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Sample records for ab initio interaction

  1. Ab initio MCDHF calculations of electron-nucleus interactions

    NASA Astrophysics Data System (ADS)

    Bieroń, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka

    2015-05-01

    We present recent advances in the development of atomic ab initio multiconfiguration Dirac-Hartree-Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac-Hartree-Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2011-01-01

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

  4. Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

    NASA Astrophysics Data System (ADS)

    Chen, Xi H.; Zhang, John Z. H.

    2004-06-01

    In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.

  5. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    NASA Astrophysics Data System (ADS)

    Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

    2015-02-01

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  6. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

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

    SciTech Connect

    Navratil, P; Ormand, W E; Forssen, C; Caurier, E

    2004-11-30

    There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

  8. Neutrino-nucleus interaction: an ab-initio perspective

    NASA Astrophysics Data System (ADS)

    Lovato, Alessandro

    2017-01-01

    Understanding of the structure and of the electroweak interactions of atomic nuclei in terms of their individual constituents is an intriguing nuclear many-body problem. I will present how the Quantum Monte Carlo community is pursuing a consistent description of the structure of atomic nuclei and their interaction with electroweak probes, providing a reliable estimate of the theoretical uncertainty of the calculation. I will also present benchmark calculations between Quantum Monte Carlo and the spectral function approach. Testing the factorization ansatz is of crucial importance, as the latter allows to combine a fully relativistic description of the interaction vertex with an accurate treatment of nuclear dynamics.

  9. Dissipative Particle Dynamics interaction parameters from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sepehr, Fatemeh; Paddison, Stephen J.

    2016-02-01

    Dissipative Particle Dynamics (DPD) is a commonly employed coarse-grained method to model complex systems. Presented here is a pragmatic approach to connect atomic-scale information to the meso-scale interactions defined between the DPD particles or beads. Specifically, electronic structure calculations were utilized for the calculation of the DPD pair-wise interaction parameters. An implicit treatment of the electrostatic interactions for charged beads is introduced. The method is successfully applied to derive the parameters for a hydrated perfluorosulfonic acid ionomer with absorbed vanadium cations.

  10. Ab Initio Study of Molecular Interactions in Cellulose Iα

    SciTech Connect

    Devarajan, Ajitha; Markutsya, Serjiy; Lamm, Monica H.; Cheng, Xiaolin; Smith, Jeremy C.; Baluyut, John Y.; Kholod, Yana; Gordon, Mark S.; Windus, Theresa L.

    2013-08-12

    Biomass recalcitrance, the resistance of cellulosic biomass to degradation, is due in part to the stability of the hydrogen bond network and stacking forces between the polysaccharide chains in cellulose microfibers. The fragment molecular orbital (FMO) method at the correlated Møller–Plesset second order perturbation level of theory was used on a model of the crystalline cellulose Iα core with a total of 144 glucose units. These computations show that the intersheet chain interactions are stronger than the intrasheet chain interactions for the crystalline structure, while they are more similar to each other for a relaxed structure. An FMO chain pair interaction energy decomposition analysis for both the crystal and relaxed structures reveals an intricate interplay between electrostatic, dispersion, charge transfer, and exchange repulsion effects. The role of the primary alcohol groups in stabilizing the interchain hydrogen bond network in the inner sheet of the crystal and relaxed structures of cellulose Iα, where edge effects are absent, was analyzed. The maximum attractive intrasheet interaction is observed for the GT-TG residue pair with one intrasheet hydrogen bond, suggesting that the relative orientation of the residues is as important as the hydrogen bond network in strengthening the interaction between the residues.

  11. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

    NASA Astrophysics Data System (ADS)

    Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki

    2015-07-01

    Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.

  12. Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

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

    1997-03-01

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

  14. Ab Initio Calculations of the Interaction between CO 2 and the Acetate Ion

    SciTech Connect

    Steckel, Janice A.

    2012-11-29

    A series of ab initio calculations designed to investigate the interaction of CO{sub 2} with acetate are presented. The lowest energy structure, AC–CO{sub 2}-η{sup 2}, is predicted by CCSD(T)/aVTZ to be bound by -10.6 kcal/mol. Six of the bound complexes have binding energies on the order of -8 kcal/mol, but analysis shows that the η{sup 1}-CT complex is fundamentally different from the others. The η{sup 1}-CT complex is characterized by geometric distortion, large polarization and induction effects and charge transfer whereas the other five complexes have little geometric distortion and negligible charge transfer. The amount of charge that is transferred from the anion to the CO{sub 2} in the η{sup 1}-CT complex is estimated to be about half an electron by NPA, DMA, CHELPG, and Mulliken analyses, whereas the EDA-ALMO-CTA (B3LYP) approach predicts a charge transfer of 75 me{sup –}. However, the transfer of this small amount of charge leads to an energy lowering of -56 kcal/mol, without which the complex would not be bound. The RI-MP2 geometries closely approximate those resulting from the CCSD optimizations, and the optimized second-order opposite spin (O2) method performs well for all the complexes except for the η{sup 1}-CT complex. DFT methods do not reproduce all the ab initio geometries, binding energies and/or energy ordering of these complexes although the range-separated hybrid meta-GGA (M11) and nonlocal (VV10 and vdwDF10) functionals are shown to yield results significantly better than other functionals considered for this system. The fact that there is such variation among DFT methods has implications for DFT-based ab initio molecular dynamics simulations and for the parametrization of classical force fields based on DFT calculations.

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

    NASA Astrophysics Data System (ADS)

    You, Y.; Yan, M. F.

    2013-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  17. Ab initio calculations in the symplectic no-core configuration interaction framework

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2015-11-19

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

  19. Ab initio calculations of nuclear structure and reactions with chiral two- and three-nucleon interactions

    NASA Astrophysics Data System (ADS)

    Navratil, Petr; Langhammer, Joachim; Hupin, Guillaume; Quaglioni, Sofia; Calci, Angelo; Roth, Robert; Soma, Vittorio; Cipollone, Andrea; Barbieri, Carlo; Duguet, T.

    2014-09-01

    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 recent years, a significant progress has been made in developing ab initio many-body approaches capable of describing both bound and scattering states in light and medium mass nuclei based on input from QCD employing Hamiltonians constructed within chiral effective field theory. We will present calculations of proton-10C scattering and resonances of the exotic nuclei 11N and 9He within the no-core shell model with continuum. Also, we will discuss calculations of binding and separation energies of neutron rich isotopes of Ar, K, Ca, Sc and Ti within the self-consistent Gorkov-Green's function approach. 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 recent years, a significant progress has been made in developing ab initio many-body approaches capable of describing both bound and scattering states in light and medium mass nuclei based on input from QCD employing Hamiltonians constructed within chiral effective field theory. We will present calculations of proton-10C scattering and resonances of the exotic nuclei 11N and 9He within the no-core shell model with continuum. Also, we will discuss calculations of binding and separation energies of neutron rich isotopes of Ar, K, Ca, Sc and Ti within the self-consistent Gorkov-Green's function approach. Support from the NSERC Grant No. 401945-2011 is acknowledged. This work was prepared in part by the LLNL under Contract No. DE-AC52-07NA27344.

  20. Do aurophilic interactions compete against hydrogen bonds? Experimental evidence and rationalization based on ab initio calculations.

    PubMed

    Codina, Antonio; Fernández, Eduardo J; Jones, Peter G; Laguna, Antonio; López-De-Luzuriaga, José M; Monge, Miguel; Olmos, M Elena; Pérez, Javier; Rodríguez, Miguel A

    2002-06-12

    [M(C6F5)(N(H)=CPh2)] (M = Ag (1) and Au (2)) complexes have been synthesized and characterized by X-ray diffraction analysis. Complex 1 shows a ladder-type structure in which two [Ag(C6F5)(N(H)=CPh2)] units are linked by a Ag(I)-Ag(I) interaction in an antiparallel disposition. The dimeric units are associated through hydrogen bonds of the type N-H...F(ortho). On the other hand, gold(I) complex 2 displays discrete dimers also in an antiparallel conformation in which both Au(I)-Au(I) interactions and N-H.F(ortho) hydrogen bonds appear within the dimeric units. The features of these coexisting interactions have been theoretically studied by ab initio calculations based on four different model systems in order to analyze them separately. The interactions have been analyzed at HF and MP2 levels of theory showing that, in this case, even at larger distances. The Au(I)-Au(I) interaction is stronger than Ag(I)-Ag(I) and that N-H.F hydrogen bonding and Au(I)-Au(I) contacts have a similar strength in the same molecule, which permits a competition between these two structural motifs giving rise to different structural arrangements.

  1. Revealing halogen bonding interactions with anomeric systems: an ab initio quantum chemical studies.

    PubMed

    Lo, Rabindranath; Ganguly, Bishwajit

    2015-02-01

    A computational study has been performed using MP2 and CCSD(T) methods on a series of O⋯X (X=Br, Cl and I) halogen bonds to evaluate the strength and characteristic of such highly directional noncovalent interactions. The study has been carried out on a series of dimeric complexes formed between interhalogen compounds (such as BrF, BrCl and BrI) and oxygen containing electron donor molecule. The existence and consequences of the anomeric effect of the electron donor molecule has also been investigated through an exploration of halogen bonding interactions in this halogen bonded complexes. The ab initio quantum chemical calculations have been employed to study both the nature and directionality of the halogen molecules toward the sp(3) oxygen atom in anomeric systems. The presence of anomeric nO→σ*CN interaction involves a dominant role for the availability of the axial and equatorial lone pairs of donor O atom to participate with interhalogen compounds in the halogen-bonded complexes. The energy difference between the axial and equatorial conformers with interhalogen compounds reaches up to 4.60 kJ/mol, which however depends upon the interacting halogen atoms and its attaching atoms. The energy decomposition analysis further suggests that the total halogen bond interaction energies are mainly contributed by the attractive electrostatic and dispersion components. The role of substituents attached with the halogen atoms has also been evaluated in this study. With the increase of halogen atom size and the positive nature of σ-hole, the halogen atom interacted more with the electron donor atom and the electrostatic contribution to the total interaction energy enhances appreciably. Further, noncovalent interaction (NCI) studies have been carried out to locate the noncovalent halogen bonding interactions in real space.

  2. Ab initio potential energy surfaces describing the interaction of CH(X2Π) with H2

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.

    2016-09-01

    We have determined four-dimensional ab initio quasi-diabatic potential energy surfaces describing the interaction of CH(X2Π) with H2, under the assumption of fixed CH and H2 internuclear separations. These calculations employed the multi-reference configuration interaction method [MRCISD+Q(Davidson)]. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants.

  3. Ab initio study of interaction of helium with edge and screw dislocations in tungsten

    NASA Astrophysics Data System (ADS)

    Bakaev, Alexander; Terentyev, Dmitry; Grigorev, Petr; Posselt, Matthias; Zhurkin, Evgeny E.

    2017-02-01

    The interaction of a single He atom with edge and screw dislocations in tungsten has been studied using ab initio calculations. It was revealed that He is strongly attracted to the core of both dislocations with the interaction energy of -1.3 and -3.0 eV for screw and edge dislocations, respectively, which corresponds to the detrapping temperature in thermal desorption spectroscopy experiments of about 500 K and 1050 K, respectively. The lowest energy positions for He around the dislocation cores are identified and the atomic structures are rationalized on the basis of elasticity theory considerations. Both types of dislocations exhibit a higher binding energy for He as compared to the He-He binding (known as self-trapping) and are weaker traps as compared to a single vacancy. It is, thus, concluded that the strong attraction to dislocation lines can contribute to the nucleation of He clusters in the temperature range which already excludes He self-trapping.

  4. Ab initio study of He-He interactions in homogeneous electron gas

    NASA Astrophysics Data System (ADS)

    Wang, Jinlong; Niu, Liang-Liang; Zhang, Ying

    2017-02-01

    We have investigated the immersion energy of a single He and the He-He interactions in homogeneous electron gas using ab initio calculations. It is found that He dislikes electrons and He-He interact via the He induced Friedel oscillations of electron densities. A critical electron density at which the global binding energy extremum shifts from the first minimum to the second one is identified. We also discover that the He-He global binding energy minimum of ∼-0.09 eV is reached at an optimal electron density of 0.04 e/Å3, corresponding to an optimal He-He separation of ∼1.7 Å. Further, the He atoms are found to gain a trivial amount of 2s and 2p states from the free electrons, inducing a hybridization between the He s- and p-states. The present results can qualitatively interpret the well-known He self-trapping behavior in metals.

  5. Acetonitrile-water hydrogen-bonded interaction: Matrix-isolation infrared and ab initio computation

    NASA Astrophysics Data System (ADS)

    Gopi, R.; Ramanathan, N.; Sundararajan, K.

    2015-08-01

    The 1:1 hydrogen-bonded complex of acetonitrile (CH3CN) and water (H2O) was trapped in Ar and N2 matrices and studied using infrared technique. Ab initio computations showed two types of complexes formed between CH3CN and H2O, a linear complex A with a Ctbnd N⋯H interaction between nitrogen of CH3CN and hydrogen of H2O and a cyclic complex B, in which the interactions are between the hydrogen of CH3CN with oxygen of H2O and hydrogen of H2O with π cloud of sbnd Ctbnd N of CH3CN. Vibrational wavenumber calculations revealed that both the complexes A and B were minima on the potential energy surface. Interaction energies computed at B3LYP/6-311++G(d,p) showed that linear complex A is more stable than cyclic complex B. Computations identified a blue shift of ∼11.5 cm-1 and a red shift of ∼6.5 cm-1 in the CN stretching mode for the complexes A and B, respectively. Experimentally, we observed a blue shift of ∼15.0 and ∼8.3 cm-1 in N2 and Ar matrices, respectively, in the CN stretching mode of CH3CN, which supports the formation of complex A. The Onsager Self Consistent Reaction Field (SCRF) model was used to explain the influence of matrices on the complexes A and B. To understand the nature of the interactions, Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were carried out for the complexes A and B.

  6. Ab initio dynamical vertex approximation

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.

  7. Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance

    NASA Astrophysics Data System (ADS)

    Spiwok, Vojtěch; Lipovová, Petra; Skálová, Tereza; Vondráčková, Eva; Dohnálek, Jan; Hašek, Jindřich; Králová, Blanka

    2005-12-01

    Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate-aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from -2.8 to -12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree-Fock method (interaction energies from +1.0 to -6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.

  8. Ab initio study of dopant-defect interactions in graphene sheets and graphene nano-ribbons

    NASA Astrophysics Data System (ADS)

    Tawalbeh, Tarek

    Theoretical studies of nanostructured systems, such as doped, defective and pristine graphene and graphene nanoribbons, present a major challenge to conventional computational methods. This thesis presents ab initio calculations based on density functional theory (DFT) to study the structural and electronic properties of doped and defective graphene and graphene 'nanoribbons. Our calculations are carried-out using density-functional pseudopotential approximations combined with the generalized gradient approximation (GGA) for the exchange-correlation functional. Structural optimizations are executed by iterative force minimization using the conjugate gradient algorithm. We investigate the effect of dopants and point defects on graphene and graphene nanoribbons and study the interactions between the two. Binding energies, equilibrium geometries, charge transfer, and exchange-splitting-induced magnetism are calculated. The dependence of dopant-defect separation distance on interaction energy and interaction energy is examined in detail. We find that the interaction energy for on-defect dopant sites is dominated by how well defect geometry accommodates the dopant-carbon interatomic distance. Depending on the site dopant-defect interaction is either attractive or repulsive. Stone-Wales defect-nitrogen pairing was found to induce exchange splitting and magnetism in certain configurations. Nitrogen was also found to passivate single-vacancy dangling bonds and eliminate exchange-splitting induced magnetism; vacancy-nitrogen interactions were found to be mostly attractive. Boron-vacancy pairing can result in a favorable symmetric sp3 configuration, this is the only vacancy-boron pairing were dangling bonds are passivated and magnetism is eliminated; other favorable boron-vacancy pairings maintain exchange splitting and can in some cases enhance it. We found that the effect of dopant-defect separation distance follows a simple inverse power law. Our results indicate that

  9. Ab-initio simulations of H2O interaction with b-SiC surfaces.

    NASA Astrophysics Data System (ADS)

    Cicero, Giancarlo

    2006-03-01

    We report on the interaction of gas phase water molecules with polar and non polar stoichiometric surfaces of cubic silicon carbide, a leading candidate semiconductor for bio-compatible devices. Finite temperature ab-initio molecular dynamics shows that the specific geometric arrangement of atoms on the outermost surface layer is responsible for water orientation and coordination and thus plays a major role in determining the surface reactivity. In particular, irrespective of coverage, water spontaneously dissociates on both polar[1] Si-terminated (001) and non-polar[2] (110) surfaces, while the C-terminated1 (001) surface is non-reactive and hydrophobic. Based on our results, we propose that STM images and photoemission experiments may detect specific changes induced by water on both the structural and electronic properties of SiC surfaces. We completed our investigation by studying a realistic solid/liquid interface[3] for the case of Si-SiC(001), after full hydroxylation takes place. We observed the formation of a thin ( 3 /AA) interfacial layer, which presents a higher density than bulk water. The liquid does not uniformly ‘wet’ the surface, rather molecules preferably bind along directions parallel to the Si dimer rows. Our calculations also predict that at 1 nm, the structural and electronic properties of liquid water are weakly affected by one-dimensional confinement between hydrophilic, solid substrates. [1] G. Cicero, A. Catellani and G. Galli Phys Rev. Lett. 93 (2004), 0161102; G. Cicero, A. Catellani and G. Galli J. Phys. Chem. B 108 (2004), 16518. [2] A. Catellani, G. Cicero and G. Galli J. Chem. Phys., in press. [3] G. Cicero, J. Grossman, A. Catellani and G. Galli J. Am. Chem. Soc. 127 (2005), 6830.

  10. Ab initio no-core properties of 7Li and 7Be with the JISP16 and chiral NNLOopt interactions

    NASA Astrophysics Data System (ADS)

    Heng, Taihua; Vary, James P.; Maris, Pieter

    2017-01-01

    We investigate the properties of 7Li with the JISP16 and chiral NNLOopt at next-to-next-to-leading order (NNLO) nucleon-nucleon interactions and 7Be with the JISP16 interaction in the ab initio no-core full configuration approach. We calculate selected observables that include energy spectra, point proton root-mean-square radii, electromagnetic moments, and transitions. We compare our results with experimental results, where available, as well as with results obtained using nucleon-nucleon plus three-nucleon interactions. We obtain reasonable agreement between theory and experiment for low-lying states that are dominated by p -shell configurations.

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

    DOE PAGES

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

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

  12. Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

    SciTech Connect

    Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D.

    2014-10-07

    We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  13. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

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

  14. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

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

  15. Ab Initio and Ab Exitu No-Core Shell Model

    SciTech Connect

    Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A

    2007-10-02

    We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.

  16. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

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

  17. Microstructure from joint analysis of experimental data and ab initio interactions: Hydrogenated amorphous silicon

    SciTech Connect

    Biswas, Parthapratim; Drabold, D. A.; Atta-Fynn, Raymond

    2014-12-28

    A study of the formation of voids and molecular hydrogen in hydrogenated amorphous silicon is presented based upon a hybrid approach that involves inversion of experimental nuclear magnetic resonance data in conjunction with ab initio total-energy relaxations in an augmented solution space. The novelty of this approach is that the voids and molecular hydrogen appear naturally in the model networks unlike conventional approaches, where voids are created artificially by removing silicon atoms from the networks. Two representative models with 16 and 18 at. % of hydrogen are studied in this work. The result shows that the microstructure of the a-Si:H network consists of several microvoids and few molecular hydrogen for concentration above 15 at. % H. The microvoids are highly irregular in shape and size, and have a linear dimension of 5–7 Å. The internal surface of a microvoid is found to be decorated with 4–9 hydrogen atoms in the form of monohydride Si–H configurations as observed in nuclear magnetic resonance experiments. The microstructure consists of (0.9–1.4)% hydrogen molecules of total hydrogen in the networks. These observations are consistent with the outcome of infrared spectroscopy, nuclear magnetic resonance, and calorimetry experiments.

  18. Molecular associations from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Iglesias, E.; Sordo, T. L.; Sordo, J. A.

    1991-12-01

    A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.

  19. Specific interactions between vitamin-D receptor and its ligands: Ab initio molecular orbital calculations in water.

    PubMed

    Takeda, Ryosuke; Kobayashi, Ittetsu; Shimamura, Kanako; Ishimura, Hiromi; Kadoya, Ryushi; Kawai, Kentaro; Kittaka, Atsushi; Takimoto-Kamimura, Midori; Kurita, Noriyuki

    2017-02-27

    Vitamin D is recognized to play important roles not only in the bone metabolism and the regulation of Ca amount in the blood but also in the onset of immunological diseases. These physiological actions caused by vitamin D are triggered by the specific interaction between vitamin D receptor (VDR) and vitamin D. In the present study, we investigated the interactions between VDR and vitamin D derivatives using ab initio molecular simulation, in order to elucidate the reason for the significant difference in their effects on VDR activity. Based on the results simulated, we elucidated which parts of the derivatives and which residues of VDR mainly contribute to the specific binding between VDR and the derivatives at an electronic level. This finding will be helpful for proposing new vitamin D derivatives as a potent modulator or inhibitor against VDR.

  20. Ab initio interaction potentials and scattering lengths for ultracold mixtures of metastable helium and alkali-metal atoms

    NASA Astrophysics Data System (ADS)

    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.

  1. Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene

    1996-01-01

    Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

  2. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations.

    PubMed

    Ahlstrand, Emma; Hermansson, Kersti; Friedman, Ran

    2017-03-24

    Zinc plays important roles in structural stabilization of proteins, enzyme catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynamics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Drude polarizable force field agreed better with the ab initio results, although the deviations between QM and MM were still rather large (40-96 kcal/mol). In order to gain further insight into Zn-ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand-ligand interactions did not play a significant role in the binding of Zn. Finally, analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn binding dynamics. An exchange between carboxylate (Asp/Glu) and imidazole (His) is less likely.

  3. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

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

  4. Ab initio no-core configuration interaction calculations of electromagnetic observables for p-shell nuclei using natural orbitals

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    The goal of ab initio nuclear theory is to provide quantitative predictions of nuclear observables, by solving the many-body problem starting from the internucleon interaction. The solution of the many-body problem involves large spaces with dimensions that grow fast with the number of nucleons and single-particle states included in the space. Convergence of nuclear observables in the employed space using an adequate set of single-particle orbitals is essential for making quantitative predictions. Long-range nuclear observables, such as the matrix elements of the E 2 operator, converge slowly when conventional oscillator single-particle orbitals are used for no-core configuration interaction (NCCI) calculations. Natural orbitals, obtained by diagonalizing the one-body density matrix from an initial NCCI calculation in the harmonic oscillator basis, provide accelerated convergence since they are adapted to the properties of the many-body wave function of the nucleus under study. We explore the convergence of electromagnetic observables of p-shell nuclei obtained using natural orbitals for NCCI calculations. Supported by the US DOE under Grants DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371. Computational resources provided by NERSC (supported by US DOE Contract DE-AC02-05CH11231) and the Notre Dame Center for Research Computing.

  5. Ab Initio Study of Polonium

    SciTech Connect

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

    2008-05-20

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

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

    SciTech Connect

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

    2015-04-21

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

  7. Ab initio based polarizable force field parametrization

    NASA Astrophysics Data System (ADS)

    Masia, Marco

    2008-05-01

    Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.

  8. Ab initio characterization of electron transfer coupling in photoinduced systems: generalized Mulliken-Hush with configuration-interaction singles.

    PubMed

    Chen, Hung-Cheng; Hsu, Chao-Ping

    2005-12-29

    To calculate electronic couplings for photoinduced electron transfer (ET) reactions, we propose and test the use of ab initio quantum chemistry calculation for excited states with the generalized Mulliken-Hush (GMH) method. Configuration-interaction singles (CIS) is proposed to model the locally excited (LE) and charge-transfer (CT) states. When the CT state couples with other high lying LE states, affecting coupling values, the image charge approximation (ICA), as a simple solvent model, can lower the energy of the CT state and decouple the undesired high-lying local excitations. We found that coupling strength is weakly dependent on many details of the solvent model, indicating the validity of the Condon approximation. Therefore, a trustworthy value can be obtained via this CIS-GMH scheme, with ICA used as a tool to improve and monitor the quality of the results. Systems we tested included a series of rigid, sigma-linked donor-bridge-acceptor compounds where "through-bond" coupling has been previously investigated, and a pair of molecules where "through-space" coupling was experimentally demonstrated. The calculated results agree well with experimentally inferred values in the coupling magnitudes (for both systems studied) and in the exponential distance dependence (for the through-bond series). Our results indicate that this new scheme can properly account for ET coupling arising from both through-bond and through-space mechanisms.

  9. The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water

    SciTech Connect

    DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2014-08-28

    In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H{sub 2}O){sub 128} significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, S{sub OO}(Q), and corresponding oxygen-oxygen radial distribution function, g{sub OO}(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, P{sub OOO}(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

  10. The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water.

    PubMed

    DiStasio, Robert A; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2014-08-28

    In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

  11. Ab initio study of pristine and Si-doped capped carbon nanotubes interacting with nimesulide molecules

    NASA Astrophysics Data System (ADS)

    Zanella, Ivana; Fagan, Solange B.; Mota, R.; Fazzio, A.

