Ab initio calculations of biomolecules
Leś, Andrzej; Adamowicz, Ludwik
1995-08-01
Ab initio quantum mechanical calculations are valuable tools for interpretation and elucidation of elemental processes in biochemical systems. With the ab initio approach one can calculate data that sometimes are difficult to obtain by experimental techniques. The most popular computational theoretical methods include the Hartree-Fock method as well as some lower-level variational and perturbational post-Hartree Fock approaches which allow to predict molecular structures and to calculate spectral properties. We have been involved in a number of joined theoretical and experimental studies in the past and some examples of these studies are given in this presentation. The systems chosen cover a wide variety of simple biomolecules, such as precursors of nucleic acids, double-proton transferring molecules, and simple systems involved in processes related to first stages of substrate-enzyme interactions. In particular, examples of some ab initio calculations used in the assignment of IR spectra of matrix isolated pyrimidine nucleic bases are shown. Some radiation-induced transformations in model chromophores are also presented. Lastly, we demonstrate how the ab-initio approach can be used to determine the initial several steps of the molecular mechanism of thymidylate synthase inhibition by dUMP analogues.
Ab initio valence calculations in chemistry
Cook, D B
1974-01-01
Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge
{ital Ab} {ital initio} calculations of biomolecules
Energy Technology Data Exchange (ETDEWEB)
Les, A. [Department of Chemistry, University of Warsaw, 02-093 Warsaw (Poland)]|[Department of Chemistry, University of Arizona, Tucson, Arizona 85721 (United States); Adamowicz, L. [Department of Theoretical Chemistry, University of Lund, Lund, S-22100 (Sweden)]|[Department of Chemistry, University of Arizona, Tucson, Arizona 85721 (United States)
1995-08-01
{ital Ab} {ital initio} quantum mechanical calculations are valuable tools for interpretation and elucidation of elemental processes in biochemical systems. With the {ital ab} {ital initio} approach one can calculate data that sometimes are difficult to obtain by experimental techniques. The most popular computational theoretical methods include the Hartree-Fock method as well as some lower-level variational and perturbational post-Hartree Fock approaches which allow to predict molecular structures and to calculate spectral properties. We have been involved in a number of joined theoretical and experimental studies in the past and some examples of these studies are given in this presentation. The systems chosen cover a wide variety of simple biomolecules, such as precursors of nucleic acids, double-proton transferring molecules, and simple systems involved in processes related to first stages of substrate-enzyme interactions. In particular, examples of some {ital ab} {ital initio} calculations used in the assignment of IR spectra of matrix isolated pyrimidine nucleic bases are shown. Some radiation-induced transformations in model chromophores are also presented. Lastly, we demonstrate how the {ital ab}-{ital initio} approach can be used to determine the initial several steps of the molecular mechanism of thymidylate synthase inhibition by dUMP analogues.
Synthesis, characterization, ab initio calculations, thermal behaviour ...
Indian Academy of Sciences (India)
Administrator
through titration of the ligands with the metal ions at constant ionic strength (0⋅1 M NaClO4) and at 25°C. According to the thermodynamic studies, as the steric character of the ligand increases, the complexation tendency to VO(IV) center decreases. Also, the ab initio calculations were carried out to determine the structural ...
Ab Initio Calculations of Oxosulfatovanadates
DEFF Research Database (Denmark)
Frøberg, Torben; Johansen, Helge
1996-01-01
Restricted Hartree-Fock and multi-configurational self-consistent-field calculations together with secondorder perturbation theory have been used to study the geometry, the electron density, and the electronicspectrum of (VO2SO4)-. A bidentate sulphate attachment to vanadium was found to be stabl...
Ab initio calculation of the Structural, Mechanical and ...
African Journals Online (AJOL)
ADOWIE PERE
ABSTRACT: An ab initio plane-wave Pseudopotential calculations using the density functional theory (DFT) .... wave Pseudopotential PWPP method with the ..... Γ the longitudinal optical LO branch shows a sharp increasing amount of upward dispersion while the TO , a flat/horizontal dispersion it was also observed that the ...
Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation
DEFF Research Database (Denmark)
Bak, Börge; Jansen, Peter; Stafast, Herbert
1975-01-01
The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes...
Graphitic nanofilms of zinc-blende materials: ab initio calculations
Hu, San-Lue; Zhao, Li; Li, Yan-Li
2017-12-01
Ab initio calculations on ultra-thin nanofilms of 25 kinds of zinc-blende semiconductors demonstrate their stable geometry structures growth along (1 1 1) surface. Our results show that the (1 1 1) surfaces of 9 kinds of zinc-blende semiconductors can transform into a stable graphitelike structure within a certain thickness. The tensile strain effect on the thickness of graphitic films is not obvious. The band gaps of stable graphitic films can be tuned over a wide range by epitaxial tensile strain, which is important for applications in microelectronic devices, solar cells and light-emitting diodes.
Ab initio MCDHF calculations of electron-nucleus interactions
Bieroń, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka
2015-05-01
We present recent advances in the development of atomic ab initio multiconfiguration Dirac-Hartree-Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac-Hartree-Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.
Ab initio calculation of the Structural, Mechanical and ...
African Journals Online (AJOL)
ADOWIE PERE
Corresponding Author: B. E. Iyorzor, Email: beniyorzor@uniben.edu. ABSTRACT: An ab initio ... by employing the first principles tight binding linear muffin-tin orbital method within the local density approximation (LDA) Kalpana et al (1998). Also the.
Ab Initio Calculations of Co Shielding in Model Complexes
Directory of Open Access Journals (Sweden)
Elaine A. Moore
2002-08-01
Full Text Available Abstract: Recent ab initio calculations of cobalt NMR shielding show that DFT-GIAO calculations using hybrid functionals are found to reproduce experimental values well. This method is used to calculate the variation of the cobalt NMR shielding tensor of sqaure pyramidal nitrosyl complexes with respect to the CoNO geometry and to differing basal ligands. The isotropic shielding is shown to have a large negative derivative with respect to CoX distance where X is a ligating atom.; the derivative with respect to NO distance is smaller but still significant. The zz component where z is along the CoN(NO bond is more sensitive to the basal ligands but the other two principal components are sensitive to the CoNO geometry.
Integral approximations in ab initio, electron propagator calculations.
Flores-Moreno, Roberto; Ortiz, J V
2009-09-28
Treatments of interelectronic repulsion that avoid four-center integrals have been incorporated in ab initio, electron-propagator calculations with diagonal self-energy matrices. Whereas the formal scaling of arithmetic operations in the propagator calculations is unaffected, the reduction of storage requirements is substantial. Moreover, the scaling of integral transformations to the molecular orbital base is lowered by one order. Four-index, electron-repulsion integrals are regenerated from three-index intermediates. Test calculations with widely applied self-energy approximations demonstrate the accuracy of this approach. Only small errors are introduced when this technique is used with quasiparticle virtual orbitals, provided that conventional techniques of integral evaluation are used in the construction of density-difference matrices.
Thermal neutron scattering law calculations using ab initio molecular dynamics
Wormald, Jonathan; Hawari, Ayman I.
2017-09-01
In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of
Quantum plasmonics: from jellium models to ab initio calculations
Directory of Open Access Journals (Sweden)
Varas Alejandro
2016-08-01
Full Text Available Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Ab-initio calculations for dilute magnetic semiconductors
Energy Technology Data Exchange (ETDEWEB)
Belhadji, Brahim
2008-03-03
This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)
Ab initio calculation of the potential bubble nucleus 34Si
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
Engineering Room-temperature Superconductors Via ab-initio Calculations
Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen
The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Energy Technology Data Exchange (ETDEWEB)
Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Ab initio calculations of reactions of light nuclei
Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr
2017-09-01
An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.
Study on the surface hydroxyl group on solid breeding materials by ab-initio calculations
Energy Technology Data Exchange (ETDEWEB)
Tanaka, Satoru; Taniguchi, Masaki [Tokyo Univ. (Japan). Faculty of Engineering
1996-10-01
The nature of -OH on the surface of Li{sub 2}O was analyzed with the ab-initio quantum chemical calculation technique. Calculation results showed that the stretching vibration of O-H is affected by the chemical species around the -OH. (author)
An ab initio SCF calculation of the polarizability tensor of sulphur dioxide
Bacskay, George G.
1983-08-01
The principal components of the static electric dipole polarizability have been calculated by an ab initio coupled perturbed Hartree-Fock (CPHF) method. The calculated components are sufficiently accurate so that a choice can be made between the two different sets of experimentally consistent values in favor of the negative anisotropy parameter αxx-ᾱ.
Mulder, Frans A. A.; Filatov, Michael
2010-01-01
In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the
Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species
DEFF Research Database (Denmark)
Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.
2011-01-01
For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine....... The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...... of the conformational energy of the S-plus-amphetamine molecule and the S-plus-amphetamine-H+ ion. The harmonic frequency calculations provide information about the characteristic features of the Raman spectra and the nature of the bonding in the molecule. It is concluded that vibrational bands from salt anions...
Towards microscopic ab initio calculations of astrophysical S-factors
Neff, Thomas; Feldmeier, Hans; Langanke, Karlheinz
2011-04-01
Low energy capture cross sections are calculated within a microscopic many-body approach using an effective Hamiltonian derived from the Argonne V18 potential. The dynamics is treated within Fermionic Molecular Dynamics (FMD) which uses a Gaussian wave-packet basis to represent the many-body states. A phase-shift equivalent effective interaction derived within the Unitary Correlation Operator Method (UCOM) that treats explicitly short-range central and tensor correlations is employed. As a first application the 3He(α,γ)7Be reaction is presented. Within the FMD approach the microscopic many-body wave functions of the 3/2- and 1/2- bound states in 7Be as well as the many-body scattering states in the 1/2+, 3/2+ and 5/2+ channels are calculated as eigenstates of the same microscopic effective Hamiltonian. Finally the S-factor is calculated from E1 transition matrix elements between the many-body scattering and bound states. For 3He(α, γ)7Be the S-factor agrees very well, both in absolute normalization and energy dependence, with the recent experimental data from the Weizmann, LUNA, Seattle and ERNA experiments. For the 3H(α, γ)7Li reaction the calculated S-factor is about 15% above the data.
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.
2004-01-01
framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
Ab initio calculations on the magnetic properties of transition metal complexes
Energy Technology Data Exchange (ETDEWEB)
Bodenstein, Tilmann; Fink, Karin [Karlsruhe Institute of Technology, Institute of Nanotechnology, POB 3640, 76021 Karlsruhe (Germany)
2015-12-31
We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.
Amino acids interacting with defected carbon nanotubes: ab initio calculations
Directory of Open Access Journals (Sweden)
M. Darvish Ganji
2016-09-01
Full Text Available The adsorption of a number of amino acids on a defected single-walled carbon nanotube (SWCNT is investigated by using the density-functional theory (DFT calculations. The adsorption energies and equilibrium distances are calculated for various configurations such as amino acid attaching to defect sites heptagon, pentagon and hexagon in defective tube and also for several molecular orientations with respect to the nanotube surface. The results showed that amino acids prefer to be physisorbed on the outer surface of the defected nanotube with different interaction strength following the hierarchy histidine > glycine > phenylalanine > cysteine. Comparing these findings with those obtained for perfect SWCNTs reveals that the adsorption energy of the amino acids increase for adsorption onto defected CNTs. The adsorption nature has also been evaluated by means of electronics structures analysis within the Mulliken population and DOS spectra for the interacting entities.
DEFF Research Database (Denmark)
Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens
2006-01-01
Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported......, and it is argued how these processes may lead to different nanofiber structures. The proposed growth model is found to be in good agreement with previous findings....
The electronic structure of LaO: Ligand field versus ab initio calculations
Schamps, Joël; Bencheikh, Mohammed; Barthelat, Jean-Claude; Field, Robert W.
1995-11-01
The potentially pathological example of LaO has been chosen to test the application of ligand field theory (LFT) to metal monoxides. The test consists of a comparison of closed-shell ligand LFT (CSLLFT) results (in which a 2+/2- ionic M2+O2- model is a priori postulated with a point-charge ligand) against ab initio multiconfiguration self-consistent-field-multireference configuration interaction (MCSCF-MRCI) results (in which no ionicity is assumed a priori and an internal structure is allowed for the ligand). Special care has been devoted to the determination of a La3+ pseudopotential and its associated atomic basis set in order to keep the ab initio model close to the LFT one, yet at the same time capable of clearly exhibiting the consequences and the importance of the restrictions imposed in the CSLLFT model. The ab initio calculations reveal that the effective (Mulliken) ionicity in LaO is not La2+O2- but quite close to La+O-. Despite this, the (2+/2-) ionic CSLLFT model leads to the correct orbital occupations in the ground state but this model cannot account for the significant covalency contribution via the nominal 2pσ and 2pπ oxygen orbitals. The CSLLFT calculations correctly reproduce the excitation energies of the four lowest-lying observed states of LaO: these states are calculated to within 2000 cm-1 and globally better than via ab initio calculations. However, the (2+/2-) ionic CSLLFT model is shown to ignore the existence of a manifold of low-lying quartet (and doublet) states of (1+/1-) ionicity that might be relevant for interpreting features of the spectrum. This result exemplifies the need for developing, beyond the first attempts made in this direction, a computationally manageable open-shell ligand theory for the frequently encountered case of predominantly ionic structures with an open-shell ligand.
Electric-field control of magnetism in graphene quantum dots: Ab initio calculations
Agapito, Luis A.; Kioussis, Nicholas; Kaxiras, Efthimios
2010-01-01
Employing ab initio calculations we predict that the magnetic states of hydrogenated diamond-shaped zigzag graphene quantum dots (GQDs), each exhibiting unique electronic structure, can be selectively tuned with gate voltage, through Stark or hybridization electric-field modulation of the spatial distribution and energy of the spin-polarized molecular orbitals, leading to transitions between these states. Electrical read-out of the GQD magnetic state can be accomplished by exploiting the dist...
Electric-field control of magnetism in graphene quantum dots: Ab initio calculations.
Agapito, Luis A; Kioussis, Nicholas; Kaxiras, Efthimios
2010-11-23
Employing ab initio calculations we predict that the magnetic states of hydrogenated diamond-shaped zigzag graphene quantum dots (GQDs), each exhibiting unique electronic structure, can be selectively tuned with gate voltage, through Stark or hybridization electric-field modulation of the spatial distribution and energy of the spin-polarized molecular orbitals, leading to transitions between these states. Electrical read-out of the GQD magnetic state can be accomplished by exploiting the distinctive electrical properties of the various magnetic configurations.
Pitsevich, G. A.; Kostopravova, A. V.; Umreiko, D. S.; Ksenofontov, M. A.
2011-11-01
A technique was suggested to transform ab initio molecular force fields calculated using a set of independent vibrational coordinates into a form corresponding to a complete set of regundand coordinates and reflecting the molecular symmetry. Conditions necessary for the appropriate transformations to be possible are formulated. The possibility of transforming the force field for the simplest fragment containing regundand coordinates was demonstrated using ethylene as an example.
Ab initio Calculations of the Isotopic Dependence of Nuclear Clustering
Elhatisari, Serdar; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Lee, Dean; Li, Ning; Lu, Bing-nan; Meißner, Ulf-G.; Rupak, Gautam
2017-12-01
Nuclear clustering describes the appearance of structures resembling smaller nuclei such as alpha particles (4He nuclei) within the interior of a larger nucleus. In this Letter, we present lattice Monte Carlo calculations based on chiral effective field theory for the ground states of helium, beryllium, carbon, and oxygen isotopes. By computing model-independent measures that probe three- and four-nucleon correlations at short distances, we determine the shape of the alpha clusters and the entanglement of nucleons comprising each alpha cluster with the outside medium. We also introduce a new computational approach called the pinhole algorithm, which solves a long-standing deficiency of auxiliary-field Monte Carlo simulations in computing density correlations relative to the center of mass. We use the pinhole algorithm to determine the proton and neutron density distributions and the geometry of cluster correlations in 12C, 14C, and 16C. The structural similarities among the carbon isotopes suggest that 14C and 16C have excitations analogous to the well-known Hoyle state resonance in 12C.
Polydopamine and eumelanin molecular structures investigated with ab initio calculations.
Chen, Chun-Teh; Martin-Martinez, Francisco J; Jung, Gang Seob; Buehler, Markus J
2017-02-01
A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin. All probable early-polymerized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically analyzed to find the most stable geometry connections as well as to propose a set of molecular models that represents the chemically diverse nature of PDA and eumelanin. Our results indicate that more planar oligomers have a tendency to be more stable. This finding is in good agreement with recent experimental observations, which suggested that PDA and eumelanin are composed of nearly planar oligomers that appear to be stacked together via π-π interactions to form graphite-like layered aggregates. We also show that there is a group of tetramers notably more stable than the others, implying that even though there is an inherent chemical diversity in PDA and eumelanin, the molecular structures of the majority of the species are quite repetitive. Our results also suggest that larger oligomers are less likely to form. This observation is also consistent with experimental measurements, supporting the existence of small oligomers instead of large polymers as main components of PDA and eumelanin. In summary, this work brings an insight into the controversial structure of PDA and eumelanin, explaining some of the most important structural features, and providing a set of molecular models for more accurate modeling of eumelanin-like materials.
A Review of Solid-Solution Models of High-Entropy Alloys Based on Ab Initio Calculations
Directory of Open Access Journals (Sweden)
Fuyang Tian
2017-11-01
Full Text Available Similar to the importance of XRD in experiments, ab initio calculations, as a powerful tool, have been applied to predict the new potential materials and investigate the intrinsic properties of materials in theory. As a typical solid-solution material, the large degree of uncertainty of high-entropy alloys (HEAs results in the difficulty of ab initio calculations application to HEAs. The present review focuses on the available ab initio based solid-solution models (virtual lattice approximation, coherent potential approximation, special quasirandom structure, similar local atomic environment, maximum-entropy method, and hybrid Monte Carlo/molecular dynamics and their applications and limits in single phase HEAs.
Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines
DEFF Research Database (Denmark)
Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.
2011-01-01
. This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation...
Energy Technology Data Exchange (ETDEWEB)
Fujiwara, Y [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 (Japan); Tanimoto, Y [Faculty of Pharmacy, Osaka Ohtani University, Nishikiorikita, Tondabayashi 584-8540 (Japan)], E-mail: fuji0710@sci.hiroshima-u.ac.jp
2009-03-01
On magnetic force evaluation necessary for magnetically levitated diamagnetic substances, isotropic diamagnetic susceptibility estimation by the ab initio quantum chemical calculation using Gaussian03W was verified for more than 300 molecules in a viewpoint of the accuracy in the absolute value and the calculation level affording good cost performance. From comparison, the method of B3PW91 / 6-311+G(d,p) was found to give the adequate absolute value by the relation of (observed) = (1.03 {+-} 0.005) x (calculated) - (1.22 {+-} 0.60) x 10{sup -6} in a unit of cm{sup 3} mol{sup -1} and good cost performance.
Thermodynamic assessment of the Ho–Te system supported by ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)
2013-03-05
Highlights: ► We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ► We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ► The thermodynamic parameters of the all phases existing in the system were determined. ► The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.
Velaga, Srinath C; Anderson, Brian J
2014-01-16
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.
Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations
Koudriachova, M. V.
2008-06-01
A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.
Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye
DEFF Research Database (Denmark)
Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan
2011-01-01
. Comparison was made with other azo dyes in the literature on natural, abundant plant pigments. The results show that there is a possibility in foodstuff analysis to distinguish Sudan I from other dyes by using Raman spectroscopy with more than one laser wavelength for resonance enhancement of the different......The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis...
Czech Academy of Sciences Publication Activity Database
Slavíček, Petr; Winter, B.; Faubel, M.; Bradforth, S. E.; Jungwirth, Pavel
2009-01-01
Roč. 131, č. 18 (2009), s. 6460-6467 ISSN 0002-7863 R&D Projects: GA MŠk LC512; GA ČR GA203/08/0114 Grant - others:GA ČR(CZ) GP203/07/P449 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40400503 Keywords : DNA bases * photoelectron spectroscopy * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.580, year: 2009
Ab initio calculation of the spectrum and structure of (16)O.
Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Lee, Dean; Meissner, Ulf-G; Rupak, Gautam
2014-03-14
We present ab initio lattice calculations of the low-energy even-parity states of 16O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.
Energy Technology Data Exchange (ETDEWEB)
Kurova, N. V., E-mail: kurova_natasha@mail.ru; Burdov, V. A. [Lobachevskii Nizhni Novgorod State University (Russian Federation)
2013-12-15
The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon.
High Accuracy ab Initio Calculations of Rotational-Vibrational Levels of the HCN/HNC System.
Makhnev, Vladimir Yu; Kyuberis, Aleksandra A; Zobov, Nikolai F; Lodi, Lorenzo; Tennyson, Jonathan; Polyansky, Oleg L
2018-02-08
Highly accurate ab initio calculations of vibrational and rotational-vibrational energy levels of the HCN/HNC (hydrogen cyanide/hydrogen isocyanide) isomerising system are presented for several isotopologues. All-electron multireference configuration interaction (MRCI) electronic structure calculations were performed using basis sets up to aug-cc-pCV6Z on a grid of 1541 geometries. The ab initio energies were used to produce an analytical potential energy surface (PES) describing the two minima simultaneously. An adiabatic Born-Oppenheimer diagonal correction (BODC) correction surface as well as a relativistic correction surface were also calculated. These surfaces were used to compute vibrational and rotational-vibrational energy levels up to 25 000 cm -1 which reproduce the extensive set of experimentally known HCN/HNC levels with a root-mean-square deviation σ = 1.5 cm -1 . We studied the effect of nonadiabatic effects by introducing opportune radial and angular corrections to the nuclear kinetic energy operator. Empirical determination of two nonadiabatic parameters results in observed energies up to 7000 cm -1 for four HCN isotopologues (HCN, DCN, H 13 CN, and HC 15 N) being reproduced with σ = 0.37 cm -1 . The height of the isomerization barrier, the isomerization energy and the dissociation energy were computed using a number of models; our best results are 16 809.4, 5312.8, and 43 729 cm -1 , respectively.
Ab initio molecular orbital calculations of the static polarizabilities of xanthone analogues
Sugino, Takushi; Kambe, Nobuaki; Sonoda, Noboru; Sakaguchi, Toru; Ohta, Koji
1996-03-01
The static polarizabilities, α, of various xanthone analogues ( 1-19) were estimated by ab initio molecular orbital calculations using the coupled perturbed Hartree-Fock (CPHF) method. The influence of basis sets on the calculated values was examined in detail and the reliability of the ECP approach was confirmed. A good linear relationship was found between the Δα values calculated using the 3-21G basis set and those using larger basis sets. The introduction of substituents generally increases , whereas Δα is strongly affected by the nature of the substituents and by the molecular geometries. According to Prasad's equation, γ orient was calculated from Δα and compared with experimental values.
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
Fast and reliable ab initio calculation of crystal field splittings in lanthanide complexes
Hallmen, P. P.; Köppl, C.; Rauhut, G.; Stoll, H.; van Slageren, J.
2017-10-01
Ab initio calculations of crystal field splittings and magnetic properties of lanthanide complexes are usually performed using state-averaged complete active space self-consistent field (CASSCF) calculations and a subsequent spin-orbit calculation mixing the CASSCF wave functions (CASSCF/state interaction with spin-orbit coupling). Because this approach becomes very time-consuming for large molecules, simplifications have been proposed in the literature to determine the state-averaged orbitals by configuration-averaged Hartree-Fock (CAHF) instead of CASSCF. We present an approach which is an extension of the CAHF method. We combine the techniques of local density fitting with CAHF and achieve a significant speedup compared to CASSCF without loss in accuracy. To assess the performance of our method, we apply it to three well-known molecules, namely, Er[N(SiMe3)2]3, Er(trensal), and the double-decker (NBu4)+ [Er(Pc)2]-.
Directory of Open Access Journals (Sweden)
Karl-Heinz Böhm
2014-04-01
Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.
Magnetic properties of vanadium doped CdTe: Ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Goumrhar, F. [Laboratory of Physics of High Energy, Modeling & Simulations (LPHE-MS), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Bahmad, L., E-mail: bahmad@fsr.ac.ma [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Mounkachi, O. [Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Benyoussef, A. [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Hassan II Academy of Sciences and Technology, Rabat (Morocco)
2017-04-15
In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa–Kohn–Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature T{sub c} for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.
VandeVondele, Joost; Rothlisberger, Ursula
2000-09-01
We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.
Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2009-01-01
that the structural resolving power of Raman spectroscopy will be appreciated by the reader, when used on crystals of known conformation and on the corresponding liquids, especially in combination with modern quantum mechanics calculations. It is hoped that these inetrdisciplinary methods will be applied to many more......A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational...... spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti...
Ab initio calculation of ICD widths in photoexcited HeNe
Energy Technology Data Exchange (ETDEWEB)
Jabbari, G.; Klaiman, S.; Chiang, Y.-C.; Gokhberg, K., E-mail: kirill@pci.uni-heidelberg.de [Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Trinter, F.; Jahnke, T. [Institut für Kernphysik, Goethe-Universität Frankfurt, Max-von-Laue-Str. 1, D-60438 Frankfurt (Germany)
2014-06-14
Excitation of HeNe by synchrotron light just below the frequency of the 1s → 3p transition of isolated He has been recently shown to be followed by resonant interatomic Coulombic decay (ICD). The vibrationally resolved widths of the ICD states were extracted with high precision from the photoion spectra. In this paper, we report the results of ab initio calculations of these widths. We show that interaction between electronic states at about the equilibrium distance of HeNe makes dark states of He accessible for the photoexcitation and subsequent electronic decay. Moreover, the values of the calculated widths are shown to be strongly sensitive to the presence of the non-adiabatic coupling between the electronic states participating in the decay. Therefore, only by considering the complete manifold of interacting decaying electronic states a good agreement between the measured and computed ICD widths can be achieved.
Ab initio potential for solids
DEFF Research Database (Denmark)
Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel
1992-01-01
. At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can...
H/sub 3/ /sup +/: Ab initio calculation of the vibration spectrum
Energy Technology Data Exchange (ETDEWEB)
Carney, G.D.; Porter, R.N.
1976-11-01
The vibration spectrum of H/sub 3/ /sup +/ is calculated from the representation of a previously reported (J. Chem Phys. 60, 4251 (1974)) ab initio potential-energy surface in a fifth degree Simons--Parr--Finlan (SPF) expansion. Morse- and harmonic-oscillator basis functions are used to describe the motions of the three oscillators and the Harris--Engerholm--Gwinn quadrature technique is used to obtain matrix elements of the Hamiltonian in the basis of vibrational configurations. Our variational method is thus analogous to configuration--interaction calculations for electronic states. The ground state is found to have a zero-point energy of 4345 cm/sup -1/ and a vibrationally averaged geometry of R/sub 1/=R/sub 2/=0.91396 A, theta=60.0012degree, where theta is the angle between the two equivalent bonds. The transition frequencies for the E and A/sub 1/ fundamentals are nu-bar/sub E/=2516 cm/sup -1/ and nu-bar/sub A/=3185 cm/sup -1/ and those for the corresponding first overtones of the bending mode are 2nu-bar/sub E/=5004 +- 4 cm/sup -1/ and 2nu-bar/sub A/=4799 cm/sup -1/. The first overtone of the breathing mode is 6264 cm/sup -1/. The first-excited A/sub 1/ vibration state is metastable with a dipole--radiation lifetime of 3 sec. Transition frequencies, Einstein coefficients, and lifetimes are reported for a total of 21 transitions. Analysis of results for Dunham number and normal-coordinate expansions in comparison with those for SPF expansion show the latter to be superior for ab initio vibrational calculations. A scheme for possible direct measurement of the fundamental A/sub 1/ and E vibrational bands is suggested. (AIP)
Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2007-01-01
A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational...... spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...... and gauche conformers that has been elucidated in remarkable papers by Hamaguchi et al. Such presence of a conformational equilibrium seems to be a general feature of the room temperature liquids. Then the ‘‘localized structure features’’ that apparently exist in ionic liquids are described. It is hoped...
Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations
Directory of Open Access Journals (Sweden)
Xiaowei Li
2015-01-01
Full Text Available Structure and properties of Cu-doped diamond-like carbon films (DLC were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.% on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.
Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Li, Xiaowei; Ke, Peiling; Wang, Aiying, E-mail: aywang@nimte.ac.cn [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China)
2015-01-15
Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.
Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations
Li, Xiaowei; Ke, Peiling; Wang, Aiying
2015-01-01
Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56˜7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.
Spectroscopy of 50Sc and ab initio calculations of B (M 3 ) strengths
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.
Jonkman, H.T.; Velde, G.A. van der; Nieuwpoort, W.C.
1974-01-01
Ab initio SCF MO calculations using a contracted double zeta basis set of 168 gaussian type functions were performed on TCNQ+, TCNQ, TCNQ- and TCNQ2-. The ionisation potentials obtained from total energy differences are generally 0.25-0.50 eV higher than the corresponding negative orbital energies
Ab Initio Calculated and Experimentally Measured Raman Spectra of Spodumene (LiAlSi2O6)
Stangarone, C.; Prencipe, M.; Mantovani, L.; Bersani, D.; Tribaudino, M.; Lottici, P. P.
2014-06-01
Polarization Raman measurements on spodumene enabled the identification of all 30 active modes (14 Ag and 16 Bg). Ab initio CRYSTAL14 calculations (WC1LYP hamiltonian) give very good agreement for frequencies (ǀΔǀ< 4.8 cm^-1) and intensities.
Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada
2017-07-14
Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .
Gas phase ion chemistry of coumarins: ab initio calculations used to ...
African Journals Online (AJOL)
The gas phase ion chemistry of coumarins using electron ionization (EI), positive chemical ionization (PCI) and negative chemical ionization (NCI) in a time of flight and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is outlined. The observations in NCI mode were complimented with Ab initio ...
Mechanical properties of carbynes investigated by ab initio total-energy calculations
DEFF Research Database (Denmark)
Castelli, Ivano E.; Salvestrini, Paolo; Manini, Nicola
2012-01-01
As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear...
Formation of star nanowires of sulfur-doped zinc oxide: Ab initio calculations
Directory of Open Access Journals (Sweden)
Qiu-Bao Lin
2016-09-01
Full Text Available ZnO nanowires are hexagonally shaped under normal growth conditions, but are transformed from a hexagon to hexagram ones when sulfur dopants are added into the growth solution. The formation mechanism of the hexagram-shaped ZnO nanowires is further studied by the ab initio calculations in this paper. The present calculations support the fact that the hexagonally shaped ZnO nanowires are transformed to hexagram shaped ones when the O atoms on the side surfaces of the nanowires are replaced by S atoms in certain quantities. It indicates that the ratio of sulfur content plays an important role in the hexagram formation. The results of the electronic charge densities indicate that the charge transfer makes the S-Zn bond longer than that of O-Zn. The new charge distribution on the side planes due to the S atoms replacement leads to the formation of the hexagram-shaped nanowires. The calculation on the electronic properties shows that a sulfur-doped hexagram ZnO nanowire is an indirect band gap semiconductor with a narrow gap. When dopant is increased, the gap will decrease.
Ab initio calculation of the real contact area on the atomic scale
Wolloch, M.; Feldbauer, G.; Mohn, P.; Redinger, J.; Vernes, A.
2015-05-01
We present an approach to determine the onset of contact between a tip and a surface. The real contact area depending on the distance is calculated using Bader's quantum theory of atoms in molecules. The jump to contact, which is often observed in atomic force microscopy experiments, is used as an indicator for the initial point of contact, which in turn is defined by atomic relaxations and thus without the need of external parameters. Within our approach the contact area is estimated by evaluating the zero flux surfaces between the touching Bader atoms, where the necessary electronic density cutoff for the Bader partitioning is calculated to depend on the initial point of contact. Our proposed approach is therefore completely ab initio and we are able to define and calculate the real area of contact without imposing restrictions or free parameters. As a prototype system we choose a tip made of a ten-atom tungsten pyramid above a moiré layer of graphene on an fcc iridium (111) substrate. We find that the contact area depends exponentially on the effective distance between the tip apex and the surface atom directly below within the atomically relaxed nanosystem.
Integration of ab-initio nuclear calculation with derivative free optimization technique
Energy Technology Data Exchange (ETDEWEB)
Sharda, Anurag [Iowa State Univ., Ames, IA (United States)
2008-01-01
Optimization techniques are finding their inroads into the field of nuclear physics calculations where the objective functions are very complex and computationally intensive. A vast space of parameters needs searching to obtain a good match between theoretical (computed) and experimental observables, such as energy levels and spectra. Manual calculation defies the scope of such complex calculation and are prone to error at the same time. This body of work attempts to formulate a design and implement it which would integrate the ab initio nuclear physics code MFDn and the VTDIRECT95 code. VTDIRECT95 is a Fortran95 suite of parallel code implementing the derivative-free optimization algorithm DIRECT. Proposed design is implemented for a serial and parallel version of the optimization technique. Experiment with the initial implementation of the design showing good matches for several single-nucleus cases are conducted. Determination and assignment of appropriate number of processors for parallel integration code is implemented to increase the efficiency and resource utilization in the case of multiple nuclei parameter search.
New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.
Fleming, Kelly L; Tiwary, Pratyush; Pfaendtner, Jim
2016-01-21
Herein, we demonstrate a convenient approach to systematically investigate chemical reaction dynamics using the metadynamics (MetaD) family of enhanced sampling methods. Using a symmetric SN2 reaction as a model system, we applied infrequent metadynamics, a theoretical framework based on acceleration factors, to quantitatively estimate the rate of reaction from biased and unbiased simulations. A systematic study of the algorithm and its application to chemical reactions was performed by sampling over 5000 independent reaction events. Additionally, we quantitatively reweighed exhaustive free-energy calculations to obtain the reaction potential-energy surface and showed that infrequent metadynamics works to effectively determine Arrhenius-like activation energies. Exact agreement with unbiased high-temperature kinetics is also shown. The feasibility of using the approach on actual ab initio molecular dynamics calculations is then presented by using Car-Parrinello MD+MetaD to sample the same reaction using only 10-20 calculations of the rare event. Owing to the ease of use and comparatively low-cost of computation, the approach has extensive potential applications for catalysis, combustion, pyrolysis, and enzymology.
Hafner, Jürgen
2010-09-29
During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.
Ab initio calculation of the electronic absorption spectrum of liquid water
Energy Technology Data Exchange (ETDEWEB)
Martiniano, Hugo F. M. C.; Galamba, Nuno [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Cabral, Benedito J. Costa, E-mail: ben@cii.fc.ul.pt [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa (Portugal); Instituto de Física da Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP (Brazil)
2014-04-28
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
Structure and Magnetic Properties in Ruthenium-Based Full-Heusler Alloys: AB INITIO Calculations
Bahlouli, S.; Aarizou, Z.; Elchikh, M.
2013-12-01
In this paper, we present ab initio calculations within density functional theory (DFT) to investigate structure, electronic and magnetic properties of Ru2CrZ (Z = Si, Ge and Sn) full-Heusler alloys. We have used the developed full-potential linearized muffin tin orbitals (FP-LMTO) based on the local spin density approximation (LSDA) with the PLane Wave expansion (PLW). In particular, we found that these Ruthenium-based Heusler alloys have the antiferromagnetic (AFM) type II as ground state. Then, we studied and discussed the magnetic properties belonging to our different magnetic structures: AFM type II, AFM type I and ferromagnetic (FM) phase. We also found that Ru2CrSi and Ru2CrGe exhibit a semiconducting behavior whereas Ru2CrSn has a semimetallic-like behavior as it is experimentally found. We made an estimation of Néel temperatures (TN) in the framework of the mean-field theory and used the energy differences approach to deduce the relevant short-range nearest-neighbor (J1) and next-nearest-neighbor (J2) interactions. The calculated TN are somewhat overestimated to the available experimental ones.
Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.
Küçük, Sami Emre; Biktagirov, Timur; Sezer, Deniz
2015-10-14
A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone.
Ab initio calculation of Ti NMR shieldings for titanium oxides and halides
Tossell, J. A.
Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.
Ab initio calculations of structural and magnetic properties of Ni-Co-Mn-Cr-Sn alloys
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Zagrebin Mikhail
2015-01-01
Full Text Available The composition dependences of crystal lattice parameters, bulk modulus, magnetic moments, magnetic exchange parameters in Ni2-yCoyMn1.5-xCrxSn0.5 (y = 0.2, 0.4; 0.0 ≤ x ≤ 0.4 Heusler alloys are investigated with the help of ab initio calculations. Our simulations have shown that crystal lattice parameter firstly increased and then decreased with Cr content (x increasing. The strongest ferromagnetic interaction for Ni1.6Co0.4Mn1.4Cr0.1Sn0.5 is nearest-neighbor interaction between Co and Mn1 (on own sites. The strongest antiferromagnetic interaction is observed between nearest-neighbor Mn1-Cr atoms in the first coordination sphere and it is equal to -15meV. Total magnetic moment of Ni2-yCoyMn1.5-xCrxSn0.5 (y =0.2, 0.4; 0.0 ≤ x ≤ 0.4 takes value in region from 6.1 μB to 6.6 μB.
Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo
2016-06-21
The nature of bonding interactions between the cation and the anion of an ionic liquid is at the heart of understanding ionic liquid properties. A particularly interesting case is a special class of ionic liquids known as protic ionic liquids. The extent of proton transfer in protic ionic liquids has been observed to vary according to the interacting species. Back proton transfer renders protic ionic liquids volatile and to be considered as inferior ionic liquids. We try to address this issue by employing modern ab initio valence bond theory calculations. The results indicate that the bonding in the cation and the anion of a prototypical ionic liquid, ethylammonium nitrate, is fundamentally different. It is neither characteristic of covalent/polar covalent bonding nor ionic bonding but rather charge shift bonding as a resonance hybrid of two competing ionic molecular electronic structure configurations. An investigation of other analogous protic ionic liquids reveals that this charge shift bonding seems to be a typical characteristic of protic ionic liquids while the ionic solid analogue compound ammonium nitrate has less charge shift bonding character as compared to protic ionic liquids. Further the extent of charge shift bonding character has been found to be congruent with the trends in many physicochemical properties such as melting point, conductivity, viscosity, and ionicity of the studied ionic liquids indicating that percentage charge shift character may serve as a key descriptor for large scale computational screening of ionic liquids with desired properties.
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Lei Li
2015-01-01
Full Text Available The ab initio calculations about the properties of the interstitials doping in the rutile TiO2 and their impact on the transport coefficients are reported. As the doping of the Zr or Ti interstitials in the TiO2, the lattice Ti4+ ions acquire the excess electrons so reduced to the Ti3+ or Ti2+ ions. However, the Cu interstitials could not lose enough electrons to reduce the lattice Ti4+ ions. Furthermore, the Ti or Cu interstitials in the ZrO2 also are unable to promote the lattice Zr4+ ions to form the lattice Zr3+ or Zr2+ ions. The high transport coefficients are observed in the defected TiO2 with the Ti or Zr interstitials as the high concentration of the Ti3+ or Ti2+ ions. So, the Zr interstitials are the favorable choice for the extra-doping to improve the transport properties in the TiO2-based resistive random access memory.
Directory of Open Access Journals (Sweden)
Hirokazu Takaki
2014-01-01
Full Text Available We present an efficient computation technique for ab-initio electron transport calculations based on density functional theory and the nonequilibrium Green’s function formalism for application to heterostructures with two-dimensional (2D interfaces. The computational load for constructing the Green’s functions, which depends not only on the energy but also on the 2D Bloch wave vector along the interfaces and is thus catastrophically heavy, is circumvented by parallel computational techniques with the message passing interface, which divides the calculations of the Green’s functions with respect to energy and wave vectors. To demonstrate the computational efficiency of the present code, we perform ab-initio electron transport calculations of Al(100-Si(100-Al(100 heterostructures, one of the most typical metal-semiconductor-metal systems, and show their transmission spectra, density of states (DOSs, and dependence on the thickness of the Si layers.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Energy Technology Data Exchange (ETDEWEB)
Dytrych, T. [Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Louisiana State Univ., Baton Rouge, LA (United States); Maris, Pieter [Iowa State Univ., Ames, IA (United States); Launey, K. D. [Louisiana State Univ., Baton Rouge, LA (United States); Draayer, J. P. [Louisiana State Univ., Baton Rouge, LA (United States); Vary, James [Iowa State Univ., Ames, IA (United States); Langr, D. [Czech Technical Univ., Prague (Czech Republic); Aerospace Research and Test Establishment, Prague (Czech Republic); Saule, E. [Univ. of North Carolina, Charlotte, NC (United States); Caprio, M. A. [Univ. of Notre Dame, IN (United States); Catalyurek, U. [The Ohio State Univ., Columbus, OH (United States). Dept. of Electrical and Computer Engineering; Sosonkina, M. [Old Dominion Univ., Norfolk, VA (United States)
2016-06-09
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for ^{6}Li and ^{12}C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
Rotational study of the NH3-CO complex: millimeter-wave measurements and ab initio calculations.
Surin, L A; Potapov, A; Dolgov, A A; Tarabukin, I V; Panfilov, V A; Schlemmer, S; Kalugina, Y N; Faure, A; van der Avoird, A
2015-03-21
The rotational spectrum of the van der Waals complex NH3-CO has been measured with the intracavity OROTRON jet spectrometer in the frequency range of 112-139 GHz. Newly observed and assigned transitions belong to the K = 0-0, K = 1-1, K = 1-0, and K = 2-1 subbands correlating with the rotationless (jk)NH3 = 00 ground state of free ortho-NH3 and the K = 0-1 and K = 2-1 subbands correlating with the (jk)NH3 = 11 ground state of free para-NH3. The (approximate) quantum number K is the projection of the total angular momentum J on the intermolecular axis. Some of these transitions are continuations to higher J values of transition series observed previously [C. Xia et al., Mol. Phys. 99, 643 (2001)], the other transitions constitute newly detected subbands. The new data were analyzed together with the known millimeter-wave and microwave transitions in order to determine the molecular parameters of the ortho-NH3-CO and para-NH3-CO complexes. Accompanying ab initio calculations of the intermolecular potential energy surface (PES) of NH3-CO has been carried out at the explicitly correlated coupled cluster level of theory with single, double, and perturbative triple excitations and an augmented correlation-consistent triple zeta basis set. The global minimum of the five-dimensional PES corresponds to an approximately T-shaped structure with the N atom closest to the CO subunit and binding energy De = 359.21 cm(-1). The bound rovibrational levels of the NH3-CO complex were calculated for total angular momentum J = 0-6 on this intermolecular potential surface and compared with the experimental results. The calculated dissociation energies D0 are 210.43 and 218.66 cm(-1) for ortho-NH3-CO and para-NH3-CO, respectively.
