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Sample records for ab initio quantum

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-06-01

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

  2. The density matrix renormalization group for ab initio quantum chemistry

    CERN Document Server

    Wouters, Sebastian

    2014-01-01

    During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational co...

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

    Science.gov (United States)

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

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Varas Alejandro

    2016-08-01

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

  6. Ab initio quantum dynamics using coupled-cluster

    CERN Document Server

    Kvaal, Simen

    2012-01-01

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

  7. Ab initio quantum dynamics using coupled-cluster.

    Science.gov (United States)

    Kvaal, Simen

    2012-05-21

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

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

    Science.gov (United States)

    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.

  9. Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry (Briefing Charts)

    Science.gov (United States)

    2015-06-28

    ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A...Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...COMBUSTION CHEMISTRY (Briefing Charts) 5a. CONTRACT NUMBER In-House 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Ghanshyam L

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...... noise limit. The demonstrated protocol opens up new opportunities for quantum microscopy, quantum metrology and quantum information processing....

  11. Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules

    CERN Document Server

    Lester, William A; Reynolds, PJ

    1994-01-01

    This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n

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

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-14

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

  14. Quantum supercharger library: hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics.

    Science.gov (United States)

    Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J

    2015-07-05

    This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.

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

    Science.gov (United States)

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

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

  16. Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study

    Science.gov (United States)

    Kawashima, Yukio; Tachikawa, Masanori

    2013-05-01

    Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.

  17. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    CERN Document Server

    Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

    2003-01-01

    The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

  18. A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data

    CERN Document Server

    Eckl, Bernhard; Hasse, Hans

    2009-01-01

    A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...

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

    Science.gov (United States)

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

    2016-10-01

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

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

    Science.gov (United States)

    Marsalek, Ondrej; Markland, Thomas E

    2016-02-07

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

  1. 360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)

    2016-09-02

    The Sanibel Symposium 2014 was held February 16-21, 2014, at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.

  2. 360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)

    2016-09-02

    The Sanibel Symposium 2014 was held February 16-21 2014 at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.

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

    Science.gov (United States)

    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.

  4. Quantum Ring-Polymer Contraction Method: Including nuclear quantum effects at no additional computational cost in comparison to ab-initio molecular dynamics

    CERN Document Server

    John, Chris; Habershon, Scott; Kühne, Thomas D

    2015-01-01

    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. This development permits to routinely include nuclear quantum effects in ab-initio molecular dynamics simulations.

  5. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    Science.gov (United States)

    Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

  6. Direct Observation of Early-stage Quantum Dot Growth Mechanisms with High-temperature Ab Initio Molecular Dynamics

    OpenAIRE

    2015-01-01

    Colloidal quantum dots (QDs) exhibit highly desirable size- and shape-dependent properties for applications from electronic devices to imaging. Indium phosphide QDs have emerged as a primary candidate to replace the more toxic CdSe QDs, but production of InP QDs with the desired properties lags behind other QD materials due to a poor understanding of how to tune the growth process. Using high-temperature ab initio molecular dynamics (AIMD) simulations, we report the first direct observation o...

  7. An ab initio quantum chemical investigation of the structure and stability of ozone-water complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Pradeep [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Sathyamurthy, N., E-mail: nsath@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140306 (India)

    2013-03-29

    Highlights: ► Eclipse geometry most stable for the 1:1 ozone-water complex. ► Cyclic structure most stable for the 1:2 complex. ► Shift in the vertical electronic excitation energy of ozone due to hydration. - Abstract: Ab initio quantum chemical calculations have been carried out to investigate the structure and stability of 1:1 and 1:2 ozone-water complexes. All the geometries have been optimized at the CCSD level of theory using aug-cc-pVDZ and aug-cc-pVTZ basis sets. The importance of correlation-consistent basis sets in deciding the nature of critical points on these complexes is emphasized. An analysis based on the dipole moment of the complexes and the charge distribution on atoms follows. The effect of ozone molecule on the structure and properties of water dimer is also investigated. Values of the vertical electronic excitation energy and the corresponding transition dipole moment have been calculated for the ozone-water complexes using the multi-reference-configuration-interaction method and the aug-cc-pVTZ basis set. The calculated shift in vibrational frequencies due to complex formation is compared with the earlier reported experimental and theoretical values.

  8. Communication: Towards ab initio self-energy embedding theory in quantum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Lan, Tran Nguyen, E-mail: latran@umich.edu [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (United States); Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States); Kananenka, Alexei A.; Zgid, Dominika [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    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.

  9. The vibration properties of the (n,0) boron nitride nanotubes from ab initio quantum chemical simulations.

    Science.gov (United States)

    Erba, A; Ferrabone, M; Baima, J; Orlando, R; Rérat, M; Dovesi, R

    2013-02-07

    The vibration spectrum of single-walled zigzag boron nitride (BN) nanotubes is simulated with an ab initio periodic quantum chemical method. The trend towards the hexagonal monolayer (h-BN) in the limit of large tube radius R is explored for a variety of properties related to the vibrational spectrum: vibration frequencies, infrared intensities, oscillator strengths, and vibration contributions to the polarizability tensor. The (n,0) family is investigated in the range from n = 6 (24 atoms in the unit cell and tube radius R = 2.5 Å) to n = 60 (240 atoms in the cell and R = 24.0 Å). Simulations are performed using the CRYSTAL program which fully exploits the rich symmetry of this class of one-dimensional periodic systems: 4n symmetry operators for the general (n,0) tube. Three sets of infrared active phonon bands are found in the spectrum. The first one lies in the 0-600 cm(-1) range and goes regularly to zero when R increases; the connection between these normal modes and the elastic and piezoelectric constants of h-BN is discussed. The second (600-800 cm(-1)) and third (1300-1600 cm(-1)) sets tend regularly, but with quite different speed, to the optical modes of the h-BN layer. The vibrational contribution of these modes to the two components (parallel and perpendicular) of the polarizability tensor is also discussed.

  10. Towards ab initio self-energy embedding theory in quantum chemistry

    CERN Document Server

    Lan, Tran Nguyen; Zgid, Dominika

    2015-01-01

    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 (GF2) method is used to describe the non-local correlations, while the full configuration interaction (FCI) 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 (NEVPT2) with the same active...

  11. Communication: Towards ab initio self-energy embedding theory in quantum chemistry.

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M. [Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States)

    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.

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

    Science.gov (United States)

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

    2015-05-21

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

  14. Ab initio optimization principle for the ground states of translationally invariant strongly correlated quantum lattice models

    Science.gov (United States)

    Ran, Shi-Ju

    2016-05-01

    In this work, a simple and fundamental numeric scheme dubbed as ab initio optimization principle (AOP) is proposed for the ground states of translational invariant strongly correlated quantum lattice models. The idea is to transform a nondeterministic-polynomial-hard ground-state simulation with infinite degrees of freedom into a single optimization problem of a local function with finite number of physical and ancillary degrees of freedom. This work contributes mainly in the following aspects: (1) AOP provides a simple and efficient scheme to simulate the ground state by solving a local optimization problem. Its solution contains two kinds of boundary states, one of which play the role of the entanglement bath that mimics the interactions between a supercell and the infinite environment, and the other gives the ground state in a tensor network (TN) form. (2) In the sense of TN, a novel decomposition named as tensor ring decomposition (TRD) is proposed to implement AOP. Instead of following the contraction-truncation scheme used by many existing TN-based algorithms, TRD solves the contraction of a uniform TN in an opposite way by encoding the contraction in a set of self-consistent equations that automatically reconstruct the whole TN, making the simulation simple and unified; (3) AOP inherits and develops the ideas of different well-established methods, including the density matrix renormalization group (DMRG), infinite time-evolving block decimation (iTEBD), network contractor dynamics, density matrix embedding theory, etc., providing a unified perspective that is previously missing in this fields. (4) AOP as well as TRD give novel implications to existing TN-based algorithms: A modified iTEBD is suggested and the two-dimensional (2D) AOP is argued to be an intrinsic 2D extension of DMRG that is based on infinite projected entangled pair state. This paper is focused on one-dimensional quantum models to present AOP. The benchmark is given on a transverse Ising

  15. Quantum chemistry the development of ab initio methods in molecular electronic structure theory

    CERN Document Server

    Schaefer III, Henry F

    2004-01-01

    This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi

  16. Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2008-08-07

    We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the "distributed approximating functional." Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born-Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.

  17. Condensed-matter ab initio approach for strongly correlated electrons: Application to a quantum spin liquid candidate

    Energy Technology Data Exchange (ETDEWEB)

    Yamaji, Youhei [Quantum-Phase Electronics Center, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656 (Japan)

    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.

  18. Fingerprints of antiaromaticity in the negative ion (Li_3Al_4)^- via an ab initio quantum-chemical study

    CERN Document Server

    Grassi, A; Angilella, G G N; March, N H; Pucci, R

    2012-01-01

    Fingerprints of antiaromaticity in the negative ion (Li_3Al_4)^-, this species being realizable via a laser vaporization technique, are revealed by means of an ab initio quantum-chemical investigation. First, the ground-state equilibrium geometry of this ion is predicted. Also, the characteristics of the HOMO are studied, both for the square and the rectangular Al_4 geometry in two low-lying isomers of the negative ion. There is no particular sensitivity to the change in geometry of the Al_4 configuration. Therefore, we have calculated theoretically chemical shifts, which contain remarkable fingerprints of antiaromaticity. As to future directions, some comments are added in relation to the Shannon entropy.

  19. Optimizing electronic structure and quantum transport at the graphene-Si(111) interface: an ab initio density-functional study.

    Science.gov (United States)

    Tayran, Ceren; Zhu, Zhen; Baldoni, Matteo; Selli, Daniele; Seifert, Gotthard; Tománek, David

    2013-04-26

    We use ab initio density-functional calculations to determine the interaction of a graphene monolayer with the Si(111) surface. We find that graphene forms strong bonds to the bare substrate and accommodates the 12% lattice mismatch by forming a wavy structure consisting of free-standing conductive ridges that are connected by ribbon-shaped regions of graphene, which bond covalently to the substrate. We perform quantum transport calculations for different geometries to study changes in the transport properties of graphene introduced by the wavy structure and bonding to the Si substrate. Our results suggest that wavy graphene combines high mobility along the ridges with efficient carrier injection into Si in the contact regions.

  20. Some implications of the Hartree product treatment of the quantum nuclei in the ab initio nuclear-electronic orbital methodology

    Science.gov (United States)

    Gharabaghi, Masumeh; Shahbazian, Shant

    2016-12-01

    In this letter the conceptual and computational implications of the Hartree product type nuclear wavefunction introduced recently within the context of the ab initio non-Born-Oppenheimer Nuclear-electronic orbital (NEO) methodology are considered. It is demonstrated that this wavefunction may imply a pseudo-adiabatic separation of the nuclei and electrons and each nucleus is conceived as a quantum oscillator while a non-Coulombic effective Hamiltonian is deduced for electrons. Using the variational principle this Hamiltonian is employed to derive a modified set of single-component Hartree-Fock equations which are equivalent to the multi-component version derived previously within the context of the NEO and, easy to be implemented computationally.

  1. Ab Initio Potential Energy Surfaces and Quantum Dynamics of Rotational Inelastic Processes in the H+ Collision with CS

    CERN Document Server

    Kaur, Rajwant

    2016-01-01

    Rate coefficient for state-to-state rotational transitions in H+ collision with CS has been obtained using accurate quantum dynamical close-coupling calculations to interpret microwave astronomical observations. Accurate three dimensional ab initio potential energy surfaces have been computed for the ground state and low-lying excited states of H+ - CS system using internally contracted MRCI method and aug-cc-pVQZ basis sets. Rotational excitation and deexcitation integral cross sections are computed at low and ultra low collision energies, respectively. Resonances have been observed at very low energies typically below 50 cm-1. Among all the transitions, Deltaj=+1 and Deltaj=-1 are found to be predominant for excitation and deexcitation, respectively. Deexcitation cross section in the ultracold region is found to obey Wigner's threshold law. The magnitude of state-to-state excitation rate obtained is maximum for j'=1 in the temperature range 2-240 K while minimum for deexcitation in ultracold region. The rot...

  2. Some implications of the Hartree product treatment of the quantum nuclei in the ab initio Nuclear-electronic orbital methodology

    CERN Document Server

    Gharabaghi, Masumeh

    2016-01-01

    In this letter the conceptual and computational implications of the Hartree product type nuclear wavefunction introduced recently within context of the ab initio non-Born-Oppenheimer Nuclear-electronic orbital (NEO) methodology are considered. It is demonstrated that this wavefunction may imply a pseudo-adiabatic separation of the nuclei and electrons and each nucleus is conceived as a quantum oscillator while a non-Coulombic effective Hamiltonian is deduced for electrons. Using variational principle this Hamiltonian is used to derive a modified set of single-component Hartree-Fock equations which are equivalent to the multi-component version derived previously within context of the NEO and, easy to be implemented computationally.

  3. {\\em Ab initio} Quantum Monte Carlo simulation of the warm dense electron gas in the thermodynamic limit

    CERN Document Server

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

    2016-01-01

    We perform \\emph{ab initio} quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with linear response theory we are able to remove finite-size errors from the potential energy over the entire warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown \\emph{et al.}~[PRL \\textbf{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 $F_{xc}$ of the macroscopic electron gas with an unprecedented accuracy of $|\\Delta V|/|V|, |\\Delta F_{xc}|/|F|_{xc} \\sim 10^{-3}$. A comparison of our new data to the recent parametrization of $F_{xc}$ by Karasiev {\\em et al.} [PRL {\\bf 112}, 076403 (2014)] reveals significant inaccuracies of the latter.

  4. Ab initio energetics, kinetics, and quantum transport characteristics of graphene nanoribbons as nanosensors for detecting nitrogen dioxide

    Science.gov (United States)

    Paulla, Kirti K.; Hassan, Ahmed J.; Knick, Cory R.; Farajian, Amir A.

    2014-03-01

    Molecules adsorption on graphene nanoribbons (GNRs) can be used to engineer and make use of their properties for applications such as energy storage and sensors. We investigate adsorption characteristics by considering nitrogen dioxide as a sample molecule for assessing nanosensor functionality of GNRs. Using ab initio modeling, energetics of various adsorption possibilities are determined and their rate constants are calculated and compared. Nonbonding and weak sp3 adsorptions at the hydrogen-terminated edges are shown to be more feasible than center adsorptions. This shows increased reactivity compared to graphene. Calculated quantum transport responses upon molecules adsorption indicate possibility of sensing extremely low nitrogen dioxide concentrations. Possible approaches for improving gas nanosensor functionality of GNRs are discussed. Reference: RSC Advances, 2013, DOI: 10.1039/c3ra46372a. This research was supported by the National Science Foundation Grant ECCS-0925939.

  5. Quantum molecular mechanics-a noniterative procedure for the fast ab Initio calculation of closed shell systems.

    Science.gov (United States)

    Moura, Gustavo L C; Simas, Alfredo M

    2012-04-05

    In this article, we advance the foundations of a strategy to develop a molecular mechanics method based not on classical mechanics and force fields but entirely on quantum mechanics and localized electron-pair orbitals, which we call quantum molecular mechanics (QMM). Accordingly, we introduce a new manner of calculating Hartree-Fock ab initio wavefunctions of closed shell systems based on variationally preoptimized nonorthogonal electron pair orbitals constructed by linear combinations of basis functions centered on the atoms. QMM is noniterative and requires only one extremely fast inversion of a single sparse matrix to arrive to the one-particle density matrix, to the electron density, and consequently, to the ab initio electrostatic potential around the molecular system, or cluster of molecules. Although QMM neglects the smaller polarization effects due to intermolecular interactions, it fully takes into consideration polarization effects due to the much stronger intramolecular geometry distortions. For the case of methane, we show that QMM was able to reproduce satisfactorily the energetics and polarization effects of all distortions of the molecule along the nine normal modes of vibration, well beyond the harmonic region. We present the first practical applications of the QMM method by examining, in detail, the cases of clusters of helium atoms, hydrogen molecules, methane molecules, as well as one molecule of HeH(+) surrounded by several methane molecules. We finally advance and discuss the potentialities of an exact formula to compute the QMM total energy, in which only two center integrals are involved, provided that the fully optimized electron-pair orbitals are known.

  6. Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    Science.gov (United States)

    KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

    2014-01-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

  7. Grid-based methods for biochemical ab initio quantum chemical applications

    Energy Technology Data Exchange (ETDEWEB)

    Colvin, M.E.; Nelson, J.S.; Mori, E. [and others

    1997-01-01

    A initio quantum chemical methods are seeing increased application in a large variety of real-world problems including biomedical applications ranging from drug design to the understanding of environmental mutagens. The vast majority of these quantum chemical methods are {open_quotes}spectral{close_quotes}, that is they describe the charge distribution around the nuclear framework in terms of a fixed analytic basis set. Despite the additional complexity they bring, methods involving grid representations of the electron or solvent charge can provide more efficient schemes for evaluating spectral operators, inexpensive methods for calculating electron correlation, and methods for treating the electrostatic energy of salvation in polar solvents. The advantage of mixed or {open_quotes}pseudospectral{close_quotes} methods is that they allow individual non-linear operators in the partial differential equations, such as coulomb operators, to be calculated in the most appropriate regime. Moreover, these molecular grids can be used to integrate empirical functionals of the electron density. These so-called density functional methods (DFT) are an extremely promising alternative to conventional post-Hartree Fock quantum chemical methods. The introduction of a grid at the molecular solvent-accessible surface allows a very sophisticated treatment of a polarizable continuum solvent model (PCM). Where most PCM approaches use a truncated expansion of the solute`s electric multipole expansion, e.g. net charge (Born model) or dipole moment (Onsager model), such a grid-based boundary-element method (BEM) yields a nearly exact treatment of the solute`s electric field. This report describes the use of both DFT and BEM methods in several biomedical chemical applications.

  8. Direct assessment of quantum nuclear effects on hydrogen bond strength by constrained-centroid ab initio path integral molecular dynamics

    Science.gov (United States)

    Walker, Brent; Michaelides, Angelos

    2010-11-01

    The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)2 is about 30% weaker when quantum nuclear effects are included, while that in (H2O)2 is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.

  9. Ab initio molecular dynamics with noisy forces: Validating the quantum Monte Carlo approach with benchmark calculations of molecular vibrational properties

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Ye, E-mail: xw111luoye@gmail.com; Sorella, Sandro, E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), and CRS Democritos, CNR-INFM, Via Bonomea 265, I-34136 Trieste (Italy); Zen, Andrea, E-mail: zen.andrea.x@gmail.com [Dipartimento di Fisica, Università di Roma “La Sapienza,” Piazzale Aldo Moro 2, I-00185 Rome (Italy)

    2014-11-21

    We present a systematic study of a recently developed ab initio simulation scheme based on molecular dynamics and quantum Monte Carlo. In this approach, a damped Langevin molecular dynamics is employed by using a statistical evaluation of the forces acting on each atom by means of quantum Monte Carlo. This allows the use of an highly correlated wave function parametrized by several variational parameters and describing quite accurately the Born-Oppenheimer energy surface, as long as these parameters are determined at the minimum energy condition. However, in a statistical method both the minimization method and the evaluation of the atomic forces are affected by the statistical noise. In this work, we study systematically the accuracy and reliability of this scheme by targeting the vibrational frequencies of simple molecules such as the water monomer, hydrogen sulfide, sulfur dioxide, ammonia, and phosphine. We show that all sources of systematic errors can be controlled and reliable frequencies can be obtained with a reasonable computational effort. This work provides convincing evidence that this molecular dynamics scheme can be safely applied also to realistic systems containing several atoms.

  10. Ab Initio Holography

    CERN Document Server

    Lunts, Peter; Miller, Jonah; Schnetter, Erik; Kim, Yong Baek; Lee, Sung-Sik

    2015-01-01

    We apply the quantum renormalization group to construct a holographic dual for the U(N) vector model for complex bosons defined on a lattice. The bulk geometry becomes dynamical as the hopping amplitudes which determine connectivity of space are promoted to quantum variables. In the large N limit, the full bulk equations of motion for the dynamical hopping fields are numerically solved for finite systems. From finite size scaling, we show that different phases exhibit distinct geometric features in the bulk. In the insulating phase, the space gets fragmented into isolated islands deep inside the bulk, exhibiting ultra-locality. In the superfluid phase, the bulk exhibits a horizon beyond which the geometry becomes non-local. Right at the horizon, the hopping fields decay with a universal power-law in coordinate distance between sites, while they decay in slower power-laws with continuously varying exponents inside the horizon. At the critical point, the bulk exhibits a local geometry whose characteristic lengt...

  11. Ab initio molecular orbital calculation considering the quantum mechanical effect of nuclei by path integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2000-12-01

    We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.

  12. Network-Forming Nanoclusters in Binary As-S/Se Glasses: From Ab Initio Quantum Chemical Modeling to Experimental Evidences

    Science.gov (United States)

    Hyla, M.

    2017-01-01

    Network-forming As2(S/Se)m nanoclusters are employed to recognize expected variations in a vicinity of some remarkable compositions in binary As-Se/S glassy systems accepted as signatures of optimally constrained intermediate topological phases in earlier temperature-modulated differential scanning calorimetry experiments. The ab initio quantum chemical calculations performed using the cation-interlinking network cluster approach show similar oscillating character in tendency to local chemical decomposition but obvious step-like behavior in preference to global phase separation on boundary chemical compounds (pure chalcogen and stoichiometric arsenic chalcogenides). The onsets of stability are defined for chalcogen-rich glasses, these being connected with As2Se5 ( Z = 2.29) and As2S6 ( Z = 2.25) nanoclusters for As-Se and As-S glasses, respectively. The physical aging effects result preferentially from global phase separation in As-S glass system due to high localization of covalent bonding and local demixing on neighboring As2Sem+1 and As2Sem-1 nanoclusters in As-Se system. These nanoclusters well explain the lower limits of reversibility windows in temperature-modulated differential scanning calorimetry, but they cannot be accepted as signatures of topological phase transitions in respect to the rigidity theory.

  13. Nuclear Quantum Effects in Liquid Water: A Highly Accurate ab initio Path-Integral Molecular Dynamics Study

    Science.gov (United States)

    Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto

    2014-03-01

    In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.

  14. [Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

    Science.gov (United States)

    Petrenko, Y M

    2015-01-01

    Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

  15. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

    Science.gov (United States)

    Liu, Haiyan; Lu, Zhenyu; Cisneros, G Andres; Yang, Weitao

    2004-07-08

    The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

  16. Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, Sergei D., E-mail: sergei.ivanov@unirostock.de; Grant, Ian M.; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr–Universität Bochum, 44780 Bochum (Germany)

    2015-09-28

    With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

  17. \\emph{Ab initio} Quantum Monte Carlo simulation of the warm dense electron gas

    CERN Document Server

    Dornheim, Tobias; Malone, Fionn; Schoof, Tim; Sjostrom, Travis; Foulkes, W M C; Bonitz, Michael

    2016-01-01

    Warm dense matter is one of the most active frontiers in plasma physics due to its relevance for dense astrophysical objects as well as for novel laboratory experiments in which matter is being strongly compressed e.g. by high-power lasers. Its description is theoretically very challenging as it contains correlated quantum electrons at finite temperature---a system that cannot be accurately modeled by standard analytical or ground state approaches. Recently several breakthroughs have been achieved in the field of fermionic quantum Monte Carlo simulations. First, it was shown that exact simulations of a finite model system ($30 \\dots 100$ electrons) is possible that avoid any simplifying approximations such as fixed nodes [Schoof {\\em et al.}, Phys. Rev. Lett. {\\bf 115}, 130402 (2015)]. Second, a novel way to accurately extrapolate these results to the thermodynamic limit was reported by Dornheim {\\em et al.} [Phys. Rev. Lett. {\\bf 117}, 156403 (2016)]. As a result, now thermodynamic results for the warm dense...

  18. Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

    KAUST Repository

    Buin, Andrei

    2015-06-18

    © 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

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

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China); Cao, Jun [Guizhou Provincial Key Laboratory of Computational Nano-material Science, Guizhou Normal College, Guiyang 550018 (China); Feng, Wei; Li, Xin-qi [Department of Physics, Beijing Normal University, Beijing 100875 (China)

    2015-11-21

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

  20. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.; Miaskiewicz, K. [Pacific Northwest Lab., Richland, WA (United States); Osman, R. [Mount Sinai School of Medicine, New York, NY (United States). Dept. of Physiology and Biophysics

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  1. Ab-initio Hamiltonian approach to light nuclei and to quantum field theory

    Indian Academy of Sciences (India)

    J P Vary; H Honkanen; Jun Li; P Maris; A M Shirokov; S J Brodsky; A Harindranath; G F De Teramond; E G Ng; C Yang; M Sosonkina

    2010-07-01

    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.

  2. Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces

    CERN Document Server

    Fujisaki, Hiroshi; Hirao, Kimihiko; Straub, John E; Stock, Gerhard

    2008-01-01

    Employing extensive quantum-chemical calculations at the DFT/B3LYP and MP2 level, a quartic force field of isolated N-methylacetamide is constructed. Taking into account 24 vibrational degrees of freedom, the model is employed to perform numerically exact vibrational configuration interaction calculations of the vibrational energy relaxation of the amide I mode. It is found that the energy transfer pathways may sensitively depend on details of the theoretical description. Moreover, the exact reference calculations were used to study the applicability and accuracy of (i) the quasiclassical trajectory method, (ii) time-dependent second-order perturbation theory, and (iii) the instantaneous normal mode description of frequency fluctuations. Based on the results, several strategies to describe vibrational energy relaxation in biomolecular systems are discussed.

  3. Heats of Segregation of BCC Metals Using Ab Initio and Quantum Approximate Methods

    Science.gov (United States)

    Good, Brian; Chaka, Anne; Bozzolo, Guillermo

    2003-01-01

    Many multicomponent alloys exhibit surface segregation, in which the composition at or near a surface may be substantially different from that of the bulk. A number of phenomenological explanations for this tendency have been suggested, involving, among other things, differences among the components' surface energies, molar volumes, and heats of solution. From a theoretical standpoint, the complexity of the problem has precluded a simple, unified explanation, thus preventing the development of computational tools that would enable the identification of the driving mechanisms for segregation. In that context, we investigate the problem of surface segregation in a variety of bcc metal alloys by computing dilute-limit heats of segregation using both the quantum-approximate energy method of Bozzolo, Ferrante and Smith (BFS), and all-electron density functional theory. In addition, the composition dependence of the heats of segregation is investigated using a BFS-based Monte Carlo procedure, and, for selected cases of interest, density functional calculations. Results are discussed in the context of a simple picture that describes segregation behavior as the result of a competition between size mismatch and alloying effects

  4. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    Science.gov (United States)

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

    1995-01-01

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

  5. P-V Relation for Mercuric Calcogenides: Ab Initio Method

    Directory of Open Access Journals (Sweden)

    G. Misra

    2011-01-01

    Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.

  6. Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects.

    Science.gov (United States)

    Marsalek, Ondrej; Markland, Thomas E

    2017-03-22

    Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to 2 orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infrared and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.