    2007-05-01

    The interaction of the nimesulide molecule with pristine and Si-doped capped carbon nanotubes is studied by first-principle calculations. The nimesulide molecules, which are basic components of an anti-inflammatory drug, combined with carbon nanostructures, could result in novel drug delivery systems. In this Letter, the nimesulide interaction with pristine capped nanotubes is shown as occuring in a physisorption regime and it is demonstrated that this interaction can be much more intense when the capped nanotube is substitutionaly doped with an Si atom. Then, the Si-doped capped nanotube can constitute a feasible novel nimesulide molecule delivery system.

  12. Electrostatically enhanced FF interactions through hydrogen bonding, halogen bonding and metal coordination: an ab initio study.

    PubMed

    Bauzá, Antonio; Frontera, Antonio

    2016-07-27

    In this manuscript the ability of hydrogen and halogen bonding interactions, as well as metal coordination to enhance FF interactions involving fluorine substituted aromatic rings has been studied at the RI-MP2/def2-TZVPD level of theory. We have used 4-fluoropyridine, 4-fluorobenzonitrile, 3-(4-fluorophenyl)propiolonitrile and their respective meta derivatives as aromatic compounds. In addition, we have used HF and IF as hydrogen and halogen bond donors, respectively, and Ag(i) as the coordination metal. Furthermore, we have also used HF as an electron rich fluorine donor entity, thus establishing FF interactions with the above mentioned aromatic systems. Moreover, a CSD (Cambridge Structural Database) search has been carried out and some interesting examples have been found, highlighting the impact of FF interactions involving aromatic fluorine atoms in solid state chemistry. Finally, cooperativity effects between FF interactions and both hydrogen and halogen bonding interactions have been analyzed and compared. We have also used Bader's theory of "atoms in molecules" to further describe the cooperative effects.

  13. Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

    SciTech Connect

    Orimoto, Yuuichi; Xie, Peng; Liu, Kai; Yamamoto, Ryohei; Imamura, Akira; Aoki, Yuriko

    2015-03-14

    An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for

  14. Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

    NASA Astrophysics Data System (ADS)

    Orimoto, Yuuichi; Yamamoto, Ryohei; Xie, Peng; Liu, Kai; Imamura, Akira; Aoki, Yuriko

    2015-03-01

    An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs' inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10-7-10-8 hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. -290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for

  15. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

    PubMed

    Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  16. Vacancy-solute interactions in ferromagnetic and paramagnetic bcc iron: Ab initio calculations

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    Vacancy-solute interactions play a crucial role in diffusion-controlled processes, such as ordering or decomposition, which occur in alloys under heat treatment or under irradiation. Detailed knowledge of these interactions is important for predicting long-term behavior of nuclear materials (such as reactor steels and nuclear-waste containers) as well as for advancing our general understanding of kinetic processes in alloys. Using first-principles calculations based on the density functional theory and employing the locally self-consistent Green's function technique, we develop a database of vacancy-solute interactions in dilute alloys of bcc Fe with 3p (Al, Si, P, S), 3d (Sc-Cu), and 4d (Y-Ag) elements. Unrelaxed interactions within the first three coordination shells have been computed in the ferromagnetic state as well as in the paramagnetic (disordered local moment) state of the iron matrix. Magnetism is found to have a strong effect on the vacancy-solute interactions. Implications of the obtained results for interpreting the effects of vacancy trapping and enhanced impurity diffusion are discussed.

  17. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-03

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

  18. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  19. Interpretation of the photoelectron, ultraviolet, and vacuum ultraviolet photoabsorption spectra of bromobenzene by ab initio configuration interaction and DFT computations

    SciTech Connect

    Palmer, Michael H. Ridley, Trevor E-mail: vronning@phys.au.dk E-mail: marcello.coreno@elettra.eu E-mail: malgorzata.biczysko@sns.it; Hoffmann, Søren Vrønning E-mail: vronning@phys.au.dk E-mail: marcello.coreno@elettra.eu E-mail: malgorzata.biczysko@sns.it Jones, Nykola C. E-mail: vronning@phys.au.dk E-mail: marcello.coreno@elettra.eu E-mail: malgorzata.biczysko@sns.it; Coreno, Marcello E-mail: vronning@phys.au.dk E-mail: marcello.coreno@elettra.eu E-mail: malgorzata.biczysko@sns.it; Grazioli, Cesare; Zhang, Teng; and others

    2015-10-28

    New photoelectron, ultraviolet (UV), and vacuum UV (VUV) spectra have been obtained for bromobenzene by synchrotron study with higher sensitivity and resolution than previous work. This, together with use of ab initio calculations with both configuration interaction and time dependent density functional theoretical methods, has led to major advances in interpretation. The VUV spectrum has led to identification of a considerable number of Rydberg states for the first time. The Franck-Condon (FC) analyses including both hot and cold bands lead to identification of the vibrational structure of both ionic and electronically excited states including two Rydberg states. The UV onset has been interpreted in some detail, and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. In a similar way, the 6 eV absorption band which is poorly resolved is analysed in terms of the presence of two ππ* states of {sup 1}A{sub 1} (higher oscillator strength) and {sup 1}B{sub 2} (lower oscillator strength) symmetries, respectively. The detailed analysis of the vibrational structure of the 2{sup 2}B{sub 1} ionic state is particularly challenging, and the best interpretation is based on equation-of-motion-coupled cluster with singles and doubles computations. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene. The equilibrium structures of the 3b{sub 1}3s and 6b{sub 2}3s (valence shell numbering) Rydberg states have been obtained and compared with the corresponding ionic limit structures.

  20. Interpretation of the photoelectron, ultraviolet, and vacuum ultraviolet photoabsorption spectra of bromobenzene by ab initio configuration interaction and DFT computations.

    PubMed

    Palmer, Michael H; Ridley, Trevor; Hoffmann, Søren Vrønning; Jones, Nykola C; Coreno, Marcello; de Simone, Monica; Grazioli, Cesare; Zhang, Teng; Biczysko, Malgorzata; Baiardi, Alberto; Peterson, Kirk

    2015-10-28

    New photoelectron, ultraviolet (UV), and vacuum UV (VUV) spectra have been obtained for bromobenzene by synchrotron study with higher sensitivity and resolution than previous work. This, together with use of ab initio calculations with both configuration interaction and time dependent density functional theoretical methods, has led to major advances in interpretation. The VUV spectrum has led to identification of a considerable number of Rydberg states for the first time. The Franck-Condon (FC) analyses including both hot and cold bands lead to identification of the vibrational structure of both ionic and electronically excited states including two Rydberg states. The UV onset has been interpreted in some detail, and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. In a similar way, the 6 eV absorption band which is poorly resolved is analysed in terms of the presence of two ππ* states of (1)A1 (higher oscillator strength) and (1)B2 (lower oscillator strength) symmetries, respectively. The detailed analysis of the vibrational structure of the 2(2)B1 ionic state is particularly challenging, and the best interpretation is based on equation-of-motion-coupled cluster with singles and doubles computations. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene. The equilibrium structures of the 3b13s and 6b23s (valence shell numbering) Rydberg states have been obtained and compared with the corresponding ionic limit structures.

  1. Chemical interaction of water molecules with framework Al in acid zeolites: a periodic ab initio study on H-clinoptilolite.

    PubMed

    Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2015-09-28

    Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed.

  2. Emergence of rotational bands in ab initio no-core configuration interaction calculations of light nuclei

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    The emergence of rotational bands has recently been observed in no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. Yrast and low-lying excited bands are found. The results demonstrate the possibility of well-developed rotational structure in NCCI calculations, using realistic nucleon-nucleon interactions, and within finite, computationally-accessible configuration spaces. This talk will focus on results for rotation in both the even-mass and odd-mass Be isotopes (7 <= A <= 12). Supported by US DOE (DE-FG02-95ER-40934, DESC0008485 SciDAC/NUCLEI, DE-FG02-87ER40371), US NSF (0904782), and Research Corporation for Science Advancement (Cottrell Scholar Award). Computational resources provided by NERSC (US DOE DE-AC02-05CH11231).

  3. Ab Initio Modeling Of Friction Reducing Agents Shows Quantum Mechanical Interactions Can Have Macroscopic Manifestation.

    PubMed

    Hernández Velázquez, J D; Barroso-Flores, J; Gama Goicochea, A

    2016-11-23

    Two of the most commonly encountered friction-reducing agents used in plastic sheet production are the amides known as erucamide and behenamide, which despite being almost identical chemically, lead to markedly different values of the friction coefficient. To understand the origin of this contrasting behavior, in this work we model brushes made of these two types of linear-chain molecules using quantum mechanical numerical simulations under the density functional theory at the B97D/6-31G(d,p) level of theory. Four chains of erucamide and behenamide were linked to a 2 × 10 zigzag graphene sheet and optimized both in vacuum and in continuous solvent using the SMD implicit solvation model. We find that erucamide chains tend to remain closer together through π-π stacking interactions arising from the double bonds located at C13-C14, a feature behenamide lacks, and thus a more spread configuration is obtained with the latter. It is argued that this arrangement of the erucamide chains is responsible for the lower friction coefficient of erucamide brushes, compared with behenamide brushes, which is a macroscopic consequence of cooperative quantum mechanical interactions. While only quantum level interactions are modeled here, we show that behenamide chains are more spread out in the brush than erucamide chains as a consequence of those interactions. The spread-out configuration allows more solvent particles to penetrate the brush, leading in turn to more friction, in agreement with macroscopic measurements and mesoscale simulations of the friction coefficient reported in the literature.

  4. Ab initio study of interstitial cluster interaction with Re, Os, and Ta in W

    NASA Astrophysics Data System (ADS)

    Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

    2017-02-01

    The stability of tungsten self-interstitial atom (SIA) clusters is studied using first-principles methods. Clusters from one to seven SIAs are systematically explored from 1264 unique configurations. Finite-size effect of the simulation cell is corrected based on the scaling of formation energy versus inverse volume cell. Furthermore, the accuracy of the calculations is improved by treating the 5p semicore states as valence states. Configurations of the three most stable clusters in each cluster size n are presented, which consist of parallel [111] dumbbells. The evolution of these clusters leading to small dislocation loops is discussed. The binding energy of size-n clusters is analyzed relative to an n → (n-1) + 1 dissociation and is shown to increase with size. Extrapolation for n > 7 is presented using a dislocation loop model. In addition, the interaction of these clusters with a substitutional Re, Os, or Ta solute is explored by replacing one of the dumbbells with the solute. Re and Os strongly attract these clusters, but Ta strongly repels. The strongest interaction is found when the solute is located on the periphery of the cluster rather than in the middle. The magnitude of this interaction decreases with cluster size. Empirical fits to describe the trend of the solute binding energy are presented.

  5. Ab initio metadynamics simulations of oxygen/ligand interactions in organoaluminum clusters

    SciTech Connect

    Alnemrat, Sufian; Hooper, Joseph P.

    2014-10-14

    Car-Parrinello molecular dynamics combined with a metadynamics algorithm is used to study the initial interaction of O{sub 2} with the low-valence organoaluminum clusters Al{sub 4}Cp{sub 4} (Cp=C{sub 5}H{sub 5}) and Al{sub 4}Cp{sub 4}{sup *} (Cp{sup *}=C{sub 5}[CH{sub 3}]{sub 5}). Prior to reaction with the aluminum core, simulations suggest that the oxygen undergoes a hindered crossing of the steric barrier presented by the outer ligand monolayer. A combination of two collective variables based on aluminum/oxygen distance and lateral oxygen displacement was found to produce distinct reactant, product, and transition states for this process. In the methylated cluster with Cp{sup *} ligands, a broad transition state of 45 kJ/mol was observed due to direct steric interactions with the ligand groups and considerable oxygen reorientation. In the non-methylated cluster the ligands distort away from the oxidizer, resulting in a barrier of roughly 34 kJ/mol with minimal O{sub 2} reorientation. A study of the oxygen/cluster system fixed in a triplet multiplicity suggests that the spin state does not affect the initial steric interaction with the ligands. The metadynamics approach appears to be a promising means of analyzing the initial steps of such oxidation reactions for ligand-protected clusters.

  6. Switching magnetic interactions in the NiFe Prussian Blue Analogue: an ab initio inspection.

    PubMed

    Krah, Tim; Amor, Nadia Ben; Robert, Vincent

    2014-05-28

    The magnetic interaction in the Ni(ii)-Fe(iii) Prussian Blue Analogue is investigated by means of Difference Dedicated Configuration Interaction (DDCI) calculations. Embedded cluster calculations are performed to extract the exchange coupling constant J with respect to an opening of the Ni-NC-Fe bridge while maintaining a rigid Fe(CN)6 unit. It is shown that such active distortion significantly modifies the magnetic interaction scheme in the material. Not only a ferromagnetic to antiferromagnetic transition is observed, but the J value is varied from +11.4 cm(-1) to -12.5 cm(-1) when the Ni-Fe cyanide bridge is opened by 20°. The enhancement of the intersite hopping electron transfer integral by a factor of 1.5 can be correlated with the observed Na(+)-ion mobility in a unified "cation-coupled electron transfer" (CCET) process. These results stress the complexity and originality of this class of compounds evidenced by the versatility of their magnetic network.

  7. Ab initio Study of Nuclear Quadrupole Interactions in Selenium and Tellurium

    NASA Astrophysics Data System (ADS)

    Maharjan, N. B.; Paudyal, D. D.; Mishra, D. R.; Byahut, S. P.; Cho, Hwa-Suck; Scheicher, R. H.; Jeong, Junho; Das, T. P.

    2004-03-01

    We are systematically studying the influence of impurities in calcogenide glasses on the glass transition temperature using the first-principles Hartree-Fock cluster method. Results of our calculations on the electronic structures of pure selenium and tellurium chain systems, and with Te and Se impurities respectively, will be reported. By comparing the theoretically obtained nuclear quadrupole interaction (NQI) tensors for ^77Se and ^125Te with available experimental NQI tensors, we were able to test the accuracy of the calculated electronic structures. Good agreement for both the pure and the impurity systems has been found. We have also studied ^125Te NQI tensors in Te-Thiourea and compared our result with experimental data to check on the choice of the ^125Te quadrupole moment used.

  8. Important factors stabilizing stacking interaction between 3-nitropyrrole and natural nucleobases revealed by ab initio calculations.

    PubMed

    Seio, Kohji; Ukawa, Hisashi; Shohda, Koh-ichiro; Sekine, Mitsuo

    2003-01-01

    Stacking energies between canonical nucleobases and a universal base, 3-nitropyrrole (3-NP), were estimated by use of molecular orbital (MO) and molecular mechanics (MM) calculations. The detailed analysis of the energy profiles revealed the importance of the London dispersion energy to stabilize the stacked dimers and electrostatic interactions to determine the orientation of 3-NP to the nucleobases in the dimers. Although the energy profiles of 3-NP/natural base dimers obtained by the MO and MM calculations were qualitatively correlated with each other, the correlations were poorer than those obtained for the stacking between natural bases. The origin of the difference between 3-NP and natural bases will be discussed to understand the possibility and limitation of the current MM calculations for the simulation and design of other universal bases.

  9. Ab Initio Petaflop-scale Particle-in-Cell Simulation of Laser-Plasma Interaction

    NASA Astrophysics Data System (ADS)

    Albright, Brian

    2008-11-01

    Large three-dimensional (3D) particle-in-cell (PIC) simulations have been performed using the VPIC code on some of the world's largest supercomputers, including the Roadrunner supercomputer, the first machine capable of a petaflop/s. These simulations have revealed the complex physical mechanisms underlying laser-plasma interactions and show an emerging universal picture of nonlinear saturation of LPI in the kinetic regime. Moreover, with the advent of peta-scale computing, we are entering an era of ``at-scale'' modeling necessary to understand the essential nonlinearity of LPI in solitary laser speckles, the building-blocks of multi-speckle beams. Under NIF-relevant conditions, stimulated Raman scattering (SRS) vs. speckle intensity shows a sharp onset at a threshold intensity (below linear estimates) and saturation at higher intensity, as validated in Trident experiments. Wavefront bowing of electron plasma waves (EPW) from trapped electron nonlinear frequency shift and amplitude-dependent damping is observed in 3D. This is followed by trapped particle modulational instability, which evolves nonlinearly into self-focusing, rapid transverse EPW phase variation, increased loss of trapped electrons, and EPW damping. In 3D, EPW turbulence may also exhibit loss of coherence through azimuthal filamentation. This reduction of source coherence for backscattered light and increased damping limit how much backscatter can obtain in a speckle. In addition, 3D modeling of novel ultraintense laser-ion acceleration mechanisms will be shown. Collaborators: L. Yin, K. J. Bowers, B. Bergen, D. S. Montgomery, J. L. Kline, H. A. Rose, B. M. Hegelich, K. A. Flippo, J. C. Fern'andez.

  10. Ab initio study of cyanoguanidine isomers

    NASA Astrophysics Data System (ADS)

    Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.

    1995-06-01

    An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers ('cyanioime' and 'cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.

  11. Ab initio study of cyanoguanidine isomers

    NASA Astrophysics Data System (ADS)

    Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.

    1995-06-01

    An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers (‘cyanioime' and ‘cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.

  12. Specific interactions between amyloid-β peptides in an amyloid-β hexamer with three-fold symmetry: Ab initio fragment molecular orbital calculations in water

    NASA Astrophysics Data System (ADS)

    Ishimura, Hiromi; Tomioka, Shogo; Kadoya, Ryushi; Shimamura, Kanako; Okamoto, Akisumi; Shulga, Sergiy; Kurita, Noriyuki

    2017-03-01

    The accumulation of amyloid-beta (Aβ) aggregates in brain contributes to the onset of Alzheimer's disease (AD). Recent structural analysis for the tissue obtained from AD patients revealed that Aβ aggregates have a single structure with three-fold symmetry. To explain why this structure possesses significant stability, we here investigated the specific interactions between Aβ peptides in the aggregate, using ab initio fragment molecular orbital calculations. The results indicate that the interactions between the Aβ peptides of the stacked Aβ pair are stronger than those between the Aβ peptides of the trimer with three-fold symmetry and that the charged amino-acids are important.

  13. Towards SiC Surface Functionalization: An Ab Initio Study

    SciTech Connect

    Cicero, G; Catellani, A

    2005-01-28

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

  14. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  15. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  16. Tryptophan interactions with glycerol/water and trehalose/sucrose cryosolvents: infrared and fluorescence spectroscopy and ab initio calculations.

    PubMed

    Dashnau, Jennifer L; Zelent, Bogumil; Vanderkooi, Jane M

    2005-04-01

    In order to correlate how the solvent affects emission properties of tryptophan, the fluorescence and phosphorescence emission spectra of tryptophan and indole model compounds were compared for solid sugar glass (trehalose/sucrose) matrix and glycerol/water solution and under the same conditions, these matrices were examined by infrared spectroscopy. Temperature was varied from 290 to 12 K. In sugar glass, the fluorescence and phosphorescence emission spectra are constant over this temperature range and the fluorescence remains red shifted; these results are consistent with the static interaction of OH groups with tryptophan in the sugar glass. In sugar glass containing water, the water retains mobility over the entire temperature range as indicated by the HOH infrared bending frequency. The fluorescence of tryptophan in glycerol/water shifts to the blue as temperature decreases and the frequency change of the absorption of the HOH bend mode is larger than in the sugar glass. These results suggest rearrangement of glycerol and water molecules over the entire temperature change. Shifts in the fluorescence emission maximum of indole and tryptophan were relatively larger than shifts for the phosphorescence emission-as expected for the relatively smaller excited triplet state dipole for tryptophan. The fluorescence emission of tryptophan in glycerol/water at low temperature has maxima at 312, 313, and 316 nm at pH 1.4, 7.0, and 10.6, respectively. The spectral shifts are interpreted to be an indication of a charge, or Stark phenomena, effect on the excited state molecule, as supported by ab initio calculations. To check whether the amino acid remains charged over the temperature range, the infrared spectrum of alanine was monitored over the entire range of temperature. The ratio of infrared absorption characteristic of carboxylate/carbonyl was constant in glycerol/water and sugar glass, which indicates that the charge was retained. Tryptophan buried in proteins, namely

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

    SciTech Connect

    Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.

    2015-01-31

    In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.

  18. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

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

    1983-06-01

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

  19. Ab initio Theory of Semiconductor Nanocrystals

    NASA Astrophysics Data System (ADS)

    Wang, Lin-Wang

    2007-03-01

    With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).

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

    PubMed

    Makarewicz, Jan; Shirkov, Leonid

    2016-05-28

    The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

  1. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

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

  2. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

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

    2014-02-28

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

  3. Ab Initio Crystal Field for Lanthanides.

    PubMed

    Ungur, Liviu; Chibotaru, Liviu F

    2017-03-13

    An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.

  4. AB initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

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

    1982-08-01

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

  5. Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: a new ab initio dipole surface for high-temperature applications.

    PubMed

    Li, Xiaoping; Mandal, Anirban; Miliordos, Evangelos; Hunt, Katharine L C

    2012-01-28

    We report new ab initio results for the interaction-induced dipole moments Δμ of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of very cool white dwarf stars, with temperatures from 3500 K to 9000 K. We have evaluated the dipoles based on finite-field calculations, with coupled cluster methods in MOLPRO 2006 and aug-cc-pV5Z (spdfg) basis sets for both the H and He centers. We have obtained values of Δμ for eight H(2) bond lengths ranging from 0.942 a.u. to 2.801 a.u., for 15 intermolecular separations R ranging from 2.0 a.u. to 10.0 a.u., and for 19 different relative orientations. In general, our values agree well with earlier ab initio results, for the geometrical configurations that are treated in common, but we have determined more points on the collision-induced dipole surface by an order of magnitude. These results make it possible to calculate transition probabilities for molecules in excited vibrational states, overtones, and rotational transitions with ΔJ > 4. We have cast our results in the symmetry-adapted form needed for absorption line shape calculations, by expressing Δμ as a series in the spherical harmonics of the orientation angles of the intermolecular vector and of a unit vector along the H(2) bond axis. The expansion coefficients depend on the H(2) bond length and the intermolecular distance R. For large separations R, we show that the ab initio values of the leading coefficients converge to the predictions from perturbation theory, including both classical multipole polarization and dispersion effects.

  6. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

  7. Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems

    SciTech Connect

    Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi

    2015-01-22

    In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.

  8. Close shell interactions in 3-ethoxycarbonyl-4-hydroxy-6-methoxymethyleneoxy-1-methyl-2-quinolone: 100 K single crystal neutron diffraction study and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Pozzi, C. G.; Fantoni, A. C.; Goeta, A. E.; Wilson, C. C.; Autino, J. C.; Punte, G.

    2005-10-01

    The molecular and crystal structures of the title compound have been determined from a single crystal neutron diffraction experiment at 100 K. A comparison between the main geometrical features and related properties of the in-crystal and the ab initio optimized free molecule structures has shown that crystal packing induces a significant distortion in the molecular geometry. Packing instead would only have a moderate effect on the observed intramolecular resonance assisted hydrogen bond. Supermolecular ab initio molecular orbital calculations have been performed on the six different dimers one molecule forms with its nine nearest neighbours. The obtained results clearly show that dispersion contributions dominate in the most strongly interacting dimers, in good qualitative accord with the predictions made by using different empirical potentials. A qualitative description of the most prominent inductive effects determined from the electron density deformation upon dimer formation is presented. Topological analyses of the dimers charge densities have been performed in the framework of the Bader's AIM theory and all the intermolecular bond critical points have been identified. An attempt to determine some of the interaction energies only from topological quantities made evident the practical limitations of such an approach.

  9. Magnitude and orientation dependence of intermolecular interaction of perfluoropropane dimer studied by high-level ab initio calculations: Comparison with propane dimer

    NASA Astrophysics Data System (ADS)

    Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro; Urata, Shingo

    2004-11-01

    Intermolecular interaction energies of 12 orientations of C3F8 dimers were calculated with electron correlation correction by the second-order Møller-Plesset perturbation method. The antiparallel C2h dimer has the largest interaction energy (-1.45 kcal/mol). Electron correlation correction increases the attraction considerably. Electrostatic energy is not large. Dispersion is mainly responsible for the attraction. Orientation dependence of the interaction energy of the C3F8 dimer is substantially smaller than that of the C3H8 dimer. The calculated interaction energy of the C3F8 dimer at the potential minimum is 78% of that of the C3H8 dimer (-1.85 kcal/mol), whereas the interaction energies of the CF4 and C2F6 dimers are larger than those of the CH4 and C2H6 dimers. The intermolecular separation in the C3F8 dimer at the potential minimum is substantially larger than that in the C3H8 dimer. The larger intermolecular separation due to the steric repulsion between fluorine atoms is the cause of the smaller interaction energy of the C3F8 dimer at the potential minimum. The calculated intermolecular interaction energy potentials of the C3F8 dimers using an all atom model OPLS-AA (OPLS all atom model) force field and a united atom model force field were compared with the ab initio calculations. Although the two force fields well reproduces the experimental vapor and liquid properties of perfluoroalkenes, the comparison shows that the united atom model underestimates the potential depth and orientation dependence of the interaction energy. The potentials obtained by the OPLS-AA force field are close to those obtained by the ab initio calculations.

  10. Ab initio no core shell model

    SciTech Connect

    Barrett, Bruce R.; Navrátil, Petr; Vary, James P.