Input/Output of ab-initio nuclear structure calculations for improved performance and portability
Energy Technology Data Exchange (ETDEWEB)
Laghave, Nikhil [Iowa State Univ., Ames, IA (United States)
2010-01-01
Many modern scientific applications rely on highly computation intensive calculations. However, most applications do not concentrate as much on the role that input/output operations can play for improved performance and portability. Parallelizing input/output operations of large files can significantly improve the performance of parallel applications where sequential I/O is a bottleneck. A proper choice of I/O library also offers a scope for making input/output operations portable across different architectures. Thus, use of parallel I/O libraries for organizing I/O of large data files offers great scope in improving performance and portability of applications. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab-initio nuclear structure calculations. We develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient I/O of large datasets along with their portability and ease of use in the down-stream processing. Even situations where the amount of data to be written is not huge, proper use of input/output operations can boost the performance of scientific applications. Application checkpointing offers enormous performance improvement and flexibility by doing a negligible amount of I/O to disk. Checkpointing saves and resumes application state in such a manner that in most cases the application is unaware that there has been an interruption to its execution. This helps in saving large amount of work that has been previously done and continue application execution. This small amount of I/O provides substantial time saving by offering restart/resume capability to applications. The need for checkpointing in optimization code NEWUOA has been identified and checkpoint/restart capability has been implemented in NEWUOA by using simple file I/O.
Ab initio calculations and mechanism of two proton migration reactions of ethoxy radical
Zhang, Yue; Zhang, Shaowen; Li, Qian Shu
2005-01-01
We present a direct ab initio and density functional theory dynamics study of the thermal rate constants of the two H-migration reactions of C 2H 5O radical. MPW1K/6-31+G(d,p) methods were employed to optimize the geometries of all stationary points and to calculate the minimum energy path (MEP). The energies of all the stationary points were refined at the QCISD(T)/aug-cc-pVTZ level of theory. The thermal gas phase rate constants were evaluated based on the energetics from the QCISD(T)/aug-cc-pVTZ//MPW1K/6-31+G(d,p) level of theory using both microcanonical variational transition state theory (μVT) and canonical variational transition state theory (CVT) with the Eckart tunneling correction in the temperature range of 200-2500 K. The extended Arrhenius expression fitted from the μVT/Eckart rate constants of 1,2 H-shift and 1,3 H-shift reactions of C 2H 5O radical in the temperature range of 200-2500 K are k = 3.90 × 10 -31T12.4e (-2.13 × 10 3/ T) and k = 2.83 × 10 -29T11.9e (-2.24 × 10 3/ T) s -1, respectively. The two isomerization rate constants exhibited positive temperature dependence in the calculated temperature region. The variational effects for the two isomerizations of ethoxy radical are small and the tunneling effects are important in the low temperature range. The titled reactions are minor and not essential compared to the decomposition pathways of ethoxy radical.
Ab initio calculation of thermodynamic, transport, and optical properties of CH{sub 2} plastics
Energy Technology Data Exchange (ETDEWEB)
Knyazev, D. V. [Joint Institute for High Temperatures RAS, Izhorskaya 13 bldg. 2, Moscow 125412 (Russian Federation); Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141700 (Russian Federation); State Scientific Center of the Russian Federation – Institute for Theoretical and Experimental Physics of National Research Centre “Kurchatov Institute,” Bolshaya Cheremushkinskaya 25, 117218 Moscow (Russian Federation); Levashov, P. R. [Joint Institute for High Temperatures RAS, Izhorskaya 13 bldg. 2, Moscow 125412 (Russian Federation); Tomsk State University, Lenin Prospekt 36, Tomsk 634050 (Russian Federation)
2015-05-15
This work covers an ab initio calculation of thermodynamic, transport, and optical properties of plastics of the effective composition CH{sub 2} at density 0.954 g/cm{sup 3} in the temperature range from 5 kK up to 100 kK. The calculation is based on the quantum molecular dynamics, density functional theory, and the Kubo-Greenwood formula. The temperature dependence of the static electrical conductivity σ{sub 1{sub D{sub C}}}(T) has a step-like shape: σ{sub 1{sub D{sub C}}}(T) grows rapidly for 5 kK ≤ T ≤ 10 kK and is almost constant for 20 kK ≤ T ≤ 60 kK. The additional analysis based on the investigation of the electron density of states (DOS) is performed. The rapid growth of σ{sub 1{sub D{sub C}}}(T) at 5 kK ≤ T ≤ 10 kK is connected with the increase of DOS at the electron energy equal to the chemical potential ϵ = μ. The frequency dependence of the dynamic electrical conductivity σ{sub 1}(ω) at 5 kK has the distinct non-Drude shape with the peak at ω ≈ 10 eV. This behavior of σ{sub 1}(ω) was explained by the dip at the electron DOS.
Tsunekawa, Tetsuya; Yamaguchi, Kizashi
1992-03-01
Ab initio CPHF calculations of static hyperpolarizabilities (β) were carried out in order to clarify the effects of nitrogen-atom substitution in π-conjugated chains with donor—acceptor substituents. The β values decrease gradually with the number of nitrogen atoms, and change drastically with the position of nitrogen-atom substitution in the polyenes. The effects of nitrogen-atom substitution are explained by the energy levels and the shapes of the frontier orbitals.
Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies
Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.
Mosyagin, I.; Lugovskoy, A. V.; Krasilnikov, O. M.; Vekilov, Yu. Kh.; Simak, S. I.; Abrikosov, I. A.
2017-11-01
We present a description of a technique for ab initio calculations of the pressure dependence of second- and third-order elastic constants. The technique is based on an evaluation of the corresponding Lagrangian stress tensor derivative of the total energy assuming finite size of the deformations. Important details and parameters of the calculations are highlighted. Considering body-centered cubic Mo as a model system, we demonstrate that the technique is highly customizable and can be used to investigate non-linear elastic properties under high-pressure conditions.
Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.
Šipr, O; Ebert, H; Minár, J
2015-02-11
A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.
Electron-phonon scattering rates in complex polar crystals from ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Prange, Micah P.; Campbell, Luke W.; Kerisit, Sebastien N.
2017-09-17
The thermalization of fast electrons by phonons is studied in CsI, NaI, SrI2, and YAP. This numerical study uses an improvement to a recently developed ab initio method based on a density functional perturbation theoretical description of the phonon modes that provides a way to go beyond widely used phonon models based on binary crystals. Improvements to this method are described, and scattering rates are presented and discussed. The results here treat polar and nonpolar scattering on equal footing and allow an assessment of the relative importance of the two types of scattering. The relative activity of the numerous phonon modes in materials with complicated structures is discussed, and a simple criterion for finding the modes that scatter strongly is presented.
Haaland, Arne; Martinsen, Kjell-Gunnar; Tafipolsky, Maxim A.; Volden, Hans Vidar; Rösler, Roland; Breunig, Hans Joachim
1997-09-01
Ab initio calculations at the MP2 level and gas electron-diffraction data of (CH 3) 2TeCl 2 show that the molecular structure is pseudo-trigonal bipyramidal with the two methyl groups occupying equatorial positions and the two Cl atoms axial positions. The bond distances are ( {GED}/{MP2 }): TeC = 213.2(5)/214.6 pm, TeCl = 250.4(3)/261.8 pm and the valence angles ∠ CTeC = {97(5)°}/{97.6°}; ∠ ClTeCl = {170(2)°}/{170.8°}.
Li, Y Q; Zhang, P Y; Han, K L
2015-03-28
A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.
Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo
2016-10-27
Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.
Electronic Structure of Hydrogenated and Surface-Modified GaAs Nanocrystals: Ab Initio Calculations
Directory of Open Access Journals (Sweden)
Hamsa Naji Nasir
2012-01-01
Full Text Available Two methods are used to simulate electronic structure of gallium arsenide nanocrystals. The cluster full geometrical optimization procedure which is suitable for small nanocrystals and large unit cell that simulates specific parts of larger nanocrystals preferably core part as in the present work. Because of symmetry consideration, large unit cells can reach sizes that are beyond the capabilities of first method. The two methods use ab initio Hartree-Fock and density functional theory, respectively. The results show that both energy gap and lattice constant decrease in their value as the nanocrystals grow in size. The inclusion of surface part in the first method makes valence band width wider than in large unit cell method that simulates the core part only. This is attributed to the broken symmetry and surface passivating atoms that split surface degenerate states and adds new levels inside and around the valence band. Bond length and tetrahedral angle result from full geometrical optimization indicate good convergence to the ideal zincblende structure at the centre of hydrogenated nanocrystal. This convergence supports large unit cell methodology. Existence of oxygen atoms at nanocrystal surface melts down density of states and reduces energy gap.
Directory of Open Access Journals (Sweden)
Basso Ernani A.
2001-01-01
Full Text Available Axial-equatorial conformational proportions for cyclohexyl-N,N-dimethyl carbamate have been measured, for the first time, by the Eliel method, ¹H and 13C dynamic nuclear magnetic resonance (DNMR. The results were compared against those determined by theoretical calculations. By the Eliel method at least five experimentally independent measureables were used in CCl4, CDCl3 and CD3CN. The ¹H and 13C low temperature experiments were performed in CF2Br2/CD2Cl2 . Semiempirical methods MNDO, AM1 and PM3 and ab initio molecular orbital calculations at the HF/STO-3G and HF/6-31G(d,p levels have been performed on the axial and equatorial conformers populations. All applied methods correctly predict the equatorial conformer preference over the axial one. The resulting equatorial preferences determined by NMR data and theoretical calculations are in good agreement.
Phonon spectra of elpasolites Cs2NaRF6 (R=Y,Yb): Ab initio calculations
Chernyshev, Vladimir; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy
2015-12-01
The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs2NaYbF6 and Cs2NaYF6 (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.
Coccia, Emanuele; Assaraf, Roland; Luppi, Eleonora; Toulouse, Julien
2017-07-01
We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificial confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on H and He atoms using Gaussian-type basis sets for the calculation of high-harmonic-generation spectra.
Energy Technology Data Exchange (ETDEWEB)
Alam, T.M.
1998-09-01
The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.
Energy Technology Data Exchange (ETDEWEB)
González-Cataldo, F. [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Wilson, Hugh F.; Militzer, B., E-mail: fgonzalez@lpmd.cl [Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA 94720 (United States)
2014-05-20
By combining density functional molecular dynamics simulations with a thermodynamic integration technique, we determine the free energy of metallic hydrogen and silica, SiO{sub 2}, at megabar pressures and thousands of degrees Kelvin. Our ab initio solubility calculations show that silica dissolves into fluid hydrogen above 5000 K for pressures from 10 and 40 Mbars, which has implications for the evolution of rocky cores in giant gas planets like Jupiter, Saturn, and a substantial fraction of known extrasolar planets. Our findings underline the necessity of considering the erosion and redistribution of core materials in giant planet evolution models, but they also demonstrate that hot metallic hydrogen is a good solvent at megabar pressures, which has implications for high-pressure experiments.
Ab initio electronic structure calculations for Mn linear chains deposited on CuN/Cu(001) surfaces
Energy Technology Data Exchange (ETDEWEB)
Barral, Maria Andrea [Departamento de Fisica ' Juan Jose Giambiagi' , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina)]. E-mail: barral@df.uba.ar; Weht, Ruben [Departamento de Fisica, Comision Nacional de Energia Atomica, Avenida del Libertador 8250, 1429 Buenos Aires (Argentina); Lozano, Gustavo [Departamento de Fisica ' Juan Jose Giambiagi' , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Maria Llois, Ana [Departamento de Fisica ' Juan Jose Giambiagi' , Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Departamento de Fisica, Comision Nacional de Energia Atomica, Avenida del Libertador 8250, 1429 Buenos Aires (Argentina)
2007-09-01
In a recent experiment, scanning tunneling microscopy has been used to obtain a direct probe of the magnetic interaction in linear manganese chains arranged by atomic manipulation on thin insulating copper nitride islands grown on Cu(001). The local spin excitation spectra of these chains have been measured with inelastic electron tunneling spectroscopy. Analyzing the spectroscopic results with a Heisenberg Hamiltonian the interatomic coupling strength within the chains has been obtained. It has been found that the coupling strength depends on the deposition sites of the Mn atoms on the islands. In this contribution, we perform ab initio calculations for different arrangements of infinite Mn chains on CuN in order to understand the influence of the environment on the value of the magnetic interactions.
Ab initio thermal rate calculations of HO + HO = O(3P) + H2O reaction and isotopologues.
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.
Energy Technology Data Exchange (ETDEWEB)
Orlando, Roberto, E-mail: roberto.orlando@unito.it; Erba, Alessandro; Dovesi, Roberto [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); De La Pierre, Marco [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845 (Australia); Zicovich-Wilson, Claudio M. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad, 1001, Col. Chamilpa, 62209 Cuernavaca (Morelos) (Mexico)
2014-09-14
Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of self-consistent-field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock, and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the symmetry adapted crystalline orbital basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative examples, referring to the implementation in the CRYSTAL code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.
Bertoldi, Dalía S.; Ramos, Susana B.; Guillermet, Armando Fernández
2017-08-01
We present a theoretical analysis of the equation of state (EOS) of metals using a quasi-harmonic Einstein model with a dimensionless cohesive energy versus distance function (F(z)) involving the Wigner-Seitz radius and a material-dependent scaling length, as suggested in classical works by Rose, Ferrante, Smith and collaborators. Using this model, and ;universal; values for the function and its first and second derivatives at the equilibrium distance (z=0), three general interrelations between EOS parameters and the cohesive energy are obtained. The first correlation involves the bulk modulus, and the second, the thermal expansion coefficient. In order to test these results an extensive database is developed, which involves available experimental data, and results of current ab initio density-functional-theory calculations using the VASP code. In particular, the 0 K values for volume, bulk modulus, its pressure derivative, and the cohesive energy of 27 elements belonging to the first (Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zn), second (Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd) and third (Hf, Ta, W, Re, Os, Ir, Pt, Au) transition row of the Periodic Table are calculated ab initio and used to test the present results. The third correlation obtained, allows an evaluation of the third derivative of F(z) at z=0 for the current elements. With this new information, a discussion is presented of the possibility of finding a ;universal; F(z) versus z function able to account accurately for the pressure derivative of the bulk modulus of the transition elements.
DEFF Research Database (Denmark)
Åstrand, Per-Olof; Ramanujam, P.S.; Hvilsted, Søren
2000-01-01
Electronic excitation energies of 16 azobenzene dyes have been calculated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Good agreement with expriment is found for the lowest singlet and triplet states for both the trans- and cis-azobenzene molecules......, the experimental singlet π → π* transitions are reproduced for a set of azobenzene dyes with different electron donor and acceptor groups and the correct shifts in excitation energy are obtained for the different substituents. It has also been demonstrated that ab initio methods can be used to determine suitable...... candidates for azo components used in materials for data storage....
Moura, Gustavo L C; Simas, Alfredo M
2012-04-05
In this article, we advance the foundations of a strategy to develop a molecular mechanics method based not on classical mechanics and force fields but entirely on quantum mechanics and localized electron-pair orbitals, which we call quantum molecular mechanics (QMM). Accordingly, we introduce a new manner of calculating Hartree-Fock ab initio wavefunctions of closed shell systems based on variationally preoptimized nonorthogonal electron pair orbitals constructed by linear combinations of basis functions centered on the atoms. QMM is noniterative and requires only one extremely fast inversion of a single sparse matrix to arrive to the one-particle density matrix, to the electron density, and consequently, to the ab initio electrostatic potential around the molecular system, or cluster of molecules. Although QMM neglects the smaller polarization effects due to intermolecular interactions, it fully takes into consideration polarization effects due to the much stronger intramolecular geometry distortions. For the case of methane, we show that QMM was able to reproduce satisfactorily the energetics and polarization effects of all distortions of the molecule along the nine normal modes of vibration, well beyond the harmonic region. We present the first practical applications of the QMM method by examining, in detail, the cases of clusters of helium atoms, hydrogen molecules, methane molecules, as well as one molecule of HeH(+) surrounded by several methane molecules. We finally advance and discuss the potentialities of an exact formula to compute the QMM total energy, in which only two center integrals are involved, provided that the fully optimized electron-pair orbitals are known. Copyright © 2012 Wiley Periodicals, Inc.
Ramya, T; Gunasekaran, S; Ramkumaar, G R
2015-01-01
The experimental and theoretical spectra of (S)-2-Oxopyrrolidin-1-yl Butanamide (S2OPB) were studied. FT-IR and FT-Raman spectra of S2OPB in the solid phase were recorded and analyzed in the range 4000-450 and 5000-50 cm(-1) respectively. The structural and spectroscopic analyses of S2OPB were calculated using ab initio Hartree Fock (HF) and density functional theory calculations (B3PW91, B3LYP) with 6-31G(d,p) basis set. A complete vibrational interpretation has been made on the basis of the calculated Potential Energy Distribution (PED). The HF, B3LYP and B3PW91 methods based NMR calculation has been used to assign the (1)H NMR and (13)C NMR chemical shift of S2OPB. Comparative study on UV-Vis spectral analysis between the experimental and theoretical (B3PW91, B3LYP) methods and the global chemical parameters and local descriptor of reactivity through the Fukui function were performed. Finally the thermodynamic properties of S2OPB were calculated at different temperatures and the corresponding relations between the properties and temperature were also studied. Copyright © 2015 Elsevier B.V. All rights reserved.
Ramya, T.; Gunasekaran, S.; Ramkumaar, G. R.
2015-10-01
The experimental and theoretical spectra of (S)-2-Oxopyrrolidin-1-yl Butanamide (S2OPB) were studied. FT-IR and FT-Raman spectra of S2OPB in the solid phase were recorded and analyzed in the range 4000-450 and 5000-50 cm-1 respectively. The structural and spectroscopic analyses of S2OPB were calculated using ab initio Hartree Fock (HF) and density functional theory calculations (B3PW91, B3LYP) with 6-31G(d,p) basis set. A complete vibrational interpretation has been made on the basis of the calculated Potential Energy Distribution (PED). The HF, B3LYP and B3PW91 methods based NMR calculation has been used to assign the 1H NMR and 13C NMR chemical shift of S2OPB. Comparative study on UV-Vis spectral analysis between the experimental and theoretical (B3PW91, B3LYP) methods and the global chemical parameters and local descriptor of reactivity through the Fukui function were performed. Finally the thermodynamic properties of S2OPB were calculated at different temperatures and the corresponding relations between the properties and temperature were also studied.
DEFF Research Database (Denmark)
Shim, Irene; Kingcade, Joseph E. , Jr.; Gingerich, Karl A.
1986-01-01
In the present work we present all-electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations of six electronic states of the PdGe molecule. The molecule is predicted to have a 3Pi ground state and two low-lying excited states 3Sigma− and 1Sigma+. The electronic structure...
Energy Technology Data Exchange (ETDEWEB)
Tohme, Samir N.; Korek, Mahmoud, E-mail: mahmoud.korek@bau.edu.lb, E-mail: fkorek@yahoo.com; Awad, Ramadan [Faculty of Science, Beirut Arab University, P.O. Box 11-5020 Riad El Solh, Beirut 1107 2809 (Lebanon)
2015-03-21
Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born–Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ω{sub e}, R{sub e}, B{sub e}, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, E{sub v}, the rotational constant, B{sub v}, the centrifugal distortion constant, D{sub v}, and the abscissas of the turning points, R{sub min} and R{sub max}, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.
Judge, P. G.; Cuntz, M.
1993-01-01
We compare ab initio calculations of semiforbidden C II line profiles near 2325 A with recently published observations of the inactive red giant Alpha Tau (K5 III) obtained using the GHRS on board the Hubble Space Telescope. Our one-dimensional, time-dependent calculations assume that the chromosphere is heated by stochastic acoustic shocks generated by photospheric convection. We calculate various models using results from traditional (mixing length) convection zone calculations as input to hydrodynamical models. The semiforbidden C II line profiles and ratios provide sensitive diagnostics of chromospheric velocity fields, electron densities, and temperatures. We identify major differences between observed and computed line profiles which are related to basic gas dynamics and which are probably not due to technical modeling restrictions. If the GHRS observations are representative of chromospheric conditions at all epochs, then one (or more) of our model assumptions must be incorrect. Several possibilities are examined. We predict time variability of semiforbidden C II lines for comparison with observations. Based upon data from the IUE archives, we argue that photospheric motions associated with supergranulation or global pulsation modes are unimportant in heating the chromosphere of Alpha Tau.
DEFF Research Database (Denmark)
Åstrand, P.-O.; Bak, K.L.; Sauer, S.P.A.
2001-01-01
The two lowest singlet excitation energies of 26 2-imidazolyl-2-thiazolylazo compounds have been investigated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Various combinations of 4- and 5-substituents at both the imidazole and thiazole units have bee...
Behzad, Somayeh
2016-09-01
Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.
Akin-Ojo, Omololu; Song, Yang; Wang, Feng
2008-08-14
A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.
Energy Technology Data Exchange (ETDEWEB)
Fleche, J.L. [CEA Saclay, Dept. des Procedes d' Enrichissement (DCC/DPE/SPCP), 91 - Gif-sur-Yvette (France)
2000-07-01
The knowledge of thermodynamic functions is essential to investigate crystal stability and chemical reactivity. These functions are not always experimentally known, as for some crystalline host phases for radioactive waste. Fortunately, it is possible to calculate them. Although possible, the full ab initio calculation is not realistic because the calculation time rapidly becomes too long. These functions are obtained using an analytical model containing physical quantities determined by ab initio calculations. This enabled us to estimate the main thermodynamic functions of zircon ZrSiO{sub 4}, fluor-apatite Ca{sub 10}(PO{sub 4}){sub 6}F{sub 2} and stoichiometric iodo-apatite Pb{sub 10}(VO{sub 4}){sub 6}I{sub 2} from the variation of cohesive energy with volume and the harmonic vibration frequencies at the center of the first Brillouin zone for the unit cell corresponding to maximum cohesive energy. These ab initio quantities are calculated with the DMOL{sup 3} code that solves the electronic Schroedinger equation using the electronic density functional theory (DFT) in local density approximation, corrected (NLDA) or not (LDA) with its gradient. To limit calculation time, we made additional approximations: - acoustic and optical vibrations beyond the first Brillouin zone center are described by the Debye and Einstein models respectively; - to allow thermal expansion of the crystal we used the quasi-harmonic approximation which assumes that frequency variations are proportional to volume variations. The proportionality coefficients known as Gruneisen coefficients are derived in this study, with specific approximations; - we used the spherical cellular approximation and considered the crystal as isotropic. The thermodynamic functions calculated with this model are the following measurable quantities : enthalpy and free enthalpy, heat capacity at constant pressure, bulk modulus and thermal expansion coefficient. For zircon and fluor-apatite, for which the main
Gonzalez, Dayana; Mebel, Alexander
2016-03-01
It has been recently shown that Titan provides a unique perspective in our solar system: its atmosphere is comparable to a model of prebiotic Earth's. Provided the organic cationic and anionic molecular species identified by the Cassini spacecraft, this research characterizes reaction pathways for the reactions of methyl derivatives of the cyclopropenyl cation, the methyl cation with methyl- and dimethyl-acetylene, and reactions of resonance structures of protonated acrylonitrile with CH2NH. Isomerization and dissociation reactions involving methyl-cyclopropenyl cations, the perinaphthenyl cation and anion, and cations of pyrimidine and purine precursors of nucleobases will be examined to locate reaction pathways, intermediates, transition states, and products of the reactions. Gaussian '09 software is used for ab initio calculations to map out the PES. Geometry optimizations and vibrational frequency computations are preformed via the double-hybrid density functional B2PLYP-D3. Single-point energies are refined by use of the explicitly-correlated coupled-cluster CCSD(T)-F12 method. Rate constants are calculated using microcanonical RRKM theory, and pressure effects evaluated used the Master Equation approach; these allow for prediction of absolute rate constants and product branching ratios at different pressures and temperatures.
Directory of Open Access Journals (Sweden)
Toshiyuki Fujii
Full Text Available Stable Zn isotopes are fractionated in roots and leaves of plants. Analyses demonstrate that the heavy Zn isotopes are enriched in the root system of plants with respect to shoots and leaves as well as the host soil, but the fractionation mechanisms remain unclear. Here we show that the origin of this isotope fractionation is due to a chemical isotope effect upon complexation by Zn malates and citrates in the aerial parts and by phosphates in the roots. We calculated the Zn isotope effect in aqueous citrates, malates, and phosphates by ab initio methods. For pH<5, the Zn isotopic compositions of the various parts of the plants are expected to be similar to those of groundwater. In the neutral to alkaline region, the calculations correctly predict that (66Zn is enriched over (64Zn in roots, which concentrate phosphates, with respect to leaves, which concentrate malates and citrates, by about one permil. It is proposed that Zn isotope fractionation represents a useful tracer of Zn availability and mobility in soils.
Directory of Open Access Journals (Sweden)
Todd M. Alam
2002-08-01
Full Text Available Abstract: Ring formation in phosphate systems is expected to influence both the magnitude and orientation of the phosphorus (31P nuclear magnetic resonance (NMR chemical shielding anisotropy (CSA tensor. Ab initio calculations of the 31P CSA tensor in both cyclic and acyclic phosphate clusters were performed as a function of the number of phosphate tetrahedral in the system. The calculation of the 31P CSA tensors employed the GAUSSIAN 98 implementation of the gauge-including atomic orbital (GIAO method at the Hartree-Fock (HF level. It is shown that both the 31P CSA tensor anisotropy, and the isotropic chemical shielding can be used for the identification of cyclic phosphates. The differences between the 31P CSA tensor in acyclic and cyclic phosphate systems become less pronounced with increasing number of phosphate groups within the ring. The orientation of the principal components for the 31P CSA tensor shows some variation due to cyclization, most notably with the smaller, highly strained ring systems.
Directory of Open Access Journals (Sweden)
A. M. Souza
2012-09-01
Full Text Available The use of nanoscale low-dimensional systems could boost the sensitivity of gas sensors. In this work we simulate a nanoscopic sensor based on carbon nanotubes with a large number of binding sites using ab initio density functional electronic structure calculations coupled to the Non-Equilibrium Green's Function formalism. We present a recipe where the adsorption process is studied followed by conductance calculations of a single defect system and of more realistic disordered system considering different coverages of molecules as one would expect experimentally. We found that the sensitivity of the disordered system is enhanced by a factor of 5 when compared to the single defect one. Finally, our results from the atomistic electronic transport are used as input to a simple model that connects them to experimental parameters such as temperature and partial gas pressure, providing a procedure for simulating a realistic nanoscopic gas sensor. Using this methodology we show that nitrogen-rich carbon nanotubes could work at room temperature with extremely high sensitivity.
Precise Tests of Ab-initio Calculations of Light Nuclei and Charge Symmetry Breaking in A=10 10B
Kuvin, S. A.; Wuosmaa, A. H.; McNeel, D. G.; Lister, C. J.; Morse, C.; Avila, M. L.; Hoffman, C. R.; Kay, B. P.; Wiringa, R. B.; McCutchan, E. A.; Sonzogni, A. A.; Santiago-Gonzalez, D.; Winkelbauer, J. R.
2017-09-01
Electromagnetic transition matrix elements have provided stringent tests of modern ab-initio calculations using realistic nuclear forces. Precise measurements of the B(E2:2 ->0) transition rates in 10 B e and 10C have been compared to recent Variational and Greens Function Monte Carlo calculations and the formulation of the 3-body forces. They revealed that these electric transitions are almost purely isoscalar in character, corresponding to tumbling of the di-alpha core. Precise measurements of the analogous transition in 10 B provide additional constraints for a possible isotensor contribution. The relevant state in 10 B , at Ex = 5.164 MeV, is particle unbound. Therefore, precise measurements of both the particle decay branch and the gamma branch are needed to extract the electric transition rate. We report on a new study of the α-particle branch by studying the 10B(p,p')10B* reaction in inverse kinematics with the HELIOS spectrometer at Argonne National Laboratory.
Kletsov, Aleksey A; Glukhovskoy, Evgeny G; Chumakov, Aleksey S; Ortiz, Joseph V
2016-01-01
The conduction properties of DNA molecule, particularly its transverse conductance (electron transfer through nucleotide bridges), represent a point of interest for DNA chemistry community, especially for DNA sequencing. However, there is no fully developed first-principles theory for molecular conductance and current that allows one to analyze the transverse flow of electrical charge through a nucleotide base. We theoretically investigate the transverse electron transport through all four DNA nucleotide bases by implementing an unbiased ab initio theoretical approach, namely, the electron propagator theory. The electrical conductance and current through DNA nucleobases (guanine [G], cytosine [C], adenine [A] and thymine [T]) inserted into a model 1-nm Ag-Ag nanogap are calculated. The magnitudes of the calculated conductance and current are ordered in the following hierarchies: gA>gG>gC>gT and IG>IA>IT>IC correspondingly. The new distinguishing parameter for the nucleobase identification is proposed, namely, the onset bias magnitude. Nucleobases exhibit the following hierarchy with respect to this parameter: Vonset(A)DNA translocation through an electrode-equipped nanopore. The results represent interest for the theorists and practitioners in the field of third generation sequencing techniques as well as in the field of DNA chemistry. Copyright © 2015 Elsevier B.V. All rights reserved.
Feshin, V. P.; Feshina, E. V.
2012-03-01
The results of ab initio calculations at the RHF/6-31G(d) and MP2/6-31G(d) levels of two stable structures of the 4-(trichlorgermyl)butan-2-one molecule with total optimization of their geometry have been represented. The structure with pentacoordinated Ge atom is energetically more advantageous as compared with that with tetracoordinated one. Using these results, the 35Cl nuclear quadrupole resonance (NQR) frequencies and asymmetry parameters of the electric field gradient (EFG) at the 35Cl nuclei in molecule with pentacoordinated Ge atom have been assessed, the frequencies satisfactorily agreeing with experimental data. Calculations at the RHF/6-31G(d) level have been performed also at various Ge⋯O distances. It has been demonstrated that convergence of the Ge and O coordination centers leads to the increase of positive charge at the Ge coordination center and of negative charge at the O coordination center, at that, electron density from the Ge atom shifts mainly to the axial Cl atom and from the C atom of carbonyl group - to its O atom. The electron density transfer from the O to Ge atom does not occur.
Adsorption effect on the formation of conductive path in defective TiO2: ab initio calculations
Li, Lei; Li, Wenshi; Qin, Han; Yang, Jianfeng; Mao, Ling-Feng
2017-10-01
Although the metal/TiO2/metal junctions providing resistive switching properties have attracted lots of attention in recent decades, revealing the atomic-nature of conductive path in TiO2 active layer remains a critical challenge. Here the effects of metal adsorption on defective TiO2(1 1 0) surface are theoretically investigated via ab initio calculations. The dependence of the conductive path on the adsorption of Ti/Zr/Cu/Pt/O atoms above a lattice Ti-ion in (1 1 0) plane and at 〈1 1 0〉 direction of the defective TiO2(0 0 1) surface are compared. It is found that Ti adsorptions in both sites give larger contributions to the presence of conductive path with more stability and larger transport coefficients at Fermi level, whereas the O adsorptions at both sites fail to produce conductive path. Moreover, the adsorptions of Zr/Cu/Pt atoms reduce the existence possibility of conductive path, especially absorbed above the lattice Ti-ion at 〈1 1 0〉 direction. Thus, it is helpful to clarify the interaction of the metal electrode and oxide layer in resistive random access memory.
DEFF Research Database (Denmark)
Berg, Rolf W.
The hydrogen bonding interactions in selected archetypal vapor molecules formed in the gas phase over protic ionic liquids are discussed, based on Raman spectroscopy assisted with ab initio molecular orbital DFT-type quantum mechanical calculations (B3LYP with 6-311+G(d,p) basis sets) on assumed......-O distances in the N-H…O bond were found as 1.730 and 1.005 Å. The comparable H-O distance in solid ethanoic acid is ~1.011 Å (neutron diffraction). [1] R. W. Berg, A. Riisager & R. Fehrmann, Formation of an ion pair molecule with a single NH+…Cl- hydrogen bond: Raman spectra of 1,1,3,3-Tetramethylguanidin...... of 1,1,3,3-tetramethylguanidinium chloride. The optimized N-H distance in the N-H…Cl bond was 1.099 Å. The H-Cl distance was 1.832 Å to compare with the ~1.27 Å in HCl gas. The bromide behaved similarly [ref 2]. Fig. 2. Not so likely 1-methylimidazolium ethanoate gas molecule. The optimized N-H and H...
Accuracy and Transferability of Ab Initio Electronic Band Structure Calculations for Doped BiFeO3
Gebhardt, Julian; Rappe, Andrew M.
2017-11-01
BiFeO3 is a multiferroic material and, therefore, highly interesting with respect to future oxide electronics. In order to realize such devices, pn junctions need to be fabricated, which are currently impeded by the lack of successful p-type doping in this material. In order to guide the numerous research efforts in this field, we recently finished a comprehensive computational study, investigating the influence of many dopants onto the electronic structure of BiFeO3. In order to allow for this large scale ab initio study, the computational setup had to be accurate and efficient. Here we discuss the details of this assessment, showing that standard density-functional theory (DFT) yields good structural properties. The obtained electronic structure, however, suffers from well-known shortcomings. By comparing the conventional DFT results for alkali and alkaline-earth metal doping with more accurate hybrid-DFT calculations, we show that, in this case, the problems of standard DFT go beyond a simple systematic error. Conventional DFT shows bad transferability and the more reliable hybrid-DFT has to be chosen for a qualitatively correct prediction of doping induced changes in the electronic structure of BiFeO3.
Energy Technology Data Exchange (ETDEWEB)
Olsson, Paer
2004-04-01
The efficiency of fast neutron reactors, such as for fusion, breeding and transmutation, depend strongly on the neutron radiation resistance of the materials used in the reactors. The binary Fe-Cr alloy, which has many attractive properties in this regard, is the base for the best steels of today which are, however, still not up to the required standards. Therefore, substantial effort has been devoted to finding new materials that can cope with the demands better. Experimental studies must be complemented with extensive theoretical modelling in order to understand the effects that different alloying elements has on the resistance properties of materials. To this end, the first steps of multi-scale modelling has been taken, starting out with ab initio calculations of the electronic structure of the complete concentration range range of the disordered binary Fe-C alloy. The mixing enthalpy of Fe-Cr has been quantitatively predicted and has, together with data from literature, been used in order to fit two sets of interatomic potentials for the purpose of simulating defect evolution with molecular dynamics and kinetic Monte-Carlo codes. These dedicated Fe-Cr alloy potentials are new and represent important additions to the pure element potentials that can be found in literature.
Structure and protonation of some indolizine derivatives studied by ab initio MO calculations
Wiench, J. W.; Stefaniak, L.; Webb, G. A.
2002-02-01
Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed 13C and 15N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.
Gaff, J F; Franzen, S; Delley, B
2010-11-04
A method for the calculation of resonance Raman cross sections is presented on the basis of calculation of structural differences between optimized ground and excited state geometries using density functional theory. A vibrational frequency calculation of the molecule is employed to obtain normal coordinate displacements for the modes of vibration. The excited state displacement relative to the ground state can be calculated in the normal coordinate basis by means of a linear transformation from a Cartesian basis to a normal coordinate one. The displacements in normal coordinates are then scaled by root-mean-square displacement of zero point motion to calculate dimensionless displacements for use in the two-time-correlator formalism for the calculation of resonance Raman spectra at an arbitrary temperature. The method is valid for Franck-Condon active modes within the harmonic approximation. The method was validated by calculation of resonance Raman cross sections and absorption spectra for chlorine dioxide, nitrate ion, trans-stilbene, 1,3,5-cycloheptatriene, and the aromatic amino acids. This method permits significant gains in the efficiency of calculating resonance Raman cross sections from first principles and, consequently, permits extension to large systems (>50 atoms).
Ab initio phonon calculations for Ll(2) Ni3Al and B2NiAl
Isaeva, E.I.; Lichtenstein, A.I.; Vekilov, Y.K.; Smirnova, E.A.; Abrikosov, I.A.; Simak, S.I.; Ahuja, R.; Johansson, B.
2004-01-01
The phonon spectra and phonon density of states of the Ni3Al and NiAl intermetallic compounds are calculated from first principles using the linear response method in conjunction with ultrasoft pseudopotentials. The calculated phonon dispersion curves are in good agreement with available
Ab initio calculations of partial molar properties in the single-site approximation
DEFF Research Database (Denmark)
Ruban, Andrei; Skriver, Hans Lomholt
1997-01-01
We discuss the application of the single-site approximation in calculations of partial molar quantities, e.g., impurity solution energy, segregation energy, and effective chemical potential, which are related to a variation of the composition of an alloy or its nonequivalent parts. We demonstrate...... properly applied in calculations of partial molar quantities....
Vocadlo, L.; Martorell, B.; Brodholt, J. P.; Wood, I. G.
2014-12-01
Seismically determined S-wave velocities in the Earth's inner core are observed to be much lower (10-30%) than those generally inferred from mineral physics. This is a remarkably large discrepancy - mineralogical models for the mantle and the outer core match the observed velocities to around 1%. In no other large volume of the Earth does such a difference exist. There have been a number of arguments put forward over the years to account for the difference, but none have been universally accepted and our inability to explain the seismic velocities of the inner core remains an uncomfortable truth. Here, we present results from ab initio molecular dynamics calculations performed at 360 GPa and core temperatures on hcp and fcc iron, and on fcc-Fe alloyed with nickel and hcp-Fe alloyed with silicon. The calculated shear modulus, and therefore seismic velocities, of pure hcp-Fe reduces dramatically just prior to melting, providing an elegant explanation for the observed velocities. Calculations on fcc-Fe show no such strong reduction in VS, with a transformation to an hcp-type structure prior to melting; addition of 6.5 atm% and 13 atm% Ni to fcc-Fe raises the temperature of this transition. When silicon is added to hcp-Fe, the pre-melting behaviour is found to be very similar to that of pure hcp-Fe with a strong nonlinear shear weakening just before melting and a corresponding reduction in VS. Because temperatures range from T/Tm = 1 at the inner-outer core boundary to T/Tm ≈ 0.99 at the centre, this strong nonlinear effect on VS should occur in the inner core, providing a compelling explanation for the low VS observed.
Wong, Kin-Yiu; Xu, Yuqing; York, Darrin M
2014-06-30
Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2'-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2'-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a "gold-standard" coupled-cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path-integral method, that is, automated integration-free path-integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. Copyright © 2014 Wiley Periodicals, Inc.
Kong, Bo; Zhang, Yachao
2016-07-01
The electronic structures of the cubic GdH3 are extensively investigated using the ab initio many-body GW calculations treating the Gd 4f electrons either in the core (4f-core) or in the valence states (4f-val). Different degrees of quasiparticle (QP) self-consistent calculations with the different starting points are used to correct the failures of the GGA/GGA + U/HSE03 calculations. In the 4f-core case, GGA + G0W0 calculations give a fundamental band gap of 1.72 eV, while GGA+ GW0 or GGA + GW calculations present a larger band gap. In the 4f-val case, the nonlocal exchange-correlation (xc) functional HSE03 can account much better for the strong localization of the 4f states than the semilocal or Hubbard U corrected xc functional in the Kohn-Sham equation. We show that the fundamental gap of the antiferromagnetic (AFM) or ferromagnetic (FM) GdH3 can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G0W0 calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW0 and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G0W0 calculations in the 4f-core case is the closest to the real result. By G0W0 calculations in the 4f-core case, we find that H or Gd defects can strongly affect the band structure, especially the H defects. We explain the mechanism in terms of the possible electron correlation on the hydrogen site. Under compression, the insulator-to-metal transition in the cubic GdH3 occurs around 40 GPa, which might be a satisfied prediction.
Swerts, Ben; Chibotaru, Liviu F; Lindh, Roland; Seijo, Luis; Barandiaran, Zoila; Clima, Sergiu; Pierloot, Kristin; Hendrickx, Marc F A
2008-04-01
In this article, we present a fragment model potential approach for the description of the crystalline environment as an extension of the use of embedding ab initio model potentials (AIMPs). The biggest limitation of the embedding AIMP method is the spherical nature of its model potentials. This poses problems as soon as the method is applied to crystals containing strongly covalently bonded structures with highly nonspherical electron densities. The newly proposed method addresses this problem by keeping the full electron density as its model potential, thus allowing one to group sets of covalently bonded atoms into fragments. The implementation in the MOLCAS 7.0 quantum chemistry package of the new method, which we call the embedding fragment ab inito model potential method (embedding FAIMP), is reported here, together with results of CASSCF/CASPT2 calculations. The developed methodology is applied for two test problems: (i) the investigation of the lowest ligand field states (2)A1 and (2)B1 of the Cr(V) defect in the YVO4 crystal and (ii) the investigation of the lowest ligand field and ligand-metal charge transfer (LMCT) states at the Mn(II) substitutional impurity doped into CaCO3. Comparison with similar calculations involving AIMPs for all environmental atoms, including those from covalently bounded units, shows that the FAIMP treatment of the YVO4 units surrounding the CrO4(3-) cluster increases the excitation energy (2)B1 → (2)A1 by ca. 1000 cm(-1) at the CASSCF level of calculation. In the case of the Mn(CO3)6(10-) cluster, the FAIMP treatment of the CO3(2-) units of the environment give smaller corrections, of ca. 100 cm(-1), for the ligand-field excitation energies, which is explained by the larger ligands of this cluster. However, the correction for the energy of the lowest LMCT transition is found to be ca. 600 cm(-1) for the CASSCF and ca. 1300 cm(-1) for the CASPT2 calculation.
Dagdigian, Paul J
2018-01-14
The potential energy surface (PES) describing the interaction of the ethynyl (C2H) radical in its ground X̃2Σ+ electronic state with molecular hydrogen has been computed through restricted coupled cluster calculations including single, double, and (perturbative) triple excitations [RCCSD(T)], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants. A representative set of energy dependent state-to-state cross sections is presented and discussed. The PES and cross sections for collisions of H2(j = 0) are compared with a previous study [F. Najar et al., Chem. Phys. Lett. 614, 251 (2014)] of collisions of C2H with H2 treated as a spherical collision partner. Good agreement is found between the two sets of calculations when the H2 molecule in the present calculation is spherically averaged.
Ab initio study of mechanical and thermal properties of GaN nanotubes by phonon calculations
Directory of Open Access Journals (Sweden)
H Tashakori
2015-01-01
Full Text Available In this work, we calculated the phonon dispersion of GaNNTs (4,0 and (4,4 by quantum ESPRESSO package using Density Functional Theory (DFT, pseudo potentials, and plane wave self-consistent field (PWscf method. For the purpose of lattice-dynamical calculation and phononic properties, we used PWscf and Phonon codes. The former produces the self-consistent electronic and all related computations (forces, stresses, structural optimization. The latter solves the DFPT equations and calculates dynamical matrices for a single wave-vector or for a uniform grid of wave-vectors. The stability of these nanotubes was studied by phonon curves. According to the calculations, the breathing mode was distinguished for both nanotubes. The mechanical properties of these nanotubes were characterized by the results obtained for phonon dispersion curves. Finally, a quantitative comparison was made between the values of stiffness of GaNNTs (4,0 and (4,4.
