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Sample records for ab initio theories

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

    PubMed

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

    2009-11-01

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

  2. 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

  3. Ab initio valence-space theory for exotic nuclei

    NASA Astrophysics Data System (ADS)

    Holt, Jason

    2015-10-01

    Recent advances in ab initio nuclear structure theory have led to groundbreaking predictions in the exotic medium-mass region, from the location of the neutron dripline to the emergence of new magic numbers far from stability. Playing a key role in this progress has been the development of sophisticated many-body techniques and chiral effective field theory, which provides a systematic basis for consistent many-nucleon forces and electroweak currents. Within the context of valence-space Hamiltonians derived from the nonperturbative in-medium similarity renormalization group (IM-SRG) approach, I will discuss the importance of 3N forces in understanding and making new discoveries in the exotic sd -shell region. Beginning in oxygen, we find that the effects of 3N forces are decisive in explaining why 24O is the last bound oxygen isotope, validating first predictions of this phenomenon from several years ago. Furthermore, 3N forces play a key role in reproducing spectroscopy, including signatures of doubly magic 22,24O, and physics beyond the dripline. Similar improvements are obtained in new spectroscopic predictions for exotic fluorine and neon isotopes, where agreement with recent experimental data is competitive with state-of-the-art phenomenology. Finally, I will discuss first applications of the IM-SRG to effective valence-space operators, such as radii and E 0 transitions, as well as extensions to general operators crucial for our future understanding of electroweak processes, such as neutrinoless double-beta decay. This work was supported by NSERC and the NRC Canada.

  4. Ab initio theory of concentration fluctuations in random alloys

    SciTech Connect

    Stocks, G.M.; Nicholson, D.M.; Gyorffy, B.L.; Wadsworth, J.S.

    1986-01-01

    This document consists of equations for the electronic mean field theory, electronic grand potential, Feynman-Pierles variational theorem, self-consistent KKR-CPa, KKR-CPA theory of direct correlation functions, first-principles Landau theory, and first-principles Cahn-Hilliard theory.

  5. Steady-state ab initio laser theory for N-level lasers.

    PubMed

    Cerjan, Alexander; Chong, Yidong; Ge, Li; Stone, A Douglas

    2012-01-01

    We show that Steady-state Ab initio Laser Theory (SALT) can be applied to find the stationary multimode lasing properties of an N-level laser. This is achieved by mapping the N-level rate equations to an effective two-level model of the type solved by the SALT algorithm. This mapping yields excellent agreement with more computationally demanding N-level time domain solutions for the steady state.

  6. Ab initio theory of spin entanglement in atoms and molecules

    NASA Astrophysics Data System (ADS)

    Pittalis, S.; Troiani, F.; Rozzi, C. A.; Vignale, G.

    2015-02-01

    We investigate spin entanglement in many-electron systems within the framework of density functional theory. We show that the entanglement length, which is extracted from the spatial dependence of the local concurrence, is a sensitive indicator of atomic shells and reveals the character, covalent or metallic, of chemical bonds. These findings shed light on the remarkable success of modern density functionals, which tacitly employ the entanglement length as a variable. This opens the way to further research on entanglement-based functionals.

  7. Ab initio no core calculations of light nuclei and preludes to Hamiltonian quantum field theory

    SciTech Connect

    Vary, J.P.; Maris, P.; Shirokov, A.M.; Honkanen, H.; li, J.; Brodsky, S.J.; Harindranath, A.; Teramond, G.F.de; /Costa Rica U.

    2009-08-03

    Recent advances in ab initio quantum many-body methods and growth in computer power now enable highly precise calculations of nuclear structure. The precision has attained a level sufficient to make clear statements on the nature of 3-body forces in nuclear physics. Total binding energies, spin-dependent structure effects, and electroweak properties of light nuclei play major roles in pinpointing properties of the underlying strong interaction. Eventually,we anticipate a theory bridge with immense predictive power from QCD through nuclear forces to nuclear structure and nuclear reactions. Light front Hamiltonian quantum field theory offers an attractive pathway and we outline key elements.

  8. Scalable numerical approach for the steady-state ab initio laser theory

    NASA Astrophysics Data System (ADS)

    Esterhazy, S.; Liu, D.; Liertzer, M.; Cerjan, A.; Ge, L.; Makris, K. G.; Stone, A. D.; Melenk, J. M.; Johnson, S. G.; Rotter, S.

    2014-08-01

    We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab initio laser theory. Our strategy is to solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate this approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal slabs. Our method paves the way for efficient and accurate simulations of microlasers which were previously inaccessible.

  9. Ab initio molecular dynamics.

    PubMed

    Laasonen, Kari

    2013-01-01

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

  10. Ab Initio Theory of Coherent Laser-Induced Magnetization in Metals

    NASA Astrophysics Data System (ADS)

    Berritta, Marco; Mondal, Ritwik; Carva, Karel; Oppeneer, Peter M.

    2016-09-01

    We present the first materials specific ab initio theory of the magnetization induced by circularly polarized laser light in metals. Our calculations are based on nonlinear density matrix theory and include the effect of absorption. We show that the induced magnetization, commonly referred to as inverse Faraday effect, is strongly materials and frequency dependent, and demonstrate the existence of both spin and orbital induced magnetizations which exhibit a surprisingly different behavior. We show that for nonmagnetic metals (such as Cu, Au, Pd, Pt) and antiferromagnetic metals the induced magnetization is antisymmetric in the light's helicity, whereas for ferromagnetic metals (Fe, Co, Ni, FePt) the imparted magnetization is only asymmetric in the helicity. We compute effective optomagnetic fields that correspond to the induced magnetizations and provide guidelines for achieving all-optical helicity-dependent switching.

  11. Epitaxial strain induced ferroelectricity in rocksalt binary compound: Hybrid functional Ab initio calculation and soft mode group theory analysis

    NASA Astrophysics Data System (ADS)

    Kim, Bog G.

    2011-05-01

    We have studied the detailed mechanism of epitaxial strain induced ferroelectricity in rocksalt binary compound by ab initio calculation and soft mode group theory analysis. By applying compressive strain, cubic binary rocksalt (F m3m) transforms into tetragonal (I 4/mmm) structure. With increasing compressive strain, tetragonal structure becomes unstable against spontaneous transformation to lower symmetry tetragonal structure (I 4/mm), evident both from ab initio calculation and from soft mode group theory analysis. For the tensile strain, phase transition sequence can be cubic binary rocksalt to tetragonal (I 4/mmm) and to orthorhombic structure (I m2m). From ab initio calculation and space group analysis, we propose that the epitaxial strain induced ferroelectricity of rocksalt binary compound is the generic property.

  12. Thermochemistry of Aqueous Hydroxyl Radical from Advances in Photoacoustic Calorimetry and ab Initio Continum Solvation Theory

    SciTech Connect

    Autrey, Thomas; Brown, Aaron K.; Camaioni, Donald M.; Dupuis, Michel; Foster, Nancy S.; Getty, April D.

    2004-03-31

    Photoacoustic signals from dilute ({approx}30 mM) solutions of H{sub 2}O{sub 2} were measured over the temperature range from 10-45 C to obtain the reaction enthalpy and volume change for H{sub 2}O{sub 2}(aq) {yields} 2 OH(aq) from which we ultimately determined {Delta}{sub f}G{sup o}, {Delta}{sub f}H{sup o} and partial molal volume, v{sup o}, of OH (aq). We find {Delta}{sub r}H = 46.8 {+-} 1.4 kcal/mol, which is 4 kcal/mol smaller than the gas phase bond energy, and {Delta}V{sub r} = 6.5 {+-} 0.4 mL/mol. The v{sup o} for OH in water is 14.4 {+-} 0.4 mL/ml: smaller than the v{sup o} of water. Using ab initio continuum theory, the hydration free energy is calculated to be -3.9 {+-} 0.3 kcal/mol (for standard states in number density concentration units) by a novel approach devised to capture in the definition of the solute cavity the strength and specific interactions of the solute with a water solvent molecule. The shape of the cavity is defined by ''rolling'' a 3 dimensional electron density isocontour of water on the ab initio water-OH minimum interaction surface. The value of the contour is selected to reproduce the volume of OH in water. We obtain for OH(aq): {Delta}{sub f}H{sup o} = -0.2 {+-} 1.4 and {Delta}{sub f}G{sup o} = 5.8 {+-} 0.4 kcal/mol that are in agreement with literature values. The results provide confidence in the pulsed PAC technique for measuring aqueous thermochemistry of radicals and open the way to obtaining thermochemistry for most radicals that can be formed by reaction of OH with aqueous substrates while advancing the field of continuum solvation theory towards ab initio-defined solute cavities.

  13. Electron transfer and localization in endohedral metallofullerenes: Ab initio density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Yang, Shenyuan; Yoon, Mina; Hicke, Christian; Zhang, Zhenyu; Wang, Enge

    2008-09-01

    Endohedral metallofullerenes constitute an appealing class of nanoscale building blocks for fabrication of a wide range of materials. One open question of fundamental importance is the precise nature of charge redistribution within the carbon cages (Cn) upon metal encapsulation. Using ab initio density functional theory, we systematically study the electronic structure of metallofullerenes, focusing on the spatial charge redistribution. For large metallofullerenes (n>32) , the valence electrons of the metal atoms are all transferred to the fullerene states. Surprisingly, the transferred charge is found to be highly localized inside the cage near the metal cations rather than uniformly distributed on the surfaces of the carbon cage as traditionally believed. This counterintuitive charge localization picture is attributed to the strong metal-cage interactions within the systems. These findings may prove to be instrumental in the design of fullerene-based functional nanomaterials.

  14. Ab initio downfolding for electron-phonon-coupled systems: Constrained density-functional perturbation theory

    NASA Astrophysics Data System (ADS)

    Nomura, Yusuke; Arita, Ryotaro

    2015-12-01

    We formulate an ab initio downfolding scheme for electron-phonon-coupled systems. In this scheme, we calculate partially renormalized phonon frequencies and electron-phonon coupling, which include the screening effects of high-energy electrons, to construct a realistic Hamiltonian consisting of low-energy electron and phonon degrees of freedom. We show that our scheme can be implemented by slightly modifying the density functional-perturbation theory (DFPT), which is one of the standard methods for calculating phonon properties from first principles. Our scheme, which we call the constrained DFPT, can be applied to various phonon-related problems, such as superconductivity, electron and thermal transport, thermoelectricity, piezoelectricity, dielectricity, and multiferroicity. We believe that the constrained DFPT provides a firm basis for the understanding of the role of phonons in strongly correlated materials. Here, we apply the scheme to fullerene superconductors and discuss how the realistic low-energy Hamiltonian is constructed.

  15. Ab-initio simulations of materials using VASP: Density-functional theory and beyond.

    PubMed

    Hafner, Jürgen

    2008-10-01

    During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces

  16. Towards a full ab initio theory of strong electronic correlations in nanoscale devices

    NASA Astrophysics Data System (ADS)

    Jacob, David

    2015-06-01

    In this paper I give a detailed account of an ab initio methodology for describing strong electronic correlations in nanoscale devices hosting transition metal atoms with open d- or f-shells. The method combines Kohn-Sham density functional theory for treating the weakly interacting electrons on a static mean-field level with non-perturbative many-body methods for the strongly interacting electrons in the open d- and f-shells. An effective description of the strongly interacting electrons in terms of a multi-orbital Anderson impurity model is obtained by projection onto the strongly correlated subspace properly taking into account the non-orthogonality of the atomic basis set. A special focus lies on the ab initio calculation of the effective screened interaction matrix U for the Anderson model. Solution of the effective Anderson model with the one-crossing approximation or other impurity solver techniques yields the dynamic correlations within the strongly correlated subspace giving rise e.g. to the Kondo effect. As an example the method is applied to the case of a Co adatom on the Cu(0 0 1) surface. The calculated low-bias tunnel spectra show Fano-Kondo lineshapes similar to those measured in experiments. The exact shape of the Fano-Kondo feature as well as its width depend quite strongly on the filling of the Co 3d-shell. Although this somewhat hampers accurate quantitative predictions regarding lineshapes and Kondo temperatures, the overall physical situation can be predicted quite reliably.

  17. Nonlocal torque operators in ab initio theory of the Gilbert damping in random ferromagnetic alloys

    NASA Astrophysics Data System (ADS)

    Turek, I.; Kudrnovský, J.; Drchal, V.

    2015-12-01

    We present an ab initio theory of the Gilbert damping in substitutionally disordered ferromagnetic alloys. The theory rests on introduced nonlocal torques which replace traditional local torque operators in the well-known torque-correlation formula and which can be formulated within the atomic-sphere approximation. The formalism is sketched in a simple tight-binding model and worked out in detail in the relativistic tight-binding linear muffin-tin orbital method and the coherent potential approximation (CPA). The resulting nonlocal torques are represented by nonrandom, non-site-diagonal, and spin-independent matrices, which simplifies the configuration averaging. The CPA-vertex corrections play a crucial role for the internal consistency of the theory and for its exact equivalence to other first-principles approaches based on the random local torques. This equivalence is also illustrated by the calculated Gilbert damping parameters for binary NiFe and FeCo random alloys, for pure iron with a model atomic-level disorder, and for stoichiometric FePt alloys with a varying degree of L 10 atomic long-range order.

  18. 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.

  19. 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

  20. Periodic Trends in Lanthanide Compounds through the Eyes of Multireference ab Initio Theory.

    PubMed

    Aravena, Daniel; Atanasov, Mihail; Neese, Frank

    2016-05-01

    Regularities among electronic configurations for common oxidation states in lanthanide complexes and the low involvement of f orbitals in bonding result in the appearance of several periodic trends along the lanthanide series. These trends can be observed on relatively different properties, such as bonding distances or ionization potentials. Well-known concepts like the lanthanide contraction, the double-double (tetrad) effect, and the similar chemistry along the lanthanide series stem from these regularities. Periodic trends on structural and spectroscopic properties are examined through complete active space self-consistent field (CASSCF) followed by second-order N-electron valence perturbation theory (NEVPT2) including both scalar relativistic and spin-orbit coupling effects. Energies and wave functions from electronic structure calculations are further analyzed in terms of ab initio ligand field theory (AILFT), which allows one to rigorously extract angular overlap model ligand field, Racah, and spin-orbit coupling parameters directly from high-level ab initio calculations. We investigated the elpasolite Cs2NaLn(III)Cl6 (Ln(III) = Ce-Nd, Sm-Eu, Tb-Yb) crystals because these compounds have been synthesized for most Ln(III) ions. Cs2NaLn(III)Cl6 elpasolites have been also thoroughly characterized with respect to their spectroscopic properties, providing an exceptionally vast and systematic experimental database allowing one to analyze the periodic trends across the lanthanide series. Particular attention was devoted to the apparent discrepancy in metal-ligand covalency trends between theory and spectroscopy described in the literature. Consistent with earlier studies, natural population analysis indicates an increase in covalency along the series, while a decrease in both the nephelauxetic (Racah) and relativistic nephelauxetic (spin-orbit coupling) reduction with increasing atomic number is calculated. These apparently conflicting results are discussed on the

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Modern ab initio valence bond theory calculations reveal charge shift bonding in protic ionic liquids.

    PubMed

    Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo

    2016-06-21

    The nature of bonding interactions between the cation and the anion of an ionic liquid is at the heart of understanding ionic liquid properties. A particularly interesting case is a special class of ionic liquids known as protic ionic liquids. The extent of proton transfer in protic ionic liquids has been observed to vary according to the interacting species. Back proton transfer renders protic ionic liquids volatile and to be considered as inferior ionic liquids. We try to address this issue by employing modern ab initio valence bond theory calculations. The results indicate that the bonding in the cation and the anion of a prototypical ionic liquid, ethylammonium nitrate, is fundamentally different. It is neither characteristic of covalent/polar covalent bonding nor ionic bonding but rather charge shift bonding as a resonance hybrid of two competing ionic molecular electronic structure configurations. An investigation of other analogous protic ionic liquids reveals that this charge shift bonding seems to be a typical characteristic of protic ionic liquids while the ionic solid analogue compound ammonium nitrate has less charge shift bonding character as compared to protic ionic liquids. Further the extent of charge shift bonding character has been found to be congruent with the trends in many physicochemical properties such as melting point, conductivity, viscosity, and ionicity of the studied ionic liquids indicating that percentage charge shift character may serve as a key descriptor for large scale computational screening of ionic liquids with desired properties.

  6. Modern ab initio valence bond theory calculations reveal charge shift bonding in protic ionic liquids.

    PubMed

    Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo

    2016-06-21

    The nature of bonding interactions between the cation and the anion of an ionic liquid is at the heart of understanding ionic liquid properties. A particularly interesting case is a special class of ionic liquids known as protic ionic liquids. The extent of proton transfer in protic ionic liquids has been observed to vary according to the interacting species. Back proton transfer renders protic ionic liquids volatile and to be considered as inferior ionic liquids. We try to address this issue by employing modern ab initio valence bond theory calculations. The results indicate that the bonding in the cation and the anion of a prototypical ionic liquid, ethylammonium nitrate, is fundamentally different. It is neither characteristic of covalent/polar covalent bonding nor ionic bonding but rather charge shift bonding as a resonance hybrid of two competing ionic molecular electronic structure configurations. An investigation of other analogous protic ionic liquids reveals that this charge shift bonding seems to be a typical characteristic of protic ionic liquids while the ionic solid analogue compound ammonium nitrate has less charge shift bonding character as compared to protic ionic liquids. Further the extent of charge shift bonding character has been found to be congruent with the trends in many physicochemical properties such as melting point, conductivity, viscosity, and ionicity of the studied ionic liquids indicating that percentage charge shift character may serve as a key descriptor for large scale computational screening of ionic liquids with desired properties. PMID:27229870

  7. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    PubMed

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-01

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes. PMID:27074500

  8. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    PubMed

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-01

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

  9. Kinetic isotope effects for Cl + CH4 ⇌ HCl + CH3 calculated using ab initio semiclassical transition state theory.

    PubMed

    Barker, John R; Nguyen, Thanh Lam; Stanton, John F

    2012-06-21

    Calculations were carried out for 25 isotopologues of the title reaction for various combinations of (35)Cl, (37)Cl, (12)C, (13)C, (14)C, H, and D. The computed rate constants are based on harmonic vibrational frequencies calculated at the CCSD(T)/aug-cc-pVTZ level of theory and X(ij) vibrational anharmonicity coefficients calculated at the CCSD(T) /aug-cc-pVDZ level of theory. For some reactions, anharmonicity coefficients were also computed at the CCSD(T)/aug-cc-pVTZ level of theory. The classical reaction barrier was taken from Eskola et al. [J. Phys. Chem. A 2008, 112, 7391-7401], who extrapolated CCSD(T) calculations to the complete basis set limit. Rate constants were calculated for temperatures from ∼100 to ∼2000 K. The computed ab initio rate constant for the normal isotopologue is in good agreement with experiments over the entire temperature range (∼10% lower than the recommended experimental value at 298 K). The ab initio H/D kinetic isotope effects (KIEs) for CH(3)D, CH(2)D(2), CHD(3), and CD(4) are in very good agreement with literature experimental data. The ab initio (12)C/(13)C KIE is in error by ∼2% at 298 K for calculations using X(ij) coefficients computed with the aug-cc-pVDZ basis set, but the error is reduced to ∼1% when X(ij) coefficients computed with the larger aug-cc-pVTZ basis set are used. Systematic improvements appear to be possible. The present SCTST results are found to be more accurate than those from other theoretical calculations. Overall, this is a very promising method for computing ab initio kinetic isotope effects.

  10. Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

    NASA Astrophysics Data System (ADS)

    Signoracci, A.; Duguet, T.; Hagen, G.; Jansen, G. R.

    2015-06-01

    Background: Ab initio many-body methods have been developed over the past 10 yr to address closed-shell nuclei up to mass A ≈130 on the basis of realistic two- and three-nucleon interactions. A current frontier relates to the extension of those many-body methods to the description of open-shell nuclei. Several routes to address open-shell nuclei are currently under investigation, including ideas that exploit spontaneous symmetry breaking. Purpose: Singly open-shell nuclei can be efficiently described via the sole breaking of U(1) gauge symmetry associated with particle-number conservation as a way to account for their superfluid character. While this route was recently followed within the framework of self-consistent Green's function theory, the goal of the present work is to formulate a similar extension within the framework of coupled cluster theory. Methods: We formulate and apply Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wave function of the system as the exponential of a quasiparticle excitation cluster operator acting on a Bogoliubov reference state. Equations for the ground-state energy and the cluster amplitudes are derived at the singles and doubles level (BCCSD) both algebraically and diagrammatically. The formalism includes three-nucleon forces at the normal-ordered two-body level. The first BCC code is implemented in m scheme, which will permit the treatment of doubly open-shell nuclei via the further breaking of SU(2) symmetry associated with angular momentum conservation. Results: Proof-of-principle calculations in an Nmax=6 spherical harmonic oscillator basis for O,1816 and 18Ne in the BCCD approximation are in good agreement with standard coupled cluster results with the same chiral two-nucleon interaction, while 20O and 20Mg display underbinding relative to experiment. The breaking of U(1) symmetry, monitored by computing the variance associated with the particle-number operator, is relatively

  11. Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

    SciTech Connect

    Signoracci, Angelo J.; Duguet, Thomas; Hagen, Gaute; Jansen, G. R.

    2015-06-29

    Background: Ab initio many-body methods have been developed over the past 10 yr to address closed-shell nuclei up to mass A≈130 on the basis of realistic two- and three-nucleon interactions. A current frontier relates to the extension of those many-body methods to the description of open-shell nuclei. Several routes to address open-shell nuclei are currently under investigation, including ideas that exploit spontaneous symmetry breaking. Purpose: Singly open-shell nuclei can be efficiently described via the sole breaking of U(1) gauge symmetry associated with particle-number conservation as a way to account for their superfluid character. While this route was recently followed within the framework of self-consistent Green's function theory, the goal of the present work is to formulate a similar extension within the framework of coupled cluster theory. Methods: We formulate and apply Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wave function of the system as the exponential of a quasiparticle excitation cluster operator acting on a Bogoliubov reference state. Equations for the ground-state energy and the cluster amplitudes are derived at the singles and doubles level (BCCSD) both algebraically and diagrammatically. The formalism includes three-nucleon forces at the normal-ordered two-body level. The first BCC code is implemented in m scheme, which will permit the treatment of doubly open-shell nuclei via the further breaking of SU(2) symmetry associated with angular momentum conservation. Results: Proof-of-principle calculations in an Nmax=6 spherical harmonic oscillator basis for 16,18O and 18Ne in the BCCD approximation are in good agreement with standard coupled cluster results with the same chiral two-nucleon interaction, while 20O and 20Mg display underbinding relative to experiment. The breaking of U(1) symmetry, monitored by computing the variance

  12. Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

    DOE PAGES

    Signoracci, Angelo J.; Duguet, Thomas; Hagen, Gaute; Jansen, G. R.

    2015-06-29

    Background: Ab initio many-body methods have been developed over the past 10 yr to address closed-shell nuclei up to mass A≈130 on the basis of realistic two- and three-nucleon interactions. A current frontier relates to the extension of those many-body methods to the description of open-shell nuclei. Several routes to address open-shell nuclei are currently under investigation, including ideas that exploit spontaneous symmetry breaking. Purpose: Singly open-shell nuclei can be efficiently described via the sole breaking of U(1) gauge symmetry associated with particle-number conservation as a way to account for their superfluid character. While this route was recently followed withinmore » the framework of self-consistent Green's function theory, the goal of the present work is to formulate a similar extension within the framework of coupled cluster theory. Methods: We formulate and apply Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wave function of the system as the exponential of a quasiparticle excitation cluster operator acting on a Bogoliubov reference state. Equations for the ground-state energy and the cluster amplitudes are derived at the singles and doubles level (BCCSD) both algebraically and diagrammatically. The formalism includes three-nucleon forces at the normal-ordered two-body level. The first BCC code is implemented in m scheme, which will permit the treatment of doubly open-shell nuclei via the further breaking of SU(2) symmetry associated with angular momentum conservation. Results: Proof-of-principle calculations in an Nmax=6 spherical harmonic oscillator basis for 16,18O and 18Ne in the BCCD approximation are in good agreement with standard coupled cluster results with the same chiral two-nucleon interaction, while 20O and 20Mg display underbinding relative to experiment. The breaking of U(1) symmetry, monitored by computing the variance associated with the particle-number operator, is

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

    NASA Astrophysics Data System (ADS)

    Borges, P. D.; Scolfaro, L.

