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Sample records for ab-initio density functional

  1. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  2. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

    PubMed Central

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2010-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations. PMID:19618944

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

    PubMed

    Marsalek, Ondrej; Markland, Thomas E

    2016-02-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our 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. PMID:26851913

  4. NMR shielding as a probe of intermolecular interactions: ab initio and density functional theory studies.

    PubMed

    Platts, James A; Gkionis, Konstantinos

    2009-11-28

    Ab initio and density functional theory (DFT) calculations of nuclear magnetic resonance shielding tensors in benzene-methane and two isomers of the benzene dimer are reported, with the aim of probing the changes in shielding induced by the formation of supramolecular complexes from isolated molecules. It is shown that the changes in shielding (and hence of chemical shift) for hydrogen nuclei are broadly in line with expectations from "shielding cones" based on aromatic ring current, but that changes for carbon nuclei are rather more subtle. More detailed analysis indicates that the change in isotropic shielding results from much larger changes in individual components of the shielding tensor and in diamagnetic/paramagnetic shielding contributions. Benchmark data were obtained using Møller-Plesset 2nd order perturbation theory with a medium-sized basis set, but it is shown that Hartree-Fock and most density functional theory methods reproduce all essential changes in shielding, and do so in a reasonably basis set independent fashion. The chosen method is then applied to a DNA-intercalator complex. PMID:19890517

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

    PubMed

    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. PMID:21386539

  6. Disulfuric acid dissociated by two water molecules: ab initio and density functional theory calculations.

    PubMed

    Kim, Seong Kyu; Lee, Han Myoung; Kim, Kwang S

    2015-11-21

    We have studied geometries, energies and vibrational spectra of disulfuric acid (H2S2O7) and its anion (HS2O7(-)) hydrated by a few water molecules, using density functional theory (M062X) and ab initio theory (SCS-MP2 and CCSD(T)). The most noteworthy result is found in H2S2O7(H2O)2 in which the lowest energy conformer shows deprotonated H2S2O7. Thus, H2S2O7 requires only two water molecules, the fewest number of water molecules for deprotonation among various hydrated monomeric acids reported so far. Even the second deprotonation of the first deprotonated species HS2O7(-) needs only four water molecules. The deprotonation is supported by vibration spectra, in which acid O-H stretching peaks disappear and specific three O-H stretching peaks for H3O(+) (eigen structure) appear. We have also kept track of variations in several geometrical parameters, atomic charges, and hybrid orbital characters upon addition of water. As the number of water molecules added increases, the S-O bond weakens in the case of H2S2O7, but strengthens in the case of HS2O7(-). It implies that the decomposition leading to H2SO4 and SO3 hardly occurs prior to the 2nd deprotonation at low temperatures. PMID:26400266

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

    SciTech Connect

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

    2014-12-14

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

  8. The vibrational problem solution in natural coordinates with the application of ab initio methods and the functional density theory (DFT-methods)

    NASA Astrophysics Data System (ADS)

    Novoselova, Anna V.; Chernavina, Mariya L.; Berezin, Kirill V.; Berezin, Valentin I.

    2015-03-01

    This article describes the algorithm and the creation of programs for the input process automate the scaling factors of quantum mechanical force fields calculated in the natural coordinates using ab initio methods and the density functional theory (DFT-methods).

  9. Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation

    NASA Astrophysics Data System (ADS)

    Arias, Tomas

    2015-03-01

    First-principles guided design of improved electrochemical systems has the potential for great societal impact by making non-fossil-fuel systems economically viable. Potential applications include improvements in fuel-cells, solar-fuel systems (``artificial photosynthesis''), supercapacitors and batteries. Economical fuel-cell systems would enable zero-carbon footprint transportation, solar-fuel systems would directly convert sunlight and water into hydrogen fuel for such fuel-cell vehicles, supercapacitors would enable nearly full recovery of energy lost during vehicle braking thus extending electric vehicle range and acceptance, and economical high-capacity batteries would be central to mitigating the indeterminacy of renewable resources such as wind and solar. Central to the operation of all of the above electrochemical systems is the electrode-electrolyte interface, whose underlying physics is quite rich, yet remains remarkably poorly understood. The essential underlying technical challenge to the first principles studies which could explore this physics is the need to properly represent simultaneously both the interaction between electron-transfer events at the electrode, which demand a quantum mechanical description, and multiscale phenomena in the liquid environment such as the electrochemical double layer (ECDL) and its associated shielding, which demand a statistical description. A direct ab initio approach to this challenge would, in principle, require statistical sampling and thousands of repetitions of already computationally demanding quantum mechanical calculations. This talk will begin with a brief review of a recent advance, joint density-functional theory (JDFT), which allows for a fully rigorous and, in principle, exact representation of the thermodynamic equilibrium between a system described at the quantum-mechanical level and a liquid environment, but without the need for costly sampling. We then shall demonstrate how this approach applies in

  10. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921

  11. Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline.

    PubMed

    Arjunan, V; Saravanan, I; Ravindran, P; Mohan, S

    2009-10-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000-400 and 4000-100 cm(-1), respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT-B3LYP gradient calculations employing the standard 6-31 G** and high level 6-311 ++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH-pi interactions and the influence of amino and methyl groups on the skeletal modes are investigated. PMID:19581121

  12. Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Saravanan, I.; Ravindran, P.; Mohan, S.

    2009-10-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000-400 and 4000-100 cm -1, respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT-B3LYP gradient calculations employing the standard 6-31G** and high level 6-311++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH -π interactions and the influence of amino and methyl groups on the skeletal modes are investigated.

  13. Ab-initio Density Functional Theory (DFT) Studies of Electronic, Transport, and Bulk Properties of Sodium Oxide (Na2O)

    NASA Astrophysics Data System (ADS)

    Polin, Daniel; Ziegler, Joshua; Malozovsky, Yuriy; Bagayoko, Diola

    We present the findings of ab-initio calculations of electronic, transport, and structural properties of cubic sodium oxide (Na2O). These results were obtained using density functional theory (DFT), specifically a local density approximation (LDA) potential, and the linear combination of Gaussian orbitals (LCGO). Our implementation of LCGO followed the Bagayoko, Zhao, and Williams method as enhanced by the work of Ekuma and Franklin (BZW-EF). We describe the electronic band structure of Na2O with a direct band gap of 2.22 eV. Our results include predicted values for the electronic band structure and associated energy eigenvalues, the total and partial density of states (DOS and pDOS), the equilibrium lattice constant of Na2O, and the bulk modulus. We have also calculated the electron and holes effective masses in the Γ to L, Γ to X, and Γ to K directions. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.

  14. Spectrochemical, ab initio and density functional studies on the conversion of 2-hydroxybenzonitrile ( o-cyanophenol) into the oxyanion

    NASA Astrophysics Data System (ADS)

    Binev, Yuri I.; Georgieva, Miglena K.; Daskalova, Lalka I.

    2004-09-01

    The spectral and structural changes caused by the conversion of 2-hydroxybenzonitrile ( o-cyanophenol) into the corresponding oxyanion have been followed by IR spectra, ab initio and density functional force field calculations. In agreement between theory and experiment, the conversion is accompanied by a 29 cm -1 frequency decrease of the cyano stretching band, 2.7-fold increase in its integrated intensity, 5.8-fold (total value) intensification of the aromatic skeletal bands of Wilson's 8 and 19 types, and other essential spectral changes. According to the calculations, the strongest structural changes are the shortening of the PhO bond with 0.10 Å, lengthenings of the adjacent CC bonds in the phenylene ring with 0.06 Å and bond angle variations near the oxyanionic center. All these changes are connected with the formation of a quasi- ortho-quinonoidal structure of the o-phenylene ring in the oxyanion. According to the electronic density analysis, 0.41 e - (Mulliken) or 0.56 e - (natural bond orbital, NBO) of the anionic charge remain localized at the oxyanionic center. Conformations and hydrogen bonds have also been discussed on the basis of experimental and theoretical data.

  15. Thermal decomposition of 1,3,3-trinitroazetidine (TNAZ): A density functional theory and ab initio study

    SciTech Connect

    Veals, Jeffrey D.; Thompson, Donald L.

    2014-04-21

    Density functional theory and ab initio methods are employed to investigate decomposition pathways of 1,3,3-trinitroazetidine initiated by unimolecular loss of NO{sub 2} or HONO. Geometry optimizations are performed using M06/cc-pVTZ and coupled-cluster (CC) theory with single, double, and perturbative triple excitations, CCSD(T), is used to calculate accurate single-point energies for those geometries. The CCSD(T)/cc-pVTZ energies for NO{sub 2} elimination by N–N and C–N bond fission are, including zero-point energy (ZPE) corrections, 43.21 kcal/mol and 50.46 kcal/mol, respectively. The decomposition initiated by trans-HONO elimination can occur by a concerted H-atom and nitramine NO{sub 2} group elimination or by a concerted H-atom and nitroalkyl NO{sub 2} group elimination via barriers (at the CCSD(T)/cc-pVTZ level with ZPE corrections) of 47.00 kcal/mol and 48.27 kcal/mol, respectively. Thus, at the CCSD(T)/cc-pVTZ level, the ordering of these four decomposition steps from energetically most favored to least favored is: NO{sub 2} elimination by N–N bond fission, HONO elimination involving the nitramine NO{sub 2} group, HONO elimination involving a nitroalkyl NO{sub 2} group, and finally NO{sub 2} elimination by C–N bond fission.

  16. Ab initio phonon dispersion in crystalline naphthalene using van der Waals density functionals

    NASA Astrophysics Data System (ADS)

    Brown-Altvater, Florian; Rangel, Tonatiuh; Neaton, Jeffrey B.

    2016-05-01

    Acene molecular crystals are of current interest in organic optoelectronics, both as active materials and for exploring and understanding new phenomena. Phonon scattering can be an important facilitator and dissipation mechanism in charge separation and carrier transport processes. Here, we carry out density functional theory (DFT) calculations of the structure and the full phonon dispersion of crystalline naphthalene, a well-characterized acene crystal for which detailed neutron-diffraction measurements, as well as infrared and Raman spectroscopy, are available. We evaluate the performance, relative to experiments, of DFT within the local density approximation (LDA); the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE); and a recent van der Waals-corrected nonlocal correlation (vdW-DF-cx) functional. We find that the vdW-DF-cx functional accurately predicts lattice parameters of naphthalene within 1%. Intermolecular and intramolecular phonon frequencies across the Brillouin zone are reproduced within 7.8% and 1%, respectively. As expected, LDA (PBE) underestimates (overestimates) the lattice parameters and overestimates (underestimates) phonon frequencies, demonstrating their shortcomings for predictive calculations of weakly bound materials. If the unit cell is fixed to the experimental lattice parameters, PBE is shown to lead to improved phonon frequencies. Our study provides a detailed understanding of the phonon spectrum of naphthalene, and highlights the importance of including van der Waals dispersion interactions in predictive calculations of lattice parameters and phonon frequencies of molecular crystals and related organic materials.

  17. Ab initio quasi-particle approximation bandgaps of silicon nanowires calculated at density functional theory/local density approximation computational effort

    SciTech Connect

    Ribeiro, M.

    2015-06-21

    Ab initio calculations of hydrogen-passivated Si nanowires were performed using density functional theory within LDA-1/2, to account for the excited states properties. A range of diameters was calculated to draw conclusions about the ability of the method to correctly describe the main trends of bandgap, quantum confinement, and self-energy corrections versus the diameter of the nanowire. Bandgaps are predicted with excellent accuracy if compared with other theoretical results like GW, and with the experiment as well, but with a low computational cost.

  18. Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei; Swanson, Jessica M. J.

    2011-05-01

    The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH/120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ = 340 a.u. and μ = 1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH/120 XC functional with μ = 340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented.

  19. Thermodynamic Properties of Elements and Compounds in Al-Sc Binary System from Ab Initio Calculations Based on Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Zhou, Zeyou; Wu, Bo; Dou, Shushi; Zhao, Chunfeng; Xiong, Yuanpeng; Wu, Yufeng; Yang, Shangjin; Wei, Zhenyi

    2014-04-01

    The thermodynamic properties of FCC Al, HCP Sc, B2 AlSc, C15 Al2Sc, B82 AlSc2, and L12 Al3Sc were studied using ab initio calculations based on density functional theory. The 0 K (-273 °C) total energies were calculated using the ab initio plane-wave pseudopotential method within the generalized gradient approximation. The ab initio calculations of the phonon dispersion curves and the density of state of FCC Al, HCP Sc, B2 AlSc, C15 Al2Sc, B82 AlSc2, and L12 Al3Sc have been performed using the density functional theory and the direct method. Deduced from Helmholtz free energy, the thermal expansion, enthalpy, heat capacity, and entropy as a function of temperature were calculated and compared considerably with the experimental data and other computational results. Our calculations show that the enthalpies of formation are temperature-dependent, and the slope is about -3.4 J/mol/K for B2 AlSc, -2.3 J/mol/K for C15 Al2Sc, -0.8 J/mol/K for B82 AlSc2, and -2.7 J/mol/K for L12 Al3Sc, respectively.

  20. Hydrogen spillover mechanism on covalent organic frameworks as investigated by ab initio density functional calculation.

    PubMed

    Guo, Jing-hua; Zhang, Hong; Tang, Yongjian; Cheng, Xinlu

    2013-02-28

    The hydrogen spillover mechanism, including the H chemisorption, diffusion, and H(2) associative desorption on the surface of COFs and H atoms migration from metal catalyst to COFs, have been studied via density functional theory (DFT) calculation. The results described herein show that each sp(2) C atom on COFs' surface can adsorb one H atom with the bond length d(C-H) between 1.11 and 1.14 Å, and the up-down arrangement of the adsorbed H atoms is the most stable configuration. By counting the chemisorption binding sites for these COFs, we can predict the saturation storage densities. High hydrogen storage densities show that the gravimetric uptakes of COFs are in the range of 5.13-6.06 wt%. The CI-NEB calculations reveal that one H atom diffusing along the C-C path on HHTP surface should overcome the 1.41-2.16 eV energy barrier. We chose tetrahedral Pt(4) cluster and HHTP as the representative catalyst and substrate, respectively, to study the H migration from metal cluster to COFs. At most, two H atoms can migrate from Pt(4) cluster to HHTP substrate. The migration reaction is an endothermic process, undergoing an activation barrier of 1.87 eV and 0.57 eV for the first and second H migration process, respectively. Three types of H(2) associative desorption from hydrogenated COFs were studied: (I) the two H adatoms recombining to one H(2) molecule with a recombination barrier of 4.28 eV, (II) the abstraction of adsorbed H atoms by gas-phase hydrogen atoms through ER type recombination reactions with a recombination barrier of 1.05 eV, (III) the H(2) desorption through the reverse spillover mechanism with an energy barrier of 2.90 eV. PMID:23338125

  1. The computation of ionization potentials for second-row elements by ab initio and density functional theory methods

    SciTech Connect

    Jursic, B.S.

    1996-12-31

    Up to four ionization potentials of elements from the second-row of the periodic table were computed using the ab initio (HF, MP2, MP3, MP4, QCISD, GI, G2, and G2MP2) and DFT (B3LY, B3P86, B3PW91, XALPHA, HFS, HFB, BLYP, BP86, BPW91, BVWN, XAPLY, XAP86, XAPW91, XAVWN, SLYR SP86, SPW91 and SVWN) methods. In all of the calculations, the large 6-311++G(3df,3pd) gaussian type of basis set was used. The computed values were compared with the experimental results and suitability of the ab initio and DFF methods were discussed, in regard to reproducing the experimental data. From the computed ionization potentials of the second-row elements, it can be concluded that the HF ab initio computation is not capable of reproducing the experimental results. The computed ionization potentials are too low. However, by using the ab initio methods that include electron correlation, the computed IPs are becoming much closer to the experimental values. In all cases, with the exception of the first ionization potential for oxygen, the G2 computation result produces ionization potentials that are indistinguishable from the experimental results.

  2. Benchmark ab Initio Conformational Energies for the Proteinogenic Amino Acids through Explicitly Correlated Methods. Assessment of Density Functional Methods.

    PubMed

    Kesharwani, Manoj K; Karton, Amir; Martin, Jan M L

    2016-01-12

    The relative energies of the YMPJ conformer database of the 20 proteinogenic amino acids, with N- and C-termination, have been re-evaluated using explicitly correlated coupled cluster methods. Lower-cost ab initio methods such as MP2-F12 and CCSD-F12b actually are outperformed by double-hybrid DFT functionals; in particular, the DSD-PBEP86-NL double hybrid performs well enough to serve as a secondary standard. Among range-separated hybrids, ωB97X-V performs well, while B3LYP-D3BJ does surprisingly well among traditional DFT functionals. Treatment of dispersion is important for the DFT functionals; for the YMPJ set, D3BJ generally works as well as the NL nonlocal dispersion functional. Basis set sensitivity for DFT calculations on these conformers is weak enough that def2-TZVP is generally adequate. For conformer corrections to heats of formation, B3LYP-D3BJ and especially DSD-PBEP86-D3BJ or DSD-PBEP86-NL are adequate for all but the most exacting applications. The revised geometries and energetics for the YMPJ database have been made available as Supporting Information and should be useful in the parametrization and validation of molecular mechanics force fields and other low-cost methods. The very recent dRPA75 method yields good performance, without resorting to an empirical dispersion correction, but is still outperformed by DSD-PBEP86-D3BJ and particularly DSD-PBEP86-NL. Core-valence corrections are comparable in importance to improvements beyond CCSD(T*)/cc-pVDZ-F12 in the valence treatment. PMID:26653705

  3. Ensemble v-representable ab initio density-functional calculation of energy and spin in atoms: A test of exchange-correlation approximations

    SciTech Connect

    Kraisler, Eli; Makov, Guy; Kelson, Itzhak

    2010-10-15

    The total energies and the spin states for atoms and their first ions with Z=1-86 are calculated within the the local spin-density approximation (LSDA) and the generalized-gradient approximation (GGA) to the exchange-correlation (xc) energy in density-functional theory. Atoms and ions for which the ground-state density is not pure-state v-representable are treated as ensemble v-representable with fractional occupations of the Kohn-Sham system. A recently developed algorithm which searches over ensemble v-representable densities [E. Kraisler et al., Phys. Rev. A 80, 032115 (2009)] is employed in calculations. It is found that for many atoms, the ionization energies obtained with the GGA are only modestly improved with respect to experimental data, as compared to the LSDA. However, even in those groups of atoms where the improvement is systematic, there remains a non-negligible difference with respect to the experiment. The ab initio electronic configuration in the Kohn-Sham reference system does not always equal the configuration obtained from the spectroscopic term within the independent-electron approximation. It was shown that use of the latter configuration can prevent the energy-minimization process from converging to the global minimum, e.g., in lanthanides. The spin values calculated ab initio fit the experiment for most atoms and are almost unaffected by the choice of the xc functional. Among the systems with incorrectly obtained spin, there exist some cases (e.g., V, Pt) for which the result is found to be stable with respect to small variations in the xc approximation. These findings suggest a necessity for a significant modification of the exchange-correlation functional, probably of a nonlocal nature, to accurately describe such systems.

  4. Ab initio-driven nuclear energy density functional method. A proposal for safe/correlated/improvable parametrizations of the off-diagonal EDF kernels

    NASA Astrophysics Data System (ADS)

    Duguet, T.; Bender, M.; Ebran, J.-P.; Lesinski, T.; Somà, V.

    2015-12-01

    This programmatic paper lays down the possibility to reconcile the necessity to resum many-body correlations into the energy kernel with the fact that safe multi-reference energy density functional (EDF) calculations cannot be achieved whenever the Pauli principle is not enforced, as is for example the case when many-body correlations are parametrized under the form of empirical density dependencies. Our proposal is to exploit a newly developed ab initio many-body formalism to guide the construction of safe, explicitly correlated and systematically improvable parametrizations of the off-diagonal energy and norm kernels that lie at the heart of the nuclear EDF method. The many-body formalism of interest relies on the concepts of symmetry breaking and restoration that have made the fortune of the nuclear EDF method and is, as such, amenable to this guidance. After elaborating on our proposal, we briefly outline the project we plan to execute in the years to come.

  5. The S66x8 benchmark for noncovalent interactions revisited: explicitly correlated ab initio methods and density functional theory.

    PubMed

    Brauer, Brina; Kesharwani, Manoj K; Kozuch, Sebastian; Martin, Jan M L

    2016-08-01

    The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol(-1) RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol(-1). The nonlocal VV10 dispersion functional is especially beneficial for the double hybrids, particularly in DSD-PBEP86-NL (RMSD = 0.12 kcal mol(-1)). Other recommended dispersion-corrected functionals with favorable price/performance ratios are ωB97X-V, and, surprisingly, B3LYP-D3BJ and BLYP-D3BJ (RMSDs of 0.23, 0.20 and 0.23 kcal mol(-1), respectively). Without dispersion correction (but parametrized for midrange interactions) M06-2X has the lead (RMSD = 0.45 kcal mol(-1)). A collection of three energy-based diagnostics yields similar information to an SAPT analysis about the nature of the noncovalent interaction. Two of those are the percentages of Hartree-Fock and of post-MP2 correlation effects in the interaction energy; the third, CSPI = [IE - IE]/[IE + IE] or its derived quantity DEBC = CSPI/(1 + CSPI(2))(1/2), describes the character of the MP2 correlation contribution, ranging from 0 (purely dispersion) to 1 (purely other effects). In addition, we propose an improved, parameter-free scaling for the (T) contribution based on the Ecorr[CCSD-F12b]/Ecorr[CCSD] and Ecorr[CCSD(F12*)]/Ecorr[CCSD] ratios. For Hartree-Fock and conventional DFT calculations, full counterpoise generally yields the fastest basis set convergence, while for double hybrids, half-counterpoise yields faster convergence, as previously established for correlated ab initio methods. PMID:26950084

  6. Ab initio and density functional computations of the vibrational spectrum, molecular geometry and some molecular properties of the antidepressant drug sertraline (Zoloft) hydrochloride

    NASA Astrophysics Data System (ADS)

    Sagdinc, Seda; Kandemirli, Fatma; Bayari, Sevgi Haman

    2007-02-01

    Sertraline hydrochloride is a highly potent and selective inhibitor of serotonin (5HT). It is a basic compound of pharmaceutical application for antidepressant treatment (brand name: Zoloft). Ab initio and density functional computations of the vibrational (IR) spectrum, the molecular geometry, the atomic charges and polarizabilities were carried out. The infrared spectrum of sertraline is recorded in the solid state. The observed IR wave numbers were analysed in light of the computed vibrational spectrum. On the basis of the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes are examined. The X-ray geometry and experimental frequencies are compared with the results of our theoretical calculations.

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  8. Recent progress in ab initio density matrix renormalization group methodology

    NASA Astrophysics Data System (ADS)

    Hachmann, Johannes; Dorando, Jonathan J.; Kin-Lic Chan, Garnet

    2008-03-01

    We present some recent developments in the ab initio density matrix renormalization group (DMRG) method for quantum chemical problems, in particular our local, quadratic scaling algorithm [1] for low dimensional systems. This method is particularly suited for the description of strong nondynamic correlation, and allows us to compute numerically exact (FCI) correlated energies for large active spaces, up to one order of magnitude larger then can be done by conventional CASCI techniques. Other features of this method are its inherent multireference nature, compactness, variational results, size-consistency and size-extensivity. In addition we will review the problems (predominantly organic electronic materials) on which we applied the ab initio DMRG: 1) metal-insulator transition in hydrogen chains [1] 2) all-trans polyacetylene [1] 3) acenes [2] 4) polydiacetylenes [3]. References [1] Hachmann, Cardoen, Chan, JCP 125 (2006), 144101. [2] Hachmann, Dorando, Avil'es, Chan, JCP 127 (2007), 134309. [3] unpublished.

  9. Towards SiC Surface Functionalization: An Ab Initio Study

    SciTech Connect

    Cicero, G; Catellani, A

    2005-01-28

    We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  11. Accuracy of Calculated Chemical Shifts in Carbon 1s Ionization Energies from Single-Reference ab Initio Methods and Density Functional Theory.

    PubMed

    Holme, Alf; Børve, Knut J; Sæthre, Leif J; Thomas, T Darrah

    2011-12-13

    A database of 77 adiabatic carbon 1s ionization energies has been prepared, covering linear and cyclic alkanes and alkenes, linear alkynes, and methyl- or fluoro-substituted benzenes. Individual entries are believed to carry uncertainties of less than 30 meV in ionization energies and less than 20 meV for shifts in ionization energies. The database provides an unprecedented opportunity for assessing the accuracy of theoretical schemes for computing inner-shell ionization energies and their corresponding chemical shifts. Chemical shifts in carbon 1s ionization energies have been computed for all molecules in the database using Hartree-Fock, Møller-Plesset (MP) many-body perturbation theory of order 2 and 3 as well as various approximations to full MP4, and the coupled-cluster approximation with single- and double-excitation operators (CCSD) and also including a perturbational estimate of the energy effect of triple-excitation operators (CCSD(T)). Moreover, a wide range of contemporary density functional theory (DFT) methods are also evaluated with respect to computing experimental shifts in C1s ionization energies. Whereas the top ab initio methods reproduce the observed shifts almost to within the experimental uncertainty, even the best-performing DFT approaches meet with twice the root-mean-squared error and thrice the maximum error compared to CCSD(T). However, a number of different density energy functionals still afford sufficient accuracy to become tools in the analysis of complex C1s photoelectron spectra. PMID:26598356

  12. Role of charge in destabilizing AlH4 and BH4 complex anions for hydrogen storage applications: Ab initio density functional calculations

    NASA Astrophysics Data System (ADS)

    Du, A. J.; Smith, Sean C.; Lu, G. Q.

    2006-11-01

    NaAlH4 and LiBH4 are potential candidate materials for mobile hydrogen storage applications, yet they have the drawback of being highly stable and desorbing hydrogen only at elevated temperatures. In this letter, ab initio density functional theory calculations reveal how the stabilities of the AlH4 and BH4 complex anions will be affected by reducing net anionic charge. Tetrahedral AlH4 and BH4 complexes are found to be distorted with the decrease of negative charge. One H-H distance becomes smaller and the charge density will overlap between them at a small anion charge. The activation energies to release of H2 from AlH4 and BH4 complexes are thus greatly decreased. We demonstrate that point defects such as neutral Na vacancies or substitution of a Na atom with Ti on the NaAlH4(001) surface can potentially cause strong distortion of neighboring AlH4 complexes and even induce spontaneous dehydrogenation. Our results help to rationalize the conjecture that the suppression of charge transfer to AlH4 and BH4 anion as a consequence of surface defects should be very effective for improving the recycling performance of H2 in NaAlH4 and LiBH4 . The understanding gained here will aid in the rational design and development of hydrogen storage materials based on these two systems.

  13. The conversion of 3- and 4-hydroxybenzonitriles ( m- and p-cyanophenols) into oxyanions, followed by IR spectra, ab initio and density functional calculations

    NASA Astrophysics Data System (ADS)

    Georgieva, Miglena K.; Angelova, Polina N.; Binev, Ivan G.

    2004-04-01

    The conversion of 3- and 4-hydroxybenzonitriles ( m- and p-cyanophenols) into oxyanions has been followed by IR spectra, ab initio HF, MP2 6-31G(d) and density functional BLYP, B3LYP 6-31G(d) force field calculations. In a general agreement between theory and experiment, the conversion causes a 34 cm -1 frequency decrease in the cyano stretching band, 3.2-fold increase in its integrated intensity and other essential spectral changes in the para-isomer; for the meta-one the corresponding values are 13 cm -1 and 2.3-fold, respectively. According to the calculations, both molecule and anion of 4-hydroxybenzonitrile are more stable (due to the polar resonance) than the corresponding meta-substituted species. The strongest structural changes, caused by deprotonation, are the 0.105 Å shortenings of the Ph-O bonds, 0.054 Å lengthenings (mean values) of the adjacent CC bonds and essential bond angle changes in the phenylene rings near the oxyanionic centers. In the case of para-isomer these changes are related to the formation of a quasi- para-quinonoidal structure of the phenylene ring in the oxyanion. According to the electronic density analysis, a bit less (Mulliken) or a bit more (natural bond orbital) than halves of the anionic charges remain localized at the oxyanionic centers. Hydrogen bonds have also been discussed.

  14. Phase diagram of the CulnSe{sub 2}-CuGaSe{sub 2} pseudobinary system studied by combined ab initio density functional theory and thermodynamic calculation

    SciTech Connect

    Xue, H. T.; Tang, F. L.; Lu, W. J.; Li, X. K.; Zhang, Y.; Feng, Y. D.

    2014-08-07

    The phase diagram of the CuInSe{sub 2}-CuGaSe{sub 2} pseudobinary system was determined using a combination of special quasirandom structure approach, ab initio density functional theory calculations, and thermodynamic modelling. It is shown that the CuIn{sub 1−x}Ga{sub x}Se{sub 2} solution phase has a tendency to phase separation at low temperature. The calculated consolute temperature is 485 K. It is found that both the binodal and spinodal curves are significantly asymmetric and on both curves there are a local maximum and a local minimum, which have not been reported in the previous studies. Our phase diagram can well explain the finding that the inhomogeneity of CuIn{sub 0.25}Ga{sub 0.75}Se{sub 2} is higher than that of CuIn{sub 0.75}Ga{sub 0.25}Se{sub 2} at the same temperature, while the previous phase diagrams cannot. Hence, our phase diagram should be more reliable and applicable.

  15. Spin-orbit decomposition of ab initio nuclear wave functions

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  16. The ab-initio density matrix renormalization group in practice

    SciTech Connect

    Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

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

    NASA Astrophysics Data System (ADS)

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

    2008-01-01

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

  18. A Comparison of Density Functional Theory with Ab initio Approaches for Systems Involving First Transition Row Metals

    NASA Technical Reports Server (NTRS)

    Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.

  19. Adsorption of TCDD molecule onto CNTs and BNNTs: Ab initio van der Waals density-functional study

    NASA Astrophysics Data System (ADS)

    Darvish Ganji, M.; Alinezhad, H.; Soleymani, E.; Tajbakhsh, M.

    2015-03-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCCD) is one of the most dangerous compounds that infect the environment and hence its removal is crucial for safety in human life. In this work, we have investigated the interaction of TCDD with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs) by using the density functional theory (DFT) calculations. Our first-principles results have been validated by experiment and also other theoretical values for the similar system. The adsorption energies for TCDD molecule on the BNNTs and CNT are calculated. It was found that TCDD adsorption ability of BNNT is slightly stronger than that of CNT and TCDD molecule prefers to be adsorbed on BNNTs with molecular axis parallel to the tube axis. The results obtained indicate that TCDD is weakly bound to the outer surface of all the considered nanotubes and the obtained adsorption energy values and binding distance are typical for the physisorption. We also evaluated the influence of curvature and introduced defects on the TCDD adsorption ability of BNNTs. Furthermore, we have analyzed the electronic structure and charge population for the energetically most favorable complexes and the results indicate that no significant hybridization between the respective orbitals of the two entities was accomplished.

  20. Ab initio density-functional theory study of NHx dehydrogenation and reverse reactions on the Rh(111) surface

    NASA Astrophysics Data System (ADS)

    Popa, C.; Offermans, W. K.; van Santen, R. A.; Jansen, A. P. J.

    2006-10-01

    The adsorption and dissociation of NHx fragments on the Rh(111) crystal surface have been studied using first-principles density-functional calculations. The stability and configurations of NHx species have been investigated and characterized using frequency analysis. The highest adsorption energies have been calculated for NH and N. Several paths of NHx (x=1-3) dehydrogenation and hydrogenation have been taken into account. The transition states have been determined and in detail analyzed. The activation barriers and thermodynamic and kinetic data have been calculated for all the elementary steps. The calculations have shown that the elementary reactions have significant barriers, between 0.7 and 1.1eV . The transition states are regarded neither early nor late with respect to the distance in hyperspace between initial and final states. The NH3 dehydrogenation has been determined as the rate limiting step. For this elementary process there has been estimated a large contribution of the zero point energy to the activation barrier and a significant entropy activation.

  1. IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-aminouracil.

    PubMed

    Singh, J S

    2014-09-15

    Infrared (IR) and Raman spectra of uracil and 5-aminouracil have been recorded and analyzed between the region 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-aminouracil by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, the most of B3LYP/6-311++G** vibrational frequencies are in the excellent agreement with available experimental assignments and helped in the reassignments of some fundamental vibrational modes. On the basis of calculated results, the assignments of some missing frequencies in the experimental study are proposed. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) are given by 25a'+11a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 6 modes (4a'+2a″) to the NH2 group. Kekule ring stretching mode is found to be comparatively higher frequency magnitude than the mode of uracil due to the involvement of hydrogen bonding of amino group. But, the ring breathing is found to be lower frequency magnitude compared to those for uracil which could be due to mass effect of the NH2 group in place of the hydrogen atom. All other bands have also been assigned different fundamentals/overtones/combinations. PMID:24793482

  2. Assessment of experimental bond dissociation energies using composite ab initio methods and evaluation of the performances of density functional methods in the calculation of bond dissociation energies.

    PubMed

    Feng, Yong; Liu, Lei; Wang, Jin-Ti; Huang, Hao; Guo, Qing-Xiang

    2003-01-01

    Composite ab initio CBS-Q and G3 methods were used to calculate the bond dissociation energies (BDEs) of over 200 compounds listed in CRC Handbook of Chemistry and Physics (2002 ed.). It was found that these two methods agree with each other excellently in the calculation of BDEs, and they can predict BDEs within 10 kJ/mol of the experimental values. Using these two methods, it was found that among the examined compounds 161 experimental BDEs are valid because the standard deviation between the experimental and theoretical values for them is only 8.6 kJ/mol. Nevertheless, 40 BDEs listed in the Handbook may be highly inaccurate as the experimental and theoretical values for them differ by over 20 kJ/mol. Furthermore, 11 BDEs listed in the Handbook may be seriously flawed as the experimental and theoretical values for them differ by over 40 kJ/mol. Using the 161 cautiously validated experimental BDEs, we then assessed the performances of the standard density functional (DFT) methods including B3LYP, B3P86, B3PW91, and BH&HLYP in the calculation of BDEs. It was found that the BH&HLYP method performed poorly for the BDE calculations. B3LYP, B3P86, and B3PW91, however, performed reasonably well for the calculation of BDEs with standard deviations of about 12.1-18.0 kJ/mol. Nonetheless, all the DFT methods underestimated the BDEs by 4-17 kJ/mol in average. Sometimes, the underestimation by the DFT methods could be as high as 40-60 kJ/mol. Therefore, the DFT methods were more reliable for relative BDE calculations than for absolute BDE calculations. Finally, it was observed that the basis set effects on the BDEs calculated by the DFT methods were usually small except for the heteroatom-hydrogen BDEs. PMID:14632451

  3. A Density Functional Theory and ab Initio Investigation of the Oxidation Reaction of CO by IO Radicals.

    PubMed

    Khanniche, Sarah; Louis, Florent; Cantrel, Laurent; Černušák, Ivan

    2016-03-17

    To get an insight into the possible reactivity between iodine oxides and CO, a first step was to study the thermochemical properties and kinetic parameters of the reaction between IO and CO using theoretical chemistry tools. All stationary points involved were optimized using the Becke's three-parameter hybrid exchange functional coupled with the Lee-Yang-Parr nonlocal correlation functional (B3LYP) and the Møller-Plesset second-order perturbation theory (MP2). Single-point energy calculations were performed using the coupled cluster theory with the iterative inclusion of singles and doubles and the perturbative estimation for triple excitations (CCSD(T)) and the aug-cc-pVnZ (n = T, Q, and 5) basis sets on geometries previously optimized at the aug-cc-pVTZ level. The energetics was then recalculated using the one-component DK-CCSD(T) approach with the relativistic ANO basis sets. The spin-orbit coupling for the iodine containing species was calculated a posteriori using the restricted active space state interaction method in conjunction with the multiconfigurational perturbation theory (CASPT2/RASSI) employing the complete active space (CASSCF) wave function as the reference. The CCSD(T) energies were also corrected for BSSE for molecular complexes and refined with the extrapolation to CBS limit while the DK-CCSD(T) values were refined with the extrapolation to FCI. The exploration of the potential energy surface revealed a two-steps mechanism with a trans and a cis pathway. The rate constants for the direct and complex mechanism were computed as a function of temperature (250-2500 K) using the canonical transition state theory. The three-parameter Arrhenius expressions obtained for the direct and indirect mechanism at the DK-CCSD(T)-cf level of theory is 1.49 × 10(-17) × T(1.77) exp(-47.4 (kJ mol(-1))/RT). PMID:26908233

  4. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine)

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2015-02-01

    FT-IR (400-4000 cm-1) and Raman spectra (200-4000 cm-1) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a‧) and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a‧ + 13a″, of which 30 modes (21a‧ + 9a″) correspond to the uracil moiety and 9 modes (5a‧ + 4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3

  5. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine).

    PubMed

    Singh, J S

    2015-02-25

    FT-IR (400-4000 cm(-1)) and Raman spectra (200-4000 cm(-1)) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G(∗∗) vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a') and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a'+13a″, of which 30 modes (21a'+9a″) correspond to the uracil moiety and 9 modes (5a'+4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3 group are

  6. Magneto-structural correlations in a family of Fe(II)Re(IV)(CN)2 single-chain magnets: density functional theory and ab initio calculations.

    PubMed

    Zhang, Yi-Quan; Luo, Cheng-Lin; Wu, Xin-Bao; Wang, Bing-Wu; Gao, Song

    2014-04-01

    Until now, the expressions of the anisotropic energy barriers Δξ and ΔA, using the uniaxial magnetic anisotropy D, the intrachain coupling strength J, and the high-spin ground state S for single-chain magnets (SCMs) in the intermediate region between the Ising and the Heisenberg limits, were unknown. To explore this relationship, we used density functional theory and ab initio methods to obtain expressions of Δξ and ΔA in terms of D, J, and S of six R4Fe(II)-Re(IV)Cl4(CN)2 (R = diethylformamide (1), dibutylformamide (2), dimethylformamide (3), dimethylbutyramide (4), dimethylpropionamide (5), and diethylacetamide (6)) SCMs in the intermediate region. The ΔA value for compounds 1-3 was very similar to the magnetic anisotropic energy of a single Fe(II), while the value of Δξ was predicted using the exchange interaction of Fe(II) with the neighboring Re(IV), which could be expressed as 2JSReSFe. Similar to compounds 1-3, the anisotropy energy barrier ΔA of compounds 4 and 5 was also equal to (Di - Ei)SFe(2), but the correlation energy Δξ was closely equal to 2JSReSFe(cos 98.4 - cos 180) due to the reversal of the spins on the opposite Fe(II). For compound 6, one unit cell of Re(IV)Fe(II) was regarded as a domain wall since it had two different Re(IV)-Fe(II) couplings. Thus, the Δξ of compound 6 was expressed as 4J″SRe1Fe1SRe2Fe2, where J″ was the coupling constant of the neighboring unit cells of Re1Fe1 and Re2Fe2, and ΔA was equal to the anisotropic energy barrier of one domain wall given by DRe1Fe1(S(2)Re1Fe1 - 1/4). PMID:24673387

  7. Electronic and transport properties edge functionalized graphene nanoribbons-An ab initio approach

    SciTech Connect

    Chauhan, Satyendra Singh; Srivastava, Pankaj; Shrivastva, A. K.