Nuclear momentum distribution in solid and liquid HF from ab initio calculation.
Krzystyniak, M
2010-10-14
A calculation of nuclear momentum distribution of liquid and solid hydrogen fluoride was performed. In both systems, density functional theory generalized gradient approximation functional of Perdew, Burke, and Ernzerhof was used for the calculation: for liquid hydrogen fluoride, using an atom centered basis set for an isolated molecule with optimized geometry, and for solid hydrogen fluoride using plane-wave basis sets on optimized orthorhombic crystal cell. For liquid hydrogen fluoride, a semiclassical approach was adopted with the vibrational contribution to momentum distribution obtained from the density functional theory calculation and translational and rotational contributions calculated classically. Nuclear momentum distribution in the solid hydrogen fluoride was calculated entirely quantum mechanically using phonon dispersion and vibrational density of states calculated in the framework of plane-wave density functional theory. Theoretical results were contrasted with recently obtained results of Compton (deep inelastic) neutron scattering on liquid and solid hydrogen fluoride. In case of liquid hydrogen fluoride, almost a perfect agreement between theory and experiment was achieved within the harmonic Born-Oppenheimer approximation. For the solid system under investigation, the harmonic approximation leads to small (4%) overestimation of the square root of the second moment indicating that neutron Compton scattering technique is sensitive to proton delocalization due to hydrogen bonding in solid hydrogen fluoride.
DEFF Research Database (Denmark)
Bludsky, O.; Bak, Keld L.; JORGENSEN, P
1995-01-01
The quartic force field and the cubic dipole moment surface are calculated for trans-2,3-dideuteriooxirane at the self-consistent field and the second order Moller-Plesset levels of theory using a triple zeta plus two polarization functions basis set. Contact transformation theory is used...... to determine the corresponding anharmonic vibrtional frequencies and intensities. Inclusion of anharmonicity improves agreement of the calculated frequencies and intensities with their experimental counterparts. The anharmonic corrections are much more sensitive to correlation effects for intensities than...
Ab initio calculation of mechanical and thermal properties of U{sub 2}Mo intermetallic
Energy Technology Data Exchange (ETDEWEB)
Jaroszewicz, S., E-mail: jaroszew@tandar.cnea.gov.ar [Gerencia de Investigación y Aplicaciones, Comisión Nacional de Energía Atómica (Argentina); Losada, E.L.; Garcés, J.E. [DAEE, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (Argentina); Mosca, H.O. [Gerencia de Investigación y Aplicaciones, Comisión Nacional de Energía Atómica (Argentina)
2013-10-15
We present a study of structural, elastic and thermodynamic properties of tetragonal (C11{sub b}) U{sub 2}Mo by means of density-functional theory based calculations using full-potential linearized augmented plane wave method. In this approach the generalized gradient approximation were used for the exchange–correlation potential calculation. The optimized lattice parameters are in excellent agreement with the experimental data. Through the Debye–Grüneisen model the temperature and pressure dependence of equation of state, bulk modulus, thermal expansion and specific heat have been obtained and discussed in the range of pressure 0–20 GPa and the temperature 0–800 K.
Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units.
Kussmann, Jörg; Ochsenfeld, Christian
2017-06-13
We present an extension of our graphics processing units (GPU)-accelerated quantum chemistry package to employ OpenCL compute kernels, which can be executed on a wide range of computing devices like CPUs, Intel Xeon Phi, and AMD GPUs. Here, we focus on the use of AMD GPUs and discuss differences as compared to CUDA-based calculations on NVIDIA GPUs. First illustrative timings are presented for hybrid density functional theory calculations using serial as well as parallel compute environments. The results show that AMD GPUs are as fast or faster than comparable NVIDIA GPUs and provide a viable alternative for quantum chemical applications.
Ab initio calculations of fundamental properties of SrTe1−xOx alloys
Indian Academy of Sciences (India)
form of the most popular Perdew–Burke–Ernzerhof (PBE), while for electronic properties, in addition to LDA, GGA corrections; Engel–Vosko GGA (EV-GGA) and modified Becke–Johnson (mBJ) schemes were also applied. The results show that the use of GGA (WC) in our calculations is more appropriate than GGA and LDA ...
The No Core Gamow Shell Model for ab-initio Nuclear Structure Calculations
Directory of Open Access Journals (Sweden)
Papadimitriou G.
2014-03-01
Full Text Available We apply the Berggren basis in a No-Core Shell Model framework to calculate ground state (g.s. energies of 3H, 4He and 5He. In our studies we use the Argonne υ18 and the chiral N3LO potentials, both of which are renormalized via a Vlow−k process.
Perlov, A.; Chadov, S.; Ebert, H.; Chioncel, L.; Lichtenstein, A.I.; Katsnelson, M.I.
2004-01-01
An approach for the calculation of the optical and magneto-optical properties of solids based on the one-particle Green function is introduced in the framework of the linear muffin-tin orbital (LMTO) method. The approach keeps all advantages of the more accurate Korringa-Kohn-Rostoker (KKR) scheme
Ab-initio calculations of electric field gradient in Ru compounds and ...
Indian Academy of Sciences (India)
S N Mishra
2017-07-11
Jul 11, 2017 ... lower than the commonly accepted literature value of +0.231(12)b. The results presented in this paper would be useful for the precise determination of quadrupole moment of high spin states in other Ru isotopes and is likely to stimulate further shell model calculations for an improved understanding of ...
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Hashemi, J.; Markussen, Troels
2009-01-01
techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure...
On the Friedel sum rule in ab initio calculations of optical properties
Knyazev, D. V.; Levashov, P. R.
2013-01-01
We investigate the influence of technical parameters in dynamic electrical conductivity calculations by the Kubo-Greenwood formula on the value of the so-called sum rule. We propose a possible explanation of the slight overestimation of the sum rule in most of our results.
Kowalski, P.; Jahn, S.; Wunder, B.
2011-12-01
Stable isotopes are excellent geochemical tracers widely used in petrology. Among them the isotopes of light elements such as Li or B strongly fractionate between minerals and aqueous fluids during fluid-rock interaction processes, which makes them excellent tracers of mass transfer processes in the subduction cycle. In order to use the full power of isotopes tracing methods the isotope fractionation mechanisms and fractionation factors between minerals and fluids of interest must be well known and characterized. One of the most important mechanisms leading to the formation of isotopic signatures is the equilibrium isotope fractionation, which nowadays can be modeled on the atomic scale by modern computational methods. However, due to high computational requirements the current works have been limited to calculations of simple materials only. In order to overcome these limitations we develop an efficient ab initio based computational approach for prediction of the equilibrium isotope fractionation factors between high pressure and temperature materials, including fluids, which would allow for efficient calculations of the isotope fractionation factors of complex minerals and fluids containing even hundreds of atoms in the supercell. We will show our results for the Li and B stable equilibrium isotope fractionation factors between complex Li/B-bearing crystalline solids (staurolite, spodumene, tourmaline, olenite and micas) and aqueous fluids. The fractionation factors were obtained in an efficient way by simplifying the consideration to calculations of the properties of fractionating atoms only. The comparison of the calculated fractionation factors, on the qualitative and quantitative levels, with the existing experimental data show the comparable to the in situ experimental techniques, predictive power of the computations. We show that with the atomistic scale modelling we are able to reproduce correctly the experimental isotope fractionation sequences
Sidi Ahmed, S.; Boujnah, M.; Bahmad, L.; Benyoussef, A.; El Kenz, A.
2017-10-01
The magnetic and electronic properties of the double perovskite Lu2MnCoO6 are studied by combining the ab-initio calculations and Monte Carlo simulation (MCs) based on the Ising model. This compound is constituted of two magnetic cubic sublattices: one occupied by Mn4+ with spin (s = 3/2) and other occupied by Co2+ with spin (σ = 3/2). By using ab-initio calculations we compute the exchange coupling between Mn-Co sublattices. We also investigate the phase transitions and the magnetic stability of this compound. The Curie temperature is determined as well as the critical exponents. We show that the Lu2MnCoO6 compound belongs to the 3D-Ising universality class.
Samdal, Svein; Strand, Tor G.; Tafipolsky, Maxim A.; Vilkov, Lev V.; Popik, M. V.; Volden, Hans Vidar
1997-11-01
The molecular structure of gaseous 4-fluorobenzaldehyde has been determined by a joint analysis of gas electron diffraction data, rotational constants from microwave spectroscopy, and constrained by results from ab initio calculations. The ab initio calculations have been performed at the {HF}/{6-311 G∗∗ } and {MP2 }/{6-31 G∗ } levels of theory. The planar C s symmetry structure was found to be the only stable conformation. The torsion of the formyl group has been treated as a large-amplitude motion. The most important structure parameters ( rg) from the joint analysis with estimates of 2σ (in parentheses) were: ( CC) mean = 1.397(1) Å, CF = 1.331(7) Å, CC(= O) = 1.488(7) Å, CO = 1.195(5) Å,
Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry.
Umer, Muhammad; Kopp, Wassja A; Leonhard, Kai
2015-12-07
We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 - both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably.
Ab initio study of the stability of beryllium clusters: accurate calculations for Be2 - 6
Šulka, Martin; Labanc, Daniel; Kováč, Martin; Pitoňák, Michal; Černušák, Ivan; Neogrády, Pavel
2012-04-01
We present results of theoretical investigation of the stability of small beryllium clusters, Be2 - 6. Due to the fact that the clusters are homonuclear, their stability is sufficiently represented by the binding energy De calculated per atom. The knowledge of this quantity offers a possibility of calculating more complex energetic effects, such as destruction or fusion of the beryllium clusters and adding or detaching a beryllium atom. The most stable structures among those of the singlet multiplicity were studied using the highly correlated coupled clusters method with iterative single- and double-excitations and the perturbative triple excitations (CCSD(T)). The effect of electron correlation, basis set saturation, basis set superposition error, relativistic effects and the core correlation were carefully investigated and discussed. The optimized virtual orbital space (OVOS) with the controlled accuracy technique is extensively applied to alleviate the computational cost of calculations. In this specific case, the use of the OVOS technique led to speed-ups in computational time by more than an order of magnitude. Finally, we present the basis set extrapolated binding energies with all of the aforementioned corrections properly included, which are the most reliable data for this key property for Be3 - 6 clusters to date. Furthermore, these values can serve as a valuable benchmark for testing the accuracy of less time consuming computational methods applicable for larger beryllium clusters. This paper is dedicated to Professor Alexander I Boldyrev on the occasion of his 60th birthday.
Numerical Exact Ab Initio Four-Nucleon Scattering Calculations: from Dream to Reality
Fonseca, A. C.; Deltuva, A.
2017-03-01
In the present manuscript we review the work of the last ten years on the pursuit to obtain numerical exact solutions of the four-nucleon scattering problem using the most advanced force models that fit two nucleon data up to pion production threshold with a χ ^2 per data point approximately one, together with the Coulomb interaction between protons; three- and four-nucleon forces are also included in the framework of a meson exchange potential model where NN couples to NΔ. Failure to describe the world data on four-nucleon scattering observables in the framework of a non relativistic scattering approach falls necessarily on the force models one uses. Four-nucleon observables pose very clear challenges, particular in the low energy region where there are a number of resonances whose position and width needs to be dynamically generated by the nucleon-nucleon (NN) interactions one uses. In addition, our calculations constitute the most advance piece of work where observables for all four-nucleon reactions involving isospin I=0, I=0 coupled to I=1 and isospin I=1 initial states are calculated at energies both below and above breakup threshold. We also present a very extensive comparison between calculated results and data for cross sections and spin observables. Therefore the present work reveals both the shortcomings and successes of some of the present NN force models in describing four-nucleon data and serve as a benchmark for future developments.
DEFF Research Database (Denmark)
Bak, KL; Bludsky, O.; Jorgensen, P
1995-01-01
A priori theory is derived for anharmonic calculations of vibrational circular dichroism (VCD). The anharmonic VCD expression is gauge origin independent and reduce to the magnetic field perturbation theory expression in the double-harmonic approximation. The theory has been implemented using...... for the atomic axial tensors and using second-order Moller-Plesset theory for the atomic polar tensors and the force fields, The changes of the vibrational rotatory strengths from anharmonicities are small, and do not explain the previously observed large discrepancies between the double-harmonic results...
Ab initio band structure calculations of the low-temperature phases of Ag2Se, Ag2Te and Ag3AuSe2
Fang, C.M.; Groot, R.A. de; Wiegers, G.A.
Ab initio band structure calculations were performed for the low-temperature modifications of the silver chalcogenides β-Ag2Se, β-Ag2Te and the ternary compound β-Ag3AuSe2 by the local spherical wave (LSW) method. Coordinates of the atoms of β-Ag2Se and β-Ag3AuSe2 were obtained from refinements
Raman spectra and ab initio calculation of a structure of aqueous solutions of methanol
Hushvaktov, H. A.; Tukhvatullin, F. H.; Jumabaev, A.; Tashkenbaev, U. N.; Absanov, A. A.; Hudoyberdiev, B. G.; Kuyliev, B.
2017-03-01
Small amount of low molecular weight alcohols leads to appearance of some special properties of alcohol-water solutions. In the literature it is associated with structural changes in solution with changing concentration. However, the problem special properties and structure of solutions at low concentration of alcohol is not very clear. Accordingly, we carried out quantum-chemical calculations and experimental studies of aqueous solutions of methyl alcohol. The calculations performed for ten molecular alcohol-water mixtures showed that with a low concentration of methyl alcohol in water the solubility of alcohol is poor: the alcohol molecules are displaced from the water structure and should form a particular structure. Thus, with low concentration of alcohol in the aqueous solution there are two types of structures: the structure of water and the structure of alcohol that should lead to the presence of specific properties. At high concentration of alcohol the structure of water is destroyed and there is just the structure made of alcohol-water aggregates. This interpretation is consistent with the experimental data of Raman spectroscopy. The band of Csbnd O vibrations of alcohol is detected to be of complex character just in the region of the presence of specific properties. Formation of intermolecular H-bonds also complicates the Raman spectra of Osbnd H or O-D vibrations of pure alcohol: a non-coincidence of peak frequencies, a shift of the band towards low-frequency region, a strong broadening of the band.
Ab initio Calculation of the n p →d γ Radiative Capture Process
Beane, Silas R.; Chang, Emmanuel; Detmold, William; Orginos, Kostas; Parreño, Assumpta; Savage, Martin J.; Tiburzi, Brian C.; Nplqcd Collaboration
2015-09-01
Lattice QCD calculations of two-nucleon systems are used to isolate the short-distance two-body electromagnetic contributions to the radiative capture process n p →d γ , and the photo-disintegration processes γ(*)d →n p . In nuclear potential models, such contributions are described by phenomenological meson-exchange currents, while in the present work, they are determined directly from the quark and gluon interactions of QCD. Calculations of neutron-proton energy levels in multiple background magnetic fields are performed at two values of the quark masses, corresponding to pion masses of mπ˜450 and 806 MeV, and are combined with pionless nuclear effective field theory to determine the amplitudes for these low-energy inelastic processes. At mπ˜806 MeV , using only lattice QCD inputs, a cross section σ806 MeV˜17 mb is found at an incident neutron speed of v =2 ,200 m /s . Extrapolating the short-distance contribution to the physical pion mass and combining the result with phenomenological scattering information and one-body couplings, a cross section of σlqcd(n p →d γ )=334.9 ( +5.2 -5.4 ) mb is obtained at the same incident neutron speed, consistent with the experimental value of σexpt(n p →d γ )=334.2 (0.5 ) mb .
Ab initio calculation of transport properties between PbSe quantum dots facets with iodide ligands
Wang, B.; Patterson, R.; Chen, W.; Zhang, Z.; Yang, J.; Huang, S.; Shrestha, S.; Conibeer, G.
2018-01-01
The transport properties between Lead Selenide (PbSe) quantum dots decorated with iodide ligands has been studied using density functional theory (DFT). Quantum conductance at each selected energy levels has been calculated along with total density of states and projected density of states. The DFT calculation is carried on using a grid-based planar augmented wave (GPAW) code incorporated with the linear combination of atomic orbital (LCAO) mode and Perdew Burke Ernzerhof (PBE) exchange-correlation functional. Three iodide ligand attached low index facets including (001), (011), (111) are investigated in this work. P-orbital of iodide ligand majorly contributes to density of state (DOS) at near top valence band resulting a significant quantum conductance, whereas DOS of Pb p-orbital shows minor influence. Various values of quantum conductance observed along different planes are possibly reasoned from a combined effect electrical field over topmost surface and total distance between adjacent facets. Ligands attached to (001) and (011) planes possess similar bond length whereas it is significantly shortened in (111) plane, whereas transport between (011) has an overall low value due to newly formed electric field. On the other hand, (111) plane with a net surface dipole perpendicular to surface layers leading to stronger electron coupling suggests an apparent increase of transport probability. Apart from previously mentioned, the maximum transport energy levels located several eVs (1 2 eVs) from the edge of valence band top.
Energy Technology Data Exchange (ETDEWEB)
Ortenzi, Luciano
2013-10-17
In this thesis I study the interplay between magnetism and superconductivity in itinerant magnets and superconductors. I do this by applying a semiphenomenological method to four representative compounds. In particular I use the discrepancies (whenever present) between density functional theory (DFT) calculations and the experiments in order to construct phenomenological models which explain the magnetic, superconducting and optical properties of four representative systems. I focus my attention on the superconducting and normal state properties of the recently discovered APt3P superconductors, on superconducting hole-doped CuBiSO, on the optical properties of LaFePO and finally on the ferromagnetic-paramagnetic transition of Ni3Al under pressure. At the end I present a new method which aims to describe the effect of spin fluctuations in itinerant magnets and superconductors that can be used to monitor the evolution of the electronic structure from non magnetic to magnetic in systems close to a quantum critical point.
Application of ab initio calculations and molecular dynamics to collagen and brome mosaic virus
Eifler, Jay Quinson
In bio-related research, large proteins are of important interest. We study two such proteins. Collagen is one such protein which forms part of the structural matrix for animals, such as in their bones and teeth. 1JS9 is another protein that is a component of the protein shell of the brome mosaic virus (BMV). And BMV is important for drug delivery and imaging. To better understand the properties of these proteins, quantum mechanically (QM) based results are needed, however computationally feasible methods are also necessary. The Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) method is well-suited for application to such large proteins. However, a new approach to reduce the computational cost is required and this extension to the method we call the Amino-Acid Based Method (AAPM) of OLCAO. The AAPM roughly calculates electronic, self-consistent field (scf) potentials for individual amino-acids with their neighboring amino-acids included as a boundary condition. This allows the costly scf part of the calculation to be skipped out. Additionally, the number of potentials used to describe the how protein i s also minimized. Results for effective charge and bond order are obtained and analyzed for Collagen and preliminary effective charge results are obtained for 1JS9. The effective charge results reproduce those already obtained with other QM based methods but without reduced cost and preserved accuracy that are characteristically different than the formal charges mostly still in use to describe the charge properties of proteins. The bond order results for Collagen nicely reproduce the observed experimentally-derived hydrogen bonding between the individual chains of the collagen triple-helix as well as the observed hydrogen bonding network.
Ab initio Calculations of the Isotopic Dependence of Nuclear Clustering.
Elhatisari, Serdar; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Lee, Dean; Li, Ning; Lu, Bing-Nan; Meißner, Ulf-G; Rupak, Gautam
2017-12-01
Nuclear clustering describes the appearance of structures resembling smaller nuclei such as alpha particles (^{4}He nuclei) within the interior of a larger nucleus. In this Letter, we present lattice Monte Carlo calculations based on chiral effective field theory for the ground states of helium, beryllium, carbon, and oxygen isotopes. By computing model-independent measures that probe three- and four-nucleon correlations at short distances, we determine the shape of the alpha clusters and the entanglement of nucleons comprising each alpha cluster with the outside medium. We also introduce a new computational approach called the pinhole algorithm, which solves a long-standing deficiency of auxiliary-field Monte Carlo simulations in computing density correlations relative to the center of mass. We use the pinhole algorithm to determine the proton and neutron density distributions and the geometry of cluster correlations in ^{12}C, ^{14}C, and ^{16}C. The structural similarities among the carbon isotopes suggest that ^{14}C and ^{16}C have excitations analogous to the well-known Hoyle state resonance in ^{12}C.
Lovato, Alessandro
2012-10-01
In this thesis, the ground state properties of nuclear matter, namely the energy per particle and the response to weak probes, are computed, studying the effects of three nucleon interactions. Both the variational approach, based on the formalism of correlated basis function, and the auxiliary field diffusion Monte Carlo method have been used. A scheme suitable to construct a density-dependent two-nucleon potential in correlated basis approach is discussed. The density dependent potential resulting from UIX three-nucleon force has been employed in auxiliary field diffusion Monte Carlo calculations that turned out to be in very good agreement with correlated basis variational results. Hence, the underbinding of symmetric nuclear matter has to be ascribed to deficiencies of the UXI potential. A comparative analysis of the equations of state of both pure neutron matter and symmetric nuclear matter obtained using a new generation of "chiral inspired" local three-body potentials has been performed. These potentials provide an excellent description of the properties of light nuclei, as well as of the neutron-deuteron doublet scattering length. The weak response of symmetric nuclear matter has been computed at three-body cluster level. Two-body effective interactions and one-body effective operators have been derived within the formalism of correlated basis functions. The inclusion of the three-body cluster term in the effective interaction allowed for a direct inclusion of the UIX three-nucleon potential. Moreover, the sizable unphysical dependence of the effective weak operator is removed once the three-body cluster term is taken into account.
Energy Technology Data Exchange (ETDEWEB)
Knyazev, D. V. [Joint Institute for High Temperatures RAS, Izhorskaya 13 Bldg. 2, Moscow 125412 (Russian Federation); Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141700 (Russian Federation); State Scientific Center of the Russian Federation—Institute for Theoretical and Experimental Physics of National Research Centre “Kurchatov Institute,” Bolshaya Cheremushkinskaya 25, 117218 Moscow (Russian Federation); Levashov, P. R. [Joint Institute for High Temperatures RAS, Izhorskaya 13 Bldg. 2, Moscow 125412 (Russian Federation); Tomsk State University, Lenin Prospekt 36, Tomsk 634050 (Russian Federation)
2014-07-15
This work is devoted to the investigation of transport and optical properties of liquid aluminum in the two-temperature case. At first optical properties, static electrical, and thermal conductivities were obtained in the ab initio calculation which is based on the quantum molecular dynamics, density functional theory, and the Kubo-Greenwood formula. Then the semiempirical approximation was constructed based on the results of our simulation. This approximation yields the dependences σ{sub 1{sub D{sub C}}}∝1/T{sub i}{sup 0.25} and K∝T{sub e}/T{sub i}{sup 0.25} for the static electrical conductivity and thermal conductivity, respectively, for liquid aluminum at ρ = 2.70 g/cm{sup 3}, 3 kK ≤ T{sub i} ≤ T{sub e} ≤ 20 kK. Our results are well described by the Drude model with the effective relaxation time τ∝T{sub i}{sup −0.25}. We have considered a number of other models for the static electrical and thermal conductivities of aluminum, they are all reduced in the low-temperature limit to the Drude model with different expressions for the relaxation time τ. Our results are not consistent with the models in which τ∝T{sub i}{sup −1} and support the models which use the expressions with the slower decrease of the relaxation time.
Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J
2014-08-07
Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the
Singla, Mallika; Rasmussen, Morten Lund; Hashemi, Hamid; Wu, Hao; Glarborg, Peter; Pelucchi, Matteo; Faravelli, Tiziano; Marshall, Paul
2018-01-24
Limitations in current hot gas cleaning methods for chlorine species from biomass gasification may be a challenge for end use such as gas turbines, engines, and fuel cells, all requiring very low levels of chlorine. During devolatilization of biomass, chlorine is released partly as methyl chloride. In the present work, the thermal conversion of CH 3 Cl under gasification conditions was investigated. A detailed chemical kinetic model for pyrolysis and oxidation of methyl chloride was developed and validated against selected experimental data from the literature. Key reactions of CH 2 Cl with O 2 and C 2 H 4 for which data are scarce were studied by ab initio methods. The model was used to analyze the fate of methyl chloride in gasification processes. The results indicate that CH 3 Cl emissions will be negligible for most gasification technologies, but could be a concern for fluidized bed gasifiers, in particular in low-temperature gasification. The present work illustrates how ab initio theory and chemical kinetic modeling can help to resolve emission issues for thermal processes in industrial scale.
Durig, James R.; Guirgis, Gamil A.; Jin, Yanping
1996-06-01
The Raman (3500-10 cm -1) and infrared (3200-50 cm -1 spectra have been recorded of the fluid and solid phases of but-2-enoyl fluoride (crotonyl fluoride) trans-CH 3CHCHCFO, where the methyl group is trans to the CFO group. From the variable temperature studies of the infrared spectrum of the sample dissolved in liquified Xe, the conformer pair at {836}/{827}cm-1 has been used to determine a ΔH value of 135 ± 11 cm -1 (387 ± 30 cal mol -1), with the s-cis ( syn) form (two double bonds oriented cis to one another) the more stable form. In the Raman and infrared spectra of the solid, the s-cis conformer seems predominant, but even with repeated annealing a spectrum free of signals from the s-trans ( anti) conformer could not be obtained. In fact, in some of the infrared spectra, there appeared to be a slight preference for the trans conformer. The asymmetric torsional fundamental of the s-trans conformer was observed at 104.3 cm -1 with two hot bands and that for the s-cis rotamer at 97.0 cm -1 with one hot band. From these data the potential function governing the conformational interchange was determined, and the potential coefficients are: V1 = -122 ± 1, V2 = 1993 ± 27, V3 = 21 ± 1 and V4 = -88 ± 8 cm -1. The s-trans to s-cis and s-cis to s-trans barriers were determined to be 2044 and 1942 cm -1, respectively, with an enthalpy difference between the conformers of 102 ± 29 cm -1(292 ± 83 cal mol -1). The barriers governing the internal rotation of the CH 3 group for the s-trans and s-cis conformers are calculated to be 1060 ± 17 cm -1 (3.03 ± 0.05 kcal mol -1) and 1042 ± 23 cm -1 (2.98 ± 0.07 kcal mol -1), respectively. A complete vibrational assignment of the normal modes is provided. The structural parameters, force constants, and vibrational frequencies have been determined from ab initio {RHF}/{3-21 G}, {RHF}/{6-31 G∗ } and {MP2 }/{6-31 G∗ } calculations, and the theoretical results are compared with the experimental values when appropriate
Energy Technology Data Exchange (ETDEWEB)
Zapukhlyak, Myroslav
2008-12-05
The present thesis gives a theoretical contribution to the understanding of the many-particle dynamics in inelastic ion-atom collisions. Many-electron dynamics in ion-helium collisions and proton-sodium collisions was theoretically studied. The description is based on the semiclassical approximation with the straight orbit for the projectile motion. The ion-atom collision problem is by this reduced to a time-dependent many-electron problem and in the non-relativistic approximation described by the time-dependent Schroedinger equation. The solution of the many-electron problem pursues in the framework of the time-dependent density functional theory. The time-dependent Schroedinger equation for the interacting many-electron problem is transformed to the system of the time-dependent Kohn-Sham equations and solved by the two-center-basis generator method. The unknown time-dependent exchange-correlation one-particle potential forces different approximation in the time-dependent Kohn-Shan scheme. In this thesis the model of the independent electrons was applied as basis model, in which the electron-electron correlation is consistently neglected in all parts and in all steps. Differential cross sections for different one- and two-electron processes were calculated in the so-called eikonal approximation for the collisional systems p-He, He{sup 2+}-He, and Ar{sup q+}-He (q=15-18). [German] Die vorliegende Arbeit leistet einen theoretischen Beitrag zum Verstaendnis der Vielteilchendynamik in inelastischen Ion-Atom-Stoessen. Vielelektronendynamik in Ion-Helium-Stoessen und Proton-Natrium-Stoessen wurde theoretisch untersucht. Die Beschreibung basiert auf der semiklassischen Naeherung mit der geraden Bahn fuer die Projektilbewegung. Das Ion-Atom- Stossproblem wird damit auf ein zeitabhaengiges Vielelektronenproblem reduziert und in der nichtrelativistischen Naeherung mit der zeitabhaengigen Schroedinger-Gleichung beschrieben. Die Loesung des Vielelektronenproblems erfolgt im
Dashnau, Jennifer L; Zelent, Bogumil; Vanderkooi, Jane M
2005-04-01
In order to correlate how the solvent affects emission properties of tryptophan, the fluorescence and phosphorescence emission spectra of tryptophan and indole model compounds were compared for solid sugar glass (trehalose/sucrose) matrix and glycerol/water solution and under the same conditions, these matrices were examined by infrared spectroscopy. Temperature was varied from 290 to 12 K. In sugar glass, the fluorescence and phosphorescence emission spectra are constant over this temperature range and the fluorescence remains red shifted; these results are consistent with the static interaction of OH groups with tryptophan in the sugar glass. In sugar glass containing water, the water retains mobility over the entire temperature range as indicated by the HOH infrared bending frequency. The fluorescence of tryptophan in glycerol/water shifts to the blue as temperature decreases and the frequency change of the absorption of the HOH bend mode is larger than in the sugar glass. These results suggest rearrangement of glycerol and water molecules over the entire temperature change. Shifts in the fluorescence emission maximum of indole and tryptophan were relatively larger than shifts for the phosphorescence emission-as expected for the relatively smaller excited triplet state dipole for tryptophan. The fluorescence emission of tryptophan in glycerol/water at low temperature has maxima at 312, 313, and 316 nm at pH 1.4, 7.0, and 10.6, respectively. The spectral shifts are interpreted to be an indication of a charge, or Stark phenomena, effect on the excited state molecule, as supported by ab initio calculations. To check whether the amino acid remains charged over the temperature range, the infrared spectrum of alanine was monitored over the entire range of temperature. The ratio of infrared absorption characteristic of carboxylate/carbonyl was constant in glycerol/water and sugar glass, which indicates that the charge was retained. Tryptophan buried in proteins, namely
Microsolvation of LiI and CsI in water: anion photoelectron spectroscopy and ab initio calculations.
Li, Ren-Zhong; Liu, Cheng-Wen; Gao, Yi Qin; Jiang, Hong; Xu, Hong-Guang; Zheng, Wei-Jun
2013-04-03
In order to understand the microsolvation of LiI and CsI in water and provide information about the dependence of solvation processes on different ions, we investigated the LiI(H2O)n(-) and CsI(H2O)n(-) (n = 0-6) clusters using photoelectron spectroscopy. The structures of these clusters and their corresponding neutrals were investigated with ab initio calculations and confirmed by comparing with the photoelectron spectroscopy experiments. Our studies show that the structural evolutions of LiI(H2O)n and CsI(H2O)n clusters are very different. The Li-I distance in LiI(H2O)n(-) increases abruptly at n = 3, whereas the abrupt elongation of the Li-I distance in neutral LiI(H2O)n occurs at n = 5. In contrast to the LiI(H2O)n(-) clusters, the Cs-I distance in CsI(H2O)n(-) increases significantly at n = 3, reaches a maximum at n = 4, and decreases again as n increases further. There is no abrupt change of the Cs-I distance in neutral CsI(H2O)n as n increases from 0 to 6. Water molecules interact strongly with the Li ion; consequently, water molecule(s) can insert within the Li(+)-I(-) ion pair. In contrast, five or six water molecules are not enough to induce obvious separation of the Cs(+)-I(-) ion pair since the Cs-water interaction is relatively weak compared to the Li-water interaction. Our work has shown that the structural variation and microsolvation in MI(H2O)n clusters are determined by the delicate balance between ion-ion, ion-water, and water-water interactions, which may have significant implications for the general understanding of salt effects in water solution.
Wang, Yimin; Carter, Stuart; Braams, Bastiaan J.; Bowman, Joel M.
2008-02-01
We report vibrational configuration interaction calculations of the monomer fundamentals of (H2O)2, (D2O)2, (H2O)3, and (D2O)3 using the code MULTIMODE and full dimensional ab initio-based global potential energies surfaces (PESs). For the dimer the HBB PES [Huang et al., J. Chem. Phys 128, 034312 (2008)] is used and for the trimer a new PES, reported here, is used. The salient properties of the new trimer PES are presented and compared to previous single-point calculations and the vibrational energies are compared with experiments.
DEFF Research Database (Denmark)
Shim, Irene; Pelino, Mario; Gingerich, Karl A.
1992-01-01
In the present work we present results of all electron ab initio multiconfiguration self-consistent-field calculations of eight electronic states of the molecule YC. Also reported are the calculated spectroscopic constants. The predicted electronic ground state is 4PI, but this state is found......, and they hardly contribute to the bonding. The chemical bond in the YC molecule is polar with charge transfer from Y to C giving rise to a dipole moment of 3.90 D at 3.9 a.u. in the 4PI ground state. Mass spectrometric equilibrium investigations in the temperature range 2365-2792 K have resulted...
DEFF Research Database (Denmark)
Singla, Mallika; Rasmussen, Morten Lund; Hashemi, Hamid
2018-01-01
Limitations in current hot gas cleaning methods for chlorine species from biomass gasification may be a challenge for end use such as gas turbines, engines, and fuel cells, all requiring very low levels of chlorine. During devolatilization of biomass, chlorine is released partly as methyl chloride....... In the present work, the thermal conversion of CH3Cl under gasification conditions was investigated. A detailed chemical kinetic model for pyrolysis and oxidation of methyl chloride was developed and validated against selected experimental data from the literature. Key reactions of CH2Cl with O2 and C2H4...... for which data are scarce were studied by ab initio methods. The model was used to analyze the fate of methyl chloride in gasification processes. The results indicate that CH3Cl emissions will be negligible for most gasification technologies, but could be a concern for fluidized bed gasifiers, in particular...
Fakhraee, Mostafa; Zandkarimi, Borna; Salari, Hadi; Gholami, Mohammad Reza
2014-12-11
The influences of hydroxyl functional group (-OH) on the thermodynamic and structural properties of ionic liquids (ILs) composed of 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C2OHmim](+)) cation and the six different conventional anions, including [Cl](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) have been extensively investigated using classical molecular dynamics (MD) simulations combined with ab initio calculations over a wide range of temperature (298-550 K). The volumetric thermodynamic properties, enthalpy of vaporization, cohesive energy density, Hildebrand solubility parameter, and heat capacity at constant pressure were estimated at desired temperature. The simulated densities were in good agreement with the experimental data with a slight overestimation. The interionic interaction of selected ILs was also computed using both the MD simulations and ab initio calculations. It was found that the highest association of cation and anion is attributed to [C2OHmim][Cl] followed by [C2OHmim][NO3], and [C2OHmim][Tf2N] with the bulkiest anion has the weakest interionic interaction among chosen ILs. The similar trend of interactions energies was nearly observed from cohesive energy density results. Additional structural details were comprehensively yielded by calculating radial distribution functions (RDFs) and spatial distribution function (SDFs) at 358 K. The most stable configurations of isolated and dimer ion pairs of these ILs were in excellent consistency with RDFs and SDFs results. Significant changes in arrangement of anions around the [C2OHmim](+) cation in comparison with conventional imidazolium-based ILs can be inferred from the MD simulations and ab initio results. Also, microscopic structural properties disclosed that the most strong cation-cation interaction is ascribed to the hydroxyl-functionalized ILs composed of bulkier anions, whereas ILs incorporating [Cl](-) and [NO3](-) anions are mainly involved in cation-anion interactions. The
CSIR Research Space (South Africa)
Kebede, MA
2014-03-01
Full Text Available . Rajalakshmi, Cerium and zinc: Dual-doped LiMn2O4 spinels as cathode material for use in lithium rechargeable batteries, J. Power Sources 187 (2009) 565-574. [12] B. Hwang, R. Santhanam, D. Liu, Y. Tsai, Effect of Al-substitution on the stability of LiMn2O... properties of aluminium doped LiMn2O4 cathode materials for Li battery: experimental and ab initio calculations Mesfin A. Kebede1,a), Maje J. Phasha1, Niki Kunjuzwa1, Lukas J. le Roux1, Donald Mkhonto2, Kenneth I. Ozoemena1 and Mkhulu K. Mathe1 1...
Directory of Open Access Journals (Sweden)
Parsaoran Siahaan
2010-06-01
Full Text Available Intermolecular interactions and molecular translational and rotational mobility are key factors in molecular material sciences, e.g. liquid crystals. One of the important substructures is given by phenylacetylene, Ph-CºCH. Its rotational behavior in its pure form and in high dilution in hexamethylphosphoric triamide OP[N(CH32]3 (HMPA has been studied by means 13C NMR T1 relaxation times at ambient temperature as measured by the inversion recovery method. HMPA is an exceptional solvent in that is has a quite large dipole moment but comparatively low relative dielectricity constant. From the molecular shape Ph-CºCH is expected to exhibit anisotropic rotational diffusion which in fact can be deduced from the measured set of T1 values of the ortho, meta and para carbon nuclei in the neat liquid as well as in the HMPA solution. This expected result rules the dominance of a linearly molecules pair Ph-CºCH...HMPA along their dipole moment axes as anticipated in view of the large HMPA dipole moment. In order to conform with the T1 data, a linear arrangement of Ph-CºCH via the interaction between its weakly acidic H-atom with negatively charge O-atom of HMPA molecules seems to lead to such an anisotropic rotational motion. This hypothesis is supported by ab initio QM calculations which come out with higher interaction energy for linear orientation than other geometries. These ab initio calculations were performed with the basis set of RHF/6-31G(d for the single molecules of Ph-CºCH and HMPA as well as for their various geometries of the molecules pair. Molecular dynamics simulations need to be performed for further confirmation. Keywords: Relaxation Times, HMPA, pheylacetylene, ab initio, intermolecular interaction, rotational diffusion
Mastail, C.; David, M.; Nita, F.; Michel, A.; Abadias, G.
2017-11-01
We use ab initio calculations to determine the preferred nucleation sites and migration pathways of Ti, Al and N adatoms on cubic NaCl-structure (B1) AlN surfaces, primary inputs towards a further thin film growth modelling of the TiAlN alloy system. The potential energy landscape is mapped out for both metallic species and nitrogen adatoms for two different AlN surface orientations, (001) and (110), using density functional theory. For all species, the adsorption energies on AlN(011) surface are larger than on AlN(001) surface. Ti and Al adatom adsorption energy landscapes determined at 0 K by ab initio show similar features, with stable binding sites being located in, or near, epitaxial surface positions, with Ti showing a stronger binding compared to Al. In direct contrast, N adatoms (Nad) adsorb preferentially close to N surface atoms (Nsurf), thus forming strong N2-molecule-like bonds on both AlN(001) and (011). Similar to N2 desorption mechanisms reported for other cubic transition metal nitride surfaces, in the present work we investigate Nad/Nsurf desorption on AlN(011) using a drag calculation method. We show that this process leaves a Nsurf vacancy accompanied with a spontaneous surface reconstruction, highlighting faceting formation during growth.
Kornobis, Karina; Wong, Bryan M; Lodowski, Piotr; Jaworska, Maria; Andruniów, Tadeusz; Rudd, Kenneth; Kozlowski, Pawel M; 10.1021/jp110914y
2011-01-01
Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to the electronically excited states of vitamin B12 (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to predict the electronic properties of these fairly complex molecules. However, the description of excited states is strongly dependent on the type of functional used in the calculations. In the present contribution, the choice of a proper functional for vitamin B12 was evaluated in terms of its agreement with both experimental results and correlated ab initio calculations. Three different functionals, i.e. B3LYP, BP86, and LC-BLYP, were tested. In addition, the effect of relative contributions of DFT and HF to the exchange-correlation functional ...
DEFF Research Database (Denmark)
Berg, Rolf W.
2007-01-01
The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures that may be formed in addition to [AlCl4]-: [Al2OCl6]2-, [Al3OCl8]-, [Al2O2Cl4]2-, [Al3O2Cl6]- and [Al4O2Cl10]2-. Ab initio Molecular Orbital (MO) calculat......The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures that may be formed in addition to [AlCl4]-: [Al2OCl6]2-, [Al3OCl8]-, [Al2O2Cl4]2-, [Al3O2Cl6]- and [Al4O2Cl10]2-. Ab initio Molecular Orbital (MO......) calculations were carried out on these various aluminium chloride and oxochloride ions, in assumed isolated gaseous free ionic state, by use of the Gaussian-03W program at the restricted Hartree-Fock (HF) level and with the 6-31+G(d,p) basis set [1]. Without any pre-assumed symmetries and with tight...... optimization convergence criteria and by using the modified GDIIS algorithm, the model calculations generally converged. The structures and their binding energies are presented. The expected geometries are supported, with one exception perhaps being the [Al2OCl6]2- ion, that gave a linear Al-O-Al bonding...
Møllendal, Harald; Gundersen, Snefrid; Tafipolsky, Maxim A.; Volden, Hans Vidar
1998-03-01
The molecular structure of gaseous 4-chlorobenzaldehyde has been determined by a joint analysis of gas electron diffraction data, rotational constants from microwave spectroscopy, and constrained by results from ab initio calculations. The ab initio calculations have been performed at the {HF}/{6-311 G∗∗ } level of theory. The plannar C s symmetry structure was found to be the only stable conformation. The torsion of the formyl group has been treated as a large amplitude motion. The most important structure parameters ( rg) from the joint analysis with estimated total errors (in parentheses) are: ( C C) mean = 1.398(1) Å, C Cl = 1.734(3) Å, C C( O) = 1.482(10) Å, C O = 1.216(5) Å,
Ab Initio Modeling of Molecular Radiation
Jaffe, Richard; Schwenke, David
2014-01-01
Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.
Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.
1991-01-01
Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.
Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile
2007-06-01
The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.
An ab initio study of hydroxylated graphane
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-01
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Giant magnetoresistance An ab-initio description
Binder, J
2000-01-01
A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...
Haaland, A.; Shorokhov, D. J.; Volden, H. V.; McMurran, J.; Kouvetakis, J.
1999-10-01
The molecular structure of CH(GeBr 3) 3 has been determined by gas electron diffraction (GED) and ab initio calculation at the HF/6-31G ∗ level. The calculations indicate that the equilibrium structure has C 3 symmetry. The most important bond distances are (GED/HF-MO); Ge-C=199.5(10)/193.6 pm, Ge-Br (mean)=228.1(2)/228.0 pm, and valence angles
Ab initio alpha-alpha scattering
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.
2015-12-01
Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Ab initio alpha-alpha scattering.