    2012-11-17

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN

  11. Study of the thermodynamic properties of CeO{sub 2} from ab initio calculations: The effect of phonon-phonon interaction

    SciTech Connect

    Niu, Zhen-Wei; Zeng, Zhao-Yi; Hu, Cui-E; Cai, Ling-Cang; Chen, Xiang-Rong

    2015-01-07

    The thermodynamic properties of CeO{sub 2} have been reevaluated by a simple but accurate scheme. All our calculations are based on the self-consistent ab initio lattice dynamical (SCAILD) method that goes beyond the quasiharmonic approximation. Through this method, the effects of phonon-phonon interactions are included. The obtained thermodynamic properties and phonon dispersion relations are in good agreement with experimental data when considering the correction of phonon-phonon interaction. We find that the correction of phonon-phonon interaction is equally important and should not be neglected. At last, by comparing with quasiharmonic approximation, the present scheme based on SCAILD method is probably more suitable for high temperature systems.

  12. Ab initio self-consistent Gorkov-Green's function calculations of semimagic nuclei: Formalism at second order with a two-nucleon interaction

    NASA Astrophysics Data System (ADS)

    Somà, V.; Duguet, T.; Barbieri, C.

    2011-12-01

    An ab initio calculation scheme for finite nuclei based on self-consistent Green's functions in the Gorkov formalism is developed. It aims at describing properties of doubly magic and semimagic nuclei employing state-of-the-art microscopic nuclear interactions and explicitly treating pairing correlations through the breaking of U(1) symmetry associated with particle number conservation. The present paper introduces the formalism necessary to undertake applications at (self-consistent) second order using two-nucleon interactions in a detailed and self-contained fashion. First applications of such a scheme will be reported soon in a forthcoming publication. Future works will extend the present scheme to include three-nucleon interactions and implement more advanced truncation schemes.

  13. Cation-specific interactions with carboxylate in amino acid and acetate aqueous solutions: X-ray absorption and ab initio calculations.

    PubMed

    Aziz, Emad F; Ottosson, Niklas; Eisebitt, Stefan; Eberhardt, Wolfgang; Jagoda-Cwiklik, Barbara; Vácha, Robert; Jungwirth, Pavel; Winter, Bernd

    2008-10-09

    Relative interaction strengths between cations (X = Li (+), Na (+), K (+), NH 4 (+)) and anionic carboxylate groups of acetate and glycine in aqueous solution are determined. These model systems mimic ion pairing of biologically relevant cations with negatively charged groups at protein surfaces. With oxygen 1s X-ray absorption spectroscopy, we can distinguish between spectral contributions from H 2O and carboxylate, which allows us to probe the electronic structure changes of the atomic site of the carboxylate group being closest to the countercation. From the intensity variations of the COO (-) aq O 1s X-ray absorption peak, which quantitatively correlate with the change in the local partial density of states from the carboxylic site, interactions are found to decrease in the sequence Na (+) > Li (+) > K (+) > NH 4 (+). This ordering, as well as the observed bidental nature of the -COO (-) aq and X (+) aq interaction, is supported by combined ab initio and molecular dynamics calculations.

  14. Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer.

    PubMed

    Řezáč, Jan; Hobza, Pavel

    2014-08-12

    Hydrogen fluoride dimer is a perfect model system for studying hydrogen bonding. Its size makes it possible to apply the most advanced theoretical methods available, yet it is a full-featured complex of molecules with nontrivial electronic structure and dynamic properties. Moreover, the dissociation energy of the HF dimer has been measured experimentally with an unparalleled accuracy of ±1 cm(-1)(Bohac et al. J. Chem. Phys. 1992, 9, 6681). In this work, we attempt to reproduce it by purely ab initio means, using advanced quantum-mechanical computational methods free of any empiricism. The purpose of this study is to demonstrate the capabilities of today's computational chemistry and to point out its limitations by identifying the contributions that introduce the largest uncertainty into the result. The dissociation energy is calculated using a composite scheme including large basis set CCSD(T) calculations, contributions of higher excitations up to CCSDTQ, relativistic and diagonal Born-Oppenheimer corrections and anharmonic vibrational calculations. The error of the calculated dissociation energy is 0.07 kcal/mol (25 cm(-1), 2.5%) when compared to the experiment. The major part of this error can be attributed to the inaccuracy of the calculations of the zero-point vibrational energy.

  15. Ab Initio Calculations Of Light-Ion Reactions

    SciTech Connect

    Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W

    2012-03-12

    The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

  16. Ab initio theories for light nuclei and neutron stars

    NASA Astrophysics Data System (ADS)

    Gezerlis, Alexandros

    2016-09-01

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

  17. Accurate ab Initio Spin Densities.

    PubMed

    Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus

    2012-06-12

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

  18. Germacrene D Cyclization: An Ab Initio Investigation

    PubMed Central

    Setzer, William N.

    2008-01-01

    Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722

  19. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

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

  20. Ab-initio phasing in protein crystallography

    NASA Astrophysics Data System (ADS)

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

    2000-11-01

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

  1. Ab-initio Studies Of Lithium Oxide

    NASA Astrophysics Data System (ADS)

    Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.

    2010-12-01

    Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.

  2. Fully relativistic ab initio calculations of the energies of chiral molecules including parity-violating weak interactions

    NASA Astrophysics Data System (ADS)

    Laerdahl, Jon K.; Schwerdtfeger, Peter

    1999-12-01

    The parity-odd perturbation operator for the inelastic electron-nucleon scattering by weak neutral currents (exchange of virtual Z0 bosons) has been implemented into a fully relativistic four-component Dirac-Hartree-Fock scheme. Dirac-Hartree-Fock electronic structure calculations on H2O2, H2S2, H2Se2, H2Te2, and H2Po2 provides a demonstration of the higher than Z5 scaling of the parity-violating energy shift (Z is the nuclear charge) in chiral molecules. To our knowledge, the calculations for H2Te2 and H2Po2 are the first for molecules containing heavy elements from period 5 or 6 of the Periodic Table, and the parity-violating energy shifts are some of the highest reported in any ab initio study. It has been shown that special care is needed in the basis set expansion of the wave function because of the coupling between the large and small components of the Dirac wave function through the γ5 matrix. Estimates of the remaining errors in the calculations have been given. A comparison with the calculated parity-violating energy shift of H2TeO have confirmed the importance of the single-center theorem, which states that the parity-violating energy shift is suppressed in molecules containing only a single heavy atomic center. Due to the close correspondence between parity-violating energy shifts and observable parity-odd properties, our results have important consequences for the current search for an experimental confirmation of parity-odd effects in molecular physics: (i) The experiments should be performed on molecules containing heavy (period 5 or 6) elements. (ii) Molecules with more than one heavy atomic center will be extremely favorable due to the single-center theorem.

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

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

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

  4. Ab initio non-relativistic spin dynamics

    SciTech Connect

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

    2014-12-07

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

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

    SciTech Connect

    Draayer, Jerry P.

    2014-09-28

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

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  7. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

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

  8. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

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

    2014-11-02

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

  9. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

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

  10. Ab Initio Calculation of the Hoyle State

    SciTech Connect

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

    2011-05-13

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

  11. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  12. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

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

    2014-01-01

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

  13. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...

    2014-11-02

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

  14. Ab initio prediction of adsorption isotherms for small molecules in metal-organic frameworks: the effect of lateral interactions for methane/CPO-27-Mg.

    PubMed

    Sillar, Kaido; Sauer, Joachim

    2012-11-07

    A hybrid method that combines density functional theory for periodic structures with wave function-based electron correlation methods for finite-size models of adsorption sites is employed to calculate energies for adsorption of CH(4) onto different sites in the metal-organic framework (MOF) CPO-27-Mg (Mg-MOF-74) with chemical accuracy. The adsorption energies for the Mg(2+), linker, second layer sites are -27.8, -18.3, and -15.1 kJ/mol. Adsorbate-adsorbate interactions increase the average CH(4) adsorption energy by about 10% (2.4 kJ/mol). The free rotor-harmonic oscillator-ideal gas model is applied to calculate free energies/equilibrium constants for adsorption on the individual sites. This information is used in a multisite Langmuir model, augmented with a Bragg-Williams model for lateral interactions, to calculate adsorption isotherms. This ab initio approach yields the contributions of the individual sites to the final isotherms and also of the lateral interactions that contribute about 15% to the maximum excess adsorption capacity. Isotherms are calculated for both absolute amounts, for calculation of isosteric heats of adsorption as function of coverage, and excess amounts, for comparison with measured isotherms. Agreement with observed excess isotherms is reached if the experimentally determined limited accessibility of adsorption sites (78%) is taken into account.

  15. Nature of noncovalent interactions in catenane supramolecular complexes: calibrating the MM3 force field with ab initio, DFT, and SAPT methods.

    PubMed

    Simeon, Tomekia M; Ratner, Mark A; Schatz, George C

    2013-08-22

    The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.

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

    SciTech Connect

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

    2010-12-20

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

  17. Ab Initio Study of Phase Equilibria in TiCx

    NASA Astrophysics Data System (ADS)

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

    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, Ti3C2, 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.

  18. Ab-Initio Shell Model with a Core

    SciTech Connect

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

    2008-06-04

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

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  20. Basis sets for ab initio periodic Hartree-Fock studies of zeolite/adsorbate interactions: He, Ne, and Ar in silica sodalite

    SciTech Connect

    Nada, R.; Nicholas, J.B.; McCarthy, M.I.; Hess, A.C.

    1996-11-15

    Silica sodalite is an ideal model system to establish base-line computer requirements of ab initio periodic Hartree-Fock (PHF) calculations of zeolites. In this article, the authors investigate the effect of various basis sets on the structural and electronic properties of bulk silica sodalite. They also study the interaction of He, Ne, and Ar with the sodalite cage. This work shows that basis-set superposition errors (BSSE) in calculations using STO-3G and 6-21G(*) basis sets are as large as the interaction energies, leading to poor confidence in the results. To cure this problem, the authors present high-quality basis sets for si, O, He, Ne, and Ar, optimized for use with PHF methods, and demonstrate that the new basis set greatly reduces BSSE. The theoretical barriers for transfer of the rare gases between sodalite cages are 5.6, 13.2, and 62.1 kcal/mol for He, Ne, and Ar. 27 refs., 6 figs., 8 tabs.

  1. Ab initio theory of many-body interaction and phonon frequencies of rare-gas crystals under pressure in the model of deformable atoms

    NASA Astrophysics Data System (ADS)

    Troitskaya, E. P.; Chabanenko, V. V.; Gorbenko, Ie. Ie.; Pilipenko, E. A.

    2015-01-01

    Ab initio calculations of phonon frequencies of compressed rare-gas crystals have been performed taking into account the many-body interaction in the model of deformable atoms. In the short-range repulsive potential, along with the previously considered three-body interaction associated with the overlap of the electron shells of atoms, the three-body forces generated by the mutual deformation of the electron shells of the nearest-neighbor atoms have been investigated in the dipole approximation. The relevant forces make no contribution to the elastic moduli but affect the equation for lattice vibrations. At high compressions, the softening of the longitudinal mode at the points L and X is observed for all the rare-gas crystals, whereas the transverse mode T 1 is softened in the direction Σ and at the point L for solid xenon. This effect is enhanced by the three-body forces. There is a good agreement between the theoretical phonon frequencies and the experimental values at zero pressure.

  2. Implementation of renormalized excitonic method at ab initio level.

    PubMed

    Zhang, Hongjiang; Malrieu, Jean-Paul; Ma, Haibo; Ma, Jing

    2012-01-05

    The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.

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

    ERIC Educational Resources Information Center

    Gesell, Laurence E.

    1995-01-01

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

  4. Ab initio two-component Ehrenfest dynamics

    SciTech Connect

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

    2015-09-21

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

  5. Ab initio phase diagram of iridium

    NASA Astrophysics Data System (ADS)

    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 Quantum Simulations of Liquid Water

    NASA Astrophysics Data System (ADS)

    Gergely, John; Ceperley, David; Gygi, Francois

    2007-03-01

    Some recent efforts at simulating liquid water have employed ``ab initio'' molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT) and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods. E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).

  7. Ab initio calculations of nitramine dimers

    NASA Astrophysics Data System (ADS)

    Koh-Fallet, Sharon; Schweigert, Igor

    2015-06-01

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

  8. Ab-initio study of hexagonal apatites

    NASA Astrophysics Data System (ADS)

    Calderin, Lazaro; Stott, Malcom J.

    2001-03-01

    A silicon stabilized mixture of calcium phosphate phases has been recognized as playing an important role in actively resorbable coatings and in ceramics as bone materials. The nature of this material is being investigated using a variety of techniques including a combination of crystallographic analysis of measured x-ray diffraction spectra, and ab initio quantum mechanics simulations. We have used all-electron, density functional based calculations to investigate a group of hexagonal apatites. The fully relaxed crystallographic structures of hydroxyapatite, and related apatites have been obtained. We will present the results and discuss the nature of the bonding in these materials. The x-ray diffraction pattern and the infra-red spectra have also been obtained and will be compared with experiment. Acknowledgments:This work is part of a collaboration with the Applied Ceramics group of M.Sayer, and with Millenium Biologix Inc. Support of the NSERC of Canada through the award of a Co-operative R & D grant to the collaboration is acknowledged.

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

    PubMed

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

    2007-07-05

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

  10. Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and Ab Initio Simulations.

    PubMed

    Xin, H; LaRue, J; Öberg, H; Beye, M; Dell'Angela, M; Turner, J J; Gladh, J; Ng, M L; Sellberg, J A; Kaya, S; Mercurio, G; Hieke, F; Nordlund, D; Schlotter, W F; Dakovski, G L; Minitti, M P; Föhlisch, A; Wolf, M; Wurth, W; Ogasawara, H; Nørskov, J K; Öström, H; Pettersson, L G M; Nilsson, A; Abild-Pedersen, F

    2015-04-17

    We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.

  11. Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

    SciTech Connect

    Xin, H.; LaRue, J.; Oberg, H.; Beye, M.; Dell'Angela, M.; Turner, J. J.; Gladh, J.; Ng, M. L.; Sellberg, J. A.; Kaya, S.; Mercurio, G.; Hieke, F.; Nordlund, D.; Schlotter, W. F.; Dakovski, G. L.; Minitti, M. P.; Fohlisch, A.; Wolf, M.; Wurth, W.; Ogasawara, H.; Norskov, J. K.; Ostrom, H.; Pettersson, L. G. M.; Nilsson, A.; Ablid-Pedersen, F.

    2015-04-16

    We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.

  12. Three-cluster dynamics within an ab initio framework

    DOE PAGES

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

    2013-09-26

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

  13. Unified ab initio approaches to nuclear structure and reactions

    DOE PAGES

    Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

    2016-04-13

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

  14. Skutterudites under pressure: An ab initio study

    SciTech Connect

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

    2014-03-07

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

  15. Emission Spectroscopy and Ab Initio Calculations for TaN

    NASA Astrophysics Data System (ADS)

    Ram, R. S.; Liévin, J.; Bernath, P. F.

    2002-10-01

    The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1Σ + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, α e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3Δ 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.

  16. Exploring "aerogen-hydride" interactions between ZOF2 (Z = Kr, Xe) and metal hydrides: An ab initio study

    NASA Astrophysics Data System (ADS)

    Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba

    2016-06-01

    In this work, a new σ-hole interaction formed between ZOF2 (Z = Kr and Xe) as the Lewis acid and a series of metal-hydrides HMX (M = Be, Mg, Zn and X = H, F, CN, CH3) is reported. The nature of this interaction, called "aerogen-hydride" interaction, is unveiled by molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. Our results indicate that the aerogen-hydride interactions are quite strong and can be comparable in strength to other σ-hole bonds. An important charge-transfer interaction is also associated with the formation of OF2Z⋯HMX complexes.

  17. Ab initio calculations of structures and interaction energies of toluene dimers including CCSD(T) level electron correlation correction

    NASA Astrophysics Data System (ADS)

    Tsuzuki, Seiji; Honda, Kazumasa; Uchimaru, Tadafumi; Mikami, Masuhiro

    2005-04-01

    The intermolecular interaction energy of the toluene dimer has been calculated with the ARS-F model (a model chemistry for the evaluation of intermolecular interaction energy between ARomatic Systems using Feller's method), which was formerly called as the AIMI model III. The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order Møller-Plesset perturbation interaction energy at the basis set limit obtained by Feller's method and the CCSD(T) correction term obtained using a medium-size basis set. The cross (C2) dimer has the largest (most negative) interaction energy (-4.08kcal/mol). The antiparallel (C2h) and parallel (CS) dimers (-3.77 and -3.41kcal/mol, respectively) are slightly less stable. The dispersion interaction is found to be the major source of attraction in the toluene dimer. The dispersion interaction mainly determines the relative stability of the stacked three dimers. The electrostatic interaction of the stacked three dimers is repulsive. Although the T-shaped and slipped-parallel benzene dimers are nearly isoenergetic, the stacked toluene dimers are substantially more stable than the T-shaped toluene dimer (-2.62kcal/mol). The large dispersion interaction in the stacked toluene dimers is the cause of their enhanced stability.

  18. Ab initio self-consistent Gorkov-Green's function calculations of semi-magic nuclei: Numerical implementation at second order with a two-nucleon interaction

    NASA Astrophysics Data System (ADS)

    Somà, V.; Barbieri, C.; Duguet, T.

    2014-02-01

    Background: The newly developed self-consistent Gorkov-Green's function approach represents a promising path to the ab initio description of mid-mass open-shell nuclei. The formalism based on a two-nucleon interaction and the second-order truncation of Gorkov's self-energy has been described in detail in Ref. [Somà, Duguet, and Barbieri, Phys. Rev. C 84, 064317 (2011), 10.1103/PhysRevC.84.064317]. Purpose: The objective is to discuss the methodology used to solve Gorkov's equation numerically and to gauge its performance in view of carrying out systematic calculations of medium-mass nuclei in the future. In doing so, different sources of theoretical error and degrees of self-consistency are investigated. Methods: We employ Krylov projection techniques with a multi-pivot Lanczos algorithm to efficiently handle the growth of poles in the one-body Green's function that arises as a result of solving Gorkov's equation self-consistently. We first characterize the numerical scaling of Gorkov's calculations based on full self-consistency and on a partially self-consistent scheme coined as "sc0". Using small model spaces, the Krylov projection technique is then benchmarked against exact diagonalization of the original Gorkov matrix. Next, the convergence of the results as a function of the number Nℓ of Lanczos iterations per pivot is investigated in large model spaces. Eventually, the convergence of the calculations with the size of the harmonic oscillator model space is examined. Results: Gorkov self-consistent Green's function (SCGF) calculations performed on the basis of Krylov projection techniques display a favorable numerical scaling that authorizes systematic calculations of mid-mass nuclei. The Krylov projection selects efficiently the appropriate degrees of freedom while spanning a very small fraction of the original space. For typical large-scale calculations of mid-mass nuclei, a Krylov projection making use of Nℓ≈50 yields a sufficient degree of accuracy

  19. Ab initio coupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone

    DOE PAGES

    Hansen, Jared A.; Bauman, Nicholas P.; Shen, Jun; ...

    2015-12-09

    In this paper, the four, closely spaced, lowest energy electronic states of the challenging, D4h-symmetric, 1,2,3,4-cyclobutanetetraone (C4O4) molecule have been investigated using high-level ab initio methods. The calculated states include the closed-shell singlet 8π(1A1g) state, the singlet 10π(1A1g) state, in which the π-type lowest unoccupied molecular orbital (LUMO) of the 8π(1A1g) reference is doubly occupied and the σ-type highest occupied molecular orbital (HOMO) is empty, and the open-shell singlet and triplet states, designated as 9π(1B2u) and 9π(3B2u), respectively, originating from single occupancy of the HOMO and LUMO. Our focus is on single-reference coupled-cluster (CC) approaches capable of handling electronic near-degeneraciesmore » in diradicals, especially the completely renormalised CR-CC(2,3) and active-space CCSDt methods, along with their CCSD and EOMCCSD counterparts. The internally contracted multi-reference configuration interaction calculations with a quasi-degenerate Davidson correction are performed as well. Our computations demonstrate that the state ordering is 9π(3B2u) < 8π(1A1g) < 9π(1B2u) < 10π(1A1g) and that the 8π(1A1g) - 9π(3B2u) gap is in the 7–11 kJ/mol range, in reasonable agreement with the negative ion photoelectron spectroscopy measurements, which give 6.27 ± 0.5 kJ/mol. Finally, in addition to the theory level used, geometry relaxation and basis set play a significant role in determining the state ordering and energy spacings. In particular, it is unsafe to use lower level, non-CC geometries and smaller basis sets.« less

  20. Molecular-dynamics simulation of liquid water with an ab initio flexible water-water interaction potential

    NASA Astrophysics Data System (ADS)

    Lie, G. C.; Clementi, E.

    1986-04-01

    The Matsuoka-Clementi-Yoshimine (MCY) configuration interaction potential for rigid water-water interactions has been extended to include the intramolecular vibrations. The extended potential (MCYL), using no empirical parameters other than the atomic masses, electron charge, and Planck constant, is used in a molecular-dynamics simulation study of the static and dynamic properties of liquid water. Among the properties studied are internal energy, heat capacity, pressure, radial distribution functions, dielectric constant, static structure factor, velocity autocorrelation functions, self-diffusion coefficients, dipole autocorrelation function, and density and current fluctuations. Comparison with experiments is made whenever possible. Most of these properties are found to improve slightly relative to the MCY model. The simulated high-frequency sound mode seems to support the results and interpretation of a recent coherent inelastic neutron scattering experiment.

  1. Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

    NASA Astrophysics Data System (ADS)

    Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

    From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

  2. Analytic ab initio-based molecular interaction potential for the BrOṡH2O complex

    NASA Astrophysics Data System (ADS)

    Hoehn, Ross D.; Yeole, Sachin D.; Kais, Sabre; Francisco, Joseph S.

    2016-05-01

    Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrOṡH2O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrOṡH2O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES scans were used both to generate a novel analytic interaction potential by modifying the existing Thole-type model used for water and to the fitted potential function. This interaction potential features anisotropic atomic polarizabilities facilitating appropriate modeling of the physics regarding the unpaired electron residing within the p-orbitals of the oxygen atom of the bromine oxide radical. The intention of this work is to facilitate future molecular dynamics simulations involving the interaction between the BrO radical and water clusters as a first step in devising possible novel chemistries taking place at the water interface of clouds within the atmosphere.

  3. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  4. THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

    SciTech Connect

    Turchi, P A

    2004-09-24

    Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.

  5. Carbon dioxide interacting with rare gases: Insights from high-level ab initio calculations of polarizability and hyperpolarizability effects

    NASA Astrophysics Data System (ADS)

    Haskopoulos, Anastasios; Maroulis, George

    2016-08-01

    We have obtained a quantitative, synthetic picture of the interaction-induced (hyper)polarizability in the sequence of the weakly bound complexes CO2⋯Rg, Rg = He, Ne, Ar, Kr, Xe. The properties are calculated from finite-field Møller-Plesset perturbation theory and coupled cluster calculations. We rely on flexible, prepared purpose-oriented atom- and molecule-specific basis set of Gaussian-type functions. We obtained interaction-induced electric properties for both the most stable T-shaped configuration and the less stable L-shaped one. Our interaction-induced first and second hyperpolarizabilities for the most stable (T-shaped) configurations, at the second order Møller-Plesset perturbation theory level are βbarint /e3a03 Eh-2 (CO2⋯Rg) = 1.14 (He), 2.02 (Ne), 2.50 (Ar), 0.50 (Kr) and -5.32 (Xe). For the second hyperpolarizability at the same level of theory γbarint /e4a04 Eh-3 (CO2⋯Rg) = -11.66 (He), -25.88 (Ne), -108.16 (Ar), -206.75 (Kr) and -460.42 (Xe). In the vicinity of the equilibrium configuration, with the Rg atom displaced on the x axis for T-shaped configuration, the first hyperpolarizability changes as (d β bar/dR / e ) e3 a02 Eh-2 (CO2⋯Rg) = -1.07 (He), -1.86 (Ne), -0.71 (Ar), 2.65 (Kr) and 9.96 (Xe). For the second hyperpolarizability (d γ ‾/dR / e ) e4 a03 Eh-3 (CO2⋯Rg) = 7.94 (He), 20.34 (Ne), 65.00 (Ar), 118.48 (Kr) and 239.84 (Xe).

  6. The interaction of NO(X2Π ) with H2: Ab initio potential energy surfaces and bound states

    NASA Astrophysics Data System (ADS)

    Kłos, Jacek; Ma, Qianli; Alexander, Millard H.; Dagdigian, Paul J.

    2017-03-01

    We determine from first principles two sets of four-dimensional diabatic potential energy surfaces (PES's) for the interaction of NO(X2Π ) with H2, under the assumption of fixed NO and H2 bond distances. The first set of PES's was computed with the explicitly correlated multi-reference configuration interaction method [MRCISD-F12 + Q(Davidson)], and the second set with an explicitly correlated, coupled-cluster method [RCCSD(T)-F12a] with the geometry scan limited to geometries possessing a plane of symmetry. The calculated PES's are then fit to an analytical form suitable for bound state and scattering calculations. The RCCSD(T)-F12a dissociation energies (D0) of the NO-para-H2(ortho-D2) and the NO-ortho-H2(para-D2) complexes are computed to be 22.7 (31.7) and 23.9 (29.2) cm-1, respectively. The values calculated with the MRCISD-F12 + Q PES's are 21.6 (31.1) and 23.3 (28.4) cm-1, respectively.