    2014-12-01

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

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

    SciTech Connect

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

    2014-12-14

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

  15. Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

    NASA Astrophysics Data System (ADS)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

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

    NASA Astrophysics Data System (ADS)

    Liang, Wenkel

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

  17. 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

  18. Ab initio determination of bond length dependence of the correlated valence shell Hamiltonian of CH: Comparison with semiempirical theories

    NASA Astrophysics Data System (ADS)

    Sun, Hosung; Freed, Karl F.

    1984-01-01

    The exact ab initio effective valence shell Hamiltonian, which is mimicked by semiempirical theories of valence, is calculated for CH at 11 bond lengths using quasidegenerate many-body perturbation theory to incorporate extensive correlation contributions. Least squares fits of the bond length dependence of the calculated CH matrix elements provide simple formulas which are compared with the intuitive forms introduced into semiempirical theories. Some of the semiempirical formulas, e.g., one-center, one-electron integrals and two-center, two-electron integrals, are in good agreement with our correlated ab initio calculations, while others display substantial departures. For example, the bond length dependence of one-center, two-electron integrals, which are assumed to be independent of bond length in semiempirical theories, is substantial but physically understandable. Corrections are found to the assumed proportionality of resonance and overlap integrals. The bond length dependence of nonclassical three-electron integrals is presented along with the hybrid and exchange integrals that are ignored in zero differential overlap methods.

  19. Defects and defect healing in amorphous Si3N4-xHy: An ab initio density functional theory study

    NASA Astrophysics Data System (ADS)

    Hintzsche, L. E.; Fang, C. M.; Marsman, M.; Jordan, G.; Lamers, M. W. P. E.; Weeber, A. W.; Kresse, G.

    2013-10-01

    We present an ab initio density functional theory study of the dominant defects in hydrogenated amorphous silicon nitrides covering different stoichiometries, the influence of hydrogen, and the influence of the annealing history. Whereas nitrogen (N) lone pair states dominate the valence band edge in stoichiometric a-Si3N4, we find that K defects, threefold coordinated silicon (Si) atoms, and Si-Si bond-related states dominate electronic defect contributions in the gap for N-deficient a-Si3N4-x. Hydrogen saturates the dangling Si bonds, significantly reducing the number of electronic defects related to undercoordinated Si atoms.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    SciTech Connect

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

    2002-12-17

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

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

    PubMed

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

    2016-05-13

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ∼1  nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory. PMID:27232042

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    DOE PAGES

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

  6. Linear optical properties and their bond length dependence of yttrium bromide from ab initio and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Alipour, Mojtaba; Mohajeri, Afshan

    2011-08-01

    We have employed conventional ab initio and density functional theory methods to study the electronic properties such as the mean static dipole polarizability, α¯, anisotropy of the polarizability, Δ α, and dipole moment, μ, of yttrium bromide. The bond length dependence of properties is determined at different levels of theory and appropriate expansions around experimental internuclear distance have been presented. Moreover, the first and second geometrical derivatives for each property are quantified and their level of theory dependence has been analyzed. To study the effect of molecular rotation and vibration on the electronic properties, the rovibrational corrections have also been carried out. It is found that these corrections are less pronounced for considered properties of YBr. In all calculations, the electron correlation effects have been considered and discussed. The obtained results show that the electron correlation is more significant in the calculation of the mean and the anisotropy of dipole polarizability.

  7. Complex Magnetism of Lanthanide Intermetallics and the Role of their Valence Electrons: Ab Initio Theory and Experiment.

    PubMed

    Petit, L; Paudyal, D; Mudryk, Y; Gschneidner, K A; Pecharsky, V K; Lüders, M; Szotek, Z; Banerjee, R; Staunton, J B

    2015-11-13

    We explain a profound complexity of magnetic interactions of some technologically relevant gadolinium intermetallics using an ab initio electronic structure theory which includes disordered local moments and strong f-electron correlations. The theory correctly finds GdZn and GdCd to be simple ferromagnets and predicts a remarkably large increase of Curie temperature with a pressure of +1.5 K kbar(-1) for GdCd confirmed by our experimental measurements of +1.6  K kbar(-1). Moreover, we find the origin of a ferromagnetic-antiferromagnetic competition in GdMg manifested by noncollinear, canted magnetic order at low temperatures. Replacing 35% of the Mg atoms with Zn removes this transition, in excellent agreement with long-standing experimental data.

  8. 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.

  9. 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.

  10. Ab initio study of temporary anions of benzene and fluorobenzenes using the multipartitioning many-body perturbation theory.

    PubMed

    Izmaylov, Artur F; Shchegoleva, Lyudmila N; Scuseria, Gustavo E; Zaitsevskii, Andréi

    2005-12-01

    We present an ab initio study of the lowest states of five temporary anions: C6H6(-), C6H5F(-), 1,4-C6H4F2(-), 1,2,3-C6H3F3(-), and 1,3,5-C6H3F3(-). Vertical positions and widths of anionic resonances have been calculated within the stabilization graph approach using the multipartitioning form of the many-body perturbation theory for state-selective effective Hamiltonians restricted to second order (MPPT-R). Good agreement with experimentally derived estimates justifies application of the MPPT-R method for theoretical investigation of haloaromatic temporary anion radicals. PMID:19810321

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

    SciTech Connect

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

    2014-06-07

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

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

    SciTech Connect

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

    2000-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Subotnik, Joseph

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

  16. 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.

  17. Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase

    NASA Astrophysics Data System (ADS)

    Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel

    2016-08-01

    We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent.

  18. 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.

  19. Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase.

    PubMed

    Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel

    2016-08-28

    We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent. PMID:27586898

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

    NASA Astrophysics Data System (ADS)

    Bacca, Sonia

    2016-04-01

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

  1. 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)

  2. An ab initio MO study of butalene

    NASA Astrophysics Data System (ADS)

    Ohta, Katsuhisa; Shima, Toru

    1994-01-01

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

  3. Ab-Initio Hamiltonian Approach to Light Nuclei And to Quantum Field Theory

    SciTech Connect

    Vary, J.P.; Honkanen, H.; Li, Jun; Maris, P.; Shirokov, A.M.; Brodsky, S.J.; Harindranath, A.; de Teramond, G.F.; Ng, E.G.; Yang, C.; Sosonkina, M.; /Ames Lab

    2012-06-22

    Nuclear structure physics is on the threshold of confronting several long-standing problems such as the origin of shell structure from basic nucleon-nucleon and three-nucleon interactions. At the same time those interactions are being developed with increasing contact to QCD, the underlying theory of the strong interactions, using effective field theory. The motivation is clear - QCD offers the promise of great predictive power spanning phenomena on multiple scales from quarks and gluons to nuclear structure. However, new tools that involve non-perturbative methods are required to build bridges from one scale to the next. We present an overview of recent theoretical and computational progress with a Hamiltonian approach to build these bridges and provide illustrative results for the nuclear structure of light nuclei and quantum field theory.

  4. Insights on co-catalyst-promoted enamine formation between dimethylamine and propanal through ab initio and density functional theory study.

    PubMed

    Patil, Mahendra P; Sunoj, Raghavan B

    2007-10-26

    The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.

  5. Ab initio theory of the scattering-independent anomalous Hall effect.

    PubMed

    Weischenberg, Jürgen; Freimuth, Frank; Sinova, Jairo; Blügel, Stefan; Mokrousov, Yuriy

    2011-09-01

    We report on first-principles calculations of the side-jump contribution to the anomalous Hall conductivity (AHC) directly from the electronic structure of a perfect crystal. We implemented our approach for a short-range scattering disorder model within the density functional theory and computed the full scattering-independent AHC in elemental bcc Fe, hcp Co, fcc Ni, and L1(0) FePd and FePt alloys. The full AHC thus calculated agrees systematically with experiment to a degree unattainable so far, correctly capturing the previously missing elements of side-jump contributions, hence paving the way to a truly predictive theory of the anomalous Hall effect and turning it from a characterization tool to a probing tool of multiband complex electronic band structures.

  6. Ab initio theory of superconductivity in a magnetic field. II. Numerical solution

    NASA Astrophysics Data System (ADS)

    Linscheid, A.; Sanna, A.; Gross, E. K. U.

    2015-07-01

    We numerically investigate the spin density functional theory for superconductors (SpinSCDFT) and the approximated exchange-correlation functional, derived and presented in the preceding Paper I [A. Linscheid et al., Phys. Rev. B 92, 024505 (2015), 10.1103/PhysRevB.92.024505]. As a test system, we employ a free-electron gas featuring an exchange splitting, a phononic pairing field, and a Coulomb repulsion. SpinSCDFT results are compared with Sarma, the Bardeen-Cooper-Schrieffer theory, and with an Eliashberg type of approach. We find that the spectrum of the superconducting Kohn-Sham SpinSCDFT system is not in agreement with the true quasiparticle structure. Therefore, starting from the Dyson equation, we derive a scheme that allows to compute the many-body excitations of the superconductor and represents the extension to superconductivity of the G0W0 method in band-structure theory. This superconducting G0W0 method vastly improves the predicted spectra.

  7. Conformers of CL-20 explosive and ab initio refinement using perturbation theory: implications to detonation mechanisms.

    PubMed

    Molt, Robert W; Bartlett, Rodney J; Watson, Thomas; Bazanté, Alexandre P

    2012-12-13

    We have identified the major conformers of CL-20 explosive, otherwise known as 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane, more formally known as 2,4,6,8,10,12-hexanitrohexaazatetracyclo[5.5.0.0]-dodecane, via Monte Carlo search in conformational space through molecular mechanics and subsequent quantum mechanical refinement using perturbation theory. Our search produced enough conformers to account for all of the various forms of CL-20 found in crystals. This suggests that our methodology will be useful in studying the conformational landscape of other nitramines. The energy levels of the conformers found are all within 0.25 eV of one another based on MBPT(2)/6-311G(d,p); consequently, without further refinement from a method such as coupled cluster theory, all conformers may reasonably be populated at STP in the gas phase. We also report the harmonic vibrational frequencies of conformers, including the implications on the mechanism of detonation. In particular, we establish that the weakest N-N nitramine of CL-20 is the cyclohexane equatorial nitramine. This preliminary mapping of the conformers of CL-20 makes it possible to study the mechanism of detonation of this explosive rigorously in future work.

  8. Conformers of CL-20 explosive and ab initio refinement using perturbation theory: implications to detonation mechanisms.

    PubMed

    Molt, Robert W; Bartlett, Rodney J; Watson, Thomas; Bazanté, Alexandre P

    2012-12-13

    We have identified the major conformers of CL-20 explosive, otherwise known as 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane, more formally known as 2,4,6,8,10,12-hexanitrohexaazatetracyclo[5.5.0.0]-dodecane, via Monte Carlo search in conformational space through molecular mechanics and subsequent quantum mechanical refinement using perturbation theory. Our search produced enough conformers to account for all of the various forms of CL-20 found in crystals. This suggests that our methodology will be useful in studying the conformational landscape of other nitramines. The energy levels of the conformers found are all within 0.25 eV of one another based on MBPT(2)/6-311G(d,p); consequently, without further refinement from a method such as coupled cluster theory, all conformers may reasonably be populated at STP in the gas phase. We also report the harmonic vibrational frequencies of conformers, including the implications on the mechanism of detonation. In particular, we establish that the weakest N-N nitramine of CL-20 is the cyclohexane equatorial nitramine. This preliminary mapping of the conformers of CL-20 makes it possible to study the mechanism of detonation of this explosive rigorously in future work. PMID:23136867

  9. Ab initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies.

    PubMed

    Suárez, Dimas; Rayón, Víctor M; Díaz, Natalia; Valdés, Haydée

    2011-10-20

    A set of benchmark results for the geometries, binding energies, and protonation affinities of 24 complexes of small organic ligands with Ca(II) is provided. The chosen level of theory is CCSD(T)/CBS obtained by means of a composite procedure. The performance of four density functionals, namely, PW91, PBE, B3LYP, and TPSS and several Pople-type basis sets, namely, 6-31G(d), 6-31+G(d), 6-31+G(2d,p) and 6-311+G(d) have been assessed. Additionally, the nature of the metal ligand bonding has been analyzed by means of the Symmetry Adapted Perturbation Theory (SAPT). We have found that the B3LYP hybrid functional, in conjunction with either the polarized double-ζ 6-31+G(2d,p) or the triple-ζ 6-311+G(d) basis sets, yields the closest results compared to the benchmark data. The SAPT analysis stresses the importance of induction effects in the binding of these complexes and suggests that consideration of classical electrostatic contributions alone may not be reliable enough for the prediction of relative binding energies for Ca(II) complexes.

  10. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-01

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  11. Ab initio molecular orbital calculations of molten salt vapor complexes using Gaussian-2 theory: LiAlF{sub 4} and NaAlF{sub 4}

    SciTech Connect

    Curtiss, L.A.

    1993-04-01

    The structures and energies of the molten salt vapor complexes LiAlF{sub 4} and NaAlF{sub 4} are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.

  12. Ab initio molecular orbital calculations of molten salt vapor complexes using Gaussian-2 theory: LiAlF[sub 4] and NaAlF[sub 4

    SciTech Connect

    Curtiss, L.A.

    1993-01-01

    The structures and energies of the molten salt vapor complexes LiAlF[sub 4] and NaAlF[sub 4] are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.

  13. 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

  14. 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.

  15. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

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

    2014-11-02

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

  16. 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.

  17. 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

  18. 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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  1. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction

    PubMed Central

    Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690

  2. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction.

    PubMed

    Willow, Soohaeng Yoo; Salim, Michael A; Kim, Kwang S; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation.

  3. 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.

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

    SciTech Connect

    Bergli, Elise; Hjorth-Jensen, Morten

    2011-05-15

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

  5. Monoligand Zn(II) Complexes:  Ab Initio Benchmark Calculations and Comparison with Density Functional Theory Methodologies.

    PubMed

    Rayón, Víctor M; Valdés, Haydee; Díaz, Natalia; Suárez, Dimas

    2008-02-01

    A systematic theoretical study on several models of Zn(II) complexes has been carried out employing both ab initio correlated wave function and density functional methods. The performance of five different functionals namely PW91, PBE, B3LYP, MPWLYP1M, and TPSS in the prediction of metal-ligand bond distances, binding energies, and proton affinities has been assessed comparing the results to those obtained with the MP2 and CCSD(T) wave function methodologies. Several basis sets ranging from double-ζ up to quintuple-ζ quality have been used, including the recently developed all-electron correlation consistent basis sets for zinc. It is shown that all the tested functionals overestimate both the metal-ligand bond distances and the binding energies, being that the B3LYP and TPSS functionals are the ones that perform the best. An analysis of the metal-ligand interaction energy shows that induction and charge-transfer effects play a prominent role in the bonding of these systems, even for those complexes with the less polarizable ligands. This finding highlights the importance of a correct description of the polarization of the monomers' charge densities by any theoretical method which aims to be applied to the study of Zn(II) complexes.

  6. Fermi surfaces, spin-mixing parameter, and colossal anisotropy of spin relaxation in transition metals from ab initio theory

    NASA Astrophysics Data System (ADS)

    Zimmermann, Bernd; Mavropoulos, Phivos; Long, Nguyen H.; Gerhorst, Christian-Roman; Blügel, Stefan; Mokrousov, Yuriy

    2016-04-01

    The Fermi surfaces and Elliott-Yafet spin-mixing parameter (EYP) of several elemental metals are studied by ab initio calculations. We focus first on the anisotropy of the EYP as a function of the direction of the spin-quantization axis [B. Zimmermann et al., Phys. Rev. Lett. 109, 236603 (2012), 10.1103/PhysRevLett.109.236603]. We analyze in detail the origin of the gigantic anisotropy in 5 d hcp metals as compared to 5 d cubic metals by band structure calculations and discuss the stability of our results against an applied magnetic field. We further present calculations of light (4 d and 3 d ) hcp crystals, where we find a huge increase of the EYP anisotropy, reaching colossal values as large as 6000 % in hcp Ti. We attribute these findings to the reduced strength of spin-orbit coupling, which promotes the anisotropic spin-flip hot loops at the Fermi surface. In order to conduct these investigations, we developed an adapted tetrahedron-based method for the precise calculation of Fermi surfaces of complicated shape and accurate Fermi-surface integrals within the full-potential relativistic Korringa-Kohn-Rostoker Green function method.

  7. Ab initio calculations of nitramine dimers

    NASA Astrophysics Data System (ADS)

    Koh-Fallet, Sharon; Schweigert, Igor

    2015-06-01

    Elevated temperatures and pressures are typically thought to have opposing effects on the reaction channels of nitramine decomposition. These high temperatures promote reactions with loose transition structures (positive activation entropies and volumes), such as N-N bond homolysis. Elevated pressures promote reactions with tight transition structures (negative activation entropies and volumes), such as intramolecular and intermolecular H transfer. However, no quantitative data exists regarding the range of temperatures and pressures at which these effects become pronounced. We are pursuing ab initio calculations of the corresponding unimolecular and bimolecular transition structures with the objective of estimating the relevant thermochemical parameters and quantifying the effects of elevated temperature and pressures on the corresponding rate constants. Here, we present density functional theory and complete active space calculations of gas-phase molecular dimers of nitramines as an intermediate step toward modeling transition structures directly in the condensed phase. This work was supported by the Naval Research Laboratory via the American Society for Engineering and Education and by the Office of Naval Research, both directly and through the Naval Research Laboratory.

  8. 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.

  9. 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.

  10. 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.

  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. Vortices of polarization in BaTiO3 core-shell nanoceramics: Calculations based on ab initio derived Hamiltonian versus Landau theory

    NASA Astrophysics Data System (ADS)

    Anoufa, M.; Kiat, J. M.; Kornev, I.; Bogicevic, C.

    2013-10-01

    In this paper, we want to emphasize the fact that many experimental properties of ceramics can be explained by the existence of a core-shell structure of the grains, particularly at small sizes. In this framework, we have studied BaTiO3 (BT) ceramics constituted of core-shell nanoparticles, nanowires, or nanoplanes by using ab initio derived effective Hamiltonian calculations whose application range is for large values of shell thickness and low values of shell permittivity. Many differences and new features compared to the situation of nanodots are induced by the core-shell structure. For instance, phase sequences are different; there is also a coexistence of vortices found by Naumov, Bellaiche, and Fu [I. I. Naumov, L. Bellaiche, and H. Fu, Nature (London)10.1038/nature03107 432, 737 (2004)] in the case of isolated dots with a homogeneous polarization, a transition from cubic paraelectric phase towards nonpolar rhombohedral phase, anomalies in dielectric permittivity associated with the onset of toroidal moments, etc. Afterwards, we compare these results with those obtained by the Landau theory of core-shell ceramics we have recently published. However, the ab initio calculations fail to capture the physics at small shell thickness and/or high shell permittivity, whereas the Landau theory fails to predict the peculiar properties of the phases in which vortices exist. Therefore, in a tentative way to build a global theory, we have constructed a Landau potential using both the polarization and the toroidal moment as competing order parameters, which allows us to propose a phase diagram, whatever the thickness and permittivity of the shell are.

  13. 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.

  14. 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.

  15. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  16. Ab-initio phasing in protein crystallography

    NASA Astrophysics Data System (ADS)

    van der Plas, J. L.; Millane, Rick P.

    2000-11-01

    The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.

  17. Ab initio Study of HZnF

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  18. 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.

  19. 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.

  20. A highly accurate ab initio potential energy surface for methane

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  1. A highly accurate ab initio potential energy surface for methane.

    PubMed

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

    2016-09-14

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement. PMID:27634258

  2. A highly accurate ab initio potential energy surface for methane.

    PubMed

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

    2016-09-14

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

  3. Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1994-01-01

    Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.

  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. Doping-enhanced hyperpolarizabilities of silicon clusters: A global ab initio and density functional theory study of Si10 (Li, Na, K)n (n = 1, 2) clusters

    NASA Astrophysics Data System (ADS)

    Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude

    2011-07-01

    A global theoretical study of the (hyper)polarizabilities of alkali doped Si10 is presented and discussed. First, a detailed picture about the low lying isomers of Si10Li, Si10Na, Si10K, Si10Li2, Si10Na2, and Si10K2 has been obtained in a global manner. Then, the microscopic first (hyper)polarizabilities of the most stable configurations have been determined by means of ab initio methods of high predictive capability such as those based on the Møller-Plesset perturbation and coupled cluster theory, paying extra attention to the (hyper)polarizabilities of the open shell mono-doped systems Si10Li, Si10Na, Si10K, and the influence of spin contamination. These results were used to assess the performance of methods of low computational cost based on density functional theory (DFT) in the reliable computation of these properties in order to proceed with an in-depth study of their evolution as a function of the alkali metal, the cluster composition, and the cluster structure. The most interesting outcomes of the performed (hyper)polarizability study indicate that while alkali doping leaves the per atom polarizability practically unaffected, influences dramatically the hyperpolarizabilities of Si10. The lowest energy structures of the mono-doped clusters are characterized by significantly enhanced hyperpolarizabilities as compared to the analogue neutral or charged bare silicon clusters Si10 and Si11, while, certain patterns governed by the type and the number of the doping agents are followed. The observed hyperpolarizability increase is found to be in close connection with specific cluster to alkali metal charge transfer excited states and to the cluster structures. Moreover, an interesting correlation between the anisotropy of the electron density, and the hyperpolarizabilities of these systems has been observed. Finally, it is important to note that the presented method assessment points out that among the various DFT functionals used in this work, (B3LYP, B3PW91

  6. 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.

  7. 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.

  8. Charge-transfer mechanism for electrophilic aromatic nitration and nitrosation via the convergence of (ab initio) molecular-orbital and Marcus-Hush theories with experiments.

    PubMed

    Gwaltney, Steven R; Rosokha, Sergiy V; Head-Gordon, Martin; Kochi, Jay K

    2003-03-19

    The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.

  9. Effects of quantum confinement on excited state properties of SrTiO3 from ab initio many-body perturbation theory

    NASA Astrophysics Data System (ADS)

    Reyes-Lillo, Sebastian E.; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

    2016-07-01

    The Ruddlesden-Popper (RP) homologous series Srn +1TinO3 n +1 provides a useful template for the study and control of the effects of dimensionality and quantum confinement on the excited state properties of the complex oxide SrTiO3. We use ab initio many-body perturbation theory within the G W approximation and the Bethe-Salpeter equation approach to calculate quasiparticle energies and absorption spectra of Srn +1TinO3 n +1 for n =1 -5 and ∞ . Our computed direct and indirect optical gaps are in excellent agreement with spectroscopic measurements. The calculated optical spectra reproduce the main experimental features and reveal excitonic structure near the gap edge. We find that electron-hole interactions are important across the series, leading to significant exciton binding energies that increase for small n and reach a value of 330 meV for n =1 , a trend attributed to increased quantum confinement. We find that the lowest-energy singlet exciton of Sr2TiO4 (n =1 ) localizes in the two-dimensional plane defined by the TiO2 layer, and we explain the origin of its localization.

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

    PubMed

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

    2014-01-24

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

  11. Double-ionization energies of some n-alkyl isocyanate molecules; studies with double-charge-transfer spectrometry and ab initio propagator theory

    NASA Astrophysics Data System (ADS)

    Bayliss, M. A.; Griffiths, I. W.; Harris, F. M.; Parry, D. E.

    2003-12-01

    Double-charge-transfer (DCT) collisions of H+, OH+ and F+ 3 keV beam ions with a series of alkyl isocyanate molecules were studied using mass spectrometric techniques. Measurement of the kinetic energies of H- ions so produced enabled the determination of double-ionization energies (DIE) for transitions to singlet doubly ionized states of the target molecules; those for triplet doubly ionized states were obtained similarly from measurements of the kinetic energies of OH- and F- ions. Values up to approximately 40 eV were obtained in most cases and were found to be in close agreement with the predictions of ab initio calculations using propagator theory, also presented here. For n-butyl isocyanate (and by implication heavier molecules in the series) the density of doubly ionized states above 30 eV was both observed and predicted to be too large and featureless for meaningful analysis, so establishing an effective upper limit on molecular size for the current application of these techniques. Significant configuration interaction was predicted for the final doubly ionized states, which justified theoretical analysis with a relatively complex method that accounts well for correlation effects.