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-12-03
Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Josefsson, Ida; Kunnus, Kristjan; Schreck, Simon; Foehlisch, Alexander; de Groot, Frank; Wernet, Philippe; Odelius, Michael
2012-01-01
A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra
Energy Technology Data Exchange (ETDEWEB)
Ferreira da Silva, F.; Lange, E. [Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Limão-Vieira, P., E-mail: plimaovieira@fct.unl.pt, E-mail: michael.brunger@flinders.edu.au, E-mail: maplima@ifi.unicamp.br [Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Jones, N. C.; Hoffmann, S. V. [ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade, DK-8000 Århus C (Denmark); Hubin-Franskin, M.-J.; Delwiche, J. [Départment de Chimie, Institut de Chimie-Bât. B6C, Université de Liège, B-4000 Liège 1 (Belgium); Brunger, M. J., E-mail: plimaovieira@fct.unl.pt, E-mail: michael.brunger@flinders.edu.au, E-mail: maplima@ifi.unicamp.br [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur (Malaysia); and others
2015-10-14
The electronic spectroscopy of isolated furfural (2-furaldehyde) in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 3.5–10.8 eV energy-range, with absolute cross section measurements derived. Electron energy loss spectra are also measured over a range of kinematical conditions. Those energy loss spectra are used to derive differential cross sections and in turn generalised oscillator strengths. These experiments are supported by ab initio calculations in order to assign the excited states of the neutral molecule. The good agreement between the theoretical results and the measurements allows us to provide the first quantitative assignment of the electronic state spectroscopy of furfural over an extended energy range.
Wang, Yu; Jin, Sheng; Li, Jiong; Zhou, Jing; Zhang, Linjuan; Wang, Jianqiang; Zhang, Shuo; Wei, Xiangjun; Jiang, Zheng; Huang, Yuying; Cui, Peixin; Zhao, Haifeng; Chu, Wangsheng
2017-08-01
Copper/zinc superoxide dismutase (CuZnSOD) is an important enzyme that plays a crucial role in protecting oxygen-metabolizing cells against harmful effects of superoxide free-radicals. In this work, the three-dimensional local structure around the copper-binding site in pH 7.0 buffer solution was determined using X-ray absorption near-edge spectroscopy (XANES) combined with ab initio calculations in the framework of the multiple-scattering theory performed by MXAN. Extremely accurate bond distances and bond angle information between ligands were returned. The result confirmed that the copper ion binds four conserved His residues and a water molecule in CuZnSOD and prefers a five-coordinated in a distorted square pyramidal geometry.
Use of ab initio quantum chemical methods in battery technology
Energy Technology Data Exchange (ETDEWEB)
Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.
Energy Technology Data Exchange (ETDEWEB)
Ciftci, Yasemin Oe. [Gazi Univ., Ankara (Turkey). Dept. of Physics; Coban, Cansu [Balikesir Univ. (Turkey). Dept. of Physics
2016-05-01
The structural, mechanical, electronic, dynamic, and optical properties of the ZrPdSn compound crystallising into the MgAgAs structure are investigated by the ab initio calculations based on the density functional theory. The lattice constant, bulk modulus, and first derivative of bulk modulus were obtained by fitting the calculated total energy-atomic volume results to the Murnaghan equation of state. These results were compared to the previous data. The band structure and corresponding density of states (DOS) were also calculated and discussed. The elastic properties were calculated by using the stress-strain method, which shows that the MgAgAs phase of this compound is mechanically stable. The presented phonon dispersion curves and one-phonon DOS confirms that this compound is dynamically stable. In addition, the heat capacity, entropy, and free energy of ZrPdSn were calculated by using the phonon frequencies. Finally, the optical properties, such as dielectric function, reflectivity function, extinction coefficient, refractive index, and energy loss spectrum, were obtained under different pressures.
Resonance and Aromaticity : An Ab Initio Valence Bond Approach
Rashid, Zahid; van Lenthe, Joop H.; Havenith, Remco W. A.
2012-01-01
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB
Ab initio study of alanine polypeptide chain twisting
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.
2006-01-01
chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...
Baesjou, PJ; Driessen, WL; Challa, G; Reedijk, J
1997-01-01
Ab initio unrestricted Hartree-Fock calculations with a 6-31G* basis set were performed on 2, 6-dimethylphenol (DMP or monomer) and 4-(2, 6-dimethylphenoxy)-2, 6-dimethylphenol (dimer) to gain more insight into the mechanism of the copper-catalyzed oxidative phenol coupling reaction. Atomic charges
Ab-initio calculations of Co-based diluted magnetic semiconductors Cd 1-xCoxX (X=S, Se, Te)
Saeed, Yasir
2010-10-01
Ab-initio calculations are performed to investigate the structural, electronic and magnetic properties of spin-polarized diluted magnetic semiconductors composed of IIVI compounds Cd1-xCoxX (X=S, Se, Te) at x=0.25. From the calculated results of band structure and density of states, the half-metallic character and stability of ferromagnetic state for Cd1-xCoxS, Cd1-xCoxSe and Cd 1-xCoxTe alloys are determined. It is found that the tetrahedral crystal field gives rise to triple degeneracy t2g and double degeneracy eg. Furthermore, we predict the values of spin-exchange splitting energies Δx(d) and Δ x(p-d) and exchange constants N0α and N 0β produced by the Co 3d states. Calculated total magnetic moments and the robustness of half-metallicity of Cd1-xCo xX (X=S, Se, Te) with respect to the variation in lattice parameters are also discussed. We also extend our calculations to x=0.50, 0.75 for S compounds in order to observe the change due to increase in Co. © 2010 Elsevier B.V.
Hahn, Seungsoo
2016-10-28
The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.
AB INITIO STUDY, INVESTIGATION OF NMR SHIELDING ...
African Journals Online (AJOL)
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Ab initio study, investigation of NMR shielding tensors, NBO and vibrational frequency. Bull. Chem. Soc. Ethiop. 2010, 24(2). 231. Gas phase results. In order to study mechanism of the reactions, structure corresponding to reactants, transition states and products were optimized in level of theory. Figure 1 shows the ...
Ab Initio molecular dynamics with excited electrons
Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.
1994-01-01
A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.
Gupta, M. K.; Mittal, R.; Chaplot, S. L.
2013-07-01
We report the ab initio density functional theory calculation of phonons in the cubic phase of ZrW2O8 in the entire Brillouin zone and identify specific anharmonic phonons that are responsible for large negative thermal expansion (NTE) in terms of the translation, rotation, and distortion of WO4 and ZrO6. We have used density functional calculations to interpret the experimental phonon spectra as a function of pressure and temperature as reported in literature. We discover that the phonons showing anharmonicity with temperature are not necessarily the same as those showing anharmonicity with pressure although both are of similar frequencies. Only the latter phonons are associated with NTE. Therefore, the cubic and/or quadratic anharmonicity of phonons is not relevant to NTE but just the volume dependence of frequencies. The calculations are able to reproduce the observed anomalous trends, namely, the softening of the low-frequency peak at about 4 meV in the phonon spectra with pressure and its hardening with temperature, whereas, both changes involve a compression of the lattice.
Zhang, Xilin; Nollett, Kenneth M.; Phillips, D. R.
2014-02-01
We report a leading-order calculation of radiative 7Li neutron captures to both the ground and first excited state of 8Li in the framework of a low-energy effective field theory (halo-EFT). Each of the possible final states is treated as a shallow bound state composed of both n +7Li and n +7Li* (core excitation) configurations. The ab initio variational Monte Carlo method is used to compute the asymptotic normalization coefficients of these bound states, which are then used to fix couplings in our EFT. We calculate the total and partial cross sections in the radiative capture process using this calibrated EFT. Fair agreement with measured total cross sections is achieved and excellent agreement with the measured branching ratio between the two final states is found. In contrast, a previous halo-EFT calculation [Rupak and Higa, Phys. Rev. Lett. 106, 222501 (2011), 10.1103/PhysRevLett.106.222501] assumes that the n-7Li couplings in different spin channels are equal, fits the P-wave "effective-range" parameter to the threshold cross section for 7Li+n→8Li+γ, and assumes the core excitation is at high enough energy scale that it can be integrated out.
Suendo, Veinardi
2011-01-01
Chlorophyll a is one the most abundant pigment on Earth, which is responsible for trapping the light energy to perform the photosynthesis process in green plants. This molecule is a metal-complex compound that consists of a porphyrins ring with high symmetry that acts as ligands with magnesium as the central ion. Chlorophyll a has been studied for many years from different point of views for both experimental and theoretical interests. In this study, the restricted Hartree-Fock configuration interaction single (RHF/CIS), time-dependent density functional theory (TDDFT) and some semi-empirical methods (CNDO/s and ZINDO) calculations were carried out and compared to reconstruct the UV-Vis absorption spectra of chlorophyll a. In some extend, the calculation results based on a single molecule calculation were succeeded to reconstruct the absorption spectra but required to be scaling and broaden to match the experimental one. Different computational methods (ab initio and semi-empirical) exhibits the differences i...
Directory of Open Access Journals (Sweden)
Veinardi Suendo
2012-07-01
Full Text Available Chlorophyll a is one the most abundant pigment on Earth that responsible for trapping the light energy to perform photosynthesis in green plants. This molecule has been studied for many years from different point of views in both experimental and theoretical interests. In this study, the restricted Hartree-Fock configuration interaction single (RHF/CIS, time-dependent density functional theory (TDDFT and several semi-empirical methods (CNDO/s and ZINDO calculations were carried out to reconstruct the UV-Vis absorption spectra of chlorophyll a. In some extend, the calculation results based on single molecule approach were succeeded to reconstruct the absorption spectra but required to be rescaled to fit the experimental one. In general, the semi-empirical methods provide better energy scaling factor that closer to unity. However, they lack of vertical transition fine features with respect to the spectrum obtained experimentally. Here, the ab initio calculations provide more complete features, especially the TDDFT at high level of basis sets that also has a good accuracy in the transition energies. The contribution of ground states and excited states orbitals in the main vertical transitions is discussed based on delocalization nature of the wavefunctions and the presence of solvent through polarizable continuum model (PCM.
Energy Technology Data Exchange (ETDEWEB)
Bouteiller, Y. [Universite Paris-Nord, CNRS, Laboratoire de Physique des Lasers UMR 7538, 93430 Villetaneuse (France); Tremblay, B. [UPMC Universite Pierre et Marie Curie, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France); CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France); Perchard, J.P., E-mail: jpp@spmol.jussieu.fr [UPMC Universite Pierre et Marie Curie, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France); CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France)
2011-07-28
Graphical abstract: The spectrum of the water dimer trapped in neon has been recorded and analysed up to 14,000 cm{sup -1}. Highlights: {yields} Observation of the vibrational spectrum of the water dimer from the far infrared to the visible. {yields} Assignment based on {sup 18}O/{sup 16}O shift and on approximate values of anharmonicity coefficients. {yields} Calculations in the framework of the second-order perturbation - resonance theory. - Abstract: The infrared spectrum of the water dimer trapped in solid neon has been recorded up to the visible by improving significantly the experimental technique used in a previous paper [Y. Bouteiller, J.P. Perchard, Chem. Phys. 305 (2004) 1]. A total of 22 intramolecular transitions of the proton donor (PD) and 23 of the proton acceptor (PA) are now identified and assigned on the basis of {sup 16}O/{sup 18}O isotopic shifts and of realistic anharmonicity corrections. From an ab initio determination of the potential energy a perturbation-resonance treatment has been carried out for each polyad P{sub n}, n = 2-8. Finally combinations of intra + intermolecular transitions were identified and assigned on the basis of calculated anharmonicity coefficients.
Tomza, Michał; Skomorowski, Wojciech; Musiał, Monika; González-Férez, Rosario; Koch, Christiane P.; Moszynski, Robert
2013-07-01
We formulate the theory for a diatomic molecule in a spatially degenerate electronic state interacting with a non-resonant laser field and investigate its rovibrational structure in the presence of the field. We report on ab initio calculations employing the double electron attachment intermediate Hamiltonian Fock space coupled cluster method restricted to single and double excitations for all electronic states of the Rb2 molecule up to 5s+5d dissociation limit of about 26,000 cm-1. In order to correctly predict the spectroscopic behaviour of Rb2, we have also calculated the electric transition dipole moments, non-adiabatic coupling and spin-orbit coupling matrix elements, and static dipole polarisabilities, using the multireference configuration interaction method. When a molecule is exposed to strong non-resonant light, its rovibrational levels get hybridised. We study the spectroscopic signatures of this effect for transitions between the X1Σ+ g electronic ground state and the A1Σ+ u and b3Π u excited state manifold. The latter is characterised by strong perturbations due to the spin-orbit interaction. We find that for non-resonant field strengths of the order 109 W/cm2, the spin-orbit interaction and coupling to the non-resonant field become comparable. The non-resonant field can then be used to control the singlet-triplet character of a rovibrational level.
Energy Technology Data Exchange (ETDEWEB)
Rosso, E.F. [Departamento de Química, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS (Brazil); Baierle, R.J., E-mail: rbaierle@smail.ufsm.br [Departamento de Física, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS (Brazil); Orellana, W. [Departamento de Ciencias Físicas, Universidad Andres Bello, República 220, 837-0134 Santiago (Chile); Miwa, R.H. [Instituto de Física, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG (Brazil)
2015-12-01
Graphical abstract: - Highlights: • β-SiC(0 0 1) surface. • Hydrogenation. • DFT calculations – PBE and HSE06 functional for the exchange correlation term. • Nanotunnel formation. • Electronic confinement. - Abstract: The structural and electronic properties of pristine and H-passivated C-terminated β-SiC(0 0 1)-c(2 × 2) surface are addressed by ab initio calculations. Here, we verify the formation of C chains composed by double-bonded dimers rows (C=C), separated by triple-bonded bridged dimers (C≡C). The surface states near the bandgap are confined along the C=C dimer rows, with no electronic contribution from the C≡C bridged dimers. After hydrogenation, the C-chains are strongly modified, forming subsurface voids or nanotunnel (NT) structures. By considering a plausible set of energy release steps for increasing hydrogenation, we obtain a C-rich NT ruled by the C=C dimer rows. Somewhat similar to that recently reported on the Si-rich termination, but 0.8 eV lower in energy. The electronic band structures of both Si-rich and C-rich NTs have been examined within the hybrid HSE06 functional, which are compared with those previously reported using a semilocal functional.
Ab initio study of phase equilibria in TiCx
DEFF Research Database (Denmark)
Korzhavyi, P.A.; Pourovskii, L.V.; Hugosson, H.W.
2002-01-01
The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, ......3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures....
Phonocatalysis. An ab initio simulation experiment
Directory of Open Access Journals (Sweden)
Kwangnam Kim
2016-06-01
Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Ab initio phonon scattering by dislocations
Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.
2017-06-01
Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.
Jong, Un-Gi; Yu, Chol-Jun; Jang, Yong-Man; Ri, Gum-Chol; Hong, Song-Nam; Pae, Yong-Hyon
2017-05-01
A little addition of Cl to MAPbI3 has been reported to improve the material stability as well as light harvesting and carrier conducting properties of organometal trihalide perovskites, the key component of perovskite solar cell (PSC). However, the mechanism of performance enhancement of PSC by Cl addition is still unclear. Here, we apply the efficient virtual crystal approximation method to revealing the effects of Cl addition on the structural, electronic, optical properties and material stability of MAPb(I1-xClx)3. Our ab initio calculations present that as the increase of Cl content cubic lattice constants and static dielectric constants decrease linearly, while band gaps and exciton binding energies increase quadratically. Moreover, we find the minimum of exciton binding energy at the Cl content of 7%, at which the chemical decomposition reaction changes coincidentally to be from exothermic to endothermic. Interactions among constituents of compound and electronic charge transferring during formation are carefully discussed. This reveals new prospects for understanding and designing of stable, high efficiency PSCs.
Strand, T. G.; Tafipolsky, M. A.; Vilkov, L. V.; Volden, H. V.
1998-02-01
The molecular structures of gaseous o-fluorobenzaldehyde and m-fluorobenzaldehyde have been determined by a joint analysis of gas electron diffraction data, rotational constants from microwave spectroscopy, and constrained by results from ab initio calculations (at HF/6-331G∗∗ level). The torsion of the formyl group has been treated as a large-amplitude motion. The most important structure parameters ( rg)) from the joint analysis with estimated total errors (in parentheses) are for o-fluorobenzaldehyde: ( C C) mean = 1.3999(2) Å, C F = 1.334(5) Å, C C( O = 1.515(6) Å, C O = 1.216(3) Å, ∠CC FC = 122.0(2)°, ∠CC CHOC = 120.3(6)° and for m-fluorobenzaldehyde: ( C C) mean = 1.394(2) Å, C F = 1.346(4) Å, C C( O = 1.494(4) Å, C O = 1.201(2) Å, ∠CC FC = 122.3(1)°, and ∠CC CHOC = 120.6(3)°. The scaled molecular force fields have been determined.
Highly scalable Ab initio genomic motif identification
Marchand, Benoit
2011-01-01
We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.
Moynier, Frédéric; Fujii, Toshiyuki; Wang, Kun; Foriel, Julien
2013-05-01
Iron is one of the most abundant transition metal in higher plants and variations in its isotopic compositions can be used to trace its utilization. In order to better understand the effect of plant-induced isotopic fractionation on the global Fe cycling, we have estimated by quantum chemical calculations the magnitude of the isotopic fractionation between different Fe species relevant to the transport and storage of Fe in higher plants: Fe(II)-citrate, Fe(III)-citrate, Fe(II)-nicotianamine, and Fe(III)-phytosiderophore. The ab initio calculations show firstly, that Fe(II)-nicotianamine is ˜3‰ (56Fe/54Fe) isotopically lighter than Fe(III)-phytosiderophore; secondly, even in the absence of redox changes of Fe, change in the speciation alone can create up to ˜1.5‰ isotopic fractionation. For example, Fe(III)-phytosiderophore is up to 1.5‰ heavier than Fe(III)-citrate2 and Fe(II)-nicotianamine is up to 1‰ heavier than Fe(II)-citrate. In addition, in order to better understand the Fe isotopic fractionation between different plant components, we have analyzed the iron isotopic composition of different organs (roots, seeds, germinated seeds, leaves and stems) from six species of higher plants: the dicot lentil (Lens culinaris), and the graminaceous monocots Virginia wild rye (Elymus virginicus), Johnsongrass (Sorghum halepense), Kentucky bluegrass (Poa pratensis), river oat (Uniola latifolia), and Indian goosegrass (Eleusine indica). The calculations may explain that the roots of strategy-II plants (Fe(III)-phytosiderophore) are isotopically heavier (by about 1‰ for the δ56Fe) than the upper parts of the plants (Fe transported as Fe(III)-citrate in the xylem or Fe(II)-nicotianamine in the phloem). In addition, we suggest that the isotopic variations observed between younger and older leaves could be explained by mixing of Fe received from the xylem and the phloem.
Directory of Open Access Journals (Sweden)
Gümüs Hacer Pir
2015-06-01
Full Text Available Quantum chemical calculations have been performed to study the molecular geometry, 1H and 13C NMR chemical shifts, conformational, natural bond orbital (NBO and nonlinear optical (NLO properties of the 2-chloro-5-(2-hydroxyethyl-4- methoxy-6-methylpyrimidine molecule in the ground state using DFT and HF methods with 6-311++G(d,p basis set. The optimized geometric parameters and 1H and 13C NMR chemical shifts have been compared with the experimental values of the title molecule. The results of the calculations show excellent agreement between the experimental and calculated frequencies at B3LYP/6-311++G(d,p level. In order to provide a full understanding of the properties of the title molecule in the context of molecular orbital picture, the highest occupied molecular energy level (EHOMO, the lowest unoccupied molecular energy level (ELUMO, the energy difference (DE between EHOMO and ELUMO, electronegativity (χ, hardness (η and softness (S have been calculated using B3LYP/6-311++G(d,p and HF/6-311++G(d,p levels. The calculated HOMO and LUMO energies show that the charge transfer occurs within the title molecule.
Coccia, Emanuele; Varsano, Daniele; Guidoni, Leonardo
2014-02-11
In this letter, we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) Å, larger than the values obtained by DFT (PBE, B3LYP, and CAM-B3LYP) and shorter than that calculated at the Hartree-Fock (HF) level. TDDFT and EOM-CCSD calculations on a reduced peridinin model confirm the HOMO-LUMO major contribution of the Bu(+)-like (S2) bright excited state. Many Body Green's Function Theory (MBGFT) calculations of the vertical excitation energy of the Bu(+)-like state for the VMC structure (VMC/MBGFT) provide an excitation energy of 2.62 eV, in agreement with experimental results in n-hexane (2.72 eV). The dependence of the excitation energy on the bond length alternation in the MBGFT and TDDFT calculations with different functionals is discussed.
Electronic states and nature of bonding in the molecule MoC by all electron ab initio calculations
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl A.
1997-01-01
by solving the Schrodinger equation for the nuclear motion numerically. Based on the results of the CASSCF calculations the (3) Sigma(-) ground state of MoC is separated from the excited states (3) Delta, (5) Sigma-, (1) Sigma, (1) Delta, (5) Pi, (1) Sigma(+), and (3) Pi by transition energies of 4500, 6178...... Darwin contact term and the relativistic mass-velocity correction have been determined in perturbation calculations. The electronic ground state is predicted as (3) Sigma(-). The spectroscopic constants for the (3) Sigma(-) electronic ground state and eight low-lying excited states have been derived......, 7207, 9312, 10 228, 11 639, and 16 864 cm(-1), respectively. The transition energy between the (3) Sigma(-) ground state and the (3) Pi state as derived in the MRCI calculations is 15 484 cm(-1). For the (3) Sigma(-) ground state the equilibrium distance has been determined as 1.688 Angstrom...
Energy Technology Data Exchange (ETDEWEB)
Sundberg, Kenneth Randall [Iowa State Univ., Ames, IA (United States). Dept. of Electrical and Computer Engineering
1976-01-01
A method is developed to optimize the separated-pair independent particle (SPIP) wave function; it is a special case of the separated-pair theory obtained by using two-term natural expansions of the geminals. The orbitals are optimized by a theory based on the generalized Brillouin theorem and iterative configuration interaction (CI) calculations in the space of the SPIP function and its single excitations. The geminal expansion coefficients are optimized by serial 2 x 2 CI calculations. Formulas are derived for the matrix elements. An algorithm to implement the method is presented, and the work needed to evaluate the molecular integrals is discussed.
DEFF Research Database (Denmark)
Bak, Keld L.; Hansen, Aage E.; Ruud, K.
1995-01-01
The second-quantization magnetic dipole operator that arises when London atomic orbitals are used as basis functions is derived. In atomic units, the magnetic dipole operator is defined as the negative of the first derivative of the electronic Hamiltonian containing the interaction with the exter......The second-quantization magnetic dipole operator that arises when London atomic orbitals are used as basis functions is derived. In atomic units, the magnetic dipole operator is defined as the negative of the first derivative of the electronic Hamiltonian containing the interaction...... that the length expression for the rotatory strength in linear response calculations gives gauge-origin-independent results. Sample calculations on ti ans-cyclooctene and its fragments are presented. Compared to conventional orbitals, the basis set convergence of the rotatory strengths calculated in the length...... form using London atomic orbitals is favourable. The rotatory strength calculated for trans-cyclooctene agrees nicely with the corresponding experimental circular dichroism spectrum, but the spectra for the fragment molecules show little resemblance with that of trans-cyclooctene....
Energy Technology Data Exchange (ETDEWEB)
Oda, Y.; Koyama, T.; Funasaka, H. [Japan Nuclear Cycle Development Institute, Tokai Works (Japan)
2000-07-01
Ab initio molecular orbital calculations on the structure and stability of the complex of uranyl nitrate with water or tri-methyl phosphate (TMP) was performed using the Density Functional Theory with the basis set including the relativistic effects. When the aqua uranyl nitrate complex structure was calculated with two water molecules at the first coordination sphere, the optimized complex structure was not in agreement with the experimental data of [UO{sub 2}(NO{sub 3}){sub 2}(H{sub 2}O){sub 6}]. The optimization of the complex structure was improved by taking into account the influence of outer four water molecules at the second coordination sphere, which should bond with inner water molecules through the water hydrogen. It means the solution effect is not negligible for the coordination of the ligands such as water. For the H{sub 3}PO{sub 4} coordination, eight models were preferred, one group had the coordination angle of U-O-P in H{sub 3}PO{sub 4} is bent, and other group had straight and the four combinations of the direction of three O-H groups. [UO{sub 2}(NO{sub 3})2(H{sub 3}PO{sub 4}){sub 2}] had greater stability, when U-O-P angle was bent, and there were on the equatorial plane. Finally, the structure of [UO{sub 2}(NO{sub 3}){sub 2}TMP{sub 2}] is optimized, and the optimized geometry has agreement with experimental values. From the comparison of H{sub 3}PO{sub 4} and TMP coordination, the alkyl group in the organophosphorus ligand strongly influences the bond angle of U-O-P. (authors)
Theoretical calculations of high-pressure phases of NiF2: An ab initio constant-pressure study
Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya
2016-12-01
We have studied the structural properties of the antiferromagnetic NiF2 tetragonal structure with P42/ mnm symmetry using density functional theory (DFT) under rapid hydrostatic pressure up to 400 GPa. For the exchange correlation energy we used the local density approximation (LDA) of Ceperley and Alder (CA). Two phase transformations are successfully observed through the simulations. The structures of XF2-type compounds crystallize in rutile-type structure. NiF2 undergoes phase transformations from the tetragonal rutile-type structure with space group P42/ mnm to orthorhombic CaCl2-type structure with space group Pnnm and from this orthorhombic phase to monoclinic structure with space group C2/ m at 152 GPa and 360 GPa, respectively. These phase changes are also studied by total energy and enthalpy calculations. According to these calculations, we perdict these phase transformations at about 1.85 and 30 GPa.
DEFF Research Database (Denmark)
Holland, D.M.P.; Shaw, D.A.; Stener, Mauro
2016-01-01
absorption bands due to excitation from the 1e00 or 6e0 orbitals. The interpretation of the experimental spectrum has been guided by transition energies and oscillator strengths, for Rydberg and valence states, calculated with the time-dependent version of density functional theory and with the coupled...... cluster linear response approach. The theoretical studies indicate that Rydberg/Rydberg and Rydberg/valence mixing is important....
GAUSSIAN 76: an ab initio molecular orbital program
Energy Technology Data Exchange (ETDEWEB)
Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.
1978-06-01
Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.
GAUSSIAN 76: An ab initio Molecular Orbital Program
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 calculation of structural and magnetic properties for Fe mono- and bilayers on Mo(1 1 0)
Qian, X; Petersen, M; Hübner, W
2000-01-01
The atomic structures were optimized and magnetic moments calculated for the pseudomorphic Fe overlayers on Mo(1 1 0) substrates employing the all-electron full-potential linearized augmented plane-wave (FP-LAPW) method. Three slabs were considered: (i) 5 monolayer (ML) Mo(1 1 0) substrate, (ii) and (iii) 1 and 2 ML pseudomorphic Fe overlayers on each side of 5 ML Mo(1 1 0) substrate. We found that for the bare Mo substrate, the top Mo-Mo interlayer spacing is contracted by 4.8% with respect to the theoretical bulk Mo(1 1 0) interlayer distance of 2.238 A. For the 1 ML Fe coverage, the Fe-Mo interlayer spacing has a contraction of 10.3% with respect to the calculated bulk Mo(1 1 0) interlayer spacing, while, for the 2 ML Fe, it is reduced by 9.5%. The Fe-Fe interlayer spacing is also contracted by as much as 11.4% with respect to the theoretical bulk Fe(1 1 0) interlayer distance of 2.004 A. The inner Mo-Mo interlayer spacings are slightly expanded (<0.5%). The magnetic moment for the 1 ML Fe overlayer on ...
Directory of Open Access Journals (Sweden)
Ali Hossein Kianfar
2017-12-01
Full Text Available In this research, structures of M(BAE (where M = VO(IV, Zn(II, Cu(II and Ni (II, BAE = bis(acetylacetoneethylenediimine, [Ni(BFE], [Ni(BBE] and [Ni(BCE] (where BFE = bis(1,1,1-triflouroacetylacetoneethylenediimine, BBE = bis(benzoylacetoneethylenediimine and BCE = bis(3-hloroacetylacetoneethylenediimine were determined by MP2 theoretical study. The thermodynamics of the tautomerism reactions was studied and the equilibrium constant of the reactions was calculated. The optimized molecular geometry and atomic charges were calculated using MP2 method with 6-31G(d basis set and compared with the reported X-ray data. Nickel and copper complexes have a planar structure while the zinc structure shows a distorted square-planar N2O2 coordination geometry. The vanadyl structure has a square-pyramide N2O3 coordination geometry. Also the bond lengths and the bond angles were studied and compared.
Energy Technology Data Exchange (ETDEWEB)
Kostko, Oleg; Ahmed, Musahid; Metz, Ricardo B.
2008-12-05
In this work we report on the detection and vacuum-ultraviolet (VUV) photoionization of gas phase SiO2 generated in situ via laser ablation of silicon in a CO2 molecular beam. The resulting species are investigated by single photon ionization with tunable VUV synchrotron radiation and mass analyzed using reflectron mass spectrometry. Photoionization efficiency (PIE) curves are recorded for SiO and SiO2 and ionization energy estimates are revealed from such measurements. A state-to-state ionizationenergy of 12.60 (+-0.05) eV is recorded by fitting two prominent peaks in the PIE curve for the following process: 1SUM O-Si-O --> 2PRODg [O-Si-O]+. Electronic structure calculations aid in the interpretation of the photoionization process and allow for identification of the symmetric stretch of 2PRODg [O-Si-O]+ which is observed in the PIE spectrum to be 0.11 eV (890 cm-1) above the ground state of the cation and agrees with the 892 cm-1 symmetric stretch frequency calculated at the CCSD(T)/aug-cc-pVTZ level.
Energy Technology Data Exchange (ETDEWEB)
Matar, Samir F. [CNRS, ICMCB, UPR 9048, Pessac (France); Bordeaux Univ., Pessac (France). ICMCB, UPR 9048; Al Alam, Adel F.; Ouaini, Naim [Univ. Saint Esprit de Kaslik (USEK), Jounieh (Lebanon). URA GREVE, CSR-USEK
2013-01-15
For equiatomic MgNi which can be hydrogenated up to the composition MgNiH{sub 1.6} at an absorption/desorption temperature of 200 C, the effects of hydrogen absorption are approached with the model structures MgNiH, MgNiH{sub 2} and MgNiH{sub 3}. From full geometry optimization and calculated cohesive energies obtained within DFT, the MgNiH{sub 2} composition close to the experimental limit is identified as most stable. Charge density analysis shows an increasingly covalent character of hydrogen: MgNiH(H{sup -0.67}) {yields} MgNiH{sub 2}(H{sup -0.63}) {yields} MgNiH{sub 3}(H{sup -0.55}). While Mg-Ni bonding prevails in MgNi and hydrogenated model phases, extra itinerant low-energy Ni states appear when hydrogen is introduced signaling Ni-H bonding which prevails over Mg-H as evidenced from total energy calculations and chemical bonding analyses. (orig.)
Directory of Open Access Journals (Sweden)
Mariya G. Ganchenkova
2015-12-01
Full Text Available Point defects play a key role in many microelectronics technologies. Knowledge of the properties of point defects and characteristics of their behavior during ion-beam synthesis of microstructures for use in silicon devices allows one to optimize the conditions of their production, improve their quality and the electronic properties. In this situation, of valuable help in studying the properties of point defects is numerical modeling, especially with the use of quantum mechanical methods based on density functional theory approach. The paper describes a systematic study of the effect of various quantum–mechanical simulation approximations on the calculated energy parameters of defects as applied to simple point defects in silicon. We demonstrate that the choice of the form of the exchange–correlation functional has the strongest effect on the predicted defect formation energy, whereas the variation of the other considered approximations is of secondary importance for simulation predictions.
Chi, C.-C.; Hsiao, C.-H.; Skoropata, E.; van Lierop, J.; Ouyang, Chuenhou Hao
2015-05-01
Significant efforts towards understanding bi-magnetic core-shell nanoparticles are underway currently as they provide a pathway towards properties unavailable with single-phased systems. Recently, we have demonstrated that the magnetism of γ-Fe2O3/CoO core-shell nanoparticles, in particular, at high temperatures, originates essentially from an interfacial doped iron-oxide layer that is formed by the migration of Co2+ from the CoO shell into the surface layers of the γ-Fe2O3 core [Skoropata et al., Phys. Rev. B 89, 024410 (2014)]. To examine directly the nature of the intermixed layer, we have used high-resolution transmission electron microscopy (HRTEM) and first-principles calculations to examine the impact of the core-shell intermixing at the atomic level. By analyzing the HRTEM images and energy dispersive spectra, the level and nature of intermixing was confirmed, mainly as doping of Co into the octahedral site vacancies of γ-Fe2O3. The average Co doping depths for different processing temperatures (150 °C and 235 °C) were 0.56 nm and 0.78 nm (determined to within 5% through simulation), respectively, establishing that the amount of core-shell intermixing can be altered purposefully with an appropriate change in synthesis conditions. Through first-principles calculations, we find that the intermixing phase of γ-Fe2O3 with Co doping is ferromagnetic, with even higher magnetization as compared to that of pure γ-Fe2O3. In addition, we show that Co doping into different octahedral sites can cause different magnetizations. This was reflected in a change in overall nanoparticle magnetization, where we observed a 25% reduction in magnetization for the 235 °C versus the 150 °C sample, despite a thicker intermixed layer.
Ab initio calculations of ideal strength and lattice instability in W-Ta and W-Re alloys
Yang, Chaoming; Qi, Liang
2018-01-01
An important theoretical criterion to evaluate the ductility of metals with a body-centered cubic (bcc) lattice is the mechanical failure mode of their perfect crystals under tension along ; directions. When the tensile stress reaches the ideal tensile strength, the pure W crystal fails by a cleavage fracture along the {100 } plane so that it is intrinsically brittle. To discover the strategy to improve its ductility, we performed density functional theory and density functional perturbation theory calculations to study the ideal tensile strength and the lattice instability under tension for both W-Ta and W-Re alloys. Anisotropic linear elastic fracture mechanics (LEFM) theory and Rice's criterion were also applied to analyze the mechanical instability at the crack tip under tension based on the competition between cleavage propagation and dislocation emission. The results show that the intrinsic ductility can be achieved in both W-Ta and W-Re, however, by different mechanisms. Even though W-Ta alloys with low Ta concentrations are still intrinsically brittle, the intrinsic ductility of W-Ta alloys with high Ta concentrations is promoted by elastic shear instability before the cleavage failure. The intrinsic ductility of W-Re alloys is produced by unstable transverse phonon waves before the cleavage failure, and the corresponding phonon mode is related to the generation of 1/2 {2 ¯11 } dislocation in bcc crystals. The ideal tensile calculations, phonon analyses, and anisotropic LEFM examinations are mutually consistent in the evaluation of intrinsic ductility. These results bring us physical insights on the ductility-brittle mechanisms of W alloys under extreme stress conditions.
Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry
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
Rafique, Muhammad; Shuai, Yong; Xu, Meng; Zhang, Guohua; Guo, Yanming
2017-09-01
Graphene-based magnetic materials have revealed great potential for developing high-performance electronic units at sub-nanometer such as spintronic data storage devices. However, a significant ferromagnetism behavior and ample band gap in the electronic structure of graphene is required before it can be used for actual engineering applications. Based on first-principles calculations, here we demonstrate the structural, electronic and magnetic behaviors of 5d transition metal (TM) atom-substituted nitrogenized monolayer graphene. We find that, during TMN(3)4 cluster-substitution, tight bonding occurs between impurity atoms and graphene with significant binding energies. Charge transfer occurs from graphene layer to the TMN(3)4 clusters. Interestingly, PtN3, TaN4 and ReN4 cluster-doped graphene structures exhibit dilute magnetic semiconductor behavior with 1.00 μB, 1.04 μB and 1.05 μB magnetic moments, respectively. While, OsN4 and PtN4 cluster-doped structures display nonmagnetic direct band gap semiconductor behavior. Remaining, TMN(3)4 cluster-doped graphene complexes exhibit half metal properties. Detailed analysis of density of states (DOS) plots indicate that d orbitals of TM atoms should be responsible for arising magnetic moments in graphene. Given results pave a new route for potential applications of dilute magnetic semiconductors and half-metals in spintronic devices by employing TMN(3)4 cluster-doped graphene complexes.
Koettgen, Julius; Schmidt, Peter C.; Bučko, Tomáš; Martin, Manfred
2018-01-01
We have studied the free energy migration barriers Δ F‡ for oxygen diffusion in pure ceria and Sm-doped ceria for the temperatures 300, 700, and 1000 K. We used the density functional theory in the generalized gradient approximation and an additional Hubbard U parameter for the Ce 4 f electronic states. We compare the results for the free energy deduced from three different methods. First, a static harmonic approach is applied in which the temperature dependent vibrational contributions to energy and entropy are deduced from the phonon frequencies of supercells with a fixed volume. Second, a static quasiharmonic approach is used in which a part of the anharmonicity effect is introduced via an implicit dependence of the harmonic frequencies on the thermally expanding cell volume. Third, the free energy barriers are calculated using metadynamics and molecular dynamics in which anharmonicity effects are naturally taken into account. The three methods examined in this study lead to distinctly different results. According to the harmonic approximation, the migration free energy difference Δ F‡ increases with increasing temperature due to an increasing entropic contribution. According to the quasiharmonic approximation, the migration free energy is independent of temperature. Finally, molecular dynamics predicts a thermally induced increase in the migration free energy. We conclude that temperature dependent experimental lattice constants cancel out the increasing entropic contribution with increasing temperature in the static quasiharmonic approach. The full consideration of anharmonicity effects in the metadynamics method again leads to a temperature dependent migration free energy.
Electronic structure of ceramic CrSi2 and WSi2: Compton spectroscopy and ab-initio calculations
Bhamu, K. C.; Sahariya, Jagrati; Ahuja, B. L.
2013-05-01
We report electron momentum densities of stable phases of transition metal disilicides CrSi2 (C40 hexagonal) and WSi2 (C11b body centered tetragonal) using a high energy 137Cs Compton spectrometer. To support the experimental investigations, we have computed theoretical Compton profiles, energy bands and density of states of both the isoelectronic compounds using density functional theory within linear combination of atomic orbitals. Theoretical calculations for the energy bands and density of states are performed for both the hexagonal and tetragonal phases of these silicides. In the tetragonal phase, both the silicides show metallic behavior. The hexagonal CrSi2 shows an energy gap (0.28 eV) between the valence band maximum at the L point and the conduction band minimum at the M point of the Brillouin zone, whereas the hexagonal WSi2 shows a semimetallic character. We have also scaled the experimental and theoretical profiles of the stable phases (hexagonal for CrSi2 and tetragonal for WSi2) on equal-valence-electron-density, which show more covalent character of WSi2 than that of CrSi2. The nature of bonding is in accordance with a present Mulliken's population analysis.
Drablia, S.; Boukhris, N.; Boulechfar, R.; Meradji, H.; Ghemid, S.; Ahmed, R.; Omran, S. Bin; El Haj Hassan, F.; Khenata, R.
2017-10-01
The alkaline earth metal chalcogenides are being intensively investigated because of their advanced technological applications, for example in photoluminescent devices. In this study, the structural, electronic, thermodynamic and thermal properties of the BaSe1-x Te x alloys at alloying composition x = 0, 0.25, 0.50, 0.75 and 1 are investigated. The full potential linearized augmented plane wave plus local orbital method designed within the density functional theory was used to perform the total energy calculations. In this research work the effect of the composition on the results of the parameters and bulk modulus as well as on the band gap energy is analyzed. From our results, we found a deviation of the obtained results for the lattice constants from Vegard’s law as well as a deviation of the value of the bulk modulus from the linear concentration dependence. We also carried out a microscopic analysis of the origin of the band gap energy bowing parameter. Furthermore, the thermodynamic stability of the considered alloys was explored through the measurement of the miscibility critical temperature. The quasi-harmonic Debye model, as implemented in the Gibbs code, was used to predict the thermal properties of the BaSe1-x Te x alloys, and these investigations comprise our first theoretical predictions concerning the BaSe1-x Te x alloys.
Fedorov, Dmitry A; Barnes, Dustin K; Varganov, Sergey A
2017-09-28
We investigate the lifetimes of vibrational states of diatomic alkali-alkaline-earth cations to determine their suitability for ultracold experiments where long decoherence time and controllability by an external electric field are desirable. The potential energy and permanent dipole moment curves for the ground electronic states of LiBe + , LiMg + , NaBe + , and NaMg + are obtained using the coupled cluster with singles doubles and triples and multireference configuration interaction methods in combination with large all-electron cc-pCVQZ and aug-cc-pCV5Z basis sets. The energies and wave functions of all vibrational states are obtained by solving the Schrödinger equation for nuclei with the B-spline basis set method. To predict the lifetimes of vibrational states, the transition dipole moments, as well as the Einstein coefficients describing spontaneous emission, and the stimulated absorption and emission induced by black body radiation are calculated. Surprisingly, in all studied ions, the lifetimes of the highest excited vibrational states are similar to the lifetimes of the ground vibrational states indicating that highly vibrationally excited ions could be useful for the ultracold experiments requiring long decoherence time.
Fedorov, Dmitry A.; Barnes, Dustin K.; Varganov, Sergey A.
2017-09-01
We investigate the lifetimes of vibrational states of diatomic alkali-alkaline-earth cations to determine their suitability for ultracold experiments where long decoherence time and controllability by an external electric field are desirable. The potential energy and permanent dipole moment curves for the ground electronic states of LiBe+, LiMg+, NaBe+, and NaMg+ are obtained using the coupled cluster with singles doubles and triples and multireference configuration interaction methods in combination with large all-electron cc-pCVQZ and aug-cc-pCV5Z basis sets. The energies and wave functions of all vibrational states are obtained by solving the Schrödinger equation for nuclei with the B-spline basis set method. To predict the lifetimes of vibrational states, the transition dipole moments, as well as the Einstein coefficients describing spontaneous emission, and the stimulated absorption and emission induced by black body radiation are calculated. Surprisingly, in all studied ions, the lifetimes of the highest excited vibrational states are similar to the lifetimes of the ground vibrational states indicating that highly vibrationally excited ions could be useful for the ultracold experiments requiring long decoherence time.