  7. Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

    Science.gov (United States)

    Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

    2014-06-10

    We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good

  8. Determination of the functional chemical structure of sulphur in asphaltenes using quantum mechanical ab-initio modelling and infra-red techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hovell, Ian; Monte, Marisa de Mello; Coelho, Roberto Rodrigues [Centro de Tecnologia Mineral (CETEM), Rio de Janeiro, RJ (Brazil); Souza, Andre Lopes de [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Escola de Quimica

    2004-07-01

    In this work a proposed methodology of the characterization of organic sulphur compounds is proposed in agreement with its functionality for the elucidation of asphaltenic structures that contain sulphur. Theoretical Infrared spectra of organic sulphur compounds were modelled using quantum mechanical ab initio Hartree-Fock calculations. Using these spectra it is possible to identify the frequency corresponding to the vibrational transition of the C-S bond of the organic sulphur compounds studied. The experimental IR spectra were studied, of these same compounds, and their respective C-S bond frequencies were obtained. A good comparison was obtained when the theoretical vibrational frequencies when compared with the experimental vibrational frequencies. Finally, this proposed methodology was applied to the experimental deconvoluted DRIFTS, and theoretical spectra of an asphaltene from Brazilian VR's, with the elucidation of the organic sulphur that is present in the average molecule. (author)

  9. Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

    Science.gov (United States)

    Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

    2013-11-01

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

  10. Local minima conformations of the Sc3N @C80 endohedral complex: Ab initio quantum chemical study and suggestions for experimental verification

    Science.gov (United States)

    Yanov, Ilya; Kholod, Yana; Simeon, Tomekia; Kaczmarek, Anna; Leszczynski, Jerzy

    The results of an ab initio quantum chemical study of the Sc3N@C80 endohedral complex are reported. The Hartree-Fock (HF) and B3LYP levels of theory were employed in conjunction with STO-3G and 6-31G(d) basis sets to determine the geometry and properties of the local minima conformations of Sc3N cluster inside the C80 cage. Weak bonding between the Sc3N and C80 molecule and a number of very close geometry and nearly identical by energy local minima structures can explain the large mobility of the endohedral cluster, but complicate determination of the global minimum structure. The effect of the endohedral cluster on the vibrational spectrum of Sc3N@C80 is revealed. Based on the theoretical infrared (IR) spectra, the experimental method to distinguish local minima structures of Sc3N@C80 is proposed.

  11. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    Science.gov (United States)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  12. Ab initio quantum mechanical study of the structure and stability of the alkaline earth metal oxides and peroxides

    Energy Technology Data Exchange (ETDEWEB)

    Koenigstein, M.; Catlow, C.R.A. [Royal Institution of Great Britain, London (United Kingdom). Davy Faraday Research Lab.

    1998-10-01

    The authors report a detailed computational study of the stability of the alkaline earth metal peroxides MO{sub 2} (M = Ba, Sr, Ca, Mg, Be) with respect to decomposition into the corresponding oxides Mo and molecular oxygen using Hartree-Fock and density functional theory (DFT) techniques. A comparison between calculated and experimental binding energies indicates that the DFT method is most suitable for a correct description of the peroxide bond. The DFT reaction energies for the peroxide decomposition MO{sub 2} {yields} MO + {1/2}O{sub 2} show that only BaO{sub 2} and SrO{sub 2} are thermodynamically stable compounds, while CaO{sub 2} (in the calcium carbide structure), MgO{sub 2}, and BeO{sub 2} (in the pyrite structure) are energetically unstable with reaction energies of {minus}24.7, {minus}26.8, and {minus}128.7 kJ/mol, respectively, and are therefore unlikely to exist as pure compounds. The published calcium carbide structure for CaO{sub 2} is probably incorrect, at least for pure calcium peroxide, since apart from the thermodynamical instability the compound is more stable in the pyrite structure by 25.5 kJ/mol. The analysis suggests that the water and/or hydrogen peroxide content of experimentally prepared MgO{sub 2} samples is necessary for the stabilization of the structure, while BeO{sub 2} is clearly unstable under ambient conditions. The authors studied also the effect of the zero point energies and the entropies on the decomposition free energies and, for this purpose, performed atomistic lattice simulations based on interatomic potentials, which they derived from their ab initio data; the results indicate a negligible effect of the zero point energies, while the entropy terms favor the decomposition reaction by ca. 20 kJ/mol at 298.15 K.

  13. Reduced dimensionality quantum dynamics of CH3 + CH4 --> CH4 + CH3: symmetric hydrogen exchange on an Ab initio potential.

    Science.gov (United States)

    Remmert, Sarah M; Banks, Simon T; Clary, David C

    2009-04-23

    The symmetric title reaction CH(3) + CH(4) --> CH(4) + CH(3) is studied using quantum scattering theory. Quantum dynamics calculations are performed in hyperspherical coordinates with a two-dimensional effective potential energy surface consisting of an analytical 18-parameter double Morse function fit to ab initio data at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. Spectator modes are treated adiabatically by inclusion of projected zero-point energy corrections in the effective potential. The close-coupled equations are solved via R-matrix propagation. Energy and J-shifted thermal rate constants are compared to experimental data and highlight the importance of quantum tunneling. Oscillating reactivity and metastable bound state resonances are observed in the cumulative and state-to-state reaction probabilities. State-to-state differential and initial state-selected integral cross sections are presented and discussed. Primary and secondary kinetic isotope effects for two symmetric deuterated variants of the title reaction are also presented.

  14. Correlation of optical and structural properties of GaN/AlN multi-quantum wells—Ab initio and experimental study

    Energy Technology Data Exchange (ETDEWEB)

    Kaminska, A., E-mail: kaminska@ifpan.edu.pl [Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 01-142 Warsaw (Poland); Department of Mathematics and Natural Sciences, College of Science, Cardinal Stefan Wyszynski University, Dewajtis 5, 01-815 Warsaw (Poland); Strak, P.; Sakowski, K. [Institute of High Pressure Physics, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw (Poland); Borysiuk, J. [Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 01-142 Warsaw (Poland); Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw (Poland); Sobczak, K.; Domagala, J. Z. [Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 01-142 Warsaw (Poland); Beeler, M.; Monroy, E. [Université Grenoble-Alpes, 38000 Grenoble (France); CEA Grenoble, INAC-SP2M, 17 av. des Martyrs, 38000 Grenoble (France); Grzanka, E. [Institute of High Pressure Physics, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw (Poland); TopGaN Ltd. Sokolowska 29/37, 01-142 Warsaw (Poland); Krukowski, S. [Institute of High Pressure Physics, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw (Poland); Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw (Poland)

    2016-01-07

    The results of comprehensive theoretical and experimental study of binary GaN/AlN multi-quantum well (MQW) systems oriented along polar c-direction of their wurtzite structure are presented. A series of structures with quantum wells and barriers of various thicknesses were grown by plasma-assisted molecular-beam epitaxy and characterized by x-ray diffraction and transmission electron microscopy. It was shown that in general the structures of good quality were obtained, with the defect density decreasing with increasing quantum well thickness. The optical transition energies in these structures were investigated comparing experimental measurements with ab initio calculations of the entire GaN/AlN MQW structure depending on the QW widths and strains, allowing for direct determination of the energies of optical transitions and the electric fields in wells/barriers by electric potential double averaging procedure. Photoluminescence (PL) measurements revealed that the emission efficiency as well as the shape of luminescence spectra correlated well with their structural quality. Additionally, due to the Quantum-Confined Stark Effect, the emission energy decreased by over 1 eV for quantum well thicknesses increasing from 1 nm up to 6 nm, and this effect was accompanied by the drastic drop of the PL efficiency. The experimental results are consistent with theoretical models. Comparison of experimental data obtained by a number of different characterization techniques with the density functional theory results received on the same geometry structure allowed to prove directly the theoretical models and to determine the polarization and the oscillator strengths in the AlN/GaN nitride systems for the first time.

  15. Structural and dynamical aspects of the unsymmetric hydration of Sb(III): an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Lim, Len Herald V; Bhattacharjee, Anirban; Asam, S Sikander; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

    2010-03-01

    An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer. The apparent domain partitioned structural behavior was probed by solvent reorientational kinetics and three-body distribution functions. The three-dimensional hydration space was conveniently segmented such that domains having different properties were properly resolved. The approach afforded a fair isolation of localized solvent structural and dynamical motifs that Sb(3+) seems to induce to a remarkable degree. Most intriguing is the apparent impact of the lone pair electrons on the second hydration shell, which offers insight into the mechanistic aspects of hydrogen bonding networks in water. Such electronic effects observed in the hydration of Sb(3+) can only be studied by applying a suitable quantum mechanical treatment including first and second hydration shell as provided by the QMCF ansatz.

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

    Science.gov (United States)

    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.

  17. Discovering chemistry with an ab initio nanoreactor

    OpenAIRE

    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 accelerat...

  18. Reciprocity Theorems for Ab Initio Force Calculations

    CERN Document Server

    Wei, C; Mele, E J; Rappe, A M; Lewis, Steven P.; Rappe, Andrew M.

    1996-01-01

    We present a method for calculating ab initio interatomic forces which scales quadratically with the size of the system and provides a physically transparent representation of the force in terms of the spatial variation of the electronic charge density. The method is based on a reciprocity theorem for evaluating an effective potential acting on a charged ion in the core of each atom. We illustrate the method with calculations for diatomic molecules.

  19. Ab initio theories for light nuclei and neutron stars

    Science.gov (United States)

    Gezerlis, Alexandros

    2016-09-01

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

  20. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

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

  1. Ab initio Bogoliubov coupled cluster theory

    Science.gov (United States)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

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

  2. Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules

    Science.gov (United States)

    Shiga, Motoyuki; Nakayama, Akira

    2008-01-01

    The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.

  3. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

    Energy Technology Data Exchange (ETDEWEB)

    Genderen, E. van; Clabbers, M. T. B. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland); Das, P. P. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Stewart, A. [Department of Physics and Energy, Materials and Surface Science Institute (MSSI), University of Limerick, Limerick (Ireland); Nederlof, I. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam (Netherlands); Barentsen, K. C. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Portillo, Q. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona (Spain); Pannu, N. S. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Nicolopoulos, S. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Gruene, T., E-mail: tim.gruene@psi.ch [Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland); Abrahams, J. P., E-mail: tim.gruene@psi.ch [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland); Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland)

    2016-02-05

    A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)

  4. Minimizing Electron-Hole Recombination on TiO2 Sensitized with PbSe Quantum Dots: Time-Domain Ab Initio Analysis.

    Science.gov (United States)

    Long, Run; English, Niall J; Prezhdo, Oleg V

    2014-09-01

    TiO2 sensitized with quantum dots (QDs) gives efficient photovoltaic and photocatalytic systems due to high stability and large absorption cross sections of QDs and rapid photoinduced charge separation at the interface. The yields of the light-induced processes are limited by electron-hole recombination that also occurs at the interface. We combine ab initio nonadiabatic molecular dynamics with analytic theory to investigate the experimentally studied charge recombination at the PbSe QD-TiO2 interface. The time-domain atomistic simulation directly mimics the laser experiment and generates important details of the recombination mechanism. The process occurs due to coupling of the electronic subsystem to polar optical modes of the TiO2 surface. The inelastic electron-phonon scattering happens on a picosecond time scale, while the elastic scattering takes 40 fs. Counter to expectations, the donor-acceptor bonding strengthens at an elevated temperature. An analytic theory extends the simulation results to larger QDs and longer QD-TiO2 bridges. It shows that the electron-hole recombination rate decreases significantly for longer bridges and larger dots and that the main effect arises due to reduced donor-acceptor coupling rather than changes in the donor-acceptor energy gap. The study indicates that by varying QD size or ligands one can reduce charge losses while still maintaining efficient charge separation, providing design principles for optimizing solar cell design and increasing photon-to-electron conversion efficiencies.

  5. Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results

    Science.gov (United States)

    Hahn, Seungsoo

    2016-10-01

    The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.

  6. On the electrical properties of the Bi2-ySryIr2O7 pyrochlore solid solution: Quantum ab initio and classic calculations

    Science.gov (United States)

    de la Mora, Pablo; Cosio-Castañeda, Carlos; Martinez-Anaya, Oliver; Morales, Francisco; Tavizon, Gustavo

    2016-09-01

    In this work, a theoretical study of the electrical properties of the Bi2-ySryIr2O7 (Bi2-ySryIr2O16O2) α-pyrochlore-type solid solution is presented. Quantum ab initio DFT(WIEN2k) calculations were performed in order to understand the electrical resistivity changes associated to the Bi substitution by Sr in this system. The main crystallographic modification associated to this substitution is the x position of the 48f oxygen (x, 1/8 , 1/8 ) (O1); this substitution substantially modifies the Bi/Sr-O1 and Ir-O1 atomic distances, increasing the former and diminishing the latter. Experimentally, the Bi2-ySryIr2O7 samples are metallic and the electrical resistivity increases with the Sr content. Electronic structure calculations for Bi2Ir2O7 and BiSrIr2O7 show that, regardless of structural changes, there is only a small change of electrical conductivity with the Sr substitution, and the experimentally observed increase of the resistivity can be explained in terms of a larger impact on the electronic structure of both; the Sr 'impurities' as well as of the thermal Sr oscillations.

  7. Full-dimensional quantum dynamics study of the H2 + C2H → H + C2H2 reaction on an ab initio potential energy surface

    Science.gov (United States)

    Chen, Liuyang; Shao, Kejie; Chen, Jun; Yang, Minghui; Zhang, Dong H.

    2016-05-01

    This work performs a time-dependent wavepacket study of the H2 + C2H → H + C2H2 reaction on a new ab initio potential energy surface (PES). The PES is constructed using neural network method based on 68 478 geometries with energies calculated at UCCSD(T)-F12a/aug-cc-pVTZ level and covers H2 + C2H↔H + C2H2, H + C2H2 → HCCH2, and HCCH2 radial isomerization reaction regions. The reaction dynamics of H2 + C2H → H + C2H2 are investigated using full-dimensional quantum dynamics method. The initial-state selected reaction probabilities are calculated for reactants in eight vibrational states. The calculated results showed that the H2 vibrational excitation predominantly enhances the reactivity while the excitation of bending mode of C2H slightly inhibits the reaction. The excitations of two stretching modes of C2H molecule have negligible effect on the reactivity. The integral cross section is calculated with J-shift approximation and the mode selectivity in this reaction is discussed. The rate constants over 200-2000 K are calculated and agree well with the experimental measured values.

  8. Structure, reactivity and spectroscopic properties of minerals from lateritic soils : insights from ab initio calculations

    OpenAIRE

    Balan, Etienne; Lazzeri, M.; Mauri, F.; Calas, G.

    2007-01-01

    We review here some recent applications of ab initio calculations to the modelling of spectroscopic and energetic properties of minerals, which are key components of lateritic soils or govern their geochemical properties. Quantum mechanical ab initio calculations are based on density functional theory and density functional perturbation theory. Among the minerals investigated, zircon is a typical resistant primary mineral. Its resistance to weathering is at the origin of the peculiar geochemi...

  9. Theoretical study on exciton recurrence motion in anthracene dimer using the Ab initio MO-CI based quantum master equation approach.

    Science.gov (United States)

    Kishi, Ryohei; Nakano, Masayoshi; Minami, Takuya; Fukui, Hitoshi; Nagai, Hiroshi; Yoneda, Kyohei; Takahashi, Hideaki

    2009-05-01

    We apply the ab initio molecular orbital (MO)-configuration interaction (CI) based quantum master equation (MOQME) method to the investigation of ultrafast exciton dynamics in an anthracene dimer modeled after anthracenophane, which is experimentally found to exhibit an oscillatory signal of fluorescence anisotropy decay. Two low-lying near-degenerate one-photon allowed excited states with a slight energy difference (42 cm(-1)) are obtained at the CIS/6-31G** level of approximation using full valence pi-orbitals. The time evolution of reduced exciton density matrices is performed by numerically solving the quantum master equation. After the creation of a superposition state of these near-degenerate states by irradiating a near-resonant laser field, we observe two kinds of oscillatory behaviors of polarizations: field-induced polarizations with faster periods, and amplitude oscillations of x- and z-polarizations, P(x) and P(z), with a slower period, in which the amplitudes of P(x) and P(z) attain maximum alternately. The latter behavior turns out to be associated with an oscillatory exciton motion between the two monomers, i.e., exciton recurrence motion, using the dynamic exciton expression based on the polarization density. From the analysis of contribution to the exciton distributions, such exciton recurrence motion is found to be characterized by both the difference in eigenfrequencies between the two near-degenerate states excited by the laser field and the relative phases among the frontier MOs primarily contributing to the near-degenerate states.

  10. Mechanism of Spectral Tuning Going from Retinal in Vacuo to Bovine Rhodopsin and its Mutants: Multireference ab initio Quantum Mechanics/Molecular Mechanics Studies

    Science.gov (United States)

    Altun, Ahmet; Yokoyama, Shozo

    2009-01-01

    We have investigated photoabsorption spectra of bovine rhodopsin and its mutants (E122Q and E113Q) by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations as well as retinal in vacuo by pure QM calculations, employing multireference (MR) ab initio and TD-B3LYP methods. The sophisticated MR-SORCI+Q and MRCISD+Q methods extrapolated with respect to adopted approximations can reproduce the experimental absorption maxima of retinal very well. The relatively inexpensive MR-DDCI2+Q method gives absorption maxima blue-shifted by ca. 65 nm from experimental values; however, this error is systematic and thus MR-DDCI2+Q can be used to estimate spectral shifts. In MR calculations, the ground state energy of retinal at B3LYP geometry is significantly lower than that at CASSCF geometry. Therefore, B3LYP geometry is more reliable than CASSCF geometry, which has blue-shift error as large as 100 nm in the gas phase. The effect of ground state geometry on the excitation energies is less critical in the polarizing field of protein environments. At the B3LYP geometry, there is no significant charge transfer upon vertical excitation to the S1 excited state either from Glu113 to retinal or from Schiff-base terminal to β-ionone ring through the polyene chain. All-trans to 11-cis isomerization of retinal in the gas phase has no influence on the calculated S1 absorbing state, in agreement with experiment. The shoulder of the experimental absorption spectrum of retinal in vacuo at the S1 absorbing band appears to be the second electronic transition (S2) in our calculations, contrary to previous tentative assignment to vibrational state of S1 or to the S1 band of a retinal isomer. PMID:19367945

  11. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations

    Science.gov (United States)

    Bankura, Arindam; Chandra, Amalendu

    2015-01-01

    The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water.

  12. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bankura, Arindam; Chandra, Amalendu, E-mail: amalen@iitk.ac.in [Department of Chemistry, Indian Institute of Technology, Kanpur 208016 (India)

    2015-01-28

    The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water.

  13. Ab-initio modeling of an anion $C_{60}^-$ pseudopotential for fullerene-based compounds

    CERN Document Server

    Vrubel, I I; Ivanov, V K

    2015-01-01

    A pseudopotential of $C_{60}^-$ has been constructed from ab-initio quantum-mechanical calculations. Since the obtained pseudopotential can be easily fitted by rather simple analytical approximation it can be effectively used both in classical and quantum molecular dynamics of fullerene-based compounds.

  14. Covalent Linking Greatly Enhances Photoinduced Electron Transfer in Fullerene-Quantum Dot Nanocomposites: Time-Domain Ab Initio Study

    DEFF Research Database (Denmark)

    Chaban, Vitaly V.; Prezhdo, Victor; Prezhdo, Oleg

    2013-01-01

    Nonadiabatic molecular dynamics combined with time-domain density functional theory are used to study electron transfer (ET) from a CdSe quantum dot (QD) to the C-60 fullerene, occurring in several types of hybrid organic/inorganic nanocomposites. By unveiling the time dependence of the ET process......, it leads to a notably weaker QD-C-60 interaction than a lengthy molecular bridge. We show that the ET rate in a nonbonded mixture of QDs and C-60 can be enhanced by doping. The photoinduced ET is promoted primarily by mid- and low-frequency vibrations. The study establishes the basic design principles...

  15. Discovering chemistry with an ab initio nanoreactor

    Science.gov (United States)

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

    2014-12-01

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

  16. Giant magnetoresistance An ab-initio description

    CERN Document Server

    Binder, J

    2000-01-01

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

  17. Operator evolution for ab initio nuclear theory

    CERN Document Server

    Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr

    2014-01-01

    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 and find at short ranges an increased contribution from such ind...

  18. Ab initio alpha-alpha scattering

    CERN Document Server

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

    2015-01-01

    Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.

  19. Ab initio quantum Monte Carlo study of the binding of a positron to alkali-metal hydrides.

    Science.gov (United States)

    Kita, Yukiumi; Maezono, Ryo; Tachikawa, Masanori; Towler, Mike D; Needs, Richard J

    2011-08-07

    Quantum Monte Carlo methods are used to investigate the binding of a positron to the alkali-metal hydrides, XH (X = Na and K). We obtain positron affinities for the NaH and KH molecules of 1.422(10) eV and 2.051(39) eV, respectively. These are considerably larger than the previous results of 1.035 eV and 1.273 eV obtained from multireference single- and double-excitation configuration interaction calculations. Together with our previous results for [LiH;e(+)] [Y. Kita et al., J. Chem. Phys. 131, 134310 (2009)], our study confirms the strong correlation between the positron affinity and dipole moment of alkali-metal hydrides.

  20. Color Tuning in Short Wavelength-Sensitive Human and Mouse Visual Pigments: Ab initio Quantum Mechanics/Molecular Mechanics Studies

    Science.gov (United States)

    Altun, Ahmet; Yokoyama, Shozo; Morokuma, Keiji

    2009-01-01

    We have investigated the protonation state and photoabsorption spectrum of Schiff-base (SB) nitrogen bound 11-cis-retinal in human blue and mouse UV cone visual pigments as well as in bovine rhodopsin by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. We have employed both multireference (MRCISD+Q, MR-SORCI+Q, and MR-DDCI2+Q) and single reference (TD-B3LYP and RI-CC2) QM methods. The calculated ground-state and vertical excitation energies show that UV-sensitive pigments have deprotonated SB nitrogen, while violet-sensitive pigments have protonated SB nitrogen, in agreement with some indirect experimental evidence. A significant blue shift of the absorption maxima of violet-sensitive pigments relative to rhodopsins arises from the increase in bond length alternation of the polyene chain of 11-cis-retinal induced by polarizing fields of these pigments. The main counterion is Glu113 in both violet-sensitive vertebrate pigments and bovine rhodopsin. Neither Glu113 nor the remaining pigment has a significant influence on the first excitation energy of 11-cis-retinal in the UV-sensitive pigments that have deprotonated SB nitrogen. There is no charge transfer between the SB and β-ionone terminals of 11-cis-retinal in the ground and first excited states. PMID:19630373

  1. Mechanism of Magnetostructural Transitions in Copper-Nitroxide-Based Switchable Molecular Magnets: Insights from ab Initio Quantum Chemistry Calculations.

    Science.gov (United States)

    Jung, Julie; Guennic, Boris Le; Fedin, Matvey V; Ovcharenko, Victor I; Calzado, Carmen J

    2015-07-20

    The gradual magnetostructural transition in breathing crystals based on copper(II) and pyrazolyl-substituted nitronyl nitroxides has been analyzed by means of DDCI quantum chemistry calculations. The magnetic coupling constants (J) within the spin triads of Cu(hfac)2L(Bu)·0.5C8H18 have been evaluated for the X-ray structures reported at different temperatures. The coupling is strongly antiferromagnetic at low temperature and becomes ferromagnetic when the temperature increases. The intercluster magnetic coupling (J') is antiferromagnetic and shows a marked dependence on temperature. The magnetostructural transition can be reproduced using the calculated J values for each structure in the simulation of the magnetic susceptibility. However, the μ(T) curve can be improved nicely by considering the coexistence of two phases in the transition region, whose ratio varies with temperature corresponding to both the weakly and strongly coupled spin states. These results complement a recent VT-FTIR study on the parent Cu(hfac)2L(Pr) compound with a gradual magnetostructural transition.

  2. On the hierarchical parallelization of ab initio simulations

    CERN Document Server

    Ruiz-Barragan, Sergi; Shiga, Motoyuki

    2016-01-01

    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.

  3. Unified ab initio approaches to nuclear structure and reactions

    CERN Document Server

    Navratil, Petr; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-01-01

    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 {\\em 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 $^6$He halo nucleus, of five- and six...

  4. Ab initio calculation of the Hoyle state

    CERN Document Server

    Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G

    2011-01-01

    The Hoyle state plays a crucial role in the hydrogen 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^{1} 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^{2,3}, 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 properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...

  5. Ab initio phase diagram of iridium

    Science.gov (United States)

    Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.

    2016-09-01

    The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.

  6. Ab initio materials physics and microscopic electrodynamics of media

    OpenAIRE

    2016-01-01

    We argue that the amazing progress of first-principles materials physics necessitates a revision of the Standard Approach to electrodynamics of media. We hence subject this Standard Approach to a thorough critique, which shows both its inherent conceptual problems and its practical inapplicability to modern ab initio calculations. We then go on to show that the common practice in ab initio materials physics has overcome these difficulties by taking a different, microscopic approach to electro...

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

    Science.gov (United States)

    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.

  8. Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization

    Science.gov (United States)

    Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng

    With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.

  9. Ab initio quantum chemical studies of fullerene molecules with substitutes C59X [XSi, Ge, Sn], C59X- [XB, Al, Ga, In], and C59X [XN, P, As, Sb

    Science.gov (United States)

    Simeon, Tomekia M.; Yanov, Ilya; Leszczynski, Jerzy

    This article presents the results of systematic ab initio quantum chemical study of charged and neutral analogues of fullerene molecules: C59X[XSi, Ge, Sn], C59X- [XB, Al, Ga, In], and C59X+ [XN, P, As, Sb]. Hartree-Fock (HF) and density functional theory (DFT) levels of theory with Stuttgart-Dresden basis set were used to investigate the structure and properties of substituted fullerene molecules. A replacement of fullerene carbon atom with a heteroatom results in a unique chemical site on the fullerene surface, which may be used as a reactive center or to modify the electronic properties. We show the possibility of utilization of substituted fullerenes as atom-like building units. Heteroatom substitution allows the tuning of the physical and chemical properties of original molecule for different material science and nanotechnology applications.

  10. Rigorous ab initio quantum embedding for quantum chemistry using Green's function theory: screened interaction, non-local self-energy relaxation, orbital basis, and chemical accuracy

    CERN Document Server

    Lan, Tran Nguyen; Zgid, Dominika

    2016-01-01

    We present a detailed discussion of self-energy embedding theory (SEET) which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower cost. We apply SEET to molecular examples where commonly our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Such a self-energy separation is very general and to make this procedure applicable to multiple systems a detailed and practical procedure for the evaluation of the system and environment self-energy is necessary. We list all the intricacies for one of the possible procedures while focusing our discussion on many practical implementation aspects such as the choice of best orbital basis, impurity solver, and many steps necessary to reach chemical accuracy. Finally, on a set of carefully chosen molecular examples, we demonstrate that SEET which is a controlled, systematically improvable Green's fu...

  11. Relaxation of Small Molecules: an ab initio Study

    Institute of Scientific and Technical Information of China (English)

    CAO Yi-Gang; JIAO Zheng-Kuan; A. Antons; K. Schroeder; S. Blügel2

    2002-01-01

    Using an ab initio total energy and force method, we have relaxed several group IV and group V elementalclusters, in detail the arsenic and antimony dimers, silicon, phosphorus, arsenic and antimony tetramers. The obtainedbond lengths and cohesive energies are more accurate than other calculating methods, and in excellent agreement withthe experimental results.

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  13. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting tr

  14. Structural flexibility of DABCO. Ab initio and DFT benchmark study

    Science.gov (United States)

    Nizovtsev, Anton S.; Ryzhikov, Maxim R.; Kozlova, Svetlana G.

    2017-01-01

    The energy and structural parameters of 1,4-diazabicyclo[2.2.2]octane (DABCO) obtained by various DFT methods are examined versus ab initio and experimental data. The features of twisting potentials of DABCO and closely-related species (1-azabicyclo[2.2.2]octane and bicyclo[2.2.2]octane) are discussed in light of computational schemes applied.

  15. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    Science.gov (United States)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  16. Rational design of electrolyte components by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

    2006-02-28

    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. (author)

  17. Ab initio calculation of the potential bubble nucleus $^{34}$Si

    CERN Document Server

    Duguet, T; Lecluse, S; Barbieri, C; Navrátil, P

    2016-01-01

    The possibility that an unconventional depletion in the center of the charge density distribution of certain nuclei occurs due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. We report on ab initio self-consistent Green's function calculations of one of such candidates, $^{34}$Si, together with its Z+2 neighbour $^{36}$S. Binding energies, rms radii and density distributions of the two nuclei as well as low-lying spectroscopy of $^{35}$Si, $^{37}$S, $^{33}$Al and $^{35}$P are discussed. The interpretation of one-nucleon removal and addition spectra in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input inter-nucleon interactions. The prediction regarding the (non-)existence of the bubble structure in $^{34}$Si varies significantly with the nuclear Hamiltonian used. However, demandin...