    2014-04-24

    With the help of ab initio approach we have investigated the electronic and transport properties of edge functionalized zigzag graphene nanoribbons using density functional theory. We have studied the energetic stability and Fermi energy of ZGNRs. We have reported that the edge functionalization of zigzag graphene nanoribbons can break the degeneracy that can be used to promote the onset of a semiconducting to metal transition or a half metal to semiconducting state. The edge functionalization also promotes a metal-semimetal transition. It has also been observed that the transmission spectrum of the edge functionalized ZGNRs are different from those of pristine.

  8. Communication: Unraveling the {sup 4}He droplet-mediated soft-landing from ab initio-assisted and time-resolved density functional simulations: Au@{sup 4}He{sub 300}/TiO{sub 2}(110)

    SciTech Connect

    Lara-Castells, María Pilar de Aguirre, Néstor F.; Stoll, Hermann; Mitrushchenkov, Alexander O.; Mateo, David; Pi, Martí

    2015-04-07

    An ab-initio-based methodological scheme for He-surface interactions and zero-temperature time-dependent density functional theory for superfluid {sup 4}He droplets motion are combined to follow the short-time collision dynamics of the Au@{sup 4}He{sub 300} system with the TiO{sub 2}(110) surface. This composite approach demonstrates the {sup 4}He droplet-assisted sticking of the metal species to the surface at low landing energy (below 0.15 eV/atom), thus providing the first theoretical evidence of the experimentally observed {sup 4}He droplet-mediated soft-landing deposition of metal nanoparticles on solid surfaces [Mozhayskiy et al., J. Chem. Phys. 127, 094701 (2007) and Loginov et al., J. Phys. Chem. A 115, 7199 (2011)].

  9. Evidence for anisotropic dielectric properties of monoclinic hafnia using valence electron energy-loss spectroscopy in high-resolution transmission electron microscopy and ab initio time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Guedj, C.; Hung, L.; Zobelli, A.; Blaise, P.; Sottile, F.; Olevano, V.

    2014-12-01

    The effect of nanocrystal orientation on the energy loss spectra of monoclinic hafnia (m-HfO2) is measured by high resolution transmission electron microscopy (HRTEM) and valence energy loss spectroscopy (VEELS) on high quality samples. For the same momentum-transfer directions, the dielectric properties are also calculated ab initio by time-dependent density-functional theory (TDDFT). Experiments and simulations evidence anisotropy in the dielectric properties of m-HfO2, most notably with the direction-dependent oscillator strength of the main bulk plasmon. The anisotropic nature of m-HfO2 may contribute to the differences among VEELS spectra reported in literature. The good agreement between the complex dielectric permittivity extracted from VEELS with nanometer spatial resolution, TDDFT modeling, and past literature demonstrates that the present HRTEM-VEELS device-oriented methodology is a possible solution to the difficult nanocharacterization challenges given in the International Technology Roadmap for Semiconductors.

  10. Evidence for anisotropic dielectric properties of monoclinic hafnia using valence electron energy-loss spectroscopy in high-resolution transmission electron microscopy and ab initio time-dependent density-functional theory

    SciTech Connect

    Guedj, C.; Hung, L.; Sottile, F.; Zobelli, A.; Blaise, P.; Olevano, V.

    2014-12-01

    The effect of nanocrystal orientation on the energy loss spectra of monoclinic hafnia (m-HfO{sub 2}) is measured by high resolution transmission electron microscopy (HRTEM) and valence energy loss spectroscopy (VEELS) on high quality samples. For the same momentum-transfer directions, the dielectric properties are also calculated ab initio by time-dependent density-functional theory (TDDFT). Experiments and simulations evidence anisotropy in the dielectric properties of m-HfO{sub 2}, most notably with the direction-dependent oscillator strength of the main bulk plasmon. The anisotropic nature of m-HfO{sub 2} may contribute to the differences among VEELS spectra reported in literature. The good agreement between the complex dielectric permittivity extracted from VEELS with nanometer spatial resolution, TDDFT modeling, and past literature demonstrates that the present HRTEM-VEELS device-oriented methodology is a possible solution to the difficult nanocharacterization challenges given in the International Technology Roadmap for Semiconductors.

  11. Vibrational analysis and ionization potentials of XCH 3 (X=Be,Mg,Ca) calculated by hybrid density functional theory and high order ab initio methods

    NASA Astrophysics Data System (ADS)

    Jalbout, Abraham F.

    2001-06-01

    The amount of attention dedicated to the theoretical and experimental investigation of small cationic organometallic systems in the literature is very limited. In this Letter we use the B3LYP method with a variety of basis sets as well as the very advanced CBS-Q, CBS-QB3, G1, G2MP2, G2, G3, and G3B3 ab initio methods in order to analyze the vibrational spectra as well as ionization potentials of BeCH 3,MgCH 3 and CaCH 3. The need for further addition of experimental data to the archives for these systems is discussed, as well as recommendations for which theoretical methods are optimum for a particular result.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms. PMID:27394094

  14. Local Current Density Calculations for Molecular Films from Ab Initio.

    PubMed

    Walz, Michael; Bagrets, Alexei; Evers, Ferdinand

    2015-11-10

    We present a formalism relying on density functional theory for the calculation of the spatially continuous electron current density j(r) and induced magnetic fields B(r) in molecular films in dc transport. The proposed method treats electron transport in graphene ribbons containing on the of order 10(3) atoms. The employed computational techniques scale efficiently when using several thousand CPUs. An application to transport through hydrogenated graphene will be presented. As we will show, the adatoms have an impact on the transmission function not only because they introduce additional states but also because their presence modifies the geometry of the carbon host lattice (lattice relaxation). PMID:26574313

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  16. Vibrational spectrum and assignments of 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole by ab initio Hartree-Fock and density functional methods

    NASA Astrophysics Data System (ADS)

    Arslan, Hakan; Algül, Öztekin

    2008-06-01

    The room temperature attenuated total reflection Fourier transform infrared spectrum of the 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole has been recorded with diamond/ZnSe prism. The conformational behaviour, structural stability of optimized geometry, frequency and intensity of the vibrational bands of the title compound were investigated by utilizing ab initio calculations with 6-311G** basis set at HF, B3LYP, BLYP, B3PW91 and mPW1PW91 levels. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental IR spectrum. The observed and the calculated frequencies are found to be in good agreement. The theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions using VEDA 4 program. Furthermore, the optimal uniform scaling factors calculated for the title compound are 0.9120, 0.9596, 0.9660, 0.9699, and 0.9993 for HF, mPW1PW91, B3PW91, B3LYP and BLYP methods, respectively.

  17. Ab initio and density functional theoretical design and screening of model crown ether based ligand (host) for extraction of lithium metal ion (guest): effect of donor and electronic induction.

    PubMed

    Boda, Anil; Ali, Sk Musharaf; Rao, Hanmanth; Ghosh, Sandip K

    2012-08-01

    The structures, energetic and thermodynamic parameters of model crown ethers with different donor, cavity and electron donating/ withdrawing functional group have been determined with ab initio MP2 and density functional theory in gas and solvent phase. The calculated values of binding energy/ enthalpy for lithium ion complexation are marginally higher for hard donor based aza and oxa crown compared to soft donor based thia and phospha crown. The calculated values of binding enthalpy for lithium metal ion with 12C4 at MP2 level of theory is in good agreement with the available experimental result. The binding energy is altered due to the inductive effect imparted by the electron donating/ withdrawing group in crown ether, which is well correlated with the values of electron transfer. The role of entropy for extraction of hydrated lithium metal ion by different donor and functional group based ligand has been demonstrated. The HOMO-LUMO gap is decreased and dipole moment of the ligand is increased from gas phase to organic phase because of the dielectric constant of the solvent. The gas phase binding energy is reduced in solvent phase as the solvent molecules weaken the metal-ligand binding. The theoretical values of extraction energy for LiCl salt from aqueous solution in different organic solvent is validated by the experimental trend. The study presented here should contribute to the design of model host ligand and screening of solvent for metal ion recognition and thus can contribute in planning the experiments. PMID:22318713

  18. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg3Si4O10(OH)2] as model system

    NASA Astrophysics Data System (ADS)

    Ulian, Gianfranco; Tosoni, Sergio; Valdrè, Giovanni

    2013-11-01

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg3Si4O10(OH)2], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

  19. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: talc [Mg3Si4O10(OH)2] as model system.

    PubMed

    Ulian, Gianfranco; Tosoni, Sergio; Valdrè, Giovanni

    2013-11-28

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg3Si4O10(OH)2], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO∕B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum. PMID:24289338

  20. Antagonistic properties of a natural product - Bicuculline with the gamma-aminobutyric acid receptor: Studied through electrostatic potential mapping, electronic and vibrational spectra using ab initio and density functional theory

    NASA Astrophysics Data System (ADS)

    Srivastava, Anubha; Tandon, Poonam; Jain, Sudha; Asthana, B. P.

    2011-12-01

    (+)-Bicuculline (hereinafter referred to as bicuculline), a phthalide isoquinoline alkaloid is of current interest as an antagonist of gamma-aminobutyric acid (GABA). Its inhibitor properties have been studied through molecular electrostatic potential (MEP) mapping of this molecule and GABA receptor. The hot site on the potential surface of bicuculline, which is also isosteric with GABA receptor, has been used to interpret the inhibitor property. A systematic quantum chemical study of the possible conformations, their relative stabilities, FT-Raman, FT-IR and UV-vis spectroscopic analysis of bicuculline has been reported. The optimized geometries, wavenumber and intensity of the vibrational bands of all the conformers of bicuculline have been calculated using ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP functional and 6-311G(d,p) basis set. Mulliken atomic charges, HOMO-LUMO gap Δ E, ionization potential, dipole moments and total energy have also been obtained for the optimized geometries of both the molecules. TD-DFT method is used to calculate the electronic absorption parameters in gas phase as well as in solvent environment using integral equation formalism-polarizable continuum model (IEF-PCM) employing 6-31G basis set and the results thus obtained are compared with the UV absorption spectra. The combination of experimental and calculated results provides an insight into the structural and vibrational spectroscopic properties of bicuculline.

  1. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

    SciTech Connect

    Ulian, Gianfranco; Valdrè, Giovanni; Tosoni, Sergio

    2013-11-28

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

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

    SciTech Connect

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

    2015-09-14

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

  3. Vibrational spectra and molecular structure of chiral and racemic 4-phenyl-1,3-oxazolidin-2-one by density functional theory and ab initio Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Atalay, Y.; Ucun, F.; Avcı, D.; Başoğlu, A.

    2006-06-01

    The vibrational frequencies and molecular geometry of (R)- and (rac)-4-phenly-1,3-oxazolidin-2-one (4-POO) in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths are described better by HF while bond angles are reproduced more accurately by DFT (B3LYP). Comparison of the observed fundamental vibrational frequencies of (R)-POO and (rac)-4-POO and calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems.

  4. Ab initio and density functional theory calculations of molecular structure and vibrational spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid

    NASA Astrophysics Data System (ADS)

    Kumar, J. Sharmi; Devi, T. S. Renuga; Ramkumaar, G. R.; Bright, A.

    2016-01-01

    The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. 1H and 13C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.

  5. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases

    SciTech Connect

    Arghavani Nia, Borhan; Sedighi, Matin; Shahrokhi, Masoud; Moradian, Rostam

    2013-11-15

    A density functional theory study of structural, electronical and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. In the exchange–correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca{sub 3}Sb{sub 2} has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated. - Graphical abstract: A density functional theory study of structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. Display Omitted - Highlights: • Physical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases are investigated. • It is found that the hexagonal phase is an indirect gap semiconductor. • Ca{sub 3}Sb{sub 2} is a direct-gap semiconductor at the Γ point in the cubic phase. • By increasing pressure the semiconducting band gap and anti-symmetry gap are decreased.

  6. Molecular structure and vibrational spectra of three substituted 4-thioflavones by density functional theory and ab initio Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Hong; Liu, Xiang-Ru; Zhang, Xian-Zhou

    2011-01-01

    The vibrational frequencies of three substituted 4-thioflavones in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G* and 6-31+G** basis sets. The structural analysis shows that there exists H-bonding in the selected compounds and the hydrogen bond lengths increase with the augment of the conjugate parameters of the substituent group on the benzene ring. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The theoretical spectrograms for FT-IR spectra of the title compounds have been constructed. In addition, it is noted that the selected compounds show significant activity against Shigella flexniri. Several electronic properties and thermodynamic parameters were also calculated.

  7. An ab-initio density functional theory investigation of fullerene/Zn-phthalocyanine (C60/ZnPc) interface with face-on orientation

    SciTech Connect

    Javaid, Saqib; Javed Akhtar, M.

    2015-07-28

    We have employed density functional theory to study the C60/ZnPc interface with face-on orientation, which has recently been tailored experimentally. For this purpose, adsorption of ZnPc on C60 has been studied, while taking into account different orientations of C60. Out of various adsorption sites investigated, 6:6 C-C bridge position in apex configuration of C60 has been found energetically the most favourable one with C60-ZnPc adsorption distance of ∼2.77 Å. The adsorption of ZnPc on C60 ensues both charge re-organization and charge transfer at the interface, resulting in the formation of interface dipole. Moreover, by comparing results with that of C60/CuPc interface, we show that the direction of interface dipole can be tuned by the change of the central atom of the phthalocyanine molecule. These results highlight the complexity of electronic interactions present at the C60/Phthalocyanine interface.

  8. An ab-initio density functional theory investigation of fullerene/Zn-phthalocyanine (C60/ZnPc) interface with face-on orientation

    NASA Astrophysics Data System (ADS)

    Javaid, Saqib; Javed Akhtar, M.

    2015-07-01

    We have employed density functional theory to study the C60/ZnPc interface with face-on orientation, which has recently been tailored experimentally. For this purpose, adsorption of ZnPc on C60 has been studied, while taking into account different orientations of C60. Out of various adsorption sites investigated, 6:6 C-C bridge position in apex configuration of C60 has been found energetically the most favourable one with C60-ZnPc adsorption distance of ˜2.77 Å. The adsorption of ZnPc on C60 ensues both charge re-organization and charge transfer at the interface, resulting in the formation of interface dipole. Moreover, by comparing results with that of C60/CuPc interface, we show that the direction of interface dipole can be tuned by the change of the central atom of the phthalocyanine molecule. These results highlight the complexity of electronic interactions present at the C60/Phthalocyanine interface.

  9. Investigation of the Fe3+ centers in perovskite KMgF3 through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations

    NASA Astrophysics Data System (ADS)

    Emül, Y.; Erbahar, D.; Açıkgöz, M.

    2015-08-01

    Analyses of the local crystal and electronic structure in the vicinity of Fe3+ centers in perovskite KMgF3 crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe3+ centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe3+ centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe3+ center case), FeF5O cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe3+ centers in KMgF3.

  10. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I).

    PubMed

    Singh, J S

    2014-01-01

    Raman (200-4000 cm(-1)) and FT-IR (400-4000 cm(-1)) spectra of uracil and 5-halogenated uracils (5-X-uracils; X=F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm(-1). The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G(**) vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X=F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations. PMID:24036044

  11. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-halogenated uracils (5-X-uracils; X = F, Cl, Br, I)

    NASA Astrophysics Data System (ADS)

    Singh, J. S.

    2014-01-01

    Raman (200-4000 cm-1) and FT-IR (400-4000 cm-1) spectra of uracil and 5-halogenated uracils (5-X-uracils; X = F, Cl, Br, I) have been recorded and analyzed in the range 200-4000 cm-1. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Ab initio and DFT calculations [using Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP)] were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-halogenated uracils by employing Gaussian-03 program. Gauss View software was used to make the vibrational analysis. Raman and IR spectra have been computed theoretically for the uracil and 5-halogenated molecules. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. Quantum chemical calculations helped in the reassignments of some fundamental vibrational modes. Most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with available experimental assignments. The ring breathing and kekule stretching modes are found to lower magnitudes compared to those for uracil which could be due to mass effect of halogen atom in place of the hydrogen atom. The C-X (X = F, Cl, Br, I) stretching frequency is distinctly separated from the CH/NH ring stretching frequencies on the pyrimidine ring. All other bands have also been assigned different fundamentals/overtones/combinations.

  12. CO Oxidation on supported single Pt atoms - Experimental and Ab Initio density functional studies of CO interaction with Pt atom on theta-alumina(010) surface

    SciTech Connect

    Narula, Chaitanya Kumar; Debusk, Melanie Moses; Yoon, Mina; Allard Jr, Lawrence Frederick; Mullins, David R; Wu, Zili; Yang, Xiaofan; Veith, Gabriel M; Stocks, George Malcolm

    2013-01-01

    Although there are only a few known examples of supported single atoms, they are unique because they bridge the gap between homogenous and heterogeneous catalysis. The metal center is single supported atoms can be isoelectronic with their homogenous catalyst counterpart and may allow mechanistic pathways normally seen in homogenous catalysts. Here, we report CO oxidation activity of mono-disperse single Pt atoms supported on an inert substrate, -alumina (Al2O3), in the presence of stoichiometric oxygen. Since CO oxidation on single Pt atoms cannot occur via a conventional Langmuir-Hinshelwood scheme (L-H scheme) which requires at least one Pt-Pt bond, we have carried out a first principles density functional theoretical study of a proposed pathway which is a variation on the conventional L-H scheme and is inspired by organometallic chemistry of platinum. We find that a single supported Pt atom prefers to bond to O2 over CO. The CO then bonds with the oxygenated Pt atom and forms a carbonate which dissociates to liberate CO2, leaving an oxygen atom on Pt. A subsequent reaction with another CO molecule regenerates the single atom catalyst. An in-situ diffuse reflectance infrared study of CO adsorption on the catalyst s supported single atoms has been carried out to infer information on CO absorption modes and compare the observed spectra with calculated ones for intermediates in the proposed CO oxidation pathway. Our results clearly show that supported Pt single atoms are catalytically active and that this catalytic activity can occur without involving the substrate. Characterization by electron microscopy and X-ray absorption studies of the mono-disperse Pt/ -Al2O3, synthesized by solution methods, are also presented.

  13. Ab initio studies of mechanical, electric, and magnetic properties of functionalized carbon nanotubes

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    We present results of extensive theoretical studies of mechanical, electric, and magnetic properties of functionalized carbon nanotubes (CNTs). Our studies are based on the ab initio calculations in the framework of the density functional theory. We have performed calculations for various metallic and semiconductor single wall CNTs, functionalized with simple organic molecules such as OH, COOH, NHn, CHn and metals, Al, Fe, Ni, Cu, Zn, and Pd. We have determined the stability of the functionalized CNTs, their elastic moduli, conductance, and magnetic moments (in the case of CNTs decorated with magnetic ions). These studies shed light on physical mechanisms governing the binding of the adsorbed molecules and also provide valuable quantitative predictions that are of importance for design of novel composite materials and functional devices. In particular, we find out that the Young's modulus of functionalized CNTs is smaller than in the case of bare CNTs, however it is large enough to provide a strong enforcement of composites. The functionalization with molecules leads also to the metallization of semiconducting CNTs, being relevant in the context of CNT interconnects, whereas the functionalization with metals might be used to cut CNTs into ribbons.

  14. Electronic and optical properties of the SiB2O4 (B=Mg, Zn, and Cd) spinel oxides: An ab initio study with the Tran-Blaha-modified Becke-Johnson density functional

    NASA Astrophysics Data System (ADS)

    Allali, D.; Bouhemadou, A.; Safi, E. Muhammad Abud Al; Bin-Omran, S.; Chegaar, M.; Khenata, R.; Reshak, A. H.

    2014-06-01

    We report ab initio density functional theory calculations of the structural, electronic and optical properties of the spinel oxides SiMg2O4, SiZng2O4, and SiCd2O4 using the full-potential linearized augmented plane-wave method. The structural parameters calculated using both the local density and generalized gradient approximations to the exchange-correlation potential are consistent with the literature data. To calculate the electronic properties, the exchange-correlation potential is treated with various functionals, and we find that the newly developed Tran-Blaha-modified Becke-Johnson functional significantly improves the band gap. We predict a direct band gap in all of the considered SiB2O4 compounds, and the band gaps continuously decrease as the atomic size of the B element increases. The decrease in the fundamental direct band gap (Γ-Γ) from SiMg2O4 to SiZn2O4 to SiCd2O4 can be attributed to p-d mixing in the upper valence bands of SiZn2O4 and SiCd2O4. The lowest conduction band is well dispersive, similar to that found for transparent conducting oxides such as ZnO. This band is mainly defined by the s and p electrons of the Si and B (B=Mg, Zn, Cd) atoms. The topmost valence band is considerably less dispersive and is defined by O-2p and B-d electrons. The charge-carrier effective masses are evaluated at the topmost valence band and at the bottommost conduction band that were calculated. The frequency-dependent complex dielectric function, absorption coefficient, refractive index, extinction coefficient, reflectivity and electron energy loss function were estimated. We find that the value of the zero-frequency limit of the dielectric function ε(0) increases as the band gap decreases. The origins of the peaks and structures in the optical spectra are determined in terms of the calculated energy band structures.

  15. Bromophenyl functionalization of carbon nanotubes: an ab initio study.

    PubMed

    Janssen, Jonathan Laflamme; Beaudin, Jason; Hine, Nicholas D M; Haynes, Peter D; Côté, Michel

    2013-09-20

    We study the thermodynamics of bromophenyl functionalization of carbon nanotubes with respect to diameter and metallic/insulating character using density-functional theory (DFT). On the one hand, we show that the functionalization of metallic nanotubes is thermodynamically favoured over that of semiconducting ones, in agreement with what binding energy calculations previously suggested. On the other hand, we show that the activation energy for the grafting of a bromophenyl molecule onto a semiconducting zigzag nanotube ranges from 0.72 to 0.75 eV without any clear diameter dependence within numerical accuracy. This implies that this functionalization is not selective with respect to diameter at room temperature, which explains the contradictory experimental selectivities reported in the literature. This contrasts with what is suggested by the clear diameter dependence of the binding energy of a single bromophenyl molecule, which ranges from 1.52 eV for an (8, 0) zigzag nanotube to 0.83 eV for a (20, 0) zigzag nanotube. Also, attaching a single bromophenyl to a nanotube creates states in the gap close to the functionalization site. It therefore becomes energetically favourable for a second bromophenyl to attach close to the first one on semiconducting nanotubes. The para configuration is found to be favoured for resulting bromophenyl pairs and their binding energy is found to decrease with increasing diameter, ranging from 4.35 eV for a (7, 0) nanotube to 2.26 eV for a (29, 0) nanotube. An analytic form for this radius dependence is derived using a tight binding Hamiltonian and first order perturbation theory. The 1/R(2) dependence obtained (where R is the nanotube radius) is verified by our DFT results within numerical accuracy. Finally, bromophenyl pairs are shown to be favoured by only 50 meV with respect to separate moieties on (9, 0) metallic nanotubes, which suggests that pair formation is not significantly favoured on some metallic nanotubes. This

  16. Isovector splitting of nucleon effective masses, ab initio benchmarks and extended stability criteria for Skyrme energy functionals

    SciTech Connect

    Lesinski, T.; Meyer, J.

    2006-10-15

    We study the effect of the splitting of neutron and proton effective masses with isospin asymmetry on the properties of the Skyrme energy density functional. We discuss the ability of the latter to predict observables of infinite matter and finite nuclei, paying particular attention to controlling the agreement with ab initio predictions of the spin-isospin content of the nuclear equation of state, as well as diagnosing the onset of finite size instabilities, which we find to be of critical importance. We show that these various constraints cannot be simultaneously fulfilled by the standard Skyrme force, calling at least for an extension of its P-wave part.

  17. Ab-initio study of germanium di-interstitial using a hybrid functional (HSE)

    NASA Astrophysics Data System (ADS)

    Igumbor, E.; Ouma, C. N. M.; Webb, G.; Meyer, W. E.

    2016-01-01

    In this work, we present ab-initio calculation results of Ge di-interstitials (I2(Ge)) in the framework of the density functional theory (DFT) using the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional. The formation energy, transition levels and minimum energy configurations were obtained for I2(Ge) -2, -1, 0, +1 and +2 charge states. The calculated formation energies show that for all charge states of I2(Ge), the double tetrahedral (T) configuration formed the most stable defect with a binding energy of 1.24 eV in the neutral state. We found the (+2/+1) charge state transition level for the T lying below the conduction band minimum and (+2/+1) for the split[110]-tetrahedral configuration lying deep at 0.41 eV above the valence band maximum. The di-interstitials in Ge exhibited the properties of both shallow and deep donor levels at (+2/+1) within the band gap and depending on the configurations. I2(Ge) gave rise to negative-U, with effective-U values of -0.61 and -1.6 eV in different configurations. We have compared our results with calculations of di-interstitials in silicon and available experimental data.

  18. The different roles of Pu-oxide overlayers in the hydrogenation of Pu-metal: an ab initio molecular dynamics study based on van der Waals density functional (vdW-DF)+U.

    PubMed

    Sun, Bo; Liu, Haifeng; Song, Haifeng; Zhang, Guangcai; Zheng, Hui; Zhao, Xian-Geng; Zhang, Ping

    2014-04-28

    Based on the non-local van der Waals density functional (vdW-DF)+U scheme, we carry out the ab initio molecular dynamics (AIMD) study of the interaction dynamics for H2 impingement against the stoichiometric PuO2(111), the reduced PuO2(111), and the stoichiometric α-Pu2O3(111) surfaces. The hydrogen molecular physisorption states, which cannot be captured by pure DFT+U method, are obtained by employing the vdW-DF+U scheme. We show that except for the weak physisorption, PuO 2(111) surfaces are so difficult of access that almost all of the H2 molecules will bounce back to the vacuum when their initial kinetic energies are not sufficient. Although the dissociative adsorption of H2 on PuO2(111) surfaces is found to be very exothermic, the collision-induced dissociation barriers of H2 are calculated to be as high as 3.2 eV and 2.0 eV for stoichiometric and reduced PuO2 surfaces, respectively. Unlike PuO2, our AIMD study directly reveals that the hydrogen molecules can penetrate into α-Pu2O3(111) surface and diffuse easily due to the 25% native O vacancies located along the ⟨111⟩ diagonals of α-Pu2O3 matrix. By examining the temperature effect and the internal vibrational excitations of H2, we provide a detailed insight into the interaction dynamics of H2 in α-Pu2O3. The optimum pathways for hydrogen penetration and diffusion, the corresponding energy barriers (1.0 eV and 0.53 eV, respectively) and rate constants are systematically calculated. Overall, our study fairly reveals the different interaction mechanisms between H2 and Pu-oxide surfaces, which have strong implications to the interpretation of experimental observations. PMID:24784301

  19. Ab initio density functional theory study of non-polar (101{sup ¯}0), (112{sup ¯}0) and semipolar (202{sup ¯}1) GaN surfaces

    SciTech Connect

    Mutombo, P.; Romanyuk, O.

    2014-05-28

    The atomic structures of non-polar GaN(101{sup ¯}0), (112{sup ¯}0) and semipolar GaN(202{sup ¯}1), (202{sup ¯}1{sup ¯}) surfaces were studied using ab initio calculations within density functional theory. The bulk-like truncated (1 × 1) structure with buckled Ga-N or Ga-Ga dimers was found stable on the non-polar GaN(101{sup ¯}0) surface in agreement with previous works. Ga-N heterodimers were found energetically stable on the GaN(112{sup ¯}0)-(1 × 1) surface. The formation of vacancies and substitution site defects was found unfavorable for non-polar GaN surfaces. Semipolar GaN(202{sup ¯}1)-(1 × 1) surface unit cells consist of non-polar (101{sup ¯}0) and semipolar (101{sup ¯}1) nano-facets. The (101{sup ¯}1) nano-facets consist of two-fold coordinated atoms, which form N-N dimers within a (2 × 1) surface unit cell on a GaN(202{sup ¯}1) surface. Dimers are not formed on the GaN(202{sup ¯}1{sup ¯}) surface. The stability of the surfaces with single (101{sup ¯}0) or (101{sup ¯}1) nano-facets was analyzed. A single non-polar (101{sup ¯}0)-(1 × 1) nano-facet was found stable on the GaN(202{sup ¯}1) surface, but unstable on the GaN(202{sup ¯}1{sup ¯}) surface. A single (101{sup ¯}1) nano-facet was found unstable. Semipolar GaN surfaces with (202{sup ¯}1) and (202{sup ¯}1{sup ¯}) polarity can be stabilized with a Ga overlayer at Ga-rich experimental conditions.

  20. Ab initio density matrix renormalization group study of magnetic coupling in dinuclear iron and chromium complexes

    SciTech Connect

    Harris, Travis V.; Morokuma, Keiji; Kurashige, Yuki; Yanai, Takeshi

    2014-02-07

    The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe{sub 2}OCl{sub 6}]{sup 2−} and [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+}. After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe{sub 2}OCl{sub 6}]{sup 2−} with (16e,26o), and considerably improving the smaller active space results for [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+} with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method.

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

    DOE PAGESBeta

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

    2016-05-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  3. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

  4. FTIR, FT-Raman, ab initio and density functional studies on 4-methyl-1,3-dioxolan-2-one and 4,5-dichloro-1,3-dioxolan-2-one

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Saravanan, I.; Ravindran, P.; Mohan, S.

    2010-09-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-methyl-1,3-dioxolan-2-one and 4,5-dichloro-1,3-dioxolan-2-one have been recorded in the range 3700-400 and 3700-100 cm -1, respectively. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the observed FTIR and FT-Raman data. The vibrational frequencies determined experimentally were compared with those obtained theoretically from ab initio HF and DFT-B3LYP gradient calculations employing 6-311++G** and cc-pVTZ basis sets for the optimised geometries of the compounds. The geometries and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. The interactions of the skeletal vibrational modes were investigated.

  5. Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.

  6. Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    2003-04-01

    The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.

  7. Transport and optical properties of CH2 plastics: Ab initio calculation and density-of-states-based analysis

    NASA Astrophysics Data System (ADS)

    Knyazev, D. V.; Levashov, P. R.

    2015-11-01

    This work covers an ab initio calculation of transport and optical properties of plastics of the effective composition CH2 at density 0.954 g/cm3 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 σ1DC (T) has an unusual shape: σ1DC(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) was performed. The rapid growth of σ1DC(T) at 5 kK ≤ T ≤ 10 kK is connected with the increase of DOS at the electron energy equal to the chemical potential ɛ = μ. The frequency dependence of the dynamic electrical conductivity σ1(ω) at 5 kK has the distinct non-Drude shape with the peak at ω ≈ 10 eV. This behavior of σ1(ω) was explained by the dip at the electron DOS.

  8. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

    PubMed

    Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

    2014-09-01

    We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar

  9. Spectroscopic and Ab Initio Determination of the Ring-Twisting Potential Energy Function for 1,3-Cyclohexadiene

    NASA Astrophysics Data System (ADS)

    Autrey, Daniel; Choo, Jaebum; Laane, Jaan

    2000-10-01

    The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.

  10. Hydroxyl-functionalized 1-(2-hydroxyethyl)-3-methyl imidazolium ionic liquids: thermodynamic and structural properties using molecular dynamics simulations and ab initio calculations.

    PubMed

    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

  11. Investigating short-range magnetism in strongly correlated materials via magnetic pair distribution function analysis and ab initio theory

    NASA Astrophysics Data System (ADS)

    Frandsen, Benjamin; Page, Katharine; Brunelli, Michela; Staunton, Julie; Billinge, Simon

    Short-range magnetic correlations are known to exist in a variety of strongly correlated electron systems, but our understanding of the role they play is challenged by the difficulty of experimentally probing such correlations. Magnetic pair distribution function (mPDF) analysis is a newly developed neutron total scattering method that can reveal short-range magnetic correlations directly in real space, and may therefore help ameliorate this difficulty. We present temperature-dependent mPDF measurements of the short-range magnetic correlations in the paramagnetic phase of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. We observe significant correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range-ordered spin arrangement. With no free parameters, ab initio calculations using the self-interaction-corrected local spin density approximation of density functional theory quantitatively reproduce the magnetic correlations to a high degree of accuracy. These results yield valuable insight into the magnetic exchange in MnO and showcase the utility of the mPDF technique for studying magnetic properties of strongly correlated electron systems.

  12. Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

    2015-02-01

    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.

  13. Physical origins of weak H2 binding on carbon nanostructures: Insight from ab initio studies of chemically functionalized graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Ulman, Kanchan; Bhaumik, Debarati; Wood, Brandon C.; Narasimhan, Shobhana

    2014-05-01

    We have performed ab initio density functional theory calculations, incorporating London dispersion corrections, to study the absorption of molecular hydrogen on zigzag graphene nanoribbons whose edges have been functionalized by OH, NH2, COOH, NO2, or H2PO3. We find that hydrogen molecules always preferentially bind at or near the functionalized edge, and display induced dipole moments. Binding is generally enhanced by the presence of polar functional groups. The largest gains are observed for groups with oxygen lone pairs that can facilitate local charge reorganization, with the biggest single enhancement in adsorption energy found for "strong functionalization" by H2PO3 (115 meV/H2 versus 52 meV/H2 on bare graphene). We show that for binding on the "outer edge" near the functional group, the presence of the group can introduce appreciable contributions from Debye interactions and higher-order multipole electrostatic terms, in addition to the dominant London dispersion interactions. For those functional groups that contain the OH moiety, the adsorption energy is linearly proportional to the number of lone pairs on oxygen atoms. Mixed functionalization with two different functional groups on a graphene edge can also have a synergistic effect, particularly when electron-donating and electron-withdrawing groups are combined. For binding on the "inner edge" somewhat farther from the functional group, most of the binding again arises from London interactions; however, there is also significant charge redistribution in the π manifold, which directly reflects the electron donating or withdrawing capacity of the functional group. Our results offer insight into the specific origins of weak binding of gas molecules on graphene, and suggest that edge functionalization could perhaps be used in combination with other strategies to increase the uptake of hydrogen in graphene. They also have relevance for the storage of hydrogen in porous carbon materials, such as activated

  14. Accurate ab initio potential for the krypton dimer and transport properties of the low-density krypton gas.

    PubMed

    Waldrop, Jonathan M; Song, Bo; Patkowski, Konrad; Wang, Xiaopo

    2015-05-28

    A new highly accurate potential energy curve for the krypton dimer was constructed using coupled-cluster calculations up to the singles, doubles, triples, and perturbative quadruples level, including corrections for core-core and core-valence correlation and for relativistic effects. The ab initio data points were fitted to an analytic potential which was used to compute the most important transport properties of the krypton gas. The viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor were calculated by the kinetic theory at low density and temperatures from 116 to 5000 K. The comparisons with literature experimental data as well as with values from other pair potentials indicate that our new potential is superior to all previous ones. The transport property values computed in this work are recommended as standard values over the complete temperature range. PMID:26026447

  15. Interpolating moving least-squares methods for fitting potential energy surfaces : computing high-density potential energy surface data from low-density ab initio data points.

    SciTech Connect

    Dawes, R.; Thompson, D. L.; Guo, Y.; Wagner, A. F.; Minkoff, M.; Chemistry; Univ. of Missouri-Columbia; Oklahoma State Univ.

    2007-05-11

    A highly accurate and efficient method for molecular global potential energy surface (PES) construction and fitting is demonstrated. An interpolating-moving-least-squares (IMLS)-based method is developed using low-density ab initio Hessian values to compute high-density PES parameters suitable for accurate and efficient PES representation. The method is automated and flexible so that a PES can be optimally generated for classical trajectories, spectroscopy, or other applications. Two important bottlenecks for fitting PESs are addressed. First, high accuracy is obtained using a minimal density of ab initio points, thus overcoming the bottleneck of ab initio point generation faced in applications of modified-Shepard-based methods. Second, high efficiency is also possible (suitable when a huge number of potential energy and gradient evaluations are required during a trajectory calculation). This overcomes the bottleneck in high-order IMLS-based methods, i.e., the high cost/accuracy ratio for potential energy evaluations. The result is a set of hybrid IMLS methods in which high-order IMLS is used with low-density ab initio Hessian data to compute a dense grid of points at which the energy, Hessian, or even high-order IMLS fitting parameters are stored. A series of hybrid methods is then possible as these data can be used for neural network fitting, modified-Shepard interpolation, or approximate IMLS. Results that are indicative of the accuracy, efficiency, and scalability are presented for one-dimensional model potentials as well as for three-dimensional (HCN) and six-dimensional (HOOH) molecular PESs

  16. Fourfold Clusters of Rovibrational Energies in H2Te Studied With an Ab Initio Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)

    1994-01-01

    We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.

  17. Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

    SciTech Connect

    Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan

    2014-04-14

    A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0–100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMX and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.

  18. Ab initio study of the effect of pressure on the structural and electronic properties of cubic LaAlO3 by density function theory using GGA, LDA and PBEsol exchange correlation potentials

    NASA Astrophysics Data System (ADS)

    Benam, M. R.; Abdoshahi, N.; Majidiyan Sarmazdeh, M.

    2014-08-01

    In this paper the effect of pressure on the structural and electronic properties of cubic-LaAlO3 including the equilibrium lattice constant, bulk modulus, derivative of bulk modulus and band structure have been calculated by density functional theory (DFT) using GGA, LDA, and PBEsol exchange correlation potentials. It is found that the change of the lattice constant with pressure has an exponential behavior: with increasing pressure, the lattice constant decreases first sharply at low pressures, and then more slowly at high pressures. Furthermore, the lattice constant calculated by the PBEsol method and the bulk modulus calculated by LDA and PBEsol methods are closer to the available experimental values than those obtained using other exchange correlation potentials. Regarding the electronic properties, it is shown that an increase in pressure increases the band gap, the change being 0.26 eV at 34.00 GPa. The total density of state (t-DOS) calculations demonstrate that increasing pressure has a significant effect on the core and conduction band, but little effect on the valence band. The band structure calculations indicate that, in this material, the band gap changes from indirect to direct at a pressure of about 25 GPa. Also, increasing pressure produces a clear curvature in the band structure near the bottom of the conduction band, a behavior consistent with the strong pressure dependence of the transport properties.