Maurer, Patrick; Iftimie, Radu
2010-02-21
We introduce a novel approach to compute dissociation free energy and entropy values in simulations that employ a density functional theory description of the acidic moiety and of the solvent. The approach consists of utilizing an alchemical transformation of a weak acid A-COOH into the strong acid B-COOH, which makes it practical to employ alchemical free energy perturbation methods in the context of ab initio molecular dynamics simulations. The present alchemical transformation circumvents the need to tackle changes in the total number of electrons and atoms by replacing the chemical residue responsible for the change in acidity with an easily tunable external effective potential. Our investigation demonstrates that (1) a simple but effective class of external potentials that control acidity changes in the acetic/trifluoroacetic acid series can be achieved by replacing the methyl and trifluoromethyl substituents by screened dipoles. Using this dipole-field/quantum-mechanics (DF/QM) approach one can predict gas-phase geometries, proton dissociation energies, total dipole moments, and water binding energies in good agreement with full-QM values. (2) The resulting alchemical perturbation calculations are stable and well converged and allow one to compute absolute pK(a) values whose accuracy is limited primarily by the exchange-correlation functional employed: H-COOH=2.5+/-0.6 (full-QM calculation), 3.7 (exp); F(3)C-COOH=0.4+/-0.6 (DF/QM calculation), 0.5 (exp); H(3)C-COOH=3.1+/-0.7 (DF/QM calculation), 4.7 (exp); 3) Our DF/QM model predicts that the difference in acidity between H-COOH and H(3)C-COOH is dominated by solvent entropy effects, in excellent agreement with experimental observations. The calculated difference between the dissociation energies of these acids is DeltaDelta(d)U=0.0+/-0.26 kcal/mol while the experimental value is 0.0+/-0.1 kcal/mol.
Goodrow, Anthony; Bell, Alexis T.; Head-Gordon, Martin
2008-11-01
Transition state search algorithms, such as the nudged elastic band can fail, if a good initial guess of the transition state structure cannot be provided. The growing string method (GSM) [J. Chem. Phys. 120, 7877 (2004)] eliminates the need for an initial guess of the transition state. While this method only requires knowledge of the reactant and product geometries, it is computationally intensive. To alleviate the bottlenecks in the GSM, several modifications were implemented: Cartesian coordinates were replaced by internal coordinates, the steepest descent method for minimization of orthogonal forces to locate the reaction path was replaced by the conjugate gradient method, and an interpolation scheme was used to estimate the energy and gradient, thereby reducing the calls to the quantum mechanical (QM) code. These modifications were tested to measure the reduction in computational time for four cases of increasing complexity: the Müller-Brown potential energy surface, alanine dipeptide isomerization, H abstraction in methanol oxidation, and C-H bond activation in oxidative carbonylation of toluene to p-toluic acid. These examples show that the modified GSM can achieve two- to threefold speedups (measured in terms of the reduction in actual QM gradients computed) over the original version of the method without compromising accuracy of the geometry and energy of the final transition state. Additional savings in computational effort can be achieved by carrying out the initial search for the minimum energy pathway (MEP) using a lower level of theory (e.g., HF/STO-3G) and then refining the MEP using density functional theory at the B3LYP level with larger basis sets (e.g., 6-31G∗, LANL2DZ). Thus, a general strategy for determining transition state structures is to initiate the modified GSM using a low level of theory with minimal basis sets and then refining the calculation at a higher level of theory with larger basis sets.
Den, Takuya; Menzi, Samuel; Frey, Hans-Martin; Leutwyler, Samuel
2017-08-01
p-Dioxane is non-polar, hence its rotational constants cannot be determined by microwave rotational coherence spectroscopy (RCS). We perform high-resolution gas-phase rotational spectroscopy of para-dioxane-h8 and -d8 using femtosecond time-resolved Raman RCS in a gas cell at T = 293 K and in a pulsed supersonic jet at T ˜130 K. The inertial tensor of p-dioxane-h8 is strongly asymmetric, leading to a large number of asymmetry transients in its RCS spectrum. In contrast, the d8-isotopomer is a near-oblate symmetric top that exhibits a much more regular RCS spectrum with few asymmetry transients. Fitting the fs Raman RCS transients of p-dioxane-h8 to an asymmetric-top model yields the ground-state rotational constants A0 = 5084.4(5) MHz, B0 = 4684(1) MHz, C0 = 2744.7(8) MHz, and (A0 + B0)/2 = 4884.5(7) MHz (±1 σ ). The analogous values for p-dioxane-d8 are A0 = 4083(2) MHz, B0 = 3925(4) MHz, C0 = 2347.1(6) MHz, and (A0 + B0)/2 = 4002.4(6) MHz. We determine the molecular structure with a semi-experimental approach involving the highly correlated coupled-cluster singles, doubles and iterated triples method and the cc-pCVXZ basis set series from double- to quadruple-zeta (X = D, T, Q). Combining the calculated vibrationally averaged rotational constants A0c a l c(X ) ,B0c a l c(X ) ,C0c a l c(X ) for increasing basis-set size X with non-linear extrapolation to the experimental constants A0e x p,B0e x p,C0e x p allows to determine the equilibrium ground state structure of p-dioxane. For instance, the equilibrium C-C and C-O bond lengths are re(CC) = 1.5135(3) Å and re(CO) = 1.4168(4) Å, and the four axial C-H bond lengths are 0.008 Å longer than the four equatorial ones. The latter is ascribed to the trans-effect (anomeric effect), i.e., the partial delocalization of the electron lone-pairs on the O atoms that are oriented trans, relative to the axial CH bonds.
Cheng, Tao; Xiao, Hai; Goddard, William A
2017-02-21
A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of -0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than -0.6 V (RHE) ethylene, the major product, is produced via the Eley-Rideal (ER) mechanism using H2O + e- The rate-determining step (RDS) is C-C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than -0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than -0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4 These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface.
Narula, Chaitanya K; Allard, Lawrence F; Wu, Zili
2017-07-24
The ab initio density functional theoretical studies show that energetics favor CO oxidation on single Pd atoms supported on θ-alumina. The diffuse reflectance infra-red spectroscopy (DRIFTS) results show that carbonates are formed as intermediates when single supported Pd atoms are exposed to a gaseous mixture of CO + O 2 . The rapid agglomeration of Pd atoms under CO oxidation conditions even at 6 °C leads to the presence of Pd particles along with single atoms during CO oxidation experiments. Thus, the observed CO oxidation has contributions from both single Pd atoms and Pd particles.
Indian Academy of Sciences (India)
Tufan Roy
2017-06-19
Jun 19, 2017 ... 2Theory and Simulations Laboratory, Human Resources Development Section, Raja Ramanna Centre for Advanced. Technology, Indore 452 013, ... We study the magnetic exchange interaction between the atoms for the materials ..... computing group, computer centre of RRCAT, Indore and P Thander are ...
Energy Technology Data Exchange (ETDEWEB)
Levesque, M.
2010-11-15
Ferritic steels possibly strengthened by oxide dispersion are candidates as structural materials for generation IV and fusion nuclear reactors. Their use is limited by incomplete knowledge of the iron-chromium phase diagram at low temperatures and of the phenomena inducing preferential segregation of one element at grain boundaries or at surfaces. In this context, this work contributes to the multi-scale study of the model iron-chromium alloy and their free surfaces by numerical simulations. This study begins with ab initio calculations of properties related to the mixture of atoms of iron and chromium. We highlight complex dependency of the magnetic moments of the chromium atoms on their local chemical environment. Surface properties are also proving sensitive to magnetism. This is the case of impurity segregation of chromium in iron and of their interactions near the surface. In a second step, we construct a simple energy model for high numerical efficiency. It is based on pair interactions on a rigid lattice to which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that we compare to Monte Carlo simulations. The last step of our work is to introduce free surfaces in our model. We then study the effect of ab initio calculated bulk and surface properties on surface segregation.Finally, we calculate segregation isotherms. We therefore propose an evolution model of surface composition of iron-chromium alloys as a function of bulk composition. which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that
Evarestov, R. A.; Bandura, A. V.; Losev, M. V.; Piskunov, S.; Zhukovskii, Yu. F.
2010-11-01
The formalism of line groups for one-periodic (1D) nanostructures with rotohelical symmetry has been applied for construction of TiO 2 nanotubes (NTs). They are formed by rolling up the stoichiometric two-periodic (2D) sheets cut from the energetically stable (1 0 1) anatase surface, which contains either six (O-Ti-O_O-Ti-O) or three (O-Ti-O) layers. After optimization of geometry the former keeps the centered rectangular symmetry of initial slab while the latter is spontaneously reconstructed to the hexagonal fluorite-type (1 1 1) sheet. We have considered the four sets of TiO 2 NTs with optimized 6- and 3-layered structures, which possess the two pairs of either anatase (- n, n) and ( n, n) or fluorite ( n, n) and ( n,0) chiralities, respectively. To analyze their structural and electronic properties, we have performed ab initio LCAO calculations on titania slabs and nanotubes using the hybrid Hartree-Fock/Kohn-Sham exchange-correlation functional PBE0. Both band gaps and strain energies of these nanotubes have been computed as functions of NT diameter consequently changed from 0.5 nm to 4.0 nm with number of atoms per nanotube unit cell increased from 30 up to 288. A ratio of the calculated strain energies between the 3- and 6-layered titania NTs achieves 2-3 for nanotubes with diameters ≤1.0 nm and remains noticeable for those with diameters ≤2.0 nm, i.e., the latter are more stable energetically. When diameters of nanotubes increase up to 4.0 nm these strain energies substantially decrease and approach each other. At the same time, the strain energy of 6-layered NTs with (- n, n) chirality is smaller than that for ( n, n) NTs of a similar diameter, while in 3-layered nanotubes of similar diameters, the difference in strain energies for fluorite-type ( n, n) and ( n,0) chiralities is rather negligible. The band gaps of 6-layered titania nanotubes are found to be noticeably larger as compared to 3-layered NTs with the same diameter. When these diameters
Energy Technology Data Exchange (ETDEWEB)
Hellmann, Robert
2009-06-16
Thermophysical properties of the pure gases helium, neon, methane and water vapor were calculated for low densities over wide temperature ranges. Statistical thermodynamics was used for the determination of the pressure virial coefficients. The kinetic theory of gases was utilized for the calculation of the transport and relaxation properties. So far kinetic theory was limited to linear molecules and has now been extended to molecules of arbitrary geometry to enable calculations on methane and water vapor. The interaction potentials, which are needed for all computations, were determined for helium, neon and methane from the supermolecular approach using quantum chemical ab initio methods. For water the interaction potentials were taken from the literature. The calculated values of the thermophysical properties for the four gases show very good agreement with the best experimental data. At very low and very high temperatures the theoretical values are more accurate than experimental data. (orig.)
Tailoring magnetoresistance at the atomic level: An ab initio study
Tao, Kun
2012-01-05
The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.
Ab initio study of a grain boundary in gold
Needels, M.; Rappe, A. M.; Bristowe, P. D.; Joannopoulos, J. D.
1992-10-01
The total energy of a grain boundary in a transition metal is calculated in an ab initio manner. Such calculations are now feasible using a plane-wave basis set provided that an optimally convergent pseudopotential is used. The investigation focuses on resolving two competing atomic models for the Σ=5 [001] twist boundary in gold. It is found that the model of lower energy, which involves small atomic displacements, corresponds to a structure determined both experimentally, using quantitative x-ray-diffraction techniques, and theoretically, using the embedded-atom method.
Ab initio study of a grain boundary in gold
Energy Technology Data Exchange (ETDEWEB)
Needels, M.; Rappe, A.M.; Bristowe, P.D.; Joannopoulos, J.D. (Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States))
1992-10-15
The total energy of a grain boundary in a transition metal is calculated in an {ital ab} {ital initio} manner. Such calculations are now feasible using a plane-wave basis set provided that an optimally convergent pseudopotential is used. The investigation focuses on resolving two competing atomic models for the {Sigma}=5 (001) twist boundary in gold. It is found that the model of lower energy, which involves small atomic displacements, corresponds to a structure determined both experimentally, using quantitative x-ray-diffraction techniques, and theoretically, using the embedded-atom method.
Energy Technology Data Exchange (ETDEWEB)
Pavloudis, Th. [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece); Zervos, M. [Nanostructured Materials and Devices Laboratory, Department of Mechanical and Manufacturing Engineering, PO Box 20537, Nicosia 1678 (Cyprus); Komninou, Ph. [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece); Kioseoglou, J., E-mail: sifisl@auth.gr [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece)
2016-08-31
We carry out ab initio electronic structure calculations of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} using density functional theory with projector augmented-wave potentials under the generalized gradient approximation. We find that the energetically favorable structure of Sn{sub 3}N{sub 4} is the face-centered cubic spinel structure, followed by the hexagonal structure which has energy band gaps of 1.85 eV and 1.44 eV respectively. The (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} ternary compound can exhibit both cubic and hexagonal crystal structures over the full range of x. However, the cubic structure is found to be energetically favorable for x < 0.3 above which the hexagonal structure of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} dominates. The energy band gap can be tuned continuously from 1.44 eV up to 5.8 eV in the case of the hexagonal crystal structure of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} and from 1.85 eV to 4.82 eV in the case of cubic (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}. Nevertheless the energy gap of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} is direct only for x < 0.3 when it is cubic and for x < 0.5 when hexagonal. - Highlights: • (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} exhibits both cubic and hexagonal crystal structures. • The cubic structure is favorable for x < 0.3 and the hexagonal structure for x > 0.3. • The bandgap of hexagonal (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} may be tuned from 1.44 eV up to 5.8 eV. • The bandgap may be tuned from 1.85 eV to 4.82 eV for the cubic (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}. • Bandgaps are direct for x < 0.3 (cubic) and for x < 0.5 3 (hexagonal (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}).
Energy Technology Data Exchange (ETDEWEB)
Sunahori, Fumie X. [Department of Chemistry and Physics, Franklin College, Franklin, Indiana 46131 (United States); Gharaibeh, Mohammed [Department of Chemistry, The University of Jordan, Amman 11942 (Jordan); Clouthier, Dennis J., E-mail: dclaser@uky.edu [Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055 (United States); Tarroni, Riccardo [Dipartimento di Chimica Industriale “Toso Montanari,” Università di Bologna, Viale Risorgimento 4, 40136 Bologna (Italy)
2015-05-07
The spectroscopy of gas phase BH{sub 2} has not been explored experimentally since the pioneering study of Herzberg and Johns in 1967. In the present work, laser-induced fluorescence (LIF) spectra of the A{sup ~} {sup 2}B{sub 1}(Π{sub u})−X{sup ~2}A{sub 1} band system of {sup 11}BH{sub 2}, {sup 10}BH{sub 2}, {sup 11}BD{sub 2}, and {sup 10}BD{sub 2} have been observed for the first time. The free radicals were “synthesized” by an electric discharge through a precursor mixture of 0.5% diborane (B{sub 2}H{sub 6} or B{sub 2}D{sub 6}) in high pressure argon at the exit of a pulsed valve. A total of 67 LIF bands have been measured and rotationally analyzed, 62 of them previously unobserved. These include transitions to a wide variety of excited state bending levels, to several stretch-bend combination levels, and to three ground state levels which gain intensity through Renner-Teller coupling to nearby excited state levels. As an aid to vibronic assignment of the spectra, very high level hybrid ab initio potential energy surfaces were built starting from the coupled cluster singles and doubles with perturbative triples (CCSD(T))/aug-cc-pV5Z level of theory for this seven-electron system. In an effort to obtain the highest possible accuracy, the potentials were corrected for core correlation, extrapolation to the complete basis set limit, electron correlation beyond CCSD(T), and diagonal Born-Oppenheimer effects. The spin-rovibronic states of the various isotopologues of BH{sub 2} were calculated for energies up to 22 000 cm{sup −1} above the X{sup ~} (000) level without any empirical adjustment of the potentials or fitting to experimental data. The agreement with the new LIF data is excellent, approaching near-spectroscopic accuracy (a few cm{sup −1}) and has allowed us to understand the complicated spin-rovibronic energy level structure even in the region of strong Renner-Teller resonances.
Fishchuk, A.V.; Merritt, J.M.; Avoird, A. van der
2007-01-01
The three adiabatic potential surfaces of the Br(P-2)-HCN complex that correlate to the P-2 ground state of the Br atom were calculated ab initio. With the aid of a geometry-dependent diabatic mixing angle, also calculated ab initio, these adiabatic potential surfaces were transformed into a set of
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice
2012-10-30
Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH. Copyright © 2012 Wiley Periodicals, Inc.
Ab initio design on new push pull sila- and germastilbene
Amatatsu, Yoshiaki; Ohara, Yuhki
2003-05-01
Ab initio complete active space self-consistent field and second order Möller-Plesset perturbation calculations have been performed to examine the capabilities of the second order non-linear optics (NLO) of 4-dimethylamino,4 '-cyano,i-sila(or germa)stilbenes (i-DCSS, or i-DCSG) where the carbon at the position i of the parent 4-dimethylamino,4 '-cyanostilbene (DCS) is replaced by more electro-positive silicon or germanium atom. 1-DCSS and 1-DCSG, which have not been synthesized yet, were found to have better NLO properties than DCS.
Parallelisation of algorithms for ab initio computation of material properties
Rignanese, G M; Michenaud, J P; Gonze, X
1995-01-01
Parallel algorithms for ab initio calculations of vibrations modes of solids are presented and implemented under PVM. Load balancing and communication problems are dealt with in order to increase parallelism efficiency. For accurate time measurements, synchronisation of processes must be achieved. The results obtained by working with 1,2,4 and 8 processors of a Convex MetaSeries computer are presented, showing a very good efficiency. Further parallelisation of the codes (involving a three-dimensional Fast Fourier Transform) with compiler directives on a Convex Exemplar, is discussed.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Energy Technology Data Exchange (ETDEWEB)
Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Xue, Sha; Liu, Yingdi; Li, Yaping; Teeters, Dale; Crunkleton, Daniel; Wang, Sanwu
The PEO3:LiCF3SO3 polymer electrolyte has attracted significant research due to its high conductivity and enhanced stability in lithium polymer batteries. Most experimental studies have shown that amorphous PEO lithium salt electrolytes have higher conductivity than the crystalline ones. Other studies, however, have shown that crystalline phase can conduct ions. In this work, we use ab initio molecular dynamics simulations to obtain the amorphous structure of PEO3:LiCF3SO3. The diffusion pathways and activation energies of lithium ions in both crystalline and amorphous PEO3:LiCF3SO3 are determined with first-principles density functional theory. In crystalline PEO3:LiCF3SO3, the activation energy for the low-barrier diffusion pathway is approximately 1.0 eV. In the amorphous phase, the value is 0.6 eV. This result would support the experimental observation that amorphous PEO3:LiCF3SO3has higher ionic conductivity than the crystalline phase. This work was supported by NASA Grant No. NNX13AN01A and by Tulsa Institute of Alternative Energy and Tulsa Institute of Nanotechnology. This research used resources of XSEDE, NERSC, and the Tandy Supercomputing Center.
Ab initio Potential Energy Surface for H-H2
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Energy Technology Data Exchange (ETDEWEB)
Śmiałek, M. A., E-mail: smialek@pg.gda.pl [Department of Control and Energy Engineering, Faculty of Ocean Engineering and Ship Technology, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk (Poland); Łabuda, M.; Guthmuller, J. [Department of Theoretical Physic and Quantum Information, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk (Poland); Hubin-Franskin, M.-J.; Delwiche, J. [Département de Chimie, Université de Liège, Institut de Chimie-Bât. B6C, B-4000 Liège (Belgium); Duflot, D. [Laboratoire de Physique des Lasers, Atomes et Molécules (PhLAM), UMR CNRS 8523, Université Lille1 Sciences et Technologies, F-59655 Villeneuve d' Ascq Cedex (France); Mason, N. J. [Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA (United Kingdom); Hoffmann, S. V.; Jones, N. C. [ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, Building 1520, DK-8000 Aarhus C (Denmark); Limão-Vieira, P., E-mail: plimaovieira@fct.unl.pt [Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)
2014-09-14
The highest resolution vacuum ultraviolet photoabsorption spectrum of ethyl formate, C{sub 2}H{sub 5}OCHO, yet reported is presented over the wavelength range 115.0–275.5 nm (10.75–4.5 eV) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series, observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. Calculations have also been carried out to determine the ionization energies and fine structure of the lowest ionic state of ethyl formate and are compared with a newly recorded He(I) photoelectron spectrum (from 10.1 to 16.1 eV). New vibrational structure is observed in the first photoelectron band. The photoabsorption cross sections have been used to calculate the photolysis lifetime of ethyl formate in the upper stratosphere (20–50 km)
Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.
Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H
2015-12-08
Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.
Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying
2017-04-28
A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.
Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying
2017-04-01
A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.
Lischner, Johannes; Vigil-Fowler, Derek; Louie, Steven G
2013-04-05
We calculate the photoemission spectra of suspended and epitaxial doped graphene using an ab initio cumulant expansion of the Green's function based on the GW self-energy. Our results are compared to experiment and to standard GW calculations. For doped graphene on a silicon carbide substrate, we find, in contrast to earlier calculations, that the spectral function from GW only does not reproduce experimental satellite properties. However, ab initio GW plus cumulant theory combined with an accurate description of the substrate screening results in good agreement with experiment, but gives no plasmaron (i.e., no extra well-defined excitation satisfying Dyson's equation).
Gellé, A.; Varignon, J.; Lepetit, M.-B.
2009-11-01
We propose a new ab initio method designed for the accurate calculation of effective exchange integrals between atoms with numerous open shells. This method applies to ferromagnetic as well as antiferromagnetic exchange, direct or ligand-mediated exchange. Test calculations on high spin transition metal oxides such as KNiF3, Ba2CoS3 or YMnO3 exhibit a very good accuracy compared either to the best ab initio calculations —when those are feasible— and with experimental evaluations.
Ab initio calculation of excess properties of La{sub 1−x}(Ln,An){sub x}PO{sub 4} solid solutions
Energy Technology Data Exchange (ETDEWEB)
Li, Yan [Institute of Energy and Climate Research (IEK-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52425 Jülich (Germany); JARA High-Performance Computing, Schinkelstrasse 2, 52062 Aachen (Germany); Kowalski, Piotr M., E-mail: p.kowalski@fz-juelich.de [Institute of Energy and Climate Research (IEK-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52425 Jülich (Germany); JARA High-Performance Computing, Schinkelstrasse 2, 52062 Aachen (Germany); Blanca-Romero, Ariadna [Institute of Energy and Climate Research (IEK-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52425 Jülich (Germany); JARA High-Performance Computing, Schinkelstrasse 2, 52062 Aachen (Germany); Vinograd, Victor [Institute of Energy and Climate Research (IEK-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52425 Jülich (Germany); Institute of Geoscience, Goethe Universität Frankfurt am Main, Altenhöferallee 1, 60438 Frankfurt (Germany); Bosbach, Dirk [Institute of Energy and Climate Research (IEK-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52425 Jülich (Germany); JARA High-Performance Computing, Schinkelstrasse 2, 52062 Aachen (Germany)
2014-12-15
We used ab initio computational approach to predict the excess enthalpy of mixing and the corresponding regular/subregular model parameters for La{sub 1−x}Ln{sub x}PO{sub 4} (Ln=Ce,…, Tb) and La{sub 1−x}An{sub x}PO{sub 4} (An=Pu, Am and Cm) monazite-type solid solutions. We found that the regular model interaction parameter W computed for La{sub 1−x}Ln{sub x}PO{sub 4} solid solutions matches the few existing experimental data. Within the lanthanide series W increases quadratically with the volume mismatch between LaPO{sub 4} and LnPO{sub 4} endmembers (ΔV=V{sub LaPO{sub 4}}−V{sub LnPO{sub 4}}), so that W(kJ/mol)=0.618(ΔV(cm{sup 3}/mol)){sup 2}. We demonstrate that this relationship also fits the interaction parameters computed for La{sub 1−x}An{sub x}PO{sub 4} solid solutions. This shows that lanthanides can be used as surrogates for investigation of the thermodynamic mixing properties of actinide-bearing solid solutions. - Highlights: • The excess enthalpies of mixing for monazite-type solid solutions are computed. • The excess enthalpies increase with the endmembers volume mismatch. • The relationship derived for lanthanides is transferable to La{sub 1−x}An{sub x}PO{sub 4} systems.
Ab initio and kinetic modeling studies of formic acid oxidation
DEFF Research Database (Denmark)
Marshall, Paul; Glarborg, Peter
2015-01-01
A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based...... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...
High-throughput ab-initio dilute solute diffusion database
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-01-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308
de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Bowman, Joel M
2014-02-20
We report a permutationally invariant, ab initio potential energy surface (PES) for the OH + HBr → Br + H2O reaction. The PES is a fit to roughly 26 000 spin-free UCCSD(T)/cc-pVDZ-F12a energies and has no classical barrier to reaction. It is used in quasiclassical trajectory calculations with a focus on the thermal rate constant, k(T), over the temperature range 5 to 500 K. Comparisons with available experimental data over the temperature range 23 to 416 K are made using three approaches to treat the OH rotational and associated electronic partition function. All display an inverse temperature dependence of k(T) below roughly 160 K and a nearly constant temperature dependence above 160 K, in agreement with experiment. The calculated rate constant with no treatment of spin-orbit coupling is overall in the best agreement with experiment, being (probably fortuitously) within 20% of it.
Energy Technology Data Exchange (ETDEWEB)
Trcera, Nicolas [Synchrotron SOLEIL, l' Orme des Merisiers, BP48, 91192 Gif-sur-Yvette CEDEX (France); Rossano, Stephanie; Madjer, Karim [Laboratoire Geomateriaux et Environnement, Universite Paris EST, EA 4508, 5 Bd Descartes, Champs sur Marne, 77454 Noisy-Champs cedex 2 (France); Cabaret, Delphine, E-mail: nicolas.trcera@synchrotron-soleil.fr [Universite Pierre et Marie Curie (UPMC), UMR 7590, IMPMC, 4 place Jussieu, 75252 Paris Cedex 5 (France)
2011-06-29
The structural environment of Mg in a K-bearing silicate glass of composition K{sub 2}MgSi{sub 3}O{sub 8} is investigated by x-ray absorption near-edge structure (XANES) spectroscopy at the Mg K-edge. XANES calculations are performed using a plane-wave electronic structure code, and a structural model obtained by classical molecular dynamics coupled to ab initio relaxation. Bond valence theory is used to validate plausible environments within the structural models. Comparison between the experimental and calculated spectra enables us to conclude that the Mg atoms are located in distorted tetrahedral sites. Site distortions are found to be correlated to the theoretical shift of the XANES edge position.
Trcera, Nicolas; Rossano, Stéphanie; Madjer, Karim; Cabaret, Delphine
2011-06-29
The structural environment of Mg in a K-bearing silicate glass of composition K(2)MgSi(3)O(8) is investigated by x-ray absorption near-edge structure (XANES) spectroscopy at the Mg K-edge. XANES calculations are performed using a plane-wave electronic structure code, and a structural model obtained by classical molecular dynamics coupled to ab initio relaxation. Bond valence theory is used to validate plausible environments within the structural models. Comparison between the experimental and calculated spectra enables us to conclude that the Mg atoms are located in distorted tetrahedral sites. Site distortions are found to be correlated to the theoretical shift of the XANES edge position.
Siskos, Michael G; Tzakos, Andreas G; Gerothanassis, Ioannis P
2015-09-07
The inability to determine precisely the location of labile protons in X-ray molecular structures has been a key barrier to progress in many areas of molecular sciences. We report an approach for predicting hydrogen bond distances beyond the limits of X-ray crystallography based on accurate ab initio calculations of O-HO proton chemical shifts, using a combination of DFT and contactor-like polarizable continuum model (PCM). Very good linear correlation between experimental and computed (at the GIAO/B3LYP/6-311++G(2d,p) level of theory) chemical shifts were obtained with a large set of 43 compounds in CHCl3 exhibiting intramolecular O-HO and intermolecular and intramolecular ionic O-H(-)O hydrogen bonds. The calculated OH chemical shifts exhibit a strong linear dependence on the computed (O)HO hydrogen bond length, in the region of 1.24 to 1.85 Å, of -19.8 ppm Å(-1) and -20.49 ppm Å(-1) with optimization of the structures at the M06-2X/6-31+G(d) and B3LYP/6-31+G(d) level of theory, respectively. A Natural Bond Orbitals (NBO) analysis demonstrates a very good linear correlation between the calculated (1)H chemical shifts and (i) the second-order perturbation stabilization energies, corresponding to charge transfer between the oxygen lone pairs and σ antibonding orbital and (ii) Wiberg bond order of the O-HO and O-H(-)O hydrogen bond. Accurate ab initio calculations of O-HO and O-H(-)O (1)H chemical shifts can provide improved structural and electronic description of hydrogen bonding and a highly accurate measure of distances of short and strong hydrogen bonds.
Ab initio study of long-period superstructures in close-packed A3B compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The ene......We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations...
Ab initio I-V characteristics of short C-20 chains
DEFF Research Database (Denmark)
Roland, C.; Larade, B.; Taylor, Jeremy Philip
2002-01-01
We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orien......We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both...
Ab initio treatment of ion-water molecule collisions with a three-center pseudo potential
Martínez, Pablo A.; Errea, L. F.; Méndez, Laura González; Rabadán, Ismanuel
2012-01-01
We calculate electron capture cross sections in collisions of protons with water molecules, using two simple ab initio approaches. The formalism involves the calculation of one-electron scattering wave functions and the use of three-center pseudo potential to represent the electron H2O+ interaction. Several methods to obtain many-electron cross sections are considered
Ab Initio Studies of Stratospheric Ozone Depletion Chemistry
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.
Symplectic ab initio no-core shell model
Energy Technology Data Exchange (ETDEWEB)
Draayer, J. P.; Dytrych, T.; Sviratcheva, K. D.; Bahri, C. [Department of Physics and Astronomy, Lousiana State University, Baton Rouge, 70803 Lousiana (United States); Vary, J. P. [Department of Physics and Astronomy, Iowa State University, Ames, 50011 Iowa (United States)
2008-12-15
The present study confirms the significance of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the first time, by examinations of realistic nucleon-nucleon interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The results reveal that the NCSM wave functions for light nuclei highly overlap (at the {approx} 90% level) with only a few of the most deformed Sp(3,R)-symmetric basis states. This points to the possibility of achieving convergence of higher-lying collective modes and reaching heavier nuclei by expanding the NCSM basis space beyond its current limits through Sp(3,R) basis states. Furthermore the symplectic symmetry is found to be favored by the JISP 16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry. (Author)
Ab initio study of electron-phonon coupling in rubrene
Ordejón, P.; Boskovic, D.; Panhans, M.; Ortmann, F.
2017-07-01
The use of ab initio methods for accurate simulations of electronic, phononic, and electron-phonon properties of molecular materials such as organic crystals is a challenge that is often tackled stepwise based on molecular properties calculated in gas phase and perturbatively treated parameters relevant for solid phases. In contrast, in this work we report a full first-principles description of such properties for the prototypical rubrene crystals. More specifically, we determine a Holstein-Peierls-type Hamiltonian for rubrene, including local and nonlocal electron-phonon couplings. Thereby, a recipe for circumventing the issue of numerical inaccuracies with low-frequency phonons is presented. In addition, we study the phenyl group motion with a molecular dynamics approach.
Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M
2013-03-15
The minimum energy path (MEP) of the reaction, CF(3)CHFCF(3) + H → transition state (TS) → CF(3)CFCF(3) + H(2), has been computed at different ab initio levels and with density functional theory (DFT) using different functionals. The computed B3LYP/6-31++G**, BH&HLYP/cc-pVDZ, BMK/6-31++G**, M05/6-31+G**, M05-2X/6-31+G**, UMP2/6-31++G**, PUMP2/6-31++G**//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVDZ//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVTZ(spd,sp)//UMP2//6-31++G**, RCCSD(T)/CBS//M05/6-31+G**, and RCCSD(T)/CBS//UMP2/6-31++G** MEPs, and associated gradients and Hessians, were used in reaction rate coefficient calculations based on the transition state theory (TST). Reaction rate coefficients were computed between 300 and 1500 K at various levels of TST, which include conventional TST, canonical variational TST (CVT) and improved CVT (ICVT), and with different tunneling corrections, namely, Wigner, zero-curvature, and small-curvature (SCT). The computed rate coefficients obtained at different ab initio, DFT and TST levels are compared with experimental values available in the 1000-1200 K temperature range. Based on the rate coefficients computed at the ICVT/SCT level, the highest TST level used in this study, the BH&HLYP functional performs best among all the functionals used, while the RCCSD(T)/CBS//MP2/6-31++G** level is the best among all the ab initio levels used. Comparing computed reaction rate coefficients obtained at different levels of theory shows that, the computed barrier height has the strongest effect on the computed reaction rate coefficients as expected. Variational effects on the computed rate coefficients are found to be negligibly small. Although tunneling effects are relatively small at high temperatures (~1500 K), SCT corrections are significant at low temperatures (~300 K), and both barrier heights and the magnitudes of the imaginary frequencies affect SCT corrections. Copyright © 2012 Wiley Periodicals, Inc.
An ab initio investigation of a grain boundary in a transition metal oxide
Energy Technology Data Exchange (ETDEWEB)
Dawson, I.; Bristowe, P.D. [Univ. of Cambridge (United Kingdom). Dept. of Materials Science and Metallurgy; Payne, M.C.; Lee, M.H. [Univ. of Cambridge (United Kingdom). Cavendish Lab.
1996-12-31
The authors have used ab initio total energy plane wave pseudopotential methods to perform the first completely ab initio investigation of the atomic and electronic structure of a grain boundary in a transition metal oxide. The {Sigma} = 15 (210)[001] tilt boundary in rutile TiO{sub 2} is studied using the conjugate gradients iterative minimization technique for performing total energy calculations within the LDA and pseudopotential approximations. The stability of the experimentally observed translation state of the boundary is confirmed, and some insight is gained into its electronic structure.
DEFF Research Database (Denmark)
Berg, Rolf W.; Riisager, Anders; Nguyen van Buu, Olivier
2010-01-01
, for example, a characteristic strong band at 2229 cm-1. This band was interpreted by some of us to show that the [tmgH]Cl gas phase should consist of monomeric ion pair “molecules” held together by a single N-H+ · · · Cl- hydrogen bond, the stretching vibration of which should be causing the band, based on ab......). The Raman spectra of all gas phases were quite identical and fitted the calculated spectrum of dimethylcyanamide. It is concluded that monomeric ion pair “molecules” held together by single N-H+ · · ·X- hydrogen bonds probably do not exist in the vapor phase over the solids at about 200-230 °C....... and Raman evidence to show that also the bromide salt contains dimeric ion pair “molecules” in the crystalline state and probably also in the liquid state. The structure of [tmgH]Br determined at 120(2) K was found to be monoclinic, space group P21/n, with a = 7.2072(14), b = 13.335(3), c = 9.378(2) Å, beta...
Ab initio and DFT study of Octanitrocubane. | Ejuh | Journal of the ...
African Journals Online (AJOL)
The molecular stability, structure, dipole moment, charge transfer, polarizability and energy of Octonitrocubane have been studied by using ab- initio Quantum Mechanical calculations. We have used the Restricted Hartree-Fock (RHF) and density functional Becke3LYP (B3LYP) theories by employing 6-31G, 6- 31++G** and ...
Ab initio and work function and surface energy anisotropy of LaB6
Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.
2006-01-01
Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of
Ab initio study of energy-level alignments in polymer-dye blends
Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.
2003-01-01
Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and
Ab initio study on the paths of oxygen abstraction of hydrogen trioxide
Indian Academy of Sciences (India)
This means that the importance of SO2 + HO3 → SO3 (D3h) + HOO• reaction increases with increasing temperature and, this reaction plays an important role in the SO3(D3h) production as the main molecule of the formation of acid rain at high temperatures. Keywords. Ab initio calculations; atmospheric chemistry; hydrogen ...
All electron ab initio investigations of the electronic states of the FeC molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl A.
1999-01-01
The low lying electronic states of the molecule FeC have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) and multi reference configuration interaction (MRCI) calculations. The relativistic corrections for the one electron Darwin contact te...
DEFF Research Database (Denmark)
Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian
2012-01-01
We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...
All-electron ab initio investigations of the electronic states of the NiC molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl. A.
1999-01-01
The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular...
Precise Ab-initio prediction of terahertz vibrational modes in crystalline systems
DEFF Research Database (Denmark)
Jepsen, Peter Uhd; Clark, Stewart J.
2007-01-01
We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...
The Hydration Structure of Carbon Monoxide by Ab Initio Methods
Awoonor-Williams, Ernest
2016-01-01
The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface it incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration is in good agreement with experiment (9.3 kJ/mol calc. vs 10.7 kJ/mol exptl.). The calculated diffusivity of CO(aq) in TIP3P-model water was 5.19 x 10-5 cm2/s ...
Senthil kumar, J; Jeyavijayan, S; Arivazhagan, M
2015-02-05
The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm(-1) and 4000-400 cm(-1), respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms. Copyright © 2014 Elsevier B.V. All rights reserved.
Ab initio adiabatic and quasidiabatic potential energy surfaces of H ...
Indian Academy of Sciences (India)
Ion-diatom collisions; Ab initio potential energy surface; quasidiabitaziation; Nonadiabatic coupling matrix elements. 1. Introduction. Proton collisions with diatomic target molecules ..... energies. Acknowledgements. B.A. thanks IIT Madras and University Grants Com- mission, New Delhi for providing a research fellowship.
Projector augmented wave method: ab initio molecular dynamics ...
Indian Academy of Sciences (India)
http://www.ias.ac.in/article/fulltext/boms/026/01/0033-0041 ... A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends ...
Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...
Indian Academy of Sciences (India)
Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.
Projector augmented wave method: ab initio molecular dynamics ...
Indian Academy of Sciences (India)
Unknown
Abstract. A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented.
Ab initio structure determination via powder X-ray diffraction
Indian Academy of Sciences (India)
Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination ...
Ab initio study of Pt induced nanowires on Ge(001)
Vanpoucke, D.E.P.
2009-01-01
The aim of this thesis: “Ab Initio Study of Pt Induced Nanowires on Ge(001)”, is to model the experimentally observed ‘Pt nanowires’ on Ge(001). These one-atom-thick wires can be hundreds of nanometers long while remaining defect and kink free, providing the ultimate wire any chip designer dreams
THEORETICAL STUDY (AB INITIO AND DFT METHODS) ON ...
African Journals Online (AJOL)
Theoretical study on acidic dissociation constant of xylenol orange in aqueous solution. Bull. Chem. Soc. Ethiop. 2017, 31(1). 129 modeled. Hartree-Fock ab initio and density functional geometry optimizations were performed with the Gaussian 09 program. The optimizations were done using HF/6-31+G(d) method. The.
Analysis of some conventional ab initio gene finders using human ...
African Journals Online (AJOL)
Yomi
2012-01-24
Jan 24, 2012 ... parts of a given protein coding sequence so that the users be able to choose the best program(s) in accordance with their research goals. MATERIALS AND METHODS. Sequence data set. In assessing five ab initio gene prediction programs, a data set consisting of 110 known orthologous genes of human ...
Ab initio computations on small copper compounds-CuO
Boer, D.H.W. den; Kaleveld, E.W.
1980-01-01
Ab initio computations on CuO were performed with the Hartree-Fock method and a proper dissociation MC SCF procedure. In particular the influence of the GTO basis set for Cu in molecular computations has been studied. A potential energy curve and a Mulliken population analysis are presented. The
Realization of prediction of materials properties by ab initio ...
Indian Academy of Sciences (India)
Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest ...
The Properties of Some Simple Covalent Hydrides: An Ab Initio ...
African Journals Online (AJOL)
Some properties of the monomeric binary hydrides of the elements of the first two rows of the periodic table have been determined using ab initio molecular orbital theory. The properties in question are the energetic, structural, electronic, topological and vibrational characteristics. In general, a gradual convergence towards ...
DEFF Research Database (Denmark)
Falkenberg, G.; Bunk, O.; Johnson, R.L.
2002-01-01
. Sci. 123/124, 104 (1998) for In on Si(001). For the (4x4) subunit, we propose a model that includes the main features of the (3x4) subunit together with additional mixed Ge-In dimers. The atomic positions were optimized using ab initio total-energy calculations. The calculated local densities......Using scanning-tunneling microscopy (STM) and first-principles total-energy calculations, we have determined the atomic geometry of the superstructures formed by the adsorption of up to 0.5 monolayer of indium on Ge(001) and annealing at temperatures above 200 degreesC. A strong interaction between...... indium adatoms and the germanium substrate atoms leads to the formation of two different In-Ge subunits on the Ge(001) surface. In the subsaturation regime separate (nx4) subunits are observed where n can be either 3 or 4 and the STM images resemble those of the Si(001)-(3x4)-In and -Al reconstructions...
Energy Technology Data Exchange (ETDEWEB)
Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)
2008-07-01
In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)
Accurate ab initio vibrational energies of methyl chloride
Energy Technology Data Exchange (ETDEWEB)
Owens, Alec, E-mail: owens@mpi-muelheim.mpg.de [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Thiel, Walter [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Moderate-Cost Ab Initio Thermochemistry with Chemical Accuracy.
Ganyecz, Ádám; Kállay, Mihály; Csontos, József
2017-09-12
A moderate-cost ab initio composite model chemistry including the explicitly correlated CCSD(T*)(F12) and conventional coupled-cluster methods up to perturbative quadruple excitations along with correlation consistent basis sets is developed. The model, named diet-HEAT-F12, is also augmented with diagonal Born-Oppenheimer and scalar relativistic corrections. The methods and basis sets used for the calculation of the individual components are selected to reproduce, as close as possible, without using any fitted parameters, the benchmark HEAT contributions. A well-defined recipe for calculating size-dependent 95% confidence intervals was also worked out for the model. The reliability of the protocol was checked using the W4-11 data set as well as a disjoint set of 23 accurate atomization energies collected from the literature and obtained by the procedure of Feller, Peterson, and Dixon. The best error statistics for the test set was yielded by the diet-HEAT-F12 protocol among the models W3X, W3X-L, and W3-F12 considered.
Energy Technology Data Exchange (ETDEWEB)
Kono, Y.; Tsuchioka, T.; Hashizume, T. (Chugoku Kayaku Co. Ltd., Hiroshima (Japan)); Azuma, N. (Ehime Univ., Ehime (Japan). Faculty of General Education); Maekawa, K.; Imamura, A. (Hiroshima Univ. (Japan). Faculty of Science)
1992-10-31
HMX, nitramine-based high performance explosive, is a ring nitramine compound called chemically octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine, and has 4 kinds of crystal polymorphs, [alpha], [beta], [gamma] and [delta]. Values of impact sensitivity of these four crystal polymorphs are different each other and the most stable [beta] is being produced. In this paper, ab initio [beta] calculations (STO-3G) based on the molecular structure in the crystal have been conducted on all of the above HMX crystal polymorphs and the X-ray structural analysis has also been done on the molecular structure of [beta]. As a result, 0.032 has been obtained as the ultimate R index for 734 independent reflections. Concerning the crystal, it is single crystal, its space group is P2[sub 1] /n, and its lattice constants are [alpha] = 6.5347(4), b=11.0296(6),c=7.3549(5), [angstrom] [beta] =102.689(5) [degree], and Zeta=2. When calculations are made on these bases, all energy and impact sensitivity correlate except[gamma]. 21 refs., 6 figs., 7 tabs.