  18. Ab initio predictions of the symmetry energy and recent constraints

    Science.gov (United States)

    Sammarruca, Francesca

    2017-01-01

    The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

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

    Science.gov (United States)

    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.

  20. Ab initio transport across bismuth selenide surface barriers

    KAUST Repository

    Narayan, Awadhesh

    2014-11-24

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

  1. Ab initio thermodynamic results for warm dense matter

    Science.gov (United States)

    Bonitz, Michael

    2016-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

    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.

  5. Spin-orbit decomposition of ab initio wavefunctions

    CERN Document Server

    Johnson, Calvin W

    2014-01-01

    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, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions 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 fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.

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

    Science.gov (United States)

    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.

  7. Toward the Ab-initio Description of Medium Mass Nuclei

    CERN Document Server

    Barbieri, C; Soma, V; Duguet, T; Navratil, P

    2012-01-01

    As ab-initio calculations of atomic nuclei enter the A=40-100 mass range, a great challenge is how to approach the vast majority of open-shell (degenerate) isotopes. We add realistic three-nucleon interactions to the state of the art many-body Green's function theory of closed-shells, and find that physics of neutron driplines is reproduced with very good quality. Further, we introduce the Gorkov formalism to extend ab-initio theory to semi-magic, fully open-shell, isotopes. Proof-of-principle calculations for Ca-44 and Ni-74 confirm that this approach is indeed feasible. Combining these two advances (open-shells and three-nucleon interactions) requires longer, technical, work but it is otherwise within reach.

  8. Serine Proteases an Ab Initio Molecular Dynamics Study

    CERN Document Server

    De Santis, L

    1999-01-01

    In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.

  9. High Level Ab Initio Kinetics as a Tool for Astrochemistry

    Science.gov (United States)

    Klippenstein, Stephen

    2015-05-01

    We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.

  10. Nuclear forces and ab initio calculations of atomic nuclei

    OpenAIRE

    Meißner, Ulf-G.

    2014-01-01

    Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.

  11. Thermochemical data for CVD modeling from ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Ho, P. [Sandia National Labs., Albuquerque, NM (United States); Melius, C.F. [Sandia National Labs., Livermore, CA (United States)

    1993-12-31

    Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

  12. GAUSSIAN 76: An ab initio Molecular Orbital Program

    Science.gov (United States)

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

    1978-01-01

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

  13. Ab initio calculation of tight-binding parameters

    Energy Technology Data Exchange (ETDEWEB)

    McMahan, A.K.; Klepeis, J.E.

    1997-12-01

    We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.

  14. Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

    Science.gov (United States)

    2015-07-15

    144306  (2010)]  and  the   cubic -­‐ spline -­‐fitted   PES   reported   by   Xu,   Xie,   Zhang,   Lin,   and   Guo...SUBTITLE 13. SUPPLEMENTARY NOTES 12. DISTRIBUTION AVAILIBILITY STATEMENT 6. AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b ...accurate global PESs and for direct dynamics simulations using interpolating moving least squares (IMLS) that guarantee high fidelity to ab initio data. A

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

    Science.gov (United States)

    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.

  16. Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective

    Science.gov (United States)

    Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge

    2013-03-01

    Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.

  17. Ab initio calculations to support accurate modelling of the rovibronic spectroscopy calculations of vanadium monoxide (VO)

    CERN Document Server

    McKemmish, Laura K; Tennyson, Jonathan

    2016-01-01

    Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity...

  18. {\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem

    CERN Document Server

    Vary, James P; Ng, Esmond; Yang, Chao; Sosonkina, Masha

    2009-01-01

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it ab initio} no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds $10^{10}$ and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving t...

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

    Science.gov (United States)

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

    2013-02-01

    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%.

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

    Science.gov (United States)

    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%.

  1. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

    Science.gov (United States)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

    We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-28

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

  3. Ab initio molecular dynamics using hybrid density functionals

    Science.gov (United States)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1998-12-31

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

  6. Multiscale modeling of femtosecond laser irradiation on copper film with electron thermal conductivity from ab initio calculation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    By combining ab initio quantum mechanics calculation and Drude model, electron temperature and lattice temperature dependent electron thermal conductivity is calculated and implemented into a multiscale model of laser material interaction, which couples the classical molecular dynamics and two-temperature model. The results indicated that the electron thermal conductivity obtained from ab initio calculation leads to faster thermal diffusion than that using the electron thermal conductivity from empirical determination, which further induces deeper melting region, larger number of density waves travelling inside the copper film and more various speeds of atomic clusters ablated from the irradiated film surface.

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

    Energy Technology Data Exchange (ETDEWEB)

    Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K. [Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green St., Urbana, Illinois 61801 (United States)

    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.

  8. Spin-orbit decomposition of ab initio wavefunctions

    OpenAIRE

    Johnson, Calvin W.

    2014-01-01

    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, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulti...

  9. Accelerating Ab Initio Nuclear Physics Calculations with GPUs

    CERN Document Server

    Potter, Hugh; Maris, Pieter; Sosonkina, Masha; Vary, James; Binder, Sven; Calci, Angelo; Langhammer, Joachim; Roth, Robert; Çatalyürek, Ümit; Saule, Erik

    2014-01-01

    This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.

  10. Ab initio study of phase equilibria in TiCx

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row

    2001-10-01

    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

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

    Directory of Open Access Journals (Sweden)

    Zhang Yang

    2007-05-01

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

  13. Benchmarks of the ab initio FCI, MCSM and NCFC methods

    CERN Document Server

    Abe, T; Otsuka, T; Shimizu, N; Utsuno, Y; Vary, J P

    2012-01-01

    We report ab initio no-core solutions for properties of light nuclei with three different approaches in order to assess the accuracy and convergence rates of each method. Full Configuration Interaction (FCI), Monte Carlo Shell Model (MCSM) and No Core Full Configuration (NCFC) approaches are solved separately for the ground state energy and other properties of seven light nuclei using the realistic JISP16 nucleon-nucleon interaction. The results are consistent among the different approaches. The methods differ significantly in how the required computational resources scale with increasing particle number for a given accuracy.

  14. Ab-initio study of transition metal hydrides

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)

    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.

  15. Morphing ab initio potential energy curve of beryllium monohydride

    Science.gov (United States)

    Špirko, Vladimír

    2016-12-01

    Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.

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

    KAUST Repository

    Tao, Kun

    2012-01-05

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

  17. Hydrogen Desorption from Mg Hydride: An Ab Initio Study

    Directory of Open Access Journals (Sweden)

    Simone Giusepponi

    2012-07-01

    Full Text Available Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Furthermore, extensive ab-initio molecular dynamics simulations are performed at several temperatures to characterize the desorption process at the interface. The numerical model successfully reproduces the experimental desorption temperature for the hydride.

  18. Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

    Science.gov (United States)

    Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

    2017-01-01

    Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

  19. Paired-permanent approach for VB theory (II) -An ab initio spin-free VB program

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Paired-permanent approach for VB theory is extensively developed. Canonical expan sion of a paired-permanent is deduced. Furthermore, it is shown that a paired-permanent may be expressed in terms of the products of sub-paired-permanents of any given order and their corre sponding minors. An ab initio spin-free valence bond program, called Xiamen, is implemented by using paired-permanent approach. Test calculation shows that Xiamen package is more efficient than some other programs based on the traditional VB algorithm, and it provides a new practical tool for quantum chemistry.

  20. Equations of state of heavy metals: ab initio approaches; Equations d'etat des metaux lourds: approches ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, S.; Jollet, F.; Jomard, G.; Siberchicot, B.; Torrent, M.; Zerah, G.; Amadon, B.; Bouchet, J.; Richard, N.; Robert, G. [CEA Bruyeres-le-Chatel, 91 (France)

    2005-07-01

    The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)

  1. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

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

  3. Ab initio based atomic scattering amplitudes and {002} electron structure factors of InxGa1-xAs/GaAs quantum wells

    Science.gov (United States)

    Titantah, J. T.; Lamoen, D.; Schowalter, M.; Rosenauer, A.

    2010-02-01

    The atomic scattering amplitudes of the various atoms of the systems Ga1-xInxAs, GaAs1-xNx and InAs1-xNx are calculated using the density functional theory (DFT) approach. The scattering amplitudes of N, Ga, As and In in the model systems are compared with the frequently used Doyle and Turner values. Deviation from the latter values is found for small scattering vectors (sMASAs) for small scattering vectors (sMASAs are exploited within zero pressure classical Metropolis Monte Carlo (MC), finite temperature calculations to investigate the effect of quantum well size on the electron {002} structure factor (SF) of Ga1-xInxAs quantum wells.

  4. Low-Scaling Quantum Chemistry Approach to Excited-State Properties via an ab Initio Exciton Model: Application to Excitation Energy Transfer in a Self-Assembled Nanotube.

    Science.gov (United States)

    Morrison, Adrian F; Herbert, John M

    2015-11-05

    We introduce a charge-embedding scheme for an excited-state quantum chemistry method aimed at weakly interacting molecular aggregates. The Hamiltonian matrix for the aggregate is constructed in a basis of direct products of configuration-state functions for the monomers, and diagonalization of this matrix affords excitation energies within ∼0.2 eV of the corresponding supersystem calculation. Both the basis states and the coupling matrix elements can be computed in a distributed way, resulting in an algorithm whose time-to-solution is independent of the number of chromophores, and we report calculations on systems with almost 55 000 basis functions using fewer than 450 processors. In a semiconducting organic nanotube, we find evidence of ultrafast, coherent dynamics followed by energy localization driven by static disorder. Truncation of the model system has a qualitative effect on the energy-transfer dynamics, demonstrating the importance of simulating an extended portion of the nanotube, which is not feasible using traditional quantum chemistry.

  5. Molecular potentials and wave function mapping by high-resolution electron spectroscopy and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kimberg, Victor, E-mail: victor.kimberg@pks.mpi.de [Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden (Germany); Miron, Catalin, E-mail: miron@synchrotron-soleil.fr [Synchrotron SOLEIL, l’Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex (France)

    2014-08-15

    Highlights: • Some studies related to the vibrational wave functions mapping phenomenon are reviewed. • The core-excited vibrational wave functions were mapped using dissociative and bound final states. • High-resolution experimental data is accompanied by ab initio calculations. • The mapping phenomenon allows one to extract constants of the molecular potentials. • The mapping techniques are general and can be applied for the study of many systems. - Abstract: The recent development of high brightness 3{sup rd} generation soft X-ray sources and high energy resolution electron spectrometers made it possible to accurately trace quantum phenomena associated to the vibrational dynamics in core-excited molecules. The present paper reviews the recent results on mapping of vibrational wave functions and molecular potentials based on electron spectroscopy. We discuss and compare the mapping phenomena in various systems, stressing the advantages of the resonant X-ray scattering for studying of the nuclear dynamics and spectroscopic constants of small molecules. The experimental results discussed in the paper are most often accompanied by state-of-the-art ab initio calculations allowing for a deeper understanding of the quantum effects. Besides its fundamental interest, the vibrational wave function mapping is shown to be useful for the analysis of core- and valence-excited molecular states based on the reflection principle.

  6. Ab initio quantum-chemical computations of the electronic states in HgBr2 and IBr: Molecules of interest on the Earth's atmosphere

    Science.gov (United States)

    Sitkiewicz, Sebastian P.; Oliva, Josep M.; Dávalos, Juan Z.; Notario, Rafael; Saiz-Lopez, Alfonso; Alcoba, Diego R.; Oña, Ofelia B.; Roca-Sanjuán, Daniel

    2016-12-01

    The electronic states of atmospheric relevant molecules IBr and HgBr2 are reported, within the UV-Vis spectrum range (170 nm ≤λp h o t o n≤600 nm) by means of the complete-active-space self-consistent field/multi-state complete-active-space second-order perturbation theory/spin-orbit restricted-active-space state-interaction (CASSCF/MS-CASPT2/SO-RASSI) quantum-chemical approach and atomic-natural-orbital relativistic-correlation-consistent (ANO-RCC) basis sets. Several analyses of the methodology were carried out in order to reach converged results and therefore to establish a highly accurate level of theory. Good agreement is found with the experimental data with errors not higher than around 0.1 eV. The presented analyses shall allow upcoming studies aimed to accurately determine the absorption cross sections of interhalogen molecules and compounds with Hg that are relevant to better comprehend the photochemical processes taking place in the atmosphere.

  7. An Efficient Approach to Ab Initio Monte Carlo Simulation

    CERN Document Server

    Leiding, Jeff

    2013-01-01

    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, is used to substantially decorrelate configurations at which the potential of interest is evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure is maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature \\beta^0), which is otherwise unconstrained. Local density approximation (LDA) results are presented for shocked states in argon at pressures from 4 to 60 GPa. Depending on the quality of the reference potential, the acceptance probability is enhanced by factors of 1.2-28 relative to unoptimized NMC sampling, and the procedure's efficiency is found to be competitive with that of standard ab initio...

  8. Ab initio study of the transition-metal carbene cations

    Institute of Scientific and Technical Information of China (English)

    李吉海; 冯大诚; 冯圣玉

    1999-01-01

    The geometries and bonding characteristics of the first-row transition-metal carbene cations MCH2+ were investigated by ab initio molecular orbital theory (HF/LANL2DZ). All of MCH2+ are coplanar. In the closed shell structures the C bonds to M with double bonds; while in the open shell structures the partial double bonds are formed, because one of the σ and π orbitals is singly occupied. It is mainly the π-type overlap between the 2px orbital of C and 4px, 3dxz, orbitals of M+ that forms the π orbitals. The dissociation energies of C—M bond appear in periodic trend from Sc to Cu. Most of the calculated bond dissociation energies are close to the experimental ones.

  9. Ab initio study of II-(VI){sub 2} dichalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, P; Vidal, J; Lincot, D, E-mail: polsson@kth.se [Institut de R and D sur l' energie photovoltaique (IRDEP), UMR 7174-EDF-CNRS-ENSCP, 6 quai Watier, 78401 Chatou Cedex (France)

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te){sub 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{sub 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. (paper)

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

    DEFF Research Database (Denmark)

    Marshall, Paul; Glarborg, Peter

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Kolorenč, Přemysl, E-mail: kolorenc@mbox.troja.mff.cuni.cz [Charles University in Prague, Faculty of Mathematics and Physics, Institute of Theoretical Physics, V Holešovičkách 2, 180 00 Prague (Czech Republic); Sisourat, Nicolas [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)

    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.

  12. Ab initio investigation of the mechanical properties of copper

    Institute of Scientific and Technical Information of China (English)

    Liu Yue-Lin; Gui Li-Jiang; Jin Shuo

    2012-01-01

    Employing the ab initio total energy method based on the density functional theory with the generalized gradient approximation,we have systematically investigated the theoretical mechanical properties of copper (Cu).The theoretical tensile strengths are calculated to be 25.3 GPa,5.9 GPa,and 37.6 GPa for the fcc Cu single crystal in the [001],[110],and [111] directions,respectively.Among the three directions,the [110] direction is the weakest one due to the occurrence of structure transition at the lower strain and the weakest interaction of atoms between the (110) planes,while the [111] direction is the strongest direction because of the strongest interaction of atoms between the (111) planes.In terms of the elastic constants of Cu single crystal,we also estimate some mechanical quantities of polycrystalline Cu,including bulk modulus B,shear modulus G,Young's modulus Ep,and Poisson's ratio v.

  13. Ab initio Molecular Dynamics Study on Small Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    叶林晖; 刘邦贵; 王鼎盛

    2001-01-01

    Ab initio molecular dynamics simulations are performed on small single wall nanotubes. By structural relaxation,the equilibrium C-C bond lengths and bond angles are determined. Our result shows that for both zigzag and armchair nanotubes there are two nonequivalent bond lengths. One bond stretches from that of the graphene sheet, while the other shrinks. Small variations on bond angles are also shown. Energy bands are calculated for the optimized structures. It is found that the intrinsic curvature of the very small nanotube greatly modifies the energy band which can no longer be well described in the tight-binding zone-folding picture. In our calculation very small nanotubes are metallic. The energy per atom fits quite well with the relation of E(R) = E0 + f/R2 even for the extreme small radius. The implications of the results on the properties of small nanotubes are discussed.

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

    Science.gov (United States)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-01

    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.

  15. Ab initio study of alanine polypeptide chains twisting

    CERN Document Server

    Solovyov, I A; Solovyov, A V; Yakubovitch, A V; Greiner, Walter; Solov'yov, Andrey V.; Solov'yov, Ilia A.; Yakubovitch, Alexander V.

    2005-01-01

    We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable corres...

  16. Ab initio electronic structure and optical conductivity of bismuth tellurohalides

    CERN Document Server

    Schwalbe, Sebastian; Starke, Ronald; Schober, Giulio A H; Kortus, Jens

    2016-01-01

    We investigate the electronic structure, dielectric and optical properties of bismuth tellurohalides BiTeX (X = I, Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. , Makhnev et al. , and Rusinov et al. . We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.

  17. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    CERN Document Server

    Ceriotti, Michele; Manolopoulos, David E

    2014-01-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.

  18. Many-body ab initio study of antiferromagnetic {Cr7M } molecular rings

    Science.gov (United States)

    Chiesa, A.; Carretta, S.; Santini, P.; Amoretti, G.; Pavarini, E.

    2016-12-01

    Antiferromagnetic molecular rings are widely studied both for fundamental quantum-mechanical issues and for technological applications, particularly in the field of quantum information processing. Here we present a detailed first-principles study of two families—purple and green—of {Cr7M } antiferromagnetic rings, where M is a divalent transition metal ion (M =Ni2 + , Mn2 +, and Zn2 +). We employ a recently developed flexible and efficient scheme to build ab initio system-specific Hubbard models. From such many-body models we systematically derive the low-energy effective spin Hamiltonian for the rings. Our approach allows us to calculate isotropic as well as anisotropic terms of the spin Hamiltonian, without any a priori assumption on its form. For each compound we calculate magnetic exchange couplings, zero-field splitting tensors, and gyromagnetic tensors, finding good agreement with experimental results.

  19. Ab initio interaction potentials for X and B excited states of He-I{sub 2} for studying dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Prosmiti, Rita; Garcia-Gutierrez, Leonor; Delgado-Tellez, Laura; Valdes, Alvaro; Villarreal, Pablo; Delgado-Barrio, Gerardo, E-mail: rita@imaff.cfmac.csic.e [Instituto de Fisica Fundamental (CSIC), Serrano 123, 28006 Madrid (Spain)

    2009-11-01

    Ab initio CCSD(T) and MRCI approaches were employed to construct potential energy surfaces of the ground and the B electronic excited states of He-I{sub 2} complex, while full quantum mechanical methods were applied to study its spectroscopy and dynamics. A description of the approach adopted, together with the results obtained and their comparison with recent experimental data, as well as further improvements are presented.

  20. Emergence of rotational bands in ab initio no-core configuration interaction calculations

    CERN Document Server

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

    2015-01-01

    Rotational bands have been observed to emerge in ab initio no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. We investigate the ab initio emergence of nuclear rotation in the Be isotopes, focusing on 9Be for illustration, and make use of basis extrapolation methods to obtain ab initio predictions of rotational band parameters for comparison with experiment. We find robust signatures for rotational motion, which reproduce both qualitative and quantitative features of the experimentally observed bands.

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

    Science.gov (United States)

    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.

  2. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  3. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    Science.gov (United States)

    Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  5. Ab initio evaluations of the He solubility in liquid Li

    Energy Technology Data Exchange (ETDEWEB)

    Sedano, Luis A. [EURATOM-CIEMAT Assoc., Materials for Fusion Program, Bd. 43 P0.04, Avda. Complutense 22, 28040 Madrid (Spain)]. E-mail: luis.sedano@ciemat.es; Hassanein, Ahmed [Argonne Nat. Lab, 9700 South Class Av., Argonne, IL (United States)]. E-mail: hassanein@anl.gov; Sanz, Javier [ETSII-UNED, c/Juan del Rosal, 12, 28040 Madrid (E) (Spain)]. E-mail: jsanz@ind.UNED.es

    2005-11-15

    Modified embedding atom methods (MEAM) are developed to have predictions of the partial molar heat of solution (-H{sub s}) by direct simulation of metal cohesion, He-metal and He-He interaction. Transitions from crystalline Li to configurations, having the liquid Li structure's factors (h-bar (q)), are simulated ab initio. Once h-bar (q) reproduced, He atoms are added, one by one, to the Li system. Parallel lines for each case, with slopes clearly independent on the number of He atoms in the system, are obtained for energy versus pressure at given temperatures. Average differences between two adjacent parallels at zero pressure, once kinetic energy of the system discounted, represents the energy gained by an He atom when added to the Li system, related to the solution energy -H{sub s}. The molar excess entropy of gas in solution (S-bar {sub l}{sup ex}) is previously evaluated following diverse fundamental approaches: a 'thermodynamic liquid-hole' (TL-H) model for alkali liquids and a statistical-mechanics (Neff and McQuarrie's) model (SMM). Between 600 and 900 deg. C, a typical range of interest for the use of Li in fusion technology, the computed values for the (He) Henry's constant in Li range from 8x10{sup -14} to 10{sup -13} at. fr. Pa{sup -1}.

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

    Science.gov (United States)

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

    2016-04-01

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

  7. Ab initio no-core solutions for $^6$Li

    CERN Document Server

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

    2016-01-01

    We solve for properties of $^6$Li in the ab initio No-Core Full Configuration approach and we separately solve for its ground state and $J^{\\pi}=2_{2}^{+}$ resonance with the Gamow Shell Model in the Berggren basis. We employ both the JISP16 and chiral NNLO$_{opt}$ realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root-mean-square radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton root-mean-square radius, and electric quadrupole moment. We attain improved estimates of these observables in the No-Core Full Configuration approach by using basis spaces up through N$_{max}$=18 that enable more definitive comparisons with experiment. Using the Density Matrix Renormalization Group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the Gamow Shell Model treatment of the $^6$Li ground state and $J^{\\pi}=2_{2}^{+}$ resonance by ...

  8. An efficient approach to ab initio Monte Carlo simulation.

    Science.gov (United States)

    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(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.

  9. Ab-initio calculations for dilute magnetic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Belhadji, Brahim

    2008-03-03

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

  10. Ab initio studies of niobium defects in uranium

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

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

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

    Science.gov (United States)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

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

  12. Ab initio modelling of boron related defects in amorphous silicon

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Tiago A.; Torres, Vitor J.B. [Department of Physics, University of Aveiro, Campus Santiago, 3810-193 Aveiro (Portugal)

    2012-10-15

    We have modeled boron related point defects in amorphous silicon, using an ab initio method, the Density functional theory-pseudopotential code Aimpro. The boron atoms were embedded in 64 atom amorphous silicon cubic supercells. The calculations were performed using boron defects in 15 different supercells. These supercells were developed using a modified Wooten-Winer-Weaire bond switching mechanism. In average, the properties of the 15 supercells agree with the observed radial and bond angle distributions, as well the electronic and vibrational density of states and Raman spectra. In amorphous silicon it has been very hard to find real self-interstitials, since for almost all the tested configurations, the amorphous lattice relaxes overall. We found that substitutional boron prefers to be 4-fold coordinated. We find also an intrinsic hole-trap in the non-doped amorphous lattice, which may explain the low efficiency of boron doping. The local vibrational modes are, in average, higher than the correspondent crystalline values (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

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

    CERN Document Server

    Awoonor-Williams, Ernest

    2016-01-01

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

  14. Ab initio modeling of decomposition in iron based alloys

    Science.gov (United States)

    Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.

    2016-12-01

    This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.

  15. Ab initio calculations of the absorption spectrum of chalcone

    Science.gov (United States)

    Oumi, Manabu; Maurice, David; Head-Gordon, Martin

    1999-03-01

    The excitation energies and excited states of trans-chalcone ( trans-( s-cis)-1,3-diphenylpropenone), and several related molecules ( trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone, propenal, trans-( s-cis)-1-(4-hydroxyphenyl)-3-phenylpropenone, trans-( s-cis)3-(4-hydroxyphenyl)-1-phenylpropenone) have been calculated using single reference ab initio molecular orbital methods, and characterized by attachment-detachment density analysis. The results suggest assignments for the lowest three electronic transitions observed experimentally for trans-( s-cis)-chalcone in solution. The extent of localization of the electronic transitions is established by calculations on the excited states of trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone and propenal, as well as analysis of the chalcone calculations. Contrary to some previous work, none of these excitations are strongly delocalized over the entire molecule. Calculated substituent shifts for the hydroxy chalcones are in qualitative agreement with experimental data, and support the localized interpretation of the main π→ π* transition.

  16. An ab initio Non-Equilibrium Green Function Approach to Charge Transport: Dithiolethine

    Institute of Scientific and Technical Information of China (English)

    Alexander Schnurpfeil; SONG Bo; Martin Albrecht

    2006-01-01

    @@ We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wavefunction-based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green function formalism. Our procedure is demonstrated for a dithiolethine molecule located between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.

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

    Science.gov (United States)

    Senese, Fredrick; Ake, Robert

    1992-01-01

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

  18. Relaxation of the excited -(2-hydroxy benzylidene) aniline molecule: An ab initio and TD DFT study

    Indian Academy of Sciences (India)

    Biswajit Chowdhury; Rina De; Pinaky Sett; Joydeep Chowdhury

    2010-11-01

    The photophysical behaviour of N-(2-hydroxy benzylidene) aniline or most commonly known as salicylideneaniline (SA) has been investigated using the ab initio and DFT levels of theory. The quantum chemical calculations show that the optimized non planar enol (1) form of the SA molecule is the most stable conformer in the ground state and is marked by the twisting of the phenolic and anilino rings of the molecule. The geometry optimizations and the subsequent frequency calculations of the excited singlet electronic states of the various tautomeric forms of SA molecule were performed with the CIS level of theory. A detail theoretical investigation on the relaxation dynamics of the SA molecule has been presented. Possible explanation on the excitation wavelength dependence of the photochromic yield of the molecule is also reported.

  19. Rotational Isomeric State Model of Poly(vinylidene chloride) Based Upon ab Initio Electronic Structure Calculations

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhi-jie; LIU Yu-hua; L(U) Zhong-yuan; LI Ze-sheng

    2009-01-01

    The rotational isomeric state(RIS) model was constructed for poly(vinylidene chloride)(PVDC) based on quantum chemistry calculations. The statistical weighted parameters were obtained from RIS representations and ab initio energies of conformers for model molecules 2,2,4,4-tetrachloropentane(TCP) and 2,2,4,4,6, 6-hexachlorohep-tane(HCH). By employing the RIS method, the characteristic ratio C∞ was calculated for PVDC. The calculated cha-racteristic ratio for PVDC is in good agreement with experiment result. Additionally, we studied the influence of the statistical weighted parameters on C∞ by calculating δC∞/δlnw. According to the values of δC∞/δlnw, the effects of second-order Cl-CH2 pentane type interaction and Cl-Cl long range interaction on C∞ were found to be important. In contrast, first-order interaction is unimportant.

  20. reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

    Science.gov (United States)

    Müller, Julian; Hartke, Bernd

    2016-08-09

    Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

  1. A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2001-11-01

    We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-28

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

  3. Ab Initio No Core Shell Model - Recent Results and Further Prospects

    CERN Document Server

    Vary, James P; Potter, Hugh; Caprio, Mark A; Smith, Robin; Binder, Sven; Calci, Angelo; Fischer, Sebastian; Langhammer, Joachim; Roth, Robert; Aktulga, Hasan Metin; Ng, Esmond; Yang, Chao; Oryspayev, Dossay; Sosonkina, Masha; Saule, Erik; Çatalyürek, Ümit

    2015-01-01

    There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant results within the ab initio No Core Shell Model (NCSM) closely tied to three major factors enabling this progress: (1) improved nuclear interactions that accurately describe the experimental two-nucleon and three-nucleon interaction data; (2) advances in algorithms to simulate the quantum many-body problem with strong interactions; and (3) continued rapid development of high-performance computers now capable of performing $20 \\times 10^{15}$ floating point operations per second. We also comment on prospects for further developments.