  19. Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 5-chloro-10-oxa-3-thia-tricyclo[5.2.1.0 1,5]dec-8-ene-3,3-dioxide

    NASA Astrophysics Data System (ADS)

    Arslan, Hakan; Demircan, Aydın; Göktürk, Ersen

    2008-01-01

    The IR spectra of 5-chloro-10-oxa-3-thia-tricyclo[5.2.1.0 1,5]dec-8-ene-3,3-dioxide (COTDO) has been recorded in the region 4000-525 cm -1. The optimized molecular geometry, frequency and intensity of the vibrational bands of COTDO in the ground state has been calculated using the Hartree-Fock and density functional using Becke's three-parameter hybrid method with the Lee, Yang, and Parr correlation functional methods with 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental IR spectra. The calculated geometrical parameters and harmonic vibrations are predicted in a very good agreement with the experimental data. The theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using VEDA 4 program. With the help of this modern technique we were able to complete the assignment of the vibrational spectra of the title compound.

  20. Molecular structure, vibrational spectroscopic (FT-IR, FT-Raman), UV-vis spectra, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis, thermodynamic properties of benzophenone 2,4-dicarboxylic acid by ab initio HF and density functional method.

    PubMed

    Chaitanya, K

    2012-02-01

    The FT-IR (4000-450 cm(-1)) and FT-Raman spectra (3500-100 cm(-1)) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals. PMID:22137747

  1. Molecular structure, vibrational spectroscopic (FT-IR, FT-Raman), UV-vis spectra, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis, thermodynamic properties of benzophenone 2,4-dicarboxylic acid by ab initio HF and density functional method

    NASA Astrophysics Data System (ADS)

    Chaitanya, K.

    2012-02-01

    The FT-IR (4000-450 cm -1) and FT-Raman spectra (3500-100 cm -1) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability ( β0) and related properties ( β, α0 and Δ α) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals.

  2. Investigation of the Fe{sup 3+} centers in perovskite KMgF{sub 3} through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations

    SciTech Connect

    Emül, Y.; Erbahar, D.; Açıkgöz, M.

    2015-08-14

    Analyses of the local crystal and electronic structure in the vicinity of Fe{sup 3+} centers in perovskite KMgF{sub 3} crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe{sup 3+} centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe{sup 3+} centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe{sup 3+} center case), FeF{sub 5}O cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe{sup 3+} centers in KMgF{sub 3}.

  3. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  4. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    SciTech Connect

    Roemelt, Michael

    2015-07-28

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  5. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    NASA Astrophysics Data System (ADS)

    Roemelt, Michael

    2015-07-01

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  6. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors.

    PubMed

    Roemelt, Michael

    2015-07-28

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method. PMID:26233112

  7. The pressure-induced ringwoodite to Mg-perovskite and periclase post-spinel phase transition: a Bader's topological analysis of the ab initio electron densities

    NASA Astrophysics Data System (ADS)

    Parisi, Filippo; Sciascia, Luciana; Princivalle, Francesco; Merli, Marcello

    2012-02-01

    In order to characterize the pressure-induced decomposition of ringwoodite (γ-Mg2SiO4), the topological analysis of the electron density ρ( r), based upon the theory of atoms in molecules (AIM) developed by Bader in the framework of the catastrophe theory, has been performed. Calculations have been carried out by means of the ab initio CRYSTAL09 code at the HF/DFT level, using Hamiltonians based on the Becke- LYP scheme containing hybrid Hartree-Fock/density functional exchange-correlation terms. The equation of state at 0 K has been constructed for the three phases involved in the post-spinel phase transition (ringwoodite → Mg-perovskite + periclase) occurring at the transition zone-lower mantel boundary. The topological results show that the decomposition of the ringwoodite at high pressures is caused by a conflict catastrophe. Furthermore, topological evidences of the central role played by the oxygen atoms to facilitate the pressure-induced ringwoodite decomposition and the subsequent phase transition have been noticed.

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

    SciTech Connect

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

    2013-12-04

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

  9. Communication: Hole localization in Al-doped quartz SiO{sub 2} within ab initio hybrid-functional DFT

    SciTech Connect

    Gerosa, Matteo; Bottani, Carlo Enrico

    2015-09-21

    We investigate the long-standing problem of hole localization at the Al impurity in quartz SiO{sub 2}, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained ab initio, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators.

  10. 7Be(p,(gamma))8B S-factor from Ab Initio No-Core Shell Model Wave Functions

    SciTech Connect

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

    2005-12-02

    Nuclear structure of {sup 7}Be, {sup 8}B and {sup 7,8}Li is studied within the ab initio no-core shell model (NCSM). Starting from high-precision nucleon-nucleon (NN) interactions, wave functions of {sup 7}Be and {sup 8}B bound states are obtained in basis spaces up to 10 h bar{Omega} and used to calculate channel cluster form factors (overlap integrals) of the {sup 8}B ground state with {sup 7}Be+p. Due to the use of the harmonic oscillator (HO) basis, the overlap integrals have incorrect asymptotic properties. We fix this problem in two alternative ways. First, by a Woods-Saxon (WS) potential solution fit to the interior of the NCSM overlap integrals. Second, by a direct matching with the Whittaker function. The corrected overlap integrals are then used for the {sup 7}Be(p,{gamma}){sup 8}B S-factor calculation. We study the convergence of the S-factor with respect to the NCSM HO frequency and the model space size. Our S-factor results are in agreement with recent direct measurement data. We also test the spectroscopic factors and the corrected overlap integrals from the NCSM in describing the momentum distributions in knockout reactions with {sup 8}B projectiles. A good agreement with the available experimental data is also found, attesting the overall consistency of the calculations.

  11. Ab initio design of low work function complex oxides for thermionic energy conversion

    NASA Astrophysics Data System (ADS)

    Mack, Stephanie; Li, Guo; Neaton, Jeffrey

    Understanding and controlling work functions, or band edge energies, is of interest for a variety of applications in optoelectronics and energy conversion. In particular, while recent advances in device design have improved the feasibility of thermionic generators, new low work function materials are needed to enable their widespread use. Perovskite-based oxides (ABO3) are a diverse class of materials that, depending on the transition metal atoms on the A and B sites, can give rise to myriad emergent and collective phenomena. Here, we use density functional theory calculations to examine how the work function of one such oxide, SrRuO3 (SRO), can be tuned by monolayers of SrTiO3 (STO) and other polar or near-polar oxides. We find that SRO work functions can be tuned by over 1 eV with one layer of STO, although the calculated reduction in work function is an order of magnitude less than would be expected from the bulk polarization. We understand the variation in work function via a detailed analysis of Born effective charges at the surface, which are as small as 10% of their bulk values, and charge rearrangement at the STO surface and SRO/STO interface.

  12. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    NASA Astrophysics Data System (ADS)

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  13. Communication: energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach.

    PubMed

    Liu, Zhen-Fei; Neaton, Jeffrey B

    2014-10-01

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals. PMID:25296777

  14. Communication: Energy-dependent resonance broadening in symmetric and asymmetric molecular junctions from an ab initio non-equilibrium Green's function approach

    SciTech Connect

    Liu, Zhen-Fei; Neaton, Jeffrey B.

    2014-10-07

    The electronic structure of organic-inorganic interfaces often features resonances originating from discrete molecular orbitals coupled to continuum lead states. An example is molecular junction, individual molecules bridging electrodes, where the shape and peak energy of such resonances dictate junction conductance, thermopower, I-V characteristics, and related transport properties. In molecular junctions where off-resonance coherent tunneling dominates transport, resonance peaks in the transmission function are often assumed to be Lorentzian functions with an energy-independent broadening parameter Γ. Here we define a new energy-dependent resonance broadening function, Γ(E), based on diagonalization of non-Hermitian matrices, which can describe resonances of a more complex, non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively. We compute this quantity via an ab initio non-equilibrium Green's function (NEGF) approach based on density functional theory (DFT) for both symmetric and asymmetric molecular junctions, and show that our definition of Γ(E), when combined with Breit-Wigner formula, reproduces the transmission calculated from DFT-NEGF. Through a series of examples, we illustrate how this approach can shed new light on experiments and understanding of junction transport properties in terms of molecular orbitals.

  15. Ab Initio Study of Polonium

    SciTech Connect

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-20

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.

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

    SciTech Connect

    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.

  17. Understanding phonon transport in thermoelectric materials using ab initio approaches

    NASA Astrophysics Data System (ADS)

    Broido, David

    Good thermoelectric materials have low phonon thermal conductivity, kph. Accurate theories to describe kph are important components in developing predictive models of thermoelectric efficiency that can help guide synthesis and measurement efforts. We have developed ab initio approaches to calculate kph, in which phonon modes and phonon scattering rates are computed using interatomic force constants determined from density functional theory, and a full solution of the Boltzmann transport equation for phonons is implemented. A recent approach to calculate interatomic force constants using ab initio molecular dynamics has yielded a good description of the thermal properties of Bi2Te3. But, the complexity of new promising candidate thermoelectric materials introduces computational challenges in assessing their thermal properties. An example is germanane, a germanium based hydrogen-terminated layered semiconductor, which we will discuss in this talk.

  18. Exploring complex chemical reactions by ab-initio simulation

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    1998-03-01

    Recent progress in the ab-initio molecular dynamics method and the power of parallel computing, allow the detailed study of complex chemical reaction of great industrial relevance. We illustrate this unprecedented capability by investigating the second generation Ziegler-Natta catalytic process. In this inhomogeneous catalyst, a polymerization reaction is induced by TiCl4 molecules deposited on an MgCl2 solid support. A density functional based ab-initio molecular dynamics calculation conducted with a minimum of initial assumption allows to understand the nature of the catalytic center and to determine the reaction path with the associated free energy barrier. Furthermore our calculation can explain in a nontrivial way the stereo-selectivity of the process.

  19. Guiding ab initio calculations by alchemical derivatives.

    PubMed

    to Baben, M; Achenbach, J O; von Lilienfeld, O A

    2016-03-14

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects. PMID:26979677

  20. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  1. Physical origins of weak H{sub 2} binding on carbon nanostructures: Insight from ab initio studies of chemically functionalized graphene nanoribbons

    SciTech Connect

    Ulman, Kanchan; Bhaumik, Debarati; Wood, Brandon C.; Narasimhan, Shobhana

    2014-05-07

    We have performed ab initio density functional theory calculations, incorporating London dispersion corrections, to study the absorption of molecular hydrogen on zigzag graphene nanoribbons whose edges have been functionalized by OH, NH{sub 2}, COOH, NO{sub 2}, or H{sub 2}PO{sub 3}. We find that hydrogen molecules always preferentially bind at or near the functionalized edge, and display induced dipole moments. Binding is generally enhanced by the presence of polar functional groups. The largest gains are observed for groups with oxygen lone pairs that can facilitate local charge reorganization, with the biggest single enhancement in adsorption energy found for “strong functionalization” by H{sub 2}PO{sub 3} (115 meV/H{sub 2} versus 52 meV/H{sub 2} on bare graphene). We show that for binding on the “outer edge” near the functional group, the presence of the group can introduce appreciable contributions from Debye interactions and higher-order multipole electrostatic terms, in addition to the dominant London dispersion interactions. For those functional groups that contain the OH moiety, the adsorption energy is linearly proportional to the number of lone pairs on oxygen atoms. Mixed functionalization with two different functional groups on a graphene edge can also have a synergistic effect, particularly when electron-donating and electron-withdrawing groups are combined. For binding on the “inner edge” somewhat farther from the functional group, most of the binding again arises from London interactions; however, there is also significant charge redistribution in the π manifold, which directly reflects the electron donating or withdrawing capacity of the functional group. Our results offer insight into the specific origins of weak binding of gas molecules on graphene, and suggest that edge functionalization could perhaps be used in combination with other strategies to increase the uptake of hydrogen in graphene. They also have relevance for the storage

  2. Ab-initio study of encapsulated and functionalized silicon nanotube with a monoatomically thin Cu wire

    SciTech Connect

    Chandel, Surjeet Kumar; Ahluwalia, P. K.; Sharma, Raman; Kumar, Arun

    2015-06-24

    First principle calculations based on DFT have been performed to study the interaction of monoatomically thin Cu wire with silicon nanotube in armchair configuration having chirality (6, 6) both by placing it inside (encapsulation) and outside (functionalisation) the tube. The lowest energy for positioning monoatomically thin Cu wire inside and outside surfaces of SiNT were found to possess cohesive energies of 4.03 eV and 4.02 eV respectively and hence the stability of both SiNTs is found to be almost same. However, From the electronic band structures study, the conductance in case of SiNT for the encapsulated and functionalized positioning of the Cu wire have been found to be 2G{sub 0} and 4G{sub 0} respectively showing enhanced conductance for the functionalized SiNT.

  3. Ab initio simulation of diffractometer instrumental function for high-resolution X-ray diffraction1

    PubMed Central

    Mikhalychev, Alexander; Benediktovitch, Andrei; Ulyanenkova, Tatjana; Ulyanenkov, Alex

    2015-01-01

    Modeling of the X-ray diffractometer instrumental function for a given optics configuration is important both for planning experiments and for the analysis of measured data. A fast and universal method for instrumental function simulation, suitable for fully automated computer realization and describing both coplanar and noncoplanar measurement geometries for any combination of X-ray optical elements, is proposed. The method can be identified as semi-analytical backward ray tracing and is based on the calculation of a detected signal as an integral of X-ray intensities for all the rays reaching the detector. The high speed of calculation is provided by the expressions for analytical integration over the spatial coordinates that describe the detection point. Consideration of the three-dimensional propagation of rays without restriction to the diffraction plane provides the applicability of the method for noncoplanar geometry and the accuracy for characterization of the signal from a two-dimensional detector. The correctness of the simulation algorithm is checked in the following two ways: by verifying the consistency of the calculated data with the patterns expected for certain simple limiting cases and by comparing measured reciprocal-space maps with the corresponding maps simulated by the proposed method for the same diffractometer configurations. Both kinds of tests demonstrate the agreement of the simulated instrumental function shape with the measured data. PMID:26089760

  4. Ab Initio Study of Defect Properties in YPO4

    SciTech Connect

    Gao, Fei; Xiao, Haiyan Y.; Zhou, Yungang; Devanathan, Ramaswami; Hu, Shenyang Y.; Li, Yulan; Sun, Xin; Khaleel, Mohammad A.

    2012-03-01

    Ab initio methods based on density functional theory have been used to calculate the formation energies of intrinsic defects, including vacancies, interstitials, antisites and Frenkel pairs in YPO4 under the O-rich and Y2O3-rich, and the O-rich and Y-rich conditions. The larger size of the yttrium atom may give rise to higher formation energy of the phosphorus antisite defect. In general, the formation energies of anion interstitials are much smaller than those of cation interstitials for both conditions considered. It is of greatly interest to find that the relative stabilities among the same types of interstitials are independent of the reference states. The most stable configuration for oxygen interstitials is an O-O split interstitial near the Ta site, while the most stable configuration for cation interstitials is a tetrahedral interstitial near the Ta site. The cation split interstitials are unfavorable in YPO4, with much higher formation energies. Furthermore, the properties of Frenkel pairs are compared with those calculated using empirical potentials. The results reveal that both ab initio and empirical potential calculations show a similar trend in the formation energies of Frenkel pairs, but the formation energies obtained by empirical potentials are much larger than those calculated by ab initio method.

  5. LETTER TO THE EDITOR: Ground-state geometries and the stability of some ? clusters investigated using density-based ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Shah, Vaishali; Kanhere, D. G.

    1996-04-01

    Density-based ab initio molecular dynamics has been used to investigate the stability and ground-state geometries of heteronuclear clusters of 0953-8984/8/17/001/img2 and 0953-8984/8/17/001/img3. Our investigations of these clusters indicate that the s - p bonded electrons favour a tetrahedral coordination, which plays a significant role in stabilizing the geometries of these clusters. We also report a remarkable ground-state structure for the 0953-8984/8/17/001/img4 cluster, namely a face-centred cube with the Al atoms at the face centres forming an octahedron and Li atoms at the corners of the cube. The stability analysis based on the energetics shows that these clusters do not conform to the magic shell numbers observed for homonuclear alkali atom clusters.

  6. Ab initio pair potential energy curve for the argon atom pair and thermophysical properties for the dilute argon gas. II. Thermophysical properties for low-density argon

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    A recent argon-argon interatomic potential energy curve determined from quantum-mechanical ab initio calculations and described with an analytical representation [B. Jäger, R. Hellmann, E. Bich, and E. Vogel, Mol. Phys. 107, 2181 (2009); 108, 105 (2010)] was used to calculate the most important thermophysical properties of argon governed by two-body interactions. Second pressure, acoustic, and dielectric virial coefficients as well as viscosity and thermal conductivity in the limit of zero density were computed for natural argon from 83 to 10,000 K. The calculated values for the different thermophysical properties are compared with available experimental data and values computed for other argon-argon potentials. This extensive analysis shows that the proposed potential is superior to all previous ones and that the calculated thermophysical property values are accurate enough to be applied as standard values for the complete temperature range of the calculations.

  7. Ab Initio and Phenomenological Modeling of the Phonon Spectrum of Superhard cp-BC2N

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Kopytov, A. V.; Pavlova, T. Yu.; Poplavnoi, A. S.

    2015-11-01

    The phonon spectrum of hypothetical superhard cp-BC2N is calculated based on ab initio method of density functional in the center of the Brillouin zone and interpolated over the entire Brillouin zone using the Keating phenomenological model. The interaction parameters are determined by optimization of the IR- and Ramanactive frequencies for a phenomenological model by their comparison with the results of ab initio calculations. Numerical values of short-range interaction constants and charges are in agreement with the characteristics of the chemical bond calculated ab initio. These parameters have transparent physical meaning and chemical nature and can further be used for both qualitative estimations of any physical and physico-chemical quantities and quantitative calculations of the phonon spectra of a number of isostructural compounds. The Keating phenomenological model is used to study the genesis of the phonon spectrum from the spectra of sublattices.

  8. Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

    NASA Astrophysics Data System (ADS)

    Lawan, Narin; Ranaghan, Kara E.; Manby, Frederick R.; Mulholland, Adrian J.

    2014-07-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthase. Good agreement with experimental data is only obtained at the SCS-MP2/CHARMM27 level for a reaction mechanism in which phosphate elimination precedes proton transfer. B3LYP predicts reaction energetics that are qualitatively wrong, stressing the need for ab initio QM/MM methods, and caution in interpretation of DFT results for this enzyme.

  9. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  10. High accuracy ab initio studies of electron-densities for the ground state of Be-like atomic systems.

    PubMed

    Komasa, J; Słupski, R; Jankowski, K; Wasilewski, J; Teale, A M

    2013-04-28

    Benchmark results for electron densities in the ground states of Li(-), Be, C(2+), Ne(6+), and Ar(14+) have been generated from very accurate variational wave functions represented in terms of extensive basis sets of exponentially correlated Gaussian functions. For Ne(6+), and Ar(14+), the upper bounds to the energies improve over previous results known from the literature. For the remaining systems our bounds are from 0.1 to 1.1 μhartree higher than the most accurate ones. We present in graphical and, partially, numerical form results both for the radial electron densities and for the difference radial density distributions (DRD) (defined with respect to the Hartree-Fock radial density) that highlight the impact of correlation effects on electron densities. Next, we have employed these DRD distributions in studies of the performance of several broadly used orbital-based quantum-chemical methods in accounting for correlation effects on the density. Our computed benchmark densities for Be have been also applied for testing the possibility of using the mathematically strict result concerning exact atomic electron densities, obtained by Ahlrichs et al. [Phys. Rev. A 23, 2106 (1981)], for the determination of the reliability range of computed densities in the long-range asymptotic region. The results obtained for Be are encouraging. PMID:23635137

  11. High accuracy ab initio studies of electron-densities for the ground state of Be-like atomic systems

    NASA Astrophysics Data System (ADS)

    Komasa, J.; Słupski, R.; Jankowski, K.; Wasilewski, J.; Teale, A. M.

    2013-04-01

    Benchmark results for electron densities in the ground states of Li-, Be, C2+, Ne6+, and Ar14+ have been generated from very accurate variational wave functions represented in terms of extensive basis sets of exponentially correlated Gaussian functions. For Ne6+, and Ar14+, the upper bounds to the energies improve over previous results known from the literature. For the remaining systems our bounds are from 0.1 to 1.1 μhartree higher than the most accurate ones. We present in graphical and, partially, numerical form results both for the radial electron densities and for the difference radial density distributions (DRD) (defined with respect to the Hartree-Fock radial density) that highlight the impact of correlation effects on electron densities. Next, we have employed these DRD distributions in studies of the performance of several broadly used orbital-based quantum-chemical methods in accounting for correlation effects on the density. Our computed benchmark densities for Be have been also applied for testing the possibility of using the mathematically strict result concerning exact atomic electron densities, obtained by Ahlrichs et al. [Phys. Rev. A 23, 2106 (1981), 10.1103/PhysRevA.23.2106], for the determination of the reliability range of computed densities in the long-range asymptotic region. The results obtained for Be are encouraging.

  12. Ab Initio Studies of Calcium Carbonate Hydration.

    PubMed

    Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M

    2015-11-25

    Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. PMID:26505205

  13. Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

    SciTech Connect

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-08-15

    The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to

  14. Ab initio vibrational and dielectric properties of Y V O

    NASA Astrophysics Data System (ADS)

    Vali, R.

    2009-10-01

    For the yttrium orthovanadate Y V O with a tetragonal zircon-type structure, the first complete set of Raman-active and IR-active phonon modes has been calculated using ab initio density functional perturbation theory. The calculated IR reflectivity spectra are in good agreement with available experimental data. We report the calculated frequencies of three Raman-active modes that could not be detected experimentally and a new assignment of the experimental Raman data. The contributions of each IR-active phonon modes to static dielectric tensor have been determined.

  15. Ab initio Study of He Stability in hcp-Ti

    SciTech Connect

    Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.

    2010-12-20

    The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.

  16. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  17. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  18. An ab initio study of the structure, torsional potential energy function, and electric properties of disilane, ethane, and their deuterated isotopomers.

    PubMed

    Puzzarini, Cristina; Taylor, Peter R

    2005-02-01

    Highly accurate ab initio computations of the molecular structure and properties, torsional potential energy function, and harmonic force field of disilane and ethane have been carried out. Equilibrium parameters as well as vibrational corrections have been evaluated. In addition, for these systems a vibrational averaging procedure has been employed for calculating the dipole moment of molecules which have no permanent dipole moment, i.e., SiH(3)SiD(3) and CH(3)CD(3). The molecular and spectroscopic properties calculated for ethane and its isotopomers provide a calibration against known experimental data, allowing us to estimate the reliability of our computed results for disilane for which there is much less experimental data. The goal of the present study is to predict the molecular parameters, with estimated uncertainties, that determine the microwave spectrum of SiH(3)SiD(3). PMID:15740330

  19. An ab initio study of the structure, torsional potential energy function, and electric properties of disilane, ethane, and their deuterated isotopomers

    NASA Astrophysics Data System (ADS)

    Puzzarini, Cristina; Taylor, Peter R.

    2005-02-01

    Highly accurate ab initio computations of the molecular structure and properties, torsional potential energy function, and harmonic force field of disilane and ethane have been carried out. Equilibrium parameters as well as vibrational corrections have been evaluated. In addition, for these systems a vibrational averaging procedure has been employed for calculating the dipole moment of molecules which have no permanent dipole moment, i.e., SiH3SiD3 and CH3CD3. The molecular and spectroscopic properties calculated for ethane and its isotopomers provide a calibration against known experimental data, allowing us to estimate the reliability of our computed results for disilane for which there is much less experimental data. The goal of the present study is to predict the molecular parameters, with estimated uncertainties, that determine the microwave spectrum of SiH3SiD3.

  20. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  1. Ab initio two-component Ehrenfest dynamics

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-01

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H2 and O2. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  2. Ab initio two-component Ehrenfest dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-21

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  3. Ab initio prediction of the critical thickness of a precipitate

    NASA Astrophysics Data System (ADS)

    Sampath, S.; Janisch, R.

    2013-09-01

    Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface. Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  5. Ab initio tight-binding Hamiltonian for transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Fang, Shiang; Kuate Defo, Rodrick; Shirodkar, Sharmila N.; Lieu, Simon; Tritsaris, Georgios A.; Kaxiras, Efthimios

    2015-11-01

    We present an accurate ab initio tight-binding Hamiltonian for the transition metal dichalcogenides, MoS2, MoSe2, WS2, WSe2, with a minimal basis (the d orbitals for the metal atoms and p orbitals for the chalcogen atoms) based on a transformation of the Kohn-Sham density functional theory Hamiltonian to a basis of maximally localized Wannier functions. The truncated tight-binding Hamiltonian, with only on-site, first, and partial second neighbor interactions, including spin-orbit coupling, provides a simple physical picture and the symmetry of the main band-structure features. Interlayer interactions between adjacent layers are modeled by transferable hopping terms between the chalcogen p orbitals. The full-range tight-binding Hamiltonian can be reduced to hybrid-orbital k .p effective Hamiltonians near the band extrema that capture important low-energy excitations. These ab initio Hamiltonians can serve as the starting point for applications to interacting many-body physics including optical transitions and Berry curvature of bands, of which we give some examples.

  6. CheMPS2: A free open-source spin-adapted implementation of the density matrix renormalization group for ab initio quantum chemistry

    NASA Astrophysics Data System (ADS)

    Wouters, Sebastian; Poelmans, Ward; Ayers, Paul W.; Van Neck, Dimitri

    2014-06-01

    The density matrix renormalization group (DMRG) has become an indispensable numerical tool to find exact eigenstates of finite-size quantum systems with strong correlation. In the fields of condensed matter, nuclear structure and molecular electronic structure, it has significantly extended the system sizes that can be handled compared to full configuration interaction, without losing numerical accuracy. For quantum chemistry (QC), the most efficient implementations of DMRG require the incorporation of particle number, spin and point group symmetries in the underlying matrix product state (MPS) ansatz, as well as the use of so-called complementary operators. The symmetries introduce a sparse block structure in the MPS ansatz and in the intermediary contracted tensors. If a symmetry is non-abelian, the Wigner-Eckart theorem allows to factorize a tensor into a Clebsch-Gordan coefficient and a reduced tensor. In addition, the fermion signs have to be carefully tracked. Because of these challenges, implementing DMRG efficiently for QC is not straightforward. Efficient and freely available implementations are therefore highly desired. In this work we present CheMPS2, our free open-source spin-adapted implementation of DMRG for ab initio QC. Around CheMPS2, we have implemented the augmented Hessian Newton-Raphson complete active space self-consistent field method, with exact Hessian. The bond dissociation curves of the 12 lowest states of the carbon dimer were obtained at the DMRG(28 orbitals, 12 electrons, DSU(2) = 2500)/cc-pVDZ level of theory. The contribution of 1 s core correlation to the X1Σg+ bond dissociation curve of the carbon dimer was estimated by comparing energies at the DMRG(36o, 12e, DSU(2) = 2500)/cc-pCVDZ and DMRG-SCF(34o, 8e, DSU(2) = 2500)/cc-pCVDZ levels of theory.

  7. Ab initio study of chemical bond interactions between covalently functionalized carbon nanotubes via amide, ester and anhydride linkages

    NASA Astrophysics Data System (ADS)

    Ben Doudou, Bessem; Chen, Jun; Vivet, Alexandre; Poilâne, Christophe

    2016-03-01

    In this paper, we have investigated the chemical bond interactions between covalently functionalized zigzag (5,0) and (8,0) SWCNT-SWCNT via various covalent linkages. Side-to-side junctions connected via amide, ester and anhydride linkages were particularly studied. The geometries and energy of the forming reaction were investigated using first-principles density functional theory. Furthermore, the band structures and the total density of states (DOS) of the junctions have also been analyzed. Our results show that several promising structures could be obtained by using chemical connection strategy and particularly the junctions formed by coupling amino functionalized SWCNT and carboxylic acid functionalized SWCNT was more favorable.

  8. Ab initio study of hot electrons in GaAs.

    PubMed

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

    2015-04-28

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287

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

    PubMed

    Chaka, Anne M; Felmy, Andrew R

    2014-09-01

    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. PMID:24679248

  10. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    SciTech Connect

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

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

  11. Variational reduced-density-matrix calculations on radicals: An alternative approach to open-shell ab initio quantum chemistry

    SciTech Connect

    Hammond, Jeff R.; Mazziotti, David A.

    2006-01-15

    An alternative approach to open-shell molecular calculations using the variational two-electron reduced-density-matrix (2-RDM) theory [Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)] is presented. The energy and 2-RDM of the open-shell molecule (or radical) are computed from the limit of dissociating one or more hydrogen atoms from a molecule in a singlet state. Because the ground-state energy of an 'infinitely' separated hydrogen atom in a given finite basis is known, we can determine the energy of the radical by subtracting the energy of one or more hydrogen atoms from the energy of the total dissociated system. The 2-RDM is constrained to have singlet symmetry in all calculations. Two sets of N-representability conditions are employed: (i) two-positivity conditions, and (ii) two-positivity conditions plus the T{sub 2} condition, which is a subset of the three-positivity conditions. Optimization of the energy with respect to the 2-RDM is performed with a first-order algorithm for solving the semidefinite program within the variational 2-RDM method. We present calculations of several radicals near equilibrium as well as the dissociation curves of the diatomic radicals CH and OH.

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

    NASA Astrophysics Data System (ADS)

    Correa, J. D.; Cisternas, E.

    2016-09-01

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

  13. Ab Initio Calculations of Excited Carrier Dynamics in Gallium Nitride

    NASA Astrophysics Data System (ADS)

    Jhalani, Vatsal; Bernardi, Marco

    Bulk wurtzite GaN is the primary material for blue light-emission technology. The radiative processes in GaN are regulated by the dynamics of excited (or so-called ``hot'') carriers, through microscopic processes not yet completely understood. We present ab initio calculations of electron-phonon (e-ph) scattering rates for hot carriers in GaN. Our work combines density functional theory to compute the electronic states, and density functional perturbation theory to obtain the phonon dispersions and e-ph coupling matrix elements. These quantities are interpolated on fine Brillouin zone grids with maximally localized Wannier functions, to converge the e-ph scattering rates within 5 eV of the band edges. We resolve the contribution of the different phonon modes to the total scattering rate, and study the impact on the relaxation times of the long-range Fröhlich interaction due to the longitudinal-optical phonon modes.

  14. Metal complexation and ion hydration in low density hydrothermal fluids: Ab initio molecular dynamics simulation of Cu(I) and Au(I) in chloride solutions (25-1000 °C, 1-5000 bar)

    NASA Astrophysics Data System (ADS)

    Mei, Yuan; Liu, Weihua; Sherman, David M.; Brugger, Joël

    2014-04-01

    Low-density supercritical fluids are suspected of being able to transport metals, but it is unclear what the speciation/complexation would be in such conditions. In this work, we used ab initio molecular dynamics simulations to investigate the complexation, ion association and hydration of Cu+ and Au+ in NaCl brines as a function of solution density, from ambient to supercritical conditions (to 1000 °C, 5000 bar). Cu(I) and Au(I) form distorted linear complexes with two chloride ligands (i.e., CuCl2- and AuCl2-) in subcritical chloride brines. We have discovered that these charged complexes remain in high density supercritical fluids even at high temperature; however, with decreasing density, these complexes become progressively neutralized by ion association with Na+ to form low-charge (NanCuCl2)n-1 and (NanAuCl2)n-1 complexes. In these species, the Na+ ion is very weakly bonded in the outer coordination sphere, resulting in highly disordered structures and fast (few picoseconds) exchange among coordinated and solvent Na+ ions. Thermodynamic models to predict the solubility of metals in low-density magmatic or metamorphic fluids must account for these species. In addition, we found that the number of water molecules (i.e., the hydration number) surrounding the Cu+, Au+, Na+ and Cl- ions decreases linearly when fluid density decreases; this supports empirical thermodynamic models that correlate the stability constants of complexation reactions with solvent density. The traditional Born-model description explains the ion association as resulting from the decreased dielectric constant of the solvent. However at a molecular level, the increased ion association results from the increase in translational entropy associated with ion dehydration.

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

    SciTech Connect

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-17

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

  16. Ab initio electronic stopping power of protons in bulk materials

    NASA Astrophysics Data System (ADS)

    Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia

    2016-01-01

    The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.

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

    SciTech Connect

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

    2015-04-14

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

  18. Water structure as a function of temperature from X-ray scatteringexperiments and ab initio molecular dynamics

    SciTech Connect

    Hura, Greg; Russo, Daniela; Glaeser, Robert M.; Head-Gordon,Teresa; Krack, Matthias; Parrinello, Michele

    2003-03-01

    We present high-quality X-ray scattering experiments on pure water taken over a temperature range of 2 to 77 C using a synchrotron beam line at the advanced light source (ALS) at Lawrence Berkeley National Laboratory. The ALS X-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older X-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead, we consider the direct calculation of X-ray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here.

  19. {sup 7}Be(p,{gamma}){sup 8}B S factor from ab initio no-core shell model wave functions

    SciTech Connect

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

    2006-06-15

    Nuclear structure of {sup 7}Be, {sup 8}B, and {sup 7,8}Li is studied within the ab initio no-core shell model (NCSM). Starting from high-precision nucleon-nucleon (NN) interactions, wave functions of {sup 7}Be and {sup 8}B bound states are obtained in basis spaces up to 10({Dirac_h}/2{pi}){omega} and used to calculate channel cluster form factors (overlap integrals) of the {sup 8}B ground state with {sup 7}Be+p. Due to the use of the harmonic oscillator (HO) basis, the overlap integrals have incorrect asymptotic properties. We fix this problem in two alternative ways. First, by a Woods-Saxon potential solution fit to the interior of the NCSM overlap integrals. Second, by a direct matching with the Whittaker function. The corrected overlap integrals are then used for the {sup 7}Be(p,{gamma}){sup 8}B S-factor calculation. We study the convergence of the S factor with respect to the NCSM HO frequency and the model space size. Our S factor results agree with recent direct measurement data. We also test the spectroscopic factors and the corrected overlap integrals from the NCSM in describing the momentum distributions in knockout reactions with {sup 8}B projectiles. A good agreement with the available experimental data is also found, attesting to the overall consistency of the calculations.

  20. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

    Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.

  1. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

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

  2. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding. PMID:25993396

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

    PubMed

    Drumm, Daniel W; Budi, Akin; Per, Manolo C; Russo, Salvy P; L Hollenberg, Lloyd C

    2013-01-01

    : The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785

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

    PubMed Central

    2013-01-01

    The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785

  5. i-TTM Model for Ab Initio-Based Ion-Water Interaction Potentials. 1. Halide-Water Potential Energy Functions.

    PubMed

    Arismendi-Arrieta, Daniel J; Riera, Marc; Bajaj, Pushp; Prosmiti, Rita; Paesani, Francesco

    2016-03-01

    New potential energy functions (i-TTM) describing the interactions between halide ions and water molecules are reported. The i-TTM potentials are derived from fits to electronic structure data and include an explicit treatment of two-body repulsion, electrostatics, and dispersion energy. Many-body effects are represented through classical polarization within an extended Thole-type model. By construction, the i-TTM potentials are compatible with the flexible and fully ab initio MB-pol potential, which has recently been shown to accurately predict the properties of water from the gas to the condensed phase. The accuracy of the i-TTM potentials is assessed through extensive comparisons with CCSD(T)-F12, DF-MP2, and DFT data as well as with results obtained with common polarizable force fields for X(-)(H2O)n clusters with X(-) = F(-), Cl(-), Br(-), and I(-), and n = 1-8. By construction, the new i-TTM potentials will enable direct simulations of vibrational spectra of halide-water systems from clusters to bulk and interfaces. PMID:26560189

  6. Ab initio theory of NMR chemical shifts in solids

    SciTech Connect

    Louie, S.G. |

    1997-12-31

    A new formalism for ab initio calculation of the orbital magnetic susceptibility and the NMR chemical shifts in solids and liquids is presented. The approach can be applied to periodic systems such as crystals, surfaces or polymers, and with a supercell technique, to nonperiodic systems such as amorphous materials, liquids, or solids with defects. The formalism is based on the density functional theory in the local density approximation and makes use of a generalized f-sum rule to eliminate the divergent terms that plagued previous theories. Calculations have been successfully carried out for the diamagnetic susceptibility of a number of insulators and for the NMR chemical shifts of a variety of systems including free molecules, ionic crystals, hydrogen-bonded materials and amorphous carbon.

  7. Ab Initio Neutron Drops with Chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

    Potter, Hugh; Maris, Pieter; Vary, James

    2015-04-01

    Ab initio calculations for neutron drops are of interest for insights into neutron-rich nuclei and neutron star matter, and for examining the neutron-only sector of nucleon-nucleon and 3-nucleon interactions. I present ab initio results calculated using the no-core shell model with 2- and 3-body chiral Hamiltonians for neutron drops up to 20 neutrons confined in a 10 MeV harmonic trap. I discuss ground state energies, internal energies, radii, and evidence for pairing. In addition, excitation energies can be used to investigate the spin-orbit splittings in the p-shell and sd -shell. Prior Green's Function Monte Carlo calculations using the Argonne v8' potential with added 3-nucleon forces serve as a comparison. Supported by DOE Grants DESC0008485 (SciDAC/NUCLEI), DE-FG02-87ER40371, and NSF Grant 0904782; computational resources provided by the Oak Ridge Leadership Computing Facility (DOE Office of Science Contract DE-AC05-00OR22725) under an INCITE award.

  8. Melting of sodium under high pressure. An ab-initio study

    SciTech Connect

    González, D. J.; González, L. E.

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Knockout reactions from p-shell nuclei : tests of ab initio structure models.

    SciTech Connect

    Grinyer, G. F.; Bazin, D.; Gade, A.; Tostevin, J. A.; Adrich, P.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Navratil, P.; Obertelli, A.; Quaglioni, S.; Siwek, K.; Terry, J. R.; Weisshaar, D.; Wiringa, R. B.

    2011-04-22

    Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.