  7. The interaction of NO(X(2)Π) with H2: Ab initio potential energy surfaces and bound states.

    PubMed

    Kłos, Jacek; Ma, Qianli; Alexander, Millard H; Dagdigian, Paul J

    2017-03-21

    We determine from first principles two sets of four-dimensional diabatic potential energy surfaces (PES's) for the interaction of NO(X(2)Π) with H2, under the assumption of fixed NO and H2 bond distances. The first set of PES's was computed with the explicitly correlated multi-reference configuration interaction method [MRCISD-F12 + Q(Davidson)], and the second set with an explicitly correlated, coupled-cluster method [RCCSD(T)-F12a] with the geometry scan limited to geometries possessing a plane of symmetry. The calculated PES's are then fit to an analytical form suitable for bound state and scattering calculations. The RCCSD(T)-F12a dissociation energies (D0) of the NO-para-H2(ortho-D2) and the NO-ortho-H2(para-D2) complexes are computed to be 22.7 (31.7) and 23.9 (29.2) cm(-1), respectively. The values calculated with the MRCISD-F12 + Q PES's are 21.6 (31.1) and 23.3 (28.4) cm(-1), respectively.

  8. Ab initio prediction of ferrimagnetism, exchange interactions and Curie temperatures in Mn₂TiZ Heusler compounds.

    PubMed

    Meinert, M; Schmalhorst, J-M; Reiss, G

    2011-01-26

    The Heusler compounds Mn(2)TiZ (Z = Al, Ga, In, Si, Ge, Sn, P, As, Sb) are of great interest due to their potential ferrimagnetic properties and high spin polarization. Here, we present calculations of the structural and magnetic properties of these materials. Their magnetic moment follows the Slater-Pauling rule m = N(V) - 24. None of them is actually a perfect half-metallic ferrimagnet, but some exhibit more than 90% spin polarization and Curie temperatures well above room temperature. The exchange interactions are complex; direct and indirect exchange contributions are identified. The Curie temperature scales with the total magnetic moment, and it has a positive pressure dependence. The role of the Z element is investigated: it influences the properties of the compounds mainly via its valence electron number and its atomic radius, which determines the lattice parameter. Based on these results, Mn(2)TiSi, Mn(2)TiGe, and Mn(2)TiSn are proposed as candidates for spintronic applications.

  9. Ab initio calculations of van der Waals interactions in one- and two-dimensional infinite periodic systems

    NASA Astrophysics Data System (ADS)

    Fink, Karin; Staemmler, Volker

    1995-08-01

    A new CEPA-PNO (coupled electron pair approach with pair natural orbitals) method for the calculation of correlation energies in infinite periodic systems is proposed and applied to one- and two-dimensional He. The method starts from a crystal orbital Hartree-Fock (COHF) wavefunction with the occupied Bloch orbitals transformed into Wannier orbitals. The coupled-cluster equations for the infinite system are simplified by CEPA-type approximations: A CEPA-0 (or linear coupled-cluster) formula is applied for the small intercell contributions to the total correlation energy while CI-SD, ACPF or other CEPA variants are used for the large intracell contributions. The enormous number of single and double excitations into the virtual space is greatly reduced by the use of pair natural orbitals (PNOs), which leads to large savings in the necessary computer time and disk storage. First applications to the van der Waals interaction in the linear chain and the hexagonal plane of He atoms, performed with medium size and large atomic basis sets, show that an accuracy can be reached for the infinite systems which is comparable to the accuracy of the corresponding calculations for small He clusters. Because of the extended use of the translational symmetry of the Wannier orbitals, the calculations for the linear infinite systems are even considerably faster than those for the oligomers He5 and He7.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  11. Ab initio water pair potential with flexible monomers.

    PubMed

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

    2015-03-26

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

  12. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  13. Ab Initio Study of KCl and NaCl Clusters

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2000-10-01

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

  15. Ab initio computations of photodissociation products of CFC alternatives

    SciTech Connect

    Tai, S.; Illinger, K.H.; Kenny, J.E.

    1995-12-31

    Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.

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

    SciTech Connect

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

    2014-09-01

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

  17. Ab Initio Infrared and Raman Spectra.

    DTIC Science & Technology

    1982-08-01

    tions. For parameters not depending on momenta, a parallel ab fhti Monte Carlo approach would use electronic energies and other parameters of... Monte Carlo approach. Specifically, as one of us has suggested,t I classical molecular dynamics may be integrated with ab iniHo quan- tum force...alternative approach, for phenomena which are not explicitly time dependent, is a Monte Carlo procedure in which at each trial nuclear configuration

  18. Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

    SciTech Connect

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

    2006-04-05

    A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

  19. Molecular-dynamics simulation of liquid water with an ab initio flexible water-water interaction potential. II. The effect of internal vibrations on the time correlation functions

    NASA Astrophysics Data System (ADS)

    Evans, M. W.; Refson, K.; Swamy, K. N.; Lie, G. C.; Clementi, E.

    1987-10-01

    A computer simulation of liquid water using the ab initio Matsuoka-Clementi-Yoshimine-Lie (MCYL) potential has been analyzed in comprehensive detail with use of pertinent auto-correlation and cross-correlation functions of the water molecule's vibrational, rotational, and translational dynamics. The autocorrelation functions (ACF's) of dynamical quantities such as atom velocity, center-of-mass velocity, molecular angular momentum, molecular angular velocity, molecular dipole moment, and molecular rotational velocity vectors have been computed with 3400 configurations generated in a simulation with 343 molecules in the laboratory frame and in the frame of the principal molecular moments of inertia. Furthermore, cross-correlation functions (CCF's) of many different kinds have been computed in both frames in order to study in detail the mutual effects of vibration, rotation, and translation at the single-molecule level. In some respects the inclusion of vibrational effects in the MCYL potential does not significantly change the pattern of dynamical information summarized in these time correlation functions. The rotation-translation CCF's which were obtained recently by Evans et al. from a rigid empirical model for the intermolecular pair potential energy in liquid water appear once more from the ab initio MCYL potential with the same symmetry and time dependence. This is a strong corroborative evidence for the correctness of the methods used in both cases. However, the inclusion of vibrational effects by Lie and Clementi in their MCYL potential leads in this work to considerable further insight obtained by a detailed study of cross-correlation functions between vibration and rotation and between vibration and center-of-mass translation.

  20. Vibrational frequency shifts of diatomic molecules in interaction with a Na + cation by ab initio calculations. Comparison with experiment on H 2 and N 2 adsorbed in NaA zeolite

    NASA Astrophysics Data System (ADS)

    Koubi, Laure; Blain, Monique; de Lara, Evelyne Cohen; Leclerq, Jean-Marie

    1994-01-01

    Ab initio calculations on H 2 and N 2 and on the same molecules in the presence of a Na + cation are presented. The equilibrium configuration and the vibrational frequency shift due to the interaction are calculated. The potential energy surfaces are obtained by local osculatory interpolations and extrapolations. The vibrational frequencies are calculated by the Numerov—Cooley method. The direction of the frequency shift is found to be related to the orientation of the diatomic molecule with respect to the cation. The results are compared with experimental data on induced infrared bands of H 2 and N 2 adsorbed in NaA zeolite.

  1. An ab initio electronic density study of the CH4-Ar, CH4-Xe, CH4-H2O and CH4-H2S complexes: insights into the nature of the intermolecular interaction

    NASA Astrophysics Data System (ADS)

    Bartocci, Alessio; Frati, Federica; Roncaratti, Luiz F.; Cappelletti, David; Tarantelli, Francesco; Belpassi, Leonardo; Pirani, Fernando

    2015-12-01

    The main point of this paper concerns the theoretical characterisation of the effects induced by the intermolecular interaction on the electron density upon the formation of CH4-H2X (X=O,S) and CH4-Ng (Ng=Ar,Xe) complexes. The work has been stimulated by recent molecular scattering beams experiments, which point out differences in both strength and anisotropy of the intermolecular potential between CH4-H2X respect to reference CH4-Ng systems. Herein, attention is focused on the electronic charge polarisation and particularly charge transfer (CT) effects between involved partners, directly related to the topology of the full potential energy surface. The modification of electron density and the occurrence of CT have been evaluated via the charge displacement function worked out by high level ab initio calculations. Moreover, in the case of a specific configuration of CH4-H2O system, we define the leading interaction components, including their relative stabilising role and test our intermolecular potential model with reference to ab initio calculations. The results obtained indicate that CT clearly affects the strength and the anisotropy of CH4-H2O complex, and covers a minor and negligible role for CH4-H2S and the noble gas complexes, respectively.

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

    NASA Astrophysics Data System (ADS)

    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

  3. Separable metamaterials: analytical ab-initio homogenization and chirality

    NASA Astrophysics Data System (ADS)

    Ciattoni, Alessandro; Rago, Domenico; Rizza, Carlo

    2016-11-01

    We investigate the ab-initio homogenization of separable metamaterials with factorized dielectric permittivity profiles, which can be achieved through suitable grey-scale permittivity design techniques. Separability allows such metamaterials to be physically regarded as the superposition of three fictitious 1D generating media. We prove that, in the long-wavelength limit, separable metamaterials admit a simple and analytical description of their electromagnetic bi-anisotropic response, which can be reconstructed from the properties of the 1D generating media. Our approach provides a strategy that allows the full ab-initio and flexible design of a complex bianisotropic response by using the simple and well-known properties of 1D metamaterials.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    DTIC Science & Technology

    2006-02-01

    Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued

  6. Thermochemical data for CVD modeling from ab initio calculations

    SciTech Connect

    Ho, P.; Melius, C.F.

    1993-12-31

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

  7. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

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

    1978-01-01

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

  8. Ab initio prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni

    NASA Astrophysics Data System (ADS)

    Zhang, Xi; Sluiter, Marcel H. F.

    2015-05-01

    Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total energies in a consistent manner without a statistical model. Essential features of such a model are knowledge of the chemical potential and imposition of invariants. In the present work, we derive the simplest model that satisfies these requirements and we compare it with models in the literature. As illustration we compute ab initio vacancy properties of fcc Cu-Ni alloys as a function of composition and temperature. Ab initio density functional calculations were performed for SQS supercells at various compositions with and without vacancies. Various methods of extracting alloy vacancy properties were examined. A ternary cluster expansion yielded effective cluster interactions (ECIs) for the Cu-Ni-Vac system. Composition and temperature dependent alloy vacancy concentrations were obtained using statistical thermodynamic models with the ab initio ECIs. An Arrhenius analysis showed that the heat of vacancy formation was well represented by a linear function of temperature. The positive slope of the temperature dependence implies a negative configurational entropy contribution to the vacancy formation free energy in the alloy. These findings can be understood by considering local coordination effects.

  9. The electronic states of buta-1,3-diene studied by ab initio configuration interaction and DFT methods, and electron energy loss spectroscopy

    NASA Astrophysics Data System (ADS)

    H., Michael; | Isobel C., Palmer; Walker

    2010-08-01

    The electronic vertical excitation energies for singlet and triplet valence, and Rydberg states of trans-buta-1,3-diene have been computed using ab initio multi-reference multi-root CI procedures with a [4s3p3d3f] set of Rydberg functions. Close numerical agreement between theory and experiment was found for a number of low-lying electronic states. The present CI and CASSCF [8MO,8e] calculations suggest that both the vertical and adiabatic order of the valence (ππ∗) states is: A˜1A

  10. The electronic states of oxazole studied by VUV absorption and electron energy-loss (EEL) spectroscopies, and ab initio configuration interaction methods

    NASA Astrophysics Data System (ADS)

    Palmer, Michael H.; Ganzenmüller, Georg; Walker, Isobel C.

    2007-04-01

    The oxazole VUV absorption spectrum over the range 5-12 eV shows intense bands centred near 6.3, 7.5, 8.3, 9.6 and 10.8 eV. The electron energy-loss (EEL) spectrum shows additional structure with a strong peak (˜1.4 eV) arising from resonant vibrational excitation of the molecule via a shape resonance, and a spin-forbidden 3ππ ∗ state at 4.6 eV. Electronic excitation energies for valence and Rydberg-type states have been computed using ab initio multi-reference multi-root CI methods. The CI studies used a triple zeta + polarisation basis set, augmented by diffuse (Rydberg) orbitals, to generate the theoretical singlet and triplet energy manifolds. The correlation of theory and experiment shows the nature of the more intense Rydberg state types, and identification of the main valence and Rydberg bands. Calculated energies for low-lying Rydberg states are relatively close (SD 0.38) to those expected, and there is generally a good correlation between the theoretical and experimental envelopes. Two of the three lowest electronic states arise from ππ ∗ excitation of the outer (3a″ and 2a″) π-orbitals, with one state (LP Nπ ∗) originating from the lone pair on nitrogen (15a') between them.

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

    PubMed

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

    2010-09-29

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

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

    PubMed

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

    2014-08-07

    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.

  13. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    1996-03-01

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

  14. Ab initio molecular dynamics using hybrid density functionals.

    PubMed

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

    2008-06-07

    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.

  15. Ab initio molecular dynamics using hybrid density functionals

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  17. Ab initio rotation-vibration spectra of HCN and HNC

    NASA Astrophysics Data System (ADS)

    Harris, Gregory J.; Polyansky, Oleg L.; Tennyson, Jonathan

    2002-03-01

    We have calculated an ab initio HCN/HNC linelist for all transitions up to J=25 and 18 000 cm -1 above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO+PES and dipole moment surface, which were reported in van Mourik et al. (J. Chem. Phys. 115 (2001) 3706). With this linelist we synthesise absorption spectra of HCN and HNC at 298 K and we present the band centre and band transition dipoles for the bands which are major features in these spectra. Several of the HCN bands and many of the HNC bands have not been previously studied. Our line intensities reproduce via fully ab initio methods the unusual intensity structure of the HCN CN stretch fundamental (00 01) for the first time and also the forbidden (02 20) HCN bending overtone. We also compare the J=1→0 pure rotational transition dipole in the HCN/HNC ground and vibrationally excited states with experimental and existing ab initio results.

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

    SciTech Connect

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

    2014-08-07

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  2. Ab initio modeling of decomposition in iron based alloys

    NASA Astrophysics Data System (ADS)

    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.

  3. Ab initio calculations of correlated electron dynamics in ultrashort pulses

    NASA Astrophysics Data System (ADS)

    Feist, Johannes

    2010-03-01

    The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.

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

    PubMed

    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.

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

    PubMed Central

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel

    2015-01-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

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

    PubMed

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.

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

    NASA Astrophysics Data System (ADS)

    Correa, J. D.; Cisternas, E.

    2016-09-01

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

  8. Comparison of hydrogen bonds, halogen bonds, Csbnd H⋯π interactions, and Csbnd X⋯π interactions using high-level ab initio methods

    NASA Astrophysics Data System (ADS)

    Riley, Kevin E.; Ford, Carey L.; Demouchet, Kamirah

    2015-02-01

    High quality CCSD(T) and DFT-SAPT potential energy curves were generated for complexes of HCN, BrCN, and HBr donors with formaldehyde and benzene acceptors in order to compare the strengths and properties of hydrogen bonds, halogen bonds, Csbnd H⋯π interactions, and Csbnd Br⋯π interactions. It is found that interactions involving BrCN, which has a large region of positive charge, are similar in strength to interactions involving HCN. Dispersion plays a pronounced role in Ysbnd Br⋯π complexes, accounting for about two thirds of attraction in the HBr⋯C6H6 complex. As might be expected, interactions involving halogens have stronger contributions from dispersion.

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

    NASA Technical Reports Server (NTRS)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

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

  10. Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule

    SciTech Connect

    Párraga, H.; Arranz, F. J. Benito, R. M.; Borondo, F.

    2013-11-21

    An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.

  11. Ab initio study of optical absorption spectra of semiconductors and conjugated polymers

    SciTech Connect

    Tiago, M.L.; Chang, Eric K.; Rohlfing, Michael; Louie, Steven G.

    2000-04-30

    The effects of electron-hole interaction on the optical properties of a variety of materials have been calculated using an ab initio method based on solving the Bethe-Salpeter equation. Results on selected semiconductors, insulators, and semiconducting polymers are presented. In the cases of alpha-quartz (SiO2) and poly-phenylene-vinylene, resonant excitonic states qualitatively alter the absorption spectra.

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

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  13. Ab initio molecular dynamics of liquid hydrogen chloride

    NASA Astrophysics Data System (ADS)

    Dubois, Vincent; Pasquarello, Alfredo

    2005-03-01

    We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.

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

    PubMed

    Rayón, Víctor M; Sordo, Jose A

    2005-05-22

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

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

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

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

  16. Morphing ab initio potential energy curve of beryllium monohydride

    NASA Astrophysics Data System (ADS)

    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.

  17. Ab initio evidence for nonthermal characteristics in ultrafast laser melting

    NASA Astrophysics Data System (ADS)

    Lian, Chao; Zhang, S. B.; Meng, Sheng

    2016-11-01

    Laser melting of semiconductors has been observed for almost 40 years; surprisingly, it is not well understood where most theoretical simulations show a laser-induced thermal process. Ab initio nonadiabatic simulations based on real-time time-dependent density functional theory reveal intrinsic nonthermal melting of silicon, at a temperature far below the thermal melting temperature of 1680 K. Both excitation threshold and time evolution of diffraction intensity agree well with experiment. Nonthermal melting is attributed to excitation-induced drastic changes in bonding electron density, and the subsequent decrease in the melting barrier, rather than lattice heating as previously assumed in the two-temperature models.

  18. Communication: Ab initio Joule-Thomson inversion data for argon

    NASA Astrophysics Data System (ADS)

    Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

    2013-02-01

    The Joule-Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

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

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

  20. Ab-initio study of transition metal hydrides

    SciTech Connect

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

    2014-04-24

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

  1. Electric field response in bilayer graphene: Ab initio investigation

    NASA Astrophysics Data System (ADS)

    Mori, Yutaro; Minamitani, Emi; Ando, Yasunobu; Kasamatsu, Shusuke; Watanabe, Satoshi

    2016-11-01

    Stimulated by quantum capacitance measurements, we have investigated the electric properties of bilayer graphene (BLG) with carrier doping under an external electric field using ab initio calculations. We found that the relative permittivity of BLG depends weakly on the applied electric field, and that the BLG can be regarded as a dielectric material rather than a pair of metallic films. We also found that carrier doping affects the band gap of BLG under electric fields, although carrier doping has a much smaller effect on the band gap and density of states than the application of electric fields.

  2. Communication: Ab initio Joule-Thomson inversion data for argon.

    PubMed

    Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

    2013-02-21

    The Joule-Thomson coefficient μ(H)(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

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

    SciTech Connect

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

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  4. Ab initio electron mobility and polar phonon scattering in GaAs

    NASA Astrophysics Data System (ADS)

    Zhou, Jin-Jian; Bernardi, Marco

    2016-11-01

    In polar semiconductors and oxides, the long-range nature of the electron-phonon (e -ph ) interaction is a bottleneck to compute charge transport from first principles. Here, we develop an efficient ab initio scheme to compute and converge the e -ph relaxation times (RTs) and electron mobility in polar materials. We apply our approach to GaAs, where by using the Boltzmann equation with state-dependent RTs, we compute mobilities in excellent agreement with experiment at 250 -500 K . The e -ph RTs and the phonon contributions to intravalley and intervalley e -ph scattering are also analyzed. Our work enables efficient ab initio computations of transport and carrier dynamics in polar materials.

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

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

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

  6. Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations.

    PubMed

    Pospíšil, Miroslav; Kovář, Petr; Vácha, Robert; Svoboda, Michal

    2012-01-01

    Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.

  7. Ab initio simulation of atomic-scale imaging in noncontact atomic force microscopy.

    PubMed

    Caciuc, V; Hölscher, H

    2009-07-01

    In this paper, we summarize some results of our ab initio simulations aimed at investigating the mechanism of the NC-AFM image contrast on semiconductor and metallic surfaces. We start with an introduction into the basic ideas behind the ab initio simulation process of the NC-AFM experimental results. Our simulations reveal that the interaction of a clean silicon tip with a semiconductor surface like InAs(110) might lead to bond-formation and bond-breaking processes during the approach and retraction of the tip. This imaging mechanism is very similar to that observed on a metallic surface like Ag(110). Interestingly, a clean silicon tip can become contaminated with Ag surface atoms. On both types of surface we observe a significant energy dissipation which is caused by a hysteresis in the tip-sample force curves calculated on the approach and retraction path.

  8. Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  10. Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Ab initio study of hot electrons in GaAs.

    PubMed

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

    2015-04-28

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

  13. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    PubMed Central

    Elenewski, Justin E.; Hackett, John C

    2015-01-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906

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

    PubMed

    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.

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

    SciTech Connect

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

    2012-09-15

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

  16. Ab initio study of hot electrons in GaAs

    PubMed Central

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

    2015-01-01

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

  17. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    SciTech Connect

    Elenewski, Justin E.; Hackett, John C

    2015-02-14

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

  18. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    SciTech Connect

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

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

  19. Ab initio study on electronically excited states of lithium isocyanide, LiNC

    NASA Astrophysics Data System (ADS)

    Yasumatsu, Hisato; Jeung, Gwang-Hi

    2014-01-01

    The electronically excited states of the lithium isocyanide molecule, LiNC, were studied by means of ab initio calculations. The bonding nature of LiNC up to ∼10 eV is discussed on the basis of the potential energy surfaces according to the interaction between the ion-pair and covalent states. The ion-pair states are described by Coulomb attractive interaction in the long distance range, while the covalent ones are almost repulsive or bound with a very shallow potential dent. These two states interact each other to form adiabatic potential energy surfaces with non-monotonic change in the potential energy with the internuclear distance.

  20. Elucidation of the physicomechanical and ab initio quantum energy transitions of a crosslinked PLGA scaffold.

    PubMed

    Sibambo, Sibongile R; Pillay, Viness; Choonara, Yahya E; Khan, Riaz A; Sweet, Joe L

    2007-09-01

    This study elucidated the in vitro physicomechanical transitions of a crosslinked polylactic-co-glycolic acid (PLGA) scaffold, utilizing quantum mechanics to compute the ab initio energy requirements of a salted-out and subsequently crosslinked PLGA scaffold interacting with simulated physiological fluid, phosphate buffered saline (PBS) (pH 7.4, 37 degrees C) at a molecular level. Twenty-six salted-out PLGA scaffolds were formulated using a four factor, two centerpoint quadratic Face-Centered Central Composite Design (FCCD). PLGA molecular mass, PLGA concentration, water volume and salting-out reaction time were the dependant formulation variables. Subsequent to PLGA solubilization in dimethyl formamide (DMF), protonated water was added to induce salting-out of PLGA into a scaffolds that were immersed in PBS, oscillated at 100 rpm, and analyzed at pre-determined time intervals for their physicomechanical and ab initio quantum energy transitions. Results indicated that the matrix resilience (MR) decreased with longer incubation periods (MR=35-45%) at day 30. Scaffolds salted-out using higher PLGA concentrations exhibited minimal changes in MR and the matrix ability to absorb energy was found to closely correlate with the scaffold residence time in PBS. Spartan-based ab initio quantum energy predictions elucidated the potential scaffold stability from a molecular viewpoint and its suitability for use in rate-modulated drug delivery.

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

    NASA Astrophysics Data System (ADS)

    Yang, Lina; Minnich, Austin J.

    2017-03-01

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

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

    PubMed Central

    Yang, Lina; Minnich, Austin J.

    2017-01-01

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials. PMID:28290484

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

    PubMed

    Yang, Lina; Minnich, Austin J

    2017-03-14

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

  4. The effect of two- and three-body interactions in ArnCO2 (n = 1,2) on the asymmetric stretching CO2 coordinate: An ab initio study

    NASA Astrophysics Data System (ADS)

    Rak, Janusz; Szcześniak, M. M.; Chałasiński, Grzegorz; Cybulski, sławomir M.

    1997-06-01

    The dependence of the two-body and three-body interactions in the ArnCO2 cluster upon the intramolecular asymmetric stretching coordinate of CO2 is studied by the ab initio method. In the T-shaped binary complex Ar-CO2, the influence of the components of the interaction energy on the shift of the asymmetric stretching frequency of CO2 (ν3) is estimated within a one-dimensional vibrational model and compared with the experimental data of Sperhac, Weida, and Nesbitt [J. Chem. Phys. 104, 2202 (1996)]. The interaction energy is dissected into Heitler-London, induction, and dispersion energies and their respective intrasystem correlation corrections. The redshift represents a delicate balance of these effects on the v=0 and v=1 levels. The highly correlated treatment is required to describe the dependence of two-body potential upon the stretching coordinate. The supermolecular coupled cluster calculations with the single, double, and noniterative triple excitations reproduce the shift observed by Sperhac et al. with excellent accuracy. In the Ar2CO2 trimer with the two Ar atoms in equatorial positions, the influence of the three-body interaction components on the v=0 and v=1 levels is analyzed. A model of the three-body potential, including three nonadditive components, exchange, induction, and dispersion is applied. It describes the departure from additivity of the two-body shifts observed by Sperhac et al. with excellent accuracy. The analytical models of the energy components are also discussed.