  4. Density functional and ab initio investigation of S2N2 and (SN)2

    Science.gov (United States)

    Moon, Jiwon; Chae, Myoungju; Kim, Joonghan

    2017-03-01

    Quantum chemical calculations were performed to calculate the molecular properties of the 1Ag state of disulfur dinitride, S2N2, and the 1A1 state of the SN dimer, (SN)2, using density functional theory (DFT) and ab initio methods. The molecular structure of (SN)2 is a trapezoid instead of a rectangle. Because the multireference character of (SN)2 is considerable, most hybrid DFTs poorly describe its molecular properties. In contrast, old generalized gradient approximations give qualitatively correct descriptions of the molecular properties of (SN)2. Multi-state second-order multiconfigurational perturbation theory gives results that are close to those from multireference configuration interaction with the Davidson correction. The multireference character should be considered when calculating the molecular properties of poly sulfur nitride systems.

  5. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation....... This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. 1Δ15N(D) and 2Δ1H(D) of the NH3+ groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show...

  6. An Ab-Initio Calculation of Raman Spectra of Binary Sodium Silicates

    Institute of Scientific and Technical Information of China (English)

    尤静林; 蒋国昌; 侯怀宇; 陈辉; 吴永全; 徐匡迪

    2004-01-01

    Raman spectra of binary sodium silicates are calculated by self-consistent field (SCF) molecular orbital ab initio calculation of the quantum chemical method with several poly silicon-oxygen tetrahedral model clusters when both the basis sets of 6-31 G and 6-31 G(d) are applied. The symmetric stretching vibrational frequency of non-bridging oxygen in a high frequency range and its Raman optical activity and scattering cross section are deduced and analysed. The correlation between this vibrational Raman shift and its microscopic environment of the silicon-oxygen tetrahedron is found based on interior stress of configuration, which depends on the connecting topology of adjacent silicon-oxygen tetrahedra (SiOT). A newly established empirical stress index of tetrahedron is introduced to elucidate the above relationship.

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

    Science.gov (United States)

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

    1997-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-03-01

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

  9. Comparison of ab initio molecular properties of EDO-TTF with the properties of the (EDO-TTF)(2)PF6 crystal

    NARCIS (Netherlands)

    Linker, Gerrit-Jan; van Loosdrecht, Paul H. M.; van Duijnen, Piet; Broer, Ria

    2010-01-01

    We performed ab initio quantum chemical calculations for the geometrical and electronic structure of the EDO-TTF (ethylenedioxy-tetrathiafulvalene) molecule using HF, CASSCF and DFT methods. We compare these in vacuo results with the properties of the (EDO-TTF)(2)PF6 crystal at near room temperature

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

    KAUST Repository

    Zhang, Qianfan

    2010-09-08

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

  11. Efficient conformational space exploration in ab initio protein folding simulation.

    Science.gov (United States)

    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.

  12. Resonance and aromaticity: an ab initio valence bond approach.

    Science.gov (United States)

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

    2012-05-17

    Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.

  13. Cosmic-Ray Modulation: an Ab Initio Approach

    Science.gov (United States)

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

    2014-10-01

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

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

    Science.gov (United States)

    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.

  15. Configuration-averaged open shell ab initio method for crystal field levels and magnetic properties of lanthanide(III) complexes

    CERN Document Server

    Heuvel, Willem Van den; Soncini, Alessandro

    2015-01-01

    We present an ab initio methodology dedicated to the determination of the electronic structure and magnetic properties of ground and low-lying excited states, i.e., the crystal field levels, in lanthanide(III) complexes. Currently, the most popular and successful ab initio approach is the CASSCF/RASSI-SO method, consisting of the optimization of multiple complete active space self-consistent field (CASSCF) spin eigenfunctions, followed by full diagonalization of the spin--orbit coupling (SOC) Hamiltonian in the basis of the CASSCF spin states featuring spin-dependent orbitals. Based on two simple observations valid for Ln(III) complexes, namely: (i) CASSCF 4f atomic orbitals are expected to change very little when optimized for different multiconfigurational states belonging to the 4f-electronic configuration, (ii) due to strong SOC the total spin is not a good quantum number, we propose here an efficient ab initio strategy which completely avoids any multiconfigurational calculation, by optimizing a unique s...

  16. Ab-Initio-Based Approach to Study Complete Metalloproteins: Divide and Conquer Geometry Optimization of Nitric-Oxide Reductase

    Science.gov (United States)

    Yue, Yutao; Chachiyo, Teepanis; Rodriguez, Jorge H.

    2007-03-01

    The direct application of ab-initio methods (Hartree-Fock or density functional theory) to study complete biomolecules has been impossible due to the huge computational cost of fully quantum mechanical calculations. As an initial step towards overcoming this problem, we implemented an ab-initio-based method to predict geometric structures of large metalloproteins using the principle of ``divide and conquer.'' The method has been applied to small test systems showing satisfactory agreement with all-atom ab initio calculations. We have successfully applied the divide and conquer approach to partially optimize the geometry of a ligand-enzyme system, namely NO binding to nitric-oxide reductases (NOR, P450nor). NOR is a metalloenzyme that catalyzes the reduction of NO to N2O. To compare our results with all atom calculations we studied a biochemically relevant subsystem (375 atoms) of the ligand-enzyme complex. The deviation between the divide and conquer geometry and the all atom partial geometry optimization is minor, on order of 10-1 å for bond lengths. The computational cost of the method is moderately expensive making its application to large (bio) molecules plausible. Supported by NSF CAREER Award CHE-0349189 (JHR).

  17. Transport and optical properties of warm dense aluminum in the two-temperature regime: Ab initio calculation and semiempirical approximation

    CERN Document Server

    Knyazev, D V

    2014-01-01

    This work is devoted to the investigation of transport and optical properties of liquid aluminum in the two-temperature case. At first optical properties, static electrical and thermal conductivities were obtained in the \\textit{ab initio} calculation. The \\textit{ab initio} calculation is based on the quantum molecular dynamics, density functional theory and the Kubo-Greenwood formula. The semiempirical approximation was constructed based on the results of the \\textit{ab initio} caculation. The approximation yields the dependences $\\sigma_{1_\\mathrm{DC}}\\propto1/T_i^{0.25}$ and $K\\propto T_e/T_i^{0.25}$ for the static electrical conductivity and thermal conductivity, respectively. The approximation is valid for liquid aluminum at $\\rho=2.70$~g/cm$^3$, 3~kK~$\\leq T_i\\leq T_e\\leq20$~kK. Our results are well described by the Drude model with the effective relaxation time $\\tau\\propto T_i^{-0.25}$. We have compared our results with a number of other models. They are all reduced in the low-temperature limit to th...

  18. Realization of prediction of materials properties by ab initio computer simulation

    Indian Academy of Sciences (India)

    Yoshiyuki Kawazoe

    2003-01-01

    Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest supercomputer efficiently. Therefore, it is very difficult to simulate realistic materials with grain boundaries and important reactions like diffusion in materials. To improve this situation, two ways have been invented. One way is to upgrade approximations to match the necessary levels according to inhomogeneous electron gas theory beyond the present day standard, i.e. local density approximation (LDA). The reason is simply that the system we are interested in is composed of many particles interacting with Coulomb forces governed by quantum mechanics. (Complete knowledge is available, and only what we should do is to make better approximations to explain the phenomena!). Another is to extract the necessary parameters from the ab initio calculations on systems with limited number of atoms, and apply these results into cluster variation, direct, or any other sophisticated methods based on classical concepts such as statistical mechanics. In this paper, several typical examples recently worked out by our research group are introduced to indicate that these methodologies are actually possible to be successfully used to predict materials properties before experiments based on the present day state-of-art supercomputing systems. It includes scientific visualization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube, tight-binding calculation of single electron conductance properties in nanotube to create nano-scale diode virtually by computer, which will be a base of future nanoscale electric device in nanometer size, Li + H reaction without Born–Oppenheimer approximation, structural phase

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-01

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

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

    Science.gov (United States)

    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

  1. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    Science.gov (United States)

    Ji, Pengfei; Zhang, Yuwen

    2016-03-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

  2. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.

  3. Path integral molecular dynamics calculations of the H6+ and D6+ clusters on an ab initio potential energy surface

    Science.gov (United States)

    Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki

    2007-11-01

    Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.

  4. Full-dimensional quantum calculations of the dissociation energy, zero-point, and 10 K properties of H7+/D7+ clusters using an ab initio potential energy surface.

    Science.gov (United States)

    Barragán, Patricia; Pérez de Tudela, Ricardo; Qu, Chen; Prosmiti, Rita; Bowman, Joel M

    2013-07-14

    Diffusion Monte Carlo (DMC) and path-integral Monte Carlo computations of the vibrational ground state and 10 K equilibrium state properties of the H7 (+)/D7 (+) cations are presented, using an ab initio full-dimensional potential energy surface. The DMC zero-point energies of dissociated fragments H5 (+)(D5 (+))+H2(D2) are also calculated and from these results and the electronic dissociation energy, dissociation energies, D0, of 752 ± 15 and 980 ± 14 cm(-1) are reported for H7 (+) and D7 (+), respectively. Due to the known error in the electronic dissociation energy of the potential surface, these quantities are underestimated by roughly 65 cm(-1). These values are rigorously determined for first time, and compared with previous theoretical estimates from electronic structure calculations using standard harmonic analysis, and available experimental measurements. Probability density distributions are also computed for the ground vibrational and 10 K state of H7 (+) and D7 (+). These are qualitatively described as a central H3 (+)/D3 (+) core surrounded by "solvent" H2/D2 molecules that nearly freely rotate.

  5. Time-dependent Wave Packet Quantum Scattering Study of Reaction S(3p)+H2→HS+H on a New ab initio Potential Energy Surface 3A'

    Institute of Scientific and Technical Information of China (English)

    Shuang-jiang Lv; Pei-yu Zhang; Guo-zhong He

    2012-01-01

    A new potential energy surface is presented for the triplet state 3A' of the chemical reaction S(3P)+H2 from a set of accurate ab initio data.The single point energies are computed using highly correlated complete active space self-consistent-field and multi-reference configuration interaction wave functions with a basis set of aug-cc-pV5Z.We have fitted the full set of energy values using many-body expansion method with an Aguado-Paniagua function.Based on the new potential energy surface,we carry out the time-dependent wave packet scattering calculations over the collision energy range of 0.8-2.2 eV.Both the centrifugalsudden approximation and Coriolis Coupling cross sections are obtained.In addition,the total reaction probabilities are calculated for the reactant H2 initially in the vibrational states v=0-3 (j=0).It is found that initial vibrational excitation enhances the title reaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Keegan, Ronan M. [STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Bibby, Jaclyn; Thomas, Jens [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Xu, Dong [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Zhang, Yang [University of Michigan, Ann Arbor, MI 48109 (United States); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom); STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom)

    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.

  7. Electrical resistivity of NaPb compound-forming liquid alloy using ab initio pseudopotentials

    Indian Academy of Sciences (India)

    Anil Thakur; N S Negi; P K Ahluwalla

    2005-08-01

    The study of electrical resistivity of compound-forming liquid alloy, NaPb, is presented as a function of concentration. Hard sphere diameters of Na and Pb are obtained through the interionic pair potentials evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate the partial structure factors (). Considering the liquid alloy to be a ternary mixture, Ziman formula, modified for complex formation has been used for calculating resistivity of binary liquid alloys. Form factors are calculated using ab initio pseudopotentials. The results suggest that Ziman formalism, when used with ab initio pseudopotentials, are quite successful in explaining the electrical resistivity data of compound-forming binary liquid alloys.

  8. Matrix Product Operators, Matrix Product States, and ab initio Density Matrix Renormalization Group algorithms

    CERN Document Server

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

    2016-01-01

    Current descriptions of the ab initio 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 par...

  9. Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

    Institute of Scientific and Technical Information of China (English)

    侯若冰; 陈志达; 义祥辉; 卞江; 徐光宪

    2000-01-01

    Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR+ are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,

  10. An ab initio study of the polytypism in InP

    Science.gov (United States)

    Dacal, Luis C. O.; Cantarero, A.

    2016-09-01

    The existence of polytypism in semiconductor nanostructures gives rise to the appearance of stacking faults which many times can be treated as quantum wells. In some cases, despite of a careful growth, the polytypism can be hardly avoided. In this work, we perform an ab initio study of zincblende stacking faults in a wurtzite InP system, using the supercell approach and taking the limit of low density of narrow stacking faults regions. Our results confirm the type II band alignment between the phases, producing a reliable qualitative description of the band gap evolution along the growth axis. These results show an spacial asymmetry in the zincblende quantum wells, that is expected due to the fact that the wurtzite stacking sequence (ABAB) is part of the zincblende one (ABCABC), but with an unexpected asymmetry between the valence and the conduction bands. We also present results for the complex dielectric function, clearly showing the influence of the stacking on the homostructure values and surprisingly proving that the correspondent bulk results can be used to reproduce the polytypism even in the limit we considered.

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

    Science.gov (United States)

    Hafner, Jürgen

    2010-09-29

    During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

  12. Ab initio calculations of third-order elastic constants and related properties for selected semiconductors

    OpenAIRE

    Lopuszynski, Michal; Majewski, Jacek A.

    2007-01-01

    We present theoretical studies for the third-order elastic constants $C_{ijk}$ in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for $C_{ijk}$ with experimental data available for Si and GaAs. We also underline the relation of the third-order ela...

  13. An ab initio study on single electron transfer between ClO2 and phenol

    Institute of Scientific and Technical Information of China (English)

    崔崇威; 黄君礼

    2004-01-01

    The SET mechanism between chlorine dioxide (ClO2 ) and phenol was studied by using ab initio method at 4-31G* level. Geometries of the reactants, intermediate and products of the reaction were optimized and the single point energy calculations of the species were performed. The relative structure data of the reactants, intermediate and products are given. The SET mechanism between ClO2 and phenol was confirmed by ab initio calculations. The reaction is exothermic about 200. 88 k J/mol.

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

    Science.gov (United States)

    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.

  15. Ab Initio Calculation on Self-Assembled Base-Functionalized Single-Walled Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    SONG Chen; XIA Yue-Yuan; ZHAO Ming-Wen; LIU Xiang-Dong; LI Ji-Ling; LI Li-Juan; LI Feng; HUANG Bo-Da

    2006-01-01

    @@ We perform ab initio calculations on the self-assembled base-functionalized single-walled carbon nanotubes (SWNTs) which exhibit the quasi-1D ‘ladder’ structure. The optimized configuration in the ab initio calculation is very similar to that obtainedfrom molecular dynamics simulation. We also calculate the electronic structures of the self-assembled base-functionalized SWNTs that exhibit distinct difference from the single-branch base-functionalized SWNT with a localized state lying just below the Fermi level, which may result from the coupling interaction between the bases accompanied by the self-assembly behaviour.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmi......An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin...

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

    Energy Technology Data Exchange (ETDEWEB)

    Ganster, P

    2004-10-15

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

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

    Science.gov (United States)

    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

  19. Quantum dynamics on a three-sheeted six-dimensional ab initio potential-energy surface of the phosphine cation: Simulation of the photoelectron spectrum and the ultrafast radiationless decay dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharyya, Swarnendu, E-mail: swarnendu.bhattacharyya@ch.tum.de; Domcke, Wolfgang, E-mail: wolfgang.domcke@ch.tum.de [Department of Chemistry, Technische Universität München, D-85748, Garching (Germany); Dai, Zuyang [Department of Physics and State Key Laboratory of Low-Dimensional Quantum Physics, Tsinghua University, Beijing 100084 (China)

    2015-11-21

    A diabatic three-sheeted six-dimensional potential-energy surface has been constructed for the ground state and the lowest excited state of the PH{sub 3}{sup +} cation. Coupling terms of Jahn-Teller and pseudo-Jahn-Teller origin up to eighth order had to be included to describe the pronounced anharmonicity of the surface due to multiple conical intersections. The parameters of the diabatic Hamiltonian have been optimized by fitting the eigenvalues of the potential-energy matrix to ab initio data calculated at the CASSCF/MRCI level employing the correlation-consistent triple-ζ basis. The theoretical photoelectron spectrum of phosphine and the non-adiabatic nuclear dynamics of the phosphine cation have been computed by propagating nuclear wave packets with the multiconfiguration time-dependent Hartree method. The theoretical photoelectron bands obtained by Fourier transformation of the autocorrelation function agree well with the experimental results. It is shown that the ultrafast non-radiative decay dynamics of the first excited state of PH{sub 3}{sup +} is dominated by the exceptionally strong Jahn-Teller coupling of the asymmetric bending vibrational mode together with a hyperline of conical intersections with the electronic ground state induced by the umbrella mode. Time-dependent population probabilities have been computed for the three adiabatic electronic states. The non-adiabatic Jahn-Teller dynamics within the excited state takes place within ≈5 fs. Almost 80% of the excited-state population decay to the ground state within about 10 fs. The wave packets become highly complex and delocalized after 20 fs and no further significant transfer of electronic population seems to occur up to 100 fs propagation time.

  20. Molecular tailoring approach: a route for ab initio treatment of large clusters.

    Science.gov (United States)

    Sahu, Nityananda; Gadre, Shridhar R

    2014-09-16

    Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large

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

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl. A.

    1999-01-01

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

  2. Ab initio study of Mg(AlH4)2

    NARCIS (Netherlands)

    Setten, van M.J.; Wijs, de G.A.; Popa, V.A.; Brocks, G.

    2005-01-01

    Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation (G

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

    DEFF Research Database (Denmark)

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

    2005-01-01

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

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

    NARCIS (Netherlands)

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

    2003-01-01

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

  5. Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc

    NARCIS (Netherlands)

    Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy

    2009-01-01

    The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation energi

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

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

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

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear...... response to small longitudinal and bending deformations and their failure limits for longitudinal compression and elongation....

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  9. An ab initio Valence Bond Study on Cyclopenta-Fused Naphthalenes and Fluoranthenes

    NARCIS (Netherlands)

    Havenith, R.W.A.; van Lenthe, J.H.; Jenneskens, L.W.

    2005-01-01

    To probe the effect of external cyclopenta-fusion on a naphthalene core, ab initio valence bond (VB) calculations have been performed, using strictly atomic benzene p-orbitals and p-orbitals that are allowed to delocalize, on naphthalene (1), acenaphthylene (2), pyracylene (3), cyclopenta[b,c]-acena

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

    Science.gov (United States)

    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.

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

    DEFF Research Database (Denmark)

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

    2012-01-01

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

  12. Ab Initio Investigations of the C2F4S Isomers and of Their Interconversions

    DEFF Research Database (Denmark)

    Shim, Irene; Vallano-Lorenzo, Sandra; Lisbona-Martin, Pilar

    2003-01-01

    The transition states and the activation energies for the unobserved isomerization reactions between the three possible C2F4S isomers with divalent sulfur, trifluorothioacetyl fluoride 1, tetrafluorothiirane 2, and trifluoroethenesulfenyl fluoride 3, have been determined by ab initio Hartree-Fock...

  13. Ab initio calculations on the structure of pyridine in its lowest triplet state

    NARCIS (Netherlands)

    Buma, W.J.; Groenen, E.J.J.; Schmidt, J.

    1990-01-01

    Recently we have experimentally shown that pyridine-d5, as a guest in a single crystal of benzene-d6, adopts a boatlike structure upon excitation into the lowest triplet state T0. Here MRDCI ab initio calculations are presented that reveal that the observed nonplanarity of the molecule is not caused

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

    Science.gov (United States)

    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.

  15. The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study

    Energy Technology Data Exchange (ETDEWEB)

    Perron, A., E-mail: perron1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Turchi, P.E.A.; Landa, A.; Söderlind, P. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Ravat, B.; Oudot, B.; Delaunay, F. [CEA-Centre de Valduc, 21120 Is sur Tille (France)

    2015-03-15

    Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.

  16. Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)

    Science.gov (United States)

    Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang

    2001-01-01

    Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.

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

    Science.gov (United States)

    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.

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported...

  19. New ab initio based pair potential for accurate simulation of phase transitions in ZnO

    NARCIS (Netherlands)

    Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H

    2014-01-01

    A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8)

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    . The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...

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

    NARCIS (Netherlands)

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

    2006-01-01

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

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

    Science.gov (United States)

    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).

  3. Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics

    Science.gov (United States)

    Marcolongo, Aris; Umari, Paolo; Baroni, Stefano

    2014-03-01

    The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.

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

    Science.gov (United States)

    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.

  5. Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.

    Science.gov (United States)

    Küçük, Sami Emre; Biktagirov, Timur; Sezer, Deniz

    2015-10-14

    A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone.

  6. Silicon and Germanium Nanostructures for Photovoltaic Applications: Ab-Initio Results

    Directory of Open Access Journals (Sweden)

    Pulci Olivia

    2010-01-01

    Full Text Available Abstract Actually, most of the electric energy is being produced by fossil fuels and great is the search for viable alternatives. The most appealing and promising technology is photovoltaics. It will become truly mainstream when its cost will be comparable to other energy sources. One way is to significantly enhance device efficiencies, for example by increasing the number of band gaps in multijunction solar cells or by favoring charge separation in the devices. This can be done by using cells based on nanostructured semiconductors. In this paper, we will present ab-initio results of the structural, electronic and optical properties of (1 silicon and germanium nanoparticles embedded in wide band gap materials and (2 mixed silicon-germanium nanowires. We show that theory can help in understanding the microscopic processes important for devices performances. In particular, we calculated for embedded Si and Ge nanoparticles the dependence of the absorption threshold on size and oxidation, the role of crystallinity and, in some cases, the recombination rates, and we demonstrated that in the case of mixed nanowires, those with a clear interface between Si and Ge show not only a reduced quantum confinement effect but display also a natural geometrical separation between electron and hole.

  7. Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study.

    Science.gov (United States)

    Brovarets', Ol'ha O; Yurenko, Yevgen P; Dubey, Igor Ya; Hovorun, Dmytro M

    2012-01-01

    Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (ϵ ∼ 4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.

  8. Ab Initio Excited States from the In-Medium Similarity Renormalization Group

    CERN Document Server

    Parzuchowski, N M; Bogner, S K

    2016-01-01

    We present two new methods for performing \\emph{ab initio} calculations of excited states for closed-shell systems within the in-medium similarity renormalization group (IMSRG) framework. Both are based on combining the IMSRG with simple many-body methods commonly used to target excited states, such as the Tamm-Dancoff approximation (TDA) and equations-of-motion (EOM) techniques. In the first approach, a two-step sequential IMSRG transformation is used to drive the Hamiltonian to a form where a simple TDA calculation (i.e., diagonalization in the space of $1$p$1$h excitations) becomes exact for a subset of eigenvalues. In the second approach, equations-of-motion (EOM) techniques are applied to the ground-state-decoupled IMSRG Hamiltonian to access excited states. We perform proof-of-principle calculations for parabolic quantum dots in two-dimensions and the closed shell nuclei $^{16}$O and $^{22}$O. We find that the TDA-IMSRG approach gives better accuracy than the EOM-IMSRG when calculations converge, but is...

  9. Matching a surface complexation model with ab initio molecular dynamics: montmorillonite case

    Energy Technology Data Exchange (ETDEWEB)

    Kulik, D.A.; Churakov, S.V. [Paul Scherrer Institute, Nuclear Energy and Safety Dpt., Lab. for Waste Management, CH-5232 Villigen PSI (Switzerland)

    2005-07-01

    Speciation modelling of sorption on mineral-water interfaces is performed with help of surface complexation models (SCM), suitable for diluted suspensions that seem to reach adsorption equilibrium within laboratory times. Electrostatic SCMs need several input parameters even for a relatively simple oxide mineral surface. Moreover, the electrolyte ion adsorption constants in triple layer (TL) or basic Stern (BS) models depend on the inner layer capacitance density Cl, but clear physical understanding of this parameter is missing so far. SCMs can fit acidimetric or metal titration data well at quite different combinations of input parameters, and this fact casts doubt on any interpretation of fitted parameter values in terms of microscopic physicochemical mechanisms. The problem is even deeper in SCMs for clay minerals like montmorillonite having at least two surface types: the edges exposing different (aluminol and silanol) functional groups, and the basal siloxane planes with permanent charge and ion exchange. A feasible way to overcome the caveat of SCMs is seen nowadays in relying on crystallographic data and ab initio calculations to restrict the EDL setup, species stoichiometries, and input parameter values when constructing the adsorption model. The aim of this contribution is to discuss how recent advances in sample surface characterization an d in quantum-chemistry calculations for pyrophyllite can help in putting together a multi-site-surface electrostatic SCM for montmorillonite implemented in GEM approach. The quality of macroscopic model fits is checked against the titration data. (authors)

  10. Ab initio carbon capture in open-site metal-organic frameworks.

    Science.gov (United States)

    Dzubak, Allison L; Lin, Li-Chiang; Kim, Jihan; Swisher, Joseph A; Poloni, Roberta; Maximoff, Sergey N; Smit, Berend; Gagliardi, Laura

    2012-10-01

    During the formation of metal-organic frameworks (MOFs), metal centres can coordinate with the intended organic linkers, but also with solvent molecules. In this case, subsequent activation by removal of the solvent molecules creates unsaturated 'open' metal sites known to have a strong affinity for CO(2) molecules, but their interactions are still poorly understood. Common force fields typically underestimate by as much as two orders of magnitude the adsorption of CO(2) in open-site Mg-MOF-74, which has emerged as a promising MOF for CO(2) capture. Here we present a systematic procedure to generate force fields using high-level quantum chemical calculations. Monte Carlo simulations based on an ab initio force field generated for CO(2) in Mg-MOF-74 shed some light on the interpretation of thermodynamic data from flue gas in this material. The force field describes accurately the chemistry of the open metal sites, and is transferable to other structures. This approach may serve in molecular simulations in general and in the study of fluid-solid interactions.

  11. Ab initio modeling of the optical properties in organometallic halide perovskites for photovoltaic applications

    Science.gov (United States)

    Neukirch, Amanda; Nei, Wanyi; Pedesseau, Laurent; Even, Jacky; Katan, Claudine; Mohite, Aditya; Tretiak, Segrei

    2015-03-01

    The need for an inexpensive, clean, and plentiful source of energy has generated large amounts of research in an assortment of solution processed organic and hybrid organic-inorganic solar cells. A relative newcomer to the field of solution processed photovoltaics is the lead halide perovskite solar cell. In the past 5 years, the efficiencies of devices made from this material have increased from 3.5% to nearly 20%. Despite the rapid development of organic-inorganic perovskite solar cells, a thorough understanding of the fundamental photophysical processes driving the high performance of these devices is not well understood. I am using state-of-the-art ab initio computational techniques in order to characterize the properties at the interface of perovskite devices in order to aide in materials design and device engineering. I will present an in-depth analysis of the electronic and optical properties of bulk and surface states of pure and mixed halide systems. The high-level static quantum mechanical calculations, including spin-orbit-coupling and the many body GW approach, identify the key electronic states involved in photoinduced dynamics. This knowledge provides important information on how the optical properties change with variations to the system. Supported by the DOE, the LANL LDRD program XW11, and CNLS.

  12. Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH4+⋯BeH2

    Science.gov (United States)

    Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori

    2005-07-01

    An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as N δ- H δ+ ⋯H δ- Be δ+ involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of H δ+ and H δ- are decreased and the dihydrogen H δ+ ⋯H δ- bond length is expanded as the thermal and zero-point quantum effects.

  13. A Theoretical Study on a Reaction of Iron(III) Hydroxide with Boron Trichloride by Ab Initio Calculation

    CERN Document Server

    Ichikawa, Kazuhide; Fukushima, Akinori; Ishihara, Yoshio; Isaki, Ryuichiro; Takeguchi, Toshio; Tachibana, Akitomo; 10.1016/j.theochem.2009.08.026

    2009-01-01

    We investigate a reaction of boron trichloride (BCl3) with iron(III) hydroxide (Fe(OH)3) by ab initio quantum chemical calculation as a simple model for a reaction of iron impurities in BCl3 gas. We also examine a reaction with water. We find that compounds such as Fe(Cl)(OBCl2)2(OHBCl2) and Fe(Cl)2(OBCl2)(OHBCl2) are formed while producing HCl and reaction paths to them are revealed. We also analyze the stabilization mechanism of these paths using newly-developed interaction energy density derived from electronic stress tensor in the framework of the Regional DFT (Density Functional Theory) and Rigged QED (Quantum ElectroDynamics).