  12. Ab initio molecular simulations with numeric atom-centered orbitals

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  13. 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.

  14. On the hierarchical parallelization of ab initio simulations

    NASA Astrophysics Data System (ADS)

    Ruiz-Barragan, Sergi; Ishimura, Kazuya; Shiga, Motoyuki

    2016-02-01

    A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.

  15. 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.

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

    PubMed

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

    2008-01-28

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

  17. Finite Elements in Ab Initio Electronic-Structure Calulations

    NASA Astrophysics Data System (ADS)

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

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

  18. 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.

  19. 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)

  20. Ab initio study of hot electrons in GaAs

    PubMed Central

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

    2015-01-01

    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

  1. 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)

  2. 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.

  3. 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.

  4. 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.

  5. 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).

  6. Low-energy electron scattering from CO. 2: Ab-initio study using the frame-transformation theory

    NASA Technical Reports Server (NTRS)

    Chandra, N.

    1976-01-01

    The Wigner-Eisenbud R matrix method has been combined with the frame transformation theory to study electron scattering from molecular systems. The R matrix, calculated at the boundary point of the molecular core radius, has been transformed to the space frame in order to continue the solution of the scattering equations in the outer region where rotational motion of the nuclei is taken into account. This procedure has been applied to a model calculation of thermal energy electron scattering from CO.

  7. Unified ab initio approaches to nuclear structure and reactions

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  8. 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.

  9. 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.

  10. 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.

  11. Accurate Prediction of Hyperfine Coupling Constants in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method.

    PubMed

    Yamada, Kenta; Kawashima, Yukio; Tachikawa, Masanori

    2014-05-13

    We performed ab initio path integral molecular dynamics (PIMD) simulations with a density functional theory (DFT) method to accurately predict hyperfine coupling constants (HFCCs) in the ethyl radical (CβH3-CαH2) and its Mu-substituted (muoniated) compound (CβH2Mu-CαH2). The substitution of a Mu atom, an ultralight isotope of the H atom, with larger nuclear quantum effect is expected to strongly affect the nature of the ethyl radical. The static conventional DFT calculations of CβH3-CαH2 find that the elongation of one Cβ-H bond causes a change in the shape of potential energy curve along the rotational angle via the imbalance of attractive and repulsive interactions between the methyl and methylene groups. Investigation of the methyl-group behavior including the nuclear quantum and thermal effects shows that an unbalanced CβH2Mu group with the elongated Cβ-Mu bond rotates around the Cβ-Cα bond in a muoniated ethyl radical, quite differently from the CβH3 group with the three equivalent Cβ-H bonds in the ethyl radical. These rotations couple with other molecular motions such as the methylene-group rocking motion (inversion), leading to difficulties in reproducing the corresponding barrier heights. Our PIMD simulations successfully predict the barrier heights to be close to the experimental values and provide a significant improvement in muon and proton HFCCs given by the static conventional DFT method. Further investigation reveals that the Cβ-Mu/H stretching motion, methyl-group rotation, methylene-group rocking motion, and HFCC values deeply intertwine with each other. Because these motions are different between the radicals, a proper description of the structural fluctuations reflecting the nuclear quantum and thermal effects is vital to evaluate HFCC values in theory to be comparable to the experimental ones. Accordingly, a fundamental difference in HFCC between the radicals arises from their intrinsic molecular motions at a finite temperature, in

  12. 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.

  13. 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.

  14. 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.

  15. 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].

  16. 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.

  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 water pair potential with flexible monomers.

    PubMed

    Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof

    2015-03-26

    A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects.

  19. Ab initio study of palladium and silicon carbide

    SciTech Connect

    Schuck, Paul C; Stoller, Roger E; Shrader, David

    2011-01-01

    Ab initio methods have been used to investigate the properties of Pd as impurity in bulk SiC at five charge states within the framework of density functional theory using the local density spin approximation. Pd interstitials and substitutionals have similar energy to their intrinsic counterparts. In addition, Pd substitutes for a vacancy, di-vacancy, and tri-vacancy with similar energies. Pd will also diffuse through SiC via an interstitial mechanism employing the tetrahedral sites and Pd can substitute for Si and C at positive charge states. Removing electrons (p-type doping) from SiC lowers the formation and migration energies of Pd defects in SiC for most configurations.

  20. Ab initio and RRKM calculations of o-benzyne pyrolysis

    NASA Astrophysics Data System (ADS)

    Deng, Wei-Qiao; Han, Ke-Li; Zhan, Ji-Ping; He, Guo-Zhong

    1998-05-01

    Recently, a new mechanism has been provided in the phenyl pyrolysis, that is, the phenyl dissociation favours the benzyne channel by losing an H atom [H. Wang, M. Frenklach, J. Phys. Chem., 98 (1994) 11465]. In this Letter, the dissociation of o-benzyne has been investigated by means of ab initio theory. The geometries and structures of o-benzyne with its pyrolysis products C 4H 2, C 2H 2 and also the transition state were optimized at the UHF/6-31G* level. The single point energies were refined by B3LYP/6-31G* calculations. The unimolecular rate constants for o-benzyne pyrolysis in different pressures were calculated by the Rice-Ramsperger-Kassel-Marcus (RRKM) method.

  1. Ab initio water pair potential with flexible monomers.

    PubMed

    Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof

    2015-03-26

    A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects. PMID:25687650

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Varas, Alejandro; García-González, Pablo; Feist, Johannes; García-Vidal, F. J.; Rubio, Angel

    2016-08-01

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

  5. 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

  6. 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.

  7. 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

  8. Transition state theory thermal rate constants and RRKM-based branching ratios for the N((2)D) + CH(4) reaction based on multi-state and multi-reference ab initio calculations of interest for the Titan's chemistry.

    PubMed

    Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice

    2012-10-30

    Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH.

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

    SciTech Connect

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

    2004-07-08

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

  10. 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.

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2000-08-01

    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

  13. 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.

  14. 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.

  15. Ab initio calculations in three-body cluster systems

    SciTech Connect

    Romero-Redondo, C.; Navratil, P.; Quaglioni, S.

    2013-06-10

    In this work we briefly outline the extension of the ab initio no-core shell model/Resonating group method (NCSM/RGM) to three-body cluster states. We present the results for {sup 6}He ground state within a {sup 4}He+n+n cluster basis under this approach.

  16. Rate coefficients of the CF3CHFCF3 + H → CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths.

    PubMed

    Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

    2013-03-15

    The minimum energy path (MEP) of the reaction, CF(3)CHFCF(3) + H → transition state (TS) → CF(3)CFCF(3) + H(2), has been computed at different ab initio levels and with density functional theory (DFT) using different functionals. The computed B3LYP/6-31++G**, BH&HLYP/cc-pVDZ, BMK/6-31++G**, M05/6-31+G**, M05-2X/6-31+G**, UMP2/6-31++G**, PUMP2/6-31++G**//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVDZ//UMP2/6-31++G**, RCCSD(T)/aug-cc-pVTZ(spd,sp)//UMP2//6-31++G**, RCCSD(T)/CBS//M05/6-31+G**, and RCCSD(T)/CBS//UMP2/6-31++G** MEPs, and associated gradients and Hessians, were used in reaction rate coefficient calculations based on the transition state theory (TST). Reaction rate coefficients were computed between 300 and 1500 K at various levels of TST, which include conventional TST, canonical variational TST (CVT) and improved CVT (ICVT), and with different tunneling corrections, namely, Wigner, zero-curvature, and small-curvature (SCT). The computed rate coefficients obtained at different ab initio, DFT and TST levels are compared with experimental values available in the 1000-1200 K temperature range. Based on the rate coefficients computed at the ICVT/SCT level, the highest TST level used in this study, the BH&HLYP functional performs best among all the functionals used, while the RCCSD(T)/CBS//MP2/6-31++G** level is the best among all the ab initio levels used. Comparing computed reaction rate coefficients obtained at different levels of theory shows that, the computed barrier height has the strongest effect on the computed reaction rate coefficients as expected. Variational effects on the computed rate coefficients are found to be negligibly small. Although tunneling effects are relatively small at high temperatures (~1500 K), SCT corrections are significant at low temperatures (~300 K), and both barrier heights and the magnitudes of the imaginary frequencies affect SCT corrections.

  17. Computer simulation of acetonitrile and methanol with ab initio-based pair potentials

    NASA Astrophysics Data System (ADS)

    Hloucha, M.; Sum, A. K.; Sandler, S. I.

    2000-10-01

    This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.

  18. Ab initio calculations of As-vacancy interactions in silicon

    SciTech Connect

    Xie, J.; Chen, S.P.

    1999-04-01

    Atomistic simulation of a vacancy-assisted dopant diffusion in silicon needs details of the dopant-vacancy interaction, i.e., the potential as a functional of dopant-vacancy separations. In this paper, the authors present a detailed study on the energetics of As-vacancy reaction in silicon and the lattice distortions surrounding the As-vacancy defect by using an ab initio plane wave pseudopotential method and the density functional theory (DFT). A potential-energy diagram as a function of As-vacancy separation is provided, which can be used in the atomistic diffusion simulations. The authors also calculate the binding energy and the formation energy of different complexes such as AsV, As{sub 2}V and AsV{sub 2} (V represents vacancy). They find that the stable configuration of As{sub 2}V is As-V-As, while the stable configuration of AsV{sub 2} is As-V-V. The nature of the binding between As and vacancy is explained from the lattice distortions and the change of chemical bond configuration introduced by the As-vacancy complex.

  19. Ab initio simulations of MgO under extreme conditions

    NASA Astrophysics Data System (ADS)

    Cebulla, Daniel; Redmer, Ronald

    2014-04-01

    We determined the phase diagram of magnesium oxide with finite-temperature density functional theory molecular dynamics simulations up to temperatures and pressures as relevant for the deep interior of super-Earths and in rocky cores of giant planets such as Jupiter. The equation of state data, the Hugoniot, and a ramp compression curve are computed and compared to earlier results from diamond anvil cell and (decaying) shock wave experiments. In addition, the dynamical electrical conductivity and the reflectivity along the experimental Hugoniot curve are calculated in order to characterize electronic structure changes under compression. The structural properties of MgO are identified using pair correlation functions and self-diffusion coefficients. The solid-solid coexistence line is calculated by comparing the free enthalpies of the B1 and the B2 phase. The free energy of the solid phases is determined via thermodynamic relations using the ab initio simulation results and phonon calculations in the harmonic approximation. Our results indicate that the solid B2 phase of MgO does not occur in the interior of the Earth but may play an important role in super-Earths and in rocky planetary cores.

  20. Predicting lattice thermal conductivity with help from ab initio methods

    NASA Astrophysics Data System (ADS)

    Broido, David

    2015-03-01

    The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.

  1. Ab Initio Study of Covalently Functionalized Graphene and Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Jha, Sanjiv; Hammouri, Mahmoud; Vasiliev, Igor; Magedov, Igor; Frolova, Liliya; Kalugin, Nikolai

    2014-03-01

    The electronic and structural properties of carbon nanomaterials can be affected by chemical functionalization. We apply ab initio computational methods based on density functional theory to study the properties of graphene and single-walled carbon nanotubes functionalized with benzyne. Our calculations are carried out using the SIESTA electronic structure code combined with the generalized gradient approximation for the exchange correlation functional. The calculated binding energies, densities of states, and band structures of functionalized graphene and carbon nanotubes are analyzed in comparison with the available experimental data. The surfaces of carbon nanotubes are found to be significantly more reactive toward benzyne molecules than the surface of graphene. The strength of interaction between benzyne and carbon nanotubes is affected by the curvature of the nanotube sidewall. The binding energies of benzyne molecules attached to both semiconducting zigzag and metallic armchair nanotubes increase with decreasing the nanotube diameter. Supported by NSF CHE-1112388, NMSU GREG Award, NSF ECCS-0925988, NIH-5P20RR016480-12, and NIH- P20 GM103451.

  2. Ab initio calculations of nuclear reactions important for astrophysics

    NASA Astrophysics Data System (ADS)

    Navratil, Petr; Dohet-Eraly, Jeremy; Calci, Angelo; Horiuchi, Wataru; Hupin, Guillaume; Quaglioni, Sofia

    2016-09-01

    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. One of the newly developed approaches is the No-Core Shell Model with Continuum (NCSMC), capable of describing both bound and scattering states in light nuclei simultaneously. We will present NCSMC results for reactions important for astrophysics that are difficult to measure at relevant low energies, such as 3He(α,γ)7Be and 3H(α,γ)7Li and 11C(p,γ)12N radiative capture, as well as the 3H(d,n)4He fusion. We will also address prospects of calculating the 2H(α,γ)6Li capture reaction within the NCSMC formalism. Prepared in part by LLNL under Contract DE-AC52-07NA27344. Supported by the U.S. DOE, OS, NP, under Work Proposal No. SCW1158, and by the NSERC Grant No. SAPIN-2016-00033. TRIUMF receives funding from the NRC Canada.

  3. Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach

    NASA Astrophysics Data System (ADS)

    Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.

    2009-08-01

    Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

  4. 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

  5. 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.

  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. 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

  8. 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.

  9. 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.

  10. Ab initio molecular dynamics: Concepts, recent developments, and future trends

    PubMed Central

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E.

    2005-01-01

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed “on the fly” from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  11. 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.

  12. 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.

  13. 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.

  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. 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.

  16. 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.

  17. 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.

  18. Acceleration of the Convergence in ab initio Atomic Relaxations

    NASA Astrophysics Data System (ADS)

    Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan

    2006-03-01

    Atomic relaxations is often required to accurately describe the properties of nanosystems. In ab initio calculations, a common practice is to use a standard search algorithm, such as BFGS (Broyden-Fletcher-Goldfarb-Shanno) or CG (conjugate gradient) method, which starts the atomic relaxations without any knowledge of the Hessian matrix of the system. For example, the initial Hessian in BFGS method is often set to identity, and there is no preconditioning to CG method. One way to accelerate the convergence of the atomic relaxations is to estimate an approximate Hessian matrix of the system and then use it as the initial Hessian in BFGS method or a preconditioner in CG method. Previous attempts to obtain the approximated Hessian were focused on the use of classical force field models which rely on the existence of good parameters. Here, we present an alternative method to estimate the Hessian matrix of a nanosystem. First, we decompose the system into motifs which consist of a few atoms, then calculate the Hessian matrix elements on different motif types from ab initio calculations for small prototype systems. Then we generate the Hessian Matrix of the whole system by putting together these motif Hessians. We have applied our motif-based Hessian matrix in ab initio atomic relaxations in several bulk (with/without impurity) and quantum dot systems, and have found a speed up factor of 2 to 4 depending on the system size.

  19. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    1996-03-01

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

  20. 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).

  1. 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.

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

    PubMed

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

    2010-09-29

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

  3. 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

  4. Ab Initio Calculations of Water Line Strengths

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Partridge, Harry

    1998-01-01

    We report on the determination of a high quality ab initiu potential energy surface (PES) and dipole moment function for water. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base with J less than 6 for H2O. The changes in the PES are small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Using this adjusted PES, we can match 30,092 of the 30,117 transitions in the HITRAN 96 data base for H2O with theoretical lines. The 10,25,50,75, and 90 percentiles of the difference between the calculated and tabulated line positions are -0.11, -0.04, -0.01, 0.02, and 0.07 l/cm. Non-adiabatic effects are not explicitly included. About 3% of the tabulated line positions appear to be incorrect. Similar agreement using this adjusted PES is obtained for the oxygen 17 and oxygen 18 isotopes. For HDO, the agreement is not as good, with root-mean-square error of 0.25 l/cm for lines with J less than 6. This error is reduced to 0.02 l/cm by including a small asymmetric correction to the PES, which is parameterized by simultaneously fitting to HDO md D2O data. Scaling this correction by mass factors yields good results for T2O and HTO. The intensities summed over vibrational bands are usually in good agreement between the calculations and the tabulated results, but individual lines strengths can differ greatly. A high temperature list consisting of 307,721,352 lines is generated for H2O using our PES and dipole moment function.

  5. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    SciTech Connect

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

    2013-07-20

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

  6. Ab initio kinetics of gas phase decomposition reactions.

    PubMed

    Sharia, Onise; Kuklja, Maija M

    2010-12-01

    The thermal and kinetic aspects of gas phase decomposition reactions can be extremely complex due to a large number of parameters, a variety of possible intermediates, and an overlap in thermal decomposition traces. The experimental determination of the activation energies is particularly difficult when several possible reaction pathways coexist in the thermal decomposition. Ab initio calculations intended to provide an interpretation of the experiment are often of little help if they produce only the activation barriers and ignore the kinetics of the decomposition process. To overcome this ambiguity, a theoretical study of a complete picture of gas phase thermo-decomposition, including reaction energies, activation barriers, and reaction rates, is illustrated with the example of the β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) molecule by means of quantum-chemical calculations. We study three types of major decomposition reactions characteristic of nitramines: the HONO elimination, the NONO rearrangement, and the N-NO(2) homolysis. The reaction rates were determined using the conventional transition state theory for the HONO and NONO decompositions and the variational transition state theory for the N-NO(2) homolysis. Our calculations show that the HMX decomposition process is more complex than it was previously believed to be and is defined by a combination of reactions at any given temperature. At all temperatures, the direct N-NO(2) homolysis prevails with the activation barrier at 38.1 kcal/mol. The nitro-nitrite isomerization and the HONO elimination, with the activation barriers at 46.3 and 39.4 kcal/mol, respectively, are slow reactions at all temperatures. The obtained conclusions provide a consistent interpretation for the reported experimental data. PMID:21077597

  7. Ab initio study of Fe(+)-benzyne

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1993-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  9. 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.

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

    PubMed

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

    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. PMID:25877566

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  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. Conformational studies by liquid crystal NMR and ab initio calculations: methyl nicotinate and methyl isonicotinate

    NASA Astrophysics Data System (ADS)

    Kon, Masao; Kurokawa, Hideki; Takeuchi, Hiroshi; Konaka, Shigehiro

    1992-04-01

    Conformational properties of methyl nicotinate and methyl isonicotinate have been studied by liquid crystal 1H-NMR spectroscopy combined with ab initio calculations. The solvent used is a mixture of 80 mol.% of EBBA and 20 mol.% of MBBA.Ab initio calculations have been performed with 4-21G and MINI-4 basis sets to estimate molecular structures and the potential functions for internal rotation. Some structural parameters and the energy difference between rotational isomers have been refined by using observed dipolar coupling constants. The correlation between internal rotation and reorientational molecular motion has been taken into account according to the theory of Emsley, Luckhurst and Stockley. The parameters of the mean external potential are found to take similar values for methyl nicotinate and methyl isonicotinate. The energy difference of the two stable conformers of methyl nicotinate is in agreement with the analysis neglecting the correlation between the two motions.

  14. Point defect modeling in materials: Coupling ab initio and elasticity approaches

    NASA Astrophysics Data System (ADS)

    Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel

    2013-10-01

    Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.

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

    PubMed

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

    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.

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Senent, M. L.

    1995-06-01

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

  18. 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.

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

    PubMed

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

    2013-02-27

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

  20. 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

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

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

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

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  3. In pursuit of the ab initio limit for conformational energy prototypes

    NASA Astrophysics Data System (ADS)

    Császár, Attila G.; Allen, Wesley D.; Schaefer, Henry F.

    1998-06-01

    The convergence of ab initio predictions to the one- and n-particle limits has been systematically explored for several conformational energy prototypes: the inversion barriers of ammonia, water, and isocyanic acid, the torsional barrier of ethane, the E/Z rotamer separation of formic acid, and the barrier to linearity of silicon dicarbide. Explicit ab initio results were obtained with atomic-orbital basis sets as large as [7s6p5d4f3g2h1i/6s5p4d3f2g1h] and electron correlation treatments as extensive as fifth-order Møller-Plesset perturbation theory (MP5), the full coupled-cluster method through triple excitations (CCSDT), and Brueckner doubles theory including perturbational corrections for both triple and quadruple excitations [BD(TQ)]. Subsequently, basis set and electron correlation extrapolation schemes were invoked to gauge any further variations in arriving at the ab initio limit. Physical effects which are tacitly neglected in most theoretical work have also been quantified by computations of non-Born-Oppenheimer (BODC), relativistic, and core correlation shifts of relative energies. Instructive conclusions are drawn for the pursuit of spectroscopic accuracy in theoretical conformational analyses, and precise predictions for the key energetic quantities of the molecular prototypes are advanced.

  4. Polymeric nitrogen in a graphene matrix: An ab initio study

    NASA Astrophysics Data System (ADS)

    Timoshevskii, V.; Ji, Wei; Abou-Rachid, Hakima; Lussier, Louis-Simon; Guo, H.

    2009-09-01

    A hybrid material where polymeric nitrogen chains are sandwiched between graphene sheets in the form of a three-dimensional crystal, is predicted by means of ab initio simulations. It is demonstrated that chainlike polymeric nitrogen phase becomes stable at ambient pressure when intercalated in a multilayer graphene matrix. The physical origin of this stabilization is identified by studying the electronic properties of the system. This approach of stabilizing polymeric nitrogen by means of external three-dimensional matrix constitutes a path toward synthesizing different types of nitrogen-based high-energy materials.

  5. Ab initio quantum chemical study of electron transfer in carboranes

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

  6. 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.

  7. Accelerating ab initio molecular dynamics simulations by linear prediction methods

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

    Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

  8. Exploring Transition Metal Catalyzed Reactions via AB Initio Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2011-06-01

    The study and prediction of chemical reactivity is one of the most influential contributions of quantum chemistry. A central concept in the theoretical treatment of chemical reactions is the reaction pathway, which can be quite difficult to integrate accurately and efficiently. This talk will outline our developments in the integration of these pathways on ab initio potential energy surfaces. We will also describe results from recent studies on the kinetics of transition metal catalyzed reactions, including the importance of vibrational coupling to the reaction coordinate and the role of this coupling in catalytic rate enhancement.

  9. Ab-initio study of napthelene based conducting polymer

    SciTech Connect

    Ruhela, Ankur; Kanchan, Reena; Srivastava, Anurag; Sinha, O. P.

    2014-04-24

    In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.

  10. Ab Initio Computation of the Energies of Circular Quantum Dots

    SciTech Connect

    Lohne, M. Pedersen; Hagen, Gaute; Hjorth-Jensen, M.; Kvaal, S.; Pederiva, F.

    2011-01-01

    We perform coupled-cluster and diffusion Monte Carlo calculations of the energies of circular quantum dots up to 20 electrons. The coupled-cluster calculations include triples corrections and a renormalized Coulomb interaction defined for a given number of low-lying oscillator shells. Using such a renormalized Coulomb interaction brings the coupled-cluster calculations with triples correlations in excellent agreement with the diffusion Monte Carlo calculations. This opens up perspectives for doing ab initio calculations for much larger systems of electrons.

  11. 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.

  12. Pseudorotation motion in tetrahydrofuran: an ab initio study.

    PubMed

    Rayón, Víctor M; Sordo, Jose A

    2005-05-22

    The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.

  13. Computational Evidence of Inversion of (1)La and (1)Lb-Derived Excited States in Naphthalene Excimer Formation from ab Initio Multireference Theory with Large Active Space: DMRG-CASPT2 Study.

    PubMed

    Shirai, Soichi; Kurashige, Yuki; Yanai, Takeshi

    2016-05-10

    The naphthalene molecule has two important lowest-lying singlet excited states, denoted (1)La and (1)Lb. Association of the excited and ground state monomers yields a metastable excited dimer (excimer), which emits characteristic fluorescence. Here, we report a first computational result based on ab initio theory to corroborate that the naphthalene excimer fluorescence is (1)La parentage, resulting from inversion of (1)La and (1)Lb-derived dimer states. This inversion was hypothesized by earlier experimental studies; however, it has not been confirmed rigorously. In this study, the advanced multireference (MR) theory based on the density matrix renormalization group that enables using unprecedented large-size active space for describing significant electron correlation effects is used to provide accurate potential energy curves (PECs) of the excited states. The results evidenced the inversion of the PECs and accurately predicted transition energies for excimer fluorescence and monomer absorption. Traditional MR calculations with smaller active spaces and single-reference theory calculations exhibit serious inconsistencies with experimental observations.