  11. Knockout Reactions from p-Shell Nuclei: Tests of Ab Initio Structure Models

    SciTech Connect

    Grinyer, G. F.; Bazin, D.; Adrich, P.; Obertelli, A.; Weisshaar, D.; Gade, A.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Siwek, K.; Terry, J. R.; Tostevin, J. A.; Navratil, P.; Quaglioni, S.; Wiringa, R. B.

    2011-04-22

    Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.

  12. Properties of metals during the heating by intense laser irradiation using ab initio simulations

    NASA Astrophysics Data System (ADS)

    Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane

    2011-10-01

    Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.

  13. Intrinsic acidity of aluminum, chromium (III) and iron (III) μ 3-hydroxo functional groups from ab initio electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Rustad, James R.; Dixon, David A.; Felmy, Andrew R.

    2000-05-01

    Density functional calculations are performed on M 3(OH) 7(H 2O) 62+ and M 3O(OH) 6(H 2O) 6+ clusters for MAl, Cr(III), and Fe(III), allowing determination of the relative acidities of the μ 3-hydroxo and aquo functional groups. Contrary to previous predictions and rationalizations, Fe 3OH and Al 3OH groups have nearly the same intrinsic acidity, while Cr 3OH groups are significantly more acidic. The gas-phase acidity of the Fe 3OH site is in good agreement with the value predicted by the molecular mechanics model previously used to estimate the relative acidities of surface sites on iron oxides. [ J. R. Rustad et al. (1996)Geochim. Cosmochim. Acta 60, 1563]. Acidities of aquo functional groups were also computed for Al and Cr. The AlOH 2 site is more acidic than the Al 3OH site, whereas the Cr 3OH site is more acidic than the CrOH 2 site. These findings predict that the surface charging behavior of chromium oxides/oxyhydroxides should be distinguishable from their Fe, Al counterparts. The calculations also provide insight into why the lepidocrocite/boehmite polymorph is not observed for CrOOH.

  14. Ab initio pseudopotential band calculation of organic conductors

    SciTech Connect

    Ishibashi, Shoji; Kohyama, Masanori

    1999-12-01

    The authors have calculated the band structures of organic conductors TTF-TCNQ and {beta}-(BEDT-TTF){sub 2}I{sub 3} using the ab initio plane-wave pseudopotential method within the local-density approximation (LDA). The Fermi-surface shape and the origin of bands near the Fermi level are investigated for each compound.

  15. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

    Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta

    2016-07-01

    In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

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

    PubMed Central

    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

  17. Ab initio calculation of the shock Hugoniot of bulk silicon

    NASA Astrophysics Data System (ADS)

    Strickson, Oliver; Artacho, Emilio

    2016-03-01

    We describe how ab initio molecular dynamics can be used to determine the Hugoniot locus (states accessible by a shock wave) for materials with a number of stable phases, and with an approximate treatment of plasticity and yield, without having to simulate these phenomena directly. We consider the case of bulk silicon, with forces from density-functional theory, up to 70 GPa. The fact that shock waves can split into multiple waves due to phase transitions or yielding is taken into account here by specifying the strength of any preceding waves explicitly based on their yield strain. Points corresponding to uniaxial elastic compression along three crystal axes and a number of postshock phases are given, including a plastically yielded state, approximated by an isotropic stress configuration following an elastic wave of predetermined strength. The results compare well to existing experimental data for shocked silicon.

  18. Ab initio calculations of grain boundaries in bcc metals

    NASA Astrophysics Data System (ADS)

    Scheiber, Daniel; Pippan, Reinhard; Puschnig, Peter; Romaner, Lorenz

    2016-03-01

    In this study, we compute grain boundary (GB) properties for a large set of GBs in bcc transition metals with a special focus on W, Mo and Fe using ab initio density functional theory (DFT) and semi-empirical second nearest neighbour modified embedded atom method (2NN-MEAM) potentials. The GB properties include GB energies, surface energies, GB excess volume and work of separation, which we analyse and then compare to experimental data. We find that the used 2NN-MEAM potentials can predict general trends of GB properties, but do not always reproduce the GB ground state structure and energy found with DFT. In particular, our results explain the experimental finding that W and Mo prefer intergranular fracture, while other bcc metals prefer transgranular cleavage.

  19. Ab initio study of helium behavior in titanium tritides

    SciTech Connect

    Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2013-03-01

    Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].

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

    PubMed

    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

  1. Ab initio based thermal property predictions at a low cost: An error analysis

    NASA Astrophysics Data System (ADS)

    Lejaeghere, Kurt; Jaeken, Jan; Van Speybroeck, Veronique; Cottenier, Stefaan

    2014-01-01

    Ab initio calculations often do not straightforwardly yield the thermal properties of a material yet. It requires considerable computational efforts, for example, to predict the volumetric thermal expansion coefficient αV or the melting temperature Tm from first principles. An alternative is to use semiempirical approaches. They relate the experimental values to first-principles predictors via fits or approximative models. Before applying such methods, however, it is of paramount importance to be aware of the expected errors. We therefore quantify these errors at the density-functional theory level using the Perdew-Burke-Ernzerhof functional for several semiempirical approximations of αV and Tm, and compare them to the errors from fully ab initio methods, which are computationally more intensive. We base our conclusions on a benchmark set of 71 ground-state elemental crystals. For the thermal expansion coefficient, it appears that simple quasiharmonic theory, in combination with different approximations to the Grüneisen parameter, provides a similar overall accuracy as exhaustive first-principles phonon calculations. For the melting temperature, expensive ab initio molecular-dynamics simulations still outperform semiempirical methods.

  2. A study of small systems containing H and O atoms using nonlocal functionals: Comparison with ab initio and experiment

    SciTech Connect

    Seminario, J.M.

    1994-12-31

    Structures and energies have been calculated for HO, H{sub 2}O, O{sub 2}, HO{sub 2}, H{sub 2}O{sub 2}, and O{sub 3} molecules using the nonlocal functionals PW 86, PW 91, B-P86, and B-LYP with the goal of obtaining their atomization energies. Results were compared with those form highly correlated methods and experiment. It was found that all nonlocal functionals perform similarly to or better than correlated methods MP4 and QCI (using relatively equivalent basis sets). All nonlocal energies were self-consistently calculated using the optimized geometries for each functional. None of the results contain any empirical correction except those inherent to some of the functionals. Increasing the size of the basis set when using the nonlocal functionals does not lead to any significant improvement of the energies and surprisingly it worsens the results for one of the functionals.

  3. Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

    SciTech Connect

    Kowalewski, Markus Mukamel, Shaul

    2015-07-28

    Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.

  4. Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

    NASA Astrophysics Data System (ADS)

    Kowalewski, Markus; Mukamel, Shaul

    2015-07-01

    Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.

  5. Density functional theory and Ab initio studies of vibrational spectroscopic (FT-IR, FT-Raman and UV) first order hyperpolarizabilities, NBO, HOMO-LUMO and TD-DFT analysis of the 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one

    NASA Astrophysics Data System (ADS)

    Ramachandran, G.; Muthu, S.; Uma Maheswari, J.

    2013-02-01

    Fourier transform Raman and Fourier transform infrared spectra of 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one were recorded in the regions 3500-100 cm-1 and 4000-400 cm-1 respectively in the solid phase. 1,2-Dihydropyrazolo (4, 3-E) Pyrimidin-4-one is used to treat hyperuricemia and its complication including chronic gout. The equilibrium geometry harmonic vibrational frequencies, infrared intensities and Raman intensities were calculated by Hartee Fock and density functional B3LYP methods with 6-31G (d, p) basis set, using Gaussian 03W program package on a Pentium IV/1.6 GHz personal computer. The thermodynamic functions of the title compound were also performed at the above methods and basis set. A detailed interpretation of the infrared and Raman spectra of 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one is reported. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis of the compound was recorded. The calculated HOMO and LUMO energies show that chemical activity of the molecule. The first order hyperpolarizability (β) of this novel molecular system and related properties of 1,2-Dihydropyrazolo (4,3-E) Pyrimidin-4-one are calculated using HF/6-31G (d, p) method on the finite field approach. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectra.

  6. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, M. A.; Maris, P.; Vary, J. P.; Smith, R.

    2015-08-01

    Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  8. Effect of nitrogen and vacancy defects on the thermal conductivity of diamond: An ab initio Green's function approach

    NASA Astrophysics Data System (ADS)

    Katcho, N. A.; Carrete, J.; Li, Wu; Mingo, N.

    2014-09-01

    We show that impurities and vacancies affect the thermal conductivity much more strongly than what is predicted by widely accepted models. When local distortions around point defects are strong, standard perturbative approaches fail, and phonon scattering can only be accounted for by an exact Green's function calculation. We apply the theory to the study, from first-principles, of nitrogen and vacancy defects in diamond. The thermal conductivity is computed by solving the linearized Boltzmann transport equation. The Born approximation underestimates the phonon scattering cross sections of nitrogen and vacancies by factors of 3 and 10, respectively. Thermal conductivity calculations are in good agreement with experiment.

  9. Ab initio nuclear structure theory

    NASA Astrophysics Data System (ADS)

    Negoita, Gianina Alina

    Ab initio no core methods have become major tools for understanding the properties of light nuclei based on realistic nucleon-nucleon (NN) and three-nucleon (NNN) interactions. A brief description is provided for the inter-nucleon interactions that fit two-body scattering and bound state data, as well as NNN interactions. Major new progress, including the goal of applying these interactions to solve for properties of nuclei, is limited by convergence issues. That is, with the goal of obtaining high precision solutions of the nuclear many-body Hamiltonian with no core methods (all nucleons treated on the same footing), one needs to proceed to very large basis spaces to achieve a convergence pattern suitable for extrapolation to the exact result. This thesis investigates (1) the similarity renormalization group (SRG) approach to soften the interaction, while preserving its phase shift properties, and (2) adoption of a realistic basis space using Woods-Saxon (WS) single-particle wavefunctions. Both have their advantages and limitations, discussed here. For (1), SRG was demonstrated by applying it to a realistic NN interaction, JISP16, in a harmonic oscillator (HO) representation. The degree of interaction softening achieved through a regulator parameter is examined. For (2), new results are obtained with the realistic JISP16 NN interaction in ab initio calculations of light nuclei 4He, 6He and 12C, using a WS basis optimized to minimize the ground-state energy within the truncated no core shell model. These are numerically-intensive many-body calculations. Finally, to gain insight into the potential for no core investigations of heavier nuclei, an initial investigation was obtained for the odd mass A = 47 - 49 region nuclei straddling 48Ca. The motivation for selecting these nuclei stems from the aim of preparing for nuclear double beta-decay studies of 48Ca. In these heavier systems, phenomenological additions to the realistic NN interaction determined by previous

  10. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

    We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)

  11. Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea.

    PubMed

    Erba, Alessandro; Maul, Jefferson; Civalleri, Bartolomeo

    2016-01-31

    An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermo-elasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data. PMID:26670006

  12. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    NASA Astrophysics Data System (ADS)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  13. Phonon spectrum of lead oxychloride Pb3O2Cl2: Ab initio calculation and experiment

    NASA Astrophysics Data System (ADS)

    Zakir'yanov, D. O.; Chernyshev, V. A.; Zakir'yanova, I. D.

    2016-02-01

    IR and Raman spectra of Pb3O2Cl2 in the range of 50-600 cm-1 have been detected for the first time. Ab initio calculations of the crystal structure and the phonon spectrum of Pb3O2Cl2 in the framework of LCAO approach have been performed by the Hartree-Fock method and in the framework of the density functional theory with the use of hybrid functionals. The results of calculations have made it possible to interpret the experimental vibration spectra and reveal silent modes, which do not manifest themselves in these spectra but influence the optical properties of the crystal.

  14. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

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

    1978-01-01

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

  15. Ab-initio calculations on melting of thorium

    NASA Astrophysics Data System (ADS)

    Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.

  16. Reactive Inorganic Membranes for CO2/N2 separations: Ab-initio Density Functional Theory Calculations

    NASA Astrophysics Data System (ADS)

    Ostwal, M.; Way, J. D.; Lusk, M.

    2009-10-01

    The selectivity (CO2/N2) of mesoporous silica membranes can be enhanced by surface modification using APTS (3-aminopropyl-triethoxy silane). The hypothesized transport mechanism in such materialsis the reaction of CO2 with surface amine groups to form a carbamate species and subsequent surface ``hopping'' of CO2. DFT calculations were performed in order to elucidate the mechanism of CO2 transport in APTS modified membranes, to compute the CO2 diffusivity through the membrane, and to calculate its binding energy on an amine strand. The computed binding energy for docking one CO2 molecule to an amine was calculated to be 15.5 kcal/mol (0.67 eV). The activation/barrier energy for a CO2 molecule to hop from one amine strand (in form of carbamate) to another computed using Transition State Theory (TST) was 7.2 kcal/mol (0.31 eV) and compares well with our experimental data (˜ 8kcal/mol; 0.35 eV). In the configuration studied, CO2 hops from one strand to another in a zigzag fashion due to thermal motion of the strands; a strand with the CO2 molecule undulates and eventually moves so that the CO2 can be attracted by an adjacent strand. The CO2 diffusivity calculated using the computed activation energy ranged from 1.1 X 10-11m^2/sec (@ 25 C) to 5.7 X 10-10m^2/sec (@100 C).

  17. Mo;ecular Modeling of Biogenic Manganese Oxides Using ab Initio Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Oconnor, M.; Sposito, G.; Refson, K.

    2003-12-01

    Layer type manganese oxides with short-range crystalline order (birnessites) are produced by many species of bacteria.Deposits of these oxides form a highly reactive catalytic surface that plays a major role in the destruction and sequestration of organic compounds and metals.Biogenic oxides also contain vacant Mn(IV)sites;these sites,with their associated negative charge, are the probable main cause of the high sorptive reactivity of the oxide surfaces. In order to acquire a deeper understanding of the molecular mechanisms involved in these processes, a model of a biogenic oxide was built and its structure was optimized using the CASTEP three-dimensional periodic system computational package. The resulting crystal structure shows good agreement with EXAFS data from crystals formed by a strain of the common soil and freshwater bacterium, Pseudomonas putida. The greatest challenge in modeling Mn oxides (like other transition metal oxides)comes in dealing with the electronic factors that lead to their magnetic and catalytic properties: they are highly correlated systems where the spin must be taken into account in order to obtain accurate predictions of their properties.

  18. Ab initio potentials of F+Li2 accessible at ultracold temperatures

    NASA Astrophysics Data System (ADS)

    Wright, K. W. A.; Lane, Ian C.

    2010-09-01

    Ab initio calculations for the strongly exoergic Li2+F harpoon reaction are presented using density-functional theory, complete active space self-consistent field, and multireference configuration interaction methods to argue that this reaction would be an ideal candidate for investigation with ultracold molecules. The lowest six states are calculated with the aug-correlation-consistent polarized valence triple-zeta basis set and at least two can be accessed by a ground rovibronic Li2 molecule with zero collision energy at all reaction geometries. The large reactive cross section (characteristic of harpoon reactions) and chemiluminescent products are additional attractive features of these reactions.

  19. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dixit, Mudit; Major, Dan Thomas; Pal, Sourav

    2016-05-01

    Primary H2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H2 molecules, as well as the H2 binding energy. The binding energy (∼25 kJ/mol per H2) at 8H2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage.

  20. A comparative ab initio and DFT study of polyaniline leucoemeraldine base and its oligomers.

    PubMed

    Mishra, Abhishek Kumar; Tandon, Poonam

    2009-11-01

    Ab initio Hartree-Fock (HF) and density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the polyaniline leucoemeraldine base (PANI-LB). Vibrational spectra of PANI-LB have been analyzed using the DFT oligomer approach, and complete assignments are being reported. Lower region spectral assignments of the PANI-LB which were not being reported earlier are being done in the present work. DFT calculations with the 6-31G** basis set produce very good results of not only vibrational modes but also of energy band gap. PMID:19827802

  1. Site occupancy trend of Co in Ni2MnIn: Ab initio approach

    NASA Astrophysics Data System (ADS)

    Pal, Soumyadipta; Mahadevan, Priya; Biswas, C.

    2015-06-01

    The trend of site occupation of Co at Ni sites of Ni2MnIn system is studied in austenitic phase having L21 structure by ab initio density functional theory (DFT) calculation. The Co atoms prefer to be at Ni sites rather than Mn site and are ferromagetically coupled with Ni and Mn. The ground state has tetragonal structure for Ni1.5Co0.5MnIn and Ni1.25Co0.75MnIn. The Co tends to form cluster.

  2. Ab initio potentials of F+Li{sub 2} accessible at ultracold temperatures

    SciTech Connect

    Wright, K. W. A.; Lane, Ian C.

    2010-09-15

    Ab initio calculations for the strongly exoergic Li{sub 2}+F harpoon reaction are presented using density-functional theory, complete active space self-consistent field, and multireference configuration interaction methods to argue that this reaction would be an ideal candidate for investigation with ultracold molecules. The lowest six states are calculated with the aug-correlation-consistent polarized valence triple-zeta basis set and at least two can be accessed by a ground rovibronic Li{sub 2} molecule with zero collision energy at all reaction geometries. The large reactive cross section (characteristic of harpoon reactions) and chemiluminescent products are additional attractive features of these reactions.

  3. Efficient Use of an Adapting Database of Ab Initio Calculations To Generate Accurate Newtonian Dynamics.

    PubMed

    Shaughnessy, M C; Jones, R E

    2016-02-01

    We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825

  4. Enhancing mechanical toughness of aluminum surfaces by nano-boron implantation: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zhu, Zhen; Kwon, Dae-Gyeon; Kwon, Young-Kyun; Tománek, David

    2015-01-01

    Searching for ways to enhance surface hardness of aluminum, we study the equilibrium structure, stability, elastic properties and formation dynamics of a boron-enriched surface using ab initio density functional calculations. We used molecular dynamics simulations to model the implantation of energetic boron nanoparticles in Al and identify structural arrangements that optimize the formation of strong covalent Bsbnd Al bonds. Nano-indentation simulations based on constrained optimization suggest that presence of boron nanostructures in the subsurface region enhances significantly the mechanical hardness of aluminum surfaces.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  6. Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

    NASA Astrophysics Data System (ADS)

    Akin-Ojo, Omololu; Song, Yang; Wang, Feng

    2008-08-01

    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.

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

    PubMed

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

    2014-07-14

    The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results. PMID:25028021

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

    SciTech Connect

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

    2014-07-14

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

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

    SciTech Connect

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

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

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

    PubMed

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

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573

  12. Ab initio calculation of a global potential, vibrational energies, and wave functions for HCN/HNC, and a simulation of the (A-tilde)-(X-tilde) emission spectrum

    NASA Technical Reports Server (NTRS)

    Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.

    1993-01-01

    A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.

  13. Ab initio modelling of methane hydrate thermophysical properties.

    PubMed

    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. PMID:27019976

  14. Ab initio simulations on rutile-based titania nanowires

    NASA Astrophysics Data System (ADS)

    Zhukovskii, Yu F.; Evarestov, R. A.

    2012-08-01

    The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 1bar 10 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.

  15. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

    Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls

  16. Ab initio calculations of reactions with light nuclei

    NASA Astrophysics Data System (ADS)

    Quaglioni, Sofia; Hupin, Guillaume; Calci, Angelo; Navrátil, Petr; Roth, Robert

    2016-03-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review ab initio calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the ab initio no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the A-nucleon system are coupled to (A-a)+a target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

  17. An efficient approach to ab initio Monte Carlo simulation

    SciTech Connect

    Leiding, Jeff; Coe, Joshua D.

    2014-01-21

    We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β{sup 0}), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where—depending on the quality of the reference system potential—acceptance probabilities were enhanced by factors of 1.2–28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

  18. Ab-initio study of magnetic properties and phase transitions in Ga (Mn) N with Monte Carlo approach

    NASA Astrophysics Data System (ADS)

    Sbai, Y.; Ait Raiss, A.; Salmani, E.; Bahmad, L.; Benyoussef, A.

    2015-12-01

    On the basis of ab-initio calculations and Monte Carlo simulations the magnetic and electronic properties of Gallium nitride (GaN) doped with the transition metal Manganese (Mn) were studied. The ab initio calculations were done using the AKAI-KKR-CPA method within the Local Density Approximation (LDA) approximation. We doped our Diluted Magnetic Semiconductor (DMS), with different concentrations of magnetic impurities Mn and plotted the density of state (DOS) for each one. Showing a half-metallic behavior and ferromagnetic state especially for Ga0.95Mn0.05N making this DMS a strong candidate for spintronic applications. Moreover, the magnetization and susceptibility of our system as a function of the temperature has been calculated and give for various system size L to study the size effect. In addition, the transition temperature was deduced from the peak of the susceptibility. The Ab initio results are in good agreement with literature especially for (x=0.05) of Mn which gives the most interesting results.

  19. Skutterudites under pressure: An ab initio study

    SciTech Connect

    Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.

    2014-03-07

    Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.

  20. An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry

    SciTech Connect

    Matthew Neurock; David A. Walthall

    2006-05-07

    One of the greatest societal challenges over the next decade is the production of cheap, renewable energy for the 10 billion people that inhabit the earth. This will require the development of various different energy sources potentially including fuels derived from methane, coal, and biomass and alternatives sources such as solar, wind and nuclear energy. One approach will be to synthesize gasoline and other fuels from simpler hydrocarbons such as CO derived from methane or other U.S. based sources such as coal. Syngas (CO and H{sub 2}) can be readily converted into higher molecular weight hydrocarbons through Fischer-Tropsch synthesis. Fischer-Tropsch synthesis involves the initiation or activation of CO and H{sub 2} bonds, the subsequent propagation steps including hydrogenation and carbon-carbon coupling, followed by chain termination reactions. Commercially viable catalysts include supported Co and Co-alloys. Over the first two years of this project we have used ab initio methods to determine the adsorption energies for all reactants, intermediates, and products along with the overall reaction energies and their corresponding activation barriers over the Co(0001) surface. Over the third year of the project we developed and advanced an ab initio-based kinetic Monte Carlo simulation code to simulate Fischer Tropsch synthesis. This report details our work over the last year which has focused on the derivation of kinetic parameters for the elementary steps involved in FT synthesis from ab initio density functional theoretical calculations and the application of the kinetic Monte Carlo algorithm to simulate the initial rates of reaction for FT over the ideal Co(0001) surface. The results from our simulations over Co(0001) indicate the importance of stepped surfaces for the activation of adsorbed CO. In addition, they demonstrate that the dominant CH{sub x}* surface intermediate under steady state conditions is CH*. This strongly suggests that hydrocarbon coupling

  1. Ab initio studies of niobium defects in uranium

    SciTech Connect

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

    Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.

  2. Ab initio simulation of gap discrete breathers in strained graphene

    NASA Astrophysics Data System (ADS)

    Lobzenko, I. P.; Chechin, G. M.; Bezuglova, G. S.; Baimova, Yu. A.; Korznikova, E. A.; Dmitriev, S. V.

    2016-03-01

    The methods of the density functional theory were used for the first time for the simulation of discrete breathers in graphene. It is demonstrated that breathers can exist with frequencies lying in the gap of the phonon spectrum, induced by uniaxial tension of a monolayer graphene sheet in the "zigzag" direction (axis X), polarized in the "armchair" direction (axis Y). The found gap breathers are highly localized dynamic objects, the core of which is formed by two adjacent carbon atoms located on the Y axis. The atoms surrounding the core vibrate at much lower amplitudes along both the axes ( X and Y). The dependence of the frequency of these breathers on amplitude is found, which shows a soft type of nonlinearity. No breathers of this type were detected in the gap induced by stretching along the Y axis. It is shown that the breather vibrations may be approximated by the Morse oscillators, the parameters of which are determined from ab initio calculations. The results are of fundamental importance, as molecular dynamics calculations based on empirical potentials cannot serve as a reliable proof of the existence of breathers in crystals.

  3. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  4. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  5. FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole.

    PubMed

    Rai, Amareshwar K; Singh, Rachana; Singh, K N; Singh, V B

    2006-02-01

    FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value. PMID:16098806

  6. Ab initio Raman spectroscopy of water under extreme conditions

    NASA Astrophysics Data System (ADS)

    Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia

    Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.

  7. An ab Initio Benchmark and DFT Validation Study on Gold(I)-Catalyzed Hydroamination of Alkynes.

    PubMed

    Ciancaleoni, Gianluca; Rampino, Sergio; Zuccaccia, Daniele; Tarantelli, Francesco; Belanzoni, Paola; Belpassi, Leonardo

    2014-03-11

    High level ab initio calculations have been carried out on an archetypal gold(I)-catalyzed reaction: hydroamination of ethyne. We studied up to 12 structures of possible gold(I)-coordinated species modeling different intermediates potentially present in a catalytic cycle for the addition of a protic nucleophile to an alkyne. The benchmark is used to evaluate the performances of some popular density functionals for describing geometries and relative energies of stationary points along the reaction profile. Most functionals (including hybrid or meta-hybrid) give accurate structures but large nonsystematic errors (4-12 kcal/mol) along the reaction energy profile. The double hybrid functional B2PLYP outperforms all considered functionals and compares very nicely with our reference ab initio benchmark energies. Moreover, we present an assessment of the accuracy of commonly used approaches to include relativistic effects, such as relativistic effective potentials and a scalar ZORA Hamiltonian, by a comparison with the results obtained using a relativistic all-electron four-component Dirac-Kohn-Sham method. The contribution of nonscalar relativistic effects in gold(I)-catalyzed reactions, as we investigated here, is expected to be on the order of 1 kcal/mol. PMID:26580180

  8. High density H2 associative absorption on Titanium alpha-borozene (Ti2B6H6): An ab-initio case study

    NASA Astrophysics Data System (ADS)

    Akbarzadeh, Alireza; Tymzcak, C. J.

    2011-03-01

    Hydrogen is considered as a clean energy carrier that could be a future replacement for our addiction to fossil fuels. However, in order to have hydrogen economy at its highest efficiently we need to store hydrogen at high volumetric and gravimetric density. Using the all electron hybrid density functional theory, we have designed a benzene-like-molecule, Ti2B6H6, which has the promise of achieving this goal. Our results show that the molecule can associatively absorb the hydrogen up to ten percent by weight of hydrogen, which exceeds the 2015 US department of energy target. In this presentation we will discuss the mechanisms of H2 absorption and possible applications of this novel molecule. This research is funded by the Welch Foundation under Grant J. 1675 and the Texas Southern University High Performance Computing Center.

  9. An ab initio molecular dynamics study of the liquid-vapor interface of an aqueous NaCl solution: inhomogeneous density, polarity, hydrogen bonds, and frequency fluctuations of interfacial molecules.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-11-21

    We have presented a first principles simulation study of the structural and dynamical properties of a liquid-vapor interfacial system of a concentrated (5.3 M) aqueous NaCl solution. We have used ab initio molecular dynamics to examine the structural and dynamical properties of the bulk and interfacial regions. The structural aspects of the system that have been considered here include the inhomogeneous density profiles of ions and water molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions in the bulk and interfacial regions. It is found that the sodium ions are mostly located in the interior, while the chloride anions occupy a significant portion of the interface of the slab. The water dipoles at the interface prefer to orient parallel to the surface. The dynamical aspects of the interfaces are investigated in terms of diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion. The results of the interfacial dynamics are compared with those of the corresponding bulk region. It is observed that the interfacial molecules exhibit faster diffusion and orientational relaxation with respect to the bulk. However, the interfacial molecules are found to have longer hydrogen bond lifetimes than those of the bulk. We have also investigated the correlations of hydrogen bond relaxation with the vibrational frequency fluctuations of interfacial water molecules. PMID:25416903

  10. An improved ab initio structure for fluorine peroxide (FOOF)

    NASA Astrophysics Data System (ADS)

    Mack, Hans-Georg; Oberhammer, Heinz

    1988-03-01

    Ab initio calculations with the 6-31G* and Dunning (9s5p/4s2p) basis sets augmented with p and d functions at various levels of theory (RHF, MP2, MP3, and MP4) were carried out on F 2O 2. The best result was obtained at the MP2 level with the Dunning basis plus one set of d functions on fluorine and two sets of d functions on oxygen. These calculations reproduce the experimental bond lengths to within 0.01 Å and the angles to within the experimental uncertainties.

  11. Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides

    NASA Astrophysics Data System (ADS)

    Sharma, Vinit; Krogel, Jaron T.; Kent, P. R. C.; Reboredo, Fernando A.

    One of the critical scientific challenges of contemporary research is to obtain an accurate theoretical description of the electronic properties of strongly correlated systems such as transition metal oxides and rare-earth compounds, since state-of-art ab-initio methods based on approximate density functionals are not always sufficiently accurate. Quantum Monte Carlo (QMC) methods, which use statistical sampling to evaluate many-body wave functions, have the potential to answer this challenge. Owing to the few fundamental approximations made and the direct treatment of electron correlation, QMC methods are among the most accurate electronic structure methods available to date. We assess the accuracy of the diffusion Monte Carlo method in the case of rocksalt manganese oxide (MnO). We study the electronic properties of this strongly-correlated oxide, which has been identified as a suitable candidate for many applications ranging from catalysts to electronic devices. ``This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.'' Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides.

  12. Ab initio electronic properties of dual phosphorus monolayers in silicon

    PubMed Central

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated. PMID:25246862

  13. Ab-initio study of transition metal hydrides

    SciTech Connect

    Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini

    2014-04-24

    We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.

  14. Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches.

    PubMed

    Ramírez-Solís, A; Poteau, R; Vela, A; Daudey, J P

    2005-04-22

    The X2Pi g-2Sigma g+, X2Pi g-2Delta g, X2Pi g-2Sigma u+, X2Pi g-2Pi u transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the X2Pi g-2Sigma g+ and X2Pi g-2Delta g transition energies, many of them even placing the 2Delta g ligand field state above the charge transfer 2Pi u and 2Sigma u+ states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the LambdaSSigma density defined by the orientation of the 3d hole (sigma, pi, or delta) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the X2Pi g state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio

  15. Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches

    NASA Astrophysics Data System (ADS)

    Ramírez-Solís, A.; Poteau, R.; Vela, A.; Daudey, J. P.

    2005-04-01

    The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large

  16. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, Mark A.; Maris, Pieter; Vary, James P.

    2015-10-01

    The challenge of ab initio nuclear theory is to quantitatively predict the complex and highly-correlated behavior of the nuclear many-body system, starting from the underlying internucleon interactions. We may now seek to understand the wealth of nuclear collective phenomena through ab initio approaches. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this talk, the intrinsic structure of these bands is discussed, and the predicted rotational bands are compared to experiment. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. 0904782. Computational resources provided by NERSC (US DOE Contract No. DE-AC02-05CH11231).

  17. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  18. An investigation of ab initio shell-model interactions derived by no-core shell model

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  19. Ab initio vel ex eventu. II

    NASA Astrophysics Data System (ADS)

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

    Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.

  20. Ab initio Bogoliubov coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

    Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.

  1. Ab initio calculations of the optical properties of crystalline and liquid InSb

    NASA Astrophysics Data System (ADS)

    Sano, Haruyuki; Mizutani, Goro

    2015-11-01

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  2. Ab Initio simulations of nonstoichiometric CdxTe1-x liquids

    NASA Astrophysics Data System (ADS)

    Ko, Eunjung; Alemany, M. M. G.; Derby, Jeffrey J.; Chelikowsky, James R.

    2005-08-01

    We present ab initio molecular-dynamics simulations for CdxTe1-x liquids where the composition is nonstoichiometric. The simulations are performed following Born-Oppenheimer molecular dynamics. The required forces are obtained from a solution of the Kohn-Sham equation using ab initio pseudopotentials. We consider stoichiometries of the form: CdxTe1-x, where x =0.2, 0.4, 0.6, and 0.8. For each composition of the melt, we consider a range of temperatures near the experimentally determined liquid temperatures. We examine the microstructural properties of the melt, the viscosity, and self-diffusion properties of the liquid as a function of the stoichiometry and temperature. We also perform an analysis of the distribution of the electronic density of states in these liquids. We find that structural changes in the local order, experimentally predicted to occur when the concentration of Cd is increased, are closely related to changes in the electronic properties of the melt.

  3. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.

    PubMed

    Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P

    2016-04-12

    This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations. PMID:26966920

  4. Vibrational spectroscopic investigations, ab initio and DFT studies on 7-bromo-5-chloro-8-hydroxyquinoline.

    PubMed

    Arjunan, V; Mohan, S; Ravindran, P; Mythili, C V

    2009-05-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of 7-bromo-5-chloro-8-hydroxyquinoline (BCHQ) have been measured in the range 4000-400 and 4000-100cm(-1), respectively. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The geometry was optimised without any symmetry constrains using the DFT/B3LYP and HF methods with 6-31G** basis set. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from ab initio HF and density functional theory (DFT) gradient calculations employing the HF/6-31G** and B3LYP/6-31G** methods for the optimised geometry of the compound. The structural parameters and normal modes of vibration obtained from HF and DFT methods are in good agreement with the experimental data. Normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. PMID:19112045

  5. Vibrational spectroscopic investigations, ab initio and DFT studies on 7-bromo-5-chloro-8-hydroxyquinoline

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Mohan, S.; Ravindran, P.; Mythili, C. V.

    2009-05-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of 7-bromo-5-chloro-8-hydroxyquinoline (BCHQ) have been measured in the range 4000-400 and 4000-100 cm -1, respectively. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The geometry was optimised without any symmetry constrains using the DFT/B3LYP and HF methods with 6-31G** basis set. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from ab initio HF and density functional theory (DFT) gradient calculations employing the HF/6-31G** and B3LYP/6-31G** methods for the optimised geometry of the compound. The structural parameters and normal modes of vibration obtained from HF and DFT methods are in good agreement with the experimental data. Normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method.

  6. Ab Initio Study of Hot Carriers in the First Picosecond after Sunlight Absorption in Silicon

    NASA Astrophysics Data System (ADS)

    Bernardi, Marco; Vigil-Fowler, Derek; Lischner, Johannes; Neaton, Jeffrey B.; Louie, Steven G.

    2014-06-01

    Hot carrier thermalization is a major source of efficiency loss in solar cells. Because of the subpicosecond time scale and complex physics involved, a microscopic characterization of hot carriers is challenging even for the simplest materials. We develop and apply an ab initio approach based on density functional theory and many-body perturbation theory to investigate hot carriers in semiconductors. Our calculations include electron-electron and electron-phonon interactions, and require no experimental input other than the structure of the material. We apply our approach to study the relaxation time and mean free path of hot carriers in Si, and map the band and k dependence of these quantities. We demonstrate that a hot carrier distribution characteristic of Si under solar illumination thermalizes within 350 fs, in excellent agreement with pump-probe experiments. Our work sheds light on the subpicosecond time scale after sunlight absorption in Si, and constitutes a first step towards ab initio quantification of hot carrier dynamics in materials.

  7. Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.

    PubMed

    Wang, Linjun; Long, Run; Prezhdo, Oleg V

    2015-04-01

    Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics. PMID:25622188

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

    PubMed

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

    2016-08-23

    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. PMID:27503889

  9. Ab initio calculations of the optical properties of crystalline and liquid InSb

    SciTech Connect

    Sano, Haruyuki; Mizutani, Goro

    2015-11-15

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  10. Recent progress with large-scale ab initio calculations: the CONQUEST code

    NASA Astrophysics Data System (ADS)

    Bowler, D. R.; Choudhury, R.; Gillan, M. J.; Miyazaki, T.

    While the success of density functional theory (DFT) has led to its use in a wide variety of fields such as physics, chemistry, materials science and biochemistry, it has long been recognised that conventional methods are very inefficient for large complex systems, because the memory requirements scale as N 2 and the cpu requirements as N 3 (where N is the number of atoms). The principles necessary to develop methods with linear scaling of the cpu and memory requirements with system size (O(N ) methods) have been established for more than ten years, but only recently have practical codes showing this scaling for DFT started to appear. We report recent progress in the development of the Conquest code, which performs O(N ) DFT calculations on parallel computers, and has a demonstrated ability to handle systems of over 10000 atoms. The code can be run at different levels of precision, ranging from empirical tight-binding, through ab initio tight-binding, to full ab initio , and techniques for calculating ionic forces in a consistent way at all levels of precision will be presented. Illustrations are given of practical Conquest calculations in the strained Ge/Si(001) system.

  11. Ab initio quantum transport calculations using plane waves

    NASA Astrophysics Data System (ADS)

    Garcia-Lekue, A.; Vergniory, M. G.; Jiang, X. W.; Wang, L. W.

    2015-08-01

    We present an ab initio method to calculate elastic quantum transport at the nanoscale. The method is based on a combination of density functional theory using plane wave nonlocal pseudopotentials and the use of auxiliary periodic boundary conditions to obtain the scattering states. The method can be applied to any applied bias voltage and the charge density and potential profile can either be calculated self-consistently, or using an approximated self-consistent field (SCF) approach. Based on the scattering states one can straightforwardly calculate the transmission coefficients and the corresponding electronic current. The overall scheme allows us to obtain accurate and numerically stable solutions for the elastic transport, with a computational time similar to that of a ground state calculation. This method is particularly suitable for calculations of tunneling currents through vacuum, that some of the nonequilibrium Greens function (NEGF) approaches based on atomic basis sets might have difficulty to deal with. Several examples are provided using this method from electron tunneling, to molecular electronics, to electronic devices: (i) On a Au nanojunction, the tunneling current dependence on the electrode-electrode distance is investigated. (ii) The tunneling through field emission resonances (FERs) is studied via an accurate description of the surface vacuum states. (iii) Based on quantum transport calculations, we have designed a molecular conformational switch, which can turn on and off a molecular junction by applying a perpendicular electric field. (iv) Finally, we have used the method to simulate tunnel field-effect transistors (TFETs) based on two-dimensional transition-metal dichalcogenides (TMDCs), where we have studied the performance and scaling limits of such nanodevices and proposed atomic doping to enhance the transistor performance.

  12. Ab initio study of heterojunction discontinuities in the ZnO/Cu2O system

    NASA Astrophysics Data System (ADS)

    Zemzemi, M.; Alaya, S.; Ben Ayadi, Z.

    2014-06-01

    Solar cells based on transparent conductive oxides such as ZnO/Cu2O constitute a very advanced way to build high-performance cells. In this work, we are interested in the characterization of the interface through nanoscale modeling based on ab initio approaches (density functional theory, local density approximation, and pseudopotential). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconducting to another phase. We build a zinc oxide in the wurtzite structure along [0001] on which we place the copper oxide in the hexagonal (CdI2-type) structure. We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well the density functional theory. Our calculation of the band offset gives a value that corresponds to other experimental and theoretical values.