  14. Communication: ab initio simulations of hydrogen-bonded ferroelectrics: collective tunneling and the origin of geometrical isotope effects.

    Science.gov (United States)

    Wikfeldt, K T; Michaelides, A

    2014-01-28

    Ab initio simulations that account for nuclear quantum effects have been used to examine the order-disorder transition in squaric acid, a prototypical H-bonded antiferroelectric crystal. Our simulations reproduce the >100 K difference in transition temperature observed upon deuteration as well as the strong geometrical isotope effect observed on intermolecular separations within the crystal. We find that collective transfer of protons along the H-bonding chains - facilitated by quantum mechanical tunneling - is critical to the order-disorder transition and the geometrical isotope effect. This sheds light on the origin of isotope effects and the importance of tunneling in squaric acid which likely extends to other H-bonded ferroelectrics.

  15. An ab initio HCN/HNC rotational-vibrational line list and opacity function for astronomy

    Science.gov (United States)

    Harris, Gregory John

    HCN/HNC is an important molecule which is found throughout the universe. For example HCN/HNC is known to exist in comets, planetary atmospheres and the interstellar medium. HCN is also an important opacity source in carbon rich stars (C-stars). HCN masers have been observed in the circumstellar material around these C-stars and also in galaxies. Jorgensen and co-workers investigated model carbon star atmospheres in which they included HCN as an opacity source. They found that including a HCN opacity function had a remarkable effect: the atmosphere expanded by five times and the pressure of the atmosphere in the surface layers dropped by one or two orders of magnitude. This suggests that a full and detailed treatment of the rotational-vibrational spectrum of HCN/HNC could have a profound effect on the models of carbon stars, this provides the main motivation in this work. The temperatures of the stars in which HCN is an important opacity source Teff = 2000 - 3000 K. If HCN and HNC are in thermodynamic equilibrium it would be expected that HNC as well as HCN are found in significant populations. The transition dipoles of the fundamental bands of HNC are more than twice as strong as their HCN counter parts. These factors mean that both HCN and HNC will be considered, which makes a semiglobal treatment of the [H,C,N] system necessary. In this thesis an ab initio HCN/HNC linelist, from which accurate spectra and opacity functions can be calculated, is computed. Within this thesis I present least squares fits for ab initio semiglobal potential energy, dipole moment, relativistic correction and adiabatic correction surfaces. The potential energy surface (PES) is morphed for HNC geometries of the potential to improve the HNC representation of the surface. The PES and dipole moment surface (DMS) are used to perform quantum mechanical nuclear motion (rotational-vibrational) calculations with the DVR3D suite of codes. Preliminary calculations are made to optimise a ro

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

    Energy Technology Data Exchange (ETDEWEB)

    Dick, Alexey

    2008-04-14

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

  17. Relaxation of Small Molecules:an ab initio Study

    Institute of Scientific and Technical Information of China (English)

    CAOYi-Gang; A.Antons; 等

    2002-01-01

    Using an ab inito total energy and force method,we have relaxed several group IV and group V elemental clusters,in detail the arsenic and antimony dimers,silicon,phosphorus,arsenic and antimony tetraners,The obtained bond lengths and cohesive energies are more accurate than other calculating methods,and in excellent agreement with the experimental results.

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

    Science.gov (United States)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

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

  19. Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

    Science.gov (United States)

    Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

    2016-10-27

    Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

  20. Reduced dimensionality spin-orbit dynamics of CH3 + HCl ⇌ CH4 + Cl on ab initio surfaces.

    Science.gov (United States)

    Remmert, Sarah M; Banks, Simon T; Harvey, Jeremy N; Orr-Ewing, Andrew J; Clary, David C

    2011-05-28

    A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH(3) + HCl ⇌ CH(4) + Cl((2)P(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions.

  1. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)

    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.

  2. Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2009-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti......A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...

  3. Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    Hagen, G; Hjorth-Jensen, M; Papenbrock, T

    2016-01-01

    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$_{\\rm sat}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to $^{56}$Ni. We derive an efficient scheme for including continuum effects in coupled-clust...

  6. Interatomic potentials for Al and Ni from experimental data and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Mishin, Y.; Farkas, D.; Miehl, M.J.; Papaconstantopoulos, D.A.

    1999-07-01

    New embedded-atom potentials for Al and Ni have been developed by fitting to both experimental data and the results of ab initio calculations. The ab initio data were obtained in the form of energies of different alternative computer-generated crystalline structures of these metals. The potentials accurately reproduce basic equilibrium properties of Al and Ni such as the elastic constants, phonon dispersion curves, vacancy formation and migration energies, stacking fault energies, and surface energies. The equilibrium energies of various alternative structures not included in the fitting database are calculated with these potentials. The results are compared with predictions of total-energy tight-binding calculations for the same structures. The embedded-atom potentials correctly reproduce the structural stability trends, which suggests that they are transferable to different local environments encountered in atomistic simulations of lattice defects.

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

    Energy Technology Data Exchange (ETDEWEB)

    González, D. J.; González, L. E. [Departamento de Física Teórica, Atómica y Optica, Universidad de Valladolid, 47011 Valladolid (Spain)

    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.

  8. Electrical Resistivity of Na-K Binary Liquid Alloy Using Ab-Initio Pseudopotentials

    Institute of Scientific and Technical Information of China (English)

    Anil Thakur; P. K. Ahluwalia

    2005-01-01

    @@ The study of electrical resistivity of simple binary liquid alloy Na-K is presented as a function of concentration.Hard sphere diameters of sodium (Na) and potassium (K) are obtained through the inter ionic pair potentials evaluated using Troullier and Martins ab-initio pseudopotentials, which have been used to calculate partial structure factors S(q). The Ziman formula for calculating resistivity of binary liquid alloys has been used. Form factors are calculated using ab-initio pseudopotentials. The results suggest that the first principle approach for calculating pseudopotentials with in the frame work of Ziman formalism is quite successful in explaining the electrical resistivity data of compound forming binary liquid alloys.

  9. Bridging a gap between continuum-QCD and ab initio predictions of hadron observables

    Directory of Open Access Journals (Sweden)

    Daniele Binosi

    2015-03-01

    Full Text Available Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.

  10. [Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].

    Science.gov (United States)

    Wu, Jun

    2015-12-01

    Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.

  11. Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

    Science.gov (United States)

    Yang, Jianjun; Tse, John S

    2011-11-17

    The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.

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

    CERN Document Server

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

    2016-01-01

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

  13. Ab Initio Calculations for the BaTiO3 (001) Surface Structure

    Institute of Scientific and Technical Information of China (English)

    XUE Xu-Yan; WANG Chun-Lei; ZHONG Wei-Lie

    2004-01-01

    @@ The ab initio method within the local density approximation is applied to calculate cubic BaTiO3 (001) surface relaxation and rumpling for two different terminations (BaO and TiO2). Our calculations demonstrate that cubic perovskite BaTiO3 crystals possess surface polarization, accompanied by the presence of the relevant electric field.We analyse their electronic structures (band structure, density of states and the electronic density redistribution with emphasis on the covalency effects). The results are also compared with that of the previous ab initio calculations. Considerable increases of Ti-O chemical bond covalency nearby the surface have been observed.The band gap reduces especially for the TiO2 termination.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-17

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

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-31

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

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-03

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

  19. Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks

    CERN Document Server

    Morillon, B; Carbonell, J

    2013-01-01

    The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.

  20. Optical and other material properties of SiO2 from ab initio studies

    Science.gov (United States)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

    The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.

  1. Ab-initio electronic structure method for substitutional disorder applied to iron-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Herbig, Alexander

    2016-02-12

    An ab-initio electronic structure method for substitutionally disordered real materials is developed within a pseudopotential density functional theory approach. The method is validated against exact diagonalization and for simple disordered CuZn alloys. The developed method is applied to iron-based superconductors. In particular, band renormalization effects due to various chemical substitutions in BaFe{sub 2}As{sub 2} are investigated and their Cooper pair breaking effects are compared.

  2. Simulation of Ab Initio Molecular Dynamics of Shock Wave on Copper

    Institute of Scientific and Technical Information of China (English)

    张林; 蔡灵仓; 向士凯; 经福谦; 陈栋泉

    2003-01-01

    The relation between particle velocity Up, up to 4 km/s, and shock wave velocity Us in copper has been simulated with ab initio molecular dynamics. The simulated relationship without considering the correction of zero-point and finite temperature effects is Us = 4.23 + 1.53Up. After considering the correction the relation becomes Us = 4.08 + 1.53Up, which is consistent with the experimental result.

  3. Ab initio verification of the analytical R-matrix theory for strong field ionization

    Science.gov (United States)

    Torlina, Lisa; Morales, Felipe; Muller, H. G.; Smirnova, Olga

    2014-10-01

    We summarize the key aspects of the recently developed analytical R-matrix (ARM) theory for strong field ionization (Torlina and Smirnova 2012 Phys. Rev. A 86 043408; Kaushal and Smirnova 2013 Phys. Rev. A 88 013421), and present tests of this theory using ab initio numerical simulations for hydrogen and helium atoms in long circularly polarized laser pulses. We find excellent agreement between the predictions of ARM and the numerical calculations.

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

    DEFF Research Database (Denmark)

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

    2003-01-01

    Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...... as its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density....

  5. Ab Initio Study on the Anti-HIV Activities of Hydroxyflavones

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yu

    2005-01-01

    Flavone and 95 hydroxyflavones have been studied with ab initio method, and their total energies, atomic charges, dipole moments, multipole moments, molecular orbital compositions, orbital energies etc. were obtained. Among them the relationship between total atomic charges and activities against HIV is basically in accordance with the experimental results. The beneficial references are provided for the extraction and synthesis of strong active anti-HIV medicines.

  6. Projector augmented wave method: ab initio molecular dynamics with full wave functions

    Indian Academy of Sciences (India)

    Peter E Blöchl; Clemens J Först; Johannes Schimpl

    2003-01-01

    A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented wave methods and the pseudopotential approach. Without sacrificing efficiency, the PAW method avoids transferability problems of the pseudopotential approach and it has been valuable to predict properties that depend on the full wave functions.

  7. Ab initio molecular dynamics simulations of the Li4F4 cluster

    Science.gov (United States)

    Heidenreich, A.; Sauer, J.

    1995-12-01

    Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li4F4, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.

  8. First fully ab initio potential energy surface of methane with a spectroscopic accuracy

    Science.gov (United States)

    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.

  9. Lattice dynamics of wurtzite CdS: Neutron scattering and ab-initio calculations

    Science.gov (United States)

    Debernardi, A.; Pyka, N. M.; Göbel, A.; Ruf, T.; Lauck, R.; Kramp, S.; Cardona, M.

    1997-08-01

    We have measured the phonon dispersion of wurtzite CdS by inelastic neutron scattering in a single crystal made from the nonabsorbing isotope 114Cd. One of the two silent B 1-modes occurs at 3.96 THz ( k = 0 ). It is significantly lower and less dispersive than so far assumed. Previous semiempirical lattice dynamical models need to be reanalyzed. However, the observed dispersion branches compare favorably with an ab-initio calculation.

  10. Steady state Ab-initio Theory of Lasers with Injected Signals

    CERN Document Server

    Cerjan, Alexander

    2013-01-01

    We present an ab-initio treatment of steady-state lasing with injected signals that treats both multimode lasing and spatial hole burning, and describes the transition to injection locking or partial locking in the multimode case. The theory shows that spatial hole burning causes a shift in the frequency of free-running laser modes away from the injection frequency, in contrast to standard approaches.

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

    Science.gov (United States)

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

    2011-01-01

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

  12. Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

    Science.gov (United States)

    Yang, Lina; Minnich, Austin J

    2017-03-14

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

  13. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Hua Y., E-mail: huay.geng@gmail.com [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan, 621900 (China); Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853 (United States)

    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.

  14. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    Science.gov (United States)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  15. Ab initio nuclear structure and reactions with chiral three-body forces

    Energy Technology Data Exchange (ETDEWEB)

    Langhammer, Joachim; Roth, Robert; Calci, Angelo [Institut fuer Kernphysik - Theoriezentrum, TU Darmstadt (Germany); Navratil, Petr [TRIUMF, Vancouver (Canada)

    2014-07-01

    One major ambition of ab initio nuclear theory is the description of nuclear-structure and reaction observables on equal footing. This is accomplished by combining the no-core shell model (NCSM) with the resonating-group method (RGM) to a unified ab initio approach to bound and continuum states, which is developed further to the no-core shell model with continuum (NCSMC). We present the formal developments to include three-nucleon interactions in both the NCSM/RGM and NCSMC formalism. This provides the possibility to assess the predictive power of chiral two- and three-nucleon forces in the variety of scattering observables. We study three-nucleon force effects on phase-shifts, cross sections and analyzing powers in first ab-initio studies of nucleon-{sup 4}He scattering with chiral two- and three-nucleon forces. Finally, we focus on heavier target nuclei using the NCSMC, e.g., in neutron-{sup 8}Be scattering and study the impact of the continuum on the spectrum of {sup 9}Be.

  16. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    CERN Document Server

    Geng, Hua Y

    2014-01-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased 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 vibration...

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

    Science.gov (United States)

    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 studies on the spin-forbidden cooling transitions of the LiRb molecule.

    Science.gov (United States)

    You, Yang; Yang, Chuan-Lu; Zhang, Qing-Qing; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang

    2016-07-20

    The spin-forbidden cooling of the LiRb molecule is investigated based on ab initio quantum chemistry calculations. The multireference configuration interaction method is used to generate the potential energy curves (PECs) of the ground state X(1)Σ(+) and the low-lying excited states a(3)Σ(+), B(1)Π, and b(3)Π. The spin-orbit coupling effects for the PECs and the transition dipole moments (TDMs) between the X(1)Σ(+), b(3)Π and a(3)Σ(+) states are also calculated. The analytical functions for the PECs are deduced. The rovibrational energy levels, the spectroscopic parameters and the Franck-Condon factors (FCF) are determined by solving the Schrödinger equation of nuclear movement with the obtained analytical functions. The b(3)Π0 ↔ X(1)Σ(+) and b(3)Π1 ↔ X(1)Σ(+) transitions have highly diagonal distributed FCFs and non-zero TDMs, demonstrating that the LiRb molecule could be a very promising candidate for laser cooling. Therefore, a three-cycle laser cooling scheme for the molecule has been proposed based on these two spin-forbidden transitions. Using the radiative lifetime and linewidth calculated from the obtained TDM functions, we present further analysis of the cooling of LiRb and the corresponding KRb molecule. The transition b(3)Π0 ↔ X(1)Σ(+) is found to be a practical transition to cool the LiRb molecule, and a sub-microkelvin cool temperature could be reached for the KRb molecule using a similar laser cooling scheme.

  19. Thermodynamics and phonon dispersion of pyrope and grossular silicate garnets from ab initio simulations

    Science.gov (United States)

    Baima, Jacopo; Ferrabone, Matteo; Orlando, Roberto; Erba, Alessandro; Dovesi, Roberto

    2016-02-01

    The phonon dispersion and thermodynamic properties of pyrope ({Mg}_3{Al}_2{Si}_3{O}_{12}) and grossular ({Ca}_3{Al}_2{Si}_3{O}_{12} ) have been computed by using an ab initio quantum mechanical approach, an all-electron variational Gaussian-type basis set and the B3LYP hybrid functional, as implemented in the Crystal program. Dispersion effects in the phonon bands have been simulated by using supercells of increasing size, containing 80, 160, 320, 640, 1280 and 2160 atoms, corresponding to 1, 2, 4, 8, 16 and 27 {k} points in the first Brillouin zone. Phonon band structures, density of states and corresponding inelastic neutron scattering spectra are reported. Full convergence of the various thermodynamic properties, in particular entropy ( S) and specific heat at constant volume (CV), with the number of {k} points is achieved with 27 {k} points. The very regular behavior of the S( T) and CV(T) curves as a function of the number of {k} points, determined by high numerical stability of the code, permits extrapolation to an infinite number of {k} points. The limiting value differs from the 27-{k} case by only 0.40 % at 100 K for S (the difference decreasing to 0.11 % at 1000 K) and by 0.29 % (0.05 % at 1000 K) for CV. The agreement with the experimental data is rather satisfactory. We also address the problem of the relative entropy of pyrope and grossular, a still debated question. Our lattice dynamical calculations correctly describe the larger entropy of pyrope than grossular by taking into account merely vibrational contributions and without invoking "static disorder" of the Mg ions in dodecahedral sites. However, as the computed entropy difference is found to be larger than the experimental one by a factor of 2-3, present calculations cannot exclude possible thermally induced structural changes, which could lead to further conformational contributions to the entropy.

  20. SPASER as a complex system: femtosecond dynamics traced by ab-initio simulations

    KAUST Repository

    Gongora, J. S. Totero

    2016-03-14

    Integrating coherent light sources at the nanoscale with spasers is one of the most promising applications of plasmonics. A spaser is a nano-plasmonic counterpart of a laser, with photons replaced by surface plasmon polaritons and the resonant cavity replaced by a nanoparticle supporting localized plasmonic modes. Despite the large body of experimental and theoretical studies, the understanding of the fundamental properties of the spaser emission is still challenging. In this work, we investigated the ultrafast dynamics of the emission from a core-shell spaser by developing a rigorous first-principle numerical model. Our results show that the spaser is a highly nonlinear system with many interacting degrees of freedom, whose emission sustain a rich manifold of different spatial phases. In the regime of strong interaction we observed that the spaser emission manifests an irreversible ergodic evolution, where energy is equally shared among all the available degrees of freedom. Under this condition, the spaser generates ultrafast vortex lasing modes that are spinning on the femtosecond scale, acquiring the character of a nanoparticle with an effective spin. Interestingly, the spin orientation is defined by spontaneous symmetry breaking induced by quantum noise, which is a fundamental component of our ab-initio model. This opens up interesting possibilities of achieving unidirectional emission from a perfectly spherical nanoparticle, stimulating a broad range of applications for nano-plasmonic lasers as unidirectional couplers, random information sources and novel form of photonics neural-networks. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  1. Clathrate formation and dissociation in vapor/water/ice/hydrate systems in SBA-15, sol-gel and CPG porous media, as probed by NMR relaxation, novel protocol NMR cryoporometry, neutron scattering and ab initio quantum-mechanical molecular dynamics simulation.

    Science.gov (United States)

    Webber, J Beau W; Anderson, Ross; Strange, John H; Tohidi, Bahman

    2007-05-01

    The Gibbs-Thomson effect modifies the pressure and temperature at which clathrates occur, hence altering the depth at which they occur in the seabed. Nuclear magnetic resonance (NMR) measurements as a function of temperature are being conducted for water/ice/hydrate systems in a range of pore geometries, including templated SBA-15 silicas, controlled pore glasses and sol-gel silicas. Rotator-phase plastic ice is shown to be present in confined geometry, and bulk tetrahydrofuran hydrate is also shown to probably have a rotator phase. A novel NMR cryoporometry protocol, which probes both melting and freezing events while avoiding the usual problem of supercooling for the freezing event, has been developed. This enables a detailed probing of the system for a given pore size and geometry and the exploration of differences between hydrate formation and dissociation processes inside pores. These process differences have an important effect on the environment, as they impact on the ability of a marine hydrate system to re-form once warmed above a critical temperature. Ab initio quantum-mechanical molecular dynamics calculations are also being employed to probe the dynamics of liquids in pores at nanometric dimensions.

  2. Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.

    Science.gov (United States)

    Bacchus-Montabonel, Marie-Christine

    2014-08-21

    Modeling-induced radiation damage in biological systems, in particular, in DNA building blocks, is of major concern in cancer therapy studies. Ion-induced charge-transfer dynamics may indeed be involved in proton and hadrontherapy treatments. We have thus performed a theoretical approach of the charge-transfer dynamics in collision of C(4+) ions and protons with isolated 2-deoxy-D-ribose in a wide collision energy range by means of ab initio quantum chemistry molecular methods. The comparison of both projectile ions has been performed with regard to previous theoretical and experimental results. The charge transfer appears markedly less efficient with the 2-deoxy-D-ribose target than that with pyrimidine nucleobases, which would induce an enhancement of the fragmentation process in agreement with experimental measurements. The mechanism has been analyzed with regard to inner orbital excitations, and qualitative tendencies have been pointed out for studies on DNA buiding block damage.

  3. Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study.

    Science.gov (United States)

    Monteiro, Norberto K V; Firme, Caio L

    2014-03-06

    The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).

  4. Challenges in modelling homogeneous catalysis: new answers from ab initio molecular dynamics to the controversy over the Wacker process.

    Science.gov (United States)

    Stirling, András; Nair, Nisanth N; Lledós, Agustí; Ujaque, Gregori

    2014-07-21

    We present here a review of the mechanistic studies of the Wacker process stressing the long controversy about the key reaction steps. We give an overview of the previous experimental and theoretical studies on the topic. Then we describe the importance of the most recent Ab Initio Molecular Dynamics (AIMD) calculations in modelling organometallic reactivity in water. As a prototypical example of homogeneous catalytic reactions, the Wacker process poses serious challenges to modelling. The adequate description of the multiple role of the water solvent is very difficult by using static quantum chemical approaches including cluster and continuum solvent models. In contrast, such reaction systems are suitable for AIMD, and by combining with rare event sampling techniques, the method provides reaction mechanisms and the corresponding free energy profiles. The review also highlights how AIMD has helped to obtain a novel understanding of the mechanism and kinetics of the Wacker process.

  5. π-Hydrogen Bonding of Aromatics on the Surface of Aerosols: Insights from Ab Initio and Molecular Dynamics Simulation.

    Science.gov (United States)

    Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei

    2016-07-14

    Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics.

  6. Towards the realization of ab initio dynamics at the speed of molecular mechanics: simulations with interpolated diabatic Hamiltonian.

    Science.gov (United States)

    Park, Jae Woo; Rhee, Young Min

    2014-10-20

    Understanding photochemical processes often requires accurate descriptions of the nonadiabatic events involved. The cost of accurate quantum chemical simulations of the nonadiabatic dynamics of complex systems is typically high. Here, we discuss the use of interpolated quasi-diabatic potential-energy matrices, which aims to reduce the computational cost with minimal sacrifices in accuracy. It is shown that interpolation reproduces the reference ab initio information satisfactorily for a sizeable chromophore in terms of its adiabatic energies and derivative coupling vectors. Actual nonadiabatic simulation results of the chromophore in the gas phase and in aqueous solution are presented, and it is demonstrated that the interpolated quasi-diabatic Hamiltonian can be applied to studying nonadiabatic events of a complex system in an ensemble manner at a much-reduced cost. Limitations, and how they can be overcome in future studies, are also discussed.

  7. High pressure elastic properties of minerals from ab initio simulations: The case of pyrope, grossular and andradite silicate garnets

    Energy Technology Data Exchange (ETDEWEB)

    Erba, A., E-mail: alessandro.erba@unito.it; Mahmoud, A.; Dovesi, R. [Dipartimento di Chimica and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, IT-10125 Torino (Italy); Belmonte, D. [DISTAV, Università di Genova, Corso Europa 26, 16132 Genoa (Italy)

    2014-03-28

    A computational strategy is devised for the accurate ab initio simulation of elastic properties of crystalline materials under pressure. The proposed scheme, based on the evaluation of the analytical stress tensor and on the automated computation of pressure-dependent elastic stiffness constants, is implemented in the CRYSTAL solid state quantum-chemical program. Elastic constants and related properties (bulk, shear and Young moduli, directional seismic wave velocities, elastic anisotropy index, Poisson's ratio, etc.) can be computed for crystals of any space group of symmetry. We apply such a technique to the study of high-pressure elastic properties of three silicate garnet end-members (namely, pyrope, grossular, and andradite) which are of great geophysical interest, being among the most important rock-forming minerals. The reliability of this theoretical approach is proved by comparing with available experimental measurements. The description of high-pressure properties provided by several equations of state is also critically discussed.

  8. Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies

    Science.gov (United States)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

    Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.

  9. An ab initio potential energy surface and vibrational states of MgH2(1(1)A').

    Science.gov (United States)

    Li, Hui; Xie, Daiqian; Guo, Hua

    2004-09-01

    A three-dimensional global potential energy surface for the ground electronic state of MgH(2) is constructed from more than 3000 ab initio points calculated using the internally contracted multireference configuration interaction method with the Davidson correction at the complete basis set limit. Low-lying vibrational energy levels of MgH(2) and MgD(2) are calculated using the Lanczos algorithm, and found to be in good agreement with known experimental band origins. The majority of the vibrational energy levels up to 8000 cm(-1) are assigned with normal mode quantum numbers. However, our results indicate a gradual transition from a normal mode regime for the stretching vibrations at low energies to a local mode regime near 7400 cm(-1), as evidenced by a decreasing energy gap between the (n(1),0,0) and (n(1)-1,0,1) vibrational states and bifurcation of the corresponding wave functions.

  10. Ab initio and DFT Studies of Be(BH42

    Directory of Open Access Journals (Sweden)

    J. S. Al-Otaibi

    2016-03-01

    Full Text Available In this study, the Ab inito and DFT calculations of optimized geometries, energy and vibrational spectra for the Beryllium borohydride Be(BH42 at different levels are achieved by Hartre – Fock (HF, perturbation theory (MP2 and density functional theory (B3LYP methods. They utilize the 6-31G(d, 6-311G(d,p, 6-311+G(d,p and 6-311++G(d,p basis sets. The theoretical results showed that Beryllium borohydride with the D2d structure which contains two identical groups of double bridging hydrogen has the lowest energy at all levels. Consequently, this compound is considered as the most stable one and the results of IR and Raman Spectra at all levels support that. We found that both structures Cs, C3v have the structure of D2d kind at all levels. The values of bond lengths for these two structures are identical for the bond lengths to the structure D2d kind which confirms this theory.

  11. Ab Initio Calculations of X-ray Spectra : Atomic Multiplet and Molecular Orbital Effects in a Multiconfigurational SCF Approach to the L-Edge Spectra of Transition Metal Complexes

    NARCIS (Netherlands)

    Josefsson, Ida; Kunnus, Kristjan; Schreck, Simon; Foehlisch, Alexander; de Groot, Frank; Wernet, Philippe; Odelius, Michael

    2012-01-01

    A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra fo

  12. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. II. Photoionization

    Science.gov (United States)

    Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr

    2011-10-01

    We have applied ab initio based reflection principle to simulate photoelectron spectra of small water clusters, ranging from monomer to octamer. The role of quantum and thermal effects on the structure of the water photoelectron spectra is discussed within the ab initio path integral molecular dynamics (PIMD) framework. We have used the PIMD method with up to 40 beads to sample the ground state quantum distribution at temperature T = 180 K. We have thoroughly tested the performance of various density functionals (B3LYP, BHandHLYP, M06HF, BNL, LC-ωPBE, and CAM-B3LYP) for the ionization process description. The benchmarking based on a comparison of simulated photoelectron spectra to experimental data and high level equation-of-motion ionization potential coupled clusters with singles and doubles calculations has singled out the BHandHLYP and LC-ωPBE functionals as the most reliable ones for simulations of light induced processes in water. The good performance of the density functional theory functionals to model the water photoelectron spectra also reflects their ability to reliably describe open shell excited states. The width of the photoelectron spectrum converges quickly with the cluster size as it is controlled by specific interactions of local character. The peak position is, on the other hand, defined by long-range non-specific solvent effects; it therefore only slowly converges to the corresponding bulk value. We are able to reproduce the experimental valence photoelectron spectrum of liquid water within the combined model of the water octamer embedded in a polarizable dielectric continuum. We demonstrate that including the long-range polarization and the state-specific treatment of the solvent response are needed for a reliable liquid water ionization description.

  13. Bound state potential energy surface construction: ab initio zero-point energies and vibrationally averaged rotational constants.