  14. Three-cluster dynamics within an ab initio framework

    DOE PAGES

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

    2013-09-26

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

  15. AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

    SciTech Connect

    French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes

    2012-09-15

    We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.

  16. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    SciTech Connect

    Elenewski, Justin E.; Hackett, John C

    2015-02-14

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

  17. A fragmentation and reassembly method for ab initio phasing.

    PubMed

    Shrestha, Rojan; Zhang, Kam Y J

    2015-02-01

    Ab initio phasing with de novo models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracy de novo models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted de novo models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the ab initio phasing by de novo models approach. The method can be used to solve structures when the best de novo models are still of low accuracy. PMID:25664740

  18. Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

    PubMed

    Moon, Jiwon; Kim, Joonghan

    2016-09-29

    Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

  19. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.

    PubMed

    Friesner, Richard A; Guallar, Victor

    2005-01-01

    We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples--methane monooxygenase, cytochrome P450, and triose phosphate isomerase--are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.

  20. Thermodynamic prediction of glass formation tendency, cluster-in-jellium model for metallic glasses, ab initio tight-binding calculations, and new density functional theory development for systems with strong electron correlation

    SciTech Connect

    Yao, Yongxin

    2009-01-01

    also plays an important role, as it may directly track the movement of every atom. Simulation time is a major limit for molecular dynamics, not only because of “slow” computer speed, but also because of the accumulation error in the numerical treatment of the motion equations. There is also a great concern about the reliability of the emperical potentials if using classical molecular dynamics. Ab initio methods based on density functional theory(DFT) do not have this problem, however, it suffers from small simulation cells and is more demanding computationally. When crystal phase is involved, size effect of the simulation cell is more pronounced since long-range elastic energy would be established. Simulation methods which are more efficient in computation but yet have similar reliability as the ab initio methods, like tight-binding method, are highly desirable. While the complexity of metallic glasses comes from the atomistic level, there is also a large field which deals with the complexity from electronic level. The only “ab initio” method applicable to solid state systems is density functional theory with local density approximation( LDA) or generalized gradient approximation(GGA) for the exchange-correlation energy. It is very successful for simple sp element, where it reaches an high accuracy for determining the surface reconstruction. However, there is a large class of materials with strong electron correlation, where DFT based on LDA or GGA fails in a fundamental way. An “ab initio” method which can generally apply to correlated materials, as LDA for simple sp element, is still to be developed. The thesis is prepared to address some of the above problems.

  1. Ab Initio Treatment of Lower Mantle Mineral Solvi.

    NASA Astrophysics Data System (ADS)

    Jung, D. Y.; Oganov, A. R.; Schmidt, M. W.

    2006-12-01

    The lower mantle of the Earth extends from about 670 to 2980 km depth and consists mainly of MgSiO3- perovskite (~ 70 vol%), (Mg,Fe)O magnesiowüstite (~ 20 vol%) and CaSiO3-perovskite (~ 10 vol%). To obtain a realistic picture of the lower mantle, it is necessary to consider the perovskite minerals as coexisting solid solutions with a large miscibility gap, as this is the case in nature. In this work we investigate the solvi of the three binaries in the Ca-perovskite - Mg-perovskite - corundum ternary, i.e. the solid solutions relevant for the Earth's lower mantle minerals in a simplified CMAS system. It is possible to calculate thermodynamic properties, structures and energetics of the individual minerals at extreme conditions of the mantle using ab initio methods, such as the density functional theory (DFT). We use the DFT together with the generalized gradient approximation (GGA) and the projector augmented wave (PAW) method, as implemented in the VASP code. The binary solvi are modelled through a subregular solid solution model together with point defect calculations at different pressures in the lower mantle regime. Point defects in the (Ca,Mg)-perovskite system are simple substitutions, but in MgSiO3-Al2O3 there is a coupled charge substitution of 2Al3+ with Mg2+Si^{4+}. Additionally, different symmetries of the perovskite (and akimotoite/ilmenite for MgSiO3) structures have been taken into account, thus allowing for phase transitions in solid solutions. At pressures and temperatures of the lower mantle, the solvus in the (Ca,Mg)SiO3 system remains wide open and solubilities of Ca in Mg-perovskite and Mg in Ca-perovskite decrease with pressure (at constant temperature and along any adiabatic geotherm). Calculations on the MgSiO3-Al2O3 (akimotoite-corundum) solvus show higher solubilities. Still, we find it unlikely that Ca-perovskite would disappear (i.e. fully dissolve in Mg-perovskite) at conditions of the lower mantle, at last not in the simplified CMAS

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

  3. 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.

  4. 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.

  5. 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.

  6. Vibrational spectral investigation, NBO, first hyperpolarizability and UV-Vis spectral analysis of 3,5-dichlorobenzonitrile and m-bromobenzonitrile by ab initio and density functional theory methods.

    PubMed

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

    2015-02-01

    The FT-IR and FT-Raman spectra of 3,5-dichlorobenzonitrile and m-bromobenzonitrile have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The optimized geometry, wave numbers and intensity of vibrational bonds of title molecules are obtained by ab initio and DFT level of theory with complete relaxation in the potential energy surface using 6-311++G(d, p) basis set. A complete vibrational assignments aided by the theoretical harmonic frequency, analysis have been proposed. The harmonic vibrational frequencies calculated have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The UV-Vis spectral analysis of the molecules has also been done which confirms the charge transfer of the molecules. Furthermore, the first hyperpolarizability and total dipole moment of the molecules have been calculated. PMID:25440585

  7. Quasi-Ab initio molecular dynamic study of Fe melting

    PubMed

    Belonoshko; Ahuja; Johansson

    2000-04-17

    We have investigated the melting of hcp Fe at high pressure by employing molecular dynamics simulations in conjunction with the full potential linear muffin tin orbital method. Apart from being of fundamental value, the melting of iron at high pressure is also important for our understanding of the Earth. The subject of iron melting at high pressures is controversial. The experimental data for the iron melting temperature can be separated into two regions, "low" and "high." Here we present an ab initio simulated iron melting curve which is in agreement with the low temperatures at lower pressures, but is in excellent agreement with the high-mostly shockwave-temperatures at high pressures. A comparison with available data lends support to the presented iron melting curve.

  8. Effective pair potentials using an ab initio variational approach

    NASA Astrophysics Data System (ADS)

    Faussurier, Gérald; Blancard, Christophe; Silvestrelli, Pier Luigi

    2010-01-01

    We used a variational approach adapted to a quantum molecular-dynamics code to determine the best reference potential for warm dense aluminum. This ab initio variational approach was based on the Gibbs-Bogolyubov inequality. We used many-body reference systems interacting through inverse-power-law potentials, among which the Coulomb potential was a particular case defining the classical one-component plasma model. By comparisons with full quantum molecular-dynamics simulations, we found that the Coulomb potential was not always the best reference potential. We calculated the self-diffusion coefficient and the shear viscosity and discussed the results obtained using the Chisolm-Wallace relation in the warm dense matter regime.

  9. Ab initio study of guanine damage by hydroxyl radical.

    PubMed

    Chaban, Galina M; Wang, Dunyou; Huo, Winifred M

    2015-01-15

    Multiconfigurational ab initio methods are used in this study to examine two initial reactions that take place during the OH radical attack of the DNA base guanine: a ring opening reaction and a hydrogen transfer reaction. The same reactions are also studied in the presence of a single water molecule. The ring opening reaction has a moderate barrier height of ∼20-25 kcal/mol that is relatively insensitive to the presence of water. The barrier of the H-transfer reaction, on the other hand, is lowered from ∼50 to ∼22 kcal/mol when one water molecule is added, thus becoming comparable to the barrier height of the ring opening reaction. PMID:25517252

  10. Ab initio engineering of materials with stacked hexagonal tin frameworks

    NASA Astrophysics Data System (ADS)

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-07-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.

  11. Ab initio engineering of materials with stacked hexagonal tin frameworks.

    PubMed

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.

  12. Ab Initio Study of KCl and NaCl Clusters

    NASA Astrophysics Data System (ADS)

    Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin

    2013-03-01

    We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.

  13. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches. PMID:27015491

  14. Reactive Monte Carlo sampling with an ab initio potential

    NASA Astrophysics Data System (ADS)

    Leiding, Jeff; Coe, Joshua D.

    2016-05-01

    We present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the "rare-event" character of chemical reactions.

  15. Ab initio X-Ray Absorption Fine Structure Cumulants

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

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

  16. Ab initio engineering of materials with stacked hexagonal tin frameworks

    PubMed Central

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  17. Ab Initio Force Fields for Imidazolium-Based Ionic Liquids.

    PubMed

    McDaniel, Jesse G; Choi, Eunsong; Son, Chang Yun; Schmidt, J R; Yethiraj, Arun

    2016-07-21

    We develop ab initio force fields for alkylimidazolium-based ionic liquids (ILs) that predict the density, heats of vaporization, diffusion, and conductivity that are in semiquantitative agreement with experimental data. These predictions are useful in light of the scarcity of and sometimes inconsistency in experimental heats of vaporization and diffusion coefficients. We illuminate physical trends in the liquid cohesive energy with cation chain length and anion. These trends are different than those based on the experimental heats of vaporization. Molecular dynamics prediction of the room temperature dynamics of such ILs is more difficult than is generally realized in the literature due to large statistical uncertainties and sensitivity to subtle force field details. We believe that our developed force fields will be useful for correctly determining the physics responsible for the structure/property relationships in neat ILs.

  18. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    SciTech Connect

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

    2015-05-21

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

  3. 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.

  4. An ab initio quartic force field and the fundamental frequencies of o-benzyne

    NASA Astrophysics Data System (ADS)

    Bludský, Ota; Pirko, Vladimír; Kobayashi, Rika; Jørgensen, Poul

    1994-10-01

    The ab initio SCF, MCSCF and MP2 molecular energies, gradients and Hessians have been evaluated at 33 points for the ground electronic state of the o-benzyne molecule. The corresponding potential energy surfaces have been fitted to obtain a quartic force field from which the fundamental frequencies have been determined using second-order perturbation theory. Theoretical predictions reproduce the majority of the experimental data to a degree of agreement which allows a complete assignment of all the fundamental frequencies of o-benzyne.

  5. An accurate potential energy curve for helium based on ab initio calculations

    NASA Astrophysics Data System (ADS)

    Janzen, A. R.; Aziz, R. A.

    1997-07-01

    Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.

  6. Converging sequences in the ab initio no-core shell model

    SciTech Connect

    Forssen, C.; Vary, J. P.; Caurier, E.; Navratil, P.

    2008-02-15

    We demonstrate the existence of multiple converging sequences in the ab initio no-core shell model. By examining the underlying theory of effective operators, we expose the physical foundations for the alternative pathways to convergence. This leads us to propose a revised strategy for evaluating effective interactions for A-body calculations in restricted model spaces. We suggest that this strategy is particularly useful for applications to nuclear processes in which states of both parities are used simultaneously, such as for transition rates. We demonstrate the utility of our strategy with large-scale calculations in light nuclei.

  7. Ab Initio Electronic Structure Calculations of Cytochrome P450 -- Ligand Interactions

    NASA Astrophysics Data System (ADS)

    Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.

    1997-03-01

    The Cytochrome P450 superfamily of enzymes are of great interest in pharmacology as they participate in an enormous range of physiological processes including drug deactivation and xenobiotic detoxification. We apply ab initio electronic structure calculations to model the interactions of the haem molecule at the P450 active site with substrate and inhibitor ligands. These calculations, based on density function theory, were performed with the CETEP code which uses a plane wave basis set and pseudopotentials to perform efficient LDA, GGA and spin dependent calculations. A change in the spin state of the haem iron atom is observed on binding of a substrate molecule, consistent with the accepted reaction mechanism.

  8. 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.

  9. Temperature-Dependent Diffusion Coefficients from ab initio Computations: Hydrogen in Nickel

    SciTech Connect

    E Wimmer; W Wolf; J Sticht; P Saxe; C Geller; R Najafabadi; G Young

    2006-03-16

    The temperature-dependent mass diffusion coefficient is computed using transition state theory. Ab initio supercell phonon calculations of the entire system provide the attempt frequency, the activation enthalpy, and the activation entropy as a function of temperature. Effects due to thermal lattice expansion are included and found to be significant. Numerical results for the case of hydrogen in nickel demonstrate a strong temperature dependence of the migration enthalpy and entropy. Trapping in local minima along the diffusion path has a pronounced effect especially at low temperatures. The computed diffusion coefficients with and without trapping bracket the available experimental values over the entire temperature range between 0 and 1400 K.

  10. Ab initio description of second-harmonic generation from crystal surfaces

    NASA Astrophysics Data System (ADS)

    Tancogne-Dejean, Nicolas; Giorgetti, Christine; Véniard, Valérie

    2016-09-01

    We propose an ab initio framework to derive the dielectric and the second-order susceptibility tensors for crystal surfaces. The single-surface response is extracted from a supercell scheme. We evaluate macroscopic quantities, taking into account the local fields. The first- and second-order susceptibilities are evaluated within time-dependent density functional theory, in the long-wavelength limit. We apply our formalism to the calculation of the second-harmonic generation for clean and hydrogenated silicon surfaces. The agreement with measured second-order susceptibility components is significantly better, illustrating the importance of local-field effects.

  11. Site occupancy trend of Co in Ni{sub 2}MnIn: Ab initio approach

    SciTech Connect

    Pal, Soumyadipta Mahadevan, Priya; Biswas, C.

    2015-06-24

    The trend of site occupation of Co at Ni sites of Ni{sub 2}MnIn system is studied in austenitic phase having L2{sub 1} 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 Ni{sub 1.5}Co{sub 0.5}MnIn and Ni{sub 1.25}Co{sub 0.75}MnIn. The Co tends to form cluster.

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

    PubMed

    Zhang, Dawei; Liu, Chungen

    2016-04-12

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

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

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

  14. Ab initio and density functional studies of hydrocarbon adsorption in zeolites.

    SciTech Connect

    Curtiss, L. A.

    1998-08-21

    The adsorption energies of methane and ethane in zeolites are investigated with ab initio molecular orbital theory and density functional theory. In this work we have used zeolite cluster models containing two, three, and five tetrahedral (Si, Al) atoms and have found equilibrium structures for complexes of methane, ethane, and propane with an acid site. If a large enough cluster is used and correlation effects are included via perturbation theory, the calculated adsorption energy for ethane is about 5 kcal/mol compared with the experimental value of 7.5 kcal/mol. The B3LYP density functional method gives a much smaller binding of {approximately}1 kcal/mol for ethane. The reason for the failure of density fictional theory is unclear.

  15. Protons in polar media: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

    The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations

  16. Differences in the surface electronic structure of Ge(001) and Si(001) from angle-resolved photoemission spectroscopy and ab-initio theory

    NASA Astrophysics Data System (ADS)

    Hatch, Richard C.; Seo, Hosung; Ponath, Patrick; Choi, Miri; Posadas, Agham B.; Demkov, Alexander A.

    2014-03-01

    Using high-resolution angle-resolved photoemission spectroscopy (ARPES) we compare the surface electronic structure of both Ge(001) and Si(001) surfaces. Unlike previous ARPES experiments, where the Ge(001) surfaces were prepared using cycles of ion sputtering and annealing, our Ge(001) surfaces were prepared using a combination of wet etching and oxygen plasma cleaning. This new technique has the advantage that it avoids the incomplete healing of surface roughening associated with sputtering and annealing cycles. The ARPES data show that the dimer-derived surface state that determines the charge neutrality level, and thus the Schottky barrier height in Si, is actually a surface resonance in Ge, and the highest occupied state is a bulk state. In order to avoid theory predicting an overlap of the valence and conduction bands, we employed first-principles, hybrid density functional theory (DFT). This theory effectively explains the presence of a number of photoemission features in both Si and Ge. We found it is necessary to incorporate spin-orbit interaction in the hybrid DFT calculations for Ge in order to model ARPES data, and we found a spin-orbit splitting of 0.28 eV both experimentally and theoretically.

  17. Operator evolution for ab initio electric dipole transitions of 4He

    DOE PAGES

    Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; Jurgenson, Eric D.; Navartil, Petr

    2015-07-24

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

  18. 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.

  19. Ab initio studies of anisotropic magnetism in uranium and cerium monopnictides and monochalcogenides

    NASA Astrophysics Data System (ADS)

    Collins, Eric Mason

    We have applied two ab initio based methods to investigate the origin in the electronic structure of the unusual magnetic behavior of the cerium and uranium monopnictides and monochalcogenides. First, we have carried out spin-polarized electronic structure calculations, based on the full potential linear muffin tin (FPLMTO) method, with spin polarization (orbital polarization only via spin-orbit coupling) and also with orbital polarization correction. Second, we have carried out ab initio based calculations synthesizing (1) a phenomenological theory of orbitally driven magnetism based on the Anderson and Kondo, lattice model which incorporates explicitly the hybridization induced and the Coulomb exchange interactions on an equal footing, and (2) FPLMTO electronic structure calculations allowing a first principles evaluation of all the parameters entering the model Hamiltonian. For the cerium compounds, we also include the crystal field interactions on an equal footing with the hybridization and Coulomb exchange interactions with a scaling determined by experiment. The results for the uranium compound calculations show that both methods are limited to the extremes to which they are best suited. The pure band structure calculations provide the best agreement for the lighter uranium compounds, while the model hamiltonian approach provides better agreement for the heavier uranium compounds. In the case of the cerium compounds, while the pure FPLMTO calculations yield values for the magnetic moment in agreement with experiment for the lighter cerium chalcogenides, they fail to give, even qualitatively, the magnetic properties for all other systems. On the other hand, the ab initio based model Hamiltonian calculations reveal for the first time the interplay of hybridization, Coulomb exchange, and crystal field interactions across the cerium series, and give results for the low-temperature moment and ordering temperature in excellent agreement with experiment, for the

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  1. Ab Initio and Density Functional Theory Modeling of the Chiroptical Response of Glycine and Alanine in Solution Using Explicit Solvation and Molecular Dynamics.

    PubMed

    Kundrat, Matthew D; Autschbach, Jochen

    2008-11-11

    We investigate ways in which simple point charge (SPC) water models can be used in place of more expensive quantum mechanical water molecules to efficiently model the solvent effect on a solute molecule's chiroptical responses. The effect that SPC waters have on the computed circular dichroism of a solvated glycine molecule are comparable to, albeit somewhat weaker than, that of quantum mechanical waters at the coupled cluster CC2 level of theory. The effects of SPC waters in fact correlate better with QM-CC2 waters than quantum mechanical waters computed with density functional theory (DFT) methods, since they do not promote spurious charge transfer excitations that are a known deficiency with most popular density functionals. Furthermore, the near zero order scaling of point charge waters allows multiple layers of explicit solvation to be modeled with negligible computational cost, which is not practical with CC2 or DFT levels. As a practical example, we model the molar rotations of glycine and alanine, and track their convergence.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  3. Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations.

    PubMed

    Tarcan, Erdoğan; Altindağ, Ozgü; Avci, Davut; Atalay, Yusuf

    2008-11-01

    The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C3H7N6+.C8H5O4(-)) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000-100 cm(-1) region where the theoretical evaluation and assignment of all observed bands were made.

  4. Effective field theory and Ab-initio calculation of p-type (Ga, Fe)N within LDA and SIC approximation

    NASA Astrophysics Data System (ADS)

    Salmani, E.; Mounkachi, O.; Ez-Zahraouy, H.; El Kenz, A.; Hamedoun, M.; Benyoussef, A.

    2013-03-01

    Based on first-principles spin-density functional calculations, using the Korringa-Kohn-Rostoker method combined with the coherent potential approximation, we investigated the half-metallic ferromagnetic behavior of (Ga, Fe)N co-doped with carbon within the self-interaction-corrected local density approximation. Mechanism of hybridization and interaction between magnetic ions in p-type (Ga, Fe)N is investigated. Stability energy of ferromagnetic and disorder local moment states was calculated for different carbon concentration. The local density and the self-interaction-corrected approximations have been used to explain the strong ferromagnetic interaction observed and the mechanism that stabilizes this state. The transition temperature to the ferromagnetic state has been calculated within the effective field theory, with a Honmura-Kaneyoshi differential operator technique.

  5. Magnetic properties of the double perovskite Sr2FeOsO6: microscopic insights from ab-initio density-functional theory study

    NASA Astrophysics Data System (ADS)

    Kanungo, Sudipta; Yan, Binghai; Jansen, Martin; Felser, Claudia

    2015-03-01

    Using density-functional theory calculations, we investigated the electronic and magnetic properties of the ordered 3d-5d double perovskite Sr2FeOsO6, which has recently drawn attention for interesting antiferromagnetic (AFM) phase transitions in low temperature observed in experiments. The calculated effective magnetic exchange interactions reveal the importance of long-range super-superexchange interactions in this compound. The competition between the ferromagnetic (FM) Os-O-Fe short-range interaction and AFM Os-O-Fe-O-Os long-range interaction induces strong magnetic frustration along the crystallographic c axis. This strong magnetic frustration is proposed to drive the magnetic phase transition between two AFM phases (AFM1 to AFM2) and related lattice distortion, which were also observed in the experiment.

  6. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca3Sb2 in hexagonal and cubic phases

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    A density functional theory study of structural, electronical and optical properties of Ca3Sb2 compound in hexagonal and cubic phases is presented. In the exchange-correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca3Sb2 has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated.

  7. Ionization Energies and Aqueous Redox Potentials of Organic Molecules: Comparison of DFT, Correlated ab Initio Theory and Pair Natural Orbital Approaches.

    PubMed

    Isegawa, Miho; Neese, Frank; Pantazis, Dimitrios A

    2016-05-10

    The calculation of redox potentials involves large energetic terms arising from gas phase ionization energies, thermodynamic contributions, and solvation energies of the reduced and oxidized species. In this work we study the performance of a wide range of wave function and density functional theory methods for the prediction of ionization energies and aqueous one-electron oxidation potentials of a set of 19 organic molecules. Emphasis is placed on evaluating methods that employ the computationally efficient local pair natural orbital (LPNO) approach, as well as several implementations of coupled cluster theory and explicitly correlated F12 methods. The electronic energies are combined with implicit solvation models for the solvation energies. With the exception of MP2 and its variants, which suffer from enormous errors arising at least partially from the poor Hartree-Fock reference, ionization energies can be systematically predicted with average errors below 0.1 eV for most of the correlated wave function based methods studies here, provided basis set extrapolation is performed. LPNO methods are the most efficient way to achieve this type of accuracy. DFT methods show in general larger errors and suffer from inconsistent behavior. The only exception is the M06-2X functional which is found to be competitive with the best LPNO-based approaches for ionization energies. Importantly, the limiting factor for the calculation of accurate redox potentials is the solvation energy. The errors in the predicted solvation energies by all continuum solvation models tested in this work dominate the final computed reduction potential, resulting in average errors typically in excess of 0.3 V and hence obscuring the gains that arise from choosing a more accurate electronic structure method.

  8. 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.

  9. Lead-Chalcogenides Under Pressure: Ab-Initio Study

    NASA Astrophysics Data System (ADS)

    Gupta, Dinesh C.; Hamid, Idris

    ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.

  10. Ab initio studies of phosphorene island single electron transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.

    2016-05-01

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.

  11. 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

  12. Ab initio description of the exotic unbound 7He nucleus

    DOE PAGES

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-01-11

    In this study, the neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2– resonance is well established, there is a controversy concerning the excited 1/2– resonance reported in some experiments as low lying and narrow (ER~1 MeV, Γ≤1 MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-coremore » shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2– resonance above 2 MeV.« less

  13. 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.