  5. Accurate ab initio potential energy computations for the H sub 4 system: Tests of some analytic potential energy surfaces

    SciTech Connect

    Boothroyd, A.I. ); Dove, J.E.; Keogh, W.J. ); Martin, P.G. ); Peterson, M.R. )

    1991-09-15

    The interaction potential energy surface (PES) of H{sub 4} is of great importance for quantum chemistry, as a test case for molecule--molecule interactions. It is also required for a detailed understanding of certain astrophysical processes, namely, collisional excitation and dissociation of H{sub 2} in molecular clouds, at densities too low to be accessible experimentally. Accurate {ital ab} {ital initio} energies were computed for 6046 conformations of H{sub 4}, using a multiple reference (single and) double excitation configuration interaction (MRD-CI) program. Both systematic and random'' errors were estimated to have an rms size of 0.6 mhartree, for a total rms error of about 0.9 mhartree (or 0.55 kcal/mol) in the final {ital ab} {ital initio} energy values. It proved possible to include in a self-consistent way {ital ab} {ital initio} energies calculated by Schwenke, bringing the number of H{sub 4} conformations to 6101. {ital Ab} {ital initio} energies were also computed for 404 conformations of H{sub 3}; adding {ital ab} {ital initio} energies calculated by other authors yielded a total of 772 conformations of H{sub 3}. (The H{sub 3} results, and an improved analytic PES for H{sub 3}, are reported elsewhere.) {ital Ab} {ital initio} energies are tabulated in this paper only for a sample of H{sub 4} conformations; a full list of all 6101 conformations of H{sub 4} (and 772 conformations of H{sub 3} ) is available from Physics Auxiliary Publication Service (PAPS), or from the authors.

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  8. Ab initio computational applications to complex biomolecular systems

    NASA Astrophysics Data System (ADS)

    Liang, Lei

    A series of biomaterial related systems---including water and DNA molecules---have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of single-molecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% x the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of ˜1.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of ˜1.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchange-correlation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing

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

    PubMed

    Rana, Malay Kumar; Chandra, Amalendu

    2013-05-28

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

  10. Ab initio insight into graphene nanofibers to destabilize hydrazine borane for hydrogen release

    NASA Astrophysics Data System (ADS)

    Qian, Zhao; Raghubanshi, Himanshu; Sterlin Leo Hudson, M.; Srivastava, O. N.; Liu, Xiangfa; Ahuja, Rajeev

    2017-02-01

    We report the potential destabilizing effects of graphene nanofibers on the hydrogen release property of hydrazine borane via state-of-the-art ab initio calculations for the first time. Interactions of a hydrazine borane cluster with two types of graphene patch edges which exist abundantly in our synthesized graphene nanofibers have been investigated. It is found that both zigzag and armchair edges can greatly weaken the H-host bonds (especially the middle Nsbnd H bond) of hydrazine borane. The dramatic decrease in hydrogen removal energy is caused by the strong interaction between hydrazine borane and the graphene patch edges concerning the electronic charge density redistribution.

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

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

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

  12. Ab initio electronic and lattice dynamical properties of cerium dihydride

    NASA Astrophysics Data System (ADS)

    Gurel, Tanju; Eryigit, Resul

    2007-03-01

    The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.

  13. Approximate ab initio calculations of electronic structure of amorphous silicon

    NASA Astrophysics Data System (ADS)

    Durandurdu, M.; Drabold, D. A.; Mousseau, N.

    2000-12-01

    We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.

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

    SciTech Connect

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

    2015-01-21

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

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

    PubMed Central

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

    2016-01-01

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

  16. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Olsson, P.; Vidal, J.; Lincot, D.

    2011-10-01

    The structural stabilities of the (Zn,Cd)(S,Se,Te)2 dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe2 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.

  19. Reactive Monte Carlo sampling with an ab initio potential

    DOE PAGES

    Leiding, Jeff; Coe, Joshua D.

    2016-05-04

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  1. Ab initio study of helium behavior in titanium tritides

    SciTech Connect

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

    2013-03-01

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

  2. Ab initio electron propagator theory of molecular wires. I. Formalism.

    PubMed

    Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V

    2005-11-08

    Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.

  3. Ab initio simulations of liquid carbon monoxide at high pressure

    NASA Astrophysics Data System (ADS)

    Leonhardi, Tanis C.; Militzer, Burkhard

    2017-03-01

    Carbon monoxide occurs as a volatile species in the interiors of terrestrial planets, and as a disequilibrium atmospheric constituent in the giant planets. It plays an important role during the accretionary stages of planet formation reacting with gases to form compounds such as CH4 and H2O. The structure of carbon monoxide is unknown over the majority of the temperature and pressure regime in giant planet interiors. Here we perform ab initio molecular dynamics simulations to characterize CO to 140 GPa and 5,000 K. We find that CO is stable as a molecular liquid at lower P-T conditions, as a polymeric liquid at higher P-T conditions found in ice giant interiors, and as a plasma at high-T.

  4. An ab initio study on anionic aerogen bonds

    NASA Astrophysics Data System (ADS)

    Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba

    2017-01-01

    An ab initio study is carried out to investigate the anionic aerogen bonds in complexes of KrO3, XeO3 and XeOF2 with F-, Cl-, Br-, CN-, NC-, N3-, SH-, SCN-, NCS-, OH- and OCH3- anions. All of the anionic aerogen bonds analyzed here have a partial covalent character. Charge transfer from the anion to the Kr-O or Xe-O σ∗ orbital stabilizes these complexes and leads to a sizable redshift in the corresponding stretching frequencies. The J(Kr-O) or J(Xe-O) spin-spin coupling constants can be regarded as a useful tool for the characterization of strength of the anionic aerogen-bonded complexes.

  5. Simple calculation of ab initio melting curves: Application to aluminum

    NASA Astrophysics Data System (ADS)

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2015-03-01

    We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003), 10.1063/1.1624057] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013), 10.1103/PhysRevE.88.062145]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

  6. Ab initio quantum transport in atomic carbon chains

    NASA Astrophysics Data System (ADS)

    Botello-Méndez, Andrés R.; Charlier, Jean-Christophe; Banhart, Florian; NAPS Team; Carbyne Collaboration

    2015-03-01

    Carbyne, the sp-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. Recently, detailed electrical measurements and first-principles electronic transport calculations have been performed on monoatomic carbon chains. When the 1D system is under strain, the current-voltage curves exhibit a semiconducting behavior, which corresponds to the polyyne structure of the atomic chain with alternating single and triple bonds. Conversely, when the chain is unstrained, the ohmic behavior is observed in agreement with the metallic cumulene structure with double bonds, confirming recent theoretical predictions, namely that a metal-insulator transition can be induced by adjusting the strain. The key role of the contacting leads is also scrutinized by ab initio quantum conductance calculations, explaining the rectifying behavior measured in monoatomic carbon chains in a non-symmetric contact configuration.

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

    NASA Astrophysics Data System (ADS)

    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.

  8. Ab-initio theory of spin fluctuations in magnets

    NASA Astrophysics Data System (ADS)

    Antropov, Vladimir; Ke, Liqin; van Schilfgaarde, Mark; Katsnelson, Mikhael

    2011-03-01

    We propose a framework for a true ab initio theory of magnetism, based on many-body perturbation theory (MPBT). It fits in naturally with methods based MPBT such as the GW approximation; but the approach can be implemented as an extension to any existing static method for electronic structure such as the local spin density approximation to density functional theory, to include spin fluctuations. Initially we calculated the spin fluctuation contributions using random phase approximation. The self consistency procedure similar to the one used in Moryia-Kawabata theory can be naturally implemented. The fluctuation dissipation theorem is used to calculate the reduction of the mean field magnetic moment in itinerant magnets. The applications of the technique includes traditional 3d ferromagnetic metals, their alloys and compounds and 5f systems.

  9. An Ab Initio Study of Alkali-C60 Complexes

    NASA Astrophysics Data System (ADS)

    Frick, Nathan; Hira, A. S.; Ray, A. K.

    2003-03-01

    We extend our previous work on fullerene-alkali complexes1-2 by presenting the results of an ab initio theoretical study of the alkali LiC60+, LiC60, NaC60+, NaC60, KC60+, and KC60 complexes. In the endohedral complexes for Li and Na, there is displacement of the adatom from the center. Of the ions, exohedral Li+ will sit closest to the cage, and among the neutrals, exohedral K remains closest. Bond lengths are consistently longer for the fivefold and threefold approaches. Adsorbates inside the fullerene donate negative charge to the carbons, but ions outside obtain a small amount, resulting in a polarization of the molecule. In the ion complexes, there is lowering of the orbital energy levels by 3 to 4 eV, resulting in an increase in the number of bound, but unoccupied, electronic orbitals. The HOMO-LUMO gap, of interest in superconductivity studies, is reduced by about 50 1. A.S. Hira and A.K. Ray, Phys. Rev. A 52, 141(1995); A 54, 2205(1996). 2. Ajit Hira and A. K. Ray, "An Initio Modeling of the Endohedral and Exohedral Complexes of C60Na2+ Complexes", Bull. Am. Phys. Soc. 47 (March 2002).

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

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

  11. Ab initio calculations of the melting temperatures of refractory bcc metals.

    PubMed

    Wang, L G; van de Walle, A

    2012-01-28

    We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Multiferroicity in TTF-CA Organic Molecular Crystals Predicted through Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Giovannetti, Gianluca; Kumar, Sanjeev; Stroppa, Alessandro; van den Brink, Jeroen; Picozzi, Silvia

    2009-12-01

    We show by means of ab initio calculations that the organic molecular crystal TTF-CA is multiferroic: it has an instability to develop spontaneously both ferroelectric and magnetic ordering. Ferroelectricity is driven by a Peierls transition of the TTF-CA in its ionic state. Subsequent antiferromagnetic ordering strongly enhances the opposing electronic contribution to the polarization. It is so large that it switches the direction of the total ferroelectric moment. Within an extended Hubbard model, we capture the essence of the electronic interactions in TTF-CA, confirm the presence of a multiferroic groundstate, and clarify how this state develops microscopically.

  14. Ab-initio method for X-ray absorption spectra simulation of hydride molecular ions

    NASA Astrophysics Data System (ADS)

    Puglisi, Alessandra; Sisourat, Nicolas; Carniato, Stéphane

    2017-03-01

    Soft X-ray absorption spectra of molecular ions are important data for the modeling and understanding of laboratory and astrophysical plasma. In this work, we present an ab-initio method, based on the Configuration Interaction (CI) approach, for the calculations of energy positions and oscillator strengths of X-ray absorption spectra. Furthermore, we investigate the effects of the choice of the nature and number of spin-orbitals used in the CI expansion on the spectra. The method is applied on three hydride molecular ions, namely CH+, OH+ and SiH+. However, the approach proposed here is general and may thus be applied to any kind of molecular ions.

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

    SciTech Connect

    Vary, J. P.; Maris, P.; Honkanen, H.; Li, J.; Shirokov, A. M.; Brodsky, S. J.; Harindranath, A.

    2009-12-17

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

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

    SciTech Connect

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

    2009-08-03

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

  17. Ab initio calculations of one-electron-scattering properties of ethyne (acetylene) and ethylene molecules

    SciTech Connect

    Tripathi, A.N.; Smith, V.H. Jr. K7L3N6); Kaijser, P.; Siemens, A.G. ); Diercksen, G.H.F. )

    1990-03-01

    Isotropic scattering functions and Compton profiles together with their directional components for several directions relevant to the molecular structure of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} have been evaluated for {ital ab} {ital initio} self-consistent field and configuration-interaction wave functions. The internally folded density (reciprocal form factor) {ital B}({ital r}) is calculated and discussed as are various momentum expectation values. Comparison is made with available experimental and other theoretical results.

  18. Testing the density matrix expansion against ab initio calculations of trapped neutron drops

    SciTech Connect

    Bogner, S. K.; Hergert, H.; Furnstahl, R. J.; Kortelainen, Erno M; Stoitsov, M. V.; Maris, Pieter; Vary, J. P.

    2011-01-01

    Microscopic input to a universal nuclear energy density functional can be provided through the density matrix expansion (DME), which has recently been revived and improved. Several DME implementation strategies are tested for neutron drop systems in harmonic traps by comparing to Hartree-Fock (HF) and ab initio no-core full configuration (NCFC) calculations with a model interaction (Minnesota potential). The new DME with exact treatment of Hartree contributions is found to best reproduce HF results and supplementing the functional with fit Skyrme-like contact terms shows systematic improvement toward the full NCFC results.

  19. Ab initio calculation of excitonic Hamiltonian of light-harvesting complex LH1 of Thermochromatium tepidum

    NASA Astrophysics Data System (ADS)

    Kozlov, Maxim I.; Poddubnyy, Vladimir V.; Glebov, Ilya O.; Belov, Aleksandr S.; Khokhlov, Daniil V.

    2016-02-01

    The electronic properties of light-harvesting complexes determine the efficiency of energy transfer in photosynthetic antennae. Ab initio calculations of the electronic properties of bacteriochlorophylls (composing the LH1 complex of the purple bacteria Thermochromatium tepidum) were performed. Based on these calculations, the excitonic Hamiltonian of a native cyclic complex and the Hamiltonians of open complexes with several removed bacteriochlorophylls were constructed. Absorption spectra calculated based on these Hamiltonians agree well with the experimental data. We found that the parameters of interaction between the neighboring bacteriochlorophylls are significantly larger than the empirical parameters suggested previously.

  20. Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study.

    PubMed

    Payal, Rajdeep Singh; Balasubramanian, Sundaram

    2014-09-07

    Interactions determining the dissolution of a monomer of β-cellulose, i.e., cellobiose in a room temperature ionic liquid, [Emim][OAc], have been studied using ab initio molecular dynamics simulations. Although anions are the predominant species in the first coordination shell of cellobiose, cations too are present to a minor extent around it. The presence of low concentration of water in the solution does not significantly alter the nature of the coordination environment of cellobiose. All intra-molecular hydrogen bonds of anti-syn cellobiose are replaced by inter-molecular hydrogen bonds formed with the anions, whereas the anti-anti conformer retains an intramolecular hydrogen bond.

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

    NASA Astrophysics Data System (ADS)

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

    1997-07-01

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

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

    SciTech Connect

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

    2008-02-15

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Ab initio study of weakly bound halogen complexes: RX⋯PH3.

    PubMed

    Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana

    2013-01-01

    Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

  6. Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.

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

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

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

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

    SciTech Connect

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

    2015-04-14

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

  9. Phenolic Polymer Solvation in Water and Ethylene Glycol II: Ab Initio Computations.

    PubMed

    Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W

    2017-03-14

    Ab initio techniques are used to study the interaction of ethylene glycol and water with phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as water, but the potential energy surface is further complicated by CH$_2$-phenolic interactions, different conformers of ethylene glycol and two OH groups on each molecule. Thus the ethylene glycol-phenolic potential is more complicated than is the water-phenolic potential. The results of the {\\it ab initio} calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibrations studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  11. Application of ab-initio calculations to modeling of nanoscale diffusion and activation in silicon

    NASA Astrophysics Data System (ADS)

    Diebel, Milan

    As ULSI devices enter the nanoscale, ultra-shallow and highly electrically active junctions become necessary. New materials and 3D device structures as well as new process technologies are under exploration to meet the requirements of future devices. A detailed understanding of the atomistic mechanisms of point-defect/dopant interactions which govern diffusion and activation behavior is required to overcome the challenges in building these devices. This dissertation describes how ab-initio calculations can be used to develop physical models of diffusion and activation in silicon. A hierarchy of approaches (ab-initio, kinetic lattice Monte Carlo, continuum) is used to bridge the gaps in time scale and system size between atomistic calculations and nanoscale devices. This modeling approach is demonstrated by investigating two very different challenges in process technology: F co-implantation and stress effects on dopant diffusion/activation. In the first application, ab-initio calculations are used to understand anomalous F diffusion behavior. A set of strongly bound fluorine vacancy complexes (FnVm ) were found. The decoration of vacancies/dangling silicon bonds by fluorine leads to fluorine accumulating in vacancy rich regions, which explains the fluorine redistribution behavior reported experimentally. The revealed interactions of F with point-defects explain the benefits of F co-implantation for B and P activation and diffusion. Based on the insight gained, a simplified F diffusion model at the continuum level (50--100 nm scale) is extracted that accounts for co-implantation effects on B and P for various implant energies and doses. The second application addresses the effect of stress on point-defect/dopant equilibrium concentration, diffusion, and activation. A methodology is developed to extract detailed stress effects from ab-initio calculations. The approach is used to extract induced strains and elasticity tensors for various defects and impurities in order

  12. Ab initio solution of macromolecular crystal structures without direct methods.

    PubMed

    McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

    2017-04-04

    The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

  13. Ab initio study of MoS2 nanotube bundles

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu; Charlier, Jean-Christophe

    2003-07-01

    Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    We investigate the electronic structure, dielectric, and optical properties of bismuth tellurohalides BiTe X (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. [Phys. Rev. B 90, 035201 (2014), 10.1103/PhysRevB.90.035201], Makhnev et al. [Opt. Spectrosc. 117, 764 (2014), 10.1134/S0030400X14110125], and Rusinov et al. [JETP Lett. 101, 507 (2015), 10.1134/S0021364015080147]. 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.

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

    NASA Astrophysics Data System (ADS)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Gupta, Dinesh C.; Hamid, Idris

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

  17. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  18. Challenges for large scale ab initio Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Kent, Paul

    2015-03-01

    Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).

  19. Ab-Initio Study of Incongruent Melting in Silicates

    NASA Astrophysics Data System (ADS)

    Pinilla, C.; Stixrude, L. P.

    2014-12-01

    Knowledge of the multi-component thermodynamics and phase equilibria of silicate melts at Earth's interior conditions are key to understand the chemical and thermal evolution of the planet. Yet they remain poorly constrained with a wide uncertainty on the eutectic composition and temperature. In this work we present results from ab-initio molecular dynamics in combination with the two-phase coexistance method to study properties of a system of MgSiO3 liquid coexisting with crystalline MgO at conditions of the deep lower mantle. During incongruent melting the crystal may either grow via partial freezing of the liquid or shrink via partial melting at a given temperature and pressure. The melting process can be studied using the two-phases method where liquid and solid are in contact at a given temperature and pressure and so under thermodynamic equilibrium. We characterise the composition and densities of the resultant solid and liquid phases, provide chemical potentials of the liquid phase and study the structural and dynamical properties of the melt. In addition, we discuss the performance of alternative computational methods applied to the study of incongruent melting in silicate systems where long simulation times and a large number of atoms are usually needed. Finally, we discuss the implication of our findings for the evolution of the Earth's interior.

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

    DOE PAGES

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-01-11

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

  1. Volumic omit maps in ab initio dual-space phasing.

    PubMed

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.

  2. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

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

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  3. Ab initio liquid water from PBE0 hybrid functional simulations

    NASA Astrophysics Data System (ADS)

    Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2010-03-01

    For reasons of computational efficiency, so far most ab initio molecular dynamics simulations of liquid water have been based on semi-local density functional approximations, such as PBE and BLYP. These approaches yield a liquid structure that, albeit qualitatively correct, is overstructured compared to experiment, even after nuclear quantum effects have been taken into account.footnotetextJ. A. Morrone and R. Car, Phys. Rev. Lett. 101, 017801(2008) A major cause of this inaccuracy is the delocalization error associated to semi-local density functional approximations, which, as a consequence, overestimate slightly the hydrogen bond strength in the liquid. In this work we adopt the PBE0 hybrid functional approximation, which, by mixing a fraction of exact (Hartree-Fock) exchange, reduces significantly the delocalization error of semi-local functionals. Our approach is based on a numerically efficient order-N implementation of exact exchange.footnotetextX. Wu, A. Selloni, and R. Car, Phys. Rev. B 79, 085102(2009) We find that PBE0 systematically improves the agreement of the simulated liquid with experiment. Our conclusion is substantiated by the calculated radial distribution functions, H-bond statistics, and molecular dipole distribution.

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

    PubMed

    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.

  5. Ab initio studies of phosphorene island single electron transistor

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Broido, David

    2015-03-01

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

  7. Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

    NASA Astrophysics Data System (ADS)

    Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

    2017-01-01

    The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

  8. Ab initio Raman spectroscopy of water under extreme conditions

    NASA Astrophysics Data System (ADS)

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

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

  9. Ab initio studies of niobium defects in uranium

    SciTech Connect

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

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

  10. Perovskite transparent conducting oxides: an ab initio study.

    PubMed

    Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B

    2013-10-16

    We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.

  11. Ab initio calculations of nuclear reactions important for astrophysics

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  12. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

  13. Electronic structure and conductivity of ferroelectric hexaferrite: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Knížek, K.; Novák, P.; Küpferling, M.

    2006-04-01

    Ba0.5Sr1.5Zn2Fe12O22 is a promising multiferroic compound in which the electric polarization is intimately connected to the magnetic state. In principle, ferroelectrity might exist above the room temperature, but the electrical conductivity that increases with increasing temperature limits it to temperatures below ≈130K . We present results of an ab initio electronic structure calculation of the (BaSr)Zn2Fe12O22 system. To improve the description of strongly correlated 3d electrons of iron, the GGA+U method is used. The results show that the electrical conductivity strongly depends on relative fractions of iron and zinc in the tetrahedral sublattice that belongs to the spinel block of the hexaferrite structure. If this sublattice is fully occupied by zinc, the system is an insulator with a gap of ≈1.5eV . If it is occupied equally by Fe and Zn the gap decreases by a factor of 2, and the system is metallic when this sublattice is filled by iron only.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  15. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

  16. Ab initio molecular dynamics calculations of ion hydration free energies.

    PubMed

    Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.

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

    DTIC Science & Technology

    2015-06-28

    Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...Unlimited. 13. SUPPLEMENTARY NOTES Briefing Charts presented at 9th Int. Conf. Chemical Kinetics; Ghent, Belgium; 28 Jun 2015. PA#15351. 14. ABSTRACT...ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A

  18. Experimental and ab initio study of the mechanical properties of hydroxyapatite

    NASA Astrophysics Data System (ADS)

    Snyders, R.; Music, D.; Sigumonrong, D.; Schelnberger, B.; Jensen, J.; Schneider, J. M.

    2007-05-01

    The authors have studied the elastic properties of radio frequency sputtered phase pure, stoichiometric, and dense hydroxyapatite films by nanoindentation. The measured elastic modulus values have been compared to ab initio calculated data. The calculation technique was based on the determination of all elastic constants. The calculated and measured elastic modulus values differ by ˜10%. The good agreement indicates that the elasticity of hydroxyapatite can be described using ab initio calculations, establishing the elastic modulus thereof.

  19. An ab initio study on the four electronically lowest-lying states of CH 2 using the state-averaged complete active space second-order configuration interaction method

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Yukio; Schaefer, Henry F., III

    1997-12-01

    Four electronically lowest-lying ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states of CH 2 have been investigated systematically using ab initio electronic structure theory. Complete active space (CAS) self-consistent-field (SCF) second-order configuration interaction (SOCI) and state-averaged (SA) CASSCF-SOCI levels of theory have been employed. The CASSCF reference wave function was constructed by minimizing the total energy of a specified state, while the SACASSCF reference wave function was obtained by minimizing the equally weighted total energy of the four ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states. The third excited state ( c˜ 1A 1 or 2 1A 1) is of particular theoretical interest because it is represented by the second root of CASSCF and SOCI Hamiltonian matrices. Theoretical treatments of states not the lowest of their symmetry require special attention due to their tendency of variational collapse to the lower-lying state(s). For these four lowest-lying states total energies and physical properties including dipole moments, harmonic vibrational frequencies, and associated infrared (IR) intensities were determined and compared with the results from the configuration interaction with single and double excitations (CISD) method and available experimental values. The CASSCF-SOCI method should provide the most reliable energetics and physical properties in the present study owing to its fully variational nature in the molecular orbital (MO) and CI spaces for a given state. It is demonstrated that the SACASSCF-SOCI wave functions produce results which are quite consistent with those from the CASSCF-SOCI method. Thus significantly increased application of the SACASSCF-SOCI method to the excited states of a wide variety of molecular systems is expected.

  20. 4He+n+n continuum within an ab initio framework

    DOE PAGES

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

    2014-07-16

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

  1. Three-cluster dynamics within an ab initio framework

    SciTech Connect

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

    2013-09-26

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

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

    SciTech Connect

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

    2016-05-17

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  6. Unified ab initio approaches to nuclear structure and reactions

    SciTech Connect

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

    2016-04-13

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

  7. The CO-Ne van der Waals complex: ab initio intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces, and second virial coefficients.

    PubMed

    Baranowska, Angelika; Fernández, Berta; Rizzo, Antonio; Jansík, Branislav

    2009-11-14

    The intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces of the CO-Ne van der Waals complex are calculated using coupled cluster methods and the d-aug-cc-pVTZ basis set extended with a set of 3s3p2d1f1g midbond functions placed in the middle of the van der Waals bond. After fitting the interaction properties to appropriate analytical functions the surfaces are further used in semiclassical calculations of the pressure, the dielectric and the refractivity second virial coefficients of the system. The interaction potential energy surface has a single minimum (-49.9952 cm(-1)), which corresponds to R = 3.383 A and theta = 79.4 degrees. The computed dielectric second virial coefficient B(epsilon) approximately -0.27 cm(6) mol(-2) around the room temperature.

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

    SciTech Connect

    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.