    Science.gov (United States)

    Bettens, Ryan P A

    2003-01-15

    Collins' method of interpolating a potential energy surface (PES) from quantum chemical calculations for reactive systems (Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 102, 5647. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 8302. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 816) has been applied to a bound state problem. The interpolation method has been combined for the first time with quantum diffusion Monte Carlo calculations to obtain an accurate ground state zero-point energy, the vibrationally average rotational constants, and the vibrationally averaged internal coordinates. In particular, the system studied was fluoromethane using a composite method approximating the QCISD(T)/6-311++G(2df,2p) level of theory. The approach adopted in this work (a) is fully automated, (b) is fully ab initio, (c) includes all nine nuclear degrees of freedom, (d) requires no assumption of the functional form of the PES, (e) possesses the full symmetry of the system, (f) does not involve fitting any parameters of any kind, and (g) is generally applicable to any system amenable to quantum chemical calculations and Collins' interpolation method. The calculated zero-point energy agrees to within 0.2% of its current best estimate. A0 and B0 are within 0.9 and 0.3%, respectively, of experiment.

  14. Symmetry-general least-squares extraction of elastic data for strained materials from ab initio calculations of stress

    Science.gov (United States)

    Le Page, Yvon; Saxe, Paul

    2002-03-01

    A symmetry-general approach for the least-squares, therefore precise, extraction of elastic coefficients for strained materials is reported. It analyzes stresses calculated ab initio for properly selected strains. The problem, its implementation, and its solution strategy all differ radically from a previous energy-strain approach that we published last year, but the normal equations turn out to be amenable to the same constrainment scheme that makes both approaches symmetry general. The symmetry considerations governing the automated selection of appropriately strained models and their Cartesian systems are detailed. The extension to materials under general stress is discussed and implemented. VASP was used for ab initio calculation of stresses. A comprehensive range of examples includes a triclinic material (kyanite) and simple materials with a range of symmetries at zero pressure, MgO under hydrostatic pressure, Ti4As3 under [001] uniaxial strain, and Si under [001] uniaxial stress. The MgO case agrees with recent experimental work including elastic coefficients as well as their first and second derivatives. The curves of elastic coefficients for Si show a gradual increase in the 33 compliance coefficient, leading to a collapse of the material at -11.7 GPa, compared with -12.0 GPa experimentally. Interpretation of results for Be using two approximations [local density (LDA), generalized gradient (GGA)], two approaches (stress strain and energy strain), two potential types (projector augmented wave and ultrasoft), and two quantum engines (VASP and ORESTES) expose the utmost importance of the cell data used for the elastic calculations and the lesser importance of the other factors. For stiffness at relaxed cell data, differences are shown to originate mostly in the considerable overestimation of the residual compressive stresses at x-ray cell data by LDA, resulting in a smaller relaxed cell, thus larger values for diagonal stiffness coefficients. The symmetry

  15. Poly(aryl-ether-ether-ketone) as a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation

    Science.gov (United States)

    2014-12-01

    Poly(aryl-ether-ether-ketone) as a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio...Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation Janet Ho and Marco Olguin Sensors...a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation 5a. CONTRACT NUMBER 5b. GRANT

  16. Ab initio aqueous thermochemistry: application to the oxidation of hydroxylamine in nitric acid solution.

    Science.gov (United States)

    Ashcraft, Robert W; Raman, Sumathy; Green, William H

    2007-10-18

    Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are

  17. Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

    Science.gov (United States)

    Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

    2017-02-01

    The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

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

    Science.gov (United States)

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

    2014-06-01

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

  19. Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2007-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti......A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational...

  20. Atomic ionization of germanium by neutrinos from an ab initio approach

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiunn-Wei [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); National Center for Theoretical Sciences and Leung Center for Cosmology and Particle Astrophysics, National Taiwan University, Taipei 10617, Taiwan (China); Chi, Hsin-Chang [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Huang, Keh-Ning [Department of Physics, Sichuan University, Chengdu, Sichuan (China); Department of Physics, Fuzhou University, Fuzhou, Fujian (China); Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Liu, C.-P. [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Shiao, Hao-Tse [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Singh, Lakhwinder [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Department of Physics, Banaras Hindu University, Varanasi 221005 (India); Wong, Henry T. [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Wu, Chih-Liang; Wu, Chih-Pan [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)

    2014-04-04

    An ab initio calculation of atomic ionization of germanium by neutrinos was carried out in the framework of multiconfiguration relativistic random phase approximation and benchmarked by related atomic structure and photoabsorption data. This improves over the conventional approach based on scattering off free electrons whose validity at sub-keV energy transfer is questionable. Limits on neutrino magnetic moments are derived using reactor neutrino data taken with low threshold germanium detectors. Future applications of these atomic techniques will greatly reduce the atomic uncertainties in low-energy neutrino and dark matter detections.

  1. Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale.

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-19

    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.

  2. Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones

    Science.gov (United States)

    Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng

    2004-04-01

    A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.

  3. Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ailin; Yan, Tianying; Shen, Panwen [Department of Material Chemistry, Institute of New Energy Material Chemistry, Nankai University, Tianjin, 300071 (China)

    2011-02-01

    Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer. (author)

  4. Relativistic k .p Hamiltonians for centrosymmetric topological insulators from ab initio wave functions

    Science.gov (United States)

    Nechaev, I. A.; Krasovskii, E. E.

    2016-11-01

    We present a method to microscopically derive a small-size k .p Hamiltonian in a Hilbert space spanned by physically chosen ab initio spinor wave functions. Without imposing any complementary symmetry constraints, our formalism equally treats three- and two-dimensional systems and simultaneously yields the Hamiltonian parameters and the true Z2 topological invariant. We consider bulk crystals and thin films of Bi2Se3 , Bi2Te3 , and Sb2Te3 . It turns out that the effective continuous k .p models with open boundary conditions often incorrectly predict the topological character of thin films.

  5. The effects of magnetic annealing of transition metal alloys deduced from ab initio electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Razee, S.S.A.; Staunton, J.B. [Department of Physics, University of Warwick, Coventry (United Kingdom); Ginatempo, B.; Bruno, E. [Dipartimento di Fisica and Unita INFM, Universita di Messina, Messina (Italy); Pinski, F.J. [Department of Physics, University of Cincinnati, OH (United States)

    2001-09-24

    A theory is presented for describing the effects of annealing magnetic alloys in magnetic fields. It has an ab initio spin-polarized relativistic Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) electronic structure basis and uses the framework of concentration waves. Alloys which would otherwise be soft magnets are found experimentally to develop directional chemical order and significant uniaxial anisotropy when annealed in magnetic fields. Our approach is able to provide a quantitative description of these effects together with the underlying electronic mechanisms. We describe applications to the soft magnetic alloys permalloy and FeCo. (author)

  6. Communication: GAIMS—Generalized Ab Initio Multiple Spawning for both internal conversion and intersystem crossing processes

    Science.gov (United States)

    Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; González, Leticia; Martínez, Todd J.

    2016-03-01

    Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.

  7. Ab initio study of the EFG at the N sites in imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Brown Goncalves, Marcos, E-mail: browngon@if.usp.br [Universidade de Sao Paulo, Instituto de Fisica (Brazil); Di Felice, R. [National Center on Nanostructures and Biosystems at Surfaces (S3) of INFM-CNR (Italy); Poleshchuk, O. Kh. [Tomsk State Pedagogical University (Russian Federation); Petrilli, H. M. [Universidade de Sao Paulo, Instituto de Fisica (Brazil)

    2008-01-15

    We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-03-16

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

  9. Ab initio studies on the mechanic and magnetic properties of PdHx

    Institute of Scientific and Technical Information of China (English)

    Cui Xin; Liang Xi-Xia; Wang Jian-Tao; Zhao Guo-Zhong

    2011-01-01

    Based on ab initio total energy calculations, the structural, electronic, mechanic, and magnetic properties of PdHx are investigated. It is found that bulk modulus of PdHx is larger than the metal Pd with the hydrogen storage except Pd4H2. The calculated results for the magnetic moments show that the hydrogen addition weakens the magnetic properties of the PdHx systems. A strong magneto-volume effect is found in PdHx structures as well as Pd. The transition from paramagnetism to ferromagnetism is discussed. The corresponding densities of states for both structures are also shown to understand the magnetic behaviour.

  10. Ab-initio simulation of photoinduced transformation of small rings in amorphous silica

    OpenAIRE

    Bernasconi, D. Donadio M.

    2004-01-01

    We have studied the photoinduced transformation of small rings (3-membered) in amorphous silica by Car-Parrinello simulations. The process of ring opening leading to the formation of a couple of paramagnetic centers, namely an E' and a non-bridging-oxygen hole center (NBOHC), has been proposed experimentally to occur in silica exposed to F2 laser irradiation (at 7.9 eV). By using a new scheme for the simulation of rare events in ab-initio molecular dynamics (Iannuzzi, Laio and Parrinello, Phy...

  11. Ab initio MO study of reaction mechanism for carbonyl migration of Co complex

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Ab initio method under the effective core potential (ECP) approximation is employed to study the reaction mechanism of carbonyl migration of the cycle of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3 at Hartree-Fock (HF) level. The structures of the reactant, transition state and product for the reaction are determined. The energy of each stationary point is corrected at MP2/LAN2DZ//LANL2DZ+ZPE (zero-point energy) level. The calculated activation barrier is 28.89 kJ/mol.

  12. Ab initio study of the epitaxial growth of Ge on Si(100) surface

    Energy Technology Data Exchange (ETDEWEB)

    Milman, V.; Pennycook, S.J.; Jesson, D.E. [Oak Ridge National Lab., TN (United States); Payne, M.C.; Stich, I. [Cambridge Univ. (United Kingdom). Dept. of Physics

    1993-11-01

    We identify the binding sites for adsorption of a single Ge atom on the Si(100) surface using ab initio total energy calculations. The calculated diffusion barriers are in excellent agreement with experimental estimates. Using a large supercell we resolve the controversy regarding the binding geometry and migration path for the adatom, and investigate the influence of the adatom on the buckling of Si dimers. The adatom induces a buckling defect that is frequently observed using scanning tunneling microscopy (STM); therefore the study of single adatoms may be experimentally accessible.

  13. Ab initio research on DNA base alkylation by the β-position metabolite of methylethylnitrosamine

    Institute of Scientific and Technical Information of China (English)

    ZHAO Lijiao; ZHONG Rugang; YUAN Xiaolong; CUI Yasong; DAI Qianhuan

    2004-01-01

    Ab initio calculation is carried out to study the different supposed mechanisms of DNA base alkylation by β-sulphate-nitrosamines at RHF/6-31G(d) and MP2/6-31G(d)levels. Full geometric structure optimization is done for all reactants, intermediates, products and transition states. The activation energy and IRC are obtained. The results show that the anchimeric assistant effect promotes the alkylation of DNA base by β-sulphate-nitrosamines. Solvent calculation is carried out with Onsager model of SCRF method at the same level. The results indicate that the activation energy is decreased obviously in water.

  14. Binding of oxygen with titanium dioxide on singlet potential energy surface: An ab initio investigation

    Science.gov (United States)

    Bogdanchikov, Georgii A.; Baklanov, Alexey V.

    2017-01-01

    Ab initio calculations have been carried out to investigate interaction of titanium dioxide TiO2 with oxygen O2 in ground triplet and excited singlet states. On a singlet potential energy surface (PES) formation of a stable compound of titanium peroxide TiO4 is revealed which should appear in reaction of TiO2 with singlet oxygen without activation barrier. This peroxide is lower in energy than the ground state of two individual molecules TiO2 + 3O2 by 34.6 kcal/mol. Location of conical intersection between triplet and singlet PESs of TiO2sbnd O2 is also investigated.

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

    Science.gov (United States)

    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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay...... replaced by ‘‘hydrogen atoms’’ having mass 15 and TRPES spectra were calculated. These showed an induction time of (108 10) fs which could directly be assigned to progress along a torsional mode leading to the intersection seam with the molecular ground state. In a stepladder-type approach, the close...

  17. Ab initio many-body calculations of the 4He photo-absorption cross section

    CERN Document Server

    Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr

    2013-01-01

    A major goal of nuclear theory is to make quantitative calculations of low-energy nuclear observables starting from microscopic internucleon forces. Computationally, this is complicated by the large model spaces needed to reach convergence in many-body approaches, such as the no-core shell model (NCSM). In recent years, the similarity renormalization group (SRG) has provided a powerful and versatile means to soften interactions for ab initio structure calculations, thus leading to convergence within smaller model spaces. Here we compute the 4He total photo absorption cross section and study, for the first time, the consistency of the SRG approach in a continuum observable.

  18. Ab initio studies of ionization potentials of hydrated hydroxide and hydronium

    CERN Document Server

    Swartz, Charles W

    2013-01-01

    The ionization potential distributions of hydrated hydroxide and hydronium are computed with many-body approach for electron excitations with configurations generated by {\\it ab initio} molecular dynamics. The experimental features are well reproduced and found to be closely related to the molecular excitations. In the stable configurations, the ionization potential is mainly perturbed by water molecules within the first solvation shell. On the other hand, electron excitation is delocalized on both proton receiving and donating complex during proton transfer, which shifts the excitation energies and broadens the spectra for both hydrated ions.

  19. Carbon dioxide capture in 2-aminoethanol aqueous solution from ab initio molecular dynamics simulations

    Science.gov (United States)

    Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš

    2017-03-01

    The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.

  20. Ab initio calculation of the spectrum and structure of $^{16}$O

    CERN Document Server

    Epelbaum, Evgeny; Lähde, Timo A; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam

    2013-01-01

    We present ab initio lattice calculations of the low-energy even-parity states of $^{16}$O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.

  1. Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations

    Science.gov (United States)

    Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.

    2008-01-01

    The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.

  2. Charge carrier motion in disordered conjugated polymers: a multiscale ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    Vukmirovic, Nenad; Wang, Lin-Wang

    2009-11-10

    We developed an ab-initio multiscale method for simulation of carrier transport in large disordered systems, based on direct calculation of electronic states and electron-phonon coupling constants. It enabled us to obtain the never seen before rich microscopic details of carrier motion in conjugated polymers, which led us to question several assumptions of phenomenological models, widely used in such systems. The macroscopic mobility of disordered poly(3- hexylthiophene) (P3HT) polymer, extracted from our simulation, is in agreement with experimental results from the literature.

  3. Ab-initio density functional theory study of a WO3 NH3-sensing mechanism

    Institute of Scientific and Technical Information of China (English)

    Hu Ming; Zhang Jie; Wang Wei-Dan; Qin Yu-Xiang

    2011-01-01

    WO3 bulk and various surfaces are studied by an ab-initio density functional theory technique.The band structures and electronic density states of WO3 bulk are investigated.The surface energies of different WO3 surfaces are compared and then the(002)surface with minimum energy is computed for its NH3 sensing mechanism which explains the results in the experiments.Three adsorption sites are considered.According to the comparisons of the energy and the charge change between before and after adsorption in the optimal adsorption site O1c,the NH3 sensing mechanism is obtained.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance....... The presence of the adsorbate causes scattering of electrons of mainly one spin type. The scattering is shown to be due to a coupling of the two armchair band states to the metal 3d orbitals with matching symmetry, giving rise to Fano antiresonances appearing as dips in the transmission function. The spin type...

  5. Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

    Science.gov (United States)

    Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki

    2012-09-01

    Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.

  6. Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data

    CERN Document Server

    White, Andrew D; Hocky, Glen M; Voth, Gregory A

    2016-01-01

    Accounting for electrons and nuclei simultaneously is a key goal of computer simulation via ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce the properties of systems such as water due to inaccuracies in the underlying electronic density functionals, shortcomings that are often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy-based approach to directly incorporate limited experimental data via a minimal bias. The biased AIMD simulations of both water and of an excess proton in water are shown to give significantly improved properties for both the biased and unbiased observables.

  7. Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations

    Institute of Scientific and Technical Information of China (English)

    LIAO Long-Zhong; LIU Zheng-Hui; ZHANG Zhao-Hui

    2008-01-01

    Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms.

  8. Ab initio adiabatic and quasidiabatic potential energy surfaces of H++ CN system

    Indian Academy of Sciences (India)

    Bhargava Anusuri; Sanjay Kumar

    2016-02-01

    We present restricted geometry (collinear and perpendicular approaches of proton) ab initio three dimensional potential energy surfaces for H++ CN system. The calculations were performed at the internally contracted multi-reference configuration interaction level of theory using Dunning’s correlation consistent polarized valence triple zeta basis set. Adiabatic and quasidiabatic surfaces have been computed for the ground and the first excited electronic states. Nonadiabatic effects arising from radial coupling have been analyzed in terms of nonadiabatic coupling matrix elements and coupling potentials.

  9. Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution from Ab Initio Potential and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    S. Tolosa

    2013-01-01

    Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

  10. Prediction of adsorption of small molecules in porous materials based on ab initio force field method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Computational prediction of adsorption of small molecules in porous materials has great impact on the basic and applied research in chemical engineering and material sciences. In this work,we report an approach based on grand canonical ensemble Monte Carlo(GCMC) simulations and ab initio force fields. We calculated the adsorption curves of ammonia in ZSM-5 zeolite and hydrogen in MOF-5(a metal-organic-framework material). The predictions agree well with experimental data. Because the predictions are based on the first principle force fields,this approach can be used for the adsorption prediction of new molecules or materials without experimental data as guidance.

  11. Assessing the Thermoelectric Properties of Sintered Compounds via High-Throughput Ab-Initio Calculations

    Science.gov (United States)

    Wang, Shidong; Wang, Zhao; Setyawan, Wahyu; Mingo, Natalio; Curtarolo, Stefano

    2011-10-01

    Several thousand compounds from the Inorganic Crystal Structure Database have been considered as nanograined, sintered-powder thermoelectrics with the high-throughput ab-initio AFLOW framework. Regression analysis unveils that the power factor is positively correlated with both the electronic band gap and the carrier effective mass, and that the probability of having large thermoelectric power factors increases with the increasing number of atoms per primitive cell. Avenues for further investigation are revealed by this work. These avenues include the role of experimental and theoretical databases in the development of novel materials.

  12. Ab Initio MO Studies on the Reaction Mechanism for Carbonyl Insertion Catalyzed by Carbonyl Cobalt Complex

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Ab initio method, under the effective core potential(ECP) approximation at HF/LANL2DZ level, has been employed to study the reaction mechanism of the carbonyl insertion of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3. The two reaction paths have been discussed. The calculated potential energy barriers for the carbonyl migration and the ethyl group migration are 105.0 kJ/mol and 39.17 kJ/mol, respectively. The results indicate that the reaction path via ethyl migration is more energetically favorable than that via carbonyl insertion.

  13. Trivacancy in silicon: A combined DLTS and ab-initio modeling study

    Science.gov (United States)

    Markevich, V. P.; Peaker, A. R.; Lastovskii, S. B.; Murin, L. I.; Coutinho, J.; Markevich, A. V.; Torres, V. J. B.; Briddon, P. R.; Dobaczewski, L.; Monakhov, E. V.; Svensson, B. G.

    2009-12-01

    Deep level transient spectroscopy and ab-initio modeling have been used for identification of energy levels and structure of trivacancy (V3) in Si. It is found that in the neutral charge state the V3 is bistable, with the "fourfold" configuration being lower in energy than the (1 1 0) planar configuration. V3 in the (1 1 0) planar configuration gives rise to two acceptor levels at Ec-0.36 eV and Ec-0.46 eV in the gap, while in the "fourfold" configuration the defect has trigonal symmetry and an acceptor level at Ec-0.075 eV.

  14. Ab Initio Calculations of Elastic Constants of Li2O under Pressure

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-Feng; CHEN Xiang-Rong; JI Guang-Fu; MENG Chuan-Min

    2006-01-01

    @@ We investigate the equilibrium lattice constant, bulk modulus, elastic constants and Debye temperature of Li2 O under pressure by using ab initio unrestricted Hartree-Fock (HF) linear combination of atomic orbital (LCAO) periodic approach. The obtained results at zero pressure are well consistent with the available experimental data and other theoretical results. It is found that the elastic constants C11, C12 and C44 and bulk modulus B increase monotonously as pressure increases. Also, the anisotropy will weaken and the Debye temperature will rise with pressure increasing.

  15. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    Science.gov (United States)

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  16. Determinação da estrutura molecular do ciclooctano por métodos ab initio e difração de elétrons na fase gasosa Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    Directory of Open Access Journals (Sweden)

    Wagner B. De Almeida

    2000-10-01

    Full Text Available The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase and ab initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions.

  17. Ab initio intermolecular potential energy surface of He-LiH

    Institute of Scientific and Technical Information of China (English)

    鄢国森; 杨明晖; 谢代前

    1997-01-01

    The intermolecular potential energy surface of He-LiH complex was studied using the full-electronic complete forth-order Miller-Plesset perturbation (MPPT) method.In ab initio calculations,the bond length of LiH was fixed at 0 159 5 nm.The potential has two local minima of Vm=-179.93 cm for the linear He LiH geormetrv at Rm=0.227 nm and Vm=-10.44 cm-1 for the linear He-HL1 geometry at Rm=0.516 nm The potemal exhibits strong anisotropy The analytic potential function with 31 parameters was determined by fitting to the calculated ab,mtio potentials The influence of variation of LiH bond length on the potential energy surface was also studied

  18. Ab initio MO calculations on the Structure and Raman and Infrared Spectra of the [Al4O2Cl10]2- oxide species in chloroaluminate melts

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2007-01-01

    optimization convergence criteria and by using the modified GDIIS algorithm, the model calculations generally converged. The structures and their binding energies are presented. The expected geometries are supported, with one exception perhaps being the [Al2OCl6]2- ion, that gave a linear Al-O-Al bonding......), without any empiric adjustments of the harmonic force constants, using constants directly predicted from the Gaussian 03W program. Previously obtained IR absorption and Raman scattering spectra of melts are assigned, by comparing to the ab initio quantum mechanical vibrational analysis results...

  19. Comparison of ab initio molecular properties of EDO-TTF with the properties of the (EDO-TTF) 2PF 6 crystal

    Science.gov (United States)

    Linker, Gerrit-Jan; Loosdrecht, Paul H. M. van; Duijnen, Piet van; Broer, Ria

    2010-03-01

    We performed ab initio quantum chemical calculations for the geometrical and electronic structure of the EDO-TTF (ethylenedioxy-tetrathiafulvalene) molecule using HF, CASSCF and DFT methods. We compare these in vacuo results with the properties of the (EDO-TTF) 2PF 6 crystal at near room temperature. We demonstrate that, by bending and charging the molecule in vacuum, the deformation that is thought to be the origin of charge ordering in this material is an inherent property of the EDO-TTF molecule. We further show that deformations can be readily made at ambient temperatures.

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

    Science.gov (United States)

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

    2014-09-04

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

  1. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  2. Thermodynamic assessment of the Ho–Te system supported by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)

    2013-03-05

    Highlights: ► We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ► We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ► The thermodynamic parameters of the all phases existing in the system were determined. ► The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.

  3. Ab initio many-body calculations of nucleon-nucleus scattering

    Science.gov (United States)

    Quaglioni, Sofia; Navrátil, Petr

    2009-04-01

    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 the Pauli principle. We outline technical details and present phase-shift results for neutron scattering on H3, He4, and Be10 and proton scattering on He3,4, 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-He4S-wave phase shifts. In contrast, the experimental nucleon-He4P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-Be10 continuum is successful in explaining the parity-inverted ground state in Be11.

  4. Ab initio many-body calculations of nucleon-nucleus scattering

    CERN Document Server

    Quaglioni, Sofia

    2009-01-01

    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 3H, 4He and 10Be and proton scattering on 3He and 4He, 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-4He S-wave phase shifts. On the contrary, the experimental nucleon-4He P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-10Be continuum is successful in explaining the parity-inverted ground state in 11Be.

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

    Science.gov (United States)

    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.

  6. Ab initio simulations of phase stability and martensitic transitions in NiTi

    Science.gov (United States)

    Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.

    2016-12-01

    For NiTi-based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. We show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing phase transformation temperatures is discussed.

  7. Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi

    Science.gov (United States)

    Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.

    2016-01-01

    For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-12-01

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

  9. Embedding parameters in ab initio theory to develop approximations based on molecular similarity

    CERN Document Server

    Tanha, Matteus; Kaul, Shiva; Cappiello, Alexander; Gordon, Geoffrey J; Yaron, David J

    2015-01-01

    A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement with results from a higher-level (HL) ab initio model. A parametrized LL (pLL) model is created by multiplying selected matrix elements of the Hamiltonian operators by scaling factors that depend on element types. Various schemes for applying the scaling factors are compared, along with the impact of making the scaling factors linear functions of variables related to bond lengths, atomic charges, and bond orders. The models are trained on ethane and ethylene, substituted with -NH2, -OH and -F, and tested on substituted propane, propylene and t-butane. Training and test datasets are created by distorting the molecular geometries and applying uniform electric fields. The fitted properties include changes in total energy arising from geometric distortions or applied fields, an...

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

    Energy Technology Data Exchange (ETDEWEB)

    Sano, Haruyuki, E-mail: h-sano@ishikawa-nct.ac.jp [National Institute of Technology, Ishikawa College, Kitacyujo, Tsubata, Ishikawa 929-0392 (Japan); Mizutani, Goro [School of Materials Science, Japan Advanced Institute of Science and Technology, Tatsunokuchi, Ishikawa 923-1292 (Japan)

    2015-11-15

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

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

    Science.gov (United States)

    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).

  12. Embedding parameters in ab initio theory to develop well-controlled approximations based on molecular similarity

    CERN Document Server

    Tanha, Matteus; Cappiello, Alex; Gordon, Geoffrey J; Yaron, David J

    2013-01-01

    A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is proposed, in which parameters are embedded into a low-cost, low-level (LL) ab initio theory and adjusted to obtain agreement with a higher level (HL) ab initio theory. This approach is explored by training such a model on data for ethane and testing the resulting model on methane, propane and butane. The electronic distribution of the molecules is varied by placing them in strong electrostatic environments consisting of random charges placed on the corners of a cube. The results find that parameters embedded in HF/STO-3G theory can be adjusted to obtain agreement, to within about 2 kcal/mol, with results of HF/6-31G theory. Obtaining this level of agreement requires the use of parameters that are functions of the bond lengths, atomic charges, and bond orders within the molecules. The argument is made that this approach provides a well-controlled means to take advantage of molecular similarity in...

  13. smyRNA: a novel Ab initio ncRNA gene finder.

    Directory of Open Access Journals (Sweden)

    Raheleh Salari

    Full Text Available BACKGROUND: Non-coding RNAs (ncRNAs have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs. METHODOLOGY/PRINCIPAL FINDINGS: We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences. CONCLUSIONS/SIGNIFICANCE: Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown ncRNA families. AVAILABILITY: (http://compbio.cs.sfu.ca/taverna/smyrna.

  14. Ab initio determination of an extended Heisenberg Hamiltonian in CuO{sub 2} layers

    Energy Technology Data Exchange (ETDEWEB)

    Calzado, C.J.; Malrieu, J.P. [Lab. de Physique Quantique, IRSAMC, Univ. Paul Sabatier, Toulouse (France)

    2001-06-01

    Accurate ab initio calculations on embedded Cu{sub 4}O{sub 12} square clusters, fragments of the La{sub 2}CuO{sub 4} lattice, confirm a value of the nearest neighbor antiferromagnetic coupling (J = 124 meV) previously obtained from ab initio calculations on bicentric clusters and in good agreement with experiment. These calculations predict non negligible antiferromagnetic second-neighbor interaction (J' = 6.5 meV) and four-spin cyclic exchange (K = 14 meV), which may affect the thermodynamic and spectroscopic properties of these materials. The dependence of the magnetic coupling on local lattice distortions has also been investigated. Among them the best candidate to induce a spin-phonon effect seems to be the movement of the Cu atoms, changing the Cu-Cu distance, for which the variation of the nearest neighbor magnetic coupling with the Cu-O distance is {delta}J/{delta}d{sub Cu} {sub -} {sub O} {proportional_to} 1700 cm {sup -1} A {sup -1}. (orig.)