  13. Ab-Initio Shell Model with a Core

    SciTech Connect

    Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P

    2008-06-04

    We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.

  14. Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

    NASA Technical Reports Server (NTRS)

    Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

    2011-01-01

    Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

  15. Ab initio study of the effect of vacancies on the thermal conductivity

    NASA Astrophysics Data System (ADS)

    Protik, Nakib; Carrete, Jesus; Mingo, Natalio; Katcho, Nebil; Broido, David

    Point defects and vacancies in particular can have a profound impact on phonon thermal transport. Examples are seen in diamond and cubic boron arsenide where large C and As vacancy concentrations give much lower thermal conductivity than expected. Here, we calculate the phonon-vacancy scattering rates using an ab initioGreen's function approach, which treats the scattering to all orders in contrast to standard perturbation theory approaches. The lattice thermal conductivity, k, is calculated from first principles by solving the Boltzmann transport equation for phonons, with interatomic force constants determined using density functional theory. The reduction in k with vacancy defect density is assessed. The phonon-vacancy scattering can show significant differences using the Green's function method compared to what would be predicted from the perturbative Born approximation, consistent with previous findings for diamond.

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

    SciTech Connect

    Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.; Malozovsky, Y.; Zhao, G. L.; Bagayoko, D.

    2014-09-14

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

  17. Interactions of foreign interstitial and substitutional atoms in bcc iron from ab initio calculations

    NASA Astrophysics Data System (ADS)

    You, Y.; Yan, M. F.

    2013-05-01

    C and N atoms are the most frequent foreign interstitial atoms (FIAs), and often incorporated into the surface layers of steels to enhance their properties by thermochemical treatments. Al, Si, Ti, V, Cr, Mn, Co, Ni, Cu, Nb and Mo are the most common alloying elements in steels, also can be called foreign substitutional atoms (FSAs). The FIA and FSA interactions play an important role in the diffusion of C and N atoms, and the microstructures and mechanical properties of surface modified layers. Ab initio calculations based on the density functional theory are carried out to investigate FIA interactions with FSA in ferromagnetic bcc iron. The FIA-FSA interactions are analyzed systematically from five aspects, including interaction energies, density of states (DOS), bond populations, electron density difference maps and local magnetic moments.

  18. Classical Magnetic Dipole Moments for the Simulation of Vibrational Circular Dichroism by ab Initio Molecular Dynamics.

    PubMed

    Thomas, Martin; Kirchner, Barbara

    2016-02-01

    We present a new approach for calculating vibrational circular dichroism spectra by ab initio molecular dynamics. In the context of molecular dynamics, these spectra are given by the Fourier transform of the cross-correlation function of magnetic dipole moment and electric dipole moment. We obtain the magnetic dipole moment from the electric current density according to the classical definition. The electric current density is computed by solving a partial differential equation derived from the continuity equation and the condition that eddy currents should be absent. In combination with a radical Voronoi tessellation, this yields an individual magnetic dipole moment for each molecule in a bulk phase simulation. Using the chiral alcohol 2-butanol as an example, we show that experimental spectra are reproduced very well. Our approach requires knowing only the electron density in each simulation step, and it is not restricted to any particular electronic structure method. PMID:26771403

  19. {ital Ab initio} study of silicon in the R8 phase

    SciTech Connect

    Pfrommer, B.G.; Cote, M.; Louie, S.G.; Cohen, M.L.

    1997-09-01

    We present a detailed {ital ab initio} study of the electronic and structural properties of the recently discovered R8 phase of silicon. Within the framework of density-functional theory in the local-density approximation and using pseudopotentials with a plane-wave basis, we study the energetics of the R8 phase compared to the other tetrahedrally bonded diamond, {beta}-Sn, and BC8 phases. The bonding properties and the pressure dependence of the bond lengths of the BC8 and R8 phases are investigated. An analysis of the band structure reveals that R8 silicon could be a semimetal or semiconductor with a small, indirect band gap. Our computed density of states of R8 silicon shows a sharpening of the valence-band edge similar to the one observed for amorphous silicon. {copyright} {ital 1997} {ital The American Physical Society}

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

    SciTech Connect

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

    2006-01-27

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

  1. {ital Ab initio} full charge-density study of the atomic volume of {alpha}-phase Fr, Ra, Ac, Th, Pa, U, Np, and Pu

    SciTech Connect

    Vitos, L.; Kollar, J.; Skriver, H.L.

    1997-02-01

    We have used a full charge-density technique based on the linear muffin-tin orbitals method in first-principles calculations of the atomic volumes of the light actinides including Fr, Ra, and Ac in their low-temperature crystallographic phases. The good agreement between the theoretical and experimental values along the series support the picture of itinerant 5f electronic states in Th to Pu. The increased deviation between theory and experiment found in Np and Pu may be an indication of correlation effects not included in the local density approximation. {copyright} {ital 1997} {ital The American Physical Society}

  2. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  3. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  4. Quantitative Comparison of a New Ab Initio Micrometeor Ablation Model with an Observationally Verifiable Standard Model

    NASA Astrophysics Data System (ADS)

    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

  5. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    SciTech Connect

    Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung

    2014-09-01

    A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

  6. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Preston, D. L.

    2015-11-01

    The melting curve of osmium up to a pressure P of 500 GPa is obtained from an extensive suite of ab initio quantum molecular dynamics (QMD) simulations using the Z method. The ab initio P =0 melting point of Os is 3370 ±75 K; this range encompasses all of the available data in the literature and corroborates the conclusion of J. W. Arblaster [Platinum Metals Rev. 49, 166 (2005)], 10.1595/147106705X70264 that the melting temperature of pure Os is 3400 ±50 K and that the 3300 K typically quoted in the literature is the melting point of impure Os. The T =0 equation of state (EOS) of Os and the P dependence of the optimized c /a ratio for the hexagonal unit cell, both to pressures ˜900 GPa, are obtained in the ab initio approach as validation of its use. Although excellent agreement with the available experimental data (P ≲80 GPa) is found, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes the QMD data to higher pressures, in agreement with the more recent experimental EOS by Godwal et al. The theoretical melting curve of Os obtained earlier by Joshi et al. is shown to be inconsistent with our QMD results, and the possible reason for this discrepancy is suggested. Regularities in the melting curves of Os and five other third-row transition metals (Ta, W, Re, Pt, Au) could be used to estimate the currently unknown melting curves of Hf and Ir.

  7. On combining temperature and pressure effects on structural properties of crystals with standard ab initio techniques

    NASA Astrophysics Data System (ADS)

    Erba, A.

    2014-09-01

    A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values.

  8. On combining temperature and pressure effects on structural properties of crystals with standard ab initio techniques.

    PubMed

    Erba, A

    2014-09-28

    A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values. PMID:25273420

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

    SciTech Connect

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

    2015-06-24

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

  10. Ab initio study of nitrogen-multisubstituted neutral and positively charged C{sub 20} fullerene

    SciTech Connect

    Rani, Anita; Kumar, Ranjan

    2014-04-24

    Ab initio investigation of structural and electronic properties of Nitrogen doped fullerenes, obtained from C{sub 20} by replacing up to 10 C atoms with N atoms, are studied by means of first principals density functional theory calculations using numerical orbitals as basis sets. We have obtained the ground state structures for C{sub 20−n}N{sub n} for n=1-10. While substituting nitrogen atoms, we cannot substitute more than 9 nitrogen atoms. Nitrogen doping in C20 shows a significant change in density of states. For a better comparison with experimental measurements, we have also considered some positively charged ions and report the differences between properties of these ions and the corresponding neutral molecules.

  11. Ab initio study of He point defects in fcc Au-Ag alloys

    SciTech Connect

    Zhu, Zi Qiang; Yang, Li; Nie, JL; Peng, SM; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2013-04-25

    The relative stabilities of He defects in two fcc Au-Ag alloys (Au3Ag2 and AuAg) are investigated using ab initio method based on density functional theory. The results show that the stabilities of He defects in the two alloys mainly depend on the atomic arrangements of the nearest neighboring host metals. A He interstitial prefers to stay at a site with more Ag neighboring atoms, while the favorable substitutional site has more Au neighboring atoms in Au-Ag alloys. Moreover, the substitutional He defects are the most stable configurations in both the alloys, and the octahedral He interstitials are energetically more favorable than the tetrahedral interstitials. It is of interest to note that the properties of He defects slightly depend on the mass-density of Au-Ag alloys. The results also demonstrate that the relative stabilities of He defects are primarily attributed to the hybridization between metals d states and He p states.

  12. Atomic and Electronic Structures of C_60+BN Nanopeapods from ab initio Pseudopotential Calculations

    NASA Astrophysics Data System (ADS)

    Trave, Andrea; Ribeiro, Filipe; Louie, Steven G.; Cohen, Marvin L.

    2004-03-01

    Nanopeapods are structures of nanometric size consisting of an external carbon nanotube encapsulating a chain or complex array of fullerenes. Recent calculations and experiments have proven that nanopeapods can be obtained assembling fullerenes within boron nitride nanotubes, creating novel materials of possible interest for electronic transport applications. To improve the understanding of the properties of these composite systems, as compared to empty nanotubes and carbon nanopeapods, ab-initio total energy calculations have been performed within the pseudopotential Density Functional Theory in local density approximation. Results of these calculations on the energetics and geometrical deformations involved in the encapsulation will be presented, followed by a discussion of the consequences on the electronic structures of these systems, with particular focus on aspects relevant to electronic transport phenomena. This work is supported by NFS (Grant DMR00-87088) and DOE (Contract DE-AC03-76SF00098), using computational resources at NERSC and NPACI.

  13. Ab initio investigation of barium-scandium-oxygen coatings on tungsten for electron emitting cathodes

    NASA Astrophysics Data System (ADS)

    Vlahos, Vasilios; Booske, John H.; Morgan, Dane

    2010-02-01

    Microwave, x-ray, and radio-frequency radiation sources require a cathode emitting electrons into vacuum. Thermionic B-type dispenser cathodes consist of BaxOz coatings on tungsten (W), where the surface coatings lower the W work function and enhance electron emission. The new and promising class of scandate cathodes modifies the B-type surface through inclusion of Sc, and their superior emissive properties are also believed to stem from the formation of a low work function surface alloy. In order to better understand these cathode systems, density-functional theory (DFT)-based ab initio modeling is used to explore the stability and work function of BaxScyOz on W(001) monolayer-type surface structures. It is demonstrated how surface depolarization effects can be calculated easily using ab initio calculations and fitted to an analytic depolarization equation. This approach enables the rapid extraction of the complete depolarization curve (work function versus coverage relation) from relatively few DFT calculations, useful for understanding and characterizing the emitting properties of novel cathode materials. It is generally believed that the B-type cathode has some concentration of Ba-O dimers on the W surface, although their structure is not known. Calculations suggest that tilted Ba-O dimers are the stable dimer surface configuration and can explain the observed work function reduction corresponding to various dimer coverages. Tilted Ba-O dimers represent a new surface coating structure not previously proposed for the activated B-type cathode. The thermodynamically stable phase of Ba and O on the W surface was identified to be the Ba0.25O configuration, possessing a significantly lower Φ value than any of the Ba-O dimer configurations investigated. The identification of a more stable Ba0.25O phase implies that if Ba-O dimers cover the surface of emitting B-type cathodes, then a nonequilibrium steady state must dominate the emitting surface. The identification of

  14. Ab-initio investigation of spin-dependent transport properties in Fe-doped armchair graphyne nanoribbons

    NASA Astrophysics Data System (ADS)

    GolafroozShahri, S.; Roknabadi, M. R.; Shahtahmasebi, N.; Behdani, M.

    2016-12-01

    An ab-initio study on the spin-polarized transport properties of H-passivated Fe-doped graphyne nanoribbons is presented. All the calculations were based on density functional theory (DFT). Doping single magnetic atom on graphyne nanoribbons leads to metallicity which can significantly improve the conductivity. The currents are not degenerate for both up and down spin electrons and they are considerably spin-polarized. Therefore a relatively good spin-filtering can be expected. For configurations with geometric symmetry spin-rectifying is also observed. Therefore they can be applied as a dual spin-filter or a dual spin-diode in spintronic equipment.

  15. Interstitial Zn atoms do the trick in thermoelectric zinc antimonide, Zn4Sb3: a combined maximum entropy method X-ray electron density and ab initio electronic structure study.

    PubMed

    Cargnoni, Fausto; Nishibori, Eiji; Rabiller, Philippe; Bertini, Luca; Snyder, G Jeffrey; Christensen, Mogens; Gatti, Carlo; Iversen, Bo Brummerstadt

    2004-08-20

    The experimental electron density of the high-performance thermoelectric material Zn4Sb3 has been determined by maximum entropy (MEM) analysis of short-wavelength synchrotron powder diffraction data. These data are found to be more accurate than conventional single-crystal data due to the reduction of common systematic errors, such as absorption, extinction and anomalous scattering. Analysis of the MEM electron density directly reveals interstitial Zn atoms and a partially occupied main Zn site. Two types of Sb atoms are observed: a free spherical ion (Sb3-) and Sb2(4-) dimers. Analysis of the MEM electron density also reveals possible Sb disorder along the c axis. The disorder, defects and vacancies are all features that contribute to the drastic reduction of the thermal conductivity of the material. Topological analysis of the thermally smeared MEM density has been carried out. Starting with the X-ray structure ab initio computational methods have been used to deconvolute structural information from the space-time data averaging inherent to the XRD experiment. The analysis reveals how interstitial Zn atoms and vacancies affect the electronic structure and transport properties of beta-Zn4Sb3. The structure consists of an ideal A12Sb10 framework in which point defects are distributed. We propose that the material is a 0.184:0.420:0.396 mixture of A12Sb10, A11BCSb10 and A10BCDSb10 cells, in which A, B, C and D are the four Zn sites in the X-ray structure. Given the similar density of states (DOS) of the A12Sb10, A11BCSb10 and A10BCDSb10 cells, one may electronically model the defective stoichiometry of the real system either by n-doping the 12-Zn atom cell or by p-doping the two 13-Zn atom cells. This leads to similar calculated Seebeck coefficients for the A12Sb10, A11BCSb10 and A10BCDSb10 cells (115.0, 123.0 and 110.3 microV K(-1) at T=670 K). The model system is therefore a p-doped semiconductor as found experimentally. The effect is dramatic if these cells are

  16. Three-cluster dynamics within an ab initio framework

    DOE PAGESBeta

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

    2013-09-26

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

  17. Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe2S3 : Combined ab initio and density matrix renormalization group study

    NASA Astrophysics Data System (ADS)

    Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; Arita, Ryotaro; Moreo, Adriana; Dagotto, Elbio

    2016-08-01

    The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe2S3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015), 10.1038/nmat4351] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe2S3 . The model is studied with the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only one Wannier orbital receiving the hole carriers while the other remains half-filled. These results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.

  18. Assessing the elastic properties and ductility of Fe-Cr-Al alloys from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Nurmi, E.; Wang, G.; Kokko, K.; Vitos, L.

    2016-01-01

    Fe-Al is one of the best corrosion resistant alloys at high temperatures. The flip side of Al addition to Fe is the deterioration of the mechanical properties. This problem can be solved by adding a suitable amount of third alloying component. In the present work, we use ab initio calculations based on density functional theory to study the elastic properties of Fe?Cr?Al? alloys for Al and Cr contents up to 20 at.%. We assess the ductility as a function of chemistry by making use of the semi-empirical correlations between the elastic parameters and mechanical properties. In particular, we derive the bulk modulus to shear modulus ratio and the Cauchy pressure and monitor their trends in terms of chemical composition. The present findings are contrasted with the previously established oxidation resistance of Fe-Cr-Al alloys.

  19. The constrained space orbital variation analysis for periodic ab initio calculations

    SciTech Connect

    Cruz Hernandez, N.; Zicovich-Wilson, Claudio Marcelo; Fdez Sanz, Javier

    2006-05-21

    The constrained space orbital variation (CSOV) method for the analysis of the interaction energy has been implemented in the periodic ab initio CRYSTAL03 code. The method allows for the partition of the energy of two interacting chemical entities, represented in turn by periodic models, into contributions which account for electrostatic effects, mutual polarization and charge transfer. The implementation permits one to carry out the analysis both at the Hartree-Fock and density functional theory levels, where in the latter the most popular exchange-correlation functionals can be used. As an illustrating example, the analysis of the interaction between CO and the MgO (001) surface has been considered. As expected by the almost fully ionic character of the support, our periodic CSOV results, in general agree with those previously obtained using the embedded cluster approach, showing the reliability of the present implementation.

  20. C and Si in the core - an experimental and ab initio approach

    NASA Astrophysics Data System (ADS)

    Vocadlo, L.; Alfe, D.; Wood, I. G.; Dobson, D.; Price, G. D.

    2003-04-01

    The fact that the core is largely composed of iron (Fe) was firmly established as a result of Birch's analysis of materials-density/sound-wave velocity systematics. Today we believe that the outer core is about 6 to 10% less dense than pure liquid Fe, while the solid inner core is a few percent less dense than pure Fe. From cosmochemical and other considerations, it is likely that the alloying elements in the core might include S, O, Si, H and C. It is also possible that the core contains minor amounts of other elements, such as Ni and K. Here we present our results from both experiments and ab initio computer calculations on Fe alloyed with C and Si at Earth's core conditions. Neutron diffraction experiments indicate that Fe3C will be non-magnetic at core conditions; ab initio calculations on the non-magnetic phase of Fe3C suggest that, at core P and T, its density and incompressibity are inconsistent with the observations from PREM. Calcuations on FeSi show that it adopts the CsCl structure at core pressures; this result has recently been validated by our high pressure experiments in which we were able to synthesise CsCl-FeSi. This is an extemely interesting result since CsCl-FeSi is iso-structural with bcc-Fe, and experiments have recently shown (Lin et al., 2002) that Si stabilises bcc-Fe with respect to hcp-Fe up to 80 GPa. Ab initio molecular dynamics simulations have been used to calculate the chemical potentials of Fe alloys. In order to match the density jump at the inner core boundary, we predict an inner core with 8 mol% S/Si and 0.3 mol% O, and an outer core containing 10 mol % S/Si and 8 mol % O. Finally we present preliminary results for the calculated high P/T elastic constants of iron alloys as a function of composition.

  1. Ab initio H2O in realistic hydrophilic confinement.

    PubMed

    Allolio, Christoph; Klameth, Felix; Vogel, Michael; Sebastiani, Daniel

    2014-12-15

    A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized. PMID:25208765

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

    SciTech Connect

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

    2005-11-15

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

  3. Ab initio non-relativistic spin dynamics

    SciTech Connect

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

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  4. Ab initio non-relativistic spin dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  5. Ab initio electronic structure study for TTF-TCNQ under uniaxial compression

    NASA Astrophysics Data System (ADS)

    Ishibashi, Shoji; Hashimoto, Tamotsu; Kohyama, Masanori; Terakura, Kiyoyuki

    2004-04-01

    We have investigated the electronic structure of TTF-TCNQ under uniaxial compression with ab initio plane-wave pseudopotential calculations within the local-density approximation and generalized gradient approximation. Depending on the compression direction, the constituent molecules are deformed in different ways. Along with these structural deformations, quasi-one-dimensional Fermi surfaces show dramatic changes in their shapes and sizes.

  6. XMVB: a program for ab initio nonorthogonal valence bond computations.

    PubMed

    Song, Lingchun; Mo, Yirong; Zhang, Qianer; Wu, Wei

    2005-04-15

    An ab initio nonorthogonal valence bond program, called XMVB, is described in this article. The XMVB package uses Heitler-London-Slater-Pauling (HLSP) functions as state functions, and calculations can be performed with either all independent state functions for a molecule or preferably a few selected important state functions. Both our proposed paired-permanent-determinant approach and conventional Slater determinant expansion algorithm are implemented for the evaluation of the Hamiltonian and overlap matrix elements among VB functions. XMVB contains the capabilities of valence bond self-consistent field (VBSCF), breathing orbital valence bond (BOVB), and valence bond configuration interaction (VBCI) computations. The VB orbitals, used to construct VB functions, can be defined flexibly in the calculations depending on particular applications and focused problems, and they may be strictly localized, delocalized, or bonded-distorted (semidelocalized). The parallel version of XMVB based on MPI (Message Passing Interface) is also available. PMID:15704237

  7. Ab initio electronic and optical spectra of free-base porphyrins: The role of electronic correlation.

    PubMed

    Palummo, Maurizia; Hogan, Conor; Sottile, Francesco; Bagalá, Paolo; Rubio, Angel

    2009-08-28

    We present a theoretical investigation of electronic and optical properties of free-base porphyrins based on density functional theory and many-body perturbation theory. The electronic levels of free-base porphine (H(2)P) and its phenyl derivative, free-base tetraphenylporphyrin (H(2)TPP) are calculated using the ab initio GW approximation for the self-energy. The approach is found to yield results that compare favorably with the available photoemission spectra. The excitonic nature of the optical peaks is revealed by solving the Bethe-Salpeter equation, which provides an accurate description of the experimental absorption spectra. The lowest triplet transition energies are in good agreement with the measured values. PMID:19725603

  8. High-Level Ab-Initio Calculation on the NiO₂ System

    SciTech Connect

    Song, Jie; Apra, Edoardo; Khait, Yuri; Hoffmann, Mark R.; Kowalski, Karol

    2006-09-20

    Several high-level ab-initio methods were employed in studies of the narrow singlet-triplet separation of the cyclic dorm of the nickel dioxide (NiO?). It is shown that the complete visions of the locally renormalized couples cluster method with singles, doubles, and noniterative triples (LR-CCSD(T)) approach, in contrast to the standard CCSD(T) method, provides results in concert with predictions of the density functional theory (DFT) and internally contracted multi-reference configuration interaction method (IIC-MCRCI), which favor the triplet state to be the lowest one. Relevant discussion of several aspects related to underlying CCSD calculations, indicate that the dominate roll of singly excited amplitudes violates the paradigm about the leading role to two-body effect in description of the correlation energy. These results are compared with the results of the second order Generalized Van Vleck Perturbation Theory (GVVPPT2) approach which supports the CCSD(T) predictions.

  9. Determination of absolute configuration using ab initio calculation of optical rotation.

    PubMed

    Stephens, P J; Devlin, F J; Cheeseman, J R; Frisch, M J; Bortolini, O; Besse, P

    2003-01-01

    Ab initio Density Functional Theory (DFT) calculations of transparent spectral region, discrete frequency specific rotations were used to assign the absolute configurations (ACs) of: 1, 2H-naphtho[1,8-bc]thiophene 1-oxide; 2, m-F-phenyl glycidic acid methyl ester; 3, o-Br-phenyl glycidic acid methyl ester; 4, p-CH(3)-phenyl glycidic acid methyl ester; 5, 2-(1-hydroxyethyl)-chromen-4-one; and 6, 6-Br-2-(1-hydroxyethyl)-chromen-4-one. The ACs of 5 and 6 were previously determined via X-ray crystallography to be: 5, R(-)/S(+); 6, R(+)/S(-). The ACs obtained using [alpha](D) are the same for both 5 and 6: R(+)/S(-). We conclude that the previously reported AC of 5 is incorrect. PMID:12884375

  10. Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide

    SciTech Connect

    Gao, Fei; Du, Jincheng; Bylaska, Eric J.; Posselt, Matthias; Weber, William J.

    2007-05-28

    The thermal stability of an antisite pair in 3C-SiC is studied using ab initio molecular dynamics within the framework of density functional theory. The lifetime of the antisite pair configuration is calculated for temperatures between 1800 and 2250 K, and the effective activation energy for antisite pair recombination is determined to be 2.52 eV. The recombination energy path and static energy barrier are also calculated using the nudged elastic band method, along with the dimer method to accurately locate the transition states. The consistency of the results suggests that the antisite pair cannot be correlated with the DI photoluminescence center, as proposed by previously theoretical interpretations. An extended exchange mechanism is found for the antisite pair recombination, and this may be a dominant mechanism for antisite pair recombination and diffusion of impurities in compound semiconductors.

  11. Ab initio determination of effective electron-phonon coupling factor in copper

    NASA Astrophysics Data System (ADS)

    Ji, Pengfei; Zhang, Yuwen

    2016-04-01

    The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.

  12. Ab initio approach to model x-ray diffraction in warm dense matter.

    PubMed

    Vorberger, J; Gericke, D O

    2015-03-01

    It is demonstrated how the static electron-electron structure factor in warm dense matter can be obtained from density functional theory in combination with quantum Monte Carlo data. In contrast to theories assuming well-separated bound and free states, this ab initio approach yields also valid results for systems close to the Mott transition (pressure ionization), where bound states are strongly modified and merge with the continuum. The approach is applied to x-ray Thomson scattering and compared to predictions of the Chihara formula whereby we use the ion-ion and electron-ion structure from the same simulations. The results show significant deviations of the screening cloud from the often applied Debye-like form. PMID:25871229

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. Ab initio calculations on magnetism induced by composite defects in magnesium oxide

    SciTech Connect

    Zhang, Yao-Fang; Feng, Min; Shao, Bin; Lu, Yuan; Zuo, Xu; Liu, Hong

    2014-05-07

    The local magnetic state induced by the composite defects, composed of an oxygen vacancy and a nitrogen substituting oxygen, in magnesium oxide has been studied by using ab initio calculation based on density functional theory. The calculated results show that local magnetic moment can be induced by the composite defects around the oxygen vacancy, when the exchange split of the oxygen vacancy is enhanced either by the hybridization between the N-p and nearest neighbor O-p orbitals or by applying on-site Coulomb repulsion (U) and exchange interaction (J). We show that the magnetic state induced by the composite defect is energetically more stable than the non-magnetic state. In addition, we show that the U and J applied on the p-orbitals of N and O atoms may significantly impact the calculated magnetic state of the composite defect, resulting in magnetic state for a configuration that is non-magnetic by generalized gradient approximation.

  15. Ab initio calculations of vacancy interactions with solute atoms in bcc Fe

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2005-01-01

    Solute Cu plays a major role in the embrittlement of reactor pressure vessel (RPV) steels under radiation. In RPV steels and dilute FeCu alloys, the tomographic atom probe has revealed the formation of Cu atmospheres under neutron flux. More recently the role of other solutes such as Ni, Mn and Si which are also within the atmospheres has been put forward. It is thus very important to characterise the interactions of these solutes with radiation-induced point defects in order to understand the elementary mechanisms behind the formation of these atmospheres. We have investigated by ab initio calculations based on the density functional theory the interactions of point defects in dilute FeX alloys (X = Cu, Mn, Ni or Si). The structure of X-vacancy complexes has been determined, as well as their binding energies. Their relative stability is discussed and compared to experimental results obtained with model alloys.

  16. Detection of Nucleic Acids with Graphene Nanopores: Ab Initio Characterization of a Novel Sequencing Device

    NASA Astrophysics Data System (ADS)

    Nelson, Tammie; Zhang, Bo; Prezhdo, Oleg

    2010-03-01

    We report an ab initio study of the interaction of two nucleobases, cytosine and adenine, with a novel graphene nanopore device for detecting the base sequence of a single-stranded nucleic acid (ssDNA or RNA). The nucleobases were inserted into a pore in a graphene nanoribbon, and the electrical current and conductance spectra were calculated as functions of voltage applied across the nanoribbon. The conductance spectra and charge densities were analyzed in the presence of each nucleobase in the graphene nanopore. The results indicate that, due to significant differences in the conductance spectra, the proposed device has adequate sensitivity to discriminate between different nucleotides. Moreover, we show that the nucleotide conductance spectra is not affected by its orientation inside the graphene nanopore. The proposed technique may be extremely useful for real applications in developing ultrafast, low cost DNA sequencing methods.

  17. Ab initio study of intrinsic, H and He point defects in hcp-Er

    SciTech Connect

    Yang, Li; Peng, SM; Long, XG; Gao, Fei; Heinisch, Howard L.; Kurtz, Richard J.; Zu, Xiaotao T.

    2010-03-01

    Ab initio calculations based on density functional theory have been performed to determine the properties of self-interstitial atoms (SIAs), vacancies, and single H and He atoms in hcp-Er. The results show that the most stable configuration for an SIA is a basal octahedral (BO) configuration, while the octahedral (O), basal split (BS) and crowdion (C) interstitial configurations are less stable, followed by the split <0001> dumbbell and tetrahedral configurations. For both H and He defects, the formation energy of an interstitial atom is less than that of a substitutional atom in hcp-Er. Furthermore, the tetrahedral interstitial position is more stable than an octahedral position for both He and H interstitials. The hybridization of the He and H defects with Er atoms has been used to explain the relative stabilities of these defects in hcp-Er.

  18. Boron and nitrogen impurities in SiC nanoribbons: an ab initio investigation

    NASA Astrophysics Data System (ADS)

    Costa, C. D.; Morbec, J. M.

    2011-05-01

    Using ab initio calculations based on density-functional theory we have performed a theoretical investigation of substitutional boron and nitrogen impurities in silicon carbide (SiC) nanoribbons. We have considered hydrogen terminated SiC ribbons with zigzag and armchair edges. In both systems we verify that the boron and nitrogen atoms energetically prefer to be localized at the edges of the nanoribbons. However, while boron preferentially substitutes a silicon atom, nitrogen prefers to occupy a carbon site. In addition, our electronic-structure calculations indicate that (i) substitutional boron and nitrogen impurities do not affect the semiconducting character of the armchair SiC nanoribbons, and (ii) the half-metallic behavior of the zigzag nanoribbons is maintained in the presence of substitutional boron impurities. In contrast, nitrogen atoms occupying edge carbon sites transform half-metallic zigzag nanoribbons into metallic systems.

  19. Boron and nitrogen impurities in SiC nanoribbons: an ab initio investigation.

    PubMed

    Costa, C D; Morbec, J M

    2011-05-25

    Using ab initio calculations based on density-functional theory we have performed a theoretical investigation of substitutional boron and nitrogen impurities in silicon carbide (SiC) nanoribbons. We have considered hydrogen terminated SiC ribbons with zigzag and armchair edges. In both systems we verify that the boron and nitrogen atoms energetically prefer to be localized at the edges of the nanoribbons. However, while boron preferentially substitutes a silicon atom, nitrogen prefers to occupy a carbon site. In addition, our electronic-structure calculations indicate that (i) substitutional boron and nitrogen impurities do not affect the semiconducting character of the armchair SiC nanoribbons, and (ii) the half-metallic behavior of the zigzag nanoribbons is maintained in the presence of substitutional boron impurities. In contrast, nitrogen atoms occupying edge carbon sites transform half-metallic zigzag nanoribbons into metallic systems. PMID:21540516

  20. Ab Initio Dynamics of AN Electron Interacting with a Lattice Defect

    NASA Astrophysics Data System (ADS)

    Ivanov, Vsevolod; Bernardi, Marco

    We study the scattering process of a charge carrier with a defect in a range of bulk and 2D materials. The scattering potential is obtained using density functional theory, the carrier is represented by a gaussian wavepacket, and the dynamics is carried out with a split-operator technique. Our parallel code can model the electron-defect scattering processes in real space and time, with an electron wavepacket of realistic size (100 - 1000 unit cells) and an accuracy typical of ab initio calculations. We apply our approach to model a carrier scattering with a vacancy in silicon and an impurity in monolayer MoS2, obtaining angular dependent scattering cross sections and resonant states.

  1. Ab initio calculation of ionization potential and electron affinity in solid-state organic semiconductors

    NASA Astrophysics Data System (ADS)

    Kang, Youngho; Jeon, Sang Ho; Cho, Youngmi; Han, Seungwu

    2016-01-01

    We investigate the vertical ionization potential (IP) and electron affinity (EA) of organic semiconductors in the solid state that govern the optoelectrical property of organic devices using a fully ab initio way. The present method combines the density functional theory and many-body perturbation theory based on G W approximations. To demonstrate the accuracy of this approach, we carry out calculations on several prototypical organic molecules. Since IP and EA depend on the molecular orientation at the surface, the molecular geometry of the surface is explicitly considered through the slab model. The computed IP and EA are in reasonable and consistent agreements with spectroscopic data on organic surfaces with various molecular arrangements. However, the transport gaps are slightly underestimated in calculations, which can be explained by different screening effects between surface and bulk regions.

  2. Electronic states of lithium passivated germanium nanowires: An ab-initio study

    SciTech Connect

    Trejo, A.; Carvajal, E.; Vázquez-Medina, R.; Cruz-Irisson, M.

    2014-05-15

    A study of the electronic and structural properties of germanium nanowires (GeNWs) was performed using the ab-initio Density Functional Theory within the generalized gradient approximation where electron-ion interactions are described by ultrasoft pseudopotentials. To study the effects of the lithium in the surface of the GeNWs we compare the electronic band structures of Hydrogen passivated GeNWs with those of partial and totally Li passivated GeNWs. The nanowires were constructed in the [001], [111] and [110] directions, using the supercell model to create different wire diameters. The results show that in the case of partial Li passivation there are localized orbitals near the valence band maximum, which would create a p-doped-kind of state. The total Li passivation created metallic states for all the wires.

  3. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics

    SciTech Connect

    Nakamura, Makoto Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki

    2014-05-14

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.

  4. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  5. A combined crystallographic analysis and ab initio calculations to interpret the reactivity of functionalized hexavanadates and their inhibitor potency toward Na(+)/K(+)-ATPase.

    PubMed

    Xu, Xiao; Bošnjaković-Pavlović, Nada; Čolović, Mirjana B; Krstić, Danijela Z; Vasić, Vesna M; Gillet, Jean-Michel; Wu, Pingfan; Wei, Yongge; Spasojević-de Biré, Anne

    2016-08-01

    In vitro influence of five synthesized functionalized hexavanadates (V6) on commercial porcine cerebral cortex Na(+)/K(+)-ATPase activity has been studied. Dose dependent Na(+)/K(+)-ATPase inhibition was obtained for all investigated compounds. Calculated half maximal inhibitory concentration IC50 values, in mol/L, for Na(+)/K(+)-ATPase were 7.6×10(-5), 1.8×10(-5), 2.9×10(-5), 5.5×10(-5) for functionalized hexavanadates (V6) with tetrabutylammonium (TBA) [V6-CH3][TBA]2, [V6-NO2][TBA]2, [V6-OH][TBA]2 and [V6-C3][TBA]2 respectively. [V6-OH][Na]2 inhibited Na(+)/K(+)-ATPase activity up to 30% at maximal investigated concentration 1×10(-3)mol/L. This reactivity has been interpreted using a study of the non-covalent interactions of functionalized hexavanadate hybrids through Cambridge Structural Database (CSD) analysis. Bibliographic searching has led to 18 different structures and 99 contacts. We have observed that C-H⋯O contacts consolidate the structures. We have also performed density functional theory (DFT) calculations and have determined electrostatic potential values at the molecular surface on a series of functionalized V6. These results enlightened their chemical reactivity and their potential biological applications such as the inhibition of the ATPase. PMID:27235271

  6. Comparative study of tight-binding and ab initio electronic structure calculations focused on magnetic anisotropy in ordered CoPt alloy

    NASA Astrophysics Data System (ADS)

    Zemen, J.; Mašek, J.; Kučera, J.; Mol, J. A.; Motloch, P.; Jungwirth, T.

    2014-04-01

    An empirical multiorbital (spd) tight binding (TB) model including magnetism and spin-orbit coupling is applied to calculations of magnetic anisotropy energy (MAE) in CoPt L10 structure. A realistic Slater-Koster parametrisation for single-element transition metals is adapted for the ordered binary alloy. Spin magnetic moment and density of states are calculated using a full-potential linearised augmented plane-wave (LAPW) ab initio method and our TB code with different variants of the interatomic parameters. Detailed mutual comparison of this data allows for determination of a subset of the compound TB parameters tuning of which improves the agreement of the TB and LAPW results. MAE calculated as a function of band filling using the refined parameters is in broad agreement with ab initio data for all valence states and in quantitative agreement with ab initio and experimental data for the natural band filling. Our work provides a practical basis for further studies of relativistic magnetotransport anisotropies by means of local Green's function formalism which is directly compatible with our TB approach.

  7. Intrinsic acidity of aluminum, chromium(III) and iron(III) {mu}{sub 3}-hydroxo functional groups from ab initio electronic structure calculations

    SciTech Connect

    Rustad, J.R.; Dixon, D.A.; Felmy, A.R.

    2000-05-01

    Density functional calculations are performed on M{sub 3}(OH){sub 7}(H{sub 2}O){sub 6}{sup 2+} and M{sub 3}O(OH){sub 6}(H{sub 2}O){sub 6}{sup +} clusters for M {double_bond} Al, Cr(III), and Fe(III), allowing determination of the relative acidities of the {mu}{sub 3}-hydroxo and aquo functional groups. Contrary to previous predictions and rationalizations, {double_bond}Fe{sub 3}OH and {double_bond}Al{sub 3}OH groups have nearly the same intrinsic acidity, while {double_bond}Cr{sub 3}OH groups are significantly more acidic. The gas-phase acidity of the Fe{sub 3}OH site is in good agreement with the value predicted by the molecular mechanics model previously used to estimate the relative acidities of surface sites on iron oxides. Acidities of aquo functional groups were also computed for Al and Cr. The {double_bond}AlOH{sub 2} site is more acidic than the {double_bond}Al{sub 3}OH site, whereas the {double_bond}Cr{sub 3}OH site is more acidic than the {double_bond}CrOH{sub 2} site. These findings predict that the surface charging behavior of chromium oxides/oxyhydroxides should be distinguishable from their Fe, Al counterparts. The calculations also provide insight into why the lepidocrocite/boehmite polymorph is not observed for CrOOH.

  8. Ab initio calculation of thermodynamic properties of silicon

    NASA Astrophysics Data System (ADS)

    Wei, Siqing; Li, Changlin; Chou, M. Y.

    1994-11-01

    We present a fully ab initio calculation of the thermodynamic properties for silicon within the quasiharmonic approximation, making use of volume-dependent phonon frequencies obtained from pseudopotential local-density calculations. The temperature dependence of the thermal-expansion coefficient, specific heat (at constant volume), and other related quantities are studied. We confirm that the thermal-expansion coefficient behaves differently in three temperature regions: positive for temperature below 15 K, negative between 15 and 125 K, and positive again above 125 K. This finding agrees with experiment. The abnormal (negative) thermal-expansion coefficient at low temperatures is explained through a detailed study of mode Grüneisen parameters. Both specific-heat and thermal-expansion-coefficient values calculated are in excellent agreement with experiment up to a few hundred kelvin.

  9. Ab initio correlated calculations of rare-gas dimer quadrupoles

    NASA Astrophysics Data System (ADS)

    Donchev, Alexander G.