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

    PubMed

    Marsalek, Ondrej; Markland, Thomas E

    2016-02-07

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

  10. New basis set superposition error free ab initio MO-VB interaction potential: Molecular-dynamics simulation of water at critical and supercritical conditions

    NASA Astrophysics Data System (ADS)

    Famulari, Antonino; Specchio, Roberto; Sironi, Maurizio; Raimondi, Mario

    1998-02-01

    Recently, a controversy has come to light in literature regarding the structure of water in nonambient conditions. Disagreement is evident between the site-site pair correlation functions of water derived from neutron diffraction and those obtained by computer simulations which employ effective pairwise potentials to express the intermolecular interactions. In this paper the SCFMI method (self-consistent field for molecular interaction) followed by nonorthogonal CI (configuration interaction) calculations was used to determine a new water-water interaction potential, which is BSSE (basis set superposition error) free in an a priori fashion. Extensive calculations were performed on water dimer and trimer and a new parametrization of a NCC-like (Niesar-Corongiu-Clementi) potential was accomplished. This was employed in the molecular-dynamics simulation of water. The effect of temperature and density variations was examined. Acceptable agreement between site-site correlation functions derived from neutron diffraction data and from computer simulation was reached. In particular, a weakening of the hydrogen bonded structure was observed on approaching the critical point, which reproduces the experimental behavior. The simulations were performed using the MOTECC (modern techniques in computational chemistry) suite of programs. The present results show the importance of BSSE-free nonorthogonal orbitals in an accurate description of the intermolecular potential of water.

  11. Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

    PubMed

    Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

    2008-12-11

    The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

  12. Photodissociation of CH{sub 3}Cl, C{sub 2}H{sub 5}Cl, and C{sub 6}H{sub 5}Cl on the Ag(111) surface: Ab initio embedded cluster and configuration interaction study

    SciTech Connect

    Kokh, Daria B.; Liebermann, Heinz-Peter; Buenker, Robert J.

    2010-02-21

    We report a comparative study of the photoinduced C-Cl bond cleavage in three Rd-Cl molecules (Rd=CH{sub 3}, C{sub 2}H{sub 5}, and C{sub 6}H{sub 5} radicals) on the Ag(111) surface. The ground, lowest excited states as well as anion states of adsorbed molecules have been computed at their equilibrium geometry and along the C-Cl dissociation pathway using the ab initio embedded cluster and multireference configuration interaction methods. The anion state can be formed by photoinduced electron transfer from the substrate to an adsorbate and is strongly bound to the surface in contrast with the electronic states of the adsorbate itself, which are only weakly perturbed by the silver surface. The excitation energy of the anion state lies lower in the Franck-Condon region than that of the lowest singlet excited state for all adsorbates and correlates directly with the dissociation products: adsorbed chlorine atom and the gas phase or adsorbed radical for Rd=CH{sub 3}, C{sub 2}H{sub 5}, and C{sub 6}H{sub 5}, respectively. The computed redshift of the photodissociation spectrum for the substrate-mediated photodissociation process relative to the corresponding gas-phase reaction is {approx}2 eV for CH{sub 3}Cl and C{sub 2}H{sub 5}Cl, and {approx}1 eV for C{sub 6}H{sub 5}Cl, which result is in good agreement with experimental data.

  13. Ab initio study of the anharmonic lattice dynamics of iron at the γ -δ phase transition

    NASA Astrophysics Data System (ADS)

    Lian, Chao-Sheng; Wang, Jian-Tao; Chen, Changfeng

    2015-11-01

    We report calculations of phonon dispersions of iron (Fe) at its γ -δ phase transition using a self-consistent ab initio lattice dynamical method in conjunction with an effective magnetic force approach via the antiferromagnetic approximation. Our results show that anharmonic phonon-phonon interactions play a crucial role in stabilizing the δ -Fe phase in the open bcc lattice. In contrast, the lattice dynamics of the close-packed fcc γ -Fe phase are dominated by magnetic interactions. Simultaneous considerations of the lattice anharmonic and magnetic interactions produced temperature-dependent phonon dispersions for δ -Fe and γ -Fe phases in excellent agreement with recent experimental measurements. The present results highlight the key role of lattice anharmonicity in determining the structural stability of iron at high temperatures, which has significant implications for other high-temperature paramagnetic metals like Ce and Pu.

  14. Ab initio based polarizable force field generation and application to liquid silica and magnesia

    NASA Astrophysics Data System (ADS)

    Beck, Philipp; Brommer, Peter; Roth, Johannes; Trebin, Hans-Rainer

    2011-12-01

    We extend the program potfit, which generates effective atomic interaction potentials from ab initio data, to electrostatic interactions and induced dipoles. The potential parametrization algorithm uses the Wolf direct, pairwise summation method with spherical truncation. The polarizability of oxygen atoms is modeled with the Tangney-Scandolo interatomic force field approach. Due to the Wolf summation, the computational effort in simulation scales linearly in the number of particles, despite the presence of electrostatic interactions. Thus, this model allows to perform large-scale molecular dynamics simulations of metal oxides with realistic potentials. Details of the implementation are given, and the generation of potentials for SiO2 and MgO is demonstrated. The approach is validated by simulations of microstructural, thermodynamic, and vibrational properties of liquid silica and magnesia.

  15. Cosmic-Ray Modulation: an Ab Initio Approach

    NASA Astrophysics Data System (ADS)

    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.

  16. The hydration structure of carbon monoxide by ab initio methods

    NASA Astrophysics Data System (ADS)

    Awoonor-Williams, Ernest; Rowley, Christopher N.

    2017-01-01

    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 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 using the TIP3P water model is in good agreement with the experiment (9.3 kJ mol-1 expt. vs 10.7 kJ mol-1 calc.). The calculated diffusivity of CO (aq) in TIP3P-model water was 5.1 ×10-5 cm2/s calc., more than double the experimental value of 2.3 ×10-5 cm2/s. The hydration energy calculated using the TIP4P-FB water model is in poorer agreement with the experiment (ΔG = 6.8 kJ/mol) but the diffusivity is in better agreement (D =2.5 ±0.1 ×10-5 cm2/s).

  17. Ab initio valence-space theory for exotic nuclei

    NASA Astrophysics Data System (ADS)

    Holt, Jason

    2015-10-01

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

  18. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    SciTech Connect

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

    2013-07-20

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

  19. Uniaxial phase transition in Si: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Cheng, C.

    2003-04-01

    Based on a previously proposed thermodynamic analysis, [C. Cheng, W. H. Huang, and H. J. Li, Phys. Rev. B 63, 153202 (2001)] we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, βSn, simple-hexagonal (sh), simple-cubic, and hexagonal closed-packed structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different contributions to the relative phase stability, we identified the most important factors in reducing the phase-transition pressures at uniaxial compression. We also show that it is possible to have phase transitions occur only when the phases are under uniaxial compression, in spite of no phase transition when under hydrostatic compression. Taking all five phases into consideration, the phase diagram at uniaxial compression was constructed for pressures up to 20 GPa. The stable phases were found to be diamond, βSn, and sh structures, i.e., the same as those when under hydrostatic condition. According to the phase diagram, direct phase transition from the diamond to the sh phase is possible if the applied uniaxial pressures, on increasing, satisfy the condition Px>Pz. Similarly, the sh-to-βSn transition on increasing pressures is also possible if the applied uniaxial pressures are varied from the condition of Px>Pz, on which the phase of sh is stable to the condition Px

  20. Actions between neonicotinoids and key residues of insect nAChR based on an ab initio quantum chemistry study: hydrogen bonding and cooperative pi-pi interaction.

    PubMed

    Wang, Yanli; Cheng, Jiagao; Qian, Xuhong; Li, Zhong

    2007-04-01

    Neonicotinoid insecticides show selective actions on insect nicotinic acetylcholine receptor (nAChR). Two key residues (Trp and Arg/Lys) have been identified as contributing to the neonicotinois binding. To investigate the selective mechanism, a computational model was set up to simulate the interaction between residues (Trp and Arg) of insect nAChR and neonicotinoids by quantum chemistry method. Three analogues of neonicotinoid derivatives without the chloropyridinyl moiety and 3-methyl-indole (3MI), guanidinium (Gua) were used to mimic the neonicotinoids and the side chain of key residues Trp and Arg accordingly. Interaction features of 3MI-analogues, analogues-Gua and 3MI-analogues -Gua complexes were analyzed comparatively. Hydrogen bonding between the nitro group of analogues and Gua was found to be the most important for binding. Moreover, the cooperative pi-pi interaction between analogues and the indole ring, which is strengthened by the existence of Gua, also contributes to the binding. The alternative binding model of neonicotinoids proposed here, although slightly different from others, might be close to the actual.

  1. ab initio study of hot carriers in the first picosecond after sunlight absorption in silicon.

    PubMed

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

    2014-06-27

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

  2. Ab initio results for intermediate-mass, open-shell nuclei

    NASA Astrophysics Data System (ADS)

    Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.

    2017-01-01

    A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.

  3. Optimized unrestricted Kohn-Sham potentials from ab initio spin densities

    NASA Astrophysics Data System (ADS)

    Boguslawski, Katharina; Jacob, Christoph R.; Reiher, Markus

    2013-01-01

    The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham (KS) potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in unrestricted KS-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011), 10.1063/1.3670414] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.

  4. Surface segregation in AuPd alloys: Ab initio analysis of the driving forces

    NASA Astrophysics Data System (ADS)

    Creuze, Jérôme; Guesmi, Hazar; Mottet, Christine; Zhu, Beien; Legrand, Bernard

    2015-09-01

    In order to determine the energetic driving forces for surface segregation in AuPd alloys, we use a combined approach coupling ab initio calculations and an analysis via an effective Ising model. Previously, this approach has been used successfully in the framework of N-body interatomic potentials to study the surface segregation in both semi-infinite alloys and nanoparticles, allowing one to determine the relative contributions of the different elementary driving forces. Here, we go beyond the use of N-body interatomic potentials by using ab initio calculations to evaluate the segregation enthalpy and the effective pair interactions, the contribution due to the size difference between the constituants being still obtained by N-body interatomic potentials. We show that the decomposition of the segregation enthalpy into its different elementary contributions is still valid at this level of description. This allows us to analyze the segregation driving forces in the two infinite dilute limits of the Au-Pd system, for both (100) and (111) surfaces. Finally, between the two infinite dilute limits, we find that our results are consistent with existing experimental data.

  5. Flexible H2O2 in water: electronic structure from photoelectron spectroscopy and ab initio calculations.

    PubMed

    Thürmer, Stephan; Seidel, Robert; Winter, Bernd; Ončák, Milan; Slavíček, Petr

    2011-06-16

    The effect of hydration on the electronic structure of H(2)O(2) is investigated by liquid-jet photoelectron spectroscopy measurements and ab initio calculations. Experimental valence electron binding energies of the H(2)O(2) orbitals in water are, on average, 1.9 eV red-shifted with respect to the gas-phase molecule. A smaller width of the first peak was observed in the photoelectron spectrum from the solution. Our experiment is complemented by simulated photoelectron spectra, calculated at the ab initio level of theory (with EOM-IP-CCSD and DFT methods), and using path-integral sampling of the ground-state density. The observed shift in ionization energy upon solvation is attributed to a combination of nonspecific electrostatic effects (long-range polarization) and of the specific interactions between H(2)O(2) and H(2)O molecules in the first solvation shell. Changes in peak widths are found to result from merging of the two lowest ionized states of H(2)O(2) in water due to conformational changes upon solvation. Hydration effects on H(2)O(2) are stronger than on the H(2)O molecule. In addition to valence spectra, we report oxygen 1s core-level photoelectron spectra from H(2)O(2)(aq), and observed energies and spectral intensities are discussed qualitatively.

  6. Ab initio many-body calculations of nucleon-nucleus scattering

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    McKemmish, Laura K.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2016-11-01

    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 of electronic transitions. We test finite-field off-diagonal dipole moments, but found that (1) the accuracy of the excitation energies were not sufficient to allow accurate dipole moments to be evaluated and (2) computer time requirements for perpendicular transitions were prohibitive. The best off-diagonal dipole moments are calculated using wavefunctions with different CASSCF orbitals.

  8. Non-covalent C-Cl…π interaction in acetylene-carbon tetrachloride adducts: Matrix isolation infrared and ab initio computational studies

    NASA Astrophysics Data System (ADS)

    Ramanathan, N.; Sundararajan, K.; Vidya, K.; Jemmis, Eluvathingal D.

    2016-03-01

    Non-covalent halogen-bonding interactions between π cloud of acetylene (C2H2) and chlorine atom of carbon tetrachloride (CCl4) have been investigated using matrix isolation infrared spectroscopy and quantum chemical computations. The structure and the energies of the 1:1 C2H2-CCl4 adducts were computed at the B3LYP, MP2 and M05-2X levels of theory using 6-311 ++G(d,p) basis set. The computations indicated two minima for the 1:1 C2H2-CCl4 adducts; with the C-Cl…π adduct being the global minimum, where π cloud of C2H2 is the electron donor. The second minimum corresponded to a C-H…Cl adduct, in which C2H2 is the proton donor. The interaction energies for the adducts A and B were found to be nearly identical. Experimentally, both C-Cl…π and C-H…Cl adducts were generated in Ar and N2 matrixes and characterized using infrared spectroscopy. This is the first report on halogen bonded adduct, stabilized through C-Cl…π interaction being identified at low temperatures using matrix isolation infrared spectroscopy. Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were performed to support the experimental results. The structures of 2:1 ((C2H2)2-CCl4) and 1:2 (C2H2-(CCl4)2) multimers and their identification in the low temperature matrixes were also discussed.

  9. Assessment of Standard Force Field Models against High-Quality ab initio Potential Curves for Prototypes of pi-pi, CH/pi, and SH/pi Interactions

    SciTech Connect

    Sumpter, Bobby G; Sherrill, David; Sinnokrot, Mutasem O; Marshall, Michael S.; Hohenstein, Edward G.; Walker, Ross; Gould, Ian R

    2009-01-01

    Several popular force fields, namely, CHARMM, AMBER, OPLS-AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechani- cal potential energy curves for noncovalent interactions in the benzene dimer, the benzene-CH4 complex, and the benzene-H2S complex. All of the force fields are semi-quantitatively correct, but none of them is consistently reliable quantitatively. Re-optimization of Lennard-Jones parameters and symmetry-adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions)are employed for the empirical force fields.

  10. Cd hyperfine interactions in DNA bases and DNA of mouse strains infected with Trypanosoma cruzi investigated by perturbed angular correlation spectroscopy and ab initio calculations.

    PubMed

    Petersen, Philippe A D; Silva, Andreia S; Gonçalves, Marcos B; Lapolli, André L; Ferreira, Ana Maria C; Carbonari, Artur W; Petrilli, Helena M

    2014-06-03

    In this work, perturbed angular correlation (PAC) spectroscopy is used to study differences in the nuclear quadrupole interactions of Cd probes in DNA molecules of mice infected with the Y-strain of Trypanosoma cruzi. The possibility of investigating the local genetic alterations in DNA, which occur along generations of mice infected with T. cruzi, using hyperfine interactions obtained from PAC measurements and density functional theory (DFT) calculations in DNA bases is discussed. A comparison of DFT calculations with PAC measurements could determine the type of Cd coordination in the studied molecules. To the best of our knowledge, this is the first attempt to use DFT calculations and PAC measurements to investigate the local environment of Cd ions bound to DNA bases in mice infected with Chagas disease. The obtained results also allowed the detection of local changes occurring in the DNA molecules of different generations of mice infected with T. cruzi, opening the possibility of using this technique as a complementary tool in the characterization of complicated biological systems.

  11. H2O and CO2 confined in cement based materials: an ab initio molecular dynamics study with van der Waals interactions

    NASA Astrophysics Data System (ADS)

    de Almeida, James; Miranda, Caetano; Fazzio, Adalberto

    2013-03-01

    Although the cement has been widely used for a long time, very little is known regarding the atomistic mechanism behind its functionality. Particularly, the dynamics of molecular systems at confined nanoporous and water hydration is largely unknown. Here, we study the dynamical and structural properties of H2O and CO2 confined between Tobermorite 9Å(T9) surfaces with Car-Parrinello molecular dynamics with and without van der Waals (vdW) interactions, at room temperature. For H2O confined, we have observed a broadening in the intra and intermolecular bond angle distribution. A shift from an ice-like to a liquid-like infrared spectrum with the inclusion of vdW interactions was observed. The bond distance for the confined CO2 was increased, followed with the appearance of shorter (larger) intramolecular (intermolecular) angles. These structural modifications result in variations on the CO2 symmetric stretching Raman active vibration modes. The diffusion coefficient obtained for both confined H2O and CO2 were found to be lower than their bulk counterparts. Interestingly, during the water dynamics, a proton exchange between H2O and the T9 surface was observed. However, for confined CO2, no chemical reactions or bond breaking were observed.

  12. Ab initio multireference configuration interaction and coupled cluster studies of potential surfaces for proton transfer in (H{sub 3}N---H---OH{sub 2}){sup +}

    SciTech Connect

    Roszak, S.; Chapman, D.A.; Kaufman, J.J.; Kaldor, U.

    1992-03-05

    Proton-transfer reactions are important in chemical and biological processes, including photosynthesis and vision. The multiple reference double-excitation configuration interaction method (MRD-CI) and the coupled cluster method (CCM) were applied for the studies of the ground-state and low-lying excited states for the proton-transfer system (H{sub 3}N---H---OH{sub 2}){sup +}. The geometry optimization at the SCF level indicates the rapid change in geometry of subunits while the proton moves between N and O atoms. The significant difference was found between the structure of potential curves for the short N-O distances (2.707, 2.95, 3.2 {Angstrom}) and the long N-O distance (5.0 {Angstrom}). The complicated multireference structure of potential curves results from the strong interactions between them. The ground state is described by a single determinant wave function for short N-O distances; however, for a distance of 5.0 {Angstrom} the multireference structure becomes significant for intermediate regions of the hydrogen bond. The correlation between the protonation potential surfaces for NH{sub 3} and H{sub 2}O and the structure of surfaces for the proton-transfer system of the complex can be recognized. The simple interpretation of the gross atomic population on the transferred proton indicates that the reaction proceeds as a {open_quotes}proton transfer{close_quotes} in the ground electronic state and a {open_quotes}hydrogen transfer{close_quotes} in low-lying excited states. 33 refs., 13 figs., 3 tabs.

  13. Thermochemistry of aqueous hydroxyl radical from advances in photoacoustic calorimetry and ab initio continuum solvation theory.

    PubMed

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

    2004-03-31

    Photoacoustic signals from dilute ( approximately 30 mM) solutions of H2O2 were measured over the temperature range from 10 to 45 degrees C to obtain the reaction enthalpy and volume change for H2O2(aq) --> 2 OH(aq) from which we ultimately determined DeltafG degrees , DeltafH degrees and partial molal volume, v degrees , of OH (aq). We find DeltarH = 46.8 +/- 1.4 kcal/mol, which is 4 kcal/mol smaller than the gas-phase bond energy, and DeltaVr = 6.5 +/- 0.4 mL/mol. The v degrees for OH in water is 14.4 +/- 0.4 mL/ml: smaller than the v degrees of water. Using ab intio continuum theory, the hydration free energy is calculated to be -3.9 +/- 0.3 kcal/mol (for standard states in number density concentration units) by a novel approach devised to capture in the definition of the solute cavity the strength and specific interactions of the solute with a water solvent molecule. The shape of the cavity is defined by "rolling" a three-dimensional electron density isocontour of water on the ab initio water-OH minimum interaction surface. The value of the contour is selected to reproduce the volume of OH in water. We obtain for OH(aq): DeltafH degrees = -0.2 +/- 1.4 and DeltafG degrees = 5.8 +/- 0.4 kcal/mol that are in agreement with literature values. The results provide confidence in the pulsed PAC technique for measuring aqueous thermochemistry of radicals and open the way to obtaining thermochemistry for most radicals that can be formed by reaction of OH with aqueous substrates while advancing the field of continuum solvation theory toward ab initio-defined solute cavities.

  14. {ital Ab initio} study of the van der Waals interaction of NH(X{sup 3}{Sigma}{sup {minus}}) with Ar({sup 1}S)

    SciTech Connect

    Kendall, R.A. Bukowski, R.; Szczesniak, M.M. Cybulski, S.M.

    1998-02-01

    The potential energy surface for the Ar({sup 1}S)+NH(X{sup 3}{Sigma}{sup {minus}}) interaction is calculated using the supermolecular unrestricted Mo/ller{endash}Plesset (UMP) perturbation theory approach and analyzed via the perturbation theory of intermolecular forces. The global minimum occurs for the approximate T-shaped geometry with Ar skewed toward the H atom at about {Theta}=67{degree} and R=6.75a{sub 0}. Our UMP4 estimate of the well depth of the global minimum is D{sub e}=100.3cm{sup {minus}1} and the related ground state dissociation energy obtained by rigid-body diffusion quantum Monte Carlo calculations (RBDQMC) is D{sub 0}=71.5{plus_minus}0.1cm{sup {minus}1}. These values are expected to be accurate to within a few percent. The potential energy surface also features a wide plateau in the proximity of Ar-N-H collinear geometry, at ca. 7.0a{sub 0}. RBDQMC calculations reveal nearly a free rotation of the NH subunit in the complex. {copyright} {ital 1998 American Institute of Physics.}

  15. Intermolecular Interactions Between Formaldehyde and Dimethyl Ether and Between Formaldehyde Abd Dimethyl Sulfide in the Complex, Investigated by Fourier Transform Microwave Spectroscopy and AB Initio Calculations

    NASA Astrophysics Data System (ADS)

    Kawashima, Yoshiyuki; Tatamitani, Yoshio; Osamura, Yoshihiro; Hirota, Eizi

    2014-06-01

    The ground-state rotational spectra of the formaldehyde-dimethyl ether (H_2CO-DME) and the formaldehyde-dimethyl sulfide (H_2CO-DMS) complexes have been studied by Fourier transform microwave spectroscopy, and a-type and c-type transitions have been observed and assigned for the H_2CO as well as D_2CO species of both the complexes. In the case of the H_2CO-DME, doublets were observed with the splitting of a few 100 kHz, whereas no such splitting was found for the H_2CO-DMS. The observed rotational constants were analyzed to conclude a Cs geometry, where DME and DMS were bound to H_2CO by the two C-H(DME/DMS)---O(H_2CO) and the two O(DME)/S(DMS)---H-C(H_2CO) hydrogen bonds. The distances Rcm between the centers of mass of the constituents were determined to be 3.102 and 3.200 Å for the two complexes, respectively. Both the H_2CO-DME and H_2CO-DMS complexes were shown by the natural bond orbital (NBO) analysis, to have strong charge transfer interactions between the constituents, as expected from the strong electron-accepting character of the H_2CO.

  16. Intermolecular interaction in the formaldehyde-dimethyl ether and formaldehyde-dimethyl sulfide complexes investigated by Fourier transform microwave spectroscopy and ab initio calculations.

    PubMed

    Tatamitani, Yoshio; Kawashima, Yoshiyuki; Osamura, Yoshihiro; Hirota, Eizi

    2015-03-12

    The ground-state rotational spectra of the formaldehyde-dimethyl ether (H2CO-DME) and formaldehyde-dimethyl sulfide (H2CO-DMS) complexes have been studied by Fourier transform microwave spectroscopy. The a-type and c-type rotational transitions have been assigned for the normal and deutrated formaldehyde-containing species of both complexes. In the case of H2CO-DME, doublets were observed with the splitting 10-300 kHz, whereas no such splittings were observed for H2CO-DMS, D2CO-DME, and D2CO-DMS. The observed rotational spectra were found consistent with a structure of Cs symmetry with DME or DMS bound to H2CO by two types of hydrogen bonds: C-H(DME/DMS)---O(H2CO) and O(DME)/S(DMS)---H-C(H2CO). The R(cm) distances between the centers of mass of the component molecules in the H2CO-DME and H2CO-DMS complexes were determined to be 3.102 and 3.200 Å, respectively, which are shorter than those in most related complexes. The spectral and NBO analyses showed that H2CO-DMS has a stronger charge transfer interaction than H2CO-DME does and that the binding energy of H2CO-DMS is larger than that of H2CO-DME.

  17. Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

    DTIC Science & Technology

    2014-08-20

    Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report

  18. Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom

    DTIC Science & Technology

    2014-08-01

    Technical Paper 3. DATES COVERED (From - To) December 2013- August 2014 4. TITLE AND SUBTITLE Ab initio Kinetics of Methylamine Radical Thermal...phase kinetics of H-abstraction reactions from CH3NHNH2 by H atoms was further investigated by ab initio second-order multireference perturbation...distribution unlimited Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom

  19. Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.

    PubMed

    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.

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

    SciTech Connect

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

    2015-06-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O 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 N2O 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.

  2. A-dependence of the Spectra of the F Isotopes from ab initio Calculations

    NASA Astrophysics Data System (ADS)

    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.

  3. Ab initio study of the optical properties of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chang, Eric

    2006-03-01

    We present an ab initio study of the optical properties of carbon nanotubes. We use state-of-the-art electronic structure methods based on many-body perturbation theory to compute the optical absorption and resonance Raman spectra of large tubes which have up to 200 atoms [1,2]. Our symmetry-based method makes the study of large tubes feasible within the many- body framework and also allows us to understand the symmetry properties of the excitons and selection rules. We include a study of the so-called dark excitons which are crucial for understanding luminescence efficiency in carbon nanotubes. The mechanism that explains the dark-bright splitting can be understood within our symmetry-based approach. Finally, we present an analysis of the two-photon spectra for several carbon nanotubes, a theoretical analysis which, in conjunction with combined one- and two-photon experiments, allows one to measure the binding energy of excitons. We find in all cases that the excitonic binding energy is large, ranging from 0.5 to 0.9 eV depending on the diameter of the tube, and that the excitonic wavefunction is Wannier-like and extended over many atoms. Our studies for the one- and two-photon absorption and resonance Raman spectra have been fruitful for understanding the corresponding experiments. In particular, our theoretical results are in good agreement with one- and two-photon absorption experiments [3-5]. The results for resonance Raman show that such a spectroscopic technique is a good alternative to optical absorption since it allows for the selection of tubes of a given diameter while probing the same excited states. 1. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. Lett. 92, 196401 (2004). 2. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. B 72, 195423 (2005). 3. M. Y. Sfeir et al., Science 306, 1540 (2004). 4. J. Maultzsch et al., to be published in Phys. Rev. B, see also cond-mat/0505150. 5. Z. M. Li et. al., Phys. Rev. Lett. 87, 127401 (2001).