  14. Local Environment Distribution in Ab Initio Liquid Water

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    We have analyzed the distribution of local environments in liquid water at ambient conditions and its inherent potential energy surface (IPES) based on state-of-the-art ab initio molecular dynamics simulations performed on 128 molecules implementing hybrid PBE0 exchange [PRB 79, 085102 (2009)] and van der Waals (vdW) interactions [PRL 102, 073005 (2009)]. The local environments of molecules are characterized in terms of the local structure index (LSI) [JCP 104, 7671 (1996)] which is able to distinguish high- and low-density molecular environments. In agreement with simulations based on model potentials, we find that the distribution of LSI is unimodal at ambient conditions and bimodal in the IPES, consistent with the existence of polymorphism in amorphous phases of water. At ambient conditions spatial LSI fluctuations extend up to ~7 Å and their dynamical correlation decays on a time scale of ~3 ps, as found for density fluctuations in a recent study [PRL 106, 037801 (2011)]. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500

  15. 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

  16. 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.

  17. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

    Rogers, J. D.; Hillman, J. J.

    1982-01-01

    Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

  18. Ab initio description of p-shell hypernuclei.

    PubMed

    Wirth, Roland; Gazda, Daniel; Navrátil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

    2014-11-01

    We present the first ab initio calculations for p-shell single-Λ hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit Λ and Σ(+),Σ(0),Σ(-) hyperons including Λ-Σ conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to (Λ)(7)Li, (Λ)(9)Be, and (Λ)(13)C. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions. PMID:25415901

  19. Ab initio calculations of free-energy reaction barriers.

    PubMed

    Bucko, T

    2008-02-13

    The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion.

  20. Ab initio calculations of free-energy reaction barriers

    NASA Astrophysics Data System (ADS)

    Bucko, T.

    2008-02-01

    The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction—the nucleophilic substitution of methyl chloride by a chlorine anion.

  1. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  2. Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures

    NASA Astrophysics Data System (ADS)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

    Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.

  3. Rational design of electrolyte components by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Johansson, Patrik; Jacobsson, Per

    This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc.

  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. The AB Initio Mia Method: Theoretical Development and Practical Applications

    NASA Astrophysics Data System (ADS)

    Peeters, Anik

    The bottleneck in conventional ab initio Hartree -Fock calculations is the storage of the electron repulsion integrals because their number increases with the fourth power of the number of basis functions. This problem can be solved by a combination of the multiplicative integral approximation (MIA) and the direct SCF method. The MIA approach was successfully applied in the geometry optimisation of some biologically interesting compounds like the neurolepticum Haloperidol and two TIBO derivatives, inactivators of HIV1. In this thesis the potency of the MIA-method is shown by the application of this method in the calculation of the forces on the nuclei. In addition, the MIA method enabled the development of a new model for performing crystal field studies: the supermolecule model. The results for this model are in better agreement with experimental data than the results for the point charge model. This is illustrated by the study of some small molecules in the solid state: 2,3-diketopiperazine, formamide oxime and two polymorphic forms of glycine, alpha-glycine and beta-glycine.

  6. 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.

  7. Ab-initio modeling of an anion C- 60 pseudopotential for fullerene-based compounds

    NASA Astrophysics Data System (ADS)

    Vrubel, Ivan I.; Polozkov, Roman G.; Ivanov, Vadim K.

    2016-08-01

    An anion C- 60 pseudopotential is determined from an ab-initio-based approach. First, ab-initio calculations are performed to calculate the electronic charge density and the total electrostatic potential. Second, the effective dependence of the pseudopotential on the radial degree of freedom is extracted from the angular average of the total electrostatic potential. Finally, the resulting effective pseudopotential is fitted to a simple analytical form which can be applied in further dynamical simulations of fullerene-based compounds.

  8. The electronic spectrum of AgCl2: Ab initio benchmark versus density-functional theory calculations on the lowest ligand-field states including spin-orbit effects

    NASA Astrophysics Data System (ADS)

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

    2006-01-01

    The XΠg2, Σg+2, and Δg2 states of AgCl2 have been studied through benchmark ab initio complete active space self-consistent field plus second-order complete active space multireference Möller-Plesset algorithm (CASSCF +CASPT2) and complete active space self-consistent field plus averaged coupled pair functional (CASSCF +ACPF) and density-functional theory (DFT) calculations using especially developed basis sets to study the transition energies, geometries, vibrational frequencies, Mulliken charges, and spin densities. The spin-orbit (SO) effects were included through the effective Hamiltonian formalism using the ΛSΣ ACPF energies as diagonal elements. At the ACPF level, the ground state is Πg2 in contradiction with ligand-field theory, SCF, and large CASSCF; the adiabatic excitation energies for the Σg+2 and Δg2 states are 1640 and 18230cm-1, respectively. The inclusion of the SO effects leads to a pure Ω =3/2(Πg2) ground state, a Ω =1/2 (66%Πg2 and 34%Σg+2) A state, a Ω =1/2 (34%Πg2 and 66%Σg+2) B state, a Ω =5/2(Δg2)C state, and a Ω =3/2(99%Δg2)D state. The X-A, X-B, X-C, and X-D transition energies are 485, 3715, 17 246, and 20110cm-1, respectively. The B97-2, B3LYP, and PBE0 functionals overestimate by ≈100% the XΠg2-Σg+2Te but provide a qualitative energetic ordering in good agreement with ACPF results. B3LYP with variable exchange leads to a 42% optimal Hartree-Fock exchange for transition energies but all equilibrium geometries get worsened. Asymptotic corrections to B3LYP do not provide improved values. The nature of the bonding in the XΠg2 state is very different from that of CuCl2 since the Mulliken charge on the metal is 1.1 while the spin density is only 0.35. DFT strongly delocalizes the spin density providing even smaller values of around 0.18 on Ag not only for the ground state, but also for the Σg+2 state.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  11. Full-dimensional (15-dimensional) ab initio analytical potential energy surface for the H7+ cluster

    NASA Astrophysics Data System (ADS)

    Barragán, Patricia; Prosmiti, Rita; Wang, Yimin; Bowman, Joel M.

    2012-06-01

    Full-dimensional ab initio potential energy surface is constructed for the H_7^+ cluster. The surface is a fit to roughly 160 000 interaction energies obtained with second-order MöllerPlesset perturbation theory and the cc-pVQZ basis set, using the invariant polynomial method [B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577 (2009), 10.1080/01442350903234923]. We employ permutationally invariant basis functions in Morse-type variables for all the internuclear distances to incorporate permutational symmetry with respect to interchange of H atoms into the representation of the surface. We describe how different configurations are selected in order to create the database of the interaction energies for the linear least squares fitting procedure. The root-mean-square error of the fit is 170 cm-1 for the entire data set. The surface dissociates correctly to the H_5^+ + H2 fragments. A detailed analysis of its topology, as well as comparison with additional ab initio calculations, including harmonic frequencies, verify the quality and accuracy of the parameterized potential. This is the first attempt to present an analytical representation of the 15-dimensional surface of the H_7^+ cluster for carrying out dynamics studies.

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

    NASA Astrophysics Data System (ADS)

    Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya

    2013-06-01

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

  13. Emergent properties of nuclei from ab initio coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-06-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon-nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

  14. a Microwave and AB Initio Study of the Nitric Acid - Trimethylamine Complex

    NASA Astrophysics Data System (ADS)

    Sedo, Galen; Leopold, Kenneth R.

    2009-06-01

    The microwave spectrum of the gas phase nitric acid - trimethylamine complex has been observed using Fourier transform microwave spectroscopy. The experimental rotational constants and (CH{_3}){_3}{^1}{^5}N-HNO{_3} isotope shifts are consistent with a complex in which the nitric acid proton forms a hydrogen bond to the nitrogen of the amine, similar to the experimentally determined structure of H{_3}N-HNO{_3} Analysis of the hyperfine structure in both the parent and (CH{_3}){_3}{^1}{^5}N-HNO{_3} spectra made it possible to determine, unambiguously, the quadrupole coupling constants of the {^1}{^5}N nuclei in both the nitric acid and trimethylamine moieties. Ab initio calculations, using the MP2/6-311++G(2df,2pd) level of theory and basis set, have been performed and are in quantitative agreement with the available experimental data. Both the experimentally determined quadrupole coupling constants and the ab initio structure have been used to assess the degree of proton transfer occurring in the nitric acid - trimethylamine complex. These results will be compared to those obtained for the H{_3}N-HNO{_3} and HNO{_3}-(H{_2}O){_n} [n = 0 - 3] complexes and discussed in terms of how binding partner basicity and the number of solvent molecules influence the incipient ionization of nitric acid moiety. M. E. Ott, and K. R. Leopold, J. Phys. Chem. A 1999, 103,1322-1328.

  15. Ab initio simulation of elastic and mechanical properties of Zn- and Mg-doped hydroxyapatite (HAP).

    PubMed

    Aryal, Sitaram; Matsunaga, Katsuyuki; Ching, Wai-Yim

    2015-07-01

    Hydroxyapatite (HAP) is an important bioceramic which constitutes the mineral components of bones and hard tissues in mammals. It is bioactive and used as bioceramic coatings for metallic implants and bone fillers. HAP readily absorbs a large amount of impurities. Knowledge on the elastic and mechanical properties of impurity-doped HAP is a subject of great importance to its potential for biomedical applications. Zn and Mg are the most common divalent cations HAP absorbs. Using density function theory based ab initio methods, we have carried out a large number of ab initio calculations to obtain the bulk elastic and mechanical properties of HAP with Zn or Mg doped in different concentration at the Ca1 and Ca2 sites using large 352-atom supercells. Detailed information on their dependece on the concetraion of the substitued impurity is obtained. Our results show that Mg enhances overall elastic and bulk mechanical properties whereas Zn tends to degrade except at low concentrations. At a higher concentration, the mechanical properties of Zn and Mg doped HAP also depend significantly on impurity distribution between the Ca1 and Ca2 sites. There is a strong evidence that Zn prefers Ca2 site for substituion whereas Mg has no such preference. These results imply that proper control of dopant concentration and their site preference must carefully considered in using doped HAP for specific biomedical applications.

  16. Higher-order elastic constants and megabar pressure effects of bcc tungsten: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Vekilov, Yu. Kh.; Krasilnikov, O. M.; Lugovskoy, A. V.; Lozovik, Yu. E.

    2016-09-01

    The general method for the calculation of n th (n ≥2 ) order elastic constants of the loaded crystal is given in the framework of the nonlinear elasticity theory. For the crystals of cubic symmetry under hydrostatic compression, the two schemes of calculation of the elastic constants of second, third, and fourth order from energy-finite strain relations and stress-finite strain relations are implemented. Both techniques are applied for the calculation of elastic constants of orders from second to fourth to the bcc phase of tungsten at a 0-600 GPa pressure range. The energy and stress at the various pressures and deformations are obtained ab initio in the framework of projector augmented wave+generalized gradient approximation (PAW+GGA) method, as implemented in Vienna Ab initio Simulation Package (VASP) code. Using the obtained results, we found the pressure dependence of Grüneisen parameters for long-wave acoustic modes in this interval. The Lamé constants of second and third order were estimated for polycrystalline tungsten. The proposed method is applicable for crystals with arbitrary symmetry.

  17. Ab initio up to the melting point: Anharmonicity and vacancies in aluminum

    NASA Astrophysics Data System (ADS)

    Grabowski, B.; Ismer, L.; Hickel, T.; Neugebauer, J.

    2009-03-01

    At elevated temperatures, the heat capacity of metals strongly deviates from the harmonic prediction. This was pointed out long agoootnotetextM. Born and E. Brody, Zeitschrift f"ur Physik 6, 132 (1921) and various explanations have been considered. Ab initio calculations showedootnotetextB. Grabowski, T. Hickel, J. Neugebauer, Phys. Rev. B 76, 24309 (2007) that a dominant part can be explained by quasiharmonic excitations. However, the detailed balance of further contributions, such as explicit anharmonicity and vacancies, is not clarified yet even for simple elementary metals. Aluminum is a prototypical example. Even though intensively studied, the ambiguous experimental situation has made a classification of the mechanisms impossible. To resolve the situation, we have calculated the full volume and temperature dependent ab initio free energy surface employing density-functional theory. In particular, we have included anharmonic and vacancy contributions using numerically highly efficient methods to coarse grain the configuration space. To obtain accurate vacancy energies, we have included the full spectrum of excitations: quasiharmonic, electronic, and explicitly anharmonic. The results are in contradiction to common belief, nevertheless the essential physics can be captured by a simple model.

  18. Deviational simulation of phonon transport in graphene ribbons with ab initio scattering

    SciTech Connect

    Landon, Colin D.; Hadjiconstantinou, Nicolas G.

    2014-10-28

    We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.

  20. Ground state analytical ab initio intermolecular potential for the Cl{sub 2}-water system

    SciTech Connect

    Hormain, Laureline; Monnerville, Maurice Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón

    2015-04-14

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.

  1. Ab initio calculation of oxygen self-diffusion coefficient in uranium dioxide UO2

    NASA Astrophysics Data System (ADS)

    Dorado, Boris; Garcia, Philippe; Torrent, Marc

    Uranium dioxide UO2 is the most widely used nuclear fuel worldwide and its atomic transport properties are relevant to practically all engineering aspects of the material. Although transport properties have already been studied in UO2 by means of first-principles calculations, the ab initio determination of self-diffusion coefficients has up to now remained unreachable because the relevant computational tools were neither available or adapted. The present work reports our results related to the ab initio calculation of the oxygen self-diffusion coefficient in UO2. We first determine the Gibbs free energies of formation of oxygen charged defects by calculating both the electronic and vibrational (hence entropic) contributions. Then, we use the transition state theory in order to compute the effective jump frequency of the defects, which in turn provides us with the value of the pre-exponential factor. The results are compared to self-diffusion data obtained experimentally with a careful monitoring of the relevant thermodynamic conditions (oxygen partial pressure, temperature, impurity content).

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

    SciTech Connect

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

    2013-11-21

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

  3. Towards an ab-initio treatment of nonlocal electronic correlations with dynamical vertex approximation

    NASA Astrophysics Data System (ADS)

    Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten

    Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.

  4. Ab initio molecular dynamics study of H2 formation inside POSS compounds.

    PubMed

    Kudo, Takako; Taketsugu, Tetsuya; Gordon, Mark S

    2011-04-01

    The mechanism and dynamics of the formation of a hydrogen molecule by incorporating two hydrogen atoms in a stepwise manner into the cavity of some POSS (polyhedral oligomeric silsesquioxanes) compounds has been investigated by ab initio molecular orbital and ab initio molecular dynamics (AIMD) methods. The host molecules in the present reactions are two types of POSS, T(8) ([HSiO(1.5)](8)) and T(12)(D(2d)) ([HSiO(1.5)](12)). AIMD simulations were performed at the CASSCF level of theory, in which two electrons and two orbitals of the colliding hydrogen atoms are included in the active space. The trajectories were started by inserting the second hydrogen atom into the hydrogen atom-encapsulated-POSS (H + H@T(n) → H(2)@T(n); n = 8 and 12). In many cases, the gradual formation of a hydrogen molecule has been observed after frequent collisions of two hydrogen atoms within the cages. The effect of the introduction of an argon atom in T(12) is discussed as well.

  5. Adsorption orientation and STM imaging of meta-benzyne resolved by scanning tunnelling microscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Simic-Milosevic, Violeta; Bocquet, Marie-Laure; Morgenstern, Karina

    2009-08-01

    Dissociative adsorption of doubly substituted benzene molecules leads to a molecule with two missing hydrogen atoms. We use scanning tunnelling microscopy at 5 K and density functional theory to investigate these benzyne molecules on Cu(1 1 1). Benzyne is either imaged as a depression, as a ring-shaped protrusion, or as a circular protrusion at different tunnelling parameters. Submolecular resolution and ab initio calculations give information on the adsorption properties about the in-situ formed biradical species.

  6. Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study

    NASA Astrophysics Data System (ADS)

    Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

    2015-04-01

    Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

  7. Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study

    SciTech Connect

    Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

    2015-04-21

    Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

  8. Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

    PubMed

    Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

    2015-04-21

    Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems. PMID:25903899

  9. Ab initio cluster calculations of hydrogenated GaAs(001) surfaces

    NASA Astrophysics Data System (ADS)

    Fu, Q.; Li, L.; Hicks, R. F.

    2000-04-01

    Hydrogen adsorption on the (2×4) and (4×2) reconstructions of gallium arsenide (001) has been studied by internal reflectance infrared spectroscopy and ab initio cluster calculations with density-functional theory. The calculations are made on Ga5As4H11,13, Ga4As5H11,13, and Ga7As8H19 clusters, which model the arsenic- and gallium-dimer termination of the semiconductor surface. Excellent agreement has been achieved between the vibrational frequencies predicted by the theory and those observed in experiments. On the (2×4), hydrogen adsorbs on arsenic dimers to form isolated and coupled arsenic-monohydrogen bonds, and arsenic-dihydrogen bonds. Conversely, on the (4×2), hydrogen adsorbs on gallium dimers to form terminal and bridged gallium hydrides. The latter species occur in isolated or coupled structures involving two or three Ga atoms.

  10. Ab Initio XAS Debye-Waller Factors Beyond the Harmonic Approximation

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

    We introduce an ab initio approach to calculate the temperature dependent vibrational effects in x-ray absorption spectra beyond the harmonic approximation. Instead of relying on empirical models, we apply electronic structure theory to determine the dynamical matrix of the system, from which the appropriate vibrational densities of state can be obtained using a Lanczos recursion algorithm [2]. By combining thermodynamic perturbation theory and the quasi-harmonic approximation we obtain x-ray absorption fine structure (XAFS) cumulants such as the mean square relative displacement (2nd cumulant), the thermal expansion (first cumulant), the asymmetry of the distribution (third cumulant) and the perpendicular motion contribution to the DW factor. Other quantities of interest such as mean square atomic displacements are also discussed. [2]H.J. Krappe and H.H. Rossner, Phys. Rev. B70, 104102 (2004).

  11. A simplified ab initio cosmic-ray modulation model: construction and predictive capabilities

    NASA Astrophysics Data System (ADS)

    Moloto, Katlego; Burger, Renier; Engelbrecht, Nicholas

    2016-07-01

    A simplified ab initio approach is followed to model cosmic-ray modulation using a steady-state three-dimensional stochastic solver of the Parker transport equation. Standard diffusion coefficients based on Quasilinear Theory (QLT) and Nonlinear Guiding Center Theory (NLGC) are used. The spatial dependence of turbulence quantities required as input for the drift- and diffusion coefficients, follow from parametric fits to results from a turbulence transport model. Effective values are used for the solar wind speed, magnetic field magnitude and tilt angle in the modulation model. The unusually high cosmic-ray intensities observed during the 2009 solar minimum follow naturally from the current model for most of the energies considered. This demonstrates that changes in turbulence contribute significantly to than usual cosmic-ray intensities during the 2009 solar minimum. We also discuss and illustrate how this model can be used to predict future cosmic-ray intensities, and comment on the reliability of such predictions.

  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 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.

  14. Communication: comparing ab initio methods of obtaining effective U parameters for closed-shell materials.

    PubMed

    Yu, Kuang; Carter, Emily A

    2014-03-28

    The density functional theory (DFT)+U method is an efficient and effective way to calculate the ground-state properties of strongly correlated transition metal compounds, with the effective U parameters typically determined empirically. Two ab initio methods have been developed to compute the U parameter based on either constrained DFT (CDFT) or unrestricted Hartree-Fock (UHF) theory. Previous studies have demonstrated the success of both methods in typical open-shell materials such as FeO and NiO. In this Communication we report numerical instability issues that arise for the CDFT method when applied to closed-shell transition metals, by using ZnO and Cu2O as examples. By contrast, the UHF method behaves much more robustly for both closed- and open-shell materials, making it more suitable for treating closed-shell transition metals, as well as main group elements. PMID:24697417

  15. Communication: Comparing ab initio methods of obtaining effective U parameters for closed-shell materials

    NASA Astrophysics Data System (ADS)

    Yu, Kuang; Carter, Emily A.

    2014-03-01

    The density functional theory (DFT)+U method is an efficient and effective way to calculate the ground-state properties of strongly correlated transition metal compounds, with the effective U parameters typically determined empirically. Two ab initio methods have been developed to compute the U parameter based on either constrained DFT (CDFT) or unrestricted Hartree-Fock (UHF) theory. Previous studies have demonstrated the success of both methods in typical open-shell materials such as FeO and NiO. In this Communication we report numerical instability issues that arise for the CDFT method when applied to closed-shell transition metals, by using ZnO and Cu2O as examples. By contrast, the UHF method behaves much more robustly for both closed- and open-shell materials, making it more suitable for treating closed-shell transition metals, as well as main group elements.

  16. Chiroptical properties of unsubstituted carbohydrates: Ab initio and semiempirical studies

    NASA Astrophysics Data System (ADS)

    Parra C., Alejandro

    Ab initio calculations support assignment of the vacuum ultraviolet circular dichroism (CD) of simple saccharides to 11A 1 --> 21B1 and 11A 1 --> 11A2 transitions centered on the oxygen atoms of the acetal group treated as two weakly coupled ether chromophores. The calculations are consistent with assignments previously made on the basis of a deconvolution of CD spectra. Estimates of the oxygen centered contributions to magnetic transition dipole moments were made. Semiempirical calculations were performed to model the NaD molar optical rotation of 1,6- and 3,6- anhydrosugars. For 1,6-anhydrosugars, current parameters produce reasonable agreement with experimental values. For 3,6-anhydrosugars, modifications to the ether parameters had to be introduced. The most relevant included a reorientation of the bond-centered s-->s* transition dipole charges in the ether chromophore to a C2v orientation, and a shift from prolate polarizability ellipsoids to general ellipsoids. These changes result in good agreement with experimental Na D molar rotations for 3,6-anhydrosugars. A low energy CD band arises in 3,6- and 1,6-anhydrosugars when agreement with the experimental NaD molar rotations is achieved. It is proposed that this band is a real feature in the spectrum. The origin of the band is primarily the interaction between b1 symmetry- oriented transition dipoles in the COC groups with other transition dipoles in the molecule. Comparison with experimental spectra leads to an assignment of this band to 11A1 --> 21B1 transitions centered on the COC groups.

  17. Ab initio molecular dynamics study of ferroelectric phase transitions

    NASA Astrophysics Data System (ADS)

    Srinivasan, Varadharajan

    We have undertaken the first ever fully first-principles simulations of ferroelectric crystals at finite temperature with an aim to understand the nature of their phase transitions. In particular, we have studied the different aspects of phase transitions in two protypical ferroelectrics - PbTiO3 and KH2PO4. In PbTiO3, we have successfully reproduced the temperature-driven transition from a tetragonal to a cubic phase by using constant-pressure Car-Parrinello molecular dynamics. By defining suitable order parameters in terms of atomic displacements, we are able to monitor the approach of the cubic phase. Using a quasi-harmonic analysis, with the inclusion of a temperature dependent volume and the average thermal atomic displacements as the most basic effects of anharmonicity, we are also able to recover the softening of ferroelectric modes as well as other features seen in experiments. These observations confirm the predominantly displacive nature of the transition, while our simulations also indicate a possible build-up of disorder near the transition temperature. We have also studied the isotope effects in the ferroelectric transition in KH2PO4 by quantifying the temperature and mass dependence of the extent of delocalization of the hydrogens. Using a recently developed ab initio Open Path-integral Molecular Dynamics scheme we have calculated both the real and momentum-space distribution of the hydrogens in both protonated and deuterated KDP above and below their respective transition temperatures. We find that the two crystals not only involve different transition mechanisms but also the fluctuations above the transition temperature are of a qualitatively different nature.

  18. 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.

  19. 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.

  20. Lithium insertion in silicon nanowires: an ab initio study.

    PubMed

    Zhang, Qianfan; Zhang, Wenxing; Wan, Wenhui; Cui, Yi; Wang, Enge

    2010-09-01

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

  1. 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

  2. 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.

  3. Novel zinc(II) and copper(II) complexes of a Mannich base derived from lawsone: Synthesis, single crystal X-ray analysis, ab initio density functional theory calculations and vibrational analysis.