    2007-10-01

    This paper reports ab initio calculations of rare gas ( RG=Kr , Ar, Ne, and He) dimer quadrupoles at the second order of Møller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG2 quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG2 quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG3 quadrupoles is discussed.

  10. Ab initio determination of light hadron masses.

    PubMed

    Dürr, S; Fodor, Z; Frison, J; Hoelbling, C; Hoffmann, R; Katz, S D; Krieg, S; Kurth, T; Lellouch, L; Lippert, T; Szabo, K K; Vulvert, G

    2008-11-21

    More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties. PMID:19023076

  11. Discovering chemistry with an ab initio nanoreactor

    DOE PAGESBeta

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

    2014-11-02

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

  12. Ab initio molar volumes and Gaussian radii.

    PubMed

    Parsons, Drew F; Ninham, Barry W

    2009-02-12

    Ab initio molar volumes are calculated and used to derive radii for ions and neutral molecules using a spatially diffuse model of the electron distribution with Gaussian spread. The Gaussian radii obtained can be used for computation of nonelectrostatic ion-ion dispersion forces that underlie Hofmeister specific ion effects. Equivalent hard-sphere radii are also derived, and these are in reasonable agreement with crystalline ionic radii. The Born electrostatic self-energy is derived for a Gaussian model of the electronic charge distribution. It is shown that the ionic volumes used in electrostatic calculations of strongly hydrated cosmotropic ions ought best to include the first hydration shell. Ionic volumes for weakly hydrated chaotropic metal cations should exclude electron overlap (in electrostatic calculations). Spherical radii are calculated as well as nonisotropic ellipsoidal radii for nonspherical ions, via their nonisotropic static polarizability tensors. PMID:19140766

  13. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  14. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

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

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881

  15. Discovering chemistry with an ab initio nanoreactor.

    PubMed

    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. PMID:25411881

  16. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    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.

  17. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

    Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

  18. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

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

    2014-11-02

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

  19. Ab Initio Calculation of the Hoyle State

    SciTech Connect

    Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.

    2011-05-13

    The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.

  20. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  1. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-01

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

  2. Ab initio calculations of the equations of state for hydrogen, helium, and water and the relevance to the giant planets

    NASA Astrophysics Data System (ADS)

    French, Martin

    2010-11-01

    Since the interior structure of giant planets inside or outside our solar system cannot be probed directly by experiments, planetary models have been developed to gain further insight. Such models require accurate equations of state (EOS) for the major components (H, He, and heavier compounds like water) up to extreme thermodynamic conditions (pressures of several ten megabars and temperatures of more than ten thousand degrees Kelvin) [1]. Ab initio methods that combine finite temperature density functional theory (FT-DFT) for the electrons with classical molecular dynamics (MD) for the ions have proven to be a powerful tool to calculate such accurate EOS data. In addition, the FT-DFT-MD also generates structural information, transport and optical properties and, most important, information on phase diagrams and demixing regions. Based on our recently calculated ab initio data for H, He, and water, we derive interior models of Saturn and Jupiter and discuss the role of H-He demixing [2] and of the plasma phase transition in hydrogen on the planetary interiors. We also present new models for Uranus and Neptune which offer conditions to allow the formation of the exotic superionic phase of water [3]. The ab initio data can also be applied in planetary evolution scenarios and dynamo simulations of solar and extrasolar planets.[4pt] [1] J. J. Fortney, N. Nettelmann, Space Sci. Rev. 152, 423 (2010)[0pt] [2] W. Lorenzen, B. Holst, R. Redmer, Phys. Rev. Lett. 102, 115701 (2009)[0pt] [3] M. French, T. R. Mattsson, N. Nettelmann, R. Redmer, Phys. Rev. B 79, 054107 (2009)

  3. 'Structure, Dynamics and Vibrational Spectrum of Supercritical CO2/H2O Mixtures from Ab Initio Molecular Dynamics as a Function of Water Cluster Formation

    SciTech Connect

    Glezakou, Vassiliki Alexandra; Rousseau, Roger J.; Dang, Liem X.; McGrail, B. Peter

    2010-08-21

    We have studied the effect of water in the supercritical phase of CO2 as a function of water self-association using DFT-based molecular dynamics simulations. The dependence of the intermolecular and intramolecular structure and dynamic properties upon water concentration in the supercritical CO2/H2O phase at a density of 0.81g/cm3 and temperature of 318.15K is investigated in detail and compared to previous studies of the pure sc-CO2 system and Monte-Carlo simulations of water in sc-CO2 phase. Analysis of radial and orientational distribution functions of the intermolecular interactions shows that the presence of water molecules does not disturb the previously established distorted T-shaped orientation of CO2 molecules, though there is strong evidence of perturbation of the second shell structure which enhances the preference for the slipped parallel orientation in this region. There is also evidence of short-lived hydrogen bonds between CO2 and water molecules. For higher water concentrations, water clustering is observed, consistent with the expected phase separation under these conditions of temperature and pressure. Finally, the water-water and water-CO2 interactions are discussed and analyzed in terms of the water self-association and thermodynamic quantities derived from the corresponding radial distribution functions. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  4. Ab initio methods for nuclear properties - a computational physics approach

    NASA Astrophysics Data System (ADS)

    Maris, Pieter

    2011-04-01

    A microscopic theory for the structure and reactions of light nuclei poses formidable challenges for high-performance computing. Several ab-initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab-initio no-core full configuration (NCFC) approach is based on basis space expansion methods and uses Slater determinants of single-nucleon basis functions to express the nuclear wave function. In this approach, the quantum many-particle problem becomes a large sparse matrix eigenvalue problem. The eigenvalues of this matrix give us the binding energies, and the corresponding eigenvectors the nuclear wave functions. These wave functions can be employed to evaluate experimental quantities. In order to reach numerical convergence for fundamental problems of interest, the matrix dimension often exceeds 1 billion, and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. I discuss different strategies for distributing and solving this large sparse matrix on current multicore computer architectures, including methods to deal with with memory bottleneck. Several of these strategies have been implemented in the code MFDn, which is a parallel fortran code for nuclear structure calculations. I will show scaling behavior and compare the performance of the pure MPI version with the hybrid MPI/OpenMP code on Cray XT4 and XT5 platforms. For large core counts (typically 5,000 and above), the hybrid version is more efficient than pure MPI. With this code, we have been able to predict properties of the unstable nucleus 14F, which have since been confirmed by experiments. I will also give an overview of other recent results for nuclei in the A = 6 to 16 range with 2- and 3-body interactions. Supported in part by US DOE Grant DE-FC02-09ER41582.

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

    SciTech Connect

    Hoy, Erik P.; Mazziotti, David A.

    2015-08-14

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

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

    PubMed

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

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

  7. Reaction barrier heights for cycloreversion of heterocyclic rings: An Achilles' heel for DFT and standard ab initio procedures

    NASA Astrophysics Data System (ADS)

    Yu, Li-Juan; Sarrami, Farzaneh; O'Reilly, Robert J.; Karton, Amir

    2015-09-01

    We introduce a database of 20 accurate cycloreversion barrier heights of 5-membered heterocyclic rings (to be known as the CRBH20 database). In these reactions, dioxazole and oxathiazole rings are fragmented to form isocyanates, isothiocyanates, and carbonyls. The reference reaction barrier heights are obtained by means of the high-level, ab initio W1-F12 and W1w thermochemical protocols. We evaluate the performance of 65 contemporary density functional theory (DFT) and double-hybrid DFT (DHDFT) procedures. The CRBH20 database represents an extremely challenging test for these methods. Most of the conventional DFT functionals (74%) result in root-mean-square deviations (RMSDs) between 10 and 81 kJ mol-1. The rest of the DFT functionals attain RMSDs = 5 - 10 kJ mol-1. Of the 12 tested DHDFT functionals, only five result in RMSDs < 10 kJ mol-1. The CRBH20 dataset also proves to be a surprisingly challenging target for composite and standard ab initio procedures.

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

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te)(2) dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. PMID:21937783

  9. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  10. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations.

    PubMed

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green's function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states. PMID:26671378

  11. Ab initio quantum dynamics using coupled-cluster.

    PubMed

    Kvaal, Simen

    2012-05-21

    The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given. PMID:22612082

  12. Polysiloxanes: ab initio force field and structural, conformational and thermophysical properties

    NASA Astrophysics Data System (ADS)

    Sun, Huai; Rigby, David

    1997-07-01

    Various levels of ab initio calculation have been performed to determine the optimum strategy for parameterization of the valence parameters of a CFF-type force field for siloxanes and polysiloxanes. Electrostatic nonbond parameters have been determined using scaled electrostatic potential (ESP) charges adjusted for known systematic differences between ab initio and experimental data, while van der Waals nonbond parameters have been determined using a classical approach involving fitting to experimental liquid density and cohesive energy density data measured at atmospheric pressure and a single temperature for a set of four small molecules. Simulations have been performed on molecular crystals, liquids and isolated molecules, yielding results which agree favorably with available experimental data. Properties calculated include unit cell parameters and crystal densities, liquid densities from 303-473 K and 0-1800 bar, dependence of oligomer density and solubility parameters on chain length and temperature, gas-phase geometries and vibrational frequencies, and gas and liquid-phase conformational behavior.

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

    NASA Astrophysics Data System (ADS)

    Trevisanutto, Paolo E.; Vignale, Giovanni

    2016-05-01

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

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

    PubMed

    Trevisanutto, Paolo E; Vignale, Giovanni

    2016-05-28

    Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is "native" to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory - density functional theory, GW approximation and Bethe-Salpeter equation - are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields. PMID:27250294

  15. Ab initio studies of low-lying 3Sigma(-), 3Pi, and 5Sigma(-) states of NH. I - Potential curves and dipole moment functions

    NASA Technical Reports Server (NTRS)

    Goldfield, Evelyn M.; Kirby, Kate P.

    1987-01-01

    Configuration interaction wave functions, potential energy curves, and dipole moment functions have been calculated for the four lowest 3Sigma(-) and the three lowest 3Pi states and 5Sigma(-) states of NH. The electronic wave functions were constructed to give a balanced description of valence-Rydberg interactions. Two repulsive states have been identified as important photodissociation pathways. Spectroscopic constants are presented for the bound states, and results are compared to other theoretical and experimental work. The possible predissociation of the A 3Pi state by the 1 5Sigma(-) state is discussed.

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

    ERIC Educational Resources Information Center

    Gesell, Laurence E.

    1995-01-01

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

  17. Phonocatalysis. An ab initio simulation experiment

    NASA Astrophysics Data System (ADS)

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-01

    Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  18. Microwave spectra and conformational studies of ethylamine from temperature dependent Raman spectra of xenon solutions and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Darkhalil, Ikhlas D.; Nagels, Nick; Herrebout, Wouter A.; van der Veken, Benjamin J.; Gurusinghe, Ranil M.; Tubergen, Michael J.; Durig, James R.

    2014-06-01

    FT-microwave spectroscopy was carried out where the trans conformer was identified to be the most stable conformer. Variable temperature (-60 to -100 °C) studies of the Raman spectra (4000-50 cm-1) of ethylamine, CH3CH2NH2 dissolved in liquefied xenon have been carried out. From these data both conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 62 ± 6 cm-1 (0.746 ± 0.072 kJ mol-1) with the trans conformer the more stable form. The percentage of the gauche conformer is estimated to be 60% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations with the Møller-Plesset perturbation method to the second order (MP2(full)) and the fourth order (MP4(SDTQ)) as well as with density functional theory by the B3LYP method by utilizing a variety of basis sets. Vibrational assignments have been made for the observed bands which have been predicted by MP2(full)/6-31G(d) ab initio calculations which includes harmonic force fields, frequencies, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are discussed and compared to the corresponding properties of some similar molecule.

  19. Vibrational dynamics of single-crystal YVO4 studied by polarized micro-Raman spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sanson, Andrea; Giarola, Marco; Rossi, Barbara; Mariotto, Gino; Cazzanelli, Enzo; Speghini, Adolfo

    2012-12-01

    The vibrational properties of yttrium orthovanadate (YVO4) single crystals, with tetragonal zircon structure, have been investigated by means of polarized micro-Raman spectroscopy and ab initio calculations. Raman spectra were taken at different polarizations and orientations carefully set by the use of a micromanipulator, so that all of the twelve Raman-active modes, expected on the basis of the group theory, were selected in turn and definitively assigned in wave number and symmetry. In particular the Eg(4) mode, assigned incorrectly in previous literature, has been observed at 387 cm-1. Moreover, the very weak Eg(1) mode, peaked at about 137 cm-1, was clearly observed only under some excitation wavelengths, and its peculiar Raman excitation profile was measured within a wide region of the visible. Finally, ab initio calculations based on density-functional theory have been performed in order to determine both Raman and infrared vibrational modes and to corroborate the experimental results. The rather good agreement between computational and experimental frequencies is slightly better than in previous computational works and supports our experimental symmetry assignments.

  20. An ab-initio study of some homolytic substitution reactions of acyl radicals at silicon, germanium and tint.

    PubMed

    Matsubara, Hiroshi; Schiesser, Carl H

    2003-12-01

    Ab initio calculations using the 6-311G**, cc-pVDZ, and (valence) double-zeta pseudopotential (DZP) basis sets, with (MP2, QCISD, CCSD(T)) and without (UHF) the inclusion of electron correlation, and density functional (BHandHLYP, B3LYP) calculations predict that homolytic substitution reactions of acetyl radicals at the silicon atoms in disilane can proceed via both backside and frontside attack mechanisms. At the highest level of theory (CCSD(T)/cc-pVDZ//MP2/cc-pVDZ), energy barriers (deltaE double dagger) of 77.2 and 81.9 kJ mol(-1) are calculated for the backside and frontside reactions respectively. Similar results are obtained for reactions involving germanium and tin with energy barriers (deltaE double dagger) of 53.7-84.2, and 55.0-89.7 kJ mol(-1) for the backside and frontside mechanisms, respectively. These data suggest that both homolytic substitution mechanisms are feasible for homolytic substitution reactions of acetyl radicals at silicon, germanium, and tin. BHandHLYP calculations provide geometries and energy barriers for backside and frontside transition states in good agreement with those obtained by traditional ab initio techniques. PMID:14685338

  1. Ultraviolet Absorption Spectra, AB Initio Calculations, and Carbonyl Wagging Potential Energy Functions of Cyclobutanone, Cyclopentanone, BICYCLO[3.1.0]HEXAN-3-ONE, and TETRAHYDROFURAN-3-ONE

    NASA Astrophysics Data System (ADS)

    Lee, Soono; Dakkouri, Marwan; Choo, Jaebum; Laane, Jaan

    2000-03-01

    The electronic absorption spectra of cyclobutanone, cyclopentanone, bicyclo[3.1.0]hexan-3-one, and tetrahydrofuran-3-one were recorded and analyzed in the 28,000 - 44,000 cm-1 region. Several dozen absorption bands were assigned for each molecule. These arise from combinations of the ring vibrations and the C=O wagging vibrations. Assigned bands were compared with previously recorded jet-cooled fluorescence excitation spectra. Additional C=O out-of-plane wagging bands were found for cyclopentanone and tetrahydrofuran-3-one, and the potential energy functions for this vibration in these molecules were recalculated. These potential energy functions have barriers to inversion reflecting the fact that the carbonyl group is bent out of the ring plane in the S1(n, π*) excited electronic state.

  2. Ab initio calculations of accurate dissociation energy and analytic potential energy function for the second excited state B1Π of 7LiH

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong

    2006-12-01

    The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.

  3. Ab Initio Geometry and Bright Excitation of Carotenoids: Quantum Monte Carlo and Many Body Green’s Function Theory Calculations on Peridinin

    PubMed Central

    Coccia, Emanuele; Varsano, Daniele; Guidoni, Leonardo

    2016-01-01

    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. PMID:26580027

  4. Ab initio calculation of accurate dissociation energy, potential energy curve and dipole moment function for the A1Σ+ state 7LiH molecule

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Yang, Xiang-Dong; Zhu, Zun-Lue

    2006-05-01

    The reasonable dissociation limit of the A1Σ+ state 7LiH molecule is obtained. The accurate dissociation energy and the equilibrium geometry of this state are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space for the first time. The whole potential energy curve and the dipole moment function for the A1Σ+ state are calculated over a wide internuclear separation range from about 0.1 to 1.4 nm. The calculated equilibrium geometry and dissociation energy of this potential energy curve are of Re=0.2487 nm and De=1.064 eV, respectively. The unusual negative values of the anharmonicity constant and the vibration-rotational coupling constant are of ωeχe=-4.7158cm-1 and αe=-0.08649cm-1, respectively. The vertical excitation energy from the ground to the A1Σ+ state is calculated and the value is of 3.613 eV at 0.15875 nm (the equilibrium position of the ground state). The highly anomalous shape of this potential energy curve, which is exceptionally flat over a wide radial range around the equilibrium position, is discussed in detail. The harmonic frequency value of 502.47cm-1 about this state is approximately estimated. Careful comparison of the theoretical determinations with those obtained by previous theories about the A1Σ+ state dissociation energy clearly shows that the present calculations are much closer to the experiments than previous theories, thus represents an improvement.

  5. Performance of the major semiempirical, ab initio, and DFT methods for isomerization enthalpies of linear to branched heptanes.

    PubMed

    Rayne, Sierra; Forest, Kaya

    2016-06-01

    The gas phase standard state (298.15 K, 1 atm) isomerization enthalpy (ΔisomH°(g)) prediction performance of the major semiempirical, ab initio, and density functional levels of theory for environmentally relevant transformations was investigated using the linear to branched heptanes as a representative case study. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are well suited for investigating the thermodynamic properties of environmentally interesting isomerizations, although the M062X functional may not be appropriate for all systems. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise. PMID:26979512

  6. Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

  7. Ab initio structural and electronic analysis of CH3SH self-assembled on a Cu(110) substrate

    NASA Astrophysics Data System (ADS)

    D'Agostino, S.; Chiodo, L.; Della Sala, F.; Cingolani, R.; Rinaldi, R.

    2007-05-01

    Ab initio Density Functional Theory calculations are here reported to characterize the adsorption of methanethiol at the Cu(110) surface. Theoretical results suggest that the binding of the adsorbate to the substrate is rather weak and the molecular geometry is correspondingly almost unaffected by the adsorption. Otherwise, when CH3SH deprotonates producing methanethiolate, a stronger chemical bond is realized between the sulfur atom of CH3S radical and Cu surface atoms. A detailed study of structural and electronic properties of methanethiolate on Cu(110) for a p(2×2) and a c(2×2) overlayer structure has been carried out. We find that, in the most stable configuration, the molecule adsorbs in the shortbridge site. The chemical bond arises due to a strong hybridization among p orbitals of sulfur and d states from the substrate, as it is deduced by an analysis of partial densities of states and charge densities.

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

    NASA Astrophysics Data System (ADS)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

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

  9. Hydrogen impurity in yttria: Ab initio and μSR perspectives

    NASA Astrophysics Data System (ADS)

    Silva, E. L.; Marinopoulos, A. G.; Vilão, R. C.; Vieira, R. B. L.; Alberto, H. V.; Piroto Duarte, J.; Gil, J. M.

    2012-04-01

    The incorporation of interstitial hydrogen in yttria was studied by means of ab initio calculations based on density-functional theory (DFT) and muonium spin polarization spectroscopy (μSR). The density-functional calculations, based on a semilocal functional within the GGA-PBE and a hybrid functional, uncovered multiple geometrical configurations for the neutral, H0, and the negatively charged, H-, states of hydrogen, thus demonstrating the existence of metastable minimum-energy sites. It was observed that the low-energy configurations for H0 and H- are similar: they prefer to relax in deep, interstitial sites, whereas the equilibrium configurations for the positively charged state, H+, were bond-type configurations with the hydrogen forming a covalent O-H bond with an O anion. For all neutral and negative configurations, localized defect levels were found inside the gap. Overall, the results for the formation energies obtained by the two different functionals are qualitatively similar; an amphoteric behavior was found for hydrogen after considering the lowest-energy structures for each charge state. The calculated acceptor transition level, obtained by the hybrid functional and seen near midgap, is consistent with μSR data from literature. The results are consistent with the present μSR data, where the observed diamagnetic signal is attributed to a donor-like muonium at the oxygen-bonded configurations and the paramagnetic signal to an acceptor-like deep muonium at the interstitial sites.

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

    PubMed

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

    2015-01-28

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

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

    SciTech Connect

    Taioli, Simone; Garberoglio, Giovanni; Simonucci, Stefano; Beccara, Silvio a; Aversa, Lucrezia; Nardi, Marco; Verucchi, Roberto; Iannotta, Salvatore; Dapor, Maurizio; and others

    2013-01-28

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

  12. Ab-initio Calculations of Accurate Electronic Properties of Wurzite AlN

    NASA Astrophysics Data System (ADS)

    Nwigboji, Ifeanyi; Malozovsky, Yuriy; Bagayoko, Diola; Bagayoko Research Group Team

    2014-03-01

    We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of wurtzite Aluminum Nitride (w-AlN). Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams' method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method verifiably obtains the minima of the occupied energies; these minima provide the most variationally and physically valid density functional theory (DFT) description of the ground states of materials under study. Our preliminary results for w-AlN show that w-AlN has a direct band gap of 5.82 eV at the Γ point. The preliminary energy bands were obtained with a basis set comprising 48 functions. None of the several, larger basis sets tested to date led to occupied energies lower than those obtained with the above 48. While most previous LDA calculations are 2 eV smaller or more than the experimental value of 5.9 eV that is in excellent agreement with our finding, considering the typical experimental uncertainty of 0.2 eV for absorption measurements on AlN. We also discuss our calculated density of states (DOS) and partial densities of states (pDOS).

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

    NASA Technical Reports Server (NTRS)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

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

  14. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  15. Generation of amorphous porous PdH: an ab initio approach

    NASA Astrophysics Data System (ADS)

    Rodriguez, Isaias; Valladares, Renela; Valladares, Ariel A.; Valladares, Alexander

    2014-03-01

    The hydrogen bubble template (HBT) method has been employed to generate amorphous porous structures in platinum, nickel, copper and gold. We used our ab initio approach to generate amorphous porous Pd50H50 ; Pd45H55 ; Pd40H60 , using an approach similar to the HBT method which keeps the interatomic distances the same as in the pure crystalline Pd, swapping palladium by hydrogen in a substitutional way, thus reducing the density and making the initial supercell metastable. We applied this HBT-like method to an initial 108-atom crystalline face-centered cubic palladium supercell, with an initial density of 12 . 02 g / cm3 . After the substitution we got three supercells: a crystalline supercell: Pd54H54, with a density of 6 . 056g/cm3 ; a supercell: Pd49H59, with a density of 5 . 506g/cm3 ; and a supercell: Pd43H65, with a density of 4 . 846g/cm3 . After the hydrogen insertion an MD process at 1000 K was applied, and the resulting structures finally relaxed. Pores appeared along well-defined spatial directions. We characterized the structures by means of the pair distribution function (PDF) and the bond-angle distribution. Our results will be discussed in the light of possible structures of amorphous porous palladium hydride. Supported by CONACYT and DGAPA, UNAM.

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

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2013-05-28

    The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations. PMID:23742495

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

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

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

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

    PubMed

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed. PMID:27357850

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

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava

    subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated

  20. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  1. Ab initio prediction of electronic, transport and bulk properties of Li2S

    NASA Astrophysics Data System (ADS)

    Malozovsky, Yuriy; Franklin, Lashounda; Ekuma, Chinedu; Bagayoko, Diola

    2015-08-01

    In this paper, we present results from ab initio, self-consistent, local density approximation (LDA) calculations of electronic and related properties of cubic antifluorite (anti-CaF2) lithium sulfide (Li2S). Our nonrelativistic computations implemented the linear combination of atomic orbital (LCAO) formalism following the Bagayoko, Zhao and Williams method, as enhanced by Ekuma and Franklin (BZW-EF). Consequently, using several self-consistent calculations with increasing basis sets, we searched for the smallest basis set that yields the absolute minima of the occupied energies. The outcomes of the calculation with this basis set, called the optimal basis set, have the full physical content of density functional theory (DFT). Our calculated indirect band gap, from Γ to X, is 3.723 eV, for the low temperature experimental lattice constant of 5.689 Å. The predicted indirect band gap of 3.702 eV is obtained for the computationally determined equilibrium lattice constant of 5.651 Å. We have also calculated the total density of states (DOS) and partial densities of states (pDOS), electron and hole effective masses and the bulk modulus of Li2S. Due to a lack of experimental results, most of the calculated ones reported here are predictions for this material suspected of exhibiting a high temperature superconductivity similar to that of MgB2.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

    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.

  4. Ab initio calculation of molecular field interactions in rare-earth transition-metal intermetallics (invited)

    NASA Astrophysics Data System (ADS)

    Brooks, M. S. S.; Gasche, T.; Auluck, S.; Nordström, L.; Severin, L.; Trygg, J.; Johansson, B.

    1991-11-01

    The interaction, KRM, between the rare-earth 4f moment and the transition-metal 3d moments in rare-earth transition-metal intermetallics is shown to depend upon the R-5d moment, which is due to 3d-5d hybridization, and local 4f-5d exchange integrals. Both the R-5d moment and KRM may be calculated ab initio from the local spin-density approximation to density functional theory in self-consistent energy-band calculations with the localized 4f-moments fixed at their Russel-Saunders values. Detailed examples are given for the RFe2 (R=Gd-Yb) series. The exchange integrals are similar to those entering into the density functional version of Stoner theory and their energy dependence must be treated carefully. The calculated local exchange integrals are shown to be related to the molecular fields derived from spin Hamiltonians, hence to the spin-wave spectra. Reasonable agreement with values of the molecular fields extracted from inelastic neutron scattering and high field susceptibility measurements is obtained.

  5. High adsorption capacity of heavy metals on two-dimensional MXenes: an ab initio study with molecular dynamics simulation.

    PubMed

    Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming

    2016-01-01

    Density functional theory (DFT) calculation is employed to study the adsorption properties of Pb and Cu on recently synthesized two-dimensional materials MXenes, including Ti3C2, V2C1 and Ti2C1. The influence of surface decoration with functional groups such as H, OH and F have also been investigated. Most of these studied MXenes exhibit excellent capability to adsorb Pb and Cu, especially the adsorption capacity of Pb on Ti2C1 is as high as 2560 mg g(-1). Both the binding energies and the adsorption capacities are sensitive to the functional groups attached to the MXenes' surface. Ab initio molecular dynamics (ab-init MD) simulation confirms that Ti2C1 remains stable at room temperature after adsorbing Pb atoms. Our calculations imply that these newly emerging two-dimensional MXenes are promising candidates for wastewater treatment and ion separation. PMID:26602974

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

    SciTech Connect

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

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  7. Ab initio molecular dynamics simulations of the static, dynamic and electronic properties of liquid lead using real-space pseudopotentials

    SciTech Connect

    Alemany, Manuel M. G.; Longo, Roberto; Gallego, Luis; Gonzales, D. J.; Gonzales, L. E.; Tiago, Murilo L; Chelikowsky, James

    2007-01-01

    We performed a comprehensive study of the static, dynamic and electronic properties of liquid Pb at T = 650 kelvins, density 0.0309 angstroms^{-3} by means of 216-particle ab initio molecular dynamics simulations based on a real-space implementation of pseudopotentials constructed within density-functional theory. The predicted results and available experimental data are very in good agreement, which confirms the adequacy of this technique to achieve a reliable description of the behavior of liquid metals, including their dynamic properties. Although some of the computed properties of liquid Pb are similar to those of simple liquid metals, others differ markedly. Our results show that an appropriate description of liquid Pb requires the inclusion of relativistic effects in the determination of the pseudopotentials of Pb.

  8. Ab-initio calculations and phase diagram assessments of An-Al systems (An = U, Np, Pu)

    NASA Astrophysics Data System (ADS)

    Sedmidubský, D.; Konings, R. J. M.; Souček, P.

    2010-02-01

    The enthalpies of formation of binary intermetallic compounds AnAl n(n=2,3,4, An=U,Np,Pu) were assessed from first principle calculations of total energies performed using full potential APW + lo technique within density functional theory ( WIEN2k). The substantial contribution to entropies, S298°, arising from lattice vibrations was calculated by direct method within harmonic crystal approximation ( Phonon software + VASP for obtaining Hellmann-Feynman forces). The electronic heat capacity and the corresponding contribution to entropy were estimated from the density of states at Fermi level obtained from electronic structure calculations. The phase diagrams of the relevant systems An-Al were calculated based on the thermodynamic data assessed from ab-initio calculations, known equilibrium and calorimetry data by employing the FactSage program.

  9. Operator evolution for ab initio theory of light nuclei

    NASA Astrophysics Data System (ADS)

    Schuster, Micah; Quaglioni, Sofia; Johnson, Calvin; Jurgenson, Eric; Navrátil, Petr

    2014-09-01

    The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range; short ranges have the largest absolute renormalization when including two- and three-body induced terms, while at long ranges the induced three-body contribution takes on increased relative importance. The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores

  10. Interpretation of the U L3-edge EXAFS in uranium dioxide using molecular dynamics and density functional theory simulations

    NASA Astrophysics Data System (ADS)

    Bocharov, Dmitry; Chollet, Melanie; Krack, Matthias; Bertsch, Johannes; Grolimund, Daniel; Martin, Matthias; Kuzmin, Alexei; Purans, Juris; Kotomin, Eugene

    2016-05-01

    X-ray absorption spectroscopy is employed to study the local structure of pure and Cr-doped UO2 at 300 K. The U L3-edge EXAFS spectrum is interpreted within the multiplescattering (MS) theory using the results of the classical and ab initio molecular dynamics simulations, allowing us to validate the accuracy of theoretical models. The Cr K-edge XANES is simulated within the full-multiple-scattering formalism considering a substitutional model (Cr at U site). It is shown that both unrelaxed and relaxed structures, produced by ab initio density functional theory (DFT) calculations, fail to describe the experiment.

  11. Ab Initio No-Core Shell Model

    SciTech Connect

    Barrett, B R; Navratil, P; Vary, J P

    2011-04-11

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

  12. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  13. THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

    SciTech Connect

    Turchi, P A

    2004-09-24

    Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.

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

    SciTech Connect

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

    2001-03-15

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

  15. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.

    PubMed

    Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R

    2016-08-01

    Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach. PMID:27337546

  16. Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

    DOE PAGESBeta

    Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; Schmidt, Jordan R.

    2016-06-23

    Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

  17. Comparative ab initio study of lattice dynamics and thermodynamics of Fe2SiO4- and Mg2SiO4-spinels.

    PubMed

    Derzsi, Mariana; Piekarz, Przemysław; Tokár, Kamil; Jochym, Paweł T; Łażewski, Jan; Sternik, Małgorzata; Parlinski, Krzysztof

    2011-03-16

    Lattice dynamics and thermodynamic properties of antiferromagnetic Fe(2)SiO(4)-spinel have been studied using density functional theory. Phonon dispersions are obtained for several hydrostatic pressures up to 20 GPa. They are used to calculate thermodynamic properties within the quasiharmonic approximation. Comparison with ab initio results obtained for Mg(2)SiO(4)-spinel is made in order to study the effect of the cation exchange on the dynamic and thermodynamic properties of (Mg, Fe)(2)SiO(4)-spinel. The obtained results have been compared with the available experimental data. PMID:21339581

  18. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and

  19. Ab initio investigation of grain boundary cohesion in Al alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Shengjun; Kontsevoi, Oleg Y.; Freeman, A. J.; Olson, G. B.

    2010-03-01

    Strength and hardness of aluminum alloys can be substantially increased by alloying with Mg, Zn, Cu, Si, and other elements. The main drawback of Al alloys is their susceptibility to stress corrosion cracking, which is caused by alloying impurities segregated at grain boundaries. We investigated the embrittling and cohesion-enhancing effects of impurities on a σ5(012)[100] grain boundary in Al by means of the full-potential linearized augmented plane-wave (FLAPW) method within the framework of the Rice-Wang thermodynamic model and within the ab initio tensile test approach. We calculated segregation energies, analyzed local atomic configurations, electronic structures and spatial charge density distributions around segregated impurities, and identified the roles of atomic size and the bonding behavior of the impurity with the surrounding Al atoms. The results show that He, H and Na are strong embrittlers, Zn is a weak embrittler, while Sc, B, Cu and Mg are cohesion enhancers. We further evaluated the effect of co-alloying with two or more elements on grain boundary strength. This work provides a fundamental basis for the design of high strength Al alloys.

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

    NASA Astrophysics Data System (ADS)

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

    2006-09-01

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

  1. Ab initio ground and the first excited adiabatic and quasidiabatic potential energy surfaces of H + + CO system

    NASA Astrophysics Data System (ADS)

    George, D. X. F.; Kumar, Sanjay

    2010-08-01

    Ab initio global adiabatic as well as quasidiabatic potential energy surfaces for the ground and the first excited electronic states of the H + + CO system have been computed as a function of the Jacobi coordinates ( R, r, γ) using Dunning's cc-pVTZ basis set at the internally contracted multi-reference (single and double) configuration interaction level of accuracy. In addition, nonadiabatic coupling matrix elements arising from radial motion, mixing angle and coupling potential have been computed using the ab initio procedure [Simah et al. (1999) [66

  2. Ab initio study of magnesium and magnesium hydride nanoclusters and nanocrystals: examining optimal structures and compositions for efficient hydrogen storage.

    PubMed

    Koukaras, Emmanuel N; Zdetsis, Aristides D; Sigalas, Michael M

    2012-09-26

    On the basis of the attractive possibility of efficient hydrogen storage in light metal hydrides, we have examined a large variety of Mg(n)H(m) nanoclusters and (MgH(2))(n) nanocrystals (n = 2-216, m = 2-436) using high level coupled cluster, CCSD(T), ab initio methods, and judicially chosen density functional calculations of comparable quality and (near chemical) accuracy. Our calculated desorption energies as a function of size and percentage of hydrogen have pinpointed optimal regions of sizes and concentrations of hydrogen which are in full agreement with recent experimental findings. Furthermore, our results reproduce the experimental desorption energy of 75.5 kJ/mol for the infinite system with remarkable accuracy (76.5 ± 1.5 kJ/mol). PMID:22920498

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

    NASA Astrophysics Data System (ADS)

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

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

  4. Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)

    NASA Astrophysics Data System (ADS)

    Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola

    Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  5. Ab initio no core configuration interaction calculations in the natural orbital basis

    NASA Astrophysics Data System (ADS)

    Constantinou, Chrysovalantis; Caprio, Mark A.; Vary, James P.; Maris, Pieter

    2015-10-01

    The natural orbital basis has been successfully used in the past in atomic and molecular structure calculations. The natural orbitals used in those calculations are calculated by diagonalizing the electron one-body density matrix. Here we develop natural orbitals for nuclear no-core configuration interaction (NCCI) calculations. A NCCI calculation using an initial single particle basis, such as the harmonic oscillator basis, must first be performed in order to obtain a one-body density matrix. The eigenvectors of the one-body density matrix are the natural orbitals, and the corresponding eigenvalues are the occupations of these natural orbitals in the nuclear wave function. According to these occupancies, the most important natural orbitals, in the sense of the most occupied, can then be selected and used in a NCCI calculation. We discuss ab initio nuclear NCCI calculations for light nuclei and assess their ability to provide faster convergence. Supported by the US DOE (under Grants DE-FG02-95ER-40934, DESC0008485 SciDAC/NUCLEI, and DE-FG02-87ER40371), and the US NSF (under Grant 0904782). Computational resources provided by NERSC (supported by US DOE Contract DE-AC02-05CH11231), and NDCRC.

  6. Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Marcolongo, Aris; Umari, Paolo; Baroni, Stefano

    2014-03-01

    The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.

  7. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  8. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    SciTech Connect

    Geng, Hua Y.

    2015-02-15

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

  9. Ab-initio crystal structure prediction. A case study: NaBH{sub 4}

    SciTech Connect

    Caputo, Riccarda; Tekin, Adem

    2011-07-15

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

  10. Regioselective synthesis and ab initio calculations of fused heterocycles thermally and under microwave irradiation

    NASA Astrophysics Data System (ADS)

    Salem, Mostafa E.; Ahmed, Ashour A.; Shaaban, Mohamed R.; Shibl, Mohamed F.; Farag, Ahmad M.

    2015-09-01

    Pyrazolo[1,5-a]pyrimidine, triazolo[1,5-a]pyrimidine, and pyrimido[1,2-a]benzimidazole, pyrido[1,2-a]benzimidazole ring systems incorporating phenylsulfonyl moiety were synthesized via the reaction of 3-(N,N-dimethylamino)-1-(thiophen-2-yl)-2-(phenylsulfonyl)prop-2-en-1-one derivatives with the appropriate aminoazoles as 1,3-binucleophiles and 1H-benzimidazol-2-ylacetonitrile using conventional methods as well as microwave irradiation. The regioselectivity of the cyclocondensation reactions was confirmed both experimentally by alternative synthesis of reaction products and theoretically using ab initio quantum chemical calculations namely the Density Functional Theory (DFT). The theoretical work was carried out using the Becke, three parameter, Lee-Yang-Parr hybrid functional (B3LYP) combined with the 6-311++G(d,p) basis set. It was found that the final cyclocondensation reaction product depends mainly on the initial addition to the activated double bond by the nitrogen atom of the 1,3-binucleophiles that has the higher electron density.

  11. Ab initio simulation of transport phenomena in rarefied gases.

    PubMed

    Sharipov, Felix; Strapasson, José L

    2012-09-01

    Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889

  12. Ab initio calculation of double ionization of atoms

    SciTech Connect

    Serov, V. V.

    2013-02-15

    The Solov'ev-Vinitsky method was used to perform an ab initio calculation of the triple-differential cross section for the double single-photon photoionization of helium for the case of equal emitted-electron energies. A Gaussian width {gamma} describing angular electron-electron correlations at the total electron energy E taking values in range between 0.1 and 100 eV was obtained for this cross section. The results agree with available experimental data, but they raise a doubt as to whether the well-known Wannier law {gamma} {proportional_to} E{sup 1/4} is applicable at experimentally accessible energies. The Gaussian width {gamma} was investigated as a function of the total emitted-electron energy for targets that have a strongly asymmetric configuration of the initial state-specifically, a negative atomic-hydrogen ion H{sup -} and heliumin the 1s2s{sup 1}S and 1s3s{sup 1}S excited states. It was found that this function, {gamma}(E), had a maximum at low energies. It was also shown that, at low energies, the dependence of the double-differential cross section on the angle between the emitted-electron momenta for the targets indicated above differed substantially from the Gaussian dependence, featuring maxima whose number was equal to the number of radial nodes in the initial state. This opens new possibilities for a qualitative analysis of the electron structure of targets.