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

    Science.gov (United States)

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

    2016-08-01

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

  16. Novel high-pressure phase of ZrO{sub 2}: An ab initio prediction

    Energy Technology Data Exchange (ETDEWEB)

    Durandurdu, Murat, E-mail: murat.durandurdu@agu.edu.tr

    2015-10-15

    The high-pressure behavior of the orthorhombic cotunnite type ZrO{sub 2} is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni{sub 2}In type) within P6{sub 3}/mmc symmetry is predicted through the simulation. The Ni{sub 2}In type crystal is the densest high-pressure phase of ZrO{sub 2} proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni{sub 2}In type hexagonal phase forms in zirconia at high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO{sub 2} through an ab initio simulation. • Cotunnite ZrO{sub 2} adopts the Ni{sub 2}In type structure at high pressure. • The Ni{sub 2}In type structure is the densest high-pressure phase of ZrO{sub 2} proposed so far. • The preferred mechanism in ZrO{sub 2} differs from the other metal dioxides.

  17. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

    Science.gov (United States)

    Kihara, D; Lu, H; Kolinski, A; Skolnick, J

    2001-08-28

    The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab initio folding. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Furthermore, to generate representative protein structures, a reduced lattice-based protein model is used with replica exchange Monte Carlo to explore conformational space. We report results on the application of this methodology, termed TOUCHSTONE, to 65 proteins whose lengths range from 39 to 146 residues. For 47 (40) proteins, a cluster centroid whose rms deviation from native is below 6.5 (5) A is found in one of the five lowest energy centroids. The number of correctly predicted proteins increases to 50 when atomic detail is added and a knowledge-based atomic potential is combined with clustered and nonclustered structures for candidate selection. The combination of the ratio of the relative number of contacts to the protein length and the number of clusters generated by the folding algorithm is a reliable indicator of the likelihood of successful fold prediction, thereby opening the way for genome-scale ab initio folding.

  18. Thermodynamic modeling of the Fe–Mo system coupled with experiments and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rajkumar, V.B.; Hari Kumar, K.C., E-mail: kchkumar@iitm.ac.in

    2014-10-25

    Highlights: • Gibbs energy functions for all stable phases in the Fe–Mo system obtained using Calphad method. • Ab initio calculation results are employed to improve Gibbs energy functions. • New experimental data have been incorporated in the optimization. • Thermochemical properties: energy of formation, cohesive energy. • Calculated values are compared with experimental results. - Abstract: In this paper we report the Gibbs energy functions for all stable phases in the Fe–Mo system obtained using Calphad method. Newly measured enthalpy increment data, tie-line data and liquidus data for selected compositions are used as input for the Gibbs energy modeling, along with carefully selected thermochemical and phase diagram data from literature. Further, ab initio generated energy of formation at 0 K for the intermetallic phases and end-members of the sublattice model for the μ phase and the σ phase are also used in the optimization of model parameters of the Gibbs energy functions. Calculated phase diagram and the thermochemical properties show good agreement with the experimental data.

  19. Ab initio study of structural, electronic, and thermal properties of Ir1-xRhx alloys

    Directory of Open Access Journals (Sweden)

    Sh. Ahmed

    2015-06-01

    Full Text Available The structural, electronic, mechanical and thermal properties of Ir1-xRhx alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.

  20. Conformational study of acyclic alcohols by NMR spectroscopic analysis, molecular force field and Ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Abe, K.; Ito, K.; Suezawa, H.; Hirota, M.; Nishio, M.

    1986-10-01

    Conformations of a series of acyclic alcohols (CH/sub 3/CH(R)CH(OH)CH/sub 3/, CH/sub 3/CH(R)CH(OH)CH(R')CH/sub 3/, and CH/sub 3/CH(R)CH(OH)Bu/sup t/) were studied (1) by measuring vicinal H-H coupling constants (/sup 3/JH-H), (2) by lanthanoid-induced shift (LIS) analysis, (3) by molecular mechanics calculations (MM2), and (4) by ab initio (STO-3G, 4-31G geometry optimization) calculations. In the case of conformationally flexible alcohols as exemplified by 2-butanol and 3-pentanol, population of conformers determined by the LIS method do not agree with those determined by the /sup 3/JH-H, MM2, and ab initio methods. The discrepancy comes from the fact that the LIS measurement gives the most stable conformation of the alcohol in the LSR-alcohol complex and not of the free alcohol. In some flexible molecules, the most stable conformer in the complex can be different from that of the free molecule. In general, the conformational equilibrium is shifted by coordination of the shift reagent to the conformer whose alkyl chain stretches opposite to the direction of the coordination site of the shift reagent. 21 references, 1 figure, 6 tables.

  1. Vibrational spectrum, ab initio calculations, conformational equilibria and torsional modes of 1,3-dichloropropane

    Science.gov (United States)

    Duffy, Daniel J.; Quenneville, Jason; Baumbaugh, T. M.; Kitchener, S. A.; McCormick, R. K.; Dormady, C. N.; Croce, T. A.; Navabi, A.; Stidham, Howard D.; Hsu, Shaw L.; Guirgis, Gamil A.; Deng, Shiping; Durig, James R.

    2004-02-01

    Ab initio calculations are reported for three of four possible conformers of 1,3-dichloropropane. The fourth conformer, with C s symmetry, has a predicted enthalpy difference of more than 1500 cm -1 from the most stable conformer from each calculation regardless of the basis set used, so there is little chance of observing it. Thus, there is no evidence in the infrared or Raman spectrum of the presence of a fourth conformer. The order of stability given by the ab initio calculations is C 2(GG)>C 1(AG)>C 2v(AA)>C s(GG'), where A indicates the anti form for one of the CH 2Cl groups and G indicates the gauche conformation for the other CH 2Cl group relative to the plane of the carbon atoms. Almost every band observed can be confidently assigned to one or another of the conformers. Many observed bands proved to be of a composite nature, with several nearly coincident vibrations of different conformers contributing to the band contour. Nonetheless, a complete assignment of fundamentals is possible for the most stable C 2 conformer, and 5 of the fundamentals of the C 2v conformer and 13 those of the C 1 conformer can be confidently assigned.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hormain, Laureline; Monnerville, Maurice, E-mail: maurice.monnerville@univ-lille1.fr; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane [Laboratoire de Physique des Lasers Atomes et Molécules, Unité Mixte de Recherche (UMR) 8523, Université Lille I, Bât. P5, 59655 Villeneuve d’Ascq Cedex (France); Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón [Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, México (Mexico)

    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.

  3. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO-

    Science.gov (United States)

    Roy, Soumendra K.; Jian, Tian; Lopez, Gary V.; Li, Wei-Li; Su, Jing; Bross, David H.; Peterson, Kirk A.; Wang, Lai-Sheng; Li, Jun

    2016-02-01

    The observation of the gaseous UFO- anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO- is linear with an O-U-F structure and a 3H4 spectral term derived from a U 7sσ25fφ15fδ1 electron configuration, whereas the ground state of neutral UFO has a 4H7/2 spectral term with a U 7sσ15fφ15fδ1 electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.

  4. Ab initio based atomic scattering amplitudes and {l_brace}002{r_brace} electron structure factors of In{sub x}Ga{sub 1-x}As/GaAs quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Titantah, J T; Lamoen, D [EMAT, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Schowalter, M; Rosenauer, A, E-mail: john.titantah@ua.ac.b [Institut fuer Festkoerperphysik, Universitaet Bremen, D 28359 Bremen (Germany)

    2010-02-01

    The atomic scattering amplitudes of the various atoms of the systems Ga{sub 1-x}In{sub x}As, GaAs{sub 1-x}N{sub x} and InAs{sub 1-x}N{sub x} are calculated using the density functional theory (DFT) approach. The scattering amplitudes of N, Ga, As and In in the model systems are compared with the frequently used Doyle and Turner values. Deviation from the latter values is found for small scattering vectors (s<0.3A{sup -1}) and for these scattering vectors dependence on the orientation of the scattering vector and the chemical environment is reported. We suggest a parametrization of these modified scattering amplitudes (MASAs) for small scattering vectors (s<1.0A{sup -1}). The MASAs are exploited within zero pressure classical Metropolis Monte Carlo (MC), finite temperature calculations to investigate the effect of quantum well size on the electron {l_brace}002{r_brace} structure factor (SF) of Ga{sub 1-x}In{sub x}As quantum wells.

  5. Ab initio interaction potentials and scattering lengths for ultracold mixtures of metastable helium and alkali-metal atoms

    Science.gov (United States)

    Kedziera, Dariusz; Mentel, Łukasz; Żuchowski, Piotr S.; Knoop, Steven

    2015-06-01

    We have obtained accurate ab initio +4Σ quartet potentials for the diatomic metastable triplet helium+alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections CCSD(T) calculations and accurate calculations of the long-range C6 coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that result in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium+alkali-metal mixture experiments.

  6. Structural phase transitions in Ruddlesden-Popper phases of strontium titanate: {\\em ab initio} and inhomogeneous Ginzburg-Landau approaches

    CERN Document Server

    Lee, Jeehye

    2010-01-01

    We present the first systematic {\\em ab initio} study of anti-ferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr$_{1+n}$Ti$_n$O$_{3n+1}$, as a function of both compressive epitaxial strain and phase number $n$. We find all RP phases to exhibit AFD order under a significant range of strains, recovering the bulk AFD order as $\\sim 1/n^2$. A Ginzburg-Landau Hamiltonian generalized to include inter-octahedral interactions reproduces our {\\em ab initio} results well, opening a pathway to understanding other nanostructured perovskite systems.

  7. Embedded atom approach for gold–silicon system from ab initio molecular dynamics simulations using the force matching method

    Indian Academy of Sciences (India)

    A NASSOUR

    2016-09-01

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.

  8. Multi-scale modeling of materials: from ab-initio calculations to kinetic simulations; Modelisation multiechelle des materiaux de l'ab-initio a la cinetique

    Energy Technology Data Exchange (ETDEWEB)

    Willaime, F. [Division de l' energie nucleaire, CEA Centre de Saclay, 91191 Gif-sur-Yvette (France); Deutsch, T.; Pochet, P. [INAC, Direction des sciences de la matiere, CEA Centre de Grenoble, 38054 Grenoble Cedex 9 (France)

    2010-07-01

    Ab-initio calculation methods, for the purposes of computing electronic structures, have made it possible, since the early nineties, to simulate the properties of perfect crystalline materials (materials free of any defect). By improving such methods, and with the increasing power of supercomputers, it has now become feasible to simulate the properties of elementary defects, which may seldom be accessed directly through experiments. This has opened up a vast, fruitful field of multi-scale simulations, where such data yield the basis for realistic simulations of the kinetics of materials evolution. The kinetic Monte-Carlo method thus provides the means to model phenomena acting at the scale of a second, or even of a year. In the issue of self-diffusion in silicon, multi-scale simulation has been successful in predicting an asymmetrical behaviour: a speeding up of vacancy diffusion under compression and a tailing off under tension, and conversely, a speeding up of interstitial diffusion under tension and a falling off under compression. Multi-scale modeling has also been successful in simulating irradiation defects in iron. (A.C.)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Ab initio study of the low-lying electronic states of the CaO molecule

    Energy Technology Data Exchange (ETDEWEB)

    Khalil, Hossain; Brites, Vincent; Quere, Frederic Le [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France); Leonard, Celine, E-mail: celine.leonard@univ-paris-est.fr [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France)

    2011-07-28

    Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1{Pi}}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: {yields} The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. {yields} Large active space, core-valence correlation and configuration interaction are required. {yields} The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. {yields} These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1}{Pi}, b{sup 3}{Sigma}{sup +} and A{sup 1

  11. Ab initio study of perovskite type oxide materials for solid oxide fuel cells

    Science.gov (United States)

    Lee, Yueh-Lin

    2011-12-01

    Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen

  12. Modeling the diffraction process of molecular crystals: computation of X-ray scattering intensities from ab initio electron densities

    NARCIS (Netherlands)

    Bruning, W.; Feil, D.

    1992-01-01

    An algorithm for calculating the scattering factors of atomic fragments in molecules as defined by the Stockholder recipe is presented. This method allows the calculation, from ab initio molecular wave functions, of structure factors including individual anisotropic atomic temperature factors. These

  13. Electronic Structure and Physical-Chemistry Property Relationship for Oxazole Derivatives by Ab Initio and DFT Methods

    OpenAIRE

    2011-01-01

    The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.

  14. Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data

    DEFF Research Database (Denmark)

    Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M

    2012-01-01

    Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...

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

    Energy Technology Data Exchange (ETDEWEB)

    Sbai, Y.; Ait Raiss, A.; Salmani, E. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Bahmad, L., E-mail: Bahmad@fsr.ac.ma [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Benyoussef, A. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco)

    2015-12-15

    On the basis of ab-initio calculations and Monte Carlo simulations the magnetic and electronic properties of Gallium nitride (GaN) doped with the transition metal Manganese (Mn) were studied. The ab initio calculations were done using the AKAI–KKR–CPA method within the Local Density Approximation (LDA) approximation. We doped our Diluted Magnetic Semiconductor (DMS), with different concentrations of magnetic impurities Mn and plotted the density of state (DOS) for each one. Showing a half-metallic behavior and ferromagnetic state especially for Ga{sub 0.95}Mn{sub 0.05}N making this DMS a strong candidate for spintronic applications. Moreover, the magnetization and susceptibility of our system as a function of the temperature has been calculated and give for various system size L to study the size effect. In addition, the transition temperature was deduced from the peak of the susceptibility. The Ab initio results are in good agreement with literature especially for (x=0.05) of Mn which gives the most interesting results. - Highlights: • The AKAI–KKR–CPA method has been applied to study the doped compound GaN:Mn. • The local density approximation (LDA) has been applied. • The ab-initio calculations have been performed. • The density of states (DOS) have been plotted for differents doping concentrations, using Monte Carlo simulations.

  16. Ab initio treatment of the chemical reaction precursor complex Cl(P-2)-HF. 2 : Bound states and infrared spectrum

    NARCIS (Netherlands)

    Fishchuk, A.V.; Groenenboom, G.C.; Avoird, A. van der

    2006-01-01

    Bound energy levels and properties of the Cl((2)p)-HF complex were obtained from full three-dimensional (3D) calculations, with the use of the ab initio computed diabatic potential surfaces from the preceding paper and the inclusion of spin-orbit coupling. For a better understanding of the dynamics

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

    Science.gov (United States)

    Zhang, Yang

    2014-02-01

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

  18. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, Gianluca; Brocks, Geert; Brink, van den Jeroen

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome

  19. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1997-01-01

    The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting t

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

    KAUST Repository

    Heryadi, Dodi

    2011-01-01

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

  1. Tunneling of electrons via rotor-stator molecular interfaces: combined ab initio and model study

    CERN Document Server

    Petreska, Irina; Pejov, Ljupco; Kocarev, Ljupco

    2015-01-01

    Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that confirmation dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previ...

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

    Science.gov (United States)

    Ji, Pengfei; Zhang, Yuwen

    2016-04-01

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

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

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    The electron temperature T_e dependent electron density of states g({\\epsilon}), Fermi-Dirac distribution f({\\epsilon}), and electron-phonon spectral function {\\alpha}^2 F({\\Omega}) are computed as prerequisites before achieving effective electron-phonon coupling factor. The obtained is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing G_(e-ph) from ab initio calculation, shows a faster decrease of T_e and increase of T_l than those using G_(e-ph) from phenomenological treatment. The approach of calculating G_(e-ph) and its implementation into MD-TTM simulation is applicable to other metals.

  4. Femtosecond Laser Processing of Germanium: An Ab Initio Molecular Dynamics Study

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtosecond laser processing is simulated by imposing the Nose Hoover thermostat to the electronic subsystem lasting for ~100 fs and continuing with microcanonical ensemble simulation of ~200 fs. The simulation results show solid, liquid and gas phases of germanium under adjusted intensities of the femtosecond laser irradiation. We find the irradiated germanium distinguishes from the usual germanium crystal by analyzing their melting and dynamic properties.

  5. Probing defects and correlations in the hydrogen-bond network of ab initio water

    CERN Document Server

    Gasparotto, Piero; Ceriotti, Michele

    2016-01-01

    The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone, but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the inter-atomic potential, finding that in most cases, the qualitative features of the hydrogen bond network are remarkably robust.

  6. Ab initio and DFT studies on vibrational spectra of some halides of group IIIB elements

    Science.gov (United States)

    Zhang, Yu; Zhao, Jianying; Tang, Guodong; Zhu, Longgen

    2005-11-01

    The vibrational spectra of some group IIIB elements halides MX 3 and their dimmers, M 2X 6 (M = Sc(III), Y(III), La(III); X = F, Cl, Br, I), have been systematically investigated by ab initio restricted Hartree-Fock (RHF) and density functional B3LYP methods with LanL2DZ and SDD basis sets. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational frequencies, calculated by two methods with different basis sets, are compared to each other. The effect of the methods and the basis sets used on the calculated vibrational frequencies are discussed. Some vibrational frequencies of these complexes are also predicted.

  7. Design of two-photon molecular tandem architectures for solar cells by ab initio theory

    DEFF Research Database (Denmark)

    Ørnsø, Kristian Baruël; García Lastra, Juan Maria; De La Torre, Gema

    2015-01-01

    An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range...... of the structural and energetic properties of several thousand porphyrin dyes. The third design is a molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels...... and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices...

  8. Piezoelectricity in two-dimensional materials: Comparative study between lattice dynamics and ab initio calculations

    Science.gov (United States)

    Michel, K. H.; ćakır, D.; Sevik, C.; Peeters, F. M.

    2017-03-01

    The elastic constant C11 and piezoelectric stress constant e1 ,11 of two-dimensional (2D) dielectric materials comprising h-BN, 2 H -MoS2 , and other transition-metal dichalcogenides and dioxides are calculated using lattice dynamical theory. The results are compared with corresponding quantities obtained with ab initio calculations. We identify the difference between clamped-ion and relaxed-ion contributions with the dependence on inner strains which are due to the relative displacements of the ions in the unit cell. Lattice dynamics allows us to express the inner-strain contributions in terms of microscopic quantities such as effective ionic charges and optoacoustical couplings, which allows us to clarify differences in the piezoelectric behavior between h-BN and MoS2. Trends in the different microscopic quantities as functions of atomic composition are discussed.

  9. Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations

    Directory of Open Access Journals (Sweden)

    Xiaowei Li

    2015-01-01

    Full Text Available Structure and properties of Cu-doped diamond-like carbon films (DLC were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.% on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

  10. Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaowei; Ke, Peiling; Wang, Aiying, E-mail: aywang@nimte.ac.cn [Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China)

    2015-01-15

    Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

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

    CERN Document Server

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

    2016-01-01

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

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

    Science.gov (United States)

    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.

  13. Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation

    Science.gov (United States)

    Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.

    2015-11-01

    The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH1.37O0.08 plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition.

  14. The ideal strength of gold under uniaxial stress: an ab initio study.

    Science.gov (United States)

    Wang, Hao; Li, Mo

    2010-07-28

    We employ an ab initio calculation based on density functional theory to investigate the ideal strength of face-centered cubic crystal Au under uniaxial stress along the [100] direction. We show that the stability of the perfect Au crystal under tensile stress is determined by the tetragonal shear stiffness modulus, with an ideal tensile strength of 4.2 GPa and the corresponding Lagrangian tensile strain of ∼ 0.07. The potential bifurcation from the primary uniaxial loading path is along the tetragonal shear. Under compressive stress, there is a stress-free body-centered cubic phase, which is unstable and ready to transform to a stress-free body-centered tetragonal phase with lower internal energy. The stable region is from - 1.6 to 4.2 GPa in the ideal strength, or from - 0.07 to 0.07 in the Lagrangian strain.

  15. Ab-initio molecular dynamics study of lanthanides in liquid sodium

    Science.gov (United States)

    Li, Xiang; Samin, Adib; Zhang, Jinsuo; Unal, C.; Mariani, R. D.

    2017-02-01

    To mitigate the fuel cladding chemical interaction (FCCI) phenomena in liquid sodium cooled fast reactors, a fundamental understanding of the lanthanide (Ln) transport through liquid Nasbnd Cs filled pores in Usbnd Zr fuel is necessary. In this study, we investigate three abundant Ln fission products diffusion coefficients in liquid Na at multiple temperatures. By utilization of Ab-initio Molecular Dynamics, the Ln diffusivities are found to be in the magnitude order of liquid diffusion (10-5cm2 /s) and the temperature dependence of the diffusivity for different lanthanides in liquid sodium was explored. It is also observed that dilute concentration of Pr and Nd led to a significant change in Na diffusivity. The structural and electronic properties of Nasbnd Ln metallic systems have been investigated. The total coordination number shows dependence on both the temperature and the composition.

  16. AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Ching, Wai-Yim

    2013-12-31

    In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.

  17. Thermal Conductivity of Pure Noble Gases at Low Density from Ab Initio Prandtl Number

    Science.gov (United States)

    Song, Bo; Wang, Xiaopo; Liu, Zhigang

    2013-03-01

    The experimental data reported in the literature after 2000 have been investigated for the viscosity and thermal conductivity of helium-4, neon, and argon at low density. The well-established values of thermal conductivity by transient hot-wire measurements are not reliable enough for noble gases in the low-pressure gas region. These facts motivate us to determine the thermal conductivity from accurate viscosity data and the ab initio Prandtl number, with an uncertainty of 0.25 % for temperatures ranging between 200 K and 700 K. The theoretical accuracy is superior to the accuracy of the best measurements. The calculated results are accurate enough to be applied as standard values for the thermal conductivity of helium-4, neon, and argon over the considered temperature range.

  18. Ab-initio Study of the Diffusion Mechanisms of Gallium in a Silicon Matrix

    Science.gov (United States)

    Levasseur-Smith, Kevin; Mousseau, Normand

    2007-03-01

    We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si. The dominant neutral configurations for single and multi-atom defects are established by ab-initio calculations using the density functional theory in the LDA approximation, with a LCAO basis as implemented in the SIESTA package. We find formation energies of 0.7 eV and 2.9 eV, respectively, for the substitutional and tetrahedral interstitial defects, while the diatomic substitutional-tetrahedral complex has a formation energy of 2.2 eV. Subsequent calculations using this same DFT package in conjunction with the activation relaxation technique (ART nouveau) allow us to determine possible diffusion pathways as well as their corresponding saddle points and energy barriers.

  19. Ab-initio simulations of self-diffusion mechanisms in semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    El-Mellouhi, Fedwa [Departement de physique and Regroupement quebecois sur les materiaux de pointe, Universite de Montreal, C.P. 6128, succ. Centre-ville, Montreal, Que., H3C 3J7 (Canada)], E-mail: f.el.mellouhi@umontreal.ca; Mousseau, Normand [Departement de physique and Regroupement quebecois sur les materiaux de pointe, Universite de Montreal, C.P. 6128, succ. Centre-ville, Montreal, Que., H3C 3J7 (Canada)], E-mail: normand.mousseau@umontreal.ca

    2007-12-15

    We present an application of SIEST-A-RT that combines the activation relaxation technique, ART nouveau, and the local-basis ab-initio code SIESTA, to study self-defect migration pathways in semiconductors. SIESTA provides reliable descriptions of defect properties in semiconductors directly comparable to experiment as well as, once combined with ART nouveau, a detailed description of their possible migration mechanisms. We use this package to characterize the properties of vacancies in silicon and GaAs, such as relaxation geometries, formation energies at low and high temperature, diffusion mechanisms and migration barriers. We show here that diffusion in bulk semiconductors is a rich and complex phenomenon that depends not only on the geometry of the defect and the surrounding lattice but also on its charge.

  20. Ab-initio simulations of self-diffusion mechanisms in semiconductors

    Science.gov (United States)

    El-Mellouhi, Fedwa; Mousseau, Normand

    2007-12-01

    We present an application of SIEST-A-RT that combines the activation relaxation technique, ART nouveau, and the local-basis ab-initio code SIESTA, to study self-defect migration pathways in semiconductors. SIESTA provides reliable descriptions of defect properties in semiconductors directly comparable to experiment as well as, once combined with ART nouveau, a detailed description of their possible migration mechanisms. We use this package to characterize the properties of vacancies in silicon and GaAs, such as relaxation geometries, formation energies at low and high temperature, diffusion mechanisms and migration barriers. We show here that diffusion in bulk semiconductors is a rich and complex phenomenon that depends not only on the geometry of the defect and the surrounding lattice but also on its charge.

  1. Estudo ab-initio da a-alanina em meio aquoso

    Directory of Open Access Journals (Sweden)

    Sambrano Júlio Ricardo

    1999-01-01

    Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

  2. Ab initio approach to the ion stopping power at the plasma-solid interface

    Science.gov (United States)

    Bonitz, Michael; Schlünzen, Niclas; Wulff, Lasse; Joost, Jan-Philip; Balzer, Karsten

    2016-10-01

    The energy loss of ions in solids is of key relevance for many applications of plasmas, ranging from plasma technology to fusion. Standard approaches are based on density functional theory or SRIM simulations, however, the applicability range and accuracy of these results are difficult to assess, in particular, for low energies. Here we present an independent approach that is based on ab initio nonequilibrium Green functions theory, e.g. that allows to incorporate electronic correlations effects of the solid. We present the first application of this method to low-temperature plasmas, concentrating on proton and alpha-particle stopping in a graphene layer. In addition to the stopping power we present time-dependent results for the local electron density, the spectral function and the photoemission spectrum that is directly accessible in optical, UV or x-ray diagnostics. http://www.itap.uni-kiel.de/theo-physik/bonitz/.

  3. Ab initio electron scattering cross-sections and transport in liquid xenon

    Science.gov (United States)

    Boyle, G. J.; McEachran, R. P.; Cocks, D. G.; Brunger, M. J.; Buckman, S. J.; Dujko, S.; White, R. D.

    2016-09-01

    Ab initio fully differential cross-sections for electron scattering in liquid xenon are developed from a solution of the Dirac-Fock scattering equations, using a recently developed framework (Boyle et al 2015 J. Chem. Phys. 142 154507) which considers multipole polarizabilities, a non-local treatment of exchange, and screening and coherent scattering effects. A multi-term solution of Boltzmann’s equation accounting for the full anisotropic nature of the differential cross-section is used to calculate transport properties of excess electrons in liquid xenon. The results were found to agree to within 25% of the measured mobilities and characteristic energies over the reduced field range of 10-4-1 Td. The accuracies are comparable to those achieved in the gas phase. A simple model, informed by highly accurate gas-phase cross-sections, is presented to improve the liquid cross-sections, which was found to enhance the accuracy of the transport coefficient calculations.

  4. Change in Inertial Confinement Fusion Implosions upon Using an Ab Initio Multiphase DT Equation of State

    Science.gov (United States)

    Caillabet, L.; Canaud, B.; Salin, G.; Mazevet, S.; Loubeyre, P.

    2011-09-01

    Improving the description of the equation of state (EOS) of deuterium-tritium (DT) has recently been shown to change significantly the gain of an inertial confinement fusion target [S. X. Hu , Phys. Rev. Lett. 104, 235003 (2010)PRLTAO0031-900710.1103/PhysRevLett.104.235003]. Here we use an advanced multiphase EOS, based on ab initio calculations, to perform a full optimization of the laser pulse shape with hydrodynamic simulations starting from 19 K in DT ice. The thermonuclear gain is shown to be a robust estimate over possible uncertainties of the EOS. Two different target designs are discussed, for shock ignition and self-ignition. In the first case, the areal density and thermonuclear energy can be recovered by slightly increasing the laser energy. In the second case, a lower in-flight adiabat is needed, leading to a significant delay (3 ns) in the shock timing of the implosion.

  5. Ab initio structure determination of new compound Ba 3(BO 3)(PO 4)

    Science.gov (United States)

    Ma, H. W.; Liang, J. K.; Wu, L.; Liu, G. Y.; Rao, G. H.; Chen, X. L.

    2004-10-01

    The crystal structure of new compound Ba3BPO7 was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to Rp=5.92%, Rwp=8.87%, Rexp=5.00% with the following details: Hexagonal, space group P63mc, a=5.4898 (1) Å, c=14.7551(1) Å, Z=2. The basic unit of the structure is the [BaO10]-[BO3]-[PO4] polar polyhedra-chain composed of Ba1-B-P-O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.