  4. ab initio MD simulations of geomaterials with ~1000 atoms

    NASA Astrophysics Data System (ADS)

    Martin, G. B.; Kirtman, B.; Spera, F. J.

    2009-12-01

    In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in

  5. Ab initio calculations of the intermolecular chemical shift in nuclear magnetic resonance in the gas phase and for adsorbed species

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; de Dios, Angel C.

    1992-07-01

    The chemical shifts observed in nuclear magnetic resonance experiments are the differences in shielding of the nuclear spin in different electronic environments. These are known to depend on intermolecular interactions as evidenced by density-dependent chemical shifts in the gas phase, gas-to-liquid shifts, and adsorption shifts on surfaces. We present the results of the first ab initio intermolecular chemical shielding function calculated for a pair of interacting atoms for a wide range of internuclear separations. We used the localized orbital local origin (LORG) approach of Hansen and Bouman and also investigated the second-order electron correlation contributions using second-order LORG (SOLO). The 39Ar shielding in Ar2 passes through zero at some very short distance, going through a minimum, and asymptotically approaches zero at larger separations. The 21Ne shielding function in Ne2 has a similar shape. The Drude model suggests a method of scaling that portion of the shielding function that is weighted most heavily by exp[-V(R)/kT]. The scaling factors, which have been verified in the comparison of 21Ne in Ne2 against 39Ar in Ar2 ab initio results, allows us to project out from the same 39Ar in Ar2 ab initio values the appropriate 129Xe shielding functions in the Xe-Ar, Xe-Kr, and Xe-Xe interacting pairs. These functions lead to temperature-dependent second virial coefficients of chemical shielding which agree with experiments in the gas phase. Ab initio calculations of 39Ar shielding in clusters of argon are used to model the observed 129Xe chemical shifts of Xe, Xe2,...,Xe8 trapped in the cages of zeolite NaA.

  6. Large basis ab initio shell model investigation of {sup 9}Be and {sup 11}Be

    SciTech Connect

    Forssen, C.; Navratil, P.; Ormand, W.E.; Caurier, E.

    2005-04-01

    We present the first ab initio structure investigation of the loosely bound {sup 11}Be nucleus, together with a study of the lighter isotope {sup 9}Be. The nuclear structure of these isotopes is particularly interesting because of the appearance of a parity-inverted ground state in {sup 11}Be. Our study is performed in the framework of the ab initio no-core shell model. Results obtained using four different, high-precision two-nucleon interactions, in model spaces up to 9({Dirac_h}/2{pi}){omega}, are shown. For both nuclei, and all potentials, we reach convergence in the level ordering of positive- and negative-parity spectra separately. Concerning their relative position, the positive-parity states are always too high in excitation energy, but a fast drop with respect to the negative-parity spectrum is observed when the model space is increased. This behavior is most dramatic for {sup 11}Be. In the largest model space we were able to reach, the 1/2{sup +} level has dropped down to become either the first or the second excited state, depending on which interaction we use. We also observe a contrasting behavior in the convergence patterns for different two-nucleon potentials and argue that a three-nucleon interaction is needed to explain the parity inversion. Furthermore, large-basis calculations of {sup 13}C and {sup 11}B are performed. This allows us to study the systematics of the position of the first unnatural-parity state in the N=7 isotone and the A=11 isobar. The {sup 11}B run in the 9({Dirac_h}/2{pi}){omega} model space involves a matrix with dimension exceeding 1.1x10{sup 9}, and is our largest calculation so far. We present results on binding energies, excitation spectra, level configurations, radii, electromagnetic observables, and {sup 10}Be+n overlap functions.

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

    SciTech Connect

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

    2004-03-31

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

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Ab initio calculation of (hyper)polarizabilities using a sum-over-states formalism.

    NASA Astrophysics Data System (ADS)

    Taylor, Caroline M.; Chaudhuri, Rajat K.; Potts, Davin M.; Freed, Karl F.

    2001-03-01

    Hyperpolarizabilities are relevant to a wide range of non-linear optical properties. Ab initio computations often require a high level of correlation for accurate determination of β and γ , and especially of thier frequency dependence. While sum-over-states methods are widely used within semi-empirical frameworks, they have not been employed with high level ab initio methods because of the computational costs associated with calculating a sufficient number of states. The effective valence shell Hamiltonian method (H^v) is a highly correlated, size-extensive, ab initio, multireference, perturbative (``perturb-then-diagonalize'') method. A single H^v calculation yields a large number of states, making it ideal for use with the sum-over-states fomalism for determination of molecular properties. The method has been used to calculate the (hyper)polarizabilities of small polyene systems.

  11. Classical and ab-initio molecular dynamic simulation of an amorphous silica surface

    NASA Astrophysics Data System (ADS)

    Mischler, C.; Kob, W.; Binder, K.

    2002-08-01

    We present the results of a classical molecular dynamic simulation as well as of an ab-initio molecular dynamic simulation of an amorphous silica surface. In the case of the classical simulation we use the potential proposed by van Beest et al. (BKS) whereas the ab-initio simulation is done with a Car-Parrinello method (CPMD). We find that the surfaces generated by BKS have a higher concentration of defects (e.g., concentration of two-membered rings) than those generated with CPMD. In addition also the distribution functions of the angles and of the distances are different for the short rings. Hence we conclude that whereas the BKS potential is able to correctly reproduce the surface on the length scale beyond ≈5 Å, it is necessary to use an ab-initio method to reliably predict the structure at small scales.

  12. Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening

    NASA Astrophysics Data System (ADS)

    de Jonge, Marc R.; Vinkers, H. Maarten; van Lenthe, Joop H.; Daeyaert, Frits; Bush, Ian J.; van Dam, Huub J. J.; Sherwood, Paul; Guest, Martyn F.

    2007-09-01

    We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of this region special care was taken to assign optimal basis functions. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.

  13. Global exploration of the energy landscape of solids on the ab initio level.

    PubMed

    Doll, K; Schön, J C; Jansen, M

    2007-12-14

    Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.

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

    PubMed

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

    2015-09-14

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

  15. Ab-initio study of quasi one-dimensional Br adsorption on Pt(110)

    NASA Astrophysics Data System (ADS)

    Franchini, Cesare; Redinger, Josef; Podloucky, Raimund

    2001-03-01

    Halogen atoms interact strongly with metal surfaces. For this reason they play an important role in many technologically important processes. The Pt(110) surface is known to reconstruct into an (1x2) structure of "missing-row" type (MR). Its strong anisotropic character can be used as template to prepare single crystal surfaces of Pt-Br-Pt chains, which exhibit quasi one-dimensional (1D) behavior. We present ab-initio investigations based on the Full-potential Linearized Augmented Plane Wave method (FLAPW), as implemented in the FLEUR package, and the Tersoff-Hamann model for simulating STM images. Structural and electronic properties of the Br/Pt(110) surface at half coverage and of the clean Pt(110) surface and its (1x2) MR reconstruction are studied in detail. Results are compared to available LEED and STM data.

  16. On potential energy models for EA-based ab initio protein structure prediction.

    PubMed

    Mijajlovic, Milan; Biggs, Mark J; Djurdjevic, Dusan P

    2010-01-01

    Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.

  17. Dynamic decomposition of aliphatic molecules on Al(111) from ab initio molecular dynamics

    SciTech Connect

    Zhong Jun; Hector, Louis G. Jr.; Adams, James B.

    2009-03-15

    Ab initio molecular dynamics based on density functional theory within the generalized gradient approximation was used to explore decomposition on Al(111) of butanol-alcohol and butanoic-acid, two important boundary additives in Al processing. Each molecule was oriented with its functional group closest to the surface and then given an initial velocity toward the surface. Decomposition occurred upon collision with Al(111) resulting in the formation of adhered fragments that represent the very initial stages in additive film formation during plastic deformation where nascent Al is liberated. Bonding interactions over the simulation time frames were explored with contours of the electron localization function. Results of the simulations were compared with existing experimental studies of chemical decomposition on clean Al surfaces and found to be in qualitative accord. The effects of other initial molecular orientations on decomposition were explored in ancillary calculations where the molecules were rotated through 90 deg. and 180 deg. prior to collision with Al(111)

  18. Ab-initio molecular dynamics study of lanthanides in liquid sodium

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2000-11-01

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

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

    SciTech Connect

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

    2014-05-15

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

  1. On the role of hydrogen filled vacancies on the embrittlement of zirconium: An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Olsson, Pär A. T.; Kese, Kwadwo; Alvarez Holston, Anna-Maria

    2015-12-01

    In this work we report the results of an ab initio study of the influence of hydrogen filled vacancies on the mechanical properties of zirconium. The modelling shows that hydrogen filled vacancies contribute to a lowering of the surface energy and an increase in the unstable stacking fault energy, which implies a reduction in ductility. The increase in unstable stacking fault energy suggests that the defects promote a change in the dislocation glide mechanism from prismatic to basal slip. To investigate the cleavage energetics, we model the decohesion process. For describing the interplanar interaction we adopt an extended version of Rose's universal binding energy relation, which is found to reproduce the behaviour accurately. The results of the modelling imply that the work of fracture and peak stress decrease as a result of the presence of hydrogen filled vacancies.

  2. Ab initio-based fracture toughness estimates and transgranular traction-separation modelling of zirconium hydrides

    NASA Astrophysics Data System (ADS)

    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.

  3. Magnetic properties of vanadium doped CdTe: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Goumrhar, F.; Bahmad, L.; Mounkachi, O.; Benyoussef, A.

    2017-04-01

    In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature Tc for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.

  4. Ab initio electronic structure, magnetism, and magnetocrystalline anisotropy of UGa2

    NASA Astrophysics Data System (ADS)

    Diviš, Martin; Richter, Manuel; Eschrig, Helmut; Steinbeck, Lutz

    1996-04-01

    Ab initio electronic structure calculations for the intermetallic compound UGa2 were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5f states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5f states, which have been treated by self-interaction corrected local-density theory. This approach with 5f2 occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant.

  5. Vicinal proton—proton coupling constants. Basis set dependence in SCF ab initio calculations

    NASA Astrophysics Data System (ADS)

    San-Fabián, Jesús; Guilleme, Joaquín; Díez, Ernesto; Lazzeretti, Paolo; Malagoli, Massimo; Zanasi, Riccardo

    1993-04-01

    An SCF ab initio study of the angular dependence and substituent effects upon the vicinal coupling constants has been carried out for the molecules CH 3CH 3, CH 2FCH 3 and CHF 2CH 3. The four contributions to 3JHH ( JFC, JSD, JOD and JOP) have been computed using the STO-3G, 6-31G, 6-31G * and 6-31G ** basis sets. The major contributions arise from the FC term. The magnitude of the SD contributions is very small and near independent of the size of the basis set. The magnitude of the orbital contributions OR (=OD+OP) decreases as the size of the basis set increases. The FC term slightly overestimates both the individual and the interaction substituent effects for basis sets larger than the STO-3G one. For this basis such effects are underestimated.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Ab initio oscillator strengths and transition probabilities in aluminum-like calcium, Ca VIII

    SciTech Connect

    Karpuskiene, R. Bogdanovich, P.

    2009-07-15

    An ab initio study of aluminum-like calcium is presented. The calculations are performed within the configuration interaction method in the basis of transformed radial orbitals with a variable parameter. Relativistic effects are accounted for within the Breit-Pauli approximation. Energy spectra, transition characteristics and lifetimes of excited levels of configurations 3s{sup 2}3p, 3s3p{sup 2}, 3s{sup 2}3d, 3p{sup 3}, 3s3p3d, 3p{sup 2}3d, 3s{sup 2}4s, 3s{sup 2}4p, 3s{sup 2}4d, 3s{sup 2}4f, 3s3p4s, and 3s3p4p are obtained. The results are compared with available experimental and theoretical data.

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

    PubMed

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

    2014-02-05

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

  9. Quantifying statistical uncertainties in ab initio nuclear physics using Lagrange multipliers

    NASA Astrophysics Data System (ADS)

    Carlsson, B. D.

    2017-03-01

    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, I 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.

  10. Thermal transmission at Si/Ge interface: ab initio lattice dynamics calculation

    NASA Astrophysics Data System (ADS)

    Alkurdi, A.; Merabia, S.

    2017-01-01

    We perform lattice dynamics calculations (LD) on silicon/germanium interfaces using ab initio interatomic force constants to predict the interfacial phonon transmission as a function of both phonon frequency and the transmission angle. We carry out a spectral and angular analysis to quantify the contribution of each phonon mode in a given scattering direction. The effect of the interaction range was studied at this interface by taking account of more or less atom layers across the interface. Moreover, we were able to predict the thermal boundary conductance (TBC) as a function of the transmission angle and temperature as well. Our results show that, the thermal energy transmission is highly anisotropic while thermal energy reflection is almost isotropic. In addition, we found that it seems there is a global critical angle of transmission beyond which almost no thermal energy is transmitted. This can be used to device high pass phonon filter via changing the orientation of the interface.

  11. Ab initio coupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone

    SciTech Connect

    Hansen, Jared A.; Bauman, Nicholas P.; Shen, Jun; Borden, Weston Thatcher; Piecuch, Piotr

    2015-12-09

    In this paper, the four, closely spaced, lowest energy electronic states of the challenging, D4h-symmetric, 1,2,3,4-cyclobutanetetraone (C4O4) molecule have been investigated using high-level ab initio methods. The calculated states include the closed-shell singlet 8π(1A1g) state, the singlet 10π(1A1g) state, in which the π-type lowest unoccupied molecular orbital (LUMO) of the 8π(1A1g) reference is doubly occupied and the σ-type highest occupied molecular orbital (HOMO) is empty, and the open-shell singlet and triplet states, designated as 9π(1B2u) and 9π(3B2u), respectively, originating from single occupancy of the HOMO and LUMO. Our focus is on single-reference coupled-cluster (CC) approaches capable of handling electronic near-degeneracies in diradicals, especially the completely renormalised CR-CC(2,3) and active-space CCSDt methods, along with their CCSD and EOMCCSD counterparts. The internally contracted multi-reference configuration interaction calculations with a quasi-degenerate Davidson correction are performed as well. Our computations demonstrate that the state ordering is 9π(3B2u) < 8π(1A1g) < 9π(1B2u) < 10π(1A1g) and that the 8π(1A1g) - 9π(3B2u) gap is in the 7–11 kJ/mol range, in reasonable agreement with the negative ion photoelectron spectroscopy measurements, which give 6.27 ± 0.5 kJ/mol. Finally, in addition to the theory level used, geometry relaxation and basis set play a significant role in determining the state ordering and energy spacings. In particular, it is unsafe to use lower level, non-CC geometries and smaller basis sets.

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

    DOE PAGES

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

    2016-05-17

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

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

    PubMed

    Hafner, Jürgen

    2008-10-01

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

  14. Ab initio study of perovskite type oxide materials for solid oxide fuel cells

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

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

    2015-02-01

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

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

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

    PubMed

    Bryk, Taras; Klevets, Ivan

    2012-12-14

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

  18. Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.

    PubMed

    Khaliullin, Rustam Z; Kühne, Thomas D

    2013-10-14

    The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

  19. A density functional and ab initio investigation of the p-aminobenzoic acid molecule

    NASA Astrophysics Data System (ADS)

    Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves

    2007-08-01

    The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.

  20. Ab initio approach to the development of interatomic potentials for the shell model of silica polymorphs

    NASA Astrophysics Data System (ADS)

    de Boer, K.; Jansen, A. P. J.; van Santen, R. A.

    1994-06-01

    We have developed a new method for deriving parameters for the shell model of silica polymorphs. All parameters for the shell model are derived in a self-consistent way from ab initio energy surfaces, polarizabilities and dipole moments of small clusters. This yields an ab initio partial charge shell model potential. The predictive power of our potential is demonstrated by presenting predictions for the structure of α-quartz, α-cristobalite, coesite, stishovite and the IR spectrum of α-quartz which are compared with experiment and predictions of the widely used potentials of Jackson and Catlow, and Kramer, Farragher, van Beest and van Santen.

  1. Calculation of second virial coefficients using ab initio intermolecular pair potentials for F2-F2 and H2-F2 dimers

    NASA Astrophysics Data System (ADS)

    Van, Tat Pham; Deiters, Ulrich K.

    2017-03-01

    The ab initio intermolecular pair potentials of dimers F2-F2 and H2-F2 were calculated from all constructed orientations, using the level of theory CCSD(T) and basis sets aug-cc-pVmZ (m = 2, 3, 23). The complete basis set limit aug-cc-pV23Z was extrapolated by ab initio interaction energies at the level of theory CCSD(T) with two basis sets aug-cc-pVmZ (m = 2, 3). Then the quantum mechanical results were used for constructing two new 5-site potential functions by fitting ab initio energies of dimers F2-F2 and H2-F2. The correlation between ab initio and the fitted ab initio energies of 5-site pair potentials for dimers F2-F2 and H2-F2 is appeared by fitness values R2 in range 0.99749-0.99997. The fitted potentials were used in standard thermodynamic relations to obtain the second virial coefficients and the results were compared to experimental data.

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

    NASA Technical Reports Server (NTRS)

    Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

    2002-01-01

    The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

  3. Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

    NASA Technical Reports Server (NTRS)

    Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

    2000-01-01

    The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

  4. Studies of solvation behaviour of LiI prevailing in diverse solvent systems conductometrically and spectrometrically supported by ab initio technique

    NASA Astrophysics Data System (ADS)

    Das, Koyeli; Bomzan, Pranish; Das, Rajesh Kumar; Rajbanshi, Biplab; Roy, Mahendra Nath

    2017-03-01

    Solvation nature of Lithium iodide (LiI) for both polar and nonpolar organic solvents viz., acetonitrile and benzonitrile have been explored by effect of geometry, spectroscopic, conductometric, ab initio methods . Results of vibrational spectroscopic data were compared with experimental values. Centre of attraction is iodide anion on significant vibrational bands of benzonitrile. Fluorescence spectra provide a supporting to the mentioned facts. Ab initio calculations used for shaping the optimum location of Li+ and I- ions in ion-solvent interactions containing varying nitriles as solvent sphere. Emission band positions, intensity, shape of solvent-sensitive molecules in organic solvents of varying polarities are studied.

  5. Interaction of a pseudo-π C—C bond with cuprous and argentous chlorides: Cyclopropane⋯CuCl and cyclopropane⋯AgCl investigated by rotational spectroscopy and ab initio calculations

    SciTech Connect

    Zaleski, Daniel P.; Mullaney, John C.; Bittner, Dror M.; Walker, Nicholas R. E-mail: nick.walker@newcastle.ac.uk; Tew, David P.; Legon, Anthony C. E-mail: nick.walker@newcastle.ac.uk

    2015-10-28

    Strongly bound complexes (CH{sub 2}){sub 3}⋯MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH{sub 2}){sub 3}⋯CuCl and (CH{sub 2}){sub 3}⋯AgCl. The geometry of each of these complexes was established unambiguously to have C{sub 2v} symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C{sub 3} triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH{sub 2}){sub 3}⋯MCl. The M atom interacts with the pseudo-π bond linking the pair of equivalent carbon atoms {sup F}C (F = front) nearest to it, so that M forms a non-covalent bond to one C—C edge of the cyclopropane molecule. The (CH{sub 2}){sub 3}⋯MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH{sub 2}){sub 3}⋯HCl and (CH{sub 2}){sub 3}⋯ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the {sup F}C—{sup F}C bond and the shrinkage of the two equivalent {sup B}C—{sup F}C (B = back) bonds relative to the C—C bond in cyclopropane itself. The expansions of the {sup F}C—{sup F}C bond are 0

  6. Interaction of a pseudo-π C—C bond with cuprous and argentous chlorides: Cyclopropane⋯CuCl and cyclopropane⋯AgCl investigated by rotational spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Zaleski, Daniel P.; Mullaney, John C.; Bittner, Dror M.; Tew, David P.; Walker, Nicholas R.; Legon, Anthony C.

    2015-10-01

    Strongly bound complexes (CH2)3⋯MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH2)3⋯CuCl and (CH2)3⋯AgCl. The geometry of each of these complexes was established unambiguously to have C2v symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C3 triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH2)3⋯MCl. The M atom interacts with the pseudo-π bond linking the pair of equivalent carbon atoms FC (F = front) nearest to it, so that M forms a non-covalent bond to one C—C edge of the cyclopropane molecule. The (CH2)3⋯MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH2)3⋯HCl and (CH2)3⋯ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the FC—FC bond and the shrinkage of the two equivalent BC—FC (B = back) bonds relative to the C—C bond in cyclopropane itself. The expansions of the FC—FC bond are 0.1024(9) Å and 0.0727(17) Å in (CH2)3⋯CuCl and (CH2)3⋯AgCl, respectively, according to the determined r0

  7. An efficient method for electron-atom scattering using ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang

    2017-02-01

    We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  9. Ab initio molecular dynamics simulations of a binary system of ionic liquids.

    PubMed

    Brüssel, Marc; Brehm, Martin; Voigt, Thomas; Kirchner, Barbara

    2011-08-14

    This work presents first insights into the structural properties of a binary mixture of ionic liquids from the perspective of ab initio molecular dynamics simulations. Simulations were carried out for a one-to-one mixture of 1-ethyl-3-methyl-imidazolium thiocyanate and 1-ethyl-3-methyl-imidazolium chloride and compared to pure 1-ethyl-3-methyl-imidazolium thiocyanate.

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

    PubMed

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

    2016-07-07

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

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

  14. Ab-initio kinetics and thermodynamics studies of ammonia-borane for hydrogen storage

    NASA Astrophysics Data System (ADS)

    Miranda, Caetano R.; Ceder, Gerbrand

    2007-03-01

    Ammonia-borane (BH3NH3) is a promising chemical hydrogen storage material given its high gravimetry and volumetric properties. However, the ammonia-borane (AB) thermal hydrogen release is not very efficient, being mainly limited by the kinetics of hydrogenation. Using ab initio calculations, we have investigated the thermodynamics and kinetics of hydrogen release on AB by calculating the free energies of the H2 release reactions for different possible decomposition products. Our results indicate that AB regeneration through the ammonia-borane polymeric and borazine-cyclotriborazane cycles is very unlikely due to the strong exothermic character of the reactions. The kinetics of hydrogen release is further investigated with the recently developed metadynamics method. This method allows us to calculate the multidimensional free energy surface of hydrogen release on AB. Our simulations reveal the atomistic mechanism of hydrogenation and provide the free energies barriers and transition states involved in inter and intramolecule H2 release on AB.

  15. Ab initio molecular treatment for charge transfer by P{sup 3+} ions on hydrogen and helium

    SciTech Connect

    Moussa, A.; Zaidi, A.; Lahmar, S.; Bacchus-Montabonel, M.-C.

    2010-02-15

    A theoretical treatment of charge-transfer processes induced by collision of phosphorus P{sup 3+}(3s{sup 2}){sup 1}S ions on atomic hydrogen and helium has been carried out using ab initio potential-energy curves and couplings at the multireference configuration interaction level of theory. The cross sections calculated by means of semiclassical collision methods show the existence of a significant charge transfer in the 0.1-700-keV laboratory energy range. Radial and rotational coupling interactions were analyzed for both collision systems.

  16. Ab initio potential energy surface for the carbon dioxide molecule pair and thermophysical properties of dilute carbon dioxide gas

    NASA Astrophysics Data System (ADS)

    Hellmann, Robert

    2014-10-01

    A four-dimensional intermolecular potential energy surface (PES) for two rigid carbon dioxide molecules was determined from quantum-chemical ab initio calculations. Interaction energies for 1229 CO2-CO2 configurations were computed at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. An analytical site-site potential function with seven sites per CO2 molecule was fitted to the interaction energies. The PES was validated by calculating the second virial coefficient as well as viscosity and thermal conductivity in the dilute-gas limit.

  17. Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent

    2012-01-01

    From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.

  18. Synthesis, characterization, and ab initio theoretical study of a molecularly imprinted polymer selective for biosensor materials.

    PubMed

    Jacob, Rebecca; Tate, Margaret; Banti, Yididya; Rix, Colin; Mainwaring, David E

    2008-01-17

    Despite the complex phenomena involved in encoding template molecule information within stable synthetic polymers to yield selective and efficient molecular recognition processes, molecularly imprinted polymers (MIP) are increasingly finding broad areas of application. Molecular interactions, both during the polymerization of the functional monomers in the presence of the template and during the processes of specific recognition after template removal, are key determinants of an effective MIP. Covalent and noncovalent template imprinting have been employed to achieve specific recognition sites. In the present study, a molecularly imprinted biocompatible polymer, having a high capacity and affinity for the dye template, nickel(II) phthalocyanine tetrasulfonic acid, has been prepared. UV-visible spectroscopy, FTIR spectroscopy, and ICP analysis were used to investigate the aspects of the synthesis, binding capacity, and adsorption kinetics of the system. Poly(allylamine) cross-linked with epichlorohydrin has been used to represent an amino-functional receptor. Binding isotherms and capacities were correlated with the degree of template removal. Kinetic studies of binding allowed diffusion mechanisms to be evaluated for the fine particulate MIP. Ab initio molecular orbital calculations were performed using Hartree-Fock, MP2, and density functional theory methods to determine the most likely mechanisms of molecular imprinting. Suitable theoretical models have been constructed to mimic the interactions between the template molecule and the polymer. Simulation of the vibrational spectra was also undertaken to make meaningful assignments to experimentally determined spectral bands resulting from these template MIP receptor interactions.