  13. Ab initio lattice dynamical studies of silicon clathrate frameworks and their negative thermal expansion

    NASA Astrophysics Data System (ADS)

    Härkönen, Ville J.; Karttunen, Antti J.

    2014-01-01

    The thermal and lattice dynamical properties of seven silicon clathrate framework structures are investigated with ab initio density functional methods (frameworks I, II, IV, V, VII, VIII, and H). The negative thermal expansion (NTE) phenomenon is investigated by means of quasiharmonic approximation and applying it to equal time displacement correlation functions. The thermal properties of the studied clathrate frameworks, excluding the VII framework, resemble those of the crystalline silicon diamond structure. The clathrate framework VII was found to have an anomalous NTE temperature range up to 300 K and it is suitable for further studies of the mechanisms of NTE. Investigation of the displacement correlation functions revealed that in NTE, the volume derivatives of the mean square displacements and mean square relative displacements of atoms behave similarly to the vibrational entropy volume derivatives and consequently to the coefficients of thermal expansion as a function of temperature. All studied clathrate frameworks, excluding the VII framework, possess a phonon band gap or even two in the case of framework V.

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

    PubMed

    Bryk, Taras; Wax, J-F

    2016-05-21

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

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

    NASA Astrophysics Data System (ADS)

    Bryk, Taras; Wax, J.-F.

    2016-05-01

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

  16. Ab initio computations of photodissociation products of CFC alternatives

    SciTech Connect

    Tai, S.; Illinger, K.H.; Kenny, J.E.

    1995-12-31

    Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.

  17. Ab Initio Structure Analysis Using Laboratory Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Sasaki, Akito

    Today, laboratory X-ray diffractometers are seeing increasingly wide use in the ab initio crystal structure analysis of organic powder samples. This is because optics and optical devices have been improved, making it possible to obtain precise integrated intensities of reflections in high 2-theta ranges. Another reason is that one can use direct-space methods, which do not require “high-resolution diffraction data”, much more easily than before. Described here are some key points to remember when performig ab initio crystal structure analysis using powder diffraction data from organic compounds.

  18. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  19. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

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

    2015-06-28

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

  20. Ab initio simulations of peptide-mineral interactions

    NASA Astrophysics Data System (ADS)

    Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko

    We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the α-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.

  1. Accurate ab initio vibrational energies of methyl chloride.

    PubMed

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

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( 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 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-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 CH3Cl without empirical refinement of the respective PESs. PMID:26133427

  2. Accurate ab initio vibrational energies of methyl chloride

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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, CH335Cl and CH337Cl. The respective PESs, CBS-35 HL, and CBS-37 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 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm-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 CH3Cl without empirical refinement of the respective PESs.

  3. Ab initio study of the bonding in diatomic nickel

    SciTech Connect

    Noell, J.O.; Newton, M.D.; Hay, P.J.; Martin, R.L.; Bobrowicz, F.W.

    1980-09-01

    Hartree--Fock, GVB, and configuration interaction calculations were performed for diatomic nickel using an ab initio effective core potential. A basis set specifically optimized for the /sup 3/D state of atomic nickel is found to be far superior to the more common basis obtained from the /sup 3/F atomic state. Correlation effects are found to be significant in determining the bond energy. In particular, the two electrons of the s--s bond must be appropriately correlated. In addition, correlation effects which one would interpret as being principally intra-atomic in character are found to have a marked effect on the molecular properties. The theoretically predicted bond dissociation energy (D/sub e/) of 43.4 kcal/mol is significantly lower than the experimental estimate of 55 +- 5 kcal/mol. However, molecular partition functions calculated using the present results indicate that the experimental value should be revised downward to a value of approx.46 +- 5 kcal/mol, in good agreement with our calculations. An interatomic distance of 4.27 bohr is computed and compared with experimental estimates. Spectroscopic parameters for dipole-allowed transitions from the ground state were determined from SCF and GVB calculations and discussed in relation to the experimentally observed visible and ultraviolet spectra attributed to Ni/sub 2/.

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

    SciTech Connect

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

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  5. Ab initio modeling of the motional Stark effect on MAST

    SciTech Connect

    De Bock, M. F. M.; Conway, N. J.; Walsh, M. J.; Carolan, P. G.; Hawkes, N. C.

    2008-10-15

    A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the {pi} and {sigma} lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic.

  6. Ab initio calculations of structure and thermodynamic properties of tetragonal-TiH2 under high temperatures and pressures

    NASA Astrophysics Data System (ADS)

    Liu, X. K.; Tang, B.; Zhang, Y.

    2013-10-01

    The structural and thermodynamic properties of tetragonal-TiH2 under high temperatures and pressures are investigated by Ab initio calculations based on pseudo-potential plane-wave density functional theory method within using the generalized gradient approximation (GGA) and quasi-harmonic Debye model. Some ground state properties such as lattice constants, bulk modulus and elastic constants are good agreement with the available experimental results and other theoretical data. Through the quasiharmonic Debye model, in which the phononic effects are considered, the thermodynamic properties of tetragonal-TiH2 such as thermal expansion coefficient, Debye temperature, heat capacity and Grüneisen parameters dependence of temperature and pressure in the range of 0-1000 K and 0-10 GPa are also presented, respectively.

  7. Thermal expansion, diffusion and melting of Li2O using a compact forcefield derived from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Asahi, Ryoji; Freeman, Clive M.; Saxe, Paul; Wimmer, Erich

    2014-10-01

    This work shows a straightforward procedure to derive forcefields (FFs) which are able to describe the structural, thermal and transport properties of condensed phases. The approach is based on ab initio molecular dynamics trajectories and an empirical calibration such as the melting point. This is demonstrated for lithium oxide using a Buckingham-type potential and optimized effective atomic charges. The present FF reproduces the density and thermal expansion of Li2O very well, including an anomaly related to the known superionic behaviour, i.e. a pre-melting of the Li sublattice at a critical temperature of Tc = 1200 K. Calculations of the diffusion coefficient as a function of temperature show a strong dependence on vacancy concentration for temperatures below Tc, consistent with previous simulations. Extensions to other ionic systems and compositions are made straightforward by the compact form of the FF and the present methodology employed in the parameter fitting.

  8. Ab initio study of hyperfine interaction parameters in C14 Hf and Zr Laves-phase compounds

    NASA Astrophysics Data System (ADS)

    Belošević-Čavor, Jelena; Koteski, V.; Radaković, J.; Cekić, B.

    2009-05-01

    Using ab initio density-functional theory approach the electric field gradients (EFGs) and hyperfine magnetic fields (HMFs) for the isostructural C14 Laves-phase compounds HfCr2 , HfFe2 , HfMn2 , ZrCr2 , and ZrMn2 are calculated and compared with the available experimental data from time differential perturbed angular-correlation (TDPAC) spectroscopy. In addition, supercell calculations of the hyperfine interaction parameters at the nucleus of the substitutional Ta impurity are used to elucidate the role played by the Ta probe in the TDPAC measurements of Hf and Zr C14 Laves phases and solve the controversy related to the origin of the HMF in the C14 HfFe2 compound.

  9. Ab initio investigations of A-site doping on the structure and electric polarization of HoMnO3

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    We have investigated the effect of A-site doping on the structure and electric polarization of orthorhombic HoMnO3 using ab initio density functional theory calculations. We find that the substitution of rare earth ions, such as Lu, Y and La in place of Ho in orthorhombic HoMnO3 modifies the local structure around Mn ions drastically, and leads to the formation of two distinct Mn sites Mn(0) and Mn(1). As a result, large variance between Mn(0)O6 and Mn(1)O6 octahedral distortions arises. This variance in the octahedral distortions drives the disparate hopping of electrons between the eg orbitals enhancing the electronic polarization with increasing rare earth ion radius. The largest polarization of 7 µC/cm2 is obtained for La doped HoMnO3. This increase in polarization has been explained on the basis of radius mismatch induced local structural effects.

  10. Effect of electric field on the mechanical properties of bilayer boron nitride with AB stacking order: An ab initio study

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Faghihnasiri, M.; Malakpour, S.; Sahmani, S.

    2015-07-01

    In the current investigation, ab initio calculations are performed to explore the influence of electric field on the mechanical properties of bilayer boron nitride with AB stacking order (AB-2LBN). To accomplish this, density functional theory (DFT) within the framework of generalized gradient approximation (GGA) is implemented. It is demonstrated that the electric field has significant effects on Young's modulus and Poisson's ratio of AB-2LBN when its magnitude is small. With increasing the magnitude of electric field, these effects diminish so that the mechanical properties with and without considering the electric field become approximately identical. Also, it is shown that the equilibrium strain energy decreases linearly by increasing the magnitude of applied electric field.

  11. Ab initio investigation of the adsorption of zoledronic acid molecule on hydroxyapatite (001) surface: an atomistic insight of bone protection

    NASA Astrophysics Data System (ADS)

    Ri, Mun-Hyok; Yu, Chol-Jun; Jang, Yong-Man; Kim, Song-Un

    2016-03-01

    We report a computational study of the adsorption of zoledronic acid molecule on hydroxyapatite (001) surface within ab initio density functional theory. The systematic study has been performed, from hydroxyapatite bulk and surface, and zoledronic acid molecule to the adsorption of the molecule on the surface. The optimized bond lengths and bond angles were obtained and analyzed, giving an evidence of structural similarity between subjects under study. The formation energies of hydroxyapatite (001) surfaces with two kinds of terminations were computed as about 1.2 and 1.5 J/m^2 with detailed atomistic structural information. We determined the adsorption energies of zoledronic acid molecule on the surfaces, which are -260 kJ/mol at 0.25 ML and -400 kJ/mol at 0.5 ML. An atomistic insight of strong binding affinity of zoledronic acid to the hydroxyapatite surface was given and discussed.

  12. Photo-induced athermal phase transitions of HgX (X = S, Se, Te) by ab initio study

    NASA Astrophysics Data System (ADS)

    Da-hua, Ren; Xin-lu, Cheng; Hong, Zhang

    2016-07-01

    Ab initio calculations of lattice constants, lattice stabilities of HgX (X = S, Se, Te) at different electronic temperatures (T e) have been performed within the density functional theory (DFT). We find that the lattice constants of HgX increase and the phonon frequencies reduce as T e increases. Especially the transverse-acoustic (TA) phonon frequencies of HgX gradually become negative with the elevation of the electron temperature. That is to say ultrafast intense laser induces lattice instabilities of HgX and athermal melting appears for the increase of laser intensity. What is more, with the X atom number increasing, the critical electronic temperatures of HgX are decreased in sequence. This result would be helpful for understanding the athermal melting processes for femtosecond laser micromachining. Project supported by the National Natural Science Foundation of China (Grant Nos. 11374217 and 11176020).

  13. AB initio free energy calculations of the solubility of silica in metallic hydrogen and application to giant planet cores

    SciTech Connect

    González-Cataldo, F.; Wilson, Hugh F.; Militzer, B.

    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.

  14. Ab initio molecular dynamics study of the static, dynamic, and electronic properties of liquid mercury at room temperature.

    PubMed

    Calderín, L; González, L E; González, D J

    2009-05-21

    We report a study on several static, dynamic, and electronic properties of liquid Hg at room temperature. We have performed ab initio molecular dynamics simulations using Kohn-Sham density functional theory combined with a nonlocal ultrasoft pseudopotential. The calculated static structure shows good agreement with the available experimental data. We present results for the single-particle dynamics, and recent experimental data are analyzed. The calculated dynamic structure factors S(q,omega) fairly agree with their experimental counterparts as measured by inelastic x-ray (and neutron) scattering experiments. The dispersion relation exhibits a positive dispersion, which however is not so marked as suggested by the experiment; moreover, its slope at the long-wavelength limit provides a good estimate of the experimental sound velocity. We have also analyzed the dynamical processes behind the S(q,omega) in terms of a model including a relaxation mechanism with both fast and slow characteristic time scales. PMID:19466841

  15. Ab initio Design of Ca-Decorated Organic Frameworks for High Capacity Molecular Hydrogen Storage with Enhanced Binding

    SciTech Connect

    Sun, Y. Y.; Lee, K.; Kim, Y. H.; Zhang, S. B.

    2009-01-01

    Ab initio calculations show that Ca can decorate organic linkers of metal-organic framework, MOF-5, with a binding energy of 1.25 eV. The Ca-decorated MOF-5 can store molecular hydrogen (H{sub 2}) in both high gravimetric (4.6 wt %) and high volumetric (36 g/l) capacities. Even higher capacities (5.7 wt % and 45 g/l) can be obtained in a rationally designed covalent organic framework system, COF-{alpha}, with decorated Ca. Both density functional theory and second-order Moller-Plesset perturbation calculations show that the H{sub 2} binding in these systems is significantly stronger than the van der Waals interactions, which is required for H{sub 2} storage at near ambient conditions.

  16. Modulation of electronic properties of silicon carbide nanotubes via sulphur-doping: An ab initio study

    NASA Astrophysics Data System (ADS)

    Singh, Ram Sevak; Solanki, Ankit

    2016-03-01

    Silicon carbide nanotubes (SiCNTs) have received a great deal of scientific and commercial interest due to their intriguing properties that include high temperature stability and electronic properties. For their efficient and widespread applications, tuning of electronic properties of SiCNTs is an attractive study. In this article, electronic properties of sulphur doped (S-doped) zigzag (9 , 0) SiCNT is investigated by ab initio calculations based on density functional theory (DFT). Energy band structures and density of states of fully optimized undoped and doped structures with varying dopant concentration are calculated. S-doped on C-site of the nanotube exhibits a monotonic reduction of energy gap with increase in dopant concentration, and the nanotube transforms from semiconductor to metal at high dopant concentration. In case of S-doped on Si-site doping has less influence on modulating electronic structures, which results in reduction of energy gap up to a moderate doping concentration. Importantly, S preferential substitutes of Si-sites and the nanotube with S-doped on Si-site are energetically more stable as compared to the nanotube with S-doped on C-site. The study of tunable electronic properties in S-doped SiCNT may have potential in fabricating nanoelectronic devices, hydrogen storage and gas sensing applications.

  17. Development of a spinor ab initio pseudopotential method and its application to spintronic materials

    NASA Astrophysics Data System (ADS)

    Theurich, Gerhard Jakob

    2001-12-01

    This thesis describes the extension of the density functional ab initio pseudopotential method to include the relativistic effect of spin-orbit coupling and non-collinear spin-polarizations within a generalized local density approximation. In contrast to conventional implementations, that neglect spin-orbit coupling and non-collinearity, the wavefunctions no longer separate into spatial and spin components, and are treated as general spinors. The implementation is applied to non-magnetic and magnetic systems with an emphasis on their spin properties. For GaAs and ZnSe the effects of relativistic corrections are studied focusing on the spin splittings of electronic bands, which are of great importance for spin relaxation in zincblende semiconductors. In the magnetic compounds MnSe and MnAs the reduced symmetry of the fully relativistic problem leads to small non-collinear arrangements of the self-consistent spin moments. Finally, the influence of spin-orbit coupling on the conduction and valence band exchange constants in dilute magnetic semiconductors is investigated, using the fully relativistic pseudopotential method. The results support the use of the scalar-relativistic approximation in such calculations.

  18. Electronic structure of silicon nitride according to ab initio quantum-chemical calculations and experimental data

    SciTech Connect

    Nekrashevich, S. S. Gritsenko, V. A.; Klauser, R.; Gwo, S.

    2010-10-15

    Charge transfer {Delta}Q = 0.35e at the Si-N bond in silicon nitride is determined experimentally using photoelectron spectroscopy, and the ionic formula of silicon nitride Si{sub 3}{sup +1.4}N{sub 4}{sup -1.05} is derived. The electronic structure of {alpha}-Si{sub 3}N{sub 4} is studied ab initio using the density functional method. The results of calculations (partial density of states) are compared with experimental data on X-ray emission spectroscopy of amorphous Si{sub 3}N{sub 4}. The electronic structure of the valence band of amorphous Si{sub 3}N{sub 4} is studied using synchrotron radiation at different excitation energies. The electron and hole effective masses m{sub e}{sup *} {approx} m{sub h}{sup *} {approx} 0.5m{sub e} are estimated theoretically. The calculated values correspond to experimental results on injection of electrons and holes into silicon nitride.

  19. Amorphous Ge quantum dots embedded in crystalline Si: ab initio results.

    PubMed

    Laubscher, M; Küfner, S; Kroll, P; Bechstedt, F

    2015-10-14

    We study amorphous Ge quantum dots embedded in a crystalline Si matrix through structure modeling and simulation using ab initio density functional theory including spin-orbit interaction and quasiparticle effects. Three models are generated by replacing a spherical region within diamond Si by Ge atoms and creating a disordered bond network with appropriate density inside the Ge quantum dot. After total-energy optimisations of the atomic geometry we compute the electronic and optical properties. We find three major effects: (i) the resulting nanostructures adopt a type-I heterostructure character; (ii) the lowest optical transitions occur only within the Ge quantum dots, and do not involve or cross the Ge-Si interface. (iii) for larger amorphous Ge quantum dots, with diameters of about 2.0 and 2.7 nm, absorption peaks appear in the mid-infrared spectral region. These are promising candidates for intense luminescence at photon energies below the gap energy of bulk Ge. PMID:26402441

  20. Engineering materials-design parameters of the Mg-Li Alloy System from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Counts, William; Friak, Martin; Raabe, Dierk; Neugebauer, Jorg

    2008-03-01

    Ab initio calculations are becoming increasingly useful to engineers interested in designing new alloys because these calculations are able to accurately predict basic material properties only knowing the atomic composition of the material. Fundamental physical properties (like formation energy and elastic constants) of 11 bcc magnesium-lithium alloys were calculated using density-functional theory (DFT) and compared with available experimental data. These DFT determined properties were in turn used to calculate engineering parameters like the bulk modulus/shear modulus (B/G) and Young's modulus/density (E/ρ). From these engineering parameters, alloys with optimal mechanical properties need for a light weight structural material were identified. It was found that the stiffest bcc magnesium-lithium alloys contain about 70 at.% magnesium while the most ductile alloys have 0-20 at.% magnesium. In addition, the specific modulus for alloys with 70 at.% magnesium was found to be equal to that of aluminum-magnesium alloys and slightly lower than that of aluminum-lithium alloys.

  1. Interplay of force constants in the lattice dynamics of disordered alloys: An ab initio study

    NASA Astrophysics Data System (ADS)

    Chouhan, Rajiv K.; Alam, Aftab; Ghosh, Subhradip; Mookerjee, Abhijit

    2014-02-01

    A reliable prediction of interatomic force constants in disordered alloys is an outstanding problem. This is due to the need for a proper treatment of multisite (at least pair) correlation within a random environment. The situation becomes even more challenging for systems with a large difference in atomic size and mass. We propose a systematic density functional theory (DFT) based study to predict the ab initio force constants in random alloys. The method is based on a combination of special quasirandom structures and the augmented space recursion to calculate phonon spectra, density of states (DOS), etc. The bcc TaW and fcc NiPt alloys are considered as the two distinct test cases. The Ta-Ta (W-W) bond distance in the alloy is predicted to be smaller (larger) than those in pure Ta (W), which, in turn, yields stiffer (softer) force constants for Ta (W). Pt-Pt force constants in the alloy, however, are predicted to be softer compared to Ni-Ni, due to the large bond distance of the former. Our calculated force constants, phonon spectra, and DOS are compared with experiments and other theoretical results, wherever available. A correct trend of the present results for the two alloys paves a path for future studies in more complex alloy systems.

  2. Yttrium aluminium garnet under pressure: Structural, elastic, and vibrational properties from ab initio studies

    SciTech Connect

    Monteseguro, V.; Rodríguez-Hernández, P.; Muñoz, A.

    2015-12-28

    The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet is mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.

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

    NASA Astrophysics Data System (ADS)

    Zemzemi, M.; Alaya, S.

    2013-12-01

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

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

    PubMed

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

    2016-03-21

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower. PMID:27004873

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. Efficient conformational space exploration in ab initio protein folding simulation.

    PubMed

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  7. Efficient conformational space exploration in ab initio protein folding simulation

    PubMed Central

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel

    2015-01-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  8. Realistic multiband k .p approach from ab initio and spin-orbit coupling effects of InAs and InP in wurtzite phase

    NASA Astrophysics Data System (ADS)

    Faria Junior, Paulo E.; Campos, Tiago; Bastos, Carlos M. O.; Gmitra, Martin; Fabian, Jaroslav; Sipahi, Guilherme M.

    2016-06-01

    Semiconductor nanowires based on non-nitride III-V compounds can be synthesized under certain growth conditions to favor the appearance of the wurtzite crystal phase. Despite reports in the literature of ab initio band structures for these wurtzite compounds, we still lack effective multiband models and parameter sets that can be simply used to investigate physical properties of such systems, for instance, under quantum confinement effects. In order to address this deficiency, in this study we calculate the ab initio band structure of bulk InAs and InP in the wurtzite phase and develop an 8 ×8 k .p Hamiltonian to describe the energy bands around the Γ point. We show that our k .p model is robust and can be fitted to describe the important features of the ab initio band structure. The correct description of the spin-splitting effects that arise due to the lack of inversion symmetry in wurtzite crystals is obtained with the k -dependent spin-orbit term in the Hamiltonian, often neglected in the literature. All the energy bands display a Rashba-like spin texture for the in-plane spin expectation value. We also provide the density of states and the carrier density as functions of the Fermi energy. Alternatively, we show an analytical description of the conduction band, valid close to the Γ point. The same fitting procedure is applied to the 6 ×6 valence band Hamiltonian. However, we find that the most reliable approach is the 8 ×8 k .p Hamiltonian for both compounds. The k .p Hamiltonians and parameter sets that we develop in this paper provide a reliable theoretical framework that can be easily applied to investigate electronic, transport, optical, and spin properties of InAs- and InP-based nanostructures.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  10. Infrared and Raman spectra, conformational analysis, ab initio calculations and vibrational assignment of 2-chloroethylsilyl chloride

    NASA Astrophysics Data System (ADS)

    Pan, Chunhua; Guirgis, Gamil A.; Durig, James R.

    2005-05-01

    The infrared (3100-40 cm -1) spectra of gaseous and solid and Raman (3200-20 cm -1) spectra of liquid 2-chloroethylsilyl chloride, ClCH 2CH 2SiH 2Cl, have been recorded. There are five possible stable conformers, Gg, Tg, Gt, Tt and Gg' for this molecule where the capital letter G ( gauche) or T ( trans) refer to rotation around the C-C bond and the lower case letters to rotation around the Si-C bond. Most ab initio calculations at the MP2(full) level predicted the order of the stability as Tg>Gg>Gt>Tt>Gg' whereas all density function theory calculations with the B3LYP method predicted the stability as Tg>Tt>Gg>Gt>Gg'. The four more stable conformers have been identified in the fluid phases with the Tg rotamer the only form remaining in the solid. Variable temperature (-105 to -150 °C) studies of the infrared spectra of the samples dissolved in liquid krypton have been recorded and the enthalpy differences determined to be: 50±20 (0.59±0.24 kJ/mol), 172±17 (2.06±0.20 kJ/mol) and 290±40 cm -1 (3.45±0.48 kJ/mol) for the Tg/Gg, Tg/Gt and Tg/Tt conformer pairs with the Tg conformer the most stable form. It is estimated that there is 42±2% of the Tg form, 33±1% of the Gg form, 20±2% of the Gt form, and 5±1% of the Tt form present at ambient temperature. A relatively complete vibrational assignment is proposed for the Tg conformer and many of the fundamentals have been identified for the other three (Gg, Gt and Tt) conformers based on the ab initio MP2(full)/6-31G(d) predicted frequencies, the relative infrared and Raman spectral intensities, and infrared band contours which are supported by normal coordinate calculations. Since the predicted energies between Tg and Gg' conformers from all calculations are very large, it is not surprising that no evidence in either the infrared or Raman spectra could be found for the Gg' conformer. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities

  11. Ab-Initio Calculations of Electronic Properties and Quantum Transport in U-Shaped Graphene Nanoribbons

    NASA Astrophysics Data System (ADS)

    Cuong, Nguyen Tien; Mizuta, Hiroshi; Cong, Bach Thanh; Otsuka, Nobuo; Chi, Dam Hieu

    2012-09-01

    Graphene is a promising candidate as a material used in nano-scale devices because of recent developments in advanced experimental techniques. Motivated by recent successful fabrications of U-shaped graphene channel transistors by using the gallium focused ion beam technology, we have performed ab-initio calculations to investigate the electronic properties and quantum transport in U-shaped graphene nanoribbons. The electronic properties are calculated using a numerical atomic orbital basis set in the framework of the density functional theory. The transport properties are investigated using the non-equilibrium Green's function method. The transmission spectra of U-shaped graphenes are analyzed in order to reveal the quantum transport of the systems. We found that the graphene nanoribbons tend to open a band gap when U-shaped structures are formed in both armchair and zigzag cases. The geometrical structures of U-shaped GNRs had enormous influences on the electron transport around the Fermi energy due to the formation of quasi-bound states at zigzag edges. The obtained results have provided valuable information for designing potential nano-scale devices based on graphenes.

  12. Infrared signature of micro-hydration in the organophosphate sarin: An ab initio study

    DOE PAGESBeta

    Alam, Todd M.; Pearce, Charles Joseph

    2015-06-28

    The infrared (IR) spectra of micro-hydrated Sarin•(H2O)n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (~1270 to 1290 cm–1) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (~810 to 815 cm–1) and the C-O-P vibrational modes (~995 to 1004 cm–1) showed that the water interactions with these functional groups were minor, and that the structures of Sarin were notmore » extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. As a result, the H2O•H2O vibrational modes (~3450 to 3660 cm–1) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters.« less

  13. Ab initio thermodynamic evaluation of Pd atom interaction with CeO(2) surfaces.

    PubMed

    Mayernick, Adam D; Janik, Michael J

    2009-08-28

    Palladium supported on ceria is an effective catalytic material for three-way automotive catalysis, catalytic combustion, and solid-oxide fuel cell (SOFC) anodes. The morphology, oxidation state, and particle size of Pd on ceria affect catalytic activity and are a function of experimental conditions. This work utilizes ab initio thermodynamics using density functional theory (DFT) (DFT+U) methods to evaluate the stability of Pd atoms, PdO(x) species, and small Pd particles in varying configurations on CeO(2) (111), (110), and (100) single crystal surfaces. Over specific oxygen partial pressure and temperature ranges, palladium incorporation to form a mixed surface oxide is thermodynamically favorable versus other single Pd atom states on each ceria surface. For example, Pd atoms may incorporate into Ce fluorite lattice positions in a Pd(4+) oxidation state on the CeO(2) (111) surface. The ceria support shifts the transition between formal Pd oxidation states (Pd(0), Pd(2+), Pd(4+)) relative to bulk palladium and stabilizes certain oxidized palladium species on each surface. We show that temperature, oxygen pressure, and cell potential in a SOFC can influence the stable states of palladium supported on ceria surfaces, providing insight into structural stability during catalytic operation. PMID:19725615

  14. Ab initio calculations of the mechanical and electronic properties of strained Si nanowires

    NASA Astrophysics Data System (ADS)

    Leu, Paul W.; Svizhenko, Alexei; Cho, Kyeongjae

    2008-06-01

    This paper reports a systematic study of the mechanical and electronic properties of strained small diameter (0.7-2.6 nm) silicon nanowires (Si NWs) using ab initio density functional theory calculations. The values of Young’s modulus, Poisson ratio, band gap, effective mass, work function, and deformation potentials are calculated for ⟨110⟩ and ⟨111⟩ Si NWs. We find that quantum confinement in ⟨110⟩ Si NWs splits conduction band valleys and decreases transport effective mass compared to the bulk case. Consequently, additional tensile strain should not lead to further significant electron mobility improvement. An interesting finding we report in this paper is that under compressive strain, there is a dramatic decrease in deformation potentials of ⟨110⟩ Si NWs, which may result in a strong increase in electron mobilities, despite a concurrent increase in effective mass. We also observe a similar strain-induced counterplay of hole deformation potentials and effective masses for both ⟨110⟩ and ⟨111⟩ Si NWs. Finally, we do not see any significant effect of tensile or compressive strain on electron effective masses and deformation potentials in ⟨111⟩ Si NWs. The sudden changes in effective mass and deformation potentials are concurrent with a change in the conduction and valence band edge states. In ⟨110⟩ NWs, this change corresponds to a transition from direct-to-indirect band gap under strain.

  15. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches.

    PubMed

    Rosenow, Phil; Tonner, Ralf

    2016-05-28

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001). PMID:27250324

  16. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    NASA Astrophysics Data System (ADS)

    Rosenow, Phil; Tonner, Ralf

    2016-05-01

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  17. The vibrational behavior of silica clusters at the glass transition: Ab initio calculations and thermodynamic implications.

    PubMed

    Ottonello, G; Zuccolini, M Vetuschi; Belmonte, D

    2010-09-14

    We present the results of a computational investigation with ab initio procedures of the structure-energy and vibrational properties of silica clusters in a dielectric continuum with dielectric constant ε=3.8, through density functional theory/B3LYP gas phase calculations coupled with a polarized continuum model approach [integral equation formalism applied to a polarized continuum (IEFPCM)] and those of the periodical structure D(6h) which leads to the α-cristobalite polymorph of silica when subjected to symmetry operations with the same functional within the linear combination of atomic orbitals (LCAO) approximation and in the framework of Bloch's theorem. Based on the computed energies and vibrational features, an aggregate of the D(6h) network and the monomer locally ordered in the short-medium range and both present in the glass in a mutual arrangement lacking of spatial continuity reproduces satisfactorily the experimentally observed low T heat capacity and the deviation from the Debye T(3) law. Above T(g), the experimental heat capacity of the liquid is perfectly reproduced summing to the internal modes the translational and rotational contributions to the bulk heat capacity and subtracting the (acoustic) terms arising from coherent motion (no longer existent). PMID:20849179

  18. Stabilization of peptide helices by length and vibrational free energies: Ab initio case study of polyalanine

    NASA Astrophysics Data System (ADS)

    Rossi, Mariana; Blum, Volker; Scheffler, Matthias

    2012-02-01

    Helices are one of the most abundant secondary structure ``building blocks" of polypeptides and proteins. Here, we explore helix stabilization as a function of peptide length and temperature [harmonic approximation to the vibrational free energy (FE)], for the alanine-based peptide, Ac-Alan-LysH^+ n=4-15, in the gas phase. For n=4-8, we predict the lowest energy structures in density-functional theory, using the van der Waals (vdW) corrected[1] PBE exchange-correlation potential. α-helices become the lowest energy structures at n 7-8 on the potential energy surface, but only barely and if including vdW interactions. At finite temperatures, the helices are further stabilized over compact conformers. While the vibrational entropy is the leading stabilizing term at 300 K, also the zero-point-energies favor the helical structures. For n>=8, the α-helix should be the only accessible conformer in the FE surface at 300 K, in agreement with experiment[2] and with our own comparison[3] of calculated ab initio anharmonic IR spectra to experimental IR multiple photon dissociation data for n=5, 10, and 15. [1] Tkatchenko and Scheffler, PRL 102, 073055 (2009); [2] Kohtani and Jarrold, JACS 108, 8454 (2004); [3] Rossi et al., JPCL 1, 3465 (2010).

  19. Large scale ab initio calculations of extended defects in materials: screw dislocations in bcc metals

    NASA Astrophysics Data System (ADS)

    Dézerald, Lucile; Ventelon, Lisa; Willaime, François; Clouet, Emmanuel; Rodney, David

    2014-06-01

    Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for supercells containing 50-to-500 atoms. The topology of the Peierls potential of screw dislocations with 1/2 <111>Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum - and not a minimum as predicted by most empirical potentials - around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions. The first results obtained within the framework of the PRACE project, DIMAIM (DIslocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning-antitwinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results

  20. Time-domain ab initio studies of photoinduced electron dynamics in nanoscale semiconductors

    NASA Astrophysics Data System (ADS)

    Prezhdo, Oleg

    2010-03-01

    Design of novel materials for energy harvesting and storage requires an understanding of the dynamical response on the nanometer scale. We have developed state-of-the-art non-adiabatic molecular dynamics techniques and implemented them within time-dependent density functional theory in order to model the ultrafast processes in these materials at the atomistic level and in real time. Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of molecular and bulk properties. As a result, QDs exhibit new physical phenomena such as the electron-phonon relaxation bottleneck and carrier multiplication, which have the potential to greatly increase solar cell efficiencies. Photoinduced charge separation across molecular/bulk interfaces drives the dye-sensitized semiconductor solar cell. A subject of active research, it creates many challenges due to the stark differences between the quantum states of molecular and periodic systems, as well as the different sets of theories and experimental tools used by physicists and chemists. Our time-domain atomistic simulations create a detailed picture of these materials. By comparing and contrasting their properties, we provide a unifying description of quantum dynamics on the nanometer scale, resolve several highly debated issues, and generate theoretical guidelines for development of novel systems for energy harvesting and storage. [4pt] [1] O. V. Prezhdo ``Photoinduced dynamics in semiconductor quantum-dots: insights from time-domain ab initio studies'', Acc. Chem. Res., available online.[0pt] [2] O. V. Prezhdo, W. R. Duncan, V. V. Prezhdo, ``Photoinduced electron dynamics at semiconductor interfaces: a time-domain ab initio prospective'', Prog. Surf. Science, 84, 39 (2009).[0pt] [3] O. V. Prezhdo, et al., ``Dynamics of the photoexcited electron at the chromophore-semiconductor interface'', Acc. Chem. Res., 41, 339 (2008).[0pt] [4] W. R. Duncan, O. V. Prezhdo, ``Theoretical studies of photoinduced electron

  1. Ab initio computational study of beta-cellobiose conformers using B3LYP/6-311++G**.

    PubMed

    Strati, Gina L; Willett, Julious L; Momany, Frank A

    2002-11-01

    The molecular structure of 27 conformers of beta-cellobiose were studied in vacuo through gradient geometry optimization using B3LYP density functionals and the 6-311++G** basis set. The conformationally dependent geometry changes and energies were explored as well as the hydrogen-bonding network. The lowest electronic energy structures found were not those suggested from available crystallographic and NMR solution data, where the glycosidic dihedral angles fall in the region (phi, psi) approximately (40 degrees, -20 degrees ). Rather, 'flipped' conformations in which the dihedral angles are in the range (phi, psi) approximately (180 degrees, 0 degrees ) are energetically more stable by approximately 2.5 kcal/mol over the 'experimentally accepted' structure. Further, when the vibrational free energy, deltaG, obtained from the calculated frequencies, is compared throughout the series, structures with (phi, psi) in the experimentally observed range still have higher free energy ( approximately 2.0 kcal/mol) than 'flipped' forms. The range of bridging dihedral angles of the 'normal' conformers, resulting from the variance in the phi dihedral is larger than that found in the 'flipped' forms. Due to this large flat energy surface for the normal conformations, we surmise that the summation of populations of these conformations will favor the 'normal' conformations, although evidence suggests that polar solvent effects may play the dominant role in providing stability for the 'normal' forms. Even though some empirical studies previously found the 'flipped' conformations to be lowest in energy, these studies have been generally discredited because they were in disagreement with experimental results. Most of the DFT/ab initio conformations reported here have not been reported previously in the ab initio literature, in part because the use of less rigorous theoretical methods, i.e. smaller basis sets, have given results in general agreement with experimental data, that is

  2. Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

    SciTech Connect

    Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan

    2006-04-05

    A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

  3. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

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

    2014-02-28

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

  4. Dialkylimidazolium chloroaluminates: Ab initio calculations, Raman and neutron scattering measurements

    SciTech Connect

    Takahasi, S. ); Curtiss, L.A.; Gosztola, D.; Koura, N. ); Loong, C.K.; Saboungi, M.L. . Materials Science Div.)

    1993-04-01

    The Raman and neutron scattering spectra of 46 mol% AlCl[sub 3] -54 mol% 1-ethyl-3-methyl imidazolium chloride (EMIC) and 67 mol% AlCl[sub 3] - 33 mol% EMIC melts are presented. Ab initio molecular orbital calculations have been carried out on structures of chloroaluminate anion and EMI cation and the interaction between anion and cation.

  5. Communication: Towards ab initio self-energy embedding theory in quantum chemistry

    NASA Astrophysics Data System (ADS)

    Lan, Tran Nguyen; Kananenka, Alexei A.; Zgid, Dominika

    2015-12-01

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

  6. A Comparative Study of Ab-Initio Thermal Conductivity Approaches: The Case of Cubic Boron Nitride

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Saikat; Lindsay, Lucas; Broido, David; Stewart, Derek

    2013-03-01

    Given its high strength and large thermal conductivity, cubic boron nitride (cBN) provides an important complement to diamond films for heat spreading applications. However, cBN, in contrast to diamond, is a polar material with significant LO-TO splitting in the phonon dispersion. In this talk, we examine the lattice thermal conductivity of cBN using several approaches based on first principles calculations. These approaches include: (1) an analytic modified Callaway-Debye model that relies on parameters from ab-initio harmonic force constants, (2) a fully self-consistent calculation of the thermal conductivity that links an iterative solution of the phonon Boltzmann transport equation (BTE) with harmonic and anharmonic interatomic force constants. The force constants for the BTE are calculated using two approaches: density functional perturbation theory and a real-space supercell approach. We will compare the results from these approaches, highlight the role of normal phonon-phonon scattering, and also examine the impact of optical modes and LO-TO splitting. In addition, we will discuss how isotope scattering affects thermal conductivity and compare this to other boron nitride structures (hexagonal BN, BN sheets and BN nanotubes).

  7. Mechanism of alkane dehydrogenation catalyzed by acidic zeolites: Ab initio transition path sampling

    NASA Astrophysics Data System (ADS)

    Bučko, Tomáš; Benco, Lubomir; Dubay, Orest; Dellago, Christoph; Hafner, Jürgen

    2009-12-01

    The dehydrogenation of propane over acidic chabazite has been studied using ab initio density-functional simulations in combination with static transition-state searches and dynamic transition path sampling (TPS) methods at elevated temperatures. The acidic zeolite has been modeled both using a small cluster and a large periodic model consisting of two unit cells, the TPS simulations allow to account for the effect of temperature and entropy. In agreement with experimental observations we find propene as the dominant reaction product and that the barrier for the dehydrogenation of a methyl group is higher than that for a methylene group. However, whereas all studies based on small cluster models (including the present one) conclude that the reaction proceeds via the formation of an alkoxy intermediate, our TPS studies based on a large periodic model lead to the conclusion that propene formation occurs via the formation of various forms of propyl cations stabilized by entropy, while the formation of an alkoxy species is a relatively rare event. It was observed only in 15% of the reactive trajectories for methyl dehydrogenation and even in only 8% of the methylene dehydrogenation reactions. Our studies demonstrate the importance of entropic effects and the need to account for the structure and flexibility of the zeolitic framework by using large periodic models.