    PubMed

    Neves, Amanda P; Vargas, Maria D; Téllez Soto, Claudio A; Ramos, Joanna M; Visentin, Lorenzo do C; Pinheiro, Carlos B; Mangrich, Antônio S; de Rezende, Edivaltrys I P

    2012-08-01

    Zinc(II) and copper(II) complexes of a tridentate Mannich base L1 derived from 2-hydroxy-1,4-naphthoquinone, pyridinecarboxyaldehyde and 2-aminomethylpyridine, [ZnL1Cl(2)]·H(2)O 1 and [CuL1Cl(2)]·2H(2)O 2, have been synthesized and fully characterized. The structure of complex 1 has been elucidated by a single crystal X-ray diffraction study: the zinc atom is pentacoordinate and the coordination geometry is a distorted square base pyramid, with a geometric structural parameter τ equal to 0.149. Vibrational spectroscopy and ab initio DFT calculations of both compounds have confirmed that the two complexes exhibit similar structures. Full assignment of the vibrational spectra was also supported by careful analysis of the distorted geometries generated by the normal modes. PMID:22513170

  4. Ab initio theory for femtosecond spin dynamics, angle-resolved fidelity analysis, and the magneto-optical Kerr effect in the Ni3(CH3OH) and Co3(+)(CH3OH) clusters.

    PubMed

    Chaudhuri, D; Jin, W; Lefkidis, G; Hübner, W

    2015-11-01

    We present a systematic analysis of the ab initio controlled femtosecond spin dynamics in Ni3(CH3OH) and Co3(+)(CH3OH) clusters achieved by a spin-orbit-coupling enabled Λ process. The distortion caused by the attachment of CH3OH to one of the active magnetic centers of the Ni3 and the Co3(+) clusters induces asymmetric geometries which result in well localized spin densities on the magnetic centers. With the use of high-level quantum chemistry methods, successful spin-flip scenarios are demonstrated for both clusters. In order to assess the experimental accessibility of those effects, we compute their tolerance with respect to two laser pulse parameters, i.e., the energy detuning as well as the deviation of the polar angle ϕ from its optimized value. Finally, we calculate the magneto-optical Kerr effect in order to connect to the susceptibility tensor χ as an experimentally measurable quantity.

  5. Ab initio Calculations of Solvation Processes in Volcanic Gases

    NASA Astrophysics Data System (ADS)

    Lemke, K.; Seward, T.

    2006-12-01

    The structures and thermochemical properties of hydrated ions and neutral molecules play an important role in our understanding of solvent clustering and hydrogen bonding in the gas phase. Considerable effort therefore has been devoted to both the experimental and theoretical determination of stepwise hydration energies of geochemically important ions and neutral molecules with solvents, for instance H2O or H2S, over a broad range of temperatures typical of those encountered in volcanic gases. Because volcanic gases contain mutiple solute and solvent components which are subject to proton transfer, competive solvation and solvent switching, characterizing individual clusters has been a fundamental challenge to a molecular-level understanding of high temperature gas-phase solvation. However, recent advances in computational chemistry methods, especially Pople´s Gaussian (G-n) and complete basis set limit (CBS-x) model chemistries, now allow characterization of the dominant cluster structures and thermochemical properties of solute-solvent and solvent-solvent interactions in high temperature volcanic gases. Building on reported measurements of volcanic gases at Vesuvio, Italy, and Showa-Shinzan, Japan, as well as our recent investigations of ion-hydration we have re-examined the high temperature clustering equilibria of the small hydronium (H3O+) and ammonium (NH4+) ions as well as neutral ammonia and sulphur species with H2O and/or H2S using ab initio quantum chemical methods. From our study, we find that most of the gas phase ions tend to associate with a small number of H2O and H2S molecules to yield a hydrated ion cluster even at low humidities. Furthermore, inspection of van´t Hoff data demonstrate that (1) hydration energies of ions are shifted to less exergonic values as the solvent shell grows and the composition shifts from water-rich to hydrogen sulphide rich, (2) ion-cluster size increases with decreasing temperature at constant humidity, (3) attachment

  6. Bulk Modulus of Sc2O3: Ab initio Calculations and Experimental Results

    SciTech Connect

    S Barzilai; I Halvey; O Yeheskel

    2011-12-31

    The bulk modulus of scandia is evaluated by ab initio calculation, based on density functional theory, and compared with bulk modulus measurement on nearly fully dense scandia and with the value attained from the equation of state based on diamond anvil cell measurements. The current results are in the upper range of the bulk moduli results in the literature. The scatter in the literature results might be explained by the differences in the specific volumes of the measured and calculated cases. For the specific volume of 59.65{+-}0.07 {angstrom}{sup 3} the average measured isothermal bulk modulus of scandia from the present study and recent literature results is 188{+-}10 GPa.

  7. Electronic and optical properties of K-doped ZnO: Ab initio study

    NASA Astrophysics Data System (ADS)

    Aimouch, D. E.; Meskine, S.; Hayn, R.; Zaoui, A.; Boukortt, A.

    2016-08-01

    We present the results of ab initio calculations of K-doped ZnO in the wurtzite structure using a supercell of 32 atoms and density functional theory. A complete analysis of its electronic, optical and magnetic properties is provided. The local spin density approximation (LSDA) has been used to analyze the density of states and to understand the K influence at different concentration values. The material is revealed to become a p-type doped semiconductor. The optical constant or refractive index, the dielectric function, and the absorption coefficient were determined and show a good agreement with available experimental data. Potassium doping leads to an absorption peak at about 380 nm. That peak might improve the absorption characteristics of ZnO for solar cell or optical applications.

  8. An ab initio model for the modulation of galactic cosmic-ray electrons

    SciTech Connect

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

    2013-12-20

    The modulation of galactic cosmic-ray electrons is studied using an ab initio three-dimensional steady state cosmic-ray modulation code in which the effects of turbulence on both the diffusion and drift of these cosmic-rays are treated as self-consistently as possible. A significant refinement is that a recent two-component turbulence transport model is used. This model yields results in reasonable agreement with observations of turbulence quantities throughout the heliosphere. The sensitivity of computed galactic electron intensities to choices of various turbulence parameters pertaining to the dissipation range of the slab turbulence spectrum, and to the choice of model of dynamical turbulence, is demonstrated using diffusion coefficients derived from the quasi-linear and extended nonlinear guiding center theories. Computed electron intensities and latitude gradients are also compared with spacecraft observations.

  9. 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.

  10. 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.

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

    PubMed

    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.

  12. Optical spectroscopy of the bulk and interfacial hydrated electron from ab initio calculations.

    PubMed

    Uhlig, Frank; Herbert, John M; Coons, Marc P; Jungwirth, Pavel

    2014-09-01

    The optical spectrum of the hydrated (aqueous) electron, e(aq)(–), is the primary observable by means of which this species is detected, monitored, and studied. In theoretical calculations, this spectrum has most often been simulated using one-electron models. Here, we present ab initio simulations of that spectrum in both bulk water and, for the first time, at the water/vapor interface, using density functional theory and its time-dependent variant. Our results indicate that this approach provides a reliable description, and quantitative agreement with the experimental spectrum for the bulk species is obtained using a “tuned” long-range corrected functional. The spectrum of the interfacial electron is found to be very similar to the bulk spectrum.

  13. HO2 + O3 Reaction: Ab Initio Study and Implications in Atmospheric Chemistry.

    PubMed

    Viegas, Luís P; Varandas, António J C

    2010-02-01

    We report a theoretical investigation on the reaction between ozone and the hydroperoxyl radical, which is part of the ozone depletion cycle. This reaction represents a great challenge to the state of the art ab initio methods, while its mechanism remains unclear to both experimentalists and theoreticians. In this work we calculated the relative energies of the stationary points along the reaction coordinate of the oxygen- and hydrogen-abstraction mechanisms using different levels of theory and extrapolating some of the results to the complete one-electron basis set limit. Oxygen abstraction is shown to be preceded by formation of hydrogen-bonded complexes, while hydrogen abstraction shows a lower energy barrier than oxygen abstraction. Both mechanisms lead to formation of HO3 + O2 in a very troublesome region of the potential-energy surface that is not correctly described by single-reference methods. The implications of the results on reaction dynamics are discussed. PMID:26617298

  14. 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.

  15. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  17. 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.

  18. Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit

    NASA Astrophysics Data System (ADS)

    Dornheim, Tobias; Groth, Simon; Sjostrom, Travis; Malone, Fionn D.; Foulkes, W. M. C.; Bonitz, Michael

    2016-10-01

    We perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N =1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy Fxc of the macroscopic electron gas with an unprecedented accuracy of |Δ V |/|V |,|Δ Fxc|/|F |xc˜10-3 . A comparison of our new data to the recent parametrization of Fxc by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.

  19. 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.

  20. Pressure-induced phase transition in wurtzite ZnTe: an ab initio study.

    PubMed

    Alptekin, Sebahaddin

    2012-03-01

    A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in wurtzite ZnTe. A first-order phase transition from the wurtzite structure to a Cmcm structure was successfully observed in a constant-pressure molecular dynamics simulation. This phase transformation was also analyzed using enthalpy calculations. We also investigated the stability of wurtzite (WZ) and zinc-blende (ZB) phases from energy-volume calculations, and found that both structures show quite similar equations of state and transform into a Cmcm structure at 16 GPa using enthalpy calculations, in agreement with experimental observations. The transition phase, lattice parameters and bulk properties we obtained are comparable with experimental and theoretical data.

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

    PubMed

    Alptekin, Sebahaddin

    2013-01-01

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

  2. High-pressure elastic properties of cubic Ir2P from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sun, Xiao-Wei; Bioud, Nadhira; Fu, Zhi-Jian; Wei, Xiao-Ping; Song, Ting; Li, Zheng-Wei

    2016-10-01

    A study of the high-pressure elastic properties of new synthetic Ir2P in the anti-fluorite structure is conducted using ab initio calculations based on density functional theory. The elastic constants C11, C12 and C44 for the cubic Ir2P are obtained by the stress-strain method and the elastic stability calculations under pressure indicate that it is stable at least 100 GPa. Additionally, the electronic density of states, the aggregate elastic moduli, that is bulk modulus, shear modulus, and Young's modulus along with the Debye temperature, Poisson's ratio, and elastic anisotropy factor are all successfully obtained. Moreover, the pressure dependence of the longitudinal and shear wave velocities in three different directions [100], [110], and [111] for Ir2P are also predicted for the first time.

  3. Ab initio investigation of the sum-frequency hyperpolarizability of small chiral molecules

    NASA Astrophysics Data System (ADS)

    Champagne, Benoı̂t; Fischer, Peer; Buckingham, A. David

    2000-11-01

    Using a sum-over-states procedure based on configuration interaction singles /6-311++G **, we have computed the sum-frequency hyperpolarizability βijk(-3 ω;2 ω, ω) of two small chiral molecules, R-monofluoro-oxirane and R-(+)-propylene oxide. Excitation energies were scaled to fit experimental UV-absorption data and checked with ab initio values from time-dependent density functional theory. The isotropic part of the computed hyperpolarizabilities, β¯(-3ω;2ω,ω) , is much smaller than that reported previously from sum-frequency generation experiments on aqueous solutions of arabinose. Comparison is made with a single-centre chiral model.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  5. Ab initio molecular orbital calculations of the vibrational frequencies of XY4/sup -n/ anions

    NASA Astrophysics Data System (ADS)

    Curtiss, L. A.; Nichols, R.

    The vibrational frequencies of a seris of XY4/sup -n/ anions (BeF4(-2), BF4(-), AlF4(-), MgCl4(-2), and AlCl4(-)) have been calculated by ab initio molecular orbital theory using the 3-21G and 6-31G* basis sets. The predicted harmonic frequencies are for the most part in good agreement with the observed frequencies of these anions in molten alkali halide mixtures. At the 3-21G basis set level the average difference between the observed and predicted frequencies is 12% while at the 6-31G* basis set level the average difference is 6%. Calculations of this type may be helpful in predicting the vibrational frequencies of other anions in molten salts.

  6. Dielectric Response and Born Dynamic Charge of BN Nanotubes from Ab Initio Finite Electric Field Calculations

    NASA Astrophysics Data System (ADS)

    Guo, Guang-Yu; Ishibashi, Shoji; Tamura, Tomoyuki; Terakura, Kiyoyuki

    2007-03-01

    Since the discovery of carbon nanotubes (CNTs) in 1991 by Iijima, carbon and other nanotubes have attracted considerable interest worldwide because of their unusual properties and also great potentials for technological applications. Though CNTs continue to attract great interest, other nanotubes such as BN nanotubes (BN-NTs) may offer different opportunities that CNTs cannot provide. In this contribution, we present the results of our recent systematic ab initio calculations of the static dielectric constant, electric polarizability, Born dynamical charge, electrostriction coefficient and piezoelectric constant of BN-NTs using the latest crystalline finite electric field theory [1]. [1] I. Souza, J. Iniguez, and D. Vanderbilt, Phys. Rev. Lett. 89, 117602 (2002); P. Umari and A. Pasquarello, Phys. Rev. Lett. 89, 157602 (2002).

  7. 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.

  8. Ab initio/DFT calculations of butyl ammonium salt of O,O'-dibornyl dithiophosphate.

    PubMed

    Kart, H H; Ozdemir Kart, S; Karakuş, M; Kurt, M

    2014-08-14

    O,O'-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other. PMID:24747929

  9. Ab initio/DFT calculations of butyl ammonium salt of O,O‧-dibornyl dithiophosphate

    NASA Astrophysics Data System (ADS)

    Kart, H. H.; Özdemir Kart, S.; Karakuş, M.; Kurt, M.

    2014-08-01

    O,O‧-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other.

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

    SciTech Connect

    Crusius, Johann-Philipp Hassel, Egon; Hellmann, Robert Bich, Eckard

    2015-06-28

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

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

    PubMed

    Rüter, Hannes R; Redmer, Ronald

    2014-04-11

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

  12. 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.

  13. Diffusion Coefficients in Liquid and Grain Boundary Predicted by Ab Initio Molecular Dynamics

    SciTech Connect

    Jablonski, P.D.; Liu, Z.; Fang, H.; Wang, B.

    2011-04-01

    Molecular dynamics (MD) is a powerful tool to probe the thermodynamic and kinetic properties of solid, glass and liquid phases. In classical molecular dynamics (CMD), empirical models are used to describe the force by considering bond, bend and dihedral angle contributions with parameters fitted to experimental data or first-principles calculations of small clusters. In the ab initio molecular dynamics (AIMD), the forces are calculated on the fly using the first-principles density functional theory as discussed above. In the present work, we use AIMD simulations to follow the random walk of atoms in the liquid state. Based on the mean square displacements (MSD), the diffusion coefficients are calculated from the Einstein equation. Furthermore, we extend this approach to understand the diffusion in grain boundaries.

  14. An ab initio analysis of electronic states associated with a silicon vacancy in cubic symmetry

    NASA Astrophysics Data System (ADS)

    Ogawa, T.; Tsuruta, K.; Iyetomi, H.

    2011-11-01

    The electronic orbitals localized in the vicinity of a vacancy in a silicon crystal are calculated by an ab initio method based on the density functional theory and analyzed in association with the elastic softening observed by the recent ultrasonic experiments, especially focused on an estimate of the electric quadrupole moments. The localized orbitals due to the existence of a vacancy show largely extended properties and the quadrupole moments calculated from the orbitals indicate the strong dependence on cell sizes up to 511 atoms in the basic cell. Asymptotic values of the quadrupole moments in the limit of large size are obtained by an extrapolating method. It is shown that the quadrupole moments are enhanced due to the extension of the orbitals and the ratio of the quadrupole moments of Γ5 and Γ3 symmetries agrees well with the value deduced from the experimental results.

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

    SciTech Connect

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

    2015-02-01

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

  16. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

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

    SciTech Connect

    Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2014-09-01

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

  18. Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-.

    PubMed

    Muller, R P; Warshel, A

    1996-01-01

    This paper describes a hybrid ab initio quantum mechanical/molecular mechanics (QM/MM) method for calculating activation free energies of chemical reactions in solution, using molecular mechanics force fields for the solvent and an ab initio technique that incorporates the potential from the solvent in its Hamiltonian for the solute. The empirical valence bond (EVB) method is used as a reference potential for the ab initio free energy calculation, and drives the reaction along the proper coordinate, thus overcoming problems encountered by direct attempts to use molecular orbital methods in calculations of activation free energies. The utility of our method is illustrated by calculating the activation free energy for proton transfer between fluoride ions in the [FHF]-system, in both polar and nonpolar solution.

  19. Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

    SciTech Connect

    Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.

    2006-09-20

    Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

  20. 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

  1. 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

  2. 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

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

    PubMed

    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. PMID:27176426

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-02-01

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

  8. Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.

    1999-01-01

    A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.

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

    PubMed

    Bryk, Taras; Klevets, Ivan

    2012-12-14

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

  10. Accurate ab initio quartic force fields for borane and BeH2

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

  12. Ab initio investigation of the stationary points on the potential energy surface for the ethylene-sulfur dioxide complex

    NASA Astrophysics Data System (ADS)

    De Almeida, Wagner B.

    1994-12-01

    The ground state potential energy surface for the C 2H 4...SO 2 complex has been extensively investigated at the Hartree-Fock (HF) level of theory employing the 6-31 G ∗∗ basis set. Electron correlation effects were assessed by second-order M∅ller-Plesset perturbation theory in single point calculations at the HF/6-31G ∗∗ optimized geometry. Various stationary points have been located and characterized through harmonic frequency analysis. The ab initio predicted global minimum energy structure is in agreement with an experimental microwave study.

  13. Ab initio molecular orbital/Rice-Ramsperger-Kassel-Marcus theory study of multichannel rate constants for the unimolecular decomposition of benzene and the H+C6H5 reaction over the ground electronic state

    NASA Astrophysics Data System (ADS)

    Mebel, A. M.; Lin, M. C.; Chakraborty, D.; Park, J.; Lin, S. H.; Lee, Y. T.

    2001-05-01

    The potential energy surface for the unimolecular decomposition of benzene and H+C6H5 recombination has been studied by the ab initio G2M(cc, MP2) method. The results show that besides direct emission of a hydrogen atom occurring without an exit channel barrier, the benzene molecule can undergo sequential 1,2-hydrogen shifts to o-, m-, and p-C6H6 and then lose a H atom with exit barriers of about 6 kcal/mol. o-C6H6 can eliminate a hydrogen molecule with a barrier of 121.4 kcal/mol relative to benzene. o- and m-C6H6 can also isomerize to acyclic isomers, ac-C6H6, with barriers of 110.7 and 100.6 kcal/mol, respectively, but in order to form m-C6H6 from benzene the system has to overcome a barrier of 108.6 kcal/mol for the 1,2-H migration from o-C6H6 to m-C6H6. The bimolecular H+C6H5 reaction is shown to be more complicated than the unimolecular fragmentation reaction due to the presence of various metathetical processes, such as H-atom disproportionation or addition to different sites of the ring. The addition to the radical site is barrierless, the additions to the o-, m-, and p-positions have entrance barriers of about 6 kcal/mol and the disproportionation channel leading to o-benzyne+H2 has a barrier of 7.6 kcal/mol. The Rice-Ramsperger-Kassel-Marcus and transition-state theory methods were used to compute the total and individual rate constants for various channels of the two title reactions under different temperature/pressure conditions. A fit of the calculated total rates for unimolecular benzene decomposition gives the expression 2.26×1014exp(-53 300/T)s-1 for T=1000-3000 K and atmospheric pressure. This finding is significantly different from the recommended rate constant, 9.0×1015exp(-54 060/T) s-1, obtained by kinetic modeling assuming only the H+C6H5 product channel. At T=1000 K, the branching ratios for the formation of H+C6H5 and ac-C6H6 are 29% and 71%, respectively. H+C6H5 becomes the major channel at T⩾1200 K. The total rate for the bimolecular H

  14. Microwave and ab initio studies of rare gas-methane van der Waals complexes

    NASA Astrophysics Data System (ADS)

    Liu, Yaqian; Jäger, Wolfgang

    2004-05-01

    Rotational spectra of the weakly bound Kr-methane van der Waals complex were recorded using a pulsed molecular beam Fourier transform microwave spectrometer in the range from 3.5 to 18 GHz. Spectra of 25 isotopomers of Kr-methane were assigned and analyzed. For isotopomers containing CH4, 13CH4, and CD4, two sets of transitions with K=0 and one with K=1 were recorded, correlating to the j=0, 1, and 2 rotational levels of free methane, respectively (j is the rotational angular momentum quantum number of the methane monomer). For isotopomers containing CH3D and CHD3, two K=0 components were recorded, correlating to the jk=00 and 11 rotational levels of free methane (k corresponds to the projection of j onto the C3 axis of CH3D and CHD3). The obtained spectroscopic results were used to derive van der Waals bond distance R, van der Waals stretching frequency νs, and the corresponding stretching force constant ks. Nuclear spin statistical weights of individual states were obtained from molecular symmetry group analyses and were compared with the observed relative transition intensities. The tentatively assigned j=2 transitions were more intense than predicted from symmetry considerations. This is attributed to a relatively large effective dipole moment of this state, supported by ab initio dipole moment calculations. Ab initio potential energy calculations of Kr-CH4 and Ar-CH4 were done at the coupled cluster level of theory, with single and double excitations and perturbative inclusion of triple excitations, using the aug-cc-pVTZ basis set supplemented with bond functions. The theoretical results show that the angular dynamics of the dimer does not change significantly when the binding partner of methane changes from Ar to Kr. The dipole moment of Ar-CH4 was calculated at various configurations, providing a qualitative explanation for the unsuccessful spectral searches for rotational transitions of Ar-CH4.

  15. Emergent properties of nuclei from ab initio coupled-cluster calculations

    DOE PAGES

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-05-17

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

  16. Ab initio thermochemistry using optimal-balance models with isodesmic corrections: The ATOMIC protocol

    NASA Astrophysics Data System (ADS)

    Bakowies, Dirk

    2009-04-01

    A theoretical composite approach, termed ATOMIC for Ab initio Thermochemistry using Optimal-balance Models with Isodesmic Corrections, is introduced for the calculation of molecular atomization energies and enthalpies of formation. Care is taken to achieve optimal balance in accuracy and cost between the various components contributing to high-level estimates of the fully correlated energy at the infinite-basis-set limit. To this end, the energy at the coupled-cluster level of theory including single, double, and quasiperturbational triple excitations is decomposed into Hartree-Fock, low-order correlation (MP2, CCSD), and connected-triples contributions and into valence-shell and core contributions. Statistical analyses for 73 representative neutral closed-shell molecules containing hydrogen and at least three first-row atoms (CNOF) are used to devise basis-set and extrapolation requirements for each of the eight components to maintain a given level of accuracy. Pople's concept of bond-separation reactions is implemented in an ab initio framework, providing for a complete set of high-level precomputed isodesmic corrections which can be used for any molecule for which a valence structure can be drawn. Use of these corrections is shown to lower basis-set requirements dramatically for each of the eight components of the composite model. A hierarchy of three levels is suggested for isodesmically corrected composite models which reproduce atomization energies at the reference level of theory to within 0.1 kcal/mol (A), 0.3 kcal/mol (B), and 1 kcal/mol (C). Large-scale statistical analysis shows that corrections beyond the CCSD(T) reference level of theory, including coupled-cluster theory with fully relaxed connected triple and quadruple excitations, first-order relativistic and diagonal Born-Oppenheimer corrections can normally be dealt with using a greatly simplified model that assumes thermoneutral bond-separation reactions and that reduces the estimate of these

  17. Ab initio thermochemistry using optimal-balance models with isodesmic corrections: the ATOMIC protocol.

    PubMed

    Bakowies, Dirk

    2009-04-14

    A theoretical composite approach, termed ATOMIC for Ab initio Thermochemistry using Optimal-balance Models with Isodesmic Corrections, is introduced for the calculation of molecular atomization energies and enthalpies of formation. Care is taken to achieve optimal balance in accuracy and cost between the various components contributing to high-level estimates of the fully correlated energy at the infinite-basis-set limit. To this end, the energy at the coupled-cluster level of theory including single, double, and quasiperturbational triple excitations is decomposed into Hartree-Fock, low-order correlation (MP2, CCSD), and connected-triples contributions and into valence-shell and core contributions. Statistical analyses for 73 representative neutral closed-shell molecules containing hydrogen and at least three first-row atoms (CNOF) are used to devise basis-set and extrapolation requirements for each of the eight components to maintain a given level of accuracy. Pople's concept of bond-separation reactions is implemented in an ab initio framework, providing for a complete set of high-level precomputed isodesmic corrections which can be used for any molecule for which a valence structure can be drawn. Use of these corrections is shown to lower basis-set requirements dramatically for each of the eight components of the composite model. A hierarchy of three levels is suggested for isodesmically corrected composite models which reproduce atomization energies at the reference level of theory to within 0.1 kcal/mol (A), 0.3 kcal/mol (B), and 1 kcal/mol (C). Large-scale statistical analysis shows that corrections beyond the CCSD(T) reference level of theory, including coupled-cluster theory with fully relaxed connected triple and quadruple excitations, first-order relativistic and diagonal Born-Oppenheimer corrections can normally be dealt with using a greatly simplified model that assumes thermoneutral bond-separation reactions and that reduces the estimate of these

  18. 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.