Ab initio simulations and neutron scattering studies of structure and dynamics in PdH
Totolici, I E
2001-01-01
The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...
Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials
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.
Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's funct......'s function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations....
Ab initio study of the electronic spectrum of BeO
Directory of Open Access Journals (Sweden)
MILJENKO PERIC
1999-12-01
Full Text Available Low-lying singlet and triplet electronic states of the BeO molecule are calculated by means of the quantum chemical ab initio method. It was found that all states in the energy range from 0 to 50000 cm-1 are of valence character. Particular attention was paid to the investigation of the dissociative behavior of the states considered. The vibrational structure of the AIP<-XIS and BIS+<-XIS+ spectral systems was calculated.
Ab initio studies of the oxidation of methane with oxo-metal cations
Nachtigallová, Dana; Roeselová, Martina; Zahradník, Rudolf
1997-05-01
Ab initio calculations have been performed to study the oxidation of methane to methanol with oxo-metal cations of MO + type. Other possible reaction channels resulting from the reaction of CH 4 are investigated in the case of LiO +. It has been found that a high level of correlation energy needs to be included in order to obtain reaction energies in reasonable agreement with experiment. The calculated complexes found on the potential energy surface are of ionic character.
Computational methods for ab initio detection of microRNAs
Directory of Open Access Journals (Sweden)
Malik eYousef
2012-10-01
Full Text Available MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the Microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.
Ab initio Monte Carlo investigation of small lithium clusters.
Energy Technology Data Exchange (ETDEWEB)
Srinivas, S.
1999-06-16
Structural and thermal properties of small lithium clusters are studied using ab initio-based Monte Carlo simulations. The ab initio scheme uses a Hartree-Fock/density functional treatment of the electronic structure combined with a jump-walking Monte Carlo sampling of nuclear configurations. Structural forms of Li{sub 8} and Li{sub 9}{sup +} clusters are obtained and their thermal properties analyzed in terms of probability distributions of the cluster potential energy, average potential energy and configurational heat capacity all considered as a function of the cluster temperature. Details of the gradual evolution with temperature of the structural forms sampled are examined. Temperatures characterizing the onset of structural changes and isomer coexistence are identified for both clusters.
Ab initio quality neural-network potential for sodium
Eshet, Hagai; Khaliullin, Rustam Z.; Kühne, Thomas D.; Behler, Jörg; Parrinello, Michele
2010-05-01
An interatomic potential for high-pressure high-temperature (HPHT) crystalline and liquid phases of sodium is created using a neural-network (NN) representation of the ab initio potential-energy surface. It is demonstrated that the NN potential provides an ab initio quality description of multiple properties of liquid sodium and bcc, fcc, and cI16 crystal phases in the P-T region up to 120 GPa and 1200 K. The unique combination of computational efficiency of the NN potential and its ability to reproduce quantitatively experimental properties of sodium in the wide P-T range enables molecular-dynamics simulations of physicochemical processes in HPHT sodium of unprecedented quality.
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Brik, M.G., E-mail: brik@fi.tartu.e [Institute of Physics, University of Tartu, Riia 142, Tartu 51014 (Estonia); Kityk, I.V. [Electrical Engineering Department, Czestochowa University of Technology, Al. Armii Krajowej 17/19, 42-200 Czestochowa (Poland); Ozga, K.; Slezak, A. [Chair of Public Health, Czestochowa University of Technology, Al. Armii Krajowej 36B, 42-200 Czestochowa (Poland)
2011-01-15
Influence of impurity Ni{sup 2+} ions on optical absorption spectra of layered CdI{sub 2} single crystals has been considered for localized level of doping. Optical properties of CdI{sub 2}:Ni{sup 2+} crystals were modeled using two independent approaches: (i) DFT-based ab initio calculations and (ii) semi-empirical crystal field theory. The former method allowed for locating the Ni{sup 2+} 3d states with respect to the host's band structure, providing a link between the properties of impurity and host itself. The latter method allowed for calculations of crystal field splitting of the Ni{sup 2+} LS terms, giving an opportunity to assign the main bands in the absorption spectrum of the doped crystal. To increase accuracy in calculating the point charge contribution to the crystal field parameters (CFP), contributions of all crystal lattice ions located at a distance of up to 72.999 A from the Ni ion were included into the crystal lattice sums. The crystal field Hamiltonian was diagonalized in the space of 25 wave functions of the spin-triplet terms {sup 3}F, {sup 3}P and the spin-singlet terms {sup 1}S, {sup 1}D, {sup 1}G of the 3d{sup 8} electron configuration of Ni{sup 2+} ion. Additional calculations of the band structure and optical functions were performed to reveal the structure of the energy bands, their role in the formation of optical properties of this system in the overlapping impurity-ligand effects. Electron density distribution in the space between atoms before and after doping was compared; hybridization of the Ni 3d states with iodine 5p states was demonstrated. The role of the crystal anisotropy in the observed effects is discussed.
Ab initio transport across bismuth selenide surface barriers
Narayan, Awadhesh
2014-11-24
© 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.
Ab initio modelling of methane hydrate thermophysical properties.
Jendi, Z M; Servio, P; Rey, A D
2016-04-21
The key thermophysical properties of methane hydrate were determined using ab initio modelling. Using density functional theory, the second-order elastic constants, heat capacity, compressibility, and thermal expansion coefficient were calculated. A wide and relevant range of pressure-temperature conditions were considered, and the structures were assessed for stability using the mean square displacement and radial distribution functions. Methane hydrate was found to be elastically isotropic with a linear dependence of the bulk modulus on pressure. Equally significant, multi-body interactions were found to be important in hydrates, and water-water interactions appear to strongly influence compressibility like in ice Ih. While the heat capacity of hydrate was found to be higher than that of ice, the thermal expansion coefficient was significantly lower, most likely due to the lower rigidity of hydrates. The mean square displacement gave important insight into stability, heat capacity, and elastic moduli, and the radial distribution functions further confirmed stability. The presented results provide a much needed atomistic thermoelastic characterization of methane hydrates and are essential input for the large-scale applications of hydrate detection and production.
Directory of Open Access Journals (Sweden)
V. Kimberg
2013-03-01
Full Text Available This paper reports an advanced study of the excited ionic states of the gas-phase nitrogen molecule in the binding-energy region of 22–34 eV, combining ultrahigh-resolution resonant photoemission (RPE and ab initio configuration-interaction calculations. The RPE spectra are recorded for nine photon energies within the N 1s→π^{*} absorption resonance of N_{2} by using a photon bandwidth that is considerably smaller than lifetime broadening, and the dependence on excitation energy of the decay spectra is analyzed and used for the first assignment of 12 highly overlapped molecular states. The effect on the RPE profile of avoided curve crossings between the final N_{2}^{+} ionic states is discussed, based on theoretical simulations that account for vibronic coupling, and compared with the experimental data. By use of synchrotron radiation with high spectral brightness, it is possible to selectively promote the molecule to highly excited vibrational sublevels of a core-excited electronic state, thereby controlling the spatial distribution of the vibrational wave packets, and to accurately image the ionic molecular potentials. In addition, the mapping of the vibrational wave functions of the core-excited states using the bound final states with far-from-equilibrium bond lengths has been achieved experimentally for the first time. Theoretical analysis has revealed the rich femtosecond nuclear dynamics underlying the mapping phenomenon.
DEFF Research Database (Denmark)
Shim, Irene; Kingcade, Joseph E.; Gingerich, Karl A.
1988-01-01
All electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations have been applied to investigate the low-lying electronic states of the NiGe molecule. The ground state of the NiGe molecule is predicted to be 1Sigma+. The chemical bond in the 1Sigma+ ground state is a double...... bond composed of one sigma and one pi bond. The sigma bond is due to a delocalized molecular orbital formed by combining the Ni 4s and the Ge 4psigma orbitals. The pi bond is a partly delocalized valence bond, originating from the coupling of the 3dpi hole on Ni with the 4ppi electron on Ge. The low...... =286.8±10.9 kJ mol−1. The standard heat of formation of the NiGe molecule has been obtained as DeltaH [open circle] f,298 =514±12 kJ mol−1. The Journal of Chemical Physics is copyrighted by The American Institute of Physics....
Baskakova, P. E.; Belyakov, Alexander V.; Colacot, Thomas; Krannich, L. K.; Haaland, Arne; Volden, Hans Vidar; Swang, Ole
1998-04-01
The molecular structures of E(NMe 2) 3, E P, As or Sb and Me CH 3, have been determined by gas electron diffraction (GED) and ab initio molecular orbital calculations at the {HF}/{6-31 G∗ } level. The equilibrium structures have Cs symmetry with two NMe 2 ligands oriented in such a manner that the direction of the electron lone pair on each N atom is orthogonal to the direction of the lone pair on the E atom, while the third ligand is oriented in such a manner that the lone pair on the N atom is antiparallel to the lone pair on E. The coordination of the antiparallel N atom is distinctly pyramidal (sum of the valence angles = 337° by GED) while the two orthogonal N atoms are nearly planar (sum of valence angles = 353° by GED). The bond distances from E to the antiparallel N atom is two to four pm longer than the bond distances to the orthogonal N atoms, and the valence angle >NEN spanned by the orthogonal N atoms is some 10° larger than the two angles spanned by the antiparallel and one orthogonal N atom. It is suggested that the equilibrium structures are stabilized by anomeric effects, i.e. delocalization of the lone pairs of the orthogonal N atoms into antibonding σ∗(E-N) orbitals.
Local Structure Analysis in $Ab$ $Initio$ Liquid Water
Santra, Biswajit; DiStasio Jr., Robert A.; Martelli, Fausto; Car, Roberto
2015-01-01
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate $ab$ $initio$ liquid water. At ambient conditions, the LSI probability distribution, P($I$), was unimodal wi...
Polariton Bose condensate in an open system: Ab initio approach
Elistratov, A. A.; Lozovik, Yu. E.
2018-01-01
In the framework of path-integral formalism and Keldysh technique for a nonequilibrium system we explore the kinetics of the polariton condensate in a quantum well embedded in an optical microcavity. We take into account pumping and leakage of excitons and photons. We make an ab initio derivation of the equations governing the dynamics of the condensates and reservoirs and show that the real open polariton system has a non-Markovian character at times comparable to the Rabi oscillation period.
Helal, Mustafa R; Yousef, Yaser A; Afaneh, Akef T
2002-07-30
HF, MP2, and B3LYP calculations with different basis sets have been used in the computation of the stabilization energies of C(3)H(7)X isomers, where X is F, Cl, and Br. The experimental stabilization energies of the structural isomers of C(3)H(7)Cl and C(3)H(7)Br have been reproduced via B3LYP calculations. However, the calculated stabilization energies of fluoropropane isomers from their reported enthalpies of formation have been reproduced in all methods of calculations in present work. The experimental relative stabilities of the gauche conformers of 1-fluoro-, 1-chloro-, and 1-bromopropanes have been also reproduced via some of the used calculations in the present work. The effect of the geminal interactions on X atomic charges and on the C-X and C-C bond lengths in halopropane isomers are also discussed. Copyright 2002 Wiley Periodicals, Inc.
Energy Technology Data Exchange (ETDEWEB)
Yao, Yongxin [Iowa State Univ., Ames, IA (United States)
2009-01-01
also plays an important role, as it may directly track the movement of every atom. Simulation time is a major limit for molecular dynamics, not only because of “slow” computer speed, but also because of the accumulation error in the numerical treatment of the motion equations. There is also a great concern about the reliability of the emperical potentials if using classical molecular dynamics. Ab initio methods based on density functional theory(DFT) do not have this problem, however, it suffers from small simulation cells and is more demanding computationally. When crystal phase is involved, size effect of the simulation cell is more pronounced since long-range elastic energy would be established. Simulation methods which are more efficient in computation but yet have similar reliability as the ab initio methods, like tight-binding method, are highly desirable. While the complexity of metallic glasses comes from the atomistic level, there is also a large field which deals with the complexity from electronic level. The only “ab initio” method applicable to solid state systems is density functional theory with local density approximation( LDA) or generalized gradient approximation(GGA) for the exchange-correlation energy. It is very successful for simple sp element, where it reaches an high accuracy for determining the surface reconstruction. However, there is a large class of materials with strong electron correlation, where DFT based on LDA or GGA fails in a fundamental way. An “ab initio” method which can generally apply to correlated materials, as LDA for simple sp element, is still to be developed. The thesis is prepared to address some of the above problems.
Machine Learning Force Field Parameters from Ab Initio Data.
Li, Ying; Li, Hui; Pickard, Frank C; Narayanan, Badri; Sen, Fatih G; Chan, Maria K Y; Sankaranarayanan, Subramanian K R S; Brooks, Bernard R; Roux, Benoît
2017-09-12
Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local "shape" of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.
Machine Learning Force Field Parameters from Ab Initio Data
Energy Technology Data Exchange (ETDEWEB)
Li, Ying [Argonne; Li, Hui [Department; Pickard, Frank C. [Laboratory; Narayanan, Badri [Center; Sen, Fatih G. [Center; Chan, Maria K. Y. [Center; Computational; Sankaranarayanan, Subramanian K. R. S. [Center; Computational; Brooks, Bernard R. [Laboratory; Roux, Benoît [Department; Center; Computational
2017-08-11
Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.
Energy Technology Data Exchange (ETDEWEB)
Kumaran, S.S.; Su, M.C.; Lim, K.P.; Michael, J.V.; Wagner, A.F.; Harding, L.B. [Argonne National Lab., IL (United States); Dixon, D.A. [DuPont Central Research and Development Experimental Station, Wilmington, DE (United States)
1996-05-02
Previously measured Cl dissociation rate constants for CCl{sub 4} and CFCl{sub 3} were analyzed with three different kinetics modeling calculations. The three models differ in detail but primarily are distinguished by the manner in which the high-pressure limiting rate constant is determined: model 1 involves a calibration to transport properties of the dissociated fragments, model 2 uses a Gorin model with a hindrance parameter, and model 3 requires variational transition state thoery on an ab initio reaction path where all low-frequency motion off the path is presumed to be a free rotation. All three models have two adjustable parameters: the dissociation energy E{sub 0} and the average energy transferred to the buffer gas [{Delta}]{sub down}. All three models are found to give comparable fits to the experiment and produce quite similar values for the adjustable parameters. The values for CCl{sub 4} and CFCl{sub 3} are compared to those obtained in similar studies for CF{sub 2}Cl{sub 2} and CF{sub 3}Cl. The results indicate a substantial and consistent decrease in the C-Cl bond energy with each additional chlorine substitution in the chlorofluoromethanes. Isodesmic electronic structure calculations at the MP2 level confirm this effect but find it to be a little smaller than the experimental results indicate. Extended electronic structure calculations provide heats of formation for all nine CF{sub x}F{sub y}Cl{sub z} methyl radicals. 42 refs., 4 figs., 5 tabs.
Energy Technology Data Exchange (ETDEWEB)
Bernard, St
1998-12-31
The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.
Suvitha, A.; Periandy, S.; Boomadevi, S.; Govindarajan, M.
2014-01-01
In this work, the vibrational spectral analysis is carried out by using Raman and infrared spectroscopy in the range 100-4000 cm-1and 50-4000 cm-1, respectively, for pycolinaldehyde oxime (PAO) (C6H6N2O) molecule. The vibrational frequencies have been calculated and scaled values are compared with experimental FT-IR and FT-Raman spectra. The structure optimizations and normal coordinate force field calculations are based on HF and B3LYP methods with 6-311++G(d,p) basis set. The results of the calculation shows excellent agreement between experimental and calculated frequencies in B3LYP/6-311++G(d,p) basis set. The optimized geometric parameters are compared with experimental values of PAO. The non linear optical properties, NBO analysis, thermodynamics properties and mulliken charges of the title molecule are also calculated and interpreted. A study on the electronic properties, such as HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) are performed. The effects due to the substitutions of CHdbnd NOH ring are investigated. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.
Ab initio calculations and analysis of chemical bonding in SrTiO3 and SrZrO3 cubic crystals
Evarestov, R. A.; Tupitsyn, I. I.; Bandura, A. V.; Alexandrov, V. E.
The possibility of the different first-principles methods to describe the chemical bonding in SrTiO3 and SrZrO3 cubic crystals is investigated. The local properties of the electronic structure (atomic charges, bond orders, atomic delocalization indexes, and polarization fractions) were calculated with different methods: traditional Mulliken population analysis in LCAO calculations, two projection techniques in plane-wave (PW) calculations, population analysis based on Wannier-type atomic orbitals, and chemical bonding analysis based on the localized Wannier functions for occupied (valence band) LCAO states. All the techniques considered except the traditional Mulliken analysis demonstrate that the ionicity of chemical bonding in SrZrO3 is larger than in SrTiO3, in agreement with the Zr and Ti electronegativities relation and the relative bandgaps observed.
Energy Technology Data Exchange (ETDEWEB)
Lee, Y.S.
1977-11-01
The effects of the 4f shell of electrons and the relativity of valence electrons are compared. The effect of 4f shell (lanthanide contraction) is estimated from the numerical Hartree-Fock (HF) calculations of pseudo-atoms corresponding to Hf, Re, Au, Hg, Tl, Pb and Bi without 4f electrons and with atomic numbers reduced by 14. The relativistic effect estimated from the numerical Dirac-Hartree-Fock (DHF) calculations of those atoms is comparable in the magnitude with that of the 4f shell of electrons. Both are larger for 6s than for 5d or 6p electrons. The various relativistic effects on valence electrons are discussed in detail to determine the proper level of the approximation for the valence electron calculations of systems with heavy elements. An effective core potential system has been developed for heavy atoms in which relativistic effects are included in the effective potentials.
Witzens, Jeremy
2014-08-01
The band diagram, deformation potential and photoelastic tensor of silicon are calculated self-consistently under uniaxial and shear strain by solving for the electronic wavefunctions with a finite-difference method. Many-body effects are accounted for by the local density approximation. In order to accommodate the large number of grid points required due to the diverging electrostatic potential near the atomic nuclei in an all-electron calculation, a non-uniform meshing is adopted. Internal displacements are taken into account by adding an additional coordinate transform to the method of Bir and Pikus. Good consistency of the calculated deformation potential and photoelastic coefficients is obtained with prior experimental and theoretical results, validating the numerical methods. Furthermore, it is shown that a slight correction of the multiplicative coefficient of the Xα approximation for conduction bands results in good agreement with experiment for both the direct and indirect bandgaps.
Ab initio lattice dynamics of complex structures
DEFF Research Database (Denmark)
Voss, Johannes
2008-01-01
atomic coordinates, we have developed a new numerical optimization scheme, which allows for a fast convergence of the coordinate relaxation. Moreover, a method for the efficient calculation of phonon frequencies has been developed, which is based on a combination of density functional theory calculations......, showing that the mobility of hydrogen is limited by high energetic barriers in the intermediate decomposition product Na3AlH6 in particular, and that the effect of titanium as a dopant on the dynamics is negligible. The presented methods and studies demonstrate possibilities for a design of new materials...
Chun, Hye Jin; Ocola, Esther J.; Laane, Jaan
2016-11-01
The vapor-phase infrared and Raman spectra of cyclohexane-d11 in the C-H stretching region show two bands at 2891 and 2921 cm-1 corresponding to the axial and equatorial C-H stretching modes respectively. Similarly, cyclohexane-d1 has two C-D stretching modes at 2145 and 2164 cm-1 (Mátrai and Gal, 1984) corresponding to the two forms. Force constants were calculated for these vibrations and these confirm the theoretical calculations, which show the equatorial bonds to be shorter and stronger. The force constant for the equatorial C-H stretching is 2% higher than for the axial.
Ab initio work function of elemental metals
DEFF Research Database (Denmark)
Skriver, Hans Lomholt; Rosengaard, N. M.
1992-01-01
We have used a recently developed self-consistent Green’s-function technique based on tight-binding linear-muffin-tin-orbital theory to calculate the work function for the close-packed surfaces of 37 elemental metals. The results agree with the limited experimental data obtained from single...
Optical properties of highly compressed polystyrene: An ab initio study
Hu, S. X.; Collins, L. A.; Colgan, J. P.; Goncharov, V. N.; Kilcrease, D. P.
2017-10-01
Using all-electron density functional theory, we have performed an ab initio study on x-ray absorption spectra of highly compressed polystyrene (CH). We found that the K -edge shifts in strongly coupled, degenerate polystyrene cannot be explained by existing continuum-lowering models adopted in traditional plasma physics. To gain insights into the K -edge shift in warm, dense CH, we have developed a model designated as "single mixture in a box" (SMIAB), which incorporates both the lowering of the continuum and the rising of the Fermi surface resulting from high compression. This simple SMIAB model correctly predicts the K -edge shift of carbon in highly compressed CH in good agreement with results from quantum molecular dynamics (QMD) calculations. Traditional opacity models failed to give the proper K -edge shifts as the CH density increased. Based on QMD calculations, we have established a first-principles opacity table (FPOT) for CH in a wide range of densities and temperatures [ρ =0.1 -100 g /c m3 and T =2000 -1 000 000 K ]. The FPOT gives much higher Rosseland mean opacity compared to the cold-opacity-patched astrophysics opacity table for warm, dense CH and favorably compares to the newly improved Los Alamos atomic model for moderately compressed CH (ρCH≤10 g /c m3 ), but remains a factor of 2 to 3 higher at extremely high densities (ρCH≥50 g /c m3 ). We anticipate the established FPOT of CH will find important applications to reliable designs of high-energy-density experiments. Moreover, the understanding of K -edge shifting revealed in this study could provide guides for improving the traditional opacity models to properly handle the strongly coupled and degenerate conditions.
Directory of Open Access Journals (Sweden)
Hanggara Sudrajat
2010-06-01
Full Text Available Molecular structures were optimized for the calix[4]arene by ab initio method at the Hartree-Fock level of theory using LANL2DZ and 6-311G basis sets. Conformational equilibrium of four calix[4]arene conformers are reported. The results are compared with experiment, force field, and semiempirical molecular orbital calculations. General trends in relative stabilities of calix[4]arene decrease in following order: cone > partial-cone > 1,2-alternate > 1,3-alternate. The most stable conformer is the cone conformer that is stabilized by an array of four hydrogen bonds and these results agree with the reported experimental observations. All structures were analyzed using theoretical IR, UV-Vis, and 1H NMR spectra attributed to the conformational equilibrium at the Hartree-Fock level of theory using LANL2DZ basis set. Keywords: ab initio calculation, calix[4]arene, conformations, cone
Acuña-Cueva, Esther R.; Faure, René; Jiménez-Pulido, Sonia B.; Moreno-Carretero, Miguel N.; Peña-Ruiz, Tomás
2004-07-01
The molecular and crystal structures of 1-methyllumazine (MLM) and 1,6,7-trimethyllumazine (MLMD) (lumazine=pteridine-2,4( 1H,3H)-dione) have been XRD determined. The compound MLM crystallizes in the monoclinic system (space group P2 1/c ) with cell dimensions: a=4.8200(2), b=9.7820(5), c=15.3230(9) Å, β=93.407(2)°. The structure was solved from 1947 reflections with I>2 σ( I). The final R[ I>2 σ( I)] was 0.0756 for 136 parameters. The compound MLMD crystallizes in the monoclinic system (space group C2) with cell dimensions: a=16.1360(4), b=6.5850(2), c=10.5380(4) Å, β=125.150(1)°. The structure was solved from 1800 reflections with I>4 σ( I). The final R[ I>4 σ( I)] was 0.0547 for 165 parameters. In both structures, the pteridine derivatives are H-bond dimerized (N-H⋯O), but whereas MLM shows a N3-H3⋯O2 H-bond, MLMD displays a N3-H3⋯O4 one, which is in accordance with the different sequence found for the carbonyl lengths. Ab initio molecular orbital calculations at the RHF/6-31G ∗ and B3LYP/6-31G ∗ levels using the GAUSSIAN94 program package have allowed us to simulate the molecular structures. The geometrical data are in good agreement with those calculated. The contribution of the atomic orbitals of the potential donor atoms to the higher occupied molecular orbitals allows us to propose theoretical arguments to justify the well-known N5-O4-bidentate coordinative behaviour found for these compounds in several metal complexes.
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 behaviour 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 counter-intuitive result: a ferromagnetism arises due to an increase of Si concentration in Fe1-x Si2+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.
An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu
Energy Technology Data Exchange (ETDEWEB)
Jomard, G.; Bottin, F.; Amadon, B
2007-07-01
By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO{sub 2} and {beta}-Pu{sub 2}O{sub 3} in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO{sub 2} in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (p{sub O{sub 2}}). We conclude that at room temperature and for p{sub O{sub 2}}{approx}10 atm., the polar O{sub 2}-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)
Ab initio Hadron structure from lattice QCD
Energy Technology Data Exchange (ETDEWEB)
J.D. Bratt; R.G. Edwards; M. Engelhardt; G.T. Fleming; Ph. Hägler; B. Musch; J.W. Negele; K. Orginos; A.V. Pochinsky; D.B. Renner; D.G. Richards; W. Schroers
2007-06-01
Early scattering experiments revealed that the proton was not a point particle but a bound state of many quarks and gluons. Deep inelastic scattering (DIS) experiments have accurately determined the probability of struck quarks carrying a fraction of the proton's momentum. The current generation of experiments and Lattice QCD calculations will provide detailed multi-dimensional pictures of the distributions of quarks and gluons inside the proton.
Ab-initio calculation of EuO doped with 5% of (Ti, V, Cr and Fe): GGA and SIC approximation
Rouchdi, M.; Salmani, E.; Bekkioui, N.; Ez-Zahraouy, H.; Hassanain, N.; Benyoussef, A.; Mzerd, A.
2017-12-01
In this research, a simple theoretical method is proposed to investigate the electronic, magnetic and optical properties of Europium oxide (EuO) doped with 5% of (Ti, V, Cr and Fe). For a basic understanding of these properties, we employed Density-Functional Theory (DFT) based calculations with the Korringa-Kohn-Rostoker code (KKR) combined with the Coherent Potential Approximation (CPA). Also we investigated the half-metallic ferromagnetic behavior of EuO doped with 5% of (Ti, V, Cr and Fe) within the self-interaction-corrected Generalized Gradient Approximation (GGA-SIC). Our calculated results revealed that the Eu0.95TM0.05O is ferromagnetic with a high transition temperature. Moreover, the optical absorption spectra revealed that the half metallicity has been also predicted.
Salmani, E.; Laghrissi, A.; Laamouri, R.; Benchafia, E.; Ez-Zahraouy, H.; Benyoussef, A.
2017-02-01
MgH2: TM (TM: V, Cr, Mn, Fe, Co, Ni) based dilute magnetic semiconductors (DMS) are investigated using first principle calculations. Our results show that the ferromagnetic state is stable when TM introduces magnetic moments as well as intrinsic carriers in TM: Co, V, Cr, Ti; Mg0.95TM0.05H2. Some of the DMS Ferro magnets under study exhibit a half-metallic behavior, which make them suitable for spintronic applications. The double exchange is shown to be the underlying mechanism responsible for the magnetism of such materials. The exchange interactions obtained from first principle calculations and used in a classical Ising model by a Monte Carlo approach resulted in ferromagnetic states with Curie temperatures within the ambient conditions.
Khandy, Shakeel Ahmad; Gupta, Dinesh C.
2017-10-01
An extensive study of rare-earth perovskite BaPaO3 and BaNpO3 has been performed by first-principles tactics based on density functional theory (DFT), because the delocalized f-electrons play an important role in the band structure formation, to reveal their impact on the overall physical and chemical properties; it has turned out to be an interesting theme. Along with critical radii and thermoelectric properties, two different theories are employed to calculate the structural properties. The DFT and empirically calculated lattice constants are in rational accord with the experimental results. The critical radius calculations show that the BaPaO3 lattice has a smaller oxygen migration activation energy than the BaNpO3. In addition, we discuss the band profile and magnetic moments for these materials, which demonstrate the half-metallic ferromagnetism with a direct energy gap of 3.91 eV for BaPaO3 and an indirect gap of 3.79 eV for BaNpO3. More interestingly, the integral magnetic moments are in accordance with the Slater-Pauling rule.
Rudysh, M. Ya.; Brik, M. G.; Stadnyk, V. Yo.; Brezvin, R. S.; Shchepanskyi, P. A.; Fedorchuk, A.; Khyzhun, O. Y.; Kityk, I. V.; Piasecki, M.
2018-01-01
In the present work complex experimental and theoretical studies of electronic and optical properties for β-lithium-ammonium sulfate crystals of good optical quality are performed using the X-ray photoelectron spectroscopy (XPS) and X-ray emission spectroscopy (XES). Standard immersion and spectroscopic techniques accompanied by the theoretical quantum-chemical calculations in the density functional theory (DFT) framework were applied. Calculations of band structure and related properties were carried out within a framework of local density and generalized gradient approximations as well as hybrid B3LYP functionals. The energy levels features and their origin are established from the DFT calculations and they were ferified by XPS and XES measurements. Theoretical and experimental refractive indices dispersions along the principal crystallographic directions (nx, ny and nz) as well as birefringence dispersion (Δnx, Δny and Δnz) in the visible spectral range are obtained. It was found a closeness of nx and ny curves for the titled crystals. More precise birefringence examining predicts their intersection at λ ≈ 190 nm.
Electronic structure and excited-state properties of Co2TiSn and Co2ZrSn from ab initio calculations
Directory of Open Access Journals (Sweden)
L.V.Bekenov
2005-01-01
Full Text Available The electronic structure, magnetism as well as the excited-state properties such as the optical and x-ray magnetic circular dichroism (XMCD spectra of the Heusler alloys Co2TiSn and Co2ZrSn were investigated theoretically from first principles using the fully relativistic Dirac LMTO band structure method. The origin of the XMCD spectra at the Co L2,3 edges in the compounds is examined. Densities of valence states, orbital and spin magnetic moments as well as optical spectra are analyzed and discussed. The calculated results are compared with the available experimental data.
Ab Initio Study of Atropisomers of Derivatives of N-Benzyl-2-phenylpyridinium Ions
Directory of Open Access Journals (Sweden)
Firouzeh Nemati
2012-01-01
Full Text Available Ab initio calculation at RHF/6-31G* level of theory for geometry optimization of conformers of N-benzyl-2-phenylpyridinium ions are reported. The series of electron-withdrawing and electron-donating groups have been replaced by 3-H phenyl and benzyl of N-benzyl-2-phenylpyridinium ions and the energy difference between the syn- and anti- forms discussed in terms of π-π stacking.
Ab-Initio Physics of Electrochemistry
Letchworth Weaver, Kendra; Arias, Tomás
2010-03-01
We present a Joint Density Functional Theory (JDFT)footnotetextS. A. Petrosyan, A. A. Rigos, and T. A. Arias, J. Phys. Chem. B, 109, 15436-15444 (2005).^,footnotetextJ. Lischner and T. A. Arias, Phys. Rev. Lett. 101, 216401 (2008). capturing the key electrostatic interactions between electronic systems and a fluid environment. This novel theory is relevant to the study of electrochemical systems and includes the dielectric properties of the fluid and charge screening due to the presence of ions in solution. We also demonstrate how DFT calculations can address the fundamental physical issues underlying electrochemistry, including the definition of a consistent reference potential, the treatment of charged surfaces under periodic boundary conditions, and the study of the solid-electrolyte interface as a function of the applied potential. Results for interfacial capacitances and potentials of zero charge calculated using these techniques will be compared to experimental values. Our theory allows simulation of a variety of materials, such as intermetallics and complex oxides, in contact with an ionic liquid environment. This method has a wide range of potential applications including catalysis in fuel cells, batteries, and photoelectrochemical cells.
HEAT: High accuracy extrapolated ab initio thermochemistry.
Tajti, Attila; Szalay, Péter G; Császár, Attila G; Kállay, Mihály; Gauss, Jürgen; Valeev, Edward F; Flowers, Bradley A; Vázquez, Juana; Stanton, John F
2004-12-15
A theoretical model chemistry designed to achieve high accuracy for enthalpies of formation of atoms and small molecules is described. This approach is entirely independent of experimental data and contains no empirical scaling factors, and includes a treatment of electron correlation up to the full coupled-cluster singles, doubles, triples and quadruples approach. Energies are further augmented by anharmonic zero-point vibrational energies, a scalar relativistic correction, first-order spin-orbit coupling, and the diagonal Born-Oppenheimer correction. The accuracy of the approach is assessed by several means. Enthalpies of formation (at 0 K) calculated for a test suite of 31 atoms and molecules via direct calculation of the corresponding elemental formation reactions are within 1 kJ mol(-1) to experiment in all cases. Given the quite different bonding environments in the product and reactant sides of these reactions, the results strongly indicate that even greater accuracy may be expected in reactions that preserve (either exactly or approximately) the number and types of chemical bonds. (c) 2004 American Institute of Physics
Energy Technology Data Exchange (ETDEWEB)
Han, Chang W. [Purdue Univ., West Lafayette, IN (United States); Iddir, Hakim [Argonne National Lab. (ANL), Argonne, IL (United States); Uzun, Alper [Koc Univ., Instanbul (Turkey); Curtiss, Larry A. [Argonne National Lab. (ANL), Argonne, IL (United States); Browning, Nigel D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gates, Bruce C. [Univ. of California, Davis, CA (United States); Ortalan, Volkan [Purdue Univ., West Lafayette, IN (United States)
2015-11-06
To address the challenge of fast, direct atomic-scale visualization of the diffusion of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as ~0.1 s per frame) to visualize the diffusion of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir_{3} cluster on MgO(110). Sequential Z-contrast images elucidate the diffusion mechanisms, including the hopping of Ir1 and the rotational migration of Ir_{3} as two Ir atoms remain anchored to the surface. Density functional theory (DFT) calculations provided estimates of the diffusion energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow real-time visualization and fundamental understanding of surface diffusion phenomena pertaining to supported catalysts and other materials.
Howard, C. M.; Wood, I. G.; Fortes, A. D.; Vocadlo, L.
2016-12-01
BackgroundInteractions between simple molecules are of fundamental interest across diverse areas of the physical sciences, and the ternary system NH3 + CO2 ± H2O is no exception. In the outer solar system, interaction of CO2 with aqueous ammonia is likely to occur, synthesizing `rock-forming' minerals [1], with CO2 perhaps playing a role in ammonia-water oceans and cryomagmas inside icy planetary bodies - the discovery of ammonium carbonates in a crater of Pluto's moon Charon [2] adds weight to CO2 occuring in these planetary environments. In the same context, ammonium carbonates may have some astrobiological relevance, since removal of water leads to the formation of urea. On Earth, combination of CO2 with aqueous ammonia has relevance to carbon capture schemes [3], and there is interest in using such materials for hydrogen storage in fuel cells [4]. Consequently, from earthly matters of climate change to the study of extraterrestrial ices, understanding the structures and properties of ammonium carbonates are important. Despite this, our knowledge of ammonium carbonates is limited under ambient conditions of pressure and temperature and is entirely absent at the higher pressures, severely limiting our ability to model the behaviour of NH3 + CO2 ± H2O solids and fluids in planetary environments. ResultsWe report the results of several experiments using variable pressure and temperature neutron diffraction work on ammonium carbonate monohydrate, ammonium bicarbonate and ammonium carbamate, with complementary Density Functional Theory (DFT) calculations. The excellent agreement between experiments and DFT calculations obtained so far adds weight to the accuracy of calculated material properties of ammonium sesquicarbonate monohydrate and several polymorphs of urea where little empirical data exists. These experimental and computational studies provide the structural, thermoelastic and vibrational information required for accurate planetary modelling and remote
Hamad, B. A.
2011-03-01
Density functional theory (DFT) calculations are performed using the full-potential linearized augmented plane wave (FP-LAPW) and generalized gradient approximation (GGA) to study the electronic and magnetic properties of perfect and defected Fe2CrSi Heusler alloy. The perfect structure was found to be a half-metallic ferromagnet with a total magnetic moment of 2 μ B and a band gap 0.6 eV. The Fermi level is found to be in the middle of this gap, which is promising for fabricating tunneling magnetoresistance (TMR) devices. Among the studied defected structures FeSi and CrSi antisite defects as well as Fe-Si and Cr-Si defects destroyed the half metallicity. However the remaining antisite, swap and vacancy defects retained the half metallicity with band gaps lower than the perfect case.
Cao, Peiyu; Tian, Fuyang; Wang, Yandong
2017-11-01
Ti-Mo alloys are promising materials for shape memory alloys and biomedical materials. Whereas, the appearance of metastable ω phase can cause embrittlement and destroy the shape memory effect. In order to avoid the ω phase, the effect of Mo on the temperature dependent lattice parameters, phase stability and elastic mechanical properties of β, α, and ω Ti1-x Mo x (x = 0-2.0) random alloys was systematically investigated by using the exact muffin-tin orbitals method in combination with the coherent potential approximation. The theoretical predictions for the lattice parameters are in good agreement with the available experiments. Results show that β Ti0.96Mo0.04 can almost transform to ω phase without lattice deformation and volume change, which suggests that the athermal ω phase is easier to precipitate and grow near 4 at.% Mo content in the β Ti1-x Mo x alloys. The critical content of Mo for the competed stabilization of β phase at T = 300 K is ~11.2 at.%. Its valence electron concentration of 4.224 is viewed as a necessary criterion for the competed phase stability. The calculations of formation energy are used to explain successfully why the partitioning of Mo can be found in Ti0.91Mo0.09 alloy after annealing. Through the analysis of formation energy, both Mo addition and increasing temperature can stabilize the β phase. The calculated Cauchy pressure, Pugh’s ratio, Poisson ratio, and Young’s modulus suggests that ω phase is intrinsically brittle and has large Young’s modulus compared with β and α phases.
Ab Initio Studies of Metal Hexaboride Materials
Schmidt, Kevin M.
Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron
Tossell, J. A.
2006-10-01
Boric acid, B(OH) 3, forms complexes in aqueous solution with a number of bidentate O-containing ligands, HL -, where H 2L is C 2O 4H 2 (oxalic acid), C 3O 4H 4 (malonic acid), C 2H 6O 2 (ethylene glycol), C 6H 6O 2 (catechol), C 10H 8O 2 (dioxynaphthalene) and C 2O 3H 4 (glycolic acid). McElligott and Byrne [McElligott, S., Byrne, R.H., 1998. Interaction of B(OH)30 and HCO3- in seawater: Formation of B(OH)CO3-. Aquat. Geochem.3, 345-356.] have also found B(OH) 3 to form an aqueous complex with HCO3-1. Recently Lemarchand et al. [Lemarchand, E., Schott, J., Gaillardeet, J., 2005. Boron isotopic fractionation related to boron sorption on humic acid and the structure of surface complexes formed. Geochim. Cosmochim. Acta69, 3519-3533] have studied the formation of surface complexes of B(OH) 3 on humic acid, determining 11B NMR shifts and fitted values of formation constants, and 11B, 10B isotope fractionations for a number of surface complexation models. Their work helps to clarify both the nature of the interaction of boric acid with the functional groups in humic acid and the nature of some of these coordinating sites on the humic acid. The determination of isotope fractionations may be seen as a form of vibrational spectroscopy, using the fractionating element as a local probe of the vibrational spectrum. We have calculated quantum mechanically the structures, stabilities, vibrational spectra, 11B NMR spectra and 11B, 10B isotope fractionations of a number of complexes B(OH) 2L - formed by reactions of the type: B(OH)3+HL-⇒B(OH)2L+HO using a 6-311G(d,p) basis set and the B3LYP method for determination of structures, vibrational frequencies and isotopic fractionations, the highly accurate Complete Basis Set-QB3 method for calculating the free energies and the GIAO HF method with a 6-311+G(2d,p) basis for the NMR shieldings. The calculations indicate that oxalic acid, malonic acid, catechol and glycolic acid all form stable complexes (Δ G Byrne, R.H., Yao, W
Ghatee, Mohammad Hadi; Bahrami, Maryam
2017-06-01
We investigate to contrasting structure, dynamic and thermophysical properties of quaternary ammonium and phosphonium ionic liquids (ILs) based on triethylalkylammonium [N222n]+ and triethylalkylphosphonium [P222n]+ cations (n = 5, 8, 12) and (bis(trifluoromethylsulfonyl)imide) anion [NTf2]- by quantum chemical calculations (QCC) and molecular dynamics (MD) simulations. QCCs conform to previous studies, showing that phosphonium cation alkyl chain rotational-energy-barrier is lower than ammonium cation. These molecular nature leads to no appreciable differences in their liquid density. However, their simulated transport properties (self-diffusion, conductivity, etc) are appreciably different. In particular, viscosity of phosphoniums are much lower than ammoniums. Ammoniums make nano-scale structural domains larger than phosphoniums. Employed analysis, vector re-orientational dynamics, ion-pair lifetime and nanostructure domain are in favor of faster dynamic for phosphoniums than ammoniums. [NTf2]- anion features a long lived pairing with ammoniums than phosphoniums. Overall, phosphoniums possess higher transference number, higher conductivity, and appreciably lower viscosity favorable for higher electrochemical performances.
Lin, Shi Ying; Guo, Hua; Honvault, Pascal; Xu, Chuanxiu; Xie, Daiqian
2008-01-07
The authors report accurate quantum mechanical studies of the O+OH reaction on the improved Xu-Xie-Zhang-Lin-Guo potential energy surface. The differential cross section was obtained at several energies near the reaction threshold using a time-independent method. The dominant forward and backward peaks in the angular distribution are consistent with a complex-forming mechanism, which is also confirmed by the extensive rotational excitation in the O2 product. However, the asymmetry of these peaks suggests a significant nonstatistical component. The initial state (upsilon i=0, j i=0) specified integral cross section, which was calculated up to 1.15 eV of collision energy using the Chebyshev wave packet method, shows no energy threshold and decreases with the increasing collision energy, consistent with the barrierless nature of the reaction. The resulting rate constant exhibits a negative temperature dependence for T>100 K and decays as the temperature is lowered, in qualitative agreement with available experimental data.
Pham Van, Tat; Deiters, Ulrich K.