  8. Ab initio calculations of the vibrational and dielectric properties of PbSnTe alloys

    NASA Astrophysics Data System (ADS)

    Scolfaro, Luisa; Rezende Neto, A. R.; Leite Alves, H. W.; Petersen, J. E.; Myers, T. H.; Borges, P. D.

    Thermoelectric devices have promise in dealing with the challenges of the growing demand for alternative clean energy and Te-based materials well-known candidates for them. Recently, we have shown that the high values for the dielectric constant, together with anharmonic LA-TO coupling, reduces the lattice thermal conductivity and enhances the electronic conductivity in PbTe. Also, it was shown that by alloying this material with Se, the electronic conductivity of the alloys is also enhanced. But, it is not clear if the same occurs when alloying with Sn. We show, in this work, our ab initio results for the vibrational and dielectric properties of Pb1-xSnxTe alloys. The calculations were carried out by using the Density Functional Theory, and the alloys were described by both the Virtual Crystal Approximation and Cluster Expansion Method. Our results show that the anharmonic LA-TO coupling enhances and reach its maximum for Sn concentration values of 0.75, corresponding to the maximum value for the dielectric constant, which is higher than that obtained for PbTe

  9. Optimized energy landscape exploration using the ab initio based activation-relaxation technique.

    PubMed

    Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal

    2011-07-21

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface. PMID:21786982

  10. Ab initio Study of Transition metal binding to the Prion Protein

    NASA Astrophysics Data System (ADS)

    Cox, Daniel L.; Singh, Rajiv R. P.; Pan, Jianping

    2004-03-01

    Fundamental understanding of the prion protein (PrP) is of critical public health importance in view of mad cow and chronic wasting diseases. In recent years, it has been shown that the normal form (PrP^c) binds copper^1), and the structure of the copper binding domain has been elaborated. Hypotheses about toxicity associated with binding of other metals (notably manganese) have been put forward, Accordingly, using the ab initio SIESTA density functional theory code^2), we calculated the binding energy E_B(M) of M-(PrP) complexes relative to initially uncomplexed M ions, with M=Cu,Ni,Zn,Mn and (PrP)^* the minimal binding domain. The binding energy trend is E_B(Ni)>E_B(Cu)>E_B(Zn)>E_B(Mn), consistent with recent experiments apart from the surprising stability of Ni. We will also present preliminary results for binding of initially complexed M ions. *-Supported by U.S. DOE, Office of Basic Energy Sciences, Division of Materials Research 1) G.S. Jackson et al., Proc. Nat. Acad. Sci. (USA) 98, 8531 (2001). 2) P. Ordejón, et al., Phys. Rev. B53, R10441 (1996); J.M. Soler et al., J. Phys. Cond. Matt. 14, 2745 (2002).

  11. Ab initio study of intrinsic defects and diffusion behaviors in solid molecular hydrogens

    NASA Astrophysics Data System (ADS)

    Sun, Qingqiang; Ye, Yingting; Yang, Tianle; Yang, Li; Peng, Shuming; Long, Xinggui; Zhou, Xiaosong; Zu, Xiaotao; Du, Jincheng

    2015-12-01

    The behaviors of intrinsic defects in solid molecular hydrogens (H2) were investigated using ab initio calculations based on density functional theory. The results show that the formation energy of a vacancy is dependent on molecule orientation in disordered hexagonal close-packed (hcp) H2 crystals, but independent of molecular orientation in face-centered cubic-Pa3 H2. Furthermore, H2 molecules generally prefer to occupy the basal octahedral sites in hcp and octahedral sites in Pa3 structures. The formation energies of an interstitial H2 depend sensitively on the volume of interstitial sites, and also on near spatial distributions of molecular axes of a H2 in hcp H2 crystals. The strong force field introduced by an interstitial H2 might induce the rotation of molecular axes and reduce the formation energy of the interstitial H2. The migration barrier energy of a vacancy in Pa3 is larger than the average in hcp structures. However, the H2 molecules prefer to jump though vacancies in the two structures of solid H2 than the interstitial migrations.

  12. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    NASA Astrophysics Data System (ADS)

    Lespade, Laure

    2016-08-01

    Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  13. Ab initio calculations of self-interstitial interaction and migration with solute atoms in bcc Fe

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2006-12-01

    The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of solute Cu. Indeed the atom probe and the small angle neutron scattering, principally, have revealed the formation of Cu clusters under neutron flux in reactor pressure vessel (RPV) steels and dilute FeCu alloys. Other solutes such as Ni, Mn and Si which are also found within the clusters, are now suspected to contribute to the embrittlement. The interactions of these solutes with radiation induced point defects need thus to be characterized properly in order to understand the elementary mechanisms behind the formation of these clusters. We have investigated by ab initio calculations based on the density functional theory the interactions of self-interstitials with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si). Different possible configurations of solute-dumbbell complexes have been studied. Their binding energies are discussed, as well as their relative stability. The migration of dumbbells with a solute atom in their vicinity was also investigated. All these results are compared to some experimental ones obtained on dilute FeX model alloys. Our results indicate that for Mn solute atoms, diffusion via an interstitial mechanism is very likely.

  14. Ab initio guided design of bcc Mg-Li alloys for ultra light-weight applications

    NASA Astrophysics Data System (ADS)

    Friák, Martin; Counts, William Art; Raabe, Dierk; Neugebauer, Jörg

    2009-03-01

    Ab initio calculations are becoming increasingly useful to engineers interested in designing new alloys because these calculations are able to accurately predict basic material properties only knowing the atomic composition of the material. In this paper, fundamental physical properties (like formation energies and elastic constants) of 11 bcc Mg-Li compounds are calculated using density-functional theory (DFT) and compared with available experimental data. These DFT-determined properties are in turn used to calculate engineering parameters like (i) specific Young's modulus (Y/ρ) or (ii) bulk over shear modulus ratio (B/G) differentiating between brittle and ductile behavior. The engineering parameters are then used to identify alloys that have optimal mechanical properties needed for a light weight structural material. It was found that the stiffest bcc magnesium-lithium alloys contain about 70 at.% Mg while the most ductile alloys have 0-20 at.% Mg. The specific modulus for alloys with 70 at.% Mg is equal to that of Al-Mg alloys. An Ashby map containing Y/ρ vs. B/G shows that it is not possible to increase both Y/ρ and B/G by changing only the composition or local order of a binary alloy (W. A. Counts, M. Fri'ak, D. Raabe and J. Neugebauer, Acta Mater 57 (2009) 69-76).

  15. Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

    NASA Astrophysics Data System (ADS)

    Liu, Shi-Yu; Liu, Shiyang; Li, De-Jun; Wang, Sanwu; Guo, Jing; Shen, Yaogen

    2015-02-01

    Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustained complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.

  16. Role of Dynamical Instability in the Ab Initio Phase Diagram of Calcium

    NASA Astrophysics Data System (ADS)

    Di Gennaro, Marco; Saha, Srijan Kumar; Verstraete, Matthieu J.

    2013-07-01

    In the 32-119 GPa pressure range and at room temperature, a simple cubic phase was reported for calcium in many different experiments. Standard linear response theory, both within density functional perturbation theory and frozen phonon calculations, presents dynamical instabilities for the simple cubic structure in the whole pressure range. Many other possible candidate phases, as well as several possible stabilization mechanisms for the simple cubic phase, have been proposed as the result of ab initio predictions but the role of temperature on the relative stability of the different phases has not been systematically investigated. We revisit the stability of the three most important candidate phases of calcium for the intermediate pressure range and for various temperatures, taking explicitly into account thermal corrections relative to electronic as well as phononic entropy and anharmonic contributions. This corrects the discrepancies among previous theoretical results and experiments and presents a different picture of the temperature driven phase transition, which results from dynamical anharmonic stabilization of simple cubic and destabilization of the tetragonal phase.

  17. The role of anharmonicity in the ab-initio phase diagram of calcium

    NASA Astrophysics Data System (ADS)

    di Gennaro, Marco; Saha, Srijan Kumar; Verstraete, Matthieu Jean

    2013-03-01

    In the 32-119 GPa pressure range and at room temperature, a simple cubic phase was reported for calcium in many different experiments. Standard linear response theory, both within density functional perturbation theory and frozen phonon calculations, presents dynamical instabilities for simple cubic in the whole pressure range. Many other possible candidate phases, as well as several possible stabilization mechanisms for simple cubic phase, have been proposed as the result of ab-initio predictions but the role of temperature on the relative stability of the different phases has not been investigated systematically. We revisit the stability of three candidate phases of calcium for the intermediate pressure range and for various value of temperatures, taking explicitly into account thermal corrections relative to electronic as well as phononic entropy and anharmonic contributions. This corrects the discrepancies among previous theoretical results and experiments, and presents a different picture of the temperature driven phase transition, which results from dynamical anharmonic stabilization of simple cubic and de-stabilization of the tetragonal phase. Transport quantities are calculated in the stabilized phases, to provide additional points of comparison with experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  19. Raman spectroscopic features of the neutral vacancy in diamond from ab initio quantum-mechanical calculations.

    PubMed

    Baima, Jacopo; Zelferino, Alessandro; Olivero, Paolo; Erba, Alessandro; Dovesi, Roberto

    2016-01-21

    Quantum-mechanical ab initio calculations are performed to elucidate the vibrational spectroscopic features of a common irradiation-induced defect in diamond, i.e. the neutral vacancy. Raman spectra are computed analytically through a Coupled-Perturbed-Hartree-Fock/Kohn-Sham approach as a function of both different defect spin states and defect concentration. The experimental Raman features of defective diamond located in the 400-1300 cm(-1) spectral range, i.e. below the first-order line of pristine diamond at 1332 cm(-1), are well reproduced, thus corroborating the picture according to which, at low damage densities, this spectral region is mostly affected by non-graphitic sp(3) defects. No peaks above 1332 cm(-1) are found, thus ruling out previous tentative assignments of different spectral features (at 1450 and 1490 cm(-1)) to the neutral vacancy. The perturbation introduced by the vacancy to the thermal nuclear motion of carbon atoms in the defective lattice is discussed in terms of atomic anisotropic displacement parameters (ADPs), computed from converged lattice dynamics calculations. PMID:26686374

  20. Communication: Towards ab initio self-energy embedding theory in quantum chemistry.

    PubMed

    Lan, Tran Nguyen; Kananenka, Alexei A; Zgid, Dominika

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces. PMID:26723581

  1. Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.

    PubMed

    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. PMID:26343351

  2. Progress in low-resolution ab initio phasing with CrowdPhase

    PubMed Central

    Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.

    2016-01-01

    Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data. PMID:26960132

  3. Reaction of Stabilized Criegee Intermediates from Ozonolysis of Limonene with Water: Ab Initio and DFT Study

    PubMed Central

    Jiang, Lei; Lan, Ru; Xu, Yi-Sheng; Zhang, Wen-Jie; Yang, Wen

    2013-01-01

    The mechanism of the chemical reaction of H2O with three stabilized Criegee intermediates (stabCI-OO, stabCI-CH3-OO and stabCIx-OO) produced via the limonene ozonolysis reaction has been investigated using ab initio and DFT (Density Functional Theory) methods. It has been shown that the formation of the hydrogen-bonded complexes is followed by two different reaction pathways, leading to the formation of either OH radicals via water-catalyzed H migration or of α-hydroxy hydroperoxide. Both pathways were found to be essential sources of atmospheric OH radical and H2O2 making a significant contribution to the formation of secondary aerosols in the Earth’s atmosphere. The activation energies at the CCSD(T)/6-31G(d) + CF level of theory were found to be in the range of 14.70–21.98 kcal mol−1. The formation of α-hydroxy hydroperoxide for the reaction of stabCIx-OO and H2O with the activation energy of 14.70 kcal mol−1 is identified as the most favorable pathway. PMID:23481640

  4. Ab initio study for the hydrogen abstraction reactions on toluene and tetralin.

    SciTech Connect

    Beste, Ariana; Harrison, Robert J; Britt, Phillip F; Buchanan III, A C

    2006-01-01

    Hydrogen abstraction reactions play a key role in many thermal and catalytic processes involved in the production of fuels and chemicals. In this paper, the hydrogen abstraction reactions on toluene and tetralin by the benzyl radical are investigated by ab initio methods. These reactions are representatives of similar reactions occurring in the thermolysis of lignin model compounds containing the phenethyl phenyl ether (PPE) structural moiety. The title reactions serve to calibrate the theoretical methods to be used in the study of PPE pyrolysis through comparison of the reaction barriers with reliable experimental values. We used two different hybrid density functionals (BHandHLYP, B3LYP) and second-order perturbation theory to obtain equilibrium and transition state geometries. We recomputed selected energy barriers at the B3LYP geometries with the coupled cluster singles and doubles (CCSD) method. Multiple transition states were found for both reactions. BHandHLYP underestimates and second-order perturbation theory overestimates the reaction barriers; B3LYP energy barriers agree well with experiment and the corresponding CCSD energy barriers. The flat potential energy surface around the saddle points causes numerical inaccuracies. We observe the break down of the harmonic approximation in the calculation of low frequencies.

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

    SciTech Connect

    Yang, Li; Peng, SM; Long, XG; Gao, Fei; Heinisch, Howard L.; Kurtz, Richard J.; Zu, Xiaotao T.

    2011-01-05

    Ab initio calculations based on density functional theory have been performed to determine the relative stabilities and migration of H and He atoms in hcp-Sc. The results show that the formation energy of an interstitial H or He atom is smaller than that of a corresponding substitutional atom. The tetrahedral (T) interstitial position is more stable than an octahedral (O) position for both He and H interstitials. The nudged elastic band method has been used to study the migration of interstitial H and He atomss in hcp-Sc. It is found that the migration energy barriers for H interstitials in hcp-Sc are significantly different from those for He interstitials, but that their migration mechanisms are similar. In addition, the formation energies of five different configurations of a He-He pair were determined, revealing that the most stable configuration consists of two He atoms located at the second-neighbor tetrahedral interstitial sites along the c axis. The formation and relative stabilities of some small He clusters have also been investigated.

  6. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

    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(H2O)62+/3+ and Ru(H2O)62+/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.

  7. Tunneling of electrons via rotor-stator molecular interfaces: Combined ab initio and model study

    NASA Astrophysics Data System (ADS)

    Petreska, Irina; Ohanesjan, Vladimir; Pejov, Ljupčo; Kocarev, Ljupčo

    2016-07-01

    Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that conformation-dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previous work where we investigated the coherent transport via strongly coupled delocalized orbital by application of Non-equilibrium Green's Function Formalism.

  8. Ab initio quasiparticle bandstructure of ABA and ABC-stacked graphene trilayers

    NASA Astrophysics Data System (ADS)

    Menezes, Marcos; Capaz, Rodrigo; Louie, Steven

    2013-03-01

    We obtain the quasiparticle band structure of ABA and ABC-stacked graphene trilayers through ab initio density functional theory (DFT) and many-body quasiparticle calculations within the GW approximation. To interpret our results, we fit the DFT and GW π bands to a low energy tight-binding model, which is found to reproduce very well the observed features near the K point. The values of the extracted hopping parameters are reported and compared with available theoretical and experimental data. For both stackings, the quasiparticle corrections lead to a renormalization of the Fermi velocity, an effect also observed in previous calculations on monolayer graphene. They also increase the separation between the higher energy bands, which is proportional to the nearest neighbor interlayer hopping parameter γ1. Both features are brought to closer agreement with experiment through the quasiparticle corrections. Finally, other effects, such as trigonal warping, electron-hole assymetry and energy gaps are discussed in terms of the associated parameters. This work was supported by the Brazilian funding agencies: CAPES, CNPq, FAPERJ and INCT-Nanomateriais de Carbono. It was also supported by NSF grant No. DMR10-1006184 and U.S. DOE under Contract No. DE-AC02-05CH11231.

  9. Insights into photodissociation dynamics of acetaldehyde from ab initio calculations and molecular dynamics simulations

    SciTech Connect

    Chen Shilu; Fang Weihai

    2009-08-07

    In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH{sub 3}CHO). Stationary structures for H{sub 2} and CO eliminations in the ground state (S{sub 0}) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH{sub 3}CHO (265 nm<{lambda}<318 nm), the T{sub 1} C-C bond fission following intersystem crossing from the S{sub 1} state is the predominant channel and the minor channel, the ground-state elimination to CH{sub 4}+CO after internal conversion (IC) from S{sub 1} to S{sub 0}, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S{sub 1}/S{sub 0} intersection point resulting from the S{sub 1} C-C bond fission, becomes accessible and increases the yield of CH{sub 4}+CO.

  10. Progress in low-resolution ab initio phasing with CrowdPhase.

    PubMed

    Jorda, Julien; Sawaya, Michael R; Yeates, Todd O

    2016-03-01

    Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data. PMID:26960132

  11. Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

    SciTech Connect

    Liu, Shi-Yu; Liu, Shiyang; Li, De-Jun; Wang, Sanwu; Guo, Jing; Shen, Yaogen

    2015-02-14

    Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustained complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.

  12. Communication: Towards ab initio self-energy embedding theory in quantum chemistry

    SciTech Connect

    Lan, Tran Nguyen; Kananenka, Alexei A.; Zgid, Dominika

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

  13. An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry

    SciTech Connect

    Matthew Neurock

    2002-09-11

    As the US seeks to develop an energy strategy that reduces the reliance on foreign oil, there is a renewed interest in research and development of the Fischer Tropsch synthesis of converting syngas into long chain hydrocarbon products. This report investigates some of the basic elementary steps for Fischer-Tropsch synthesis over ideal Co and Ru metal surfaces by using ab initio density functional theoretical calculations. This includes activation of CO of CO, the hydrogenation of CH{sub x} intermediates, and the adsorption and dissociation of water. The activation of CO is studied in detail showing a strong dependence on the surface coverage, defect sites and Co-Ru alloy formation. The barriers for CO activation over the ideal (0001) surfaces are quite high making CO activation at the terrace sites unlikely under operating conditions. The calculations for the overall reaction energies at the step edges indicate that these sites are much more reactive. The hydrogenation of the CHx intermediates occurs in a sequential fashion. CH1 was found to be the most stable intermediate over various surfaces. The barriers to form both CH* as well as CH{sub 4} are both found to be highly activated and potentially difficult steps. Water which is a reaction product was found to be weakly adsorbed on Co. Analysis of the microscopic reverse reaction of water activation indicates that this process has a very low activation barrier. Consequently, any water which forms desorbs or is activated to form surface hydroxyl intermediates.

  14. Ab initio study of point defects near stacking faults in 3C-SiC

    DOE PAGESBeta

    Xi, Jianqi; Liu, Bin; Zhang, Yanwen; Weber, William J.

    2016-07-02

    Interactions between point defects and stacking faults in 3C-SiC are studied using an ab initio method based on density functional theory. The results show that the discontinuity of the stacking sequence considerably affects the configurations and behavior of intrinsic defects, especially in the case of silicon interstitials. The existence of an intrinsic stacking fault (missing a C-Si bilayer) shortens the distance between the tetrahedral-center site and its second-nearest-neighboring silicon layer, making the tetrahedral silicon interstitial unstable. Instead of a tetrahedral configuration with four C neighbors, a pyramid-like interstitial structure with a defect state within the band gap becomes a stablemore » configuration. In addition, orientation rotation occurs in the split interstitials that has diverse effects on the energy landscape of silicon and carbon split interstitials in the stacking fault region. Moreover, our analyses of ionic relaxation and electronic structure of vacancies show that the built-in strain field, owing to the existence of the stacking fault, makes the local environment around vacancies more complex than that in the bulk.« less

  15. Argon Interaction with Gold Surfaces: Ab Initio-Assisted Determination of Pair Ar-Au Potentials for Molecular Dynamics Simulations.

    PubMed

    Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline

    2015-07-01

    Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588

  16. AB INITIO EQUATION OF STATE FOR HYDROGEN-HELIUM MIXTURES WITH RECALIBRATION OF THE GIANT-PLANET MASS-RADIUS RELATION

    SciTech Connect

    Militzer, B.; Hubbard, W. B.

    2013-09-10

    Using density functional molecular dynamics simulations, we determine the equation of state (EOS) for hydrogen-helium mixtures spanning density-temperature conditions typical of giant-planet interiors, {approx}0.2-9 g cm{sup -3} and 1000-80,000 K for a typical helium mass fraction of 0.245. In addition to computing internal energy and pressure, we determine the entropy using an ab initio thermodynamic integration technique. A comprehensive EOS table with 391 density-temperature points is constructed and the results are presented in the form of a two-dimensional free energy fit for interpolation. Deviations between our ab initio EOS and the semi-analytical EOS model by Saumon and Chabrier are analyzed in detail, and we use the results for initial revision of the inferred thermal state of giant planets with known values for mass and radius. Changes are most pronounced for planets in the Jupiter mass range and below. We present a revision to the mass-radius relationship that makes the hottest exoplanets increase in radius by {approx}0.2 Jupiter radii at fixed entropy and for masses greater than {approx}0.5 Jupiter mass. This change is large enough to have possible implications for some discrepant ''inflated giant exoplanets''.

  17. Ab Initio Calculations of Singlet and Triplet Excited States of Chlorine Nitrate and Nitric Acid

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    Ab initio calculations of vertical excitations to singlet and triplet excited states of chlorine nitrate and nitric acid are reported. The nature of the electronic transitions are examined by decomposing the difference density into the sum of detachment and attachment densities. Counterparts for the three lowest singlet excited states of nitric acid survive relatively unperturbed in chlorine nitrate, while other low-lying singlet states of chlorine nitrate appear to be directly dissociative in the ClO chromophore. These results suggest an assignment of the two main peaks in the experimental chlorine nitrate absorption spectrum. In addition, triplet vertical excitations and the lowest optimized triplet geometries of both molecules are studied.

  18. Internal dynamics in azetidine: A microwave and ab initio study

    NASA Astrophysics Data System (ADS)

    López, Juan C.; Blanco, Susana; Lesarri, Alberto; Alonso, José L.

    2001-02-01

    The internal dynamics of interconversion between equivalent conformations due to the coupling between ring puckering and NH inversion in azetidine has been investigated by rotational spectroscopy and ab initio computations. Analysis of the rotational spectra in the 8-220 GHz region has been completed for the ground state and first four excited states of the ring-puckering vibration. Rotational transitions exhibit a characteristic doubling originated by tunneling between equivalent conformations through a C2v barrier, which is related to symmetric (A1) and antisymmetric (B1) inversion states. Additionally, nuclear quadrupole hyperfine structure arising from the N nucleus could be resolved for low-J transitions. Accurate rotational and centrifugal distortion parameters together with the energy difference between inversion states derived from μc-type inversion transitions have been derived for each ring-puckering state using a two-state Hamiltonian. An effective monodimensional reduced potential function for the ring-puckering vibration V(X)=10.82(X4+14.29X-8.93X2-0.28X3) has been found consistent with the observed experimental variation of the rotational and centrifugal distortion constants with ring-puckering. This asymmetric single minimum potential function supports the existence of only one stable equatorial form. The barrier to interconversion between equivalent equatorial conformers, related to the C2v conformation of azetidine in which the ring atoms and the NH group are coplanar, has been estimated to range between 1900 and 2600 cm-1. The strong dependence of the dipole moment and quadrupole coupling constants with ring-puckering vibrational state evidence structural changes that occur along the ring-puckering coordinate.

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

    PubMed

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

    2016-07-27

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

  20. Ab initio and DFT study of the geometric structures and static dipole (hyper)polarizabilities of aromatic anions.

    PubMed

    Castellano, O; Bermúdez, Y; Giffard, M; Mabon, G; Cubillan, N; Sylla, M; Nguyen-Phu, X; Hinchliffe, A; Soscún, H

    2005-11-17

    The geometries and the static dipole (hyper)polarizabilities (alpha, beta, gamma) of a series of aromatic anions were investigated at the ab initio (HF, MP2, and MP4) and density functional theory DFT (B3LYP) levels of theory. The anions chosen for the present study are the benzenethiolate (Ph-S-), benzenecarboxylate (Ph-CO2-), benzenesulfinate (Ph-SO2-), benzenesulfonate (Ph-SO3-), and 1,3-benzenedicarboxylate (1,3-Ph-(CO2)2(2-)). For benzenethiolate anion, additional alpha, beta, and gamma calculations were performed at the coupled cluster CCSD level with MP2 optimized geometries. The standard diffuse and polarized 6-31+G(d,p) basis set was employed in conjunction to the ab initio and DFT methods. Additional HF calculations were performed with the 6-311++G(3d,3p) basis set for all the anions. The correlated electric properties were evaluated numerically within the formalism of finite field. The optimized geometries were analyzed in terms of the few reports about the phenolate and sulfonate ions. The results show that electron correlation effects on the polarizabilities are very important in all the anion series. Was found that Ph-SO2- is highly polarizable in terms of alpha and beta, and the Ph-S- is the highest second hyperpolarizable in the series. The results of alpha were rationalized in terms of the analysis of the polarization of charge based in Mulliken atomic population and the structural features of the optimized geometries of anions, whereas the large differences in the beta and gamma values in the series were respectively interpreted in terms of the bond length alternation BLA and the separation of charge in the aromatic ring by effects of the substitution. These results allowed us to suggest the benzenesulfinate and benzenethiolate anions as promising candidates that should be incorporated in ionic materials for second and third-order nonlinear optical devices. PMID:16833334

  1. The ab initio calculation of molecular electric, magnetic and geometric properties.

    PubMed

    Bast, Radovan; Ekström, Ulf; Gao, Bin; Helgaker, Trygve; Ruud, Kenneth; Thorvaldsen, Andreas J

    2011-02-21

    We give an account of some recent advances in the development of ab initio methods for the calculation of molecular response properties, involving electric, magnetic, and geometric perturbations. Particular attention is given to properties in which the basis functions depend explicitly both on time and on the applied perturbations such as perturbations involving nuclear displacements or external magnetic fields when London atomic orbitals are used. We summarize a general framework based on the quasienergy for the calculation of arbitrary-order molecular properties using the elements of the density matrix in the atomic-orbital basis as the basic variables. We demonstrate that the necessary perturbed density matrices of arbitrary order can be determined from a set of linear equations that have the same formal structure as the set of linear equations encountered when determining the linear response equations (or time-dependent self-consistent-field equations). Additional components needed to calculate properties involving perturbation-dependent basis sets are flexible one- and two-electron integral techniques for geometric or magnetic-field differentiated integrals; in Kohn-Sham density-functional theory (KS-DFT), we also need to calculate derivatives of the exchange-correlation functional. We describe a recent proposal for evaluating these contributions based on automatic differentiation. Within this framework, it is now possible to calculate any molecular property for an arbitrary self-consistent-field reference state, including two- and four-component relativistic self-consistent-field wave functions. Examples of calculations that can be performed with this formulation are presented. PMID:21180690

  2. Ab initio cluster study of crystalline NaF

    SciTech Connect

    Temple, D.K.

    1992-01-01

    A highly-accurate ab initio cluster model of crystalline NaF has been constructed to explore the limits of cluster methods in the treatment of ionic solids. The focus of this model was the characterization of the lattice environment and its influence on the easily-polarizable fluorine anion. The model consisted of a central all-electron fluorine anion coordinated by pseudopotentials, to represent the nearest-neighbor sodium cations, and a finite array of point charges chosen to generate the correct crystal field from the surrounding infinite ionic lattice. The wavefunction and properties of the anion were calculated using the restricted Hartree-Fock and configuration interaction techniques from quantum chemistry. An extensive analysis of basis set incompleteness errors in the anion wavefunction was performed. Important features were identified in the embedded anion, such as its distortion under the influence of the lattice compressions, its stabilization from the Madelung potential, and its changes in size due to electron correlations. Bulk properties of the rocksalt-structure (B1) NaF crystal were derived from the total mode energies, calculated as a function of the crystal volume. The properties included the zero-pressure lattice constant, cohesive energy, and bulk modulus, and the pressure-volume equation-of-state. A series of test calculations explored the relationships, and their underlying physical mechanisms, between the features of the embedded anion and the bulk properties of the crystal. These features often produced opposing changes in the properties, demonstrating the importance of a thorough and systematic treatment of the embedded anion. The most thorough test calculation gave bulk properties that were within 1% of experiment. Using an embedded anion model for the high-pressure cesium-chloride (B2) phase of NaF, the B1-to-B2 structural transition was correctly predicted at 25 GPa, in excellent agreement with the experimental values of 23 to 27 GPa.

  3. Ab-Initio Physics of Electrochemistry

    NASA Astrophysics Data System (ADS)

    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.

  4. Ab initio pseudopotential calculation for TTF-TCNQ and TSeF-TCNQ

    NASA Astrophysics Data System (ADS)

    Ishibashi, Shoji; Kohyama, Masanori

    2000-09-01

    We have investigated the electronic structure of the quasi-one-dimensional organic conductor TTF-TCNQ [at room temperature (RT) and 100 K] and TSeF-TCNQ (RT), which have isomorphic crystal structure, by an ab initio plane-wave pseudopotential band calculation. To express the exchange and correlation energy for electrons, we used both the local density approximation and generalized gradient approximation for comparison. For each case, electronic band dispersions were calculated along several symmetric lines and tight-binding parameters were evaluated. The Fermi surface shape was also obtained. The six sets of results (for three structures and two approximations) were compared systematically.

  5. Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

    SciTech Connect

    Holst, Bastian; French, Martin; Redmer, Ronald

    2011-06-15

    Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

  6. Ab initio molecular dynamics: concepts, recent developments, and future trends.

    PubMed

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E

    2005-05-10

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  7. Ab Initio Calculations Of Light-Ion Reactions

    SciTech Connect

    Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W

    2012-03-12

    The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

  8. Ab Initio Electronic Relaxation Times and Transport in Noble Metals

    NASA Astrophysics Data System (ADS)

    Mustafa, Jamal I.; Bernardi, Marco; Neaton, Jeffrey B.; Louie, Steven G.

    Relaxation times employed to study electron transport in metals are typically assumed to be constants and obtained empirically using the Drude model. Here, we employ ab initio calculations to compute the electron-phonon relaxation times of Cu, Ag, and Au, and find that they vary significantly on the Fermi surface, spanning ~15 -45 fs. We compute room temperature resistivities in excellent agreement with experiment by combining GW bandstructures, Wannier-interpolated band velocities, and ab initio relaxation times. Our calculations are compared to other approximations used for the relaxation times. Additionally, an importance sampling scheme is introduced to speed up the convergence of resistivity and transport calculations by sampling directly points on the Fermi surface. This work was supported by NSF Grant No. DMR15-1508412 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at LBNL's NERSC facility.

  9. Towards AB Initio Calculation of the Circular Dichroism of Peptides

    NASA Astrophysics Data System (ADS)

    Molteni, E.; Onida, G.; Tiana, G.

    2012-08-01

    In this work we plan to use ab initio spectroscopy calculations to compute circular dichroism (CD) spectra of peptides. CD provides information on protein secondary structure content; peptides, instead, remain difficult to address, due to their tendency to adopt multiple conformations in equilibrium. Therefore peptides are an interesting test-case for ab initio calculation of CD spectra. As a first application, we focus on the (83-92) fragment of HIV-1 protease, which is known to be involved in the folding and dimerization of this protein. As a preliminary step, we performed classical molecular dynamics (MD) simulations, in order to obtain a set of representative conformers of the peptide. Then, on some of the obtained conformations, we calculated absorption spectra at the independent particle, RPA and TDLDA levels, showing the presence of charge transfer excitations, and their influence on spectral features.

  10. Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations

    SciTech Connect

    Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.

    2013-12-12

    Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

  11. Structural stability and thermodynamics of CrN magnetic phases from ab initio calculations and experiment

    NASA Astrophysics Data System (ADS)

    Zhou, Liangcai; Körmann, Fritz; Holec, David; Bartosik, Matthias; Grabowski, Blazej; Neugebauer, Jörg; Mayrhofer, Paul H.

    2014-11-01

    The dynamical and thermodynamic phase stabilities of the stoichiometric compound CrN including different structural and magnetic configurations are comprehensively investigated using a first-principles density functional theory (DFT) plus U (DFT +U ) approach in conjunction with experimental measurements of the thermal expansion. Comparing DFT and DFT +U results with experimental data reveals that the treatment of electron correlations using methods beyond standard DFT is crucial. The nonmagnetic face-centered cubic B1-CrN phase is both elastically and dynamically unstable, even under high pressure, while CrN phases with nonzero local magnetic moments are predicted to be dynamically stable within the framework of the DFT +U scheme. Furthermore, the impact of different treatments for the exchange-correlation (xc)-functional is investigated by carrying out all computations employing the local density approximation and generalized gradient approximation. To address finite-temperature properties, both magnetic and vibrational contributions to the free energy have been computed employing our recently developed spin-space averaging method. The calculated phase transition temperature between low-temperature antiferromagnetic and high-temperature paramagnetic (PM) CrN variants is in excellent agreement with experimental values and reveals the strong impact of the choice of the xc-functional. The temperature-dependent linear thermal expansion coefficient of CrN is experimentally determined by the wafer curvature method from a reactive magnetron sputter deposited single-phase B1-CrN thin film with dense film morphology. A good agreement is found between experimental and ab initio calculated linear thermal expansion coefficients of PM B1-CrN. Other thermodynamic properties, such as the specific heat capacity, have been computed as well and compared to previous experimental data.

  12. Thermochemical data for CVD modeling from ab initio calculations

    SciTech Connect

    Ho, P.; Melius, C.F.

    1993-12-31

    Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

  13. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

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

    SciTech Connect

    Draayer, Jerry P.

    2014-09-28

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

  15. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    PubMed

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  17. Ab initio phonon properties of half-Heusler NiTiSn, NiZrSn and NiHfSn

    NASA Astrophysics Data System (ADS)

    Andrea, Luc; Hug, Gilles; Chaput, Laurent

    2015-10-01

    A theoretical investigation of phonon properties from first-principles calculations is carried out for the half-Heusler compounds NiXSn, X=\\text{Ti} , Zr and Hf. The crystal structures are optimised via ab initio calculations within the framework of density functional theory. The phonon properties are retrieved from harmonic and anharmonic interatomic force constants calculations using the finite size displacements method and many-body perturbation theory. A solution to the linearized phonon Boltzmann transport equation is then used to compute the ab initio thermal conductivities. For X   =   Ti, Zr and Hf, we found 15.4, 13.3 and 15.8 W m-1 K-1 at 300 K, respectively. Thanks to a spectral analysis of the velocities and lifetimes we were able appreciate the differences in the thermal conductivities between the three compounds under study. Our results provide insights to understand the behaviour of the thermal conductivity and therefore to improve the thermoelectric figure of merit for such materials.

  18. Ab initio phonon properties of half-Heusler NiTiSn, NiZrSn and NiHfSn.

    PubMed

    Andrea, Luc; Hug, Gilles; Chaput, Laurent

    2015-10-28

    A theoretical investigation of phonon properties from first-principles calculations is carried out for the half-Heusler compounds NiXSn, [Formula: see text], Zr and Hf. The crystal structures are optimised via ab initio calculations within the framework of density functional theory. The phonon properties are retrieved from harmonic and anharmonic interatomic force constants calculations using the finite size displacements method and many-body perturbation theory. A solution to the linearized phonon Boltzmann transport equation is then used to compute the ab initio thermal conductivities. For X   =   Ti, Zr and Hf, we found 15.4, 13.3 and 15.8 W m(-1) K(-1) at 300 K, respectively. Thanks to a spectral analysis of the velocities and lifetimes we were able appreciate the differences in the thermal conductivities between the three compounds under study. Our results provide insights to understand the behaviour of the thermal conductivity and therefore to improve the thermoelectric figure of merit for such materials. PMID:26441218

  19. Unified theory of quantized electrons, phonons, and photons out of equilibrium: A simplified ab initio approach based on the generalized Baym-Kadanoff ansatz

    NASA Astrophysics Data System (ADS)

    de Melo, Pedro Miguel M. C.; Marini, Andrea

    2016-04-01

    We present a full ab initio description of the coupled out-of-equilibrium dynamics of photons, phonons, and electrons. In the present approach, the quantized nature of the electromagnetic field as well as of the nuclear oscillations is fully taken into account. The result is a set of integrodifferential equations, written on the Keldysh contour, for the Green's functions of electrons, phonons, and photons where the different kinds of interactions are merged together. We then concentrate on the electronic dynamics in order to reduce the problem to a computationally feasible approach. By using the generalized Baym-Kadanoff ansatz and the completed collision approximation, we introduce a series of efficient but controllable approximations. In this way, we reduce all equations to a set of decoupled equations for the density matrix that describe all kinds of static and dynamical correlations. The final result is a coherent, general, and inclusive scheme to calculate several physical quantities: carrier dynamics, transient photoabsorption, and light emission, all of which include, at the same time, electron-electron, electron-phonon, and electron-photon interactions. We further discuss how all these observables can be easily calculated within the present scheme using a fully atomistic ab initio approach.

  20. Ab initio and relativistic DFT study of spin–rotation and NMR shielding constants in XF{sub 6} molecules, X = S, Se, Te, Mo, and W

    SciTech Connect

    Ruud, Kenneth; Demissie, Taye B.; Jaszuński, Michał

    2014-05-21

    We present an analysis of the spin–rotation and absolute shielding constants of XF{sub 6} molecules (X = S, Se, Te, Mo, W) based on ab initio coupled cluster and four-component relativistic density-functional theory (DFT) calculations. The results show that the relativistic contributions to the spin–rotation and shielding constants are large both for the heavy elements as well as for the fluorine nuclei. In most cases, incorporating the computed relativistic corrections significantly improves the agreement between our results and the well-established experimental values for the isotropic spin–rotation constants and their anisotropic components. This suggests that also for the other molecules, for which accurate and reliable experimental data are not available, reliable values of spin–rotation and absolute shielding constants were determined combining ab initio and relativistic DFT calculations. For the heavy nuclei, the breakdown of the relationship between the spin–rotation constant and the paramagnetic contribution to the shielding constant, due to relativistic effects, causes a significant error in the total absolute shielding constants.