  19. 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.

  20. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  2. New approaches for molecular conformer force field analysis in combination with ab initio results

    NASA Astrophysics Data System (ADS)

    Kuramshina, G. M.; Pentin, Yu. A.; Yagola, A. G.

    1999-10-01

    Ab initio and DFT results on harmonic force constants for trans- and gauche-conformers of CH 3CH 2CH 2Cl, CF 3CH 2CH 2Cl and CCl 3CH 2CH 2Cl are used for formulating constraints in molecular force field models described compounds with hindered internal rotation around the C-C bond.

  3. 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

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

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2011-01-01

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

  5. The Use of Ab Initio Wavefunctions in Line-Shape Calculations for Water Vapor

    NASA Astrophysics Data System (ADS)

    Gamache, Robert R.; Lamouroux, Julien; Schwenke, David W.

    2014-06-01

    In semi-classical line-shape calculations, the internal motions of the colliding pair are treated via quantum mechanics and the collision trajectory is determined by classical dynamics. The quantum mechanical component, i.e. the determination of reduced matrix elements (RME) for the colliding pair, requires the wavefunctions of the radiating and the perturbing molecules be known. Here the reduced matrix elements for collisions in the ground vibrational state of water vapor are calculated by two methods and compared. First, wavefunctions determined by diagonalizing an effective (Watson) Hamiltonian are used to calculate the RMEs and, second, the ab initio wavefunctions of Partridge and Schwenke are used. While the ground vibrational state will yield the best approximation of the wavefunctions from the effective Hamiltonian approach, this study clearly identifies problems for states not included in the fit of the Hamiltonian and for extrapolated states. RMEs determined using ab initio wavefunctions use ˜100000 times more computational time; however, all ro-vibrational interactions are included. Hence, the ab initio approach will yield better RMEs as the number of vibrational quanta exchanged in the optical transition increases, resulting in improvements in calculated half-widths and line shifts. It is important to note that even for pure rotational transitions the use of ab initio wavefunctions will yield improved results.

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

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo

    2011-05-01

    Ab initio molecular dynamics simulations with the Car-Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.

  8. Unified ab initio formulation of flexoelectricity and strain-gradient elasticity

    NASA Astrophysics Data System (ADS)

    Stengel, Massimiliano

    2016-06-01

    The theory of flexoelectricity and that of nonlocal elasticity are closely related, and are often considered together when modeling strain-gradient effects in solids. Here I show, based on a first-principles lattice-dynamical analysis, that their relationship is much more intimate than previously thought, and their consistent simultaneous treatment is crucial for obtaining correct physical answers. In particular, I identify a gauge invariance in the theory, whereby the energies associated to strain-gradient elasticity and flexoelectrically induced electric fields are individually reference dependent, and only when summed up they yield a well-defined result. To illustrate this, I construct a minimal thermodynamic functional incorporating strain-gradient effects, and establish a formal link between the continuum description and ab initio phonon dispersion curves to calculate the relevant tensor quantities. As a practical demonstration, I apply such a formalism to bulk SrTiO3, where I find an unusually strong contribution of nonlocal elasticity, mediated by the interaction between the ferroelectric soft mode and the transverse acoustic branches. These results have important implications towards the construction of well-defined thermodynamic theories where flexoelectricity and ferroelectricity coexist. More generally, they open exciting new avenues for the implementation of hierarchical multiscale concepts in the first-principles simulation of crystalline insulators.

  9. 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.

  10. 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.

    PubMed

    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. PMID:25448928

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

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

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

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

    PubMed

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

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

  13. High-level ab-initio calculation of gas-phase NMR chemical shifts and secondary isotope effects of methanol

    NASA Astrophysics Data System (ADS)

    Auer, Alexander A.

    2009-01-01

    In this contribution high-level ab-initio calculations of the chemical shifts of methanol including zero-point vibrational and temperature corrections are presented. For the first time, secondary isotope effects have been calculated via second order vibrational perturbation theory. In comparison with recent experimental gas-phase data and in contrast to other quantum-chemical methods the results are consistent and in very good agreement with the experimental 13C, 17O and 1H chemical shifts reported by Makulski [W. Makulski, J. Mol. Struct. 872 (2008) 81]. Secondary isotope effects can be calculated with remarkable accuracy of a few hundredths of a ppm in comparison to experiment.

  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. Ab initio study of the cubic-to-hexagonal phase transition promoted by interstitial hydrogen in iron

    NASA Astrophysics Data System (ADS)

    Castedo, A.; Sanchez, J.; Fullea, J.; Andrade, M. C.; de Andres, P. L.

    2011-09-01

    Using ab initio density-functional theory, we study the role of interstitial hydrogen on the energetics of the phase transformation of iron from bcc to hcp along Bain’s pathway. The impurity creates an internal stress field that can be released through a tetragonal distortion of the lattice, promoting the bcc (ferromagnetic) → fcc (frustrated antiferromagnetic) → hcp (ferromagnetic) transition. The transformation between crystal systems is accompanied by a drastic magnetic reorganization and sudden variations of the unit cell volume, which can be one of the reasons for embrittlement and mechanical failure of iron upon hydrogen adsorption.

  16. Taming the resistive switching in Fe/MgO/V/Fe magnetic tunnel junctions: An ab initio study

    NASA Astrophysics Data System (ADS)

    Aguiar-Hualde, J. M.; Alouani, M.

    2014-12-01

    A possible mechanism for the resistive switching observed experimentally in Fe/MgO/V/Fe junctions is presented. Ab initio total energy calculations within the local density approximation and pseudopotential theory shows that by moving the oxygen ions across the MgO/V interface one obtains a metastable state. It is argued that this state can be reached by applying an electric field across the interface. In addition, the ground state and the metastable state show different electric conductances. The latter results are discussed in terms of the changes of the density of states at the Fermi level and the charge transfer at the interface due to the oxygen ion motion.

  17. Ab-Initio Based Computation of Rate Constants for Spin Forbidden Metalloprotein-Substrate Reactions

    NASA Astrophysics Data System (ADS)

    Ozkanlar, Abdullah; Rodriguez, Jorge H.

    2007-03-01

    Some chemical and biochemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of ab-initio methods, such as spin density functional theory (SDFT), to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory (NA-TST) in conjuntion with SDFT to predict the rate constant of the spin- forbidden recombination of carbon monoxide with iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in very good agreement with experiment. In addition, we present results for the spin- forbidden ligand binding reactions of iron-containing heme proteins such as myoglobin.

  18. Determination of a silane intermolecular force field potential model from an ab initio calculation

    SciTech Connect

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng

    2010-12-15

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  19. Solvation properties of microhydrated sulfate anion clusters: insights from ab initio calculations.

    PubMed

    Wan, Quan; Spanu, Leonardo; Galli, Giulia

    2012-08-01

    Sulfate-water clusters play an important role in environmental and industrial processes, yet open questions remain on their physical and chemical properties. We investigated the smallest hydrated sulfate anion clusters believed to have a full solvation shell, with 12 or 13 water molecules. We used ab initio molecular dynamics and electronic structure calculations based on density functional theory, with semilocal and hybrid functionals. At both levels of theory we found that configurations with the anion at the surface of the cluster are energetically favored compared to fully solvated ones, which are instead metastable. We show that infrared spectra of the anion with different solvation shells have similar vibrational signatures, indicating that a mixture of surface and internally solvated geometries are likely to be present in the experimental samples at low temperature. In addition, the computed electronic density of states of surface and internally solvated clusters are hardly distinguishable at finite temperature, with the highest occupied molecular orbital belonging to the anion in all cases. The equilibrium structure determined for SO(4)(2-)·(H(2)O)(13) differs from that previously reported; we find that the addition of one water molecule to a 12-water cluster modifies its hydration shell and that water-water bonds are preferred over water-anion bonds.

  20. High-level ab initio computations of the absorption spectra of organic iridium complexes.

    PubMed

    Plasser, Felix; Dreuw, Andreas

    2015-02-12

    The excited states of fac-tris(phenylpyridinato)iridium [Ir(ppy)3] and the smaller model complex Ir(C3H4N)3 are computed using a number of high-level ab initio methods, including the recently implemented algebraic diagrammatic construction method to third-order ADC(3). A detailed description of the states is provided through advanced analysis methods, which allow a quantification of different charge transfer and orbital relaxation effects and give extended insight into the many-body wave functions. Compared to the ADC(3) benchmark an unexpected striking difference of ADC(2) is found for Ir(C3H4N)3, which derives from an overstabilization of charge transfer effects. Time-dependent density functional theory (TDDFT) using the B3LYP functional shows an analogous but less severe error for charge transfer states, whereas the ωB97 results are in good agreement with ADC(3). Multireference configuration interaction computations, which are in reasonable agreement with ADC(3), reveal that static correlation does not play a significant role. In the case of the larger Ir(ppy)3 complex, results at the TDDFT/B3LYP and TDDFT/ωB97 levels of theory are presented. Strong discrepancies between the two functionals, which are found with respect to the energies, characters, as well as the density of the low lying states, are discussed in detail and compared to experiment. PMID:25584785

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  4. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.

    PubMed

    Steele, Ryan P

    2015-12-17

    This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.

  5. 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

  6. Microwave and ab initio studies of rare gas-methane van der Waals complexes.

    PubMed

    Liu, Yaqian; Jäger, Wolfgang

    2004-05-15

    Rotational spectra of the weakly bound Kr-methane van der Waals complex were recorded using a pulsed molecular beam Fourier transform microwave spectrometer in the range from 3.5 to 18 GHz. Spectra of 25 isotopomers of Kr-methane were assigned and analyzed. For isotopomers containing CH4, 13CH4, and CD4, two sets of transitions with K = 0 and one with K = 1 were recorded, correlating to the j = 0, 1, and 2 rotational levels of free methane, respectively (j is the rotational angular momentum quantum number of the methane monomer). For isotopomers containing CH3D and CHD3, two K = 0 components were recorded, correlating to the j(k) = 0(0) and 1(1) rotational levels of free methane (k corresponds to the projection of j onto the C3 axis of CH3D and CHD3). The obtained spectroscopic results were used to derive van der Waals bond distance R, van der Waals stretching frequency nu(s), and the corresponding stretching force constant k(s). Nuclear spin statistical weights of individual states were obtained from molecular symmetry group analyses and were compared with the observed relative transition intensities. The tentatively assigned j = 2 transitions were more intense than predicted from symmetry considerations. This is attributed to a relatively large effective dipole moment of this state, supported by ab initio dipole moment calculations. Ab initio potential energy calculations of Kr-CH4 and Ar-CH4 were done at the coupled cluster level of theory, with single and double excitations and perturbative inclusion of triple excitations, using the aug-cc-pVTZ basis set supplemented with bond functions. The theoretical results show that the angular dynamics of the dimer does not change significantly when the binding partner of methane changes from Ar to Kr. The dipole moment of Ar-CH4 was calculated at various configurations, providing a qualitative explanation for the unsuccessful spectral searches for rotational transitions of Ar-CH4.

  7. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1996-07-01

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

  10. Proton transport in triflic acid pentahydrate studied via ab initio path integral molecular dynamics.

    PubMed

    Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E

    2011-06-16

    Trifluoromethanesulfonic acid hydrates provide a well-defined system to study proton dissociation and transport in perfluorosulfonic acid membranes, typically used as the electrolyte in hydrogen fuel cells, in the limit of minimal water. The triflic acid pentahydrate crystal (CF(3)SO(3)H·5H(2)O) is sufficiently aqueous that it contains an extended three-dimensional water network. Despite it being extended, however, long-range proton transport along the network is structurally unfavorable and would require considerable rearrangement. Nevertheless, the triflic acid pentahydrate crystal system can provide a clear picture of the preferred locations of local protonic defects in the water network, which provides insights about related structures in the disordered, low-hydration environment of perfluorosulfonic acid membranes. Ab initio molecular dynamics simulations reveal that the proton defect is most likely to transfer to the closest water that has the expected presolvation and only contains water in its first solvation shell. Unlike the tetrahydrate of triflic acid (CF(3)SO(3)H·4H(2)O), there is no evidence of the proton preferentially transferring to a water molecule bridging two of the sulfonate groups. However, this could be an artifact of the crystal structure since the only such water molecule is separated from the proton by long O-O distances. Hydrogen bonding criteria, using the two-dimensional potential of mean force, are extracted. Radial distribution functions, free energy profiles, radii of gyration, and the root-mean-square displacement computed from ab initio path integral molecular dynamics simulations reveal that quantum effects do significantly extend the size of the protonic defect and increase the frequency of proton transfer events by nearly 15%. The calculated IR spectra confirm that the dominant protonic defect mostly exists as an Eigen cation but contains some Zundel ion characteristics. Chain lengths and ring sizes determined from the

  11. 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

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

    PubMed

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

    2012-01-17

    liquid cluster and becomes indistinguishable from an equilibrated, solvated electron on a picosecond time scale. In contrast, for solid, cryogenic systems, the electron only partially localizes outside of the cluster, being trapped in a metastable, weakly bound "cushion-like" state. Strongly bound states under cryogenic conditions could only be prepared by cooling equilibrated, liquid, negatively charged clusters. These calculations allow us to rationalize how different isomers of electrons in cryogenic clusters can be observed experimentally. Our results also bring into question the direct extrapolation of properties of cryogenic, negatively charged water clusters to those of electrons in the bulk liquid. Ab initio molecular dynamics represents a unique computational tool for investigating the reactivity of the solvated electron in water. As a prototype, the electron-proton reaction was followed in the 32-water cluster. In accord with experiment, the molecular mechanism is a proton transfer process that is not diffusion limited, but rather controlled by a proton-induced deformation of the excess electron's solvent shell. We demonstrate the necessary ingredients of a successful density functional methodology for the hydrated electron that avoids potential pitfalls, such as self-interaction error, insufficient basis set, or lack of dispersion interactions. We also benchmark the density functional theory methods and outline the path to faithful ab initio simulations of dynamics and reactivity of electrons solvated in extended aqueous systems.

  13. 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.

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

    PubMed

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

    2008-08-14

    A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.

  15. Yttrium aluminium garnet under pressure: Structural, elastic, and vibrational properties from ab initio studies

    SciTech Connect

    Monteseguro, V.; Rodríguez-Hernández, P.; Muñoz, A.

    2015-12-28

    The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet is mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.

  16. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach

    SciTech Connect

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

    2008-03-28

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

  17. 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.

  18. Ab-initio crystal structure prediction. A case study: NaBH{sub 4}

    SciTech Connect

    Caputo, Riccarda; Tekin, Adem

    2011-07-15

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

  19. Synthesis, characterization and ab initio simulation of magnesium-substituted hydroxyapatite.

    PubMed

    Ren, F; Leng, Y; Xin, R; Ge, X

    2010-07-01

    The substitution of magnesium in hydroxyapatite (HA) was examined in HA nano-crystals synthesized by the wet-chemical precipitation method at 90 degrees C. Comprehensive characterization techniques, including X-ray diffraction, X-ray fluorescence, field emission scanning electron microscopy, high-resolution transmission electron microscopy, thermogravimetric analysis and Rietveld refinement, provided experimental evidence of the effects of Mg substitution on the phase, crystallinity, chemical composition, crystal size, morphology, thermal stability and crystal lattice structure of HA. A computational study using ab initio generalized gradient approximation density functional theory was performed to reveal changes in lattice parameters and preferential calcium sites for Mg substitution in HA. The experimental results showed that a limited amount of Mg (Mg/(Mg+Ca) between 5 and 7 mol.%) could successfully substitute for Ca in HA. HA crystallites became smaller and more irregular, and they formed greater agglomerates with Mg substitution. Mg substitution resulted in decreases in the crystallinity and thermal stability of HA. The lattice constants, a and c, decreased with increasing Mg substitution. The simulation results revealed that the Ca(1) sites in HA lattices were energetically favored sites for Mg substitution.

  20. Hydrogen-vacancy interaction in bcc iron: ab initio calculations and thermodynamics

    NASA Astrophysics Data System (ADS)

    Mirzaev, D. A.; Mirzoev, A. A.; Okishev, K. Yu.; Verkhovykh, A. V.

    2014-07-01

    The paper presents results of ab initio modelling of formation energies of vacancy-hydrogen complexes VHn and an extended variant of thermodynamic theory describing equilibrium concentrations of such complexes. A single H atom is shifted from vacancy to a neighbouring O-site by 1.19 Å. Two H atoms in a vacancy form a dumbbell with H-H distance of 2.38 Å being much greater than in H2 molecule. Configurations of three, four and five H atoms in a vacancy are more complex, and H-H distances gradually increase showing repulsion between hydrogen atoms. Binding energy of a VHn-1 complex with the next hydrogen atom to form VHn is 0.60, 0.61, 0.39, 0.37 and 0.31 for n = 1-5, which is close to other researchers' data. These results were used to construct an improved variant of thermodynamic description of vacancy-hydrogen interaction in a bcc solid solution taking into account both binding energies and hydrogen atom configurations in different VHn complexes. Calculations show that at low temperatures most vacancies are bound to several hydrogen atoms, and the equilibrium concentration of vacancies themselves significantly increases, in accordance with existing experiments.

  1. 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.

  2. Ab initio thermodynamic properties of point defects and O-vacancy diffusion in Mg spinels

    NASA Astrophysics Data System (ADS)

    Łodziana, Zbigniew; Piechota, Jacek

    2006-11-01

    We report ab initio plane wave density functional theory studies of thermodynamic properties of isolated cation substitutions and oxygen vacancies in magnesium spinel, MgAl2O4 . The formation enthalpy of Ca, Cu, and Zn substitutions of Mg cation indicate that transition metal dopants are energetically stable in the bulk of MgAl2O4 at low oxygen chemical potential. The electronic and thermodynamic properties of isolated defects in ternary spinel show close similarities with those in binary oxides; MgO and α-Al2O3 . The formation enthalpy of the oxygen vacancies are also similar in pure magnesium spinel and in binary oxides, but presence of impurity cations in MgAl2O4 significantly lowers formation enthalpy of the oxygen vacancy in their vicinity. Calculated energy barriers for oxygen vacancy hopping are lower in the vicinity of impurity atoms in the spinel structure. Our calculations indicate that the charge state of doped cation is modified by the accompanying oxygen vacancy and the vacancy diffusion is more facile around impurity. The present studies suggest that point defects play an important role in diffusion of oxygen vacancies in MgAl2O4 .

  3. 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.

  4. Optimized energy landscape exploration using the ab initio based activation-relaxation technique

    NASA Astrophysics Data System (ADS)

    Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal

    2011-07-01

    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 C20 clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

  5. 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.

  6. Ab initio study of protonated nitrosamide: a possible intermediate in the deNO x process

    NASA Astrophysics Data System (ADS)

    Kulkarni, Sudhir A.; Pundlik, Savita S.

    1995-10-01

    Ab initio calculations on protonated nitrosamide, a possible intermediate in the deNO x process, have been performed. A mechanism involving the formation of an intermediate NH 3NO + was proposed by Egsgaard, Carlsen and Madsen and tested by performing flame experiments with mass spectrometry. In the present work, the absence of NH 3NO + in the flame has been supported on the basis of its structure. This cation is observed to be a loosely bound adduct of NH 3 and NO + at and beyond the HF level of theory. On the other hand, NH 2NOH + is found to be a covalently bonded compound at all theoretical levels. Topographical analysis of electron density and electrostatic potential has been utilized to gain insight into bonding properties and to predict the possible sites of protonation. The vibrational spectra of both protonated nitrosamide cations are reported. The feasibility of proton transfer reactions of NH 3NO + with ammonia and water are investigated using heats of reactions. These values indicate that such a reaction is possible with NH 3 but unfavorable with H 2O.

  7. Ab initio random structure search for 13-atom clusters of fcc elements.

    PubMed

    Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M

    2013-03-27

    The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.

  8. Infrared signature of micro-hydration in the organophosphate sarin: An ab initio study

    DOE PAGES

    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

  9. 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.

  10. Ab initio Calculations of Charge Symmetry Breaking in the A =4 Hypernuclei

    NASA Astrophysics Data System (ADS)

    Gazda, Daniel; Gal, Avraham

    2016-03-01

    We report on ab initio no-core shell model calculations of the mirror Λ hypernuclei H4Λ and He4Λ , using the Bonn-Jülich leading-order chiral effective field theory hyperon-nucleon potentials plus a charge symmetry breaking Λ -Σ0 mixing vertex. In addition to reproducing rather well the 0g.s . + and 1exc+ binding energies, these four-body calculations demonstrate for the first time that the observed charge symmetry breaking splitting of mirror levels, reaching hundreds of keV for 0g.s . +, can be reproduced using realistic theoretical interaction models, although with a non-negligible momentum cutoff dependence. Our results are discussed in relation to recent measurements of the H4Λ(0g.s . +) binding energy at the Mainz Microtron [A. Esser et al. (A1 Collaboration), Phys. Rev. Lett. 114, 232501 (2015)] and the He4Λ(1exc+) excitation energy [T.O. Yamamoto et al. (J-PARC E13 Collaboration), Phys. Rev. Lett. 115, 222501 (2015)].

  11. 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.

  12. A Simple ab Initio Model for the Hydrated Electron That Matches Experiment.

    PubMed

    Kumar, Anil; Walker, Jonathan A; Bartels, David M; Sevilla, Michael D

    2015-08-27

    Since its discovery over 50 years ago, the "structure" and properties of the hydrated electron have been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy "zero Kelvin" structure found for any 4-water (or larger) anion cluster, at any post-Hartree–Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (Uhlig, Marsalek, and Jungwirth, J. Phys. Chem. Lett. 2012, 3, 3071−3075), with four OH bonds oriented toward the maximum charge density in a small central "void". The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

  13. 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.

  14. 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).

  15. Ab initio study of point defects near stacking faults in 3C-SiC

    DOE PAGES

    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

  16. 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).

  17. Microwave and ab initio studies of the Xe-CH4 van der Waals complex

    NASA Astrophysics Data System (ADS)

    Wen, Qing; Jäger, Wolfgang

    2006-01-01

    An ab initio potential-energy surface of the Xe-CH4 van der Waals complex was constructed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations. The recently developed small-core pseudopotential and augmented correlation-consistent polarized valence quadruple-zeta basis set was used for the xenon atom and Dunning's augmented correlation-consistent polarized valence triple-zeta basis set for the other atoms. The basis sets were supplemented with bond functions. Dipole moments were also calculated at various configurations. Rotational spectra of the Xe-CH4 van der Waals complex were recorded using a pulsed-nozzle Fourier transform microwave spectrometer. The isotopomers studied include those of CH4,CH134,CD4,CH3D, and CHD3 with the five most abundant Xe isotopes. Transitions within three internal rotor states, namely, the j =0,K=0;j=1,K=0; and j =2,K=1 states, were observed and assigned. Nuclear quadrupole hyperfine structures due to the presence of Xe131(I=3/2) were detected and analyzed. It was found that the j =1,K=0 state is perturbed by a Coriolis interaction with a nearby j =1,K=1 state. For isotopomers containing CH3D and CHD3, the j =2 states are no longer metastable and could not be observed. The spectroscopic results were used to derive structural and dynamical information of the Xe-CH4 complex.