2015-08-01
The intermolecular interaction potentials of the dimers H2sbnd H2 and H2sbnd O2 were calculated from quantum mechanics, using coupled-cluster theory CCSD(T) and correlation-consistent basis sets aug-cc-pVmZ (m = 2, 3); the results were extrapolated to the basis set limit aug-cc-pV23Z. The interaction energies were corrected for the basis set superposition error with the counterpoise scheme. For comparison also Møller-Plesset perturbation theory (at levels 2-4) with the basis sets aug-cc-pVTZ were considered, but the results proved inferior. The quantum mechanical results were used to construct analytical pair potential functions. From these functions the second virial coefficients of hydrogen and the cross virial coefficients of the hydrogen-oxygen system were obtained by integration; in both cases corrections for quantum effects were included. The results agree well with experimental data, if available, or with empirical correlations.
Kundu, Ashis; Ghosh, Sheuly; Ghosh, Subhradip
2017-11-01
We investigate the effects of Fe and Co substitutions on the phase stability of the martensitic phase and mechanical, electronic, and magnetic properties of the magnetic shape memory system Mn2NiGa by first-principles density functional theory calculations. The evolution of these aspects upon substitution of Fe and Co at different crystallographic sites is investigated by computing the electronic structure, mechanical properties (tetragonal shear constant, Pugh ratio, and Cauchy pressure), and magnetic exchange parameters. We find that the austenite phase of Mn2NiGa gradually stabilizes with increase in concentration of Fe/Co due to the weakening of the minority spin hybridization of Ni and Mn atoms occupying crystallographically equivalent sites. The interplay between relative structural stability and the compositional changes is understood from the variations in the elastic moduli and electronic structures. We find that like in the Ni2MnGa -based systems, the elastic shear modulus C' can be considered as a predictor of composition dependence of martensitic transformation temperature Tm in substituted Mn2NiGa , thus singling it out as the universally acceptable predictor for martensitic transformation in Ni-Mn-Ga compounds over a wide composition range. The magnetic properties of Mn2NiGa are found to be greatly improved by the substitutions due to stronger ferromagnetic interactions in the compounds. The gradually weaker (stronger) Jahn-Teller distortion (covalent bonding) in the minority spin densities of states due to substitutions leads to a half-metallic-like gap in these compounds resulting in materials with high spin polarization when the substitutions are complete. The substitutions at the Ga site result in the two compounds Mn2NiFe and Mn2NiCo with very high magnetic moments and Curie temperatures. Thus, our work indicates that although the substitutions destroy the martensitic transformation and thus the possibility of realization of shape memory
Lithium Insertion In Silicon Nanowires: An ab Initio Study
Zhang, Qianfan
2010-09-08
The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.
Suturina, Elizaveta A; Nehrkorn, Joscha; Zadrozny, Joseph M; Liu, Junjie; Atanasov, Mihail; Weyhermüller, Thomas; Maganas, Dimitrios; Hill, Stephen; Schnegg, Alexander; Bill, Eckhard; Long, Jeffrey R; Neese, Frank
2017-03-06
The magnetic properties of pseudotetrahedral Co(II) complexes spawned intense interest after (PPh4)2[Co(SPh)4] was shown to be the first mononuclear transition-metal complex displaying slow relaxation of the magnetization in the absence of a direct current magnetic field. However, there are differing reports on its fundamental magnetic spin Hamiltonian (SH) parameters, which arise from inherent experimental challenges in detecting large zero-field splittings. There are also remarkable changes in the SH parameters of [Co(SPh)4]2- upon structural variations, depending on the counterion and crystallization conditions. In this work, four complementary experimental techniques are utilized to unambiguously determine the SH parameters for two different salts of [Co(SPh)4]2-: (PPh4)2[Co(SPh)4] (1) and (NEt4)2[Co(SPh)4] (2). The characterization methods employed include multifield SQUID magnetometry, high-field/high-frequency electron paramagnetic resonance (HF-EPR), variable-field variable-temperature magnetic circular dichroism (VTVH-MCD), and frequency domain Fourier transform THz-EPR (FD-FT THz-EPR). Notably, the paramagnetic Co(II) complex [Co(SPh)4]2- shows strong axial magnetic anisotropy in 1, with D = -55(1) cm-1 and E/D = 0.00(3), but rhombic anisotropy is seen for 2, with D = +11(1) cm-1 and E/D = 0.18(3). Multireference ab initio CASSCF/NEVPT2 calculations enable interpretation of the remarkable variation of D and its dependence on the electronic structure and geometry.
Energy Technology Data Exchange (ETDEWEB)
Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.; Nguyen, Kiet T.; Williams, Stephen D.; Johnson, Timothy J.
2017-07-25
Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, we report high quality quantitative vapor-phase infrared spectra of all three isomers over the 540-6500 cm^{-1} range. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C_{2v} symmetry for ortho-xylene, and two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have C_{s} and C_{2} symmetry, and for para-xylene these conformers have C_{2v} or C_{2h} symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, we made an arbitrary choice to discuss the C_{s} conformer for meta-xylene and the C_{2v} conformer for para-xylene. We report integrated band intensities for all isomers. Using the quantitative infrared data, we determine the global warming potential values of each isomer and discuss potential bands for atmospheric monitoring.
GAS PHASE ION CHEMISTRY OF COUMARINS: AB INITIO ...
African Journals Online (AJOL)
B. S. Chandravanshi
Initio calculations favoured ionization by resonance electron capture for acetyl coumarin derivatives and dissociative electron capture by methyl substituted coumarins. Those coumarins that underwent resonance electron capture showed much higher intensities of M˙¯ than [M– H]¯ ions. These observations will be useful in ...
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.
DEFF Research Database (Denmark)
Luntz, A. C.; Kratzer, Peter
1996-01-01
Dynamical calculations are reported for D-2 dissociative chemisorption on and associative desorption from a Si(100) surface. These calculations use the dynamically relevant effective potential which is based on an ab initio potential energy surface for the ''pre-paired'' species. Three coordinates...
Entropy of liquid water from ab initio molecular dynamics.
Zhang, Cui; Spanu, Leonardo; Galli, Giulia
2011-12-08
We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations. We present the results obtained with semilocal, hybrid, and van der Waals density functionals. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. The underestimate is more severe for the PBE and PBE0 functionals than for several van der Waals functionals. © 2011 American Chemical Society
Stretching siloxanes: An ab initio molecular dynamics study
Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.
2005-10-01
We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.
Ab initio modeling of small proteins by iterative TASSER simulations
Directory of Open Access Journals (Sweden)
Zhang Yang
2007-05-01
Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (α-root mean square deviation (RMSD of 3.8Å, with 6 of them having a Cα-RMSD α-RMSD α-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (α-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Rio, B. G. del; González, L. E. [Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid (Spain)
2015-08-17
Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.
Electronic structure of the Ca3Co4O9 compound from ab initio local interactions
Soret, Julien; Lepetit, Marie-Bernadette
2012-04-01
We used fully correlated ab initio calculations to determine the effective parameters of Hubbard and t-J models for the thermoelectric misfit compound Ca3Co4O9. As for the NaxCoO2 family, the Fermi level orbitals are the a1g orbitals of the cobalt atoms; the eg' being always lower in energy by more than 240 meV. The electron correlation is found very large U/t˜26 as well as the parameters fluctuations as a function of the structural modulation. The main consequences are a partial a1g electrons localization and a fluctuation of the in-plane magnetic exchange from antiferromagnetic to ferromagnetic. The behavior of the Seebeck coefficient and the figure of merit are discussed in view of the ab initio results, as well as the 496 K phase transition.
A highly accurate {\\it ab initio} potential energy surface for methane
Owens, Alec; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-01-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \\textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include: core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of $^{12}$CH$_4$ reproduced with a root-mean-square error of $0.70{\\,}$cm$^{-1}$. The computed \\textit{ab initio} equilibrium C{--}H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as $J$ (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the e...
Siddick, M M; Ackland, G J; Morrison, C A
2006-08-14
We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.
Trapping of hydrogen and helium at dislocations in tungsten: an ab initio study
Bakaev, A.; Grigorev, P.; Terentyev, D.; Bakaeva, A.; Zhurkin, E. E.; Mastrikov, Yu. A.
2017-12-01
The interaction of H or He atoms with a core of edge and screw dislocations (SDs), with Burgers vector a 0/2≤ft , is studied by means of ab initio calculations. The results show that the edge dislocations are stronger traps for H and He compared to the SDs, while the H/He affinity to both types of dislocation is significantly weaker than to a single vacancy. The lowest energy atomic configurations are rationalized on the basis of the charge density distribution and elasticity theory considerations. The results obtained contribute to the rationalization of the thermal desorption spectroscopy analysis by attributing certain peaks of the release of plasma components to the detrapping from dislocations. Complementary molecular statics (MS) calculations are performed to validate the accuracy of the recently developed W-H-He embedded atom method (EAM) and bond-order potentials. It is revealed that the EAM potential can reproduce correctly the magnitude of the interaction of H with both dislocations as compared to the ab initio results. All the potentials underestimate significantly the He-dislocation interaction and cannot describe correctly the lowest energy positions for H and He around the dislocation core. The reason for the discrepancy between ab initio and the MS results is rationalized by the analysis of the fully relaxed atomic configurations.
Synthesis, characterization, ab initio calculations, thermal behaviour ...
Indian Academy of Sciences (India)
Author Affiliations. Mozaffar Asadi1 Mohammad Hadi Ghatee1 Susan Torabi1 Khosro Mohammadi2 Fatemeh Moosavi1. Chemistry Department, College of Sciences, Shiraz University, Shiraz 71454, I.R. Iran; Chemistry Department, Faculty of Sciences, Persian Gulf University, Bushehr 75169, I.R. Iran ...
Suzuki, Nobuaki; Asahi, Ryoji; Kishida, Yoshihiro; Masuoka, Yumi; Sugiyama, Jun
2017-04-01
In this study, 3d transition metal phosphides TiMP, where M = Cr, Mn, Fe, Co, or Ni, were synthesized via solid-state reactions. At 293 K, both TiCrP and TiMnP exhibited hexagonal symmetry with P6-2m space groups, while TiFeP, TiCoP, and TiNiP possessed orthorhombic symmetry with Pnma space groups. The electrical resistivity ρ of each compound was on the order of 10-5 Ω m and was relatively temperature independent above 2 K, except in the case of TiFeP, for which ρ linearly decreased with decreasing temperature. The absolute value of the Seebeck coefficient was small (<30 µV K-1) between 2 K and 300 K and exhibited linear temperature dependence except in the case of TiNiP. The magnetic susceptibilities χ for TiCrP, TiCoP, and TiNiP, which ranged from 1 × 10-4 emu mol-1 to 3 × 10-4 emu mol-1, were temperature independent above 2 K, indicating that these species exhibit Pauli paramagnetism. The temperature-independent χ of TiFeP was relatively high, ~2.5 × 10-3 emu mol-1. The Stoner enhancement factor estimated from the Pauli paramagnetic susceptibility that was determined based on the calculated density of states and the Wilson ratio were 21.2 and 14.1, respectively, for TiFeP, suggesting that the magnetism of TiFeP may be exchange-enhanced Pauli paramagnetism. In contrast, for TiMnP, χ obeyed a Curie-Weiss law, and an effective magnetic moment per TiMnP formula unit of 1.07 μ B and a Weiss temperature of -8.0 K were obtained. The ab initio calculations for TiMnP yielded a predicted magnetic moment of 1.0 μ B per TiMnP formula unit, which is consistent with the experimental result. On the other hand, the measured electronic specific heat coefficient of TiMnP (48.1 mJ mol-1 · K-2) was about seven times higher than that estimated based on the calculated density of states. These results for TiMnP imply that spin fluctuations may determine its properties.
Ab initio thermodynamic model for magnesium carbonates and hydrates.
Chaka, Anne M; Felmy, Andrew R
2014-09-04
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
Microhydration of protonated glycine: an ab initio family tree.
Michaux, Catherine; Wouters, Johan; Perpète, Eric A; Jacquemin, Denis
2008-02-28
The incremental hydration of the glycine cation is investigated using an ab initio approach fully correcting for basis set superposition errors and explicitly incorporating electron-correlation effects. Structures with zero to four surrounding water molecules have been determined. It is demonstrated that the successive aggregates follow a Darwinian family tree, the most stable complexes systematically belonging to the same branch of the tree. In strong contrast with neutral glycine, the direct hydrogen bonding to the glycine cation is favored over bridging water structures. The agreement between experimental and theoretical hydration enthalpies and Gibbs free energies is impressive, as ab initio estimates almost systematically fit the experimental error bars. For GlyH(+)-(H2O) and GlyH(+)-(H2O)3, we show that two structures are generated by the experimental setup. The present approach also resolves most of the previous theory/experiment discrepancies and provides patterns for the evolution of the vibrational spectra: a decrease of the hydrogen-bond stretching frequency indicating second-shell water molecules. Additionally, the impact of bulk solvent solvation is investigated, as four discrete water molecules still do not fully hydrate the protonated glycine.
Wu, Xiangyang
1999-07-01
The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B
Embedded atom approach for gold–silicon system from ab initio ...
Indian Academy of Sciences (India)
In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...
Khaliullin, Rustam Z.; Eshet, Hagai; Kühne, Thomas D.; Behler, Jörg; Parrinello, Michele
2010-03-01
An interatomic potential for the diamond and graphite phases of carbon has been created using a neural-network (NN) representation of the ab initio potential energy surface. The NN potential combines the accuracy of a first-principles description of both phases with the efficiency of empirical force fields and allows one to perform a molecular-dynamics study, of ab initio quality, of the thermodynamics of graphite-diamond coexistence. Good agreement between the experimental and calculated coexistence curves is achieved if nuclear quantum effects are included in the simulation.
Physisorption of an organometallic platinum complex on silica. An ab initio study
Shen, Juan; Muthukumar, Kaliappan; Jeschke, Harald O.; Valenti, Roser
2012-01-01
The interaction of trimethyl methylcyclopentadienyl platinum (MeCpPtMe3) with a fully hydroxylated SiO2 surface has been explored by means of ab initio calculations. A large slab model cut out from the hydroxylated beta-cristobalite SiO2 (111) surface was chosen to simulate a silica surface. Density functional theory calculations were performed to evaluate the energies of MeCpPtMe3 adsorption to the SiO2 surface. Our results show that the physisorption of the molecule is dependent on both (i)...
Hayashi, T; Jansen, TL; Zhuang, W; Mukamel, S
2005-01-01
An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D2O solvent obtained from molecular dynamics simulations, we calculate
Giovannetti, G.; Brocks, G.; van den Brink, J.
2008-01-01
We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic
Ab initio study of structural, electronic, and thermal properties of Ir1-xRhx alloys
Directory of Open Access Journals (Sweden)
Sh. Ahmed
2015-06-01
Full Text Available The structural, electronic, mechanical and thermal properties of Ir1-xRhx alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.
Ab initio studies on complexes formed by melamine and cyclotrione
Directory of Open Access Journals (Sweden)
LIANGIANG ZHU
2007-04-01
Full Text Available Ab initio methods were used to study the binding energies of non-bonded complexes formed by melamine and cyclotrione, with the STO-3G, 3-21G and 6-31G (d basis sets. The electronic spectra were computed using the INDO/CIS method, and the IR spectra, Raman and NMR spectra with the RHF/6-31G (dmethod. It was demonstrated that the complexes could be formed because of the negative binding energies, which were changed with the change in the electronic properties of the monomers. A red-shift of the first absorptions in the electronic spectra and the vibrational frequencies of the N–H bonds in the IR and Raman spectra of the complexes, compared with those of the monomers, occurred; simultaneously, the 1Hand 13C chemical shifts were altered, due to the non-bonded interaction.
Efficient approach to compute melting properties fully from ab initio with application to Cu
Zhu, Li-Fang; Grabowski, Blazej; Neugebauer, Jörg
2017-12-01
Applying thermodynamic integration within an ab initio-based free-energy approach is a state-of-the-art method to calculate melting points of materials. However, the high computational cost and the reliance on a good reference system for calculating the liquid free energy have so far hindered a general application. To overcome these challenges, we propose the two-optimized references thermodynamic integration using Langevin dynamics (TOR-TILD) method in this work by extending the two-stage upsampled thermodynamic integration using Langevin dynamics (TU-TILD) method, which has been originally developed to obtain anharmonic free energies of solids, to the calculation of liquid free energies. The core idea of TOR-TILD is to fit two empirical potentials to the energies from density functional theory based molecular dynamics runs for the solid and the liquid phase and to use these potentials as reference systems for thermodynamic integration. Because the empirical potentials closely reproduce the ab initio system in the relevant part of the phase space the convergence of the thermodynamic integration is very rapid. Therefore, the proposed approach improves significantly the computational efficiency while preserving the required accuracy. As a test case, we apply TOR-TILD to fcc Cu computing not only the melting point but various other melting properties, such as the entropy and enthalpy of fusion and the volume change upon melting. The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the local-density approximation (LDA) are used. Using both functionals gives a reliable ab initio confidence interval for the melting point, the enthalpy of fusion, and entropy of fusion.
Rezaee, Mohammadreza; Compton, Robert
2015-05-01
Collision induced dissociation (CID) and ab initio calculations were utilized to study a few derivatives of azobenzene molecule and their product ions. High level computational methods along with large basis set size yield values in close agreement with the experimental results. Möller-Plesset and coupled-cluster theory including perturbative triple excitations, CCSD(T), method were performed to obtain a high accuracy estimation of the bond dissociation energy value. The electron affinities have been studied experimentally using the photoelectron spectroscopy method as well as theoretically using ab inito calculations. For the trans-2,2',6,6' tetra-fluoro azobenzene the bond dissociation has been experimentally determined to be 1.88 eV and the vertical detachment energy is 1.78 eV.
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.
Temperature-Dependent Diffusion Coefficients from ab initio Computations: Hydrogen in Nickel
Energy Technology Data Exchange (ETDEWEB)
E Wimmer; W Wolf; J Sticht; P Saxe; C Geller; R Najafabadi; G Young
2006-03-16
The temperature-dependent mass diffusion coefficient is computed using transition state theory. Ab initio supercell phonon calculations of the entire system provide the attempt frequency, the activation enthalpy, and the activation entropy as a function of temperature. Effects due to thermal lattice expansion are included and found to be significant. Numerical results for the case of hydrogen in nickel demonstrate a strong temperature dependence of the migration enthalpy and entropy. Trapping in local minima along the diffusion path has a pronounced effect especially at low temperatures. The computed diffusion coefficients with and without trapping bracket the available experimental values over the entire temperature range between 0 and 1400 K.
Orbital free ab initio study of static and dynamic properties of some liquid transition metals
Directory of Open Access Journals (Sweden)
Bhuiyan G. M.
2017-01-01
Full Text Available Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD. This method is based on the density functional theory (DFT which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.
Scalable numerical approach for the steady-state ab initio laser theory
Esterhazy, S.; Liu, D.; Liertzer, M.; Cerjan, A.; Ge, L.; Makris, K. G.; Stone, A. D.; Melenk, J. M.; Johnson, S. G.; Rotter, S.
2014-08-01
We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab initio laser theory. Our strategy is to solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate this approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal slabs. Our method paves the way for efficient and accurate simulations of microlasers which were previously inaccessible.
FTIR cryospectroscopic and ab initio studies of desflurane-dimethyl ether H-bonded complexes
Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.
2017-09-01
The IR spectra of mixtures of desflurane and dimethyl ether are studied with the help of FTIR cryospectroscopy in liquefied Kr at T 118-158 K. Comparative analysis of the experimental data and results of ab initio calculations show that either of the two C-H groups of desflurane is involved in heterodimer formation of comparable strengths. The blue frequency shift is found for stretching vibrations of those C-H donors which directly participate in H-bond formation. Additionally the complexes are stabilized by weaker contacts between hydrogen atoms of dimethyl ether and fluorine atoms of desflurane.
Orbital free ab initio study of static and dynamic properties of some liquid transition metals
Bhuiyan, G. M.; Molla, Mohammad Riazuddin; Ziauddin Ahmed, A. Z.; Gonzalez, L. E.; Gonzalez, D. J.
2017-08-01
Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD). This method is based on the density functional theory (DFT) which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.
Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations.
Mo, Yirong; Gao, Jiali
2006-02-23
Combined ab initio quantum mechanical and molecular mechanical (QM/MM) simulations coupled with the block-localized wave function energy decomposition (BLW-ED) method have been conducted to study the solvation of two prototypical ionic systems, acetate and methylammonium ions in aqueous solution. Calculations reveal that the electronic polarization between the targeted solutes and water is the primary many-body effect, whereas the charge-transfer term only makes a small fraction of the total solute-solvent interaction energy. In particular, the polarization effect is dominated by the solvent (water) polarization.
Ab initio studies of complexes of ozone with some positive ions
Snyder, G.; Sapse, D.
1994-02-01
Ab initio calculations using the 6-31G * and the 6-311G * basis sets are performed on HeO +3, LiO +3 and N 2O +3 comp the HeO +3 and N 2O +3 complexes the positive charge is on the oxygen and the complexes are not bound with respect to dissociation into He or N 2 and O +3. In the LiO +3 complex the positive charge is on lithium and the complex is strongly bound with respect to the Li + and O 3.
Ab initio determination of the structure of a grain boundary by simulated quenching
Energy Technology Data Exchange (ETDEWEB)
Payne, M.C.; Bristowe, P.D.; Joannopoulos, J.D.
1987-03-30
Results of the first completely ab initio investigation of the microscopic structure of a grain boundary in a semiconductor are presented. By use of the molecular-dynamics--simulated annealing method for performing total-energy calculations within the local-density--functional and pseudopotential approximation, the ..sigma.. = 5 (001) twist boundary in germanium is studied. A number of rotation-and-translation states are investigated leading to a prediction for the structure of this geometry. Evidence for the possible presence of novel defects and glasslike tunneling mode states at grain boundaries is presented.
Ab-initio determination of the structure of a grain boundary by simulated quenching
Energy Technology Data Exchange (ETDEWEB)
Payne, M.C.; Bristowe, P.D.; Joannopoulos, J.D.
1987-02-01
Results of the first completely ab-initio investigation of the microscopic structure of a grain boundary in a semiconductor are presented. Using the molecular dynamics simulated annealing method for performing total energy calculations within the local density functional and pseudopotential approximations, the ..sigma.. = 5(001) twist boundary in germanium is studied. A number of rotation-and-translation states are investigated leading to a prediction for the structure of this geometry. Evidence for the possible presence of novel defects and glass-like tunneling mode states at grain boundaries is presented.
Ab initio determination of the structure of a grain boundary by simulated quenching
Payne, M. C.; Bristowe, P. D.; Joannopoulos, J. D.
1987-03-01
Results of the first completely ab initio investigation of the microscopic structure of a grain boundary in a semiconductor are presented. By use of the molecular-dynamics-simulated annealing method for performing total-energy calculations within the local-density-functional and pseudopotential approximations, the Sigma = 5 (001) twist boundary is germanium is studied. A number of rotation-and-translation states are investigated leading to a prediction for the structure of this geometry. Evidence for the possible presence of novel defects and glasslike tunneling-mode states at grain boundaries is presented.
Yusuf, Muhammad; Roza, Destria; Nasution, Ahmad Kamil
2017-11-01
The computational calculation was performed on the acetalization of 2-hydroxybenzaldehyde by using ab initio method. Ab initio method is derived directly from theoretical principles with no inclusion of experimental data and this is an approximate quantum mechanical calculation. The aim of this research was to studies the acetalization of 2-hydroxybenzaldehyde mechanism using halogen acid catalysts. Computational calculation which was applied on the acetalization of 2-hydroxybenzaldehyde using halogen acid catalysts provided possible reaction steps. The first step was formation of a labile hemiacetal because it is essentially tetrahedral intermediates containing a leaving group. The second step was formation of a stable acetal. The results of computational calculation of acetalization of 2-hydroxybenzaldehyde provided possible energy change in the each step of the reaction process. A labile hemiacetal showed higher energy (481.04 kJ/mol) than 2-hydroxybenzaldehyde dimethyl acetal (65.32 kJ/mol) and 2-hydroxybenzaldehyde (0 kJ/mol) due to its instability. In general, acetalization of 2-hydroxybenzaldehyde reaction is a reversible reaction. The effect of Lewis acidity on halogen acid catalysts was also studied in this research. Based on the Mulliken charge on the H atom, it is found that HF has the highest Lewis acidity compared to other halogen acids with order HF> HCl> HBr> HI. As a result, HF was the efficient catalysts for acetalization of 2-Hydroxybenzaldehyde.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos
2016-08-01
Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.
Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.
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.
Knight, Chris; Maupin, C Mark; Izvekov, Sergei; Voth, Gregory A
2010-10-12
In this report, a general methodology is presented for the parametrization of a reactive force field using data from a condensed phase ab initio molecular dynamics (AIMD) simulation. This algorithm allows for the creation of an empirical reactive force field that accurately reproduces the underlying ab initio reactive surface while providing the ability to achieve long-time statistical sampling for large systems not possible with AIMD alone. In this work, a model for the hydrated excess proton is constructed where the hydronium cation and proton hopping portions of the model are statistically force-matched to the results of Car-Parrinello Molecular Dynamics (CPMD) simulations. The flexible nature of the algorithm also allows for the use of the more accurate classical simple point-charge flexible water (SPC/Fw) model to describe the water-water interactions while utilizing the ab initio data to create an overall multistate molecular dynamics (MS-MD) reactive model of the hydrated excess proton in water. The resulting empirical model for the system qualitatively reproduces thermodynamic and dynamic properties calculated from the ab initio simulation while being in good agreement with experimental results and previously developed multistate empirical valence bond (MS-EVB) models. The present methodology, therefore, bridges the AIMD technique with the MS-MD modeling of reactive events, while incorporating key strengths of both.
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 Molecular Orbital Studies of the Vibrational Spectra of some ...
African Journals Online (AJOL)
Ab initio Molecular Orbital Studies of the Vibrational Spectra of some van der Waals Complexes. Part 4. Complexes of Sulphur Dioxide with Carbon Dioxide, Carbonyl Sulphide, Carbon Disulphide and Nitrous Oxide.
MONTE CARLO SIMULATION OF I-, Br-, AND Cl- IN WATER USING AB INITIO PAIR POTENSIAL FUNCTIONS
Directory of Open Access Journals (Sweden)
Harno Dwi Pranowo
2010-06-01
Full Text Available Monte Carlo simulations were performed for I-, Br- and Cl-, in water using ab initio pair potential. The systems consisting of one anion in 215 solvent molecules have been simulated at 298 K. Anion-water pair potentials have been newly developed based on ab initio calculations of split valence basis set plus polarization quality. The structure of the solvated ion is discussed in terms of radial distribution functions, coordination number and pair potential distribution. Structural properties were investigated by means of radial distribution functions and their running integration numbers, leading for the first solvation shell to an average 12.60 H2O around I- with I--O distance of 3.74 Å and I--H distance of 2.86 Å, 11.84 H2O around Br- with Br--O distance of 3.40 Å and Br--H distance of 2.42 Å, and 10.68 H2O around Cl- with Cl--O distance of 3.20 Å and Cl--H distance of 2.24 Å, respectively. The structure of the water-anion complexes are agreed with dipole orientation. Pair energy distribution of hydrated anions showed that the pair interaction energy are increase from I-, Cl-, to Br-, namely, -6.28, -9.98 and -13.67 kcal/mol, respectively. The coordination number distribution analysis for the first solvation shell of the all hydrated anions indicated a high exchange rate for the first solvation shell ligands. Keywords: Monte Carlo simulation, halogen anion, ab initio
Transition strengths in 21 , 22 , 23Mg as tests of ab initio theory
Henderson, Jack; Ruotsalainen, Panu; Hackman, Greg; Experiment S1480 Team; Experiment S1624 Team; Experiment S1646 Team
2017-09-01
Effective charges compensate for insufficiencies arising from truncations of the nuclear model-space by performing a crude inflation of nucleon charges to account for missing electric-quadrupole (E 2) transition strength. Recent theoretical developments in ab initio nuclear theory might allow for the calculation of this strength using evolved effective-operators arising from first-principles, removing the need for effective charges and enhancing predictive power. To that end, Coulomb excitation measurements were performed of neutron-deficient 21 , 22 , 23Mg at TRIUMF-ISAC, with the goal of extracting precision E 2 strengths for comparison with state-of-the-art models. Results will be presented and compared with ab initio in-medium similarity renormalization group (IM-SRG) and symplectic no-core shell-model calculations, as well as phenomenological shell-model results. Results will also be presented in the context of mirror-pairs in the sd -shell, providing a systematic evaluation of the reproduction of E 2 strength with respect to isospin.
DEFF Research Database (Denmark)
Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.
2014-01-01
Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.......Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom....
Ab initio thermodynamic results for warm dense matter
Bonitz, Michael
2016-10-01
Warm dense matter (WDM) - an exotic state where electrons are quantum degenerate and ions may be strongly correlated - is ubiquitous in dense astrophysical plasmas and highly compressed laboratory systems including inertial fusion. Accurate theoretical predictions require precision thermodynamic data for the electron gas at high density and finite temperature around the Fermi temperature. First such data have been obtained by restricted path integral Monte Carlo (restricted PIMC) simulations and transformed into analytical fits for the free energy. Such results are also key input for novel finite temperature density functional theory. However, the RPIMC data of Ref. 1 are limited to moderate densities, and even there turned out to be surprisingly inaccurate, which is a consequence of the fermion sign problem. These problems were recently overcome by the development of alternative QMC approaches in Kiel (configuration PIMC and permutation blocking PIMC) and Imperial College (Density matrix QMC). The three methods have their strengths and limitations in complementary parameter regions and provide highly accurate thermodynamic data for the electronic contributions in WDM. While the original results were obtained for small particle numbers, recently accurate finite size corrections were derived allowing to compute ab initio thermodynamic data with an unprecedented accuracy of better than 0.3 percent. This provides the final step for the use as benchmark data for experiments and models of Warm dense matter. Co-authors: T. Schoof, S. Groth, T. Dornheim, F. D. Malone, M. Foulkes, and T. Sjostroem, Funded by: DFG via SFB-TR24 and project BO1366-10.
Volumic omit maps in ab initio dual-space phasing.
Oszlányi, Gábor; Sütő, András
2016-07-01
Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.
Challenges for large scale ab initio Quantum Monte Carlo
Kent, Paul
2015-03-01
Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).
An Ab Initio Based Potential Energy Surface for Water
Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.
Ab initio no-core solutions for 6Li
Shin, Ik Jae; Kim, Youngman; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy; Michel, Nicolas
2017-07-01
We solve for properties of 6Li in the ab initio no-core full configuration (NCFC) approach and we separately solve for its ground state and {J}π ={2}2+ resonance with the Gamow shell model (GSM) in the Berggren basis. We employ both the JISP16 and chiral {{NNLO}}{opt} realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root mean square (rms) radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton rms radius, and electric quadrupole moment. We attain improved estimates of these observables in the NCFC approach by using basis spaces up through {N}\\max =18 that enable more definitive comparisons with experiment. Using the density matrix renormalization group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the GSM treatment of the 6Li ground state and {J}π ={2}2+ resonance by adopting a natural orbital single-particle basis.
Double-walled silicon nanotubes: an ab initio investigation
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.
Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface
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 Hartree-Fock study of tritium desorption from Li{sub 2}O
Energy Technology Data Exchange (ETDEWEB)
Taniguchi, Masaki; Tanaka, Satoru [Tokyo Univ. (Japan). Faculty of Engineering
1998-03-01
Dissociative adsorption of hydrogen on Li{sub 2}O (110) surface has been investigated with ab-initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and potential energy surface for H{sub 2} dissociative adsorption was evaluated by calculating the total energy of the system. Calculation results on adsorption heat indicated that H{sub 2} adsorption is endothermic. However, when oxygen vacancy exists adjacent to the adsorption sites, heat of adsorption energy became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (author)
All Electron ab initio Investigations of the Electronic States of the MoN Molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl A.
1999-01-01
The low lying electronic states of the molecule MoN have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction have...... been determined in perturbation calculations. The electronic ground state is confirmed as being 4 . The chemical bond of MoN has triple bond character due to the approximately fully occupied delocalized bonding and orbitals. The spectroscopic constants for the ground state and ten excited states have...... been derived. The excited doublet states, 2 , 2 , 2 , and 2 + are found to be lower lying than the 4 state that has been investigated experimentally. Elaborate multi configuration configuration interaction (MRCI) calculations have been carried out for the states 4 and 4 using various basis sets...
Ab Initio Computation of Dynamical Properties: Pressure Broadening
Wiesenfeld, Laurent; Drouin, Brian
2014-06-01
Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into
Han, Huixian; Li, Anyang; Guo, Hua
2014-12-01
A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
Energy Technology Data Exchange (ETDEWEB)
Lespade, Laure, E-mail: l.lespade@ism.u-bordeaux1.fr
2016-08-22
Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH{sup ·} or ABTS{sup ·+} is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.
Vibrational predissociation dynamics of the aniline-neon Van der Waals complex: an ab initio study
Energy Technology Data Exchange (ETDEWEB)
Lopez-Tocon, I.; Otero, J.C.; Soto, J.; Becucci, M.; Pietraperzia, G.; Castellucci, E
2004-08-02
The aniline-neon van der Waals complex has been investigated from a theoretical point of view. The intermolecular distance, structure and rotational constants in the ground electronic state have been obtained by ab initio calculations using second-order Moeller-Plesset (MP2) theory. The potential energy surface has also been determined. It has been found that two conformers exist: the anti, where the neon atom and the NH bonds are located on opposite sides of the ring, is slightly more stable than the syn conformer. All the ab initio results agree with those obtained by the analysis of the rotational and laser induced fluorescence spectra of this complex. We have also modeled the interaction of the van der Waals bending mode with others internal motions of the aniline molecule such as the inversion mode of the amino group and the breathing mode of the ring. The theoretical results predict that there is a significant coupling between the van der Waals bending and the inversion mode in agreement with the experimental behavior found in both the ground and the first excited electronic states of this complex.
Phenolic Polymer Solvation in Water and Ethylene Glycol, II: Ab Initio Computations.
Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W
2017-04-06
Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH2-phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule. Thus, the ethylene glycol-phenolic potential is more complicated than the water-phenolic potential. The results of the ab initio calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibration studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.
Ab initio quantum chemistry in parallel-portable tools and applications
Energy Technology Data Exchange (ETDEWEB)
Harrison, R.J.; Shepard, R. (Argonne National Lab., IL (United States)); Kendall, R.A. (Battelle Pacific Northwest Lab., Richland, WA (United States))
1991-01-01
In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10{sup 5}) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs.
Ab initio thermodynamics for the growth of ultra-thin Cu film on a perfect Mg O(001) surface
Energy Technology Data Exchange (ETDEWEB)
Zhukovskii, Yuri F. [Institute for Solid State Physics, University of Latvia, Kengaraga str. 8, Riga LV-1063 (Latvia)]. E-mail: quantzh@latnet.lv; Fuks, David [Materials Engineering Department, Ben-Gurion University of the Negev, POB 653, Beer-Sheva IL-84105 (Israel); Kotomin, Eugene A. [Institute for Solid State Physics, University of Latvia, Kengaraga str. 8, Riga LV-1063 (Latvia); Dorfman, Simon [Department of Physics, Israel Institute of Technology-Technion, Haifa IL-32000 (Israel)
2005-12-15
Controlled growth of thin metallic films on oxide substrates is important for numerous micro-and nano electronic applications. Our ab initio study is devoted to the periodic slab simulations for a series of ordered 2a Cu superlattices on the regular Mg O(001) substrate. Submonolayer and monolayer substrate Cu coverages were calculated using the Daft-Gaga method, as implemented into the Crystal-98 code. The results of ab initio calculations have been combined with thermodynamic theory which allows US to predict the growth mode of ultra-thin metal films (spinodal decomposition vs. nucleation-and-growth regime) as a function of the metal coverage and the temperature, and to estimate the metal density in clusters. We show that 3a cluster formation becomes predominant already at low Cu coverages, in agreement with the experiment.
Energy Technology Data Exchange (ETDEWEB)
Lucas, G
2006-10-15
The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)
Cosmic-Ray Modulation: an Ab Initio Approach
Engelbrecht, N. E.; Burger, R. A.
2014-10-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.
Cosmic-ray modulation: an ab initio approach
Energy Technology Data Exchange (ETDEWEB)
Engelbrecht, N.E.; Burger, R.A., E-mail: 12580996@nwu.ac.za [Center for Space Research, North-West University, Potchefstroom (South Africa)
2014-07-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented. (author)
AN AB INITIO MODEL FOR COSMIC-RAY MODULATION
Energy Technology Data Exchange (ETDEWEB)
Engelbrecht, N. E.; Burger, R. A. [Center for Space Research, North-West University, Potchefstroom 2520 (South Africa)
2013-07-20
A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.
DEFF Research Database (Denmark)
Pedersen, Kim Vestergaard; Christensen, Henrik; Shim, Irene
2004-01-01
Trichlorothioacetyl chloride 1, tetrachlorothiirane 2, and trichloroethenesulfenyl chloride 3 and the equilibria between them have been investigated by ab initio Hartree-Fock (HF), Møller-Plesset second order perturbation (MP2) calculations, and by Gaussian-3 theory, G3(MP2). The transition states...... of the isomerization reactions have been identified. Also investigated were possible reactions leading to the isomers and their possible decomposition products. The results show that the unobserved isomerization reactions are feasible....
Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study
Energy Technology Data Exchange (ETDEWEB)
Steinkasserer, Lukas Eugen Marsoner, E-mail: marsoner@zedat.fu-berlin.de [Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin (Germany); MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140 Wellington (New Zealand); Gaston, Nicola [MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140 Wellington (New Zealand); Paulus, Beate [Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin (Germany)
2015-04-21
Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.
Ab initio study of energetics and magnetism of sigma phase in Co–Mo and Fe–Mo systems
Czech Academy of Sciences Publication Activity Database
Pavlů, Jana; Vřešťál, Jan; Šob, Mojmír
2016-01-01
Roč. 24, č. 2 (2016), č. článku Art. Number 025009. ISSN 0965-0393 R&D Projects: GA ČR GA14-15576S Institutional support: RVO:68081723 Keywords : intermetallics * magnetic properties * phase stability * thermodynamic properties * site occupancy * ab-initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.891, year: 2016
Surface Tension of Ab Initio Liquid Water at the Water-Air Interface
Nagata, Yuki; Bonn, Mischa; Kühne, Thomas D
2016-01-01
We report calculations of the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the simulation cell size dependence of the surface tension of water from force field molecular dynamics (MD) simulations, which show that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is required for the small system used in the AIMD simulation. The AIMD simulations reveal that the double-{\\xi} basis set overestimates the experimentally measured surface tension due to the Pulay stress, while the triple and quadruple-{\\xi} basis sets give similar results. We further demonstrate that the van der Waals corrections critically affect the surface tension. AIMD simulations without the van der Waals correction substantially underestimate the surface tension, while van der Waals correction with the Grimme's D2 technique results in the value for the surface tension that is too high. T...
A room temperature CO$_2$ line list with ab initio computed intensities
Zak, Emil; Polyansky, Oleg L; Lodi, Lorenzo; Zobov, Nikolay F; Tashkun, Sergey A; Perevalov, Valery I
2016-01-01
Atmospheric carbon dioxide concentrations are being closely monitored by remote sensing experiments which rely on knowing line intensities with an uncertainty of 0.5% or better. We report a theoretical study providing rotation-vibration line intensities substantially within the required accuracy based on the use of a highly accurate {\\it ab initio} dipole moment surface (DMS). The theoretical model developed is used to compute CO$_2$ intensities with uncertainty estimates informed by cross comparing line lists calculated using pairs of potential energy surfaces (PES) and DMS's of similar high quality. This yields lines sensitivities which are utilized in reliability analysis of our results. The final outcome is compared to recent accurate measurements as well as the HITRAN2012 database. Transition frequencies are obtained from effective Hamiltonian calculations to produce a comprehensive line list covering all $^{12}$C$^{16}$O$_2$ transitions below 8000 cm$^{-1}$ and stronger than 10$^{-30}$ cm / molecule at ...
DEFF Research Database (Denmark)
Andersen, Vinca Bonde; Berg, Rolf W.; Shim, Irene
2017-01-01
The iminodisulfonate, [N(SO3)2]3–, and phosphinodisulfonate, [P(SO3)2]3–, ions have been investigated by performing ab initio MP2/6-311+G**calculations. The nitrogen and phosphorus atoms as part of the ions are shown to be divalent with a negative charge and two lone pairs on the nitrogen...... and phosphorus atoms. The experimentally known calcium sodium iminodisulfonate trihydrate and the analogous unknown compound calcium sodium phosphinodisulfonate trihydrate have also been investigated using the MP2/6-311+G** calculations. For the nitrogen compound, only minor changes occur in the iminodisulfonate...... ion when it becomes part of the calcium sodium iminodisulfonate trihydrate. For the phosphorus compound, the geometry of the phosphinodisulfonate ion changes significantly as part of calcium sodium phosphinodisulfonate trihydrate. Furthermore, the charges associated with the atoms in calcium sodium...
Ab initio molecular dynamics simulation of pressure-induced phase transition in MgS
Begeç, Ebru; Eker, Sıtkı; Bozdemir, Süleyman
2017-08-01
Pressure-induced phase transition in MgS is studied using a constant pressure ab initio molecular dynamics method, and a solid evidence of existence of its high-pressure phase is provided. As predicted by total energy calculations, MgS undergoes a structural phase transformation from the rocksalt structure to a CsCl-type structure under hydrostatic pressure. The transformation mechanism is characterized, and two intermediate phases having P4/ nmm and P21/ m symmetries for the rocksalt-to-CsCl-type phase transformation of MgS are proposed, which is different from the previously proposed mechanisms. We also study this phase transition using the total energy calculations. Our predicted transition parameters and bulk properties are in good agreement with the earlier first principle simulations.
High-accuracy extrapolated ab initio thermochemistry of the vinyl, allyl, and vinoxy radicals.
Tabor, Daniel P; Harding, Michael E; Ichino, Takatoshi; Stanton, John F
2012-07-26
Enthalpies of formation at both 0 and 298 K were calculated according to the HEAT (High-accuracy Extrapolated Ab initio Thermochemistry) protocol for the title molecules, all of which play important roles in combustion chemistry. At the HEAT345-(Q) level of theory, recommended enthalpies of formation at 0 K are 301.5 ± 1.3, 180.3 ± 1.8, and 23.4 ± 1.5 kJ mol(-1) for vinyl, allyl, and vinoxy, respectively. At 298 K, the corresponding values are 297.3, 168.6, and 16.1 kJ mol(-1), with the same uncertainties. The calculated values for the three radicals are in excellent agreement with the corresponding experimental values, but the uncertainties associated with the HEAT values for vinoxy are considerably smaller than those based on experimental studies.
Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.
1989-01-01
Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.
Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface
Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
Energy Technology Data Exchange (ETDEWEB)
Nakamura, Makoto, E-mail: nakamura@cphys.s.kanazawa-u.ac.jp; Obata, Masao [Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192 (Japan); Morishita, Tetsuya [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568 (Japan); Oda, Tatsuki, E-mail: oda@cphys.s.kanazawa-u.ac.jp [Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192 (Japan); Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192 (Japan)
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
Structure and dynamics of liquid Zn: an analysis of ab-initio simulations
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del Rio B. G.