  6. Ab initio study of the electronic structure andelastic properties of Al5C3N

    Institute of Scientific and Technical Information of China (English)

    Xu Xue-Wen; Hu Long; Yu Xiao; Lu Zun-Ming; Fan Ying; Li Yang-xian; Tang Cheng-Chun

    2011-01-01

    We investigate the electronic structure,chemical bonding and elastic properties of the hexagonal aluminum carbonitride,Al5C3N,by ab initio calculations.Al5C3N is a semiconductor with a narrow indirect gap of 0.81 eV.The valence bands below the Fermi level (EF) originate from the hybridized Al p-C p and Al p-N p states.The calculated bulk and Young's moduli are 201 GPa and 292 GPa,which are slightly lower than those of Ti3SiC2.The values of the bulk-to-shear-modulus and bulk-modulus-to-c44 are 1.73 and 1.97,respectively,which axe higher than those of Ti2AlCand Ti2AlN,indicating that Al5C3N is a ductile ceramic.

  7. Ab initio-based fracture toughness estimates and transgranular traction-separation modelling of zirconium hydrides

    Science.gov (United States)

    Olsson, P. A. T.; Kese, K.; Kroon, M.; Alvarez Holston, A.-M.

    2015-06-01

    In this work we report the results of an ab initio study of the transgranular fracture toughness and cleavage of brittle zirconium hydrides. We use the Griffith-Irwin relation to assess the fracture toughness using calculated surface energy and estimated isotropic Voigt-Reuss-Hill averages of the elastic constants. The calculated fracture toughness values are found to concur well with experimental data, which implies that fracture is dominated by cleavage failure. To investigate the cleavage energetics, we model the decohesion process. To describe the interplanar interaction we adopt Rose’s universal binding energy relation, which is found to reproduce the behaviour accurately. The modelling shows that the work of fracture and ductility decreases with increasing hydrogen content.

  8. A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters.

    Science.gov (United States)

    Rafiee, Marjan A; Hadipour, Nasser L; Naderi-manesh, Hossein

    2004-03-01

    In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory.

  9. Ab initio modeling of radiation damage in MgF{sub 2} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Abuova, F.U. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Kotomin, E.A., E-mail: kotomin@latnet.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Lisitsyn, V.M. [Tomsk Polytechnical University, Tomsk 634003 (Russian Federation); Akilbekov, A.T. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Piskunov, S. [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia)

    2014-05-01

    MgF{sub 2} with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F−H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F{sub 2} interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.

  10. Minimal parameter implicit solvent model for ab initio electronic structure calculations

    CERN Document Server

    Dziedzic, Jacek; Skylaris, Chris-Kriton; Mostofi, Arash A; Payne, Mike C

    2011-01-01

    We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.

  11. Ab-initio study of magnetism behavior in TiO2 semiconductor with structural defects

    Science.gov (United States)

    Zarhri, Z.; Houmad, M.; Ziat, Y.; El Rhazouani, O.; Slassi, A.; Benyoussef, A.; El Kenz, A.

    2016-05-01

    Magnetic, electronic and structural properties of titanium dioxide material with different structural defects are studied using the first-principles ab-initio calculations and the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA) method in connection with the local density approximation (LDA). We investigated all structural defects in rutile TiO2 such as Titanium interstitial (Tii), Titanium anti-sites (Tio), Titanium vacancies (VTi), Oxygen interstitial (Oi), Oxygen anti-sites (OTi) and oxygen vacancies (Vo). Mechanisms of hybridization and interaction between magnetic atoms are investigated. The transition temperature is computed using the Mean Field Approximation (MFA).Magnetic stability energy of ferromagnetic and disordered local moment states is calculated to determine the most stable state. Titanium anti-sites have a half-metallic aspect. We also studied the change type caused by structural defects in this material.

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

    CERN Document Server

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

    2016-01-01

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

  13. Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations

    Science.gov (United States)

    Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.

    2016-06-01

    The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.

  14. Ab-initio calculations on two-electron ions in strongly coupled plasma environment

    CERN Document Server

    Bhattacharyya, S; Mukherjee, T K

    2015-01-01

    In this work, the controversy between the interpretations of recent measurements on dense aluminum plasma created with Linac coherent light sources (LCLS) X-ray free electron laser (FEL) and Orion laser has been addressed. In both kind of experiments, helium-like and hydrogen-like spectral lines are used for plasma diagnostics . However, there exist no precise theoretical calculations for He-like ions within dense plasma environment. The strong need for an accurate theoretical estimates for spectral properties of He-like ions in strongly coupled plasma environment leads us to perform ab initio calculations in the framework of Rayleigh-Ritz variation principle in Hylleraas coordinates where ion-sphere potential is used. An approach to resolve the long-drawn problem of numerical instability for evaluating two-electron integrals with extended basis inside a finite domain is presented here. The present values of electron densities corresponding to disappearance of different spectral lines obtained within the fram...

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

    Science.gov (United States)

    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.

  16. Ab initio study of the optical properties of crystalline phenanthrene, including the excitonic effects

    Science.gov (United States)

    Dadsetani, Mehrdad; Nejatipour, Hajar; Ebrahimian, Ali

    2015-05-01

    Using the ab initio methods for solving the Bethe-Salpeter equation on the basis of the FPLAPW method, optical properties of crystalline phenanthrene were calculated, in a comparison to its isomer, anthracene. It was found that despite the similarity of the structural, electronic, and the overall optical properties in a 40 eV energy range, phenanthrene and anthracene show significant differences in their optical spectra in the energy range below band gaps. Phenanthrene has two spin singlet excitonic features whereas anthracene shows one. The singlet and the lowest triplet binding energies of phenanthrene were found to be larger than anthracene. In this study, in addition, a comparison has been made between the optical spectra in RPA and the existing experimental data.

  17. Ab Initio Simulation of Electrical Currents Induced by Ultrafast Laser Excitation of Dielectric Materials

    Science.gov (United States)

    Wachter, Georg; Lemell, Christoph; Burgdörfer, Joachim; Sato, Shunsuke A.; Tong, Xiao-Min; Yabana, Kazuhiro

    2014-08-01

    We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab initio simulations based on time-dependent density functional theory give insight into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunnelinglike excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis, suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [A. Schiffrin et al., Nature (London) 493, 70 (2013)].

  18. The {\\it ab initio} calculation of spectra of open shell diatomic molecules

    CERN Document Server

    Tennyson, Jonathan; McKemmish, Laura K; Yurchenko, Sergei N

    2016-01-01

    The spectra (rotational, rotation-vibrational or electronic) of diatomic molecules due to transitions involving only closed-shell ($^1\\Sigma$) electronic states follow very regular, simple patterns and their theoretical analysis is usually straightforward. On the other hand, open-shell electronic states lead to more complicated spectral patterns and, moreover, often appear as a manifold of closely lying electronic states, leading to perturbations with even larger complexity. This is especially true when at least one of the atoms is a transition metal. Traditionally these complex cases have been analysed using approaches based on perturbation theory, with semi-empirical parameters determined by fitting to spectral data. Recently the needs of two rather diverse scientific areas have driven the demand for improved theoretical models of open-shell diatomic systems based on an \\emph{ab initio} approach, these areas are ultracold chemistry and the astrophysics of "cool" stars, brown dwarfs and most recently extraso...

  19. Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

    Science.gov (United States)

    Šipr, O; Ebert, H; Minár, J

    2015-02-11

    A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

  20. Ab initio multiple spawning dynamics using multi-state second-order perturbation theory.

    Science.gov (United States)

    Tao, Hongli; Levine, Benjamin G; Martínez, Todd J

    2009-12-10

    We have implemented multi-state second-order perturbation theory (MS-CASPT2) in the ab initio multiple spawning (AIMS) method for first-principles molecular dynamics including nonadiabatic effects. The nonadiabatic couplings between states are calculated numerically using an efficient method which requires only two extra energy calculations per time step. As a representative example, we carry out AIMS-MSPT2 calculations of the excited state dynamics of ethylene. Two distinct types of conical intersections, previously denoted as the twisted-pyramidalized and ethylidene intersections, are responsible for ultrafast population transfer from the excited state to the ground state. Although these two pathways have been observed in prior dynamics simulations, we show here that the branching ratio is affected by dynamic correlation with the twisted-pyramidalized intersection overweighting the ethylidene-like intersection during the decay process at the AIMS-MSPT2 level of description.

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

    Science.gov (United States)

    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.

  2. Ab initio calculations in the symplectic no-core configuration interaction framework

    Science.gov (United States)

    McCoy, Anna; Caprio, Mark; Dytrych, Tomas

    2016-09-01

    A major challenge in quantitatively predicting nuclear structure directly from realistic nucleon-nucleon interactions, i.e., ab initio, arises due to an explosion in the dimension of the traditional Slater determinant basis as the number of nucleons and included shells increases. The need for including highly excited configurations arises, in large part, because the kinetic energy induces strong coupling across shells. However, the kinetic energy conserves symplectic symmetry. By combining this symplectic symmetry with the no-core configuration interaction (NCCI) framework, we reduce the size of basis necessary to obtain accurate results for p-shell nuclei. Supported by the US DOE under Grants DE-AC05-06OR23100 and DE-FG02-95ER-40934, and the Czech Science Foundation under Grant No. 16-16772S.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  5. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data

    Science.gov (United States)

    White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.

    2017-01-01

    Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.

  6. Ab initio calculation of structure and thermodynamic properties of Zintl aluminide SrAl{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Zhi-Jian [Chongqing Key Laboratory of Micro/Nano Materials Engineering and Technology, Chongqing (China); Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics; Jia, Li-Jun [Chongqing Univ. of Arts and Sciences Library (China); Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong [Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; Sun, Xiao-Wei [Lanzhou Jiaotong Univ. (China). School of Mathematics and Physics; Chen, Qi-Feng [China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics

    2015-07-01

    The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl{sub 2} at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory method within 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 SrAl{sub 2} are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations in the thermal expansion a are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.

  7. A-dependence of the Spectra of the F Isotopes from ab initio Calculations

    Science.gov (United States)

    Barrett, Bruce R.; Dikmen, Erdal; Maris, Pieter; Vary, James P.; Shirokov, Andrey M.

    2016-03-01

    Using a succession of Okubo-Lee-Suzuki transformations within the No Core Shell Model (NCSM) formalism, we derive an ab initio, non-perturbative procedure for calculating the input for standard shell-model (SSM) calculations within one major shell. We have used this approach for calculating the spectra of the F isotopes from A=18 to A=25, so as to study the A-dependence of the results. In particular, we are interested in seeing if the theoretical input is weak enough, so that a single set of two-body effective interactions can be used for all of the F isotopes investigated. We will present results from SSM calculations based on input obtained with the JISP16 nucleon-nucleon interaction in an initial 4 ℏΩ NCSM basis space. This work supported in part by TUBITAK-BIDEB, the US DOE, the US NSF, NERSC, and the Russian Ministry of Education and Science.

  8. An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

    CERN Document Server

    Iftimie, R; Schofield, J P; Iftimie, Radu; Salahub, Dennis; Schofield, Jeremy

    2003-01-01

    In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.

  9. Ab initio research of stopping power for energetic ions in solids

    Science.gov (United States)

    He, Bin; Meng, Xu-Jun; Wang, Jian-Guo

    2017-03-01

    A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.

  10. Ab initio density functional theory investigation of structural and electronic properties of silicon carbide nanotube bundles

    Energy Technology Data Exchange (ETDEWEB)

    Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Department of Nano Science, Computational Physical Science Research Laboratory, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

    2008-10-01

    By using ab initio density functional theory the structural and electronic properties of isolated and bundled (8,0) and (6,6) silicon carbide nanotubes (SiCNTs) are investigated. Our results show that for such small diameter nanotubes the inter-tube interaction causes a very small radial deformation, while band splitting and reduction of the semiconducting energy band gap are significant. We compared the equilibrium interaction energy and inter-tube separation distance of (8,0) SiCNT bundle with (10,0) carbon nanotube (CNT) bundle where they have the same radius. We found that there is a larger inter-tube separation and weaker inter-tube interaction in the (8,0) SiCNT bundle with respect to (10,0) CNT bundle, although they have the same radius.

  11. Ab initio density functional theory investigation of Li-intercalated silicon carbide nanotube bundles

    Energy Technology Data Exchange (ETDEWEB)

    Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Computational Physical Science Research Laboratory, Department of Nano Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), PO Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

    2009-06-15

    We present the results of ab initio density functional theory calculations on the energetic, and geometric and electronic structure of Li-intercalated (6,6) silicon carbide nanotube (SiCNT) bundles. Our results show that intercalation of lithium leads to the significant changes in the geometrical structure. The most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the SiCNTs. All the Li-intercalated (6,6) SiCNT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial space are susceptible for intercalation. The present calculations suggest that the SiCNT bundle is a promising candidate for the anode material in battery applications.

  12. Electronic Transport in Monolayer Graphene with Extreme Physical Deformation: ab Initio Density Functional Calculation

    CERN Document Server

    Gao, Haiyuan; Li, Meijiao; Guo, Zhendong; Chen, Hongshen; Jin, Zhonghe; Yu, Bin

    2011-01-01

    Electronic transport properties of monolayer graphene with extreme physical bending up to 90o angle are studied using ab Initio first-principle calculations. The importance of key structural parameters including step height, curvature radius and bending angle are discussed how they modify the transport properties of the deformed graphene sheet comparing to the corresponding flat ones. The local density of state reveals that energy state modification caused by the physical bending is highly localized. It is observed that the transport properties of bent graphene with a wide range of geometrical configurations are insensitive to the structural deformation in the low-energy transmission spectra, even in the extreme case of bending. The results support that graphene, with its superb electromechanical robustness, could serve as a viable material platform in a spectrum of applications such as photovoltaics, flexible electronics, OLED, and 3D electronic chips.

  13. Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.

    Science.gov (United States)

    Steinmann, Casper; Fedorov, Dmitri G; Jensen, Jan H

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.

  14. Implementation of $ab$ $initio$ perturbed angular correlation observables for analysis of fluctuating quadrupole interactions

    CERN Document Server

    Barbosa, Marcelo

    A review about the nuclear properties, namely the nuclear moments (magnetic dipole moment and electric quadrupole moment) and their interaction with electromagnetic fields external to the nucleus (hyperfine interactions), as well as the angular distribution of radiation produced by $\\gamma$-decay, is presented. A detailed description about the theory of Perturbed Angular Correlations was done, including the comparison between $\\gamma-\\gamma$- correlations and $e^{-}- \\gamma$ correlations. For dynamic nuclear interactions, an introduction to the theory of stochastic states in PAC was performed. We focused on ab-initio implementation of observables for analyzing fluctuating quadrupole hyperfine interactions on time dependent perturbed angular correlations experiments. The development of computacional codes solving the full problem, adapted to fit data obtained on single crystals or polycrystals for two-state transient fields with any axial symmetry and orientation was the main purpose of this work. The final pa...

  15. Scaling factors for ab initio vibrational frequencies: comparison of uncertainty models for quantified prediction

    CERN Document Server

    Pernot, Pascal

    2009-01-01

    Bayesian Model Calibration is used to revisit the problem of scaling factor calibration for semi-empirical correction of ab initio calculations. A particular attention is devoted to uncertainty evaluation for scaling factors, and to their effect on prediction of observables involving scaled properties. We argue that linear models used for calibration of scaling factors are generally not statistically valid, in the sense that they are not able to fit calibration data within their uncertainty limits. Uncertainty evaluation and uncertainty propagation by statistical methods from such invalid models are doomed to failure. To relieve this problem, a stochastic function is included in the model to account for model inadequacy, according to the Bayesian Model Calibration approach. In this framework, we demonstrate that standard calibration summary statistics, as optimal scaling factor and root mean square, can be safely used for uncertainty propagation only when large calibration sets of precise data are used. For s...

  16. Ab initio study of Ni2MnGa under shear deformation

    Directory of Open Access Journals (Sweden)

    Zelený Martin

    2015-01-01

    Full Text Available The effect of shear deformation on Ni2MnGa magnetic shape memory alloy has been investigated using ab initio electronic structure calculations. We used the projector-augmented wave method for the calculations of total energies and stresses as functions of applied affine shear deformation. The studied nonmodulated martensite (NM phase exhibits a tetragonally distorted L21 structure with c/a > 1. A large strain corresponding to simple shears in {001}, {100} and {100} systems was applied to describe a full path between two equivalent NM lattices. We also studied {101} shear which is related to twining of NM phase. Twin reorientation in this system is possible, because applied positive shear results in path with significantly smaller energetic barrier than for negative shear and for shears in other studied systems. When the full relaxation of lattice parameters is allowed, the barriers further strongly decrease and the structures along the twinning path can be considered as orthorhombic.

  17. Extend of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    CERN Document Server

    Rosenow, Phil

    2016-01-01

    The extent of hydrogen coverage of the Si(001)c(4x2) 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 computationa...

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

    Science.gov (United States)

    Enlow, Mark A

    2012-03-01

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

  19. Ab initio study of the phononic origin of negative thermal expansion

    Science.gov (United States)

    Argaman, Uri; Eidelstein, Eitan; Levy, Ohad; Makov, Guy

    2016-11-01

    Negative thermal expansion is an uncommon phenomenon of theoretical interest. Multiple hypotheses regarding its microscopic origins have been suggested. In this paper, the thermal expansion of a representative semiconductor, Si, and a representative metal, Ti, are calculated ab initio using density-functional perturbation theory. The phonon modes' contributions to the thermal expansion are analyzed and the negative thermal expansion is shown to be dominated by negative mode Grüneisen parameters at specific points on the Brillouin zone boundaries. Thus, the elastic (Debye) theory for negative thermal expansion is shown to be irrelevant for these phenomena. The anomalous behavior of these modes in Ti is shown to be unaffected by an electronic topological transition as previously suggested, instead it arises from complex interplay of atomic displacements of the anomalous mode.

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

    Science.gov (United States)

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

    2014-02-05

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

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

    Science.gov (United States)

    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.

  2. A New Generation of Cool White Dwarf Atmosphere Models Using Ab Initio Calculations

    Science.gov (United States)

    Blouin, S.; Dufour, P.; Kowalski, P. M.

    2017-03-01

    Due to their high photospheric density, cool helium-rich white dwarfs (particularly DZ, DQpec and ultracool) are often poorly described by current atmosphere models. As part of our ongoing efforts to design atmosphere models suitable for all cool white dwarfs, we investigate how the ionization ratio of heavy elements and the H2-He collision-induced absorption (CIA) spectrum are altered under fluid-like densities. For the conditions encountered at the photosphere of cool helium-rich white dwarfs, our ab initio calculations show that the ionization of most metals is inhibited and that the H2-He CIA spectrum is significantly distorted for densities higher than 0.1 g/cm3.

  3. A New Generation of Cool White Dwarf Atmosphere Models Using Ab Initio Calculations

    CERN Document Server

    Blouin, Simon; Kowalski, Piotr M

    2016-01-01

    Due to their high photospheric density, cool helium-rich white dwarfs (particularly DZ, DQpec and ultracool) are often poorly described by current atmosphere models. As part of our ongoing efforts to design atmosphere models suitable for all cool white dwarfs, we investigate how the ionization ratio of heavy elements and the H$_2$-He collision-induced absorption (CIA) spectrum are altered under fluid-like densities. For the conditions encountered at the photosphere of cool helium-rich white dwarfs, our ab initio calculations show that the ionization of most metals is inhibited and that the H$_2$-He CIA spectrum is significantly distorted for densities higher than 0.1 g/cm$^3$.

  4. Ab initio STUDIES ON MAGNETISM OF 3d TRANSITION METAL DIMERS

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Ab initio calculations with the self-consistent full-potential linearized augmented-plane-wave method (FLAPW), under generalized gradient approximation, have been carried out to describe the electronic and magnetic properties of 3d transition metal dimers. It predicted the antiferromagneticity of Cr2 and ferromagneticity of other species. The Mn2 dimer was shown to be ferromagnetic coupling with a local magnetic moment of 5μB. Retaining the value of its free atom state. The V2 and Ni2 exhibited low spin-polarization with local magnetic moment of only 1μB per atom. On the other hand, Fe2 and Co2 were highly spin-polarized with local magnetic moments of 3 and 2μB.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  7. Tailoring oxygen vacancies at ZnO( 1 1 ¯ 00 ) surface: An ab initio study

    Science.gov (United States)

    Korir, K. K.; Catellani, A.; Cicero, G.

    2016-09-01

    Oxygen vacancies in ZnO crystals have significant impacts on its properties and applications. On the basis of ab initio results, we describe the oxygen vacancy distribution and diffusion paths away from the ZnO( 1 1 ¯ 00 ) surface, aiming to elucidate thermodynamics and kinetic stability of the vacancies and a possible control mechanism. In view of defect engineering and sensor applications, we propose efficient routes to chemically control the equilibrium concentration of the oxygen vacancies at ZnO surfaces by exposure to specific reactive gases: we show that the oxygen vacancy concentration can be increased using sulfur oxide as post-growth treatment, while under exposure to ozone, no significant amount of oxygen vacancies can be sustained on the surface.

  8. Ab initio molecular dynamics study of hydrogen removal by ion-surface interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, Johanna [Materials Chemistry, RWTH-Aachen, D-52056 Aachen (Germany); Larsson, Karin [Department of Materials Chemistry, Angstroem Laboratory, Uppsala University, Box 538, 751 21 Uppsala (Sweden); Schneider, Jochen M [Materials Chemistry, RWTH-Aachen, D-52056 Aachen (Germany)

    2005-04-20

    The energy dependence of surface reactions has been investigated through ab initio MD simulations for collisions between Al{sup 1+} and a gibbsite surface. No change in surface composition was observed for 0 eV initial kinetic energy of Al{sup 1+}. An increase in energy to 3.5 eV resulted in extended surface migration of hydrogen, subsequent H{sub 2} formation and desorption from the surface. These results may be understood based on thermodynamics and an increase in entropy upon H{sub 2} formation. They are of fundamental importance for an increased understanding of thin film growth through the correlation between ion energy and film composition. They may also indicate a pathway to affect impurity incorporation during film growth. (letter to the editor)

  9. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  10. Convergence from cluster to surface:ab initio calculations of Pd_n clusters

    Institute of Scientific and Technical Information of China (English)

    徐昕; 王南钦; 吕鑫; 陈明旦; 张乾二

    1995-01-01

    The"Metallic State Principle"and a way to constitute the metallic basis set are proposed,the latter is a modification of atomic basis set based on the free electron theory in solid state physics.Pd_n dusters have been carefully studied by means of ab initio calculations with atomic and metallic basis sets.Three rules,namely the"Ground State Principle",the"Lowest-Spin State Principle"and the"Metallic StatePrinciple"have been investigated and the calculation results based on these three rules are compared with eachother in terms of metallic configuration of bulk Pd,d-band width,Fermi level,etc.The calculation resultsdemonstrate that the characteristic properties of bulk Pd may be reproduced to some extent even with a smallduster if the"Metallic State Principle"is adopted.

  11. Quantifying statistical uncertainties in ab initio nuclear physics using Lagrange multipliers

    CERN Document Server

    Carlsson, B D

    2016-01-01

    Theoretical predictions need quantified uncertainties for a meaningful comparison to experimental results. This is an idea which presently permeates the field of theoretical nuclear physics. In light of the recent progress in estimating theoretical uncertainties in ab initio nuclear physics, we here present and compare methods for evaluating the statistical part of the uncertainties. A special focus is put on the (for the field) novel method of Lagrange multipliers (LM). Uncertainties from the fit of the nuclear interaction to experimental data are propagated to a few observables in light-mass nuclei to highlight any differences between the presented methods. The main conclusion is that the LM method is more robust, while covariance based methods are less demanding in their evaluation.

  12. Ab initio phonon coupling and optical response of hot electrons in plasmonic metals

    CERN Document Server

    Brown, Ana M; Narang, Prineha; Goddard, William A; Atwater, Harry A

    2016-01-01

    Ultrafast laser measurements probe the non-equilibrium dynamics of excited electrons in metals with increasing temporal resolution. Electronic structure calculations can provide a detailed microscopic understanding of hot electron dynamics, but a parameter-free description of pump-probe measurements has not yet been possible, despite intensive research, because of the phenomenological treatment of electron-phonon interactions. We present ab initio predictions of the electron-temperature dependent heat capacities and electron-phonon coupling coefficients of plasmonic metals. We find substantial differences from free-electron and semi-empirical estimates, especially in noble metals above transient electron temperatures of 2000 K, because of the previously-neglected strong dependence of electron-phonon matrix elements on electron energy. We also present first-principles calculations of the electron-temperature dependent dielectric response of hot electrons in plasmonic metals, including direct interband and phon...

  13. Ultrafast transformation of graphite to diamond: an ab initio study of graphite under shock compression.

    Science.gov (United States)

    Mundy, Christopher J; Curioni, Alessandro; Goldman, Nir; Will Kuo, I-F; Reed, Evan J; Fried, Laurence E; Ianuzzi, Marcella

    2008-05-14

    We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12 kms (longitudinal stress>130 GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.

  14. Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO

    Institute of Scientific and Technical Information of China (English)

    HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)

    2002-01-01

    The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.

  15. The Ab Initio Studies of NO Chemisorption on TiO2(110) Surface

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The studies of NO chemisorption on TiO2(110) surface are the base of research to NO decomposed to N2O on TiO2 surface. In this paper, 12 kinds of possible models of NO adsorbed on TiO2 perfect and defect surface were calculated by use of ab initio cluster method. We carried out optimization of the geometry, calculation of the chemisorption energy and analysis of the Mulliken population to those adsorption models. According to the calculation results, it can be got that the adsorbed decomposition of NO on defect surface is more advantageous and M6 and M12 are the important models to NO chemisorption and decomposition on TiO2 surface.

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

    Science.gov (United States)

    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.

  17. Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.

    Science.gov (United States)

    Ionescu, Andrei R; Whitfield, Dennis M; Zgierski, Marek Z; Nukada, Tomoo

    2006-12-29

    We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.

  18. Ab initio calculation of the growth of Te nanorods and Bi2Te3 nanoplatelets

    Institute of Scientific and Technical Information of China (English)

    Tian Xiao-Qing; Du Shi-Xuan; Gao Hong-Jun

    2008-01-01

    In this paper the growth mechanism of a Te/Bi2Te3 novel structure is studied by ab-initio calculations.The results show that the growth of Te nanorods is determined by the adsorption energy of Te atoms on different crystalline Te surfaces.The adsorption energy of Te on the Te (001) surface is 3.29 eV,which is about 0.25 eV higher than that of Te on the Te (110).This energy difference makes the preferential growth direction along the < 001> direction.In addition,the higher surface energy of Bi2Te3 (110) and the lattice misfit between crystalline Bi2Te3 and Te along < 001> direction are considered to explain the growth of the Bi2Te3 nanoplatelets,in which Volmer-Weber model is used.The theoretical results axe in agreement with experimental observation.

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

    Science.gov (United States)

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

    2016-11-01

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

  20. Ab initio study of transport properties in defected carbon nanotubes: an O(N) approach

    Energy Technology Data Exchange (ETDEWEB)

    Biel, Blanca; GarcIa-Vidal, F J; Flores, Fernando [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, E-28049 Madrid (Spain); Rubio, Angel [European Theoretical Spectroscopy Facility (ETSF), Departamento de Fisica de Materiales, Universidad PaIs Vasco, Edificio Korta, Avenida Tolosa 72, 20018 San Sebastian (Spain)], E-mail: blanca.biel@cea.fr

    2008-07-23

    A combination of ab initio simulations and linear-scaling Green's functions techniques is used to analyze the transport properties of long (up to 1 {mu}m) carbon nanotubes with realistic disorder. The energetics and the influence of single defects (monovacancies and divacancies) on the electronic and transport properties of single-walled armchair carbon nanotubes are analyzed as a function of the tube diameter by means of the local orbital first-principles Fireball code. Efficient O(N) Green's functions techniques framed within the Landauer-Buettiker formalism allow a statistical study of the nanotube conductance averaged over a large sample of defected tubes and thus extraction of the nanotube localization length. The cases of zero and room temperature are both addressed.