  18. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  19. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    PubMed

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

  20. Geometry of AN Isolated Dimer of Imidazole Characterised by Rotational Spectroscopy and AB Initio Calculations

    NASA Astrophysics Data System (ADS)

    Mullaney, John C.; Zaleski, Daniel P.; Tew, David Peter; Walker, Nick; Legon, Anthony

    2016-06-01

    An isolated, gas-phase dimer of imidazole is generated through laser vaporisation of a solid rod containing a 1:1 mixture of imidazole and copper in the presence of an argon buffer gas undergoing supersonic expansion. The complex is characterised through broadband rotational spectroscopy and is shown to have a twisted, hydrogen-bonded geometry. Calculations at the CCSD(T)(F12*)/cc-pVDZ-F12 level of theory confirm this to be the lowest-energy conformer of the imidazole dimer. The distance between the respective centres of mass of the imidazole monomer subunits is determined to be 5.2751(1) Å, and the twist angle γ describing rotation of one monomer with respect to the other about a line connecting the centres of mass of the monomers is determined to be 87.9(4)o. Four out of six intermolecular parameters in the model geometry are precisely determined from the experimental rotational constants and are consistent with results calculated ab initio.

  1. 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.

  2. Ab initio-predicted micro-mechanical performance of refractory high-entropy alloys

    PubMed Central

    Li, Xiaoqing; Tian, Fuyang; Schönecker, Stephan; Zhao, Jijun; Vitos, Levente

    2015-01-01

    Recently developed high-entropy alloys (HEAs) consisting of multiple principal elements represent a new field of metallurgy and have demonstrated appealing properties for a wide range of applications. Using ab initio alloy theory, we reveal the alloying effect on the elastic properties and the ideal tensile strength (ITS) in the [001] direction of four body-centered cubic (bcc) refractory HEAs based on Zr, V, Ti, Nb, and Hf. We find that these HEAs show high elastic anisotropy and large positive Cauchy pressure, suggesting good extrinsic ductility. Starting from ZrNbHf, it is found that the ITS decreases with equimolar Ti addition. On the other hand, if both Ti and V are added to ZrNbHf, the ITS is enhanced by about 42%. An even more captivating effect is the ITS increase by about 170%, if Ti and V are substituted for Hf. The alloying effect on the ITS is explained by the d-band filling. An intrinsic brittle-to-ductile transition is found in terms of the failure mode under uniaxial tension. These investigations suggest that intrinsically ductile HEAs with high ideal strength can be achieved by controlling the proportion of group four elements to group five elements. PMID:26199145

  3. Microwave Spectra and AB Initio Studies of the Ne-Acetone Complex

    NASA Astrophysics Data System (ADS)

    Gao, Jiao; Thomas, Javix; Xu, Yunjie; Jäger, Wolfgang

    2015-06-01

    Microwave spectra of the neon-acetone van der Waals complex were measured using a cavity-based molecular beam Fourier-transform microwave spectrometer in the region from 5 to 18 GHz. Both 20Ne and 22Ne containing isotopologues were studied and both c- and weaker a-type rotational transitions were observed. The transitions are split into multiplets due to the internal rotation of two methyl groups in acetone. Electronic structure calculations were done at the MP2 level of theory with the 6-311++g (2d, p) basis set for all atoms and the internal rotation barrier height of the methyl groups was determined to be about 2.8 kJ/mol. The ab initio rotational constants were the basis for our spectroscopic searches, but the multiplet structures and floppiness of the complex made the quantum number assignment very difficult. The assignment was finally achieved with the aid of constructing closed frequency loops and predicting internal rotation splittings using the XIAM code. Analyses of the spectra yielded rotational and centrifugal distortion constants, as well as internal rotation parameters, which were interpreted in terms of structure and internal dynamics of the complex. H. Hartwig and H. Dreizler, Z. Naturforsch. A 51, 923 (1996).

  4. 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).

  5. A Simple ab initio Model for the Hydrated Electron that Matches Experiment

    PubMed Central

    Kumar, Anil; Walker, Jonathan A.; Bartels, David M.; Sevilla, Michael D.

    2015-01-01

    Since its discovery over 50 years ago, the “structure” and properties of the hydrated electron has been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy zero “Kelvin” structure found for any 4-water (or larger) anion cluster, at any post-Hartree-Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (UMJ: Uhlig, Marsalek, and Jungwirth, Journal of Physical Chemistry Letters 2012, 3, 3071-5), with four OH bonds oriented toward the maximum charge density in a small central “void”. The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

  6. Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels

    SciTech Connect

    Morgan, Dane; Yang, Yong Austin

    2013-10-28

    The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-{Np,Am}, leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling.

  7. Ab initio cluster studies of La sub 2 CuO sub 4

    SciTech Connect

    Martin, R.L.

    1991-01-01

    In this paper we examine the properties of small cluster models of La{sub 2}CuO{sub 4}. In Section 2, the Madelung/Pauli background potential used to imbed the primary cluster and the basis sets used to expand the cluster wavefunction are discussed. Section 3 presents the results of calculations on CuO{sub 6} in which the optical absorption and the photoemission spectrum are examined. The calculation on CuO{sub 6} and our earlier work on larger clusters suggest that a single-band Pariser-Parr-Pople (PPP) model be developed. Therefore, in Section 4 the PPP model and extensions which relax the zero-differential-overlap (ZDO) approximation upon which it is based are reviewed. Calculations on the states of Cu{sub 2}O{sub 7} necessary to parameterize the PPP model are presented in Section 5 and compared with analogous calculations for Cu{sub 2}O{sub 11}. Section 6 discusses the problems associated with the direct ab initio determination of the anti-ferromagnetic exchange interaction, examines the magnitudes of the occupation-dependent hopping and direct exchange interactions which arise when the ZDO approximation is relaxed, and provides estimates of the uncertainties in the parameters due to electron correlation and polarization effects not recoverable with the present basis sets and finite clusters. A comparison of the parameters with those extracted from constrained LDF theory concludes Section 6. Finally, Section 7 summarizes the conclusions of this research.

  8. 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.

  9. Ab initio many-body calculations of nucleon-4He scattering with three-nucleon forces

    DOE PAGES

    Hupin, Guillaume; Langhammer, Joachim; Navratil, Petr; Quaglioni, Sofia; Calci, Angelo; Roth, Robert

    2013-11-27

    We extend the ab initio no-core shell model/resonating-group method to include three-nucleon (3N) interactions for the description of nucleon-nucleus collisions. We outline the formalism, give algebraic expressions for the 3N-force integration kernels, and discuss computational aspects of two alternative implementations. The extended theoretical framework is then applied to nucleon-4He elastic scattering using similarity-renormalization-group (SRG)-evolved nucleon-nucleon plus 3N potentials derived from chiral effective field theory. We analyze the convergence properties of the calculated phase shifts and explore their dependence upon the SRG evolution parameter. We include up to six excited states of the 4He target and find significant effects from themore » inclusion of the chiral 3N force, e.g., it enhances the spin-orbit splitting between the 3/2– and 1/2– resonances and leads to an improved agreement with the phase shifts obtained from an accurate R-matrix analysis of the five-nucleon experimental data. As a result, we find remarkably good agreement with measured differential cross sections at various energies below the d+3H threshold, while analyzing powers manifest larger deviations from experiment for certain energies and angles.« less

  10. Ab initio phase stability at high temperatures and pressures in the V-Cr system

    NASA Astrophysics Data System (ADS)

    Landa, Alexander; Soderlind, Per; Yang, Lin

    2015-03-01

    Vanadium metal has seen a surge in research, experimental and theoretical, driven mainly by its importance in applications but also because of its surprising destabilization of the body-centered cubic (bcc) ground-state phase close to 60 GPa. The phase stability of vanadium metal and vanadium-chromium alloys at high temperatures and pressures is explored by means of first-principles electronic-structure calculations. Utilizing the self-consistent ab initio lattice dynamics approach in conjunction with density-functional theory, we show that pressure-induced mechanical instability of body-centered cubic vanadium metal, which results in formation of a rhombohedral phase at around 60 GPa at room temperatures, will prevail significant heating and compression. Furthermore, alloying with chromium decreases the temperature at which stabilization of the body-centered cubic phase occurs at elevated pressure. Computing support for this work came from the LLNL Computing Grand Challenge program. This work performed under the auspices of the U.S. DOE by LLNL under Contract DE-AC52-07NA27344 and funded by the Laboratory Directed Research and Development Program at LLNL under project tracking code 11-ER-033.

  11. Ab initio study of the dipole polarizability and the first hyperpolarizability of heterocyclics

    NASA Astrophysics Data System (ADS)

    Humberto, J.; Soscún, M.; Hinchliffe, Alan

    1995-04-01

    An Ab Initio treatment of the molecular structures, dipole polarizability and the first hyperpolarizability of a series of B, Al, C, Si, N, P, O and S heterocyclics is presented. The molecular geometries were fully optimized at Hartree-Fock level and using the standard STO/6-31G** basis set. At these structures, the static dipole polarizability and the first hyperpolarizability were calculated by using a direct and analytic coupled perturbed Hartree-Fock HF method and the family of diffuse and multiple polarized STO/6-31+G(nd,mp) basis sets. Electron correlation effects on the polarizability were accounted at second order Mo/ller-Plesset MP2 level of theory by using a finite field energy based procedure and the STO/6-31+G(d,p) basis set. The polarizabilities of these compounds, discussed in terms of the delocalization of the ring π electrons and the intrinsec properties of the heteroatoms, shown that the HF/6-31+G(3d,3p) approach lead to values that are within the 96% of the available experimental data. Finally, the contribution of the MP2 correlation effects to the polarizability are analyzed taking as reference the Hartree-Fock results.

  12. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    SciTech Connect

    Valentini, Paolo Schwartzentruber, Thomas E. Bender, Jason D. Nompelis, Ioannis Candler, Graham V.

    2015-08-15

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.

  13. Ab initio thermochemistry of some geochemically relevant molecules in the system Cr-O-H-Cl

    NASA Astrophysics Data System (ADS)

    Ottonello, G.; Vetuschi Zuccolini, M.

    2005-07-01

    A complete theoretical model chemistry algorithm (TMCA) for the prediction of thermodynamic properties of geochemically relevant gaseous and aqueous complexes, based on molecular quantum mechanics, is presented and discussed. Cr species are selected as a case study due to the high nuclear mass and the complex electronic structure of this transition metal. The various derived magnitudes are internally consistent and sufficiently accurate to warrant comparison with the existing (and often conflictual) experimental data and literature estimates. The TMCA is based on density functional theory (DFT) B3LYP/6-31G(d,p) gas phase computations followed by computation of solvation effects by the integral polarized continuum model approach at HF/STO-3G level. Energy corrections due to relativistic effects and electron-electron correlation are accounted for by a newly developed periodic function based on computed ionization potentials and electron affinity of the central metal. Electrostatic entropy contributions to the bulk solvation entropy are accounted for by a Born-model equation based on the electrostatic component of the Integral Equation Formalism—Polarized Continuum Model (IEFPCM) coupling work. As an ancillary result, the TMCA model confirms the validity of the absolute solvation energy terms of the aqueous proton. The TMCA model is of general validity and could be eventually adopted as a standard procedure in the ab initio assessment of gas-phase and aqueous-phase energetics of geochemically relevant species.

  14. Ab initio-predicted micro-mechanical performance of refractory high-entropy alloys.

    PubMed

    Li, Xiaoqing; Tian, Fuyang; Schönecker, Stephan; Zhao, Jijun; Vitos, Levente

    2015-01-01

    Recently developed high-entropy alloys (HEAs) consisting of multiple principal elements represent a new field of metallurgy and have demonstrated appealing properties for a wide range of applications. Using ab initio alloy theory, we reveal the alloying effect on the elastic properties and the ideal tensile strength (ITS) in the [001] direction of four body-centered cubic (bcc) refractory HEAs based on Zr, V, Ti, Nb, and Hf. We find that these HEAs show high elastic anisotropy and large positive Cauchy pressure, suggesting good extrinsic ductility. Starting from ZrNbHf, it is found that the ITS decreases with equimolar Ti addition. On the other hand, if both Ti and V are added to ZrNbHf, the ITS is enhanced by about 42%. An even more captivating effect is the ITS increase by about 170%, if Ti and V are substituted for Hf. The alloying effect on the ITS is explained by the d-band filling. An intrinsic brittle-to-ductile transition is found in terms of the failure mode under uniaxial tension. These investigations suggest that intrinsically ductile HEAs with high ideal strength can be achieved by controlling the proportion of group four elements to group five elements. PMID:26199145

  15. Ab initio calculations of many-body interactions for compressed solid argon.

    PubMed

    Tian, Chunling; Liu, Fusheng; Cai, Lingcang; Yuan, Hongkuan; Chen, Hong; Zhong, Mingmin

    2015-11-01

    An investigation on many-body effects of solid argon at high pressure was conducted based on a many-body expansion of interaction energy. The three- and four-body terms in the expansion were calculated using the coupled-cluster method with single, double, and noniterative triple theory and incremental method, in which the configurations of argon trimers and tetramers were chosen as the same as those in the actual lattice. The four-body interactions in compressed solid argon were estimated for the first time, and the three-body interaction ab initio calculations were extended to a small distance. It shows that the four-body contribution is repulsive at high densities and effectively cancels the three-body lattice energy. The dimer potential plus three-body interaction can well reproduce the measurements of equation of state at pressure approximately lower than ∼60 GPa, when including the four-body effects extends the agreement up to the maximum experimental pressure of 114 GPa. PMID:26547175

  16. Silicene-derived phases on Ag(111) substrate versus coverage: Ab initio studies

    NASA Astrophysics Data System (ADS)

    Pflugradt, P.; Matthes, L.; Bechstedt, F.

    2014-01-01

    Silicene is systematically investigated as an epitaxial overlayer on an Ag(111) substrate based on the ab initio density functional theory. The geometry and stability of five silicene-silver adsorbate systems with four coincidence lattices, √7 ×√7 on √13 ×√13 , 3×3 on 4×4, 2×2 on √7 ×√7 , and √7 ×√7 on 2√3 ×2√3 , are related to the Si coverage, biaxial strain, and preparation conditions. Their phase diagram is calculated for varying chemical potential of the Si reservoir. The scanning tunneling microscopy images calculated for the optimized atomic geometries agree with those observed experimentally. The destruction of the original honeycomb symmetry and the strong adsorbate-substrate interaction significantly influence the electronic structure. Four peeled-off silicene sheets show conical linear bands, with small gaps. However, the band edges of the 3×3 on 4×4 geometry cannot be explained in terms of gap opening between Dirac cones for symmetry reasons. We confirm the conclusion that the linear bands observed by ARPES are due to folded Ag bands.

  17. 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.

  18. 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.

  19. Operator evolution for ab initio electric dipole transitions of 4He

    SciTech Connect

    Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; Jurgenson, Eric D.; Navartil, Petr

    2015-07-24

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

  20. 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.

  1. 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

  2. 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.

  3. Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models

    NASA Technical Reports Server (NTRS)

    Rammacher, W.; Cuntz, M.

    1991-01-01

    Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.

  4. Accelerating chemical reactions: Exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics

    PubMed Central

    Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.

    2011-01-01

    A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673

  5. B28: the smallest all-boron cage from an ab initio global search

    NASA Astrophysics Data System (ADS)

    Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce

    2015-09-01

    Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e

  6. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    PubMed

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations. PMID:26733483

  7. Prediction of the material with highest known melting point from ab initio molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Hong, Qi-Jun; van de Walle, Axel

    2015-07-01

    Using electronic structure calculations, we conduct an extensive investigation into the Hf-Ta-C system, which includes the compounds that have the highest melting points known to date. We identify three major chemical factors that contribute to the high melting temperatures. Based on these factors, we propose a class of materials that may possess even higher melting temperatures and explore it via efficient ab initio molecular dynamics calculations in order to identify the composition maximizing the melting point. This study demonstrates the feasibility of automated and high-throughput materials screening and discovery via ab initio calculations for the optimization of "higher-level" properties, such as melting points, whose determination requires extensive sampling of atomic configuration space.

  8. 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.

  9. Ethanol decomposition on transition metal nanoparticles during carbon nanotube growth: ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu

    2015-03-01

    The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.

  10. Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering

    SciTech Connect

    Quaglioni, S; Navratil, P

    2008-12-17

    We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and Pauli principle. We outline technical details and present phase shift results for neutron scattering on {sup 3}H, {sup 4}He and {sup 10}Be and proton scattering on {sup 3,4}He, using realistic nucleon-nucleon (NN) potentials. Our A = 4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-{sup 4}He S-wave phase shifts. We demonstrate that a proper treatment of the coupling to the n-{sup 10}Be continuum is successful in explaining the parity-inverted ground state in {sup 11}Be.

  11. Like-charge guanidinium pairing from molecular dynamics and ab initio calculations.

    PubMed

    Vazdar, Mario; Vymětal, Jiři; Heyda, Jan; Vondrášek, Jiři; Jungwirth, Pavel

    2011-10-20

    Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

  12. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

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

    SciTech Connect

    Bodenstein, Tilmann; Fink, Karin

    2015-12-31

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

  14. 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

  15. Ab initio study of AlxMoNbTiV high-entropy alloys.

    PubMed

    Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K; Vitos, Levente

    2015-02-25

    The Al(x)MoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of Al(x)MoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al(0.4)MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ∼ 4.72 obtained for the isotropic Gum metals and refractory--HEAs. PMID:25640032

  16. Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

    SciTech Connect

    Navratil, P; Ormand, W E; Forssen, C; Caurier, E

    2004-11-30

    There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

  17. Ab initio calculation of relative ion concentrations of protonated water clusters at equilibrium

    NASA Astrophysics Data System (ADS)

    Lee, E. P. F.; Dyke, J. M.; Wilders, A. E.; Watts, P.

    Relative concentrations of protonated water clusters, H(H2O)+n, are determined for the equilibria H(H2O)+n-1 + H2O ⇌ H(H2O)+n (for n = 1, …, 5), by ab initio molecular-orbital calculations (at the MP2/6-31G* level), using standard thermodynamic and statistical-mechanical methods. The calculated relative cluster-ion concentrations, at water concentrations of between 1 and 90 ppm at 308 K, are compared with the corresponding relative ion intensities measured with an ion-mobility mass spectrometer. The comparison shows that the observed cluster-ion intensity distributions agree well with those found from ab initio calculations for an equilibrium mixture of protonated water clusters.

  18. A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

    An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

  19. 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.

  20. 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.

  1. Conductivity of carbon-based molecular junctions from ab-initio methods

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Fei; Luo, Yi

    2014-12-01

    Carbon nanomaterials (CNMs) are prompting candidates for next generational electronics. In this review we provide a mini overview of recent results on the conductivity of carbon-based molecular junctions obtained from ab-initio methods. CNMs used as nanoelectrodes and molecular materials in molecular junctions are discussed. The functionalities that include the nanomechanically controlled molecular conductance switches, negative differential resistance devices, and electronic rectifiers realized by using CNMs have been demonstrated.

  2. 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.

  3. Methylchloride adsorbed on Si(0 0 1): an ab initio study

    NASA Astrophysics Data System (ADS)

    Preuss, M.; Schmidt, W. G.; Seino, K.; Bechstedt, F.

    2004-07-01

    We present ab initio calculations of the adsorption of methylchloride (CH 3Cl) on Si(0 0 1). Among multiple plausible adsorption geometries, we find five thermodynamically favorable configurations. These lead to strong geometrical changes in the Si surface structure as well as to significant charge transfer processes. The stability of the adsorption structures is discussed in terms of electrostatics. The results are compared to recent experimental and theoretical findings.

  4. An ab initio MIA study of TIBO derivatives R79882 and R82913

    NASA Astrophysics Data System (ADS)

    Peeters, Anik; Van Alsenoy, C.

    1995-04-01

    The gas phase structure of two TIBO compounds (R79882 and R82913), potent inhibitors of the reverse transcriptase of HIV1, was studied with ab initio Hartree-Fock methods using the MIA approach. For compound R82913 the geometry of a dimer and of the respective monomers was fully optimized and compared with experiment. For compound R79882 a complete geometry optimization of 15 different conformers was performed.

  5. Ab initio calculations in a uniform magnetic field using periodic supercells

    SciTech Connect

    Cai, W; Galli, G

    2003-10-21

    We present a formulation of ab initio electronic structure calculations in a finite magnetic field, which retains the simplicity and efficiency of techniques widely used in first principles molecular dynamics simulations, based on plane-wave basis sets and Fourier transforms. In addition we discuss results obtained with this method for the energy spectrum of interacting electrons in quantum wells, and for the electronic properties of dense fluid deuterium in a uniform magnetic field.

  6. On limits of ab initio calculations of pairing gap in nuclei

    SciTech Connect

    Saperstein, E. E.; Baldo, M.; Lombardo, U.; Pankratov, S. S.; Zverev, M. V.

    2011-11-15

    A brief review of recent microscopic calculations of nuclear pairing gap is given. A semi-microscopic model is suggested in which the ab initio effective pairing interaction is supplemented with a small phenomenological addendum. It involves a parameter which is universal for all medium and heavy nuclei. Calculations for several isotopic and isotonic chains of semi-magic nuclei confirm the relevance of the model.

  7. First fully ab initio potential energy surface of methane with a spectroscopic accuracy

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2016-09-01

    Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.

  8. Conformational properties of molecules by ab initio quantum mechanical energy minimization.

    PubMed Central

    Pedersen, L

    1985-01-01

    The recent literature on the determination of minimum energy conformations by ab initio quantum mechanical techniques is reviewed. The availability of computer-coded analytical first and second derivatives of the Hartree-Fock energy makes possible calculations that will be of significant assistance in structure determination of molecules. A short review of recent progress in empirical energy minimization and molecular dynamics is provided. PMID:3905373

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

    PubMed Central

    2011-01-01

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

  10. Ab initio study of the kinetics of hydrogen abstraction reactions on toluene and tetralin

    SciTech Connect

    Beste, Ariana; Britt, Phillip F; Buchanan III, A C; Harrison, Robert J; Hathorn, Bryan C

    2008-01-01

    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 reaction barriers and rate constants for the hydrogen abstraction reactions on toluene and tetralin by the benzyl radical are calculated 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. Thermolysis of PPE occurs by a free radical chain mechanism in which the product selectivity arises from competitive hydrogen abstraction at the benzylic and nonbenzylic methylen sites by chain carrying benzyl and phenoxyl radicals. The title reactions serve to calibrate the theoretical methods to be used in the study of PPE through comparison of the rate constants and the reaction enthalpies with reliable experimental values. In this study, we used two different hybrid density functionals (BHandHLYP, B3LYP) and second-order perturbation theory to obtain equilibrium and transition state geometries. 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. Absolute and relative rate constants were calculated using transition state theory. We found that the relative rate constant using the B3LYP functional agrees within a factor of 2.0 with experiment at the experimental temperature of 333 K, indicating that the B3LYP functional will be successful in predicting relative rate constants for hydrogen abstraction reactions participating in the pyrolysis of PPE.

  11. Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

    NASA Technical Reports Server (NTRS)

    Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

    2012-01-01

    Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

  12. 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.

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

    PubMed

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

    2016-01-01

    In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools. PMID:27536341

  14. Ab initio molecular dynamics simulation of pressure-induced phase transformation of BeO

    SciTech Connect

    Xiao, H. Y.; Duan, G.; Zu, X. T.; Weber, W. J.

    2011-05-05

    Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ → RS and ZB → RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ → RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange–correlation functional employed and the way of applying pressure.

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

    NASA Astrophysics Data System (ADS)

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

    2006-11-01

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

  16. 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.

  17. 7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

    SciTech Connect

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

    2006-10-12

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

  18. Ab initio quantum mechanical models of peptide helices and their vibrational spectra.

    PubMed

    Bour, Petr; Kubelka, Jan; Keiderling, Timothy A

    2002-10-01

    Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.

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

    PubMed

    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(∗)/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. PMID:26374007

  20. Condensed-matter ab initio approach for strongly correlated electrons: Application to a quantum spin liquid candidate

    SciTech Connect

    Yamaji, Youhei

    2015-12-31

    Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.