2017-01-01
Full Text Available The static and dynamic properties of liquid Zn have been studied using an ab initio molecular dynamics method. Results are reported for the thermodynamic states at 723K near which inelastic neutron and x-ray scattering data are available. The calculated static structure shows very good agreement with experimental measurements, including an asymmetric main peak. The dynamic structure reveals the existence of propagating density fluctuations, and the associated dispersion relation has also been calculated. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in several liquid metals under high pressures; the second region is around qp/2, as suggested by inelastic scattering experiments for liquid Zn and other metals.
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Abid Hussain
2017-09-01
Full Text Available Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN. Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.
EFFECT OF SCANDIUM ON HIDROGEN DISSOCIATION ENERGY AT MAGNESIUM SURFACE: AB INITIO DFT STUDY
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I Wayan Sutapa
2010-07-01
Full Text Available The dissociative chemisorption of hydrogen on both pure and Sc-incorporated Mg(0001 surfaces have been studied by ab initio density functional theory (DFT calculation. The calculated dissociation energy of hydrogen molecule on a pure Mg(0001 surface (1.200 eV is in good agreement with comparable theoretical studies. For the Sc-incorporated Mg(0001 surface, the activated barrier decreases to 0.780 eV due to the strong interaction between the molecular orbital of hydrogen and the d metal state of Sc. This could explain the experimentally observed improvement in absorption kinetics of hydrogen when transition metals have been introduced into the magnesium materials. Keywords: Dissociation, Adsorption, Chemisorptions, DFT, Magnesium
Ab initio contribution to the study of complexes formed during dilute FeCu alloys radiation
Becquart, C S
2003-01-01
Cu plays an important role in the embrittlement of pressure vessel steels under radiation and entities containing both Cu atoms and vacancies seem to appear as a consequence of displacement cascades. The characterisation of the stability as well as the migration of small Cu-vacancy complexes is thus necessary to understand and simulate the formation of these entities. For instance, cascade ageing studied by kinetic Monte Carlo or by rate theory models requires a good characterisation of such complexes which are parameters for these methods. We have investigated, by ab initio calculations based on the density functional theory, point defects and small defects in dilute FeCu alloys. The structure of small Cu clusters and Cu-vacancy complexes has been determined, as well as their formation and binding energies. Their relative stability is discussed. Vacancy migration energies in the presence of Cu atoms have been calculated and analysed. All the results are compared to the figures obtained with empirical interat...
Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos
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Cirino José Jair Vianna
2002-01-01
Full Text Available A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitude of the free energy obtained from this simulation did not permit us to conclude that urea is non-planar in water.
DEFF Research Database (Denmark)
Palmer, Michael H.; Hoffmann, Søren Vrønning; Jones, Nykola C.
2011-01-01
The Rydberg states in the vacuum ultraviolet photoabsorption spectrum of 1,2,3-triazole have been measured and analyzed with the aid of comparison to the UV valence photoelectron ionizations and the results of ab initio configuration interaction (CI) calculations. Calculated electronic ionization...
Cryospectroscopic and ab initio anharmonic studies of acetylene-trimethylamine H-bonded complex
Energy Technology Data Exchange (ETDEWEB)
Rutkowski, K.S., E-mail: rutkowsk@molsp.phys.spbu.ru [Department of Physics, St. Petersburg University, Uljanovskaja 1, 198504 St. Petersburg (Russian Federation); Melikova, S.M. [Department of Physics, St. Petersburg University, Uljanovskaja 1, 198504 St. Petersburg (Russian Federation); Janski, J.; Koll, A. [Faculty of Chemistry, University of Wroclaw, 14 F. Joliot-Curie, 50-383 Wroclaw (Poland)
2010-09-14
Graphical abstract: FTIR spectroscopy in the range of fundamental and overtone bands and ab initio calculations show weak complex formation between acetylene and trimethylamine stabilized by a conventional H-bond predominantly. - Abstract: The FTIR spectra of C{sub 2}H{sub 2} in mixtures with trimethylamine (TMA) have been studied in liquefied Kr in the frequency range of {approx}800-7000 cm{sup -1}. The data obtained for C{sub 2}H{sub 2} subunit suggest the formation of 1:1 complexes stabilized by a moderate strength conventional H-bond. CH and CN stretching vibrations, related to the vicinal bonds of proton acceptor, were found to shift in opposite directions - blue in the former and red in the latter case. New weak bands, revealed in the range of {approx}6000-7000 cm{sup -1}, were ascribed to the overtone and combination bands of C-H stretching vibrations of acetylene which participates in the H-bond formation. The relative stability of the complex has been determined in a series of temperature (T = 118-157 K) measurements of integrated intensities of vibrational bands ascribed to monomer and complex species. Ab initio MP2/6-311++G(2d,2p) a priory counterpoise corrected calculations, made for acetylene, TMA, and the complex reproduce the main spectroscopic observations. They suggest that the most stable non-linear structure of the complex is very floppy. Evaluations of anharmonic effects on position and integrated intensity of selected bands of C-H stretching modes of C{sub 2}H{sub 2} subunit have been made within perturbation theory on the basis of single point potential energy surface (PES) and dipole moment function calculations.
Ab-initio electronic and magnetic properties of Fe-Al alloys
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Apiñaniz, E.
2000-06-01
Full Text Available This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performed for the previously mentioned compositions. These results show that by disordering the alloy magnetism is enhanced and that the equilibrium lattice parameter increases.
En este trabajo se presentan cálculos autoconsistentes ab-initio realizados con el método TB-LMTO (Tight Binding Linear Muffin Tin Orbital con el fin de estudiar las diferentes estructuras que se presentan en el diagrama de fases de las aleaciones Fe-Al. Se han estudiado las estructuras ordenadas B2, DO3 y B32 para las siguientes concentraciones: Fe50Al50 y Fe3Al. Asimismo, se han realizado cálculos teniendo y sin tener en cuenta la polarización de spin con el fin de poder deducir la diferencia energética entre los estados ferromágneticos y paramágneticos de la misma estructura. Por otra parte se han realizado estos mismos cálculos para estructuras desordenadas y las mismas concentraciones. Los resultados muestran que mediante el desorden aumenta el magnetismo de estas aleaciones y crece el parámetro de red.
14N NQR lineshape in nanocrystals: An ab initio investigation of urea
Gregorovič, Alan
2017-05-01
14N nuclear quadrupole resonance (NQR) lineshapes mostly contain information of low interest, although in nanocrystals they may display some unexpected behaviour. In this work, we present an ab initio computational study of the 14N NQR lineshapes in urea nanocrystals as a function of the nanocrystal size and geometry, focusing on the surface induced broadening of the lineshapes. The lineshapes were obtained through a calculation of the electric field gradient for each nitrogen site in the nanocrystal separately, taking into account the individual crystal field by embedding the molecule of interest in a suitable lattice of point multipoles representing other urea molecules in the nanocrystal. The small influence of distant molecules is found with a series expansion, using the in-crystal Sternheimer shieldings which we also calculated ab initio. We have considered nanocrystals with two geometries: a sphere and a cube, with characteristic sizes between 5 and 100 nm. Our calculations suggest that there is a dramatic difference between the linewidths for the two geometries. For spheres, we find a steep drop in linewidths at ˜10 nm; at 5 nm the linewidth is ˜11 kHz, whereas for sizes above 20 nm the linewidth is practically negligible (<100 Hz). For cubes, on the other hand, we find a steady 1/size decrease, from 12 kHz at 10 nm to 1.2 kHz at 100 nm. This analysis is important for 14N NQR spectroscopy of crystalline pharmaceuticals, where nanoparticles are increasingly more often embedded in some sort of matrix. Although this is only a theoretical analysis, we believe that this work can serve as a guidance for the forthcoming experimental analysis.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic
Raimondi, Francesco; Hupin, Guillaume; Navrátil, Petr; Quaglioni, Sofia
2016-05-01
Background: Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Ab initio approaches have been successfully applied to describe the 3H (d ,n )4He and 3He(d ,p )4He fusion processes. Purpose: An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d ,p ) reactions to processes with light p -shell nuclei. As a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d ,p )8Li transfer reaction based on a two-body Hamiltonian. Methods: We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. Results: The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d -7Li and p -8Li particle-decay channels determines some features of the 9Be spectrum above the d +7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Conclusions: Deuteron stripping reactions with p -shell targets can now be computed ab initio, but calculations are very demanding. A quantitative description of the 7Li(d ,p )8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.
Ab initio theory for current-induced molecular switching: Melamine on Cu(001)
Ohto, Tatsuhiko
2013-05-28
Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.
Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide
Energy Technology Data Exchange (ETDEWEB)
Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)
2015-06-28
We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.
Caillabet, L; Canaud, B; Salin, G; Mazevet, S; Loubeyre, P
2011-09-09
Improving the description of the equation of state (EOS) of deuterium-tritium (DT) has recently been shown to change significantly the gain of an inertial confinement fusion target [S. X. Hu et al., Phys. Rev. Lett. 104, 235003 (2010)]. Here we use an advanced multiphase EOS, based on ab initio calculations, to perform a full optimization of the laser pulse shape with hydrodynamic simulations starting from 19 K in DT ice. The thermonuclear gain is shown to be a robust estimate over possible uncertainties of the EOS. Two different target designs are discussed, for shock ignition and self-ignition. In the first case, the areal density and thermonuclear energy can be recovered by slightly increasing the laser energy. In the second case, a lower in-flight adiabat is needed, leading to a significant delay (3 ns) in the shock timing of the implosion.
Estudo ab-initio da a-alanina em meio aquoso
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Sambrano Júlio Ricardo
1999-01-01
Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.
AB INITIO STUDY OF AMMONIA CLUSTERS: (NH3n (n = 2-6
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Herudi Kandau
2010-06-01
Full Text Available Hydrogen bonded neutral clusters of ammonia, (NH3n (n = 2-6, have been theoretically investigated employing the D95++(d,p (and wherever necessary, higher basis sets at the Hartree-Fock (HF level as well as with second-order Møller-Plesset (MP2 perturbation theory. While the ammonia trimer and tetramer exhibit perfect molecular symmetries and are nonpolar, the pentamer and hexamer both optimize with slight deviations from perfect symmetries and are seen to posses marginal, but nonzero dipole moments. The (NH3n linear clusters are seen to be chemically softer than the corresponding cyclic ones. Keywords: ab initio calculation, ammonia clusters, Hartree-Fock, Møller-Plesset
Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures
Clay, Raymond; Morales, Miguel
2017-06-01
In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Li, Yan; Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry
Functionalized carbon nanotubes have great potential for nanoscale sensing applications, yet many aspects of their sensing mechanisms are not understood. We investigate two paradigmatic sensor configurations for detection of biologically important molecules through ab initio calculations: a non-covalently functionalized nanotube for glucose detection and a covalently functionalized nanotube for ethylene detection. Despite of their structural and chemical simplicities, glucose and ethylene control key life processes of humans and plants, respectively. We evaluate the sensors' electrical conductance and transmission coefficients at the full density-functional theory level via the non-equilibrium Green's function method. A clear atomistic picture emerges about the mechanisms involved in glucose and ethylene sensing. While functionalized semiconducting nanotubes exhibit good sensitivities in both cases, the current through metallic nanotubes is only weakly affected by analyte attachment. We also investigate the effects of band gaps of the nanotubes and changes to the receptors on the detection sensitivities. These quantitative results can guide the design of improved sensors.
Ab initio potential energy surface and vibration-rotation energy levels of beryllium monohydroxide.
Koput, Jacek
2017-01-05
The accurate potential energy surface of beryllium monohydroxide, BeOH, in its ground electronic state X 2A' has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The BeOH molecule was confirmed to be bent at equilibrium, with the BeOH angle of 141.2° and the barrier to linearity of 129 cm-1 . The vibration-rotation energy levels of the BeOH and BeOD isotopologues were predicted using a variational approach and compared with recent experimental data. The results can be useful in a further analysis of high-resolution vibration-rotation spectra of these interesting species. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Ab initio potential energy surface and vibration-rotation energy levels of sulfur dioxide.
Koput, Jacek
2017-05-05
An accurate potential energy surface of sulfur dioxide, SO2 , in its ground electronic state X∼ 1A1 has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. The results obtained with the conventional and explicitly correlated coupled-cluster methods are compared. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, and adiabatic effects in determining the structure and dynamics of the SO2 molecule is discussed. The vibration-rotation energy levels of the 32 SO2 and 34 SO2 isotopologues were predicted using a variational approach. It was shown that the inclusion of the aforementioned effects was mandatory to attain the "spectroscopic" accuracy. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Ab initio atomic recombination reaction energetics on model heat shield surfaces
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.
Brigot, N.; Cohen De Lara, E.; Blain, M.
1981-01-01
Pour retrouver un certain nombre de grandeurs expérimentales tirées des spectres infrarouges de la molécule d'azote adsorbée dans la zéolithe NaA, nous présentons ici un calcul quantique ab initio sur le couple N 2-Na+. Après avoir déterminé sa géométrie d'équilibre nous calculons le glissement de la fréquence de vibration N-N et son moment dipolaire de transition induit par la présence du cation. Les résultats obtenus sont en bon accord avec l'expérience ainsi qu'avec ceux déterminés à parti...
Ab initio excited states from the in-medium similarity renormalization group
Parzuchowski, N. M.; Morris, T. D.; Bogner, S. K.
2017-04-01
We present two new methods for performing ab initio calculations of excited states for closed-shell systems within the in-medium similarity renormalization group (IMSRG) framework. Both are based on combining the IMSRG with simple many-body methods commonly used to target excited states, such as the Tamm-Dancoff approximation (TDA) and equations-of-motion (EOM) techniques. In the first approach, a two-step sequential IMSRG transformation is used to drive the Hamiltonian to a form where a simple TDA calculation (i.e., diagonalization in the space of 1 p 1 h excitations) becomes exact for a subset of eigenvalues. In the second approach, EOM techniques are applied to the IMSRG ground-state-decoupled Hamiltonian to access excited states. We perform proof-of-principle calculations for parabolic quantum dots in two dimensions and the closed-shell nuclei 16O and 22O. We find that the TDA-IMSRG approach gives better accuracy than the EOM-IMSRG when calculations converge, but it is otherwise lacking the versatility and numerical stability of the latter. Our calculated spectra are in reasonable agreement with analogous EOM-coupled-cluster calculations. This work paves the way for more interesting applications of the EOM-IMSRG approach to calculations of consistently evolved observables such as electromagnetic strength functions and nuclear matrix elements, and extensions to nuclei within one or two nucleons of a closed shell by generalizing the EOM ladder operator to include particle-number nonconserving terms.
Meisel, David D.; Szasz, Csilla; Kero, Johan
2008-06-01
The Arecibo UHF radar is able to detect the head-echos of micron-sized meteoroids up to velocities of 75 km/s over a height range of 80 140 km. Because of their small size there are many uncertainties involved in calculating their above atmosphere properties as needed for orbit determination. An ab initio model of meteor ablation has been devised that should work over the mass range 10-16 kg to 10-7 kg, but the faint end of this range cannot be observed by any other method and so direct verification is not possible. On the other hand, the EISCAT UHF radar system detects micrometeors in the high mass part of this range and its observations can be fit to a “standard” ablation model and calibrated to optical observations (Szasz et al. 2007). In this paper, we present a preliminary comparison of the two models, one observationally confirmable. Among the features of the ab initio model that are different from the “standard” model are: (1) uses the experimentally based low pressure vaporization theory of O’Hanlon (A users’s guide to vacuum technology, 2003) for ablation, (2) uses velocity dependent functions fit from experimental data on heat transfer, luminosity and ionization efficiencies measured by Friichtenicht and Becker (NASA Special Publication 319: 53, 1973) for micron sized particles, (3) assumes a density and temperature dependence of the micrometeoroids and ablation product specific heats, (4) assumes a density and size dependent value for the thermal emissivity and (5) uses a unified synthesis of experimental data for the most important meteoroid elements and their oxides through least square fits (as functions of temperature, density, and/or melting point) of the tables of thermodynamic parameters given in Weast (CRC Handbook of Physics and Chemistry, 1984), Gray (American Institute of Physics Handbook, 1972), and Cox (Allen’s Astrophysical Quantities 2000). This utilization of mostly experimentally determined data is the main reason for
Rutigliano, M; Zazza, C; Sanna, N; Pieretti, A; Mancini, G; Barone, V; Cacciatore, M
2009-12-31
The adsorption dynamics of atomic oxygen on a model beta-cristobalite silica surface has been studied by combining ab initio electronic structure calculations with a molecular dynamics semiclassical approach. We have evaluated the interaction potential of atomic and molecular oxygen interacting with an active Si site of a model beta-cristobalite surface by performing DFT electronic structure calculations. As expected, O is strongly chemisorbed, E(b) = 5.57 eV, whereas molecular oxygen can be weakly adsorbed with a high-energy barrier to the adsorption state of approximately 2 eV. The binding energies calculated for silica clusters of different sizes have revealed the local nature of the O,O(2)-silica interaction. Semiclassical collision dynamic calculations show that O is mainly adsorbed in single-bounce collisions, with a smaller probability for adsorption via a multicollision mechanism. The probability for adsorption/desorption (reflected) collisions at the three impact energies is small but not negligible at the higher energy considered in the trajectory calculations, about P(r) = 0.2 at E(kin) = 0.8 eV. The calculations give evidence of a complex multiphonon excitation-deexcitation mechanism underlying the dynamics of stable adsorption and inelastic reflection collisions.
Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei
The possibility of calculating dynamical correlation functions from first principles provides a unique opportunity to explore the manifold of the excited states of a quantum many-body system. Such calculations allow us to predict interesting physical properties like spectral functions, excitation spectra and charge and spin gaps, which are more difficult to access from usual equilibrium calculations. We address the ab-initio calculation of dynamical Green functions and two-body correlation functions in the Auxiliary-field Quantum Monte Carlo method, using the two-dimensional Hubbard model as an example. When the sign problem is not present, an unbiased estimation of imaginary time correlation functions is obtained. We discuss in detail the complexity and the stability of the calculations. Moreover, we propose a new approach which is expected to be very useful when dealing with dilute systems, e.g. for cold gases, allowing calculations with a very favorable complexity in the system size. Supported by NSF, DOE SciDAC, and Simons Foundation.
Ab initio total energy study of brucite, diaspore and hypothetical hydrous wadsleyite
Winkler, B.; Milman, V.; Hennion, B.; Payne, M. C.; Lee, M.-H.; Lin, J. S.
1995-10-01
Ab initio total energy calculations based on the local density approximation (LDA) and the generalised gradient approximation (GGA) of density functional theory have been performed for brucite, Mg(OH)2, diaspore, AlOOH and hypothetical hydrous wadsleyite, Mg7Si4O14(OH)2. The use of a general gradient approximation (GGA) is essential to obtain a good agreement (≈ 1%) of the calculated lattice parameters to diffraction data. The calculated fractional coordinates of brucite and diaspore are in good agreement (≈ 1.5%) with experimental data. The angle of the non-linear hydrogen bond in diaspore is reproduced well, and the calculated Raman active OH stretching frequency in brucite is in very good agreement with spectroscopic data. There are no significant differences between the calculated fractional coordinates and the second derivative of the energy when GGA is used instead of standard LDA. It is concluded that the description of the static and the dynamic behavior of the OH groups in these hydroxides is very good. It is therefore inferred that the parameter free model is predictive and it has been used to evaluate a hypothetical structure of hydrous wadsleyite. The model reproduces the unusual Si-O bond length of 1.7 Å, observed in β-Mg2SiO4. It predicts an O-H distance of 0.97 Å, which is significantly shorter than the distance obtained from earlier model calculations.
Energy Technology Data Exchange (ETDEWEB)
Terki, R. [Laboratoire d' Etude et de Recherche sur les Materiaux, les Procedes et les Surfaces, universite de Technologie de Belfort-Montbeliard, Site de Sevenans, 90010 Belfort (France)]. E-mail: rashida_terki@yahoo.fr; Bertrand, G. [Laboratoire d' Etude et de Recherche sur les Materiaux, les Procedes et les Surfaces, universite de Technologie de Belfort-Montbeliard, Site de Sevenans, 90010 Belfort (France); Aourag, H. [Laboratoire d' Etude et de Prediction de Materiaux, URMER, Universite de Tlemcen 13000 (Algeria); Coddet, C. [Laboratoire d' Etude et de Recherche sur les Materiaux, les Procedes et les Surfaces, universite de Technologie de Belfort-Montbeliard, Site de Sevenans, 90010 Belfort (France)
2007-04-15
The full-potential linearized augmented plane wave (FP-LAPW) method within the density functional theory was used to investigate the structural and electronic properties of Y{sub 2}Ti{sub 2}O{sub 7} and Cd{sub 2}Nb{sub 2}O{sub 7}. In this approach, the generalized gradient approximation was used for the exchange-correlation potential. We have firstly optimized the internal parameter and used it to calculate the ground state properties such as lattice constant, bulk modulus and its derivative as well as angles and inter-atomic distances. The results were in good agreement with available experimental measurements. We find that Y{sub 2}Ti{sub 2}O{sub 7} and Cd{sub 2}Nb{sub 2}O{sub 7} are highly incompressible and thus can be good candidates for hard materials. Calculations of band structure, density of state and charge density were also performed to describe the orbital mixing and the nature of chemical bonding. Both Y{sub 2}Ti{sub 2}O{sub 7} and Cd{sub 2}Nb{sub 2}O{sub 7} exhibit indirect band gaps. The mixture of B-d and O-2p states emphasis the covalent nature of the B-O bond that should explain the hardness of pyrochlore compounds. The small distances between oxygen and A/B atoms also lead to higher covalency of the bonds.
Energy Technology Data Exchange (ETDEWEB)
Dane Morgan
2010-06-10
The project began March 13, 2006, allocated for three years, and received a one year extension from March 13, 2009 to March 12, 2010. It has now completed 48 of 48 total months. The project was focused on using ab initio methods to gain insights into radiation induced segregation (RIS) in Ni-Fe-Cr alloys. The project had the following key accomplishments • Development of a large database of ab initio energetics that can be used by many researchers in the future for increased understanding of this system. For example, we have the first calculations showing a dramatic stabilization effect of Cr-Cr interstitial dumbbells in Ni. • Prediction of both vacancy and interstitial diffusion constants for Ni-Cr and Ni-Fe for dilute Cr and Fe. This work included generalization of widely used multifrequency models to make use of ab initio derived energetics and thermodynamics. • Prediction of qualitative trends of RIS from vacancy and interstitial mechanisms, suggesting the two types of defect fluxes drive Cr RIS in opposite directions. • Detailed kinetic Monte Carlo modeling of diffusion by vacancy mechanism in Ni-Cr as a function of Cr concentration. The results demonstrate that Cr content can have a significant effect on RIS. • Development of a quantitative RIS transport model, including models for thermodynamic factors and boundary conditions.
Heuvel, Willem Van den; Soncini, Alessandro
2015-01-01
We present an ab initio methodology dedicated to the determination of the electronic structure and magnetic properties of ground and low-lying excited states, i.e., the crystal field levels, in lanthanide(III) complexes. Currently, the most popular and successful ab initio approach is the CASSCF/RASSI-SO method, consisting of the optimization of multiple complete active space self-consistent field (CASSCF) spin eigenfunctions, followed by full diagonalization of the spin--orbit coupling (SOC) Hamiltonian in the basis of the CASSCF spin states featuring spin-dependent orbitals. Based on two simple observations valid for Ln(III) complexes, namely: (i) CASSCF 4f atomic orbitals are expected to change very little when optimized for different multiconfigurational states belonging to the 4f-electronic configuration, (ii) due to strong SOC the total spin is not a good quantum number, we propose here an efficient ab initio strategy which completely avoids any multiconfigurational calculation, by optimizing a unique s...
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Vadym V. Kulish
2017-12-01
Full Text Available Rational design of active electrode materials is important for the development of advanced lithium and post-lithium batteries. Ab initio modeling can provide mechanistic understanding of the performance of prospective materials and guide design. We review our recent comparative ab initio studies of lithium, sodium, potassium, magnesium, and aluminum interactions with different phases of several actively experimentally studied electrode materials, including monoelemental materials carbon, silicon, tin, and germanium, oxides TiO2 and VxOy as well as sulphur-based spinels MS2 (M = transition metal. These studies are unique in that they provided reliable comparisons, i.e., at the same level of theory and using the same computational parameters, among different materials and among Li, Na, K, Mg, and Al. Specifically, insertion energetics (related to the electrode voltage and diffusion barriers (related to rate capability, as well as phononic effects, are compared. These studies facilitate identification of phases most suitable as anode or cathode for different types of batteries. We highlight the possibility of increasing the voltage, or enabling electrochemical activity, by amorphization and p-doping, of rational choice of phases of oxides to maximize the insertion potential of Li, Na, K, Mg, Al, as well as of rational choice of the optimum sulfur-based spinel for Mg and Al insertion, based on ab initio calculations. Some methodological issues are also addressed, including construction of effective localized basis sets, applications of Hubbard correction, generation of amorphous structures, and the use of a posteriori dispersion corrections.
Energy Technology Data Exchange (ETDEWEB)
Ganster, P
2004-10-15
A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Matrix Isolation and ab initio study of the noncovalent complexes between formamide and acetylene.
Mardyukov, Artur; Sánchez-García, Elsa; Sander, Wolfram
2009-02-12
Matrix isolation spectroscopy in combination with ab initio calculations is a powerful technique for the identification of weakly bound intermolecular complexes. Here, weak complexes between formamide and acetylene are studied, and three 1:1 complexes with binding energies of -2.96, -2.46, and -1.79 kcal/mol have been found at the MP2 level of theory (MP2/cc-pVTZ + ZPE + BSSE). The two most stable dimers A and B are identified in argon and nitrogen matrices by comparison between the experimental and calculated infrared frequencies. Both complexes are stabilized by the formamide C=O...HC acetylene and H...pi interactions. Large shifts have been observed experimentally for the C-H stretching vibrations of the acetylene molecule, in very good agreement with the calculated values. Eight 1:2 FMA-acetylene trimers (T-A to T-H) with binding energies between -5.44 and -2.62 kcal/mol (MP2/aug-cc-pVDZ + ZPE + BSSE) were calculated. The two most stable trimers T-A and T-B are very close in energy and have similar infrared spectra. Several weak bands that are in agreement with the calculated frequencies of the trimers T-A and T-B are observed under matrix isolation conditions. However, the differences are too small for a definitive assignment.
Ab initio based State Specific Modeling of N2+O System
Luo, Han
Nitrogen and atomic oxygen play an important role in high temperature gas systems. Their Zeldovich reaction product nitric oxide not only affects aerothermal loads and emissions of hypersonic vehicles, but also has the possibility to influence the efficiency of hypersonic propulsion. Atomic oxygen induced nitrogen dissociation is another reaction mechanism of the N2+O system. However, due to the difficulty of conducting ground tests, there are no experimental data for this reaction now. Thermo-chemical nonequilibrium could make the problem more difficult since experiments could only track macroscopic gas properties instead of internal energy distribution. On the other hand, current reaction and internal energy exchange models are able to reproduce equilibrium condition. Whether their predictions at nonequilibrium conditions are reliable is still questionable. The work in this thesis employs quasi-classical trajectory (QCT) method based on an ab-initio chemistry calculated potential energy surface for the N2+O system. Through QCT calculations of different initial condition, high fidelity cross sections and rates are obtained. The cross sections are further used to generate a ME-QCT-VT model for vibrational excitation/relaxation, a state-specific exchange (SSE) model and a state-specific dissociation (SSD) model. These models are verified by comparison with direct QCT calculated rates and other experimental data or models. Although there are no flowfield calculations in this work, the models are able to be applied easily in DSMC calculations.
High pressure behaviour of uranium dicarbide (UC{sub 2}): Ab-initio study
Energy Technology Data Exchange (ETDEWEB)
Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C. [Applied Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)
2016-08-28
The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ∼8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressures placed at ∼24 GPa and ∼50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ∼17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC{sub 2} sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as
Di Palma, Tonia M.; Bende, Attila
2013-03-01
The structures and energetics of neutral, ionized and protonated methyl tert-butyl ether (MTBE) clusters and (MTBE)m(H2O)n clusters are investigated by tunable vacuum-UV photoionization mass spectrometry and DFT calculations. While the mass spectra of bare MTBE clusters show unprotonated and protonated clusters ions, the mass spectra of mixed clusters show protonated ions that exhibit magic numbers that correspond to n = m - 2 combinations. Ab initio calculations show that in the larger clusters a multiple proton transfer leads to a protonated water core where all available hydrogen bonds interact with MTBE molecules. The resulting bond structure explains the cluster stability.
Vibrational infrared spectra of biuret and its thioanalogs. An ab initio SCF/3-21G study
Sullivan, Richard H.; Kwiatkowski, Józef S.; Leszczyński, Jerzy; Jabalameli, Ali
1993-05-01
The results of ab initio SCF/3-21G * calculations are reported for vibrational IR spectra (harmonic wavenumbers, absolute intensities) of biuret, thiobiuret, dithiobiuret and their model systems, formamide and thioformamide. The predicted vibrational spectra of both biurets and model systems compare well with the available experimental data, and the observed shifts of the IR wavenumbers upon deuteration of the molecules are correctly predicted by the calculations. The positions and relative intensities of characteristic IR bands of formamide and thioformamide correlate well with the corresponding data for the biurets.
Directory of Open Access Journals (Sweden)
G.M. Bhuiyan
2012-10-01
Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.
Energy Technology Data Exchange (ETDEWEB)
Ikeno, Hidekazu; Groot, Frank M F de [Department of Inorganic Chemistry and Catalysis, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht (Netherlands); Tanaka, Isao, E-mail: H.Ikeno@uu.n [Department of Materials Science and Engineering, Kyoto University, Yoshida, Sakyo, Kyoto 606-8501 (Japan)
2009-11-15
X-ray-absorption near-edge structures (XANES) at the transition metal (TM) L{sub 2,3}-edge of TiCl{sub 4} and VOCl{sub 3} are calculated by the all-electron configuration interaction (CI) method using fully-relativistic molecular spinors with density functional theory (DFT). The electronic excitation from molecular spinors mainly composed of ligand p atomic spinors to those of TM-3d spinors, i.e., the charge transfer, is included by taking additional electronic configurations in the CI. The effects of the ligand field and the charge transfer on the TM-L{sub 2,3} XANES are investigated by an ab-intio method. The reduction of inter-electron interaction due to the covalent bonding between TM and ligand atoms has been found. The contribution of charge transferred configuration is small at the initial state of TM-L{sub 2,3} XANES while the significant amount of charge transferred configuration is found at the final states. The spectral shapes of TM-L{sub 2,3} XANES of both TiCl{sub 4} and VOCl{sub 3} are strongly modified by the charge transfer effects.
DEFF Research Database (Denmark)
Shim, Irene; Baba, M. Sai; Gingerich, K.A.
2002-01-01
The low-lying states of the molecule Ge-2 and of the ion Ge-2(-) have been investigated by all electron ab initio multiconfiguration self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations. The relativistic corrections for the Darwin contact term and for t...
Linker, Gerrit-Jan; van Loosdrecht, Paul H. M.; van Duijnen, Piet; Broer, Ria
2010-01-01
We performed ab initio quantum chemical calculations for the geometrical and electronic structure of the EDO-TTF (ethylenedioxy-tetrathiafulvalene) molecule using HF, CASSCF and DFT methods. We compare these in vacuo results with the properties of the (EDO-TTF)(2)PF6 crystal at near room
Transport coefficients of helium-neon mixtures at low density computed from ab initio potentials.
Sharipov, Felix; Benites, Victor J
2017-12-14
The viscosity, thermal conductivity, diffusion coefficient, and thermal diffusion factor of helium-neon mixtures at low density are calculated for a wide range of temperature and for various molar fractions. The Chapman-Enskog method is employed considering the 10th order of the Sonine polynomial expansion. Ab initio potentials for intermolecular interactions are used to calculate the omega-integrals. The relative numerical error of the present results obtained for the potentials used here is less than 7 × 10-5 for the thermal diffusion factor and 2 × 10-5 for all the other coefficients. Since each employed potential has a different accuracy, the uncertainty related to such accuracies was analyzed, considering the contribution of each potential uncertainty. It was found that the total uncertainty due to the potentials is larger than the numerical error and it varies depending on the temperature and molar fraction. A comparison of the calculated transport coefficients with those available in the open literature shows that the present calculations provide the most accurate values currently available for the transport coefficients of helium-neon binary mixtures at low density.
Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J; Yang, Weitao
2008-03-28
Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.
Ab initio-based approach to structural change of compound semiconductor surfaces during MBE growth
Ito, Tomonori; Akiyama, Toru; Nakamura, Kohji
2009-01-01
Phase diagrams of GaAs and GaN surfaces are systematically investigated by using our ab initio-based approach in conjunction with molecular beam epitaxy (MBE). The phase diagrams are obtained as a function of growth parameters such as temperature and beam equivalent pressure (BEP). The versatility of our approach is exemplified by the phase diagram calculations for GaAs(0 0 1) surfaces, where the stable phases and those phase boundaries are successfully determined as functions of temperature and As 2 and As 4 BEPs. The initial growth processes are clarified by the phase diagram calculations for GaAs(1 1 1)B-(2×2). The calculated results demonstrate that the As-trimer desorption on the GaAs(1 1 1)B-(2×2) with Ga adatoms occurs beyond 500-700 K while the desorption without Ga adatoms does beyond 800-1000 K. This self-surfactant effect induced by Ga adsorption crucially affects the initial growth of GaAs on the GaAs(1 1 1)B-(2×2). Furthermore, the phase diagram calculations for GaN(0 0 0 1) suggests that Ga adsorption or desorption during GaN MBE growth can easily change the pseudo-(1×1) to the (2×2)-Ga via newly found (1×1) and vice versa. On the basis of this finding, the possibility of ghost island formation during MBE growth is discussed.
Characterization of Elastic Properties of Porous Graphene Using an Ab Initio Study
Directory of Open Access Journals (Sweden)
Reza Ansari
2016-12-01
Full Text Available Importance of covalent bonded two-dimensional monolayer nanostructures and also hydrocarbons is undeniably responsible for creation of new fascinating materials like polyphenylene polymer, a hydrocarbon super honeycomb network, so-called porous graphene. The mechanical properties of porous graphene such as its Young’s modulus, Poisson’s ratio and the bulk modulus as the determinative properties are calculated in this paper using ab initio calculations. To accomplish this aim, the density functional theory on the basis of generalized gradient approximation and the Perdew–Burke–Ernzerhof exchange correlation is employed. Density functional theory calculations are used to calculate strain energy of porous graphene with respect to applied strain. Selected numerical results are then presented to study the properties of porous graphene. Comparisons are made between the properties of porous graphene and those of other analogous nanostructures. The results demonstrated lower stiffness of porous graphene than those of graphene and graphyne, and higher stiffness than that of graphdyine and other graphyne families. Unlikely, Poisson’s ratio is observed to be more than that of graphene and also less than that of graphyne. It is further observed that the presence of porosity and also formation of C-H bond in the pore sites is responsible for these discrepancies. Porous graphene is found to behave as the isotropic material.
An ab initio study of magneto-electric coupling of YMnO3
Varignon, J.; Petit, S.; Gellé, A.; Lepetit, M. B.
2013-12-01
This paper proposes the direct calculation of the microscopic contributions to the magneto-electric coupling, using ab initio methods. The electrostrictive and the Dzyaloshinskii-Moriya contributions were evaluated individually. For this purpose a specific method was designed, combining density functional theory calculations and embedded fragment, explicitly correlated, quantum chemical calculations. This method allowed us to calculate the evolution of the magnetic couplings as a function of an applied electric field. We found that in YMnO3 the Dzyaloshinskii-Moriya contribution to the magneto-electric effect is three orders of magnitude weaker than the electrostrictive contribution. Strictive effects are thus dominant in the magnetic exchange evolution under an applied electric field, and by extension in the magneto-electric effect. These effects however, remain quite small, and the modifications of the magnetic excitations under an applied electric field will be difficult to observe experimentally. Another important conclusion is that it can be shown that the linear magneto-electric tensor is null due to the inter-layer symmetry operations.
An ab initio study of magneto-electric coupling of YMnO3.
Varignon, J; Petit, S; Gellé, A; Lepetit, M B
2013-12-11
This paper proposes the direct calculation of the microscopic contributions to the magneto-electric coupling, using ab initio methods. The electrostrictive and the Dzyaloshinskii-Moriya contributions were evaluated individually. For this purpose a specific method was designed, combining density functional theory calculations and embedded fragment, explicitly correlated, quantum chemical calculations. This method allowed us to calculate the evolution of the magnetic couplings as a function of an applied electric field. We found that in YMnO3 the Dzyaloshinskii-Moriya contribution to the magneto-electric effect is three orders of magnitude weaker than the electrostrictive contribution. Strictive effects are thus dominant in the magnetic exchange evolution under an applied electric field, and by extension in the magneto-electric effect. These effects however, remain quite small, and the modifications of the magnetic excitations under an applied electric field will be difficult to observe experimentally. Another important conclusion is that it can be shown that the linear magneto-electric tensor is null due to the inter-layer symmetry operations.
Tarannum, Nazia; Singh, Meenakshi; Yadav, Anil K.
2017-10-01
Here, we have explored the antibacterial activity, thermal stability and theoretical study of two copolymers that contain sulfobetaine and carboetaine moiety. Copolymers were synthesized based on Schiff base chemistry with generation of zwitterionic centres by nucleophilic addition of sultone/lactone. To predict and confirm the molecular structure of zwitterionic polyelectrolyte molecule, the theoretical study of structural features and other thermodynamic characteristics of copolymer constituents was obtained by ab initio calculations. Various parameters such as geometry optimization, energy calculations, frequency calculations and intrinsic reaction coefficient (IRC) are simulated using Hartree Fock (HF) method. The geometry optimizations are analyzed at HF/3-21 G default level of theory. The vibrational frequency is calculated via density functional theory (DFT)/B3LYP 6-31G*(d) level whose values are in accord with the experimental observed frequency. Both copolymers have been successfully assessed for antibacterial activity against Staphylococcus aureus and Pseudomonas aeuroginosa bacterial strains by disc diffusion method. The antibacterial study helped in evaluating zone of inhibition, minimum inhibitory concentration and minimum bactericidal concentration. Sulfobetaine copolymer is found to be more effective in curtailing the infection caused by bacteria as compared to carbobetaine.
Ab initio study of structural, electronic, and thermal properties of Ir_{1-x}Rh_{x} alloys
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Sh. Ahmed
2015-06-01
Full Text Available The structural, electronic, mechanical and thermal properties of Ir_{1-x}Rh_{x} alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.
Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids
DEFF Research Database (Denmark)
Berg, R.W.; Deetlefs, M.; Seddon, K.R.
2005-01-01
Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2...
A fragment-based approach towards ab-initio treatment of polymeric ...
Indian Academy of Sciences (India)
Reshma S Pingale
2017-06-20
Jun 20, 2017 ... textiles, packaging, medical etc. have led to their extensive studies in both academic and industrial fields. Predicting the structure of these polymers is important for the study of their properties. The present work uses a 'divide and conquer'-type approach for the ab-initio studies of these polymeric systems.
Ab initio Molecular Orbital Studies of the Vibrational Spectra of some ...
African Journals Online (AJOL)
NJD
2004-06-15
Jun 15, 2004 ... The binary complexes formed between sulphur dioxide, as electron donor, and the series carbon dioxide, carbonyl sulphide and carbon disulphide, as electron acceptors, have been studied by means of ab initio molecular orbital theory. The optimized structures, the interaction energies and the vibrational ...
Sprik, M.; Meijer, E.M.
1998-01-01
Ab initio molecular dynamics methods have been used to study the reaction mechanism of acidcatalyzed addition of water to formaldehyde in a model system of an aqueous solution of sulfuric acid. Using the method of constraints we find that an H
Ab initio quantum dynamical study of the multi-state nonadiabatic photodissociation of pyrrole
Faraji, S.; Vazdar, M.; Reddy, V. Sivaranjana; Eckert-Maksic, M.; Lischka, H.; Koeppel, H.
2011-01-01
There has been a substantial amount of theoretical investigations on the photodynamics of pyrrole, often relying on surface hopping techniques or, if fully quantal, confining the study to the lowest two or three singlet states. In this study we extend ab initio based quantum dynamical investigations
Ab initio prediction of vacancy properties in concentrated alloys : The case of fcc Cu-Ni
Zhang, X.; Sluiter, M.H.F.
2015-01-01
Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total
Pressure induced structural phase transition in SnS—An ab initio study
Indian Academy of Sciences (India)
Unknown
25. Pressure induced structural phase transition in SnS—An ab initio study. M RAJAGOPALAN*, G KALPANA and V PRIYAMVADHA. Department of Physics, Anna University, Chennai 600 025, India. MS received 21 June 2005; revised 16 November 2005. Abstract. The structural behaviour of SnS under pressure has been ...
Advances in the ab initio description of nuclear three-cluster systems
Directory of Open Access Journals (Sweden)
Romero-Redondo Carolina
2016-01-01
Full Text Available We introduce the extension of the ab initio no-core shell model with continuum to describe three-body cluster systems. We present results for the ground state of 6He and show improvements with respect to the description obtained within the no-core shell model and the no-core shell model/resonating group methods.
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.
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.
Ab Initio Molecular Orbital Studies on the Active Site of Papain
Broer, Ria; Duijnen, P.Th. van; Nieuwpoort, W.C.
1976-01-01
Ab initio molecular orbital calcuiations using a contracted basis of gaussian orbitals on the system methanethiol/imidazole are reported. For the hydrogen bond S---H---N in this system, which was chosen as a model for the active site of papain, a double-well potential was found at a S-N separation
Ab initio study of spin-dependent transport in carbon nanotubes with iron and vanadium adatoms
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka
2008-01-01
We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance. The ...
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 Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials
DEFF Research Database (Denmark)
Lee, Yueh-Lin; Morgan, Dane; Kleis, Jesper
2009-01-01
Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas...
Ab initio study of solute transition-metal interactions with point defects in bcc Fe
Olsson, P.; Klaver, T.P.C.; Domain, C.
2010-01-01
The properties of 3d, 4d, and 5d transition-metal elements in ?-Fe have been studied using ab initio density-functional theory. The intrinsic properties of the solutes have been characterized as well as their interaction with point defects. Vacancies and interstitials of (110) and (111) orientations
Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states
DEFF Research Database (Denmark)
Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen
2003-01-01
Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...
Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo
2011-05-01
Ab initio molecular dynamics simulations with the Car-Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.