  19. Ab initio intermolecular potential energy surface and second pressure virial coefficients of methane.

    PubMed

    Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

    2008-06-07

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid methane molecules was determined from high-level quantum-mechanical ab initio computations. A total of 272 points for 17 different angular orientations on the PES were calculated utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory with basis sets of aug-cc-pVTZ and aug-cc-pVQZ qualities. The calculated interaction energies were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites per methane molecule was fitted to the interaction energies. In addition, a semiempirical correction to the analytical potential function was introduced to take into account the effects of zero-point vibrations. This correction includes adjustments of the dispersion coefficients and of a single-parameter within the fit to the measured values of the second virial coefficient B(T) at room temperature. Quantitative agreement was then obtained with the measured B values over the whole temperature range of the measurements. The calculated B values should definitely be more reliable at very low temperatures (T<150 K) than values extrapolated using the currently recommended equation of state.

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

    NASA Astrophysics Data System (ADS)

    Hafner, Jürgen

    2010-09-01

    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.

  1. Liquid water with an ab initio potential - X-ray and neutron scattering from 238 to 368 K

    NASA Astrophysics Data System (ADS)

    Corongiu, Giorgina; Clementi, Enrico

    1992-08-01

    The study reports molecular dynamics simulations with the Nieser-Corongiu-Clementi flexible water molecules (NCC-vib) ab initio potential at a number of temperatures ranging from 242 to 361 K for H2O and from 238 to 368 K for D2O. Each simulation was carried out, after equilibration, for 12 pcs. The computed trajectories are used to study structural properties as a function of the temperature. Water geometry in the liquid, pair correlation functions, coordination numbers, and X-ray and neutron scattering structure functions are compared with available experiments. The overall agreement is quite satisfactory, validating the reliability of the NCC-vib interaction potential.

  2. Ab initio parameterization of YFF1, a universal force field for drug-design applications.

    PubMed

    Yakovenko, Olexandr Ya; Li, Yvonne Y; Oliferenko, Alexander A; Vashchenko, Ganna M; Bdzhola, Volodymyr G; Jones, Steven J M

    2012-02-01

    The YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special "closure" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds.

  3. Ab initio study of the Br(2P)-HBr van der Waals complex.

    PubMed

    Toboła, R; Chałasiński, G; Kłos, J; Szcześniak, M M

    2009-05-14

    This study reports an ab initio characterization of a prereactive van der Waals complex between an open-shell atom Br((2)P) and a closed shell molecule HBr. The three adiabatic potential surfaces 1 (2)A('), 2 (2)A('), and 1 (2)A("), which result from the splitting of degenerate P state of Br are obtained from coupled cluster calculations. The coupling between same-symmetry states is calculated by multireference configuration-interaction method. A transformation to a diabatic representation and inclusion of the spin-orbit coupling effects on the interactions are also discussed. Bound states are calculated using an adiabatic bender model. The global minimum on the lowest adiabatic potential surface corresponds to a T-shaped geometry and has a well depth of D(e)=762.5 cm(-1) at R(e)=3.22 A. A secondary minimum occurs for a hydrogen-bonded geometry with D(e)=445.3 cm(-1) at R(e)=4.24 A. Upon inclusion of spin-orbit coupling the hydrogen-bonded minimum remains at the same depth, but the T-shaped minimum washes out to less than half of its spin-free value. The lowest bound state is localized in the linear minimum. The spin-orbit coupling plays a very important role in shaping of the potential energy surfaces of Br-HBr.

  4. Ab-initio calculation of electron-phonon coupling for spin relaxation in metals.

    NASA Astrophysics Data System (ADS)

    Pruneda, Miguel; Souza, Ivo

    2007-03-01

    Spin-electronic devices have motivated an important effort in understanding the mechanisms for spin-relaxation, because the operation of such devices requires long spin-diffusion lenghts. Two main factors contribute to spin relaxation: (i) spin-orbit interaction, which mixes the spin-up and spin-down components of the electronic wavefunction, and (ii) electron scattering from defects or phonons. In metals, the phonon-mediated Elliot-Yafet mechanism is believed to be dominant. Realistic calculations are computationally demanding, requiring an accurate description of the electronic states near the Fermi surface and their coupling to the lattice (phonons). Here we use a Density Functional Perturbation Theory implementation to calculate from first-principles the electron-phonon interaction in systems with spin-orbit coupling. Combined with recently-developed Wannier-interpolation methods for sampling efficiently the Brillouin zone, this will allow for a fully ab-initio calculation of the spin relaxation in metals. J. Fabian and S. Das Sarma, Phys. Rev. Lett. 83, 1211 (1999).

  5. Potential energy surface and second virial coefficient of methane-water from ab initio calculations.

    PubMed

    Akin-Ojo, Omololu; Szalewicz, Krzysztof

    2005-10-01

    Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03 kcal/mol at a geometry where H2O is the proton donor, HO-H...CH4, with the O-H-C angle of 165 degrees, while the secondary minimum, with an energy of -0.72 kcal/mol, has CH4 in the role of the proton donor (H3C-H...OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06 kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653 K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.

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

    PubMed

    Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo

    2016-06-21

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

  7. Ab initio Mapping of Interlayer Coupling in Transition Metal Dichalcogenides and Graphene

    NASA Astrophysics Data System (ADS)

    Fang, Shiang; Kaxiras, Efthimios

    Two-dimensional layered materials cover a wide variety of physics phenomena, such as topological phases, superconductivity, magnetism and charge density waves. Owing to the layered geometry and the van der Waals interactions in between, stacks of these van der Waals layered materials provide a venue to create a heterostructure with various physics properties. The interaction between different physics properties is particular interesting to engineer the material with the desired properties. One of the crucial ingredient in understanding the heterostructure is the interlayer coupling in between. In the literature, such kind of coupling has been proposed in various empirical forms. However, a true ab initio coupling model is still lacking. For the first time, here we have derived such interlayer coupling model from the first principle calculations based on the Wannier transformation of graphene stacks. We further investigate the Fermi velocity renormalization, van Hove singularities and the moire pattern for electron localization. Such microscopic understanding of the interlayer coupling would shed light on orbital hybridization and transport in multilayer stacks. This work was supported by the STC Center for Integrated Quantum Materials, NSF Grant No. DMR-1231319, and by ARO MURI Award No. W911NF-14-0247.

  8. Ab initio calculations of cooperativity effects on clusters of methanol, ethanol, 1-propanol, and methanethiol

    SciTech Connect

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

    2000-02-17

    The results of ab initio calculations for cyclic clusters of methanol, ethanol, 1-propanol, and methanethiol are presented. Dimer, trimer, and tetramer clusters of all four compounds are studied, as are pentamer and hexamer clusters of methanol. From optimized clusters at HG/6--31G**, total energies and binding energies were calculated with both the HF and MP2 theories using the aug-cc-pVDZ basis set. Accurate binding energies were also calculated for the dimer and trimer of methanol using symmetry-adapted perturbation theory with the same basis set. Intermolecular and intramolecular distances, charge distribution of binding sites, binding energies, and equilibrium constants were computed to determine the hydrogen bond cooperativity effect for each species. The cooperativity effect, exclusive to hydrogen bonding systems, results form specific forces among the molecules, in particular charge-transfer processes and the greater importance of interactions between molecules not directly hydrogen bonded because of the longer range of the interactions. The ratios of equilibrium constants for forming multimer hydrogen bonds to that for dimer hydrogen bond formation increase rapidly with the cluster size, in contrast to the constant value commonly used in thermodynamic models for hydrogen bonding liquids.

  9. Ab-initio based calculations of vacancy formation and clustering energies including lattice relaxation in Fe{sub 3}Al

    SciTech Connect

    Muratov, L.S.; Cooper, B.R.; Wills, J.M.

    1999-03-01

    Vacancy formation and clustering significantly affect structural properties of transition-metal aluminides. Ab-initio quantum mechanical total-energy calculations using a full-potential linear combination of muffin-tin orbitals (LMTO) technique provide a convenient method of studying relevant characteristics such as changes in density of states, and charge redistribution around defects. Augmented with Hellmann-Feymann forces, LMTO allows calculations of relaxation geometries and relaxation energies. The authors have performed such calculations for vacancies and antisite substitutional point defects in Fe{sub 3}Al with DO{sub 3} crystallographic structure. There are two limiting factors complicating calculations of defect formation energies directly from ab-initio calculations. The first is that a single defect, due to the lattice periodicity necessitated by the use of ab-initio total energy techniques, cannot be considered as an isolated defect, even in the maximum computable simulation cell. Unlike previous calculations, which did not find a dependency on the size of the simulation cell, the calculations have shown a significant difference in results for 32- and 16- atom cells. This difference provides information about vacancy clustering since it can be explained by a relatively small attractive interaction energy {approximately} 0.2 eV between two vacancies located in adjacent simulation cells and separated by the lattice constant distance (5.52 {angstrom}). By comparing the internal energies for two configurations of 30 atom cells (32 atom--2 vacancies), the authors were able to estimate that the attractive interaction between two vacancies could reach 1.2 eV. The second complication is the fact that chemical potentials of elements cannot be directly extracted from the total energy calculations for the compound. To deal with this problem, they considered two possible approximations and compared results, which were found to be quite similar for iron vacancies.

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

    PubMed

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

    2016-05-05

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

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

    DOE PAGES

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

    2016-05-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  14. Hydrogen bond effects in the vibrational spectra of 1,3-propanediol in acetonitrile: Ab initio and experimental study

    NASA Astrophysics Data System (ADS)

    Muniz-Miranda, Francesco; Pagliai, Marco; Cardini, Gianni; Righini, Roberto

    2012-12-01

    Hydrogen bond interactions strongly affect vibrational properties and frequencies, the most common consequence being a redshift of the stretching vibration involved; there are, however, few exceptions to this general trend. In previous works, we have proved the effectiveness of ab initio simulations combined with wavelet analysis to investigate these effects and put them into relation to structural environment. In this work, we investigate the hydrogen bond effects on the structural and vibrational properties of 1,3-propanediol in acetonitrile by a combined experimental and computational approach. We explain the appearance of two spectral components in the O-H stretching band on the basis of intra- and intermolecular hydrogen bond interactions. We also elucidate the blueshift of the C≡N stretching band as due to a hydrogen bond interaction between the glycol and acetonitrile that modify the electron density distribution inside the CN group. This effect is well reproduced by ab initio molecular dynamics simulations and density functional calculations reported in this work.

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

    SciTech Connect

    González, D. J.; González, L. E.

    2015-08-17

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

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

    SciTech Connect

    Bodenstein, Tilmann; Fink, Karin

    2015-12-31

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  18. Ab initio study of AlxMoNbTiV high-entropy alloys.

    PubMed

    Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K; Vitos, Levente

    2015-02-25

    The Al(x)MoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of Al(x)MoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al(0.4)MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ∼ 4.72 obtained for the isotropic Gum metals and refractory--HEAs.

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

    SciTech Connect

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

    2015-04-14

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

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

    NASA Technical Reports Server (NTRS)

    Rammacher, W.; Cuntz, M.

    1991-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed Central

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  4. Ab initio studies of equations of state and chemical reactions of reactive structural materials

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava

    subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated

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

    PubMed

    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.

  6. The Pu-U-Am system: An ab initio informed CALPHAD thermodynamic study

    NASA Astrophysics Data System (ADS)

    Perron, A.; Turchi, P. E. A.; Landa, A.; Söderlind, P.; Ravat, B.; Oudot, B.; Delaunay, F.

    2015-03-01

    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.

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

    PubMed

    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.

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2015-04-14

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

    Halasyamani, Shiv; Fennie, Craig

    2016-11-03

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

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

    PubMed

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

    2012-01-02

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

  13. Ab initio dipole moment and theoretical rovibrational intensities in the electronic ground state of PH 3

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Carvajal, Miguel; Thiel, Walter; Jensen, Per

    2006-09-01

    We report a six-dimensional CCSD(T)/aug-cc-pVTZ dipole moment surface for the electronic ground state of PH 3 computed ab initio on a large grid of 10 080 molecular geometries. Parameterized, analytical functions are fitted through the ab initio data, and the resulting dipole moment functions are used, together with a potential energy function determined by refining an existing ab initio surface in fittings to experimental wavenumber data, for simulating absorption spectra of the first three polyads of PH 3, i.e., ( ν2, ν4), ( ν1, ν3, 2 ν2, 2 ν4, ν2 + ν4), and ( ν1 + ν2, ν3 + ν2, ν1 + ν4, ν3 + ν4, 2 ν2 + ν4, ν2 + 2 ν4, 3 ν2, 3 ν4). The resulting theoretical transition moments show excellent agreement with experiment. A line-by-line comparison of the simulated intensities of the ν2/ ν4 band system with 955 experimental intensity values reported by Brown et al. [L.R. Brown, R.L. Sams, I. Kleiner, C. Cottaz, L. Sagui, J. Mol. Spectrosc. 215 (2002) 178-203] gives an average absolute percentage deviation of 8.7% (and a root-mean-square deviation of 0.94 cm -1 for the transition wavenumbers). This is very remarkable since the calculations rely entirely on ab initio dipole moment surfaces and do not involve any adjustment of these surfaces to reproduce the experimental intensities. Finally, we predict the line strengths for transitions between so-called cluster levels (near-degenerate levels formed at high rotational excitation) for J up to 60.

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

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2016-09-01

    Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.

  15. Ab initio equation of state of hydrogen for inertial fusion applications

    NASA Astrophysics Data System (ADS)

    Benedict, Lorin X.; Morales, Miguel A.; Schwegler, Eric; Tamblyn, Isaac; Bonev, Stanimir A.; Correa, Alfredo A.; Clark, Daniel S.; Haan, Steven W.; LLNL Collaboration

    2011-06-01

    We describe ab initio electronic structure calculations (DFT molecular dynamics and quantum Monte Carlo) of the equation of state of hydrogen in a regime relevant for ICF applications. We find the computed EOS to be quite close to that of the most recent SESAME table (constructed by G. Kerley, 2004). A simple density-dependent correction brings the recent SESAME EOS into nearly perfect agreement with ours in the chosen region. Simulations of ICF applications with this corrected SESAME table are discussed.

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

    SciTech Connect

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-17

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

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

    NASA Astrophysics Data System (ADS)

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

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

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

    PubMed

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

    2016-11-01

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

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

    SciTech Connect

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

    2015-09-14

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

  1. Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

    PubMed

    Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

    2016-10-17

    For CO and N2 on Mg(2+) sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

  2. An ab initio calculation of the fundamental and overtone HCl stretching vibrations for the HCl dimer

    NASA Astrophysics Data System (ADS)

    Jensen, Per; Bunker, P. R.; Epa, V. C.; Karpfen, A.

    1992-02-01

    We have previously determined an analytical ab initio six-dimensional potential energy surface for the HCl dimer, and have used it to determine the minimum energy path for the trans-tunneling motion. In the present paper we refine this path by fitting to data. We calculate a further 178 ab initio points in order to determine the HCl stretching energies, and HCl stretching dipole moment functions, at eight positions along the minimum energy path. We use these ab initio results to compute the stretching wavenumbers and transition moments from the v1 = v2 = 0 state to all states of (HCl) 2 that have v1 + v2 ≤ 3, where v1 and v2 are the local mode quantum numbers for the HCl stretching vibrations. In doing this calculation we have assumed an adiabatic separation of the HCl stretching motion from the other vibrational motions in the dimer, and have used the semirigid bender Hamiltonian to average over the trans-tunneling motion. We obtain the fundamental "free-H" stretch v1 at 2877 cm -1 and the fundamental "bound-H" stretch v2 at 2861 cm -1; the experimental values are 2880 and 2854 cm -1, respectively.

  3. Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

    NASA Astrophysics Data System (ADS)

    Tachikawa, Masanori; Shiga, Motoyuki

    2004-09-01

    We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

    Geng, Hua Y.

    2015-02-15

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

  6. Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si.

  7. Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO

    SciTech Connect

    Xiao, Haiyan; Duan, G; Zu, X T; Weber, William J

    2011-01-01

    Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ {yields} RS and ZB {yields} RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ {yields} RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange-correlation functional employed and the way of applying pressure.

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

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

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

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

    SciTech Connect

    Lan, Tran Nguyen; Kananenka, Alexei A.; Zgid, Dominika

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

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

    DOE PAGES

    Hupin, Guillaume; Langhammer, Joachim; Navratil, Petr; ...

    2013-11-27

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

  11. Ab initio calculations for the first-positive bands of N2

    NASA Astrophysics Data System (ADS)

    Ni, Chao; Cheng, Junxia; Cheng, Xinlu

    2017-01-01

    The absolute absorption spectral line intensities of the 0-0, 1-1, 2-2, 3-3, and 4-4 bands of N2(A3Σu+ - B3Пg) are computed for the first time with the accurate potential energy curves (PECs) and transition dipole moment curves (TDMCs) using the ab initio calculation. During the calculation process, the precise multireference configuration interaction (MRCI) approach with the augmented correlation consistent polarized valence quadruple-zeta set (aug-cc-pVQZ) and active space 3110311 are used. The calculated PECs of the two states (A3Σu+, B3Пg) agree well with Rydberg-Klein-Rees (RKR) potential, and the calculated TDMCs are more reasonable than the results of other studies. Our calculated Einstein A coefficients are also well consistent with the recent experiment results. The intensities of five bands are obtained from the summation of their respective absolute line intensities, for instance, the 0-0 band intensities are 3.25 × 10-16 cm-1/(molecule cm-2) at 300 K and 1.65 × 10-16 cm-1/(molecule cm-2) at 3000 K. The theoretical results are credible. They are also beneficial for astrophysics where high temperature dominates.

  12. Physical properties and spectra of IO, IO- and HOI studied by ab initio methods.

    PubMed

    Minaev, Boris; Loboda, Oleksandr; Vahtras, Olav; Agren, Hans; Bilan, Elena

    2002-03-15

    Structure and properties of the IO, IO- and HOI species, which are of potential importance for the ozone destruction catalytic cycle in the troposphere, have been calculated together with the EPR, NMR and UV-visible spectra by ab initio methodology with account of spin-orbit coupling (SOC) effects. Multi-configuration self-consistent field calculations with linear and quadratic response techniques and the multi-reference configuration interaction method have been employed. Photodissociation of these species, crucial for the catalytic ozone-destruction cycle, is critically reviewed and analyzed. Calculations predict that the singlet-triplet (S-T) transition to the lowest triplet state (X1 A' --> 3A'') should be responsible for the weak long-wavelength tail absorption (approximately 450-560 nm) and photodissociation of the HOI molecule. The second, more intense, band around 400 nm is produced by two overlapping S-S and S-T transitions. In order to check this assignment of the HOI photodissociation the isoelectronic IO- anion and IO radical have been studied by the same methods. Comparison with the EPR spectrum of the IO radical indicates that the methods are reliable which gives credit to the accuracy of the HOI spectral interpretation. NMR spectra of HOI and IO- molecules and some other properties are calculated for the first time.

  13. Interatomic Coulombic decay in a He dimer: Ab initio potential-energy curves and decay widths

    SciTech Connect

    Kolorenc, Premysl; Kryzhevoi, Nikolai V.; Sisourat, Nicolas; Cederbaum, Lorenz S.

    2010-07-15

    The energy gained by either of the two helium atoms in a helium dimer through simultaneous ionization and excitation can be efficiently transferred to the other helium atom, which then ionizes. The respective relaxation process called interatomic Coulombic decay (ICD) is the subject of the present paper. Specifically, we are interested in ICD of the lowest of the ionized excited states, namely, the He{sup +}(n=2)He states, for which we calculated the relevant potential-energy curves and the interatomic decay widths. The full-configuration interaction method was used to obtain the potential-energy curves. The decay widths were computed by utilizing the Fano ansatz, Green's-function methods, and the Stieltjes imaging technique. The behavior of the decay widths with the interatomic distance is examined and is elucidated, whereby special emphasis is given to the asymptotically large interatomic separations. Our calculations show that the electronic ICD processes dominate over the radiative decay mechanisms over a wide range of interatomic distances. The ICD in the helium dimer has recently been measured by Havermeier et al. [Phys. Rev. Lett. 104, 133401 (2010)]. The impact of nuclear dynamics on the ICD process is extremely important and is discussed by Sisourat et al. [Nat. Phys. 6, 508 (2010)] based on the ab initio data computed in the present paper.

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

    DOE PAGES

    Alam, Todd M.; Pearce, Charles Joseph

    2015-06-28

    The infrared (IR) spectra of micro-hydrated Sarin•(H2O)n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (~1270 to 1290 cm–1) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (~810 to 815 cm–1) and the C-O-P vibrational modes (~995 to 1004 cm–1) showed that the water interactions with these functional groups were minor, and that the structures of Sarin were notmore » extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. As a result, the H2O•H2O vibrational modes (~3450 to 3660 cm–1) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters.« less

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

    PubMed

    Plasser, Felix; Dreuw, Andreas

    2015-02-12

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

  16. Ab initio transport calculations of molecular wires with electron-phonon couplings

    NASA Astrophysics Data System (ADS)

    Hirose, Kenji; Kobayashi, Nobuhiko

    2009-03-01

    Understanding of electron transport through nanostructures becomes important with the advancement of fabrication process to construct atomic-scale devices. Due to the drastic change of transport properties by contact conditions to electrodes in local electric fields, first-principles calculation approaches are indispensable to understand and characterize the transport properties of nanometer-scale molecular devices. Here we study the transport properties of molecular wires between metallic electrodes, especially focusing on the effects of contacts to electrodes and of the electron-phonon interactions. We use an ab initio calculation method based on the scattering waves, which are obtained by the recursion-transfer-matrix (RTM) method, combined with non-equilibrium Green's function (NEGF) method including the electron-phonon scatterings. We find that conductance shows exponential behaviors as a function of the length of molecular wires due to tunneling process determined by the HOMO-LUMO energy gap. From the voltage drop behaviors inside the molecular wires, we show that the contact resistances are dominant source for the bias drop and thus are related to local heating. We will present the electron-phonon coupling effects at contact on the inelastic scattering and discuss on the local heating and local temperature, comparing them with those of metallic atomic wires.

  17. Electronic and magnetic properties of α-MnO2 from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Crespo, Y.; Seriani, N.

    2013-10-01

    α-MnO2, an active catalyst for oxygen reduction and evolution reactions, has been investigated using ab initio calculations with different exchange-correlation functionals: the generalized-gradient approximation in the version of Perdew, Burke, and Ernzerhof (PBE), PBE+U, and hybrid functionals. Both hybrid functionals and PBE+U (U≥2.0 eV) fail to capture the antiferromagnetic (AFM) ground state found experimentally, and a ferromagnetic configuration has the lowest energy. An AFM ground state is then recovered when using PBE or PBE+U (U≤1.6 eV). Interestingly, a reduction of the gap is observed at increasing values of the U parameter. We offer a qualitative explanation for the change in the calculated ground state employing the results for the electronic structure and physical arguments similar to those exposed in the Goodenough-Kanamori-Anderson rules. It is argued that the pz orbital of oxygen atoms with sp2 hybridization plays a fundamental role in the superexchange AFM interaction and in the reduction of the gap.

  18. Semiconductiong Properties of Clathrates Ba8@Ge43: ab initio Study

    NASA Astrophysics Data System (ADS)

    Eguchi, Haruki; Tsumuraya, Kazuo; Takenaka, Hiroyuki; Suzuki, Akihiko; Tanigaki, Katsumi

    2003-03-01

    The Si-clathrates have been usually synthesized when alkaline or alkaline-earth atoms are coexisted with the host Si atoms, which is also the case for the Ge-clathrates. The I-encapsulating Si-clathrates have been also synthesized recently. In the case of the hydrate clathrates, the formation has been controlled by both the sizes of the endohedral molecules and the hydrophobic interactions of the molecules in the water.[1] We study the mechanism of the clathrate formation through the binding nature of the Si-X and Ge-X dimers, where X is selected elements in the periodic table. We calculate the charge transfers (population analysis), the binding energies, and the bonding distances using the ab-initio molecular dynamics method with planewaves and pseudo-potentials. We discuss the mechanism of the formation of the Si-clathrates comparing with that of the hydrate clathrates and evaluate the stability of clathrates predicted by the present study. [1]E.Dendy Sloan,Jr, Clathrate Hydrates of Natural Gasses, Marcel Dekker, 1998.

  19. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods.

    PubMed

    Slavíček, Petr; Fárník, Michal

    2011-07-14

    In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N-H···π interaction, N-H···N hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron-proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.

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

    NASA Astrophysics Data System (ADS)

    Stengel, Massimiliano

    2016-06-01

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

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

    SciTech Connect

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

    2015-08-15

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

  2. Matrix Isolation and ab initio study of the noncovalent complexes between formamide and acetylene.

    PubMed

    Mardyukov, Artur; Sánchez-García, Elsa; Sander, Wolfram

    2009-02-12

    Matrix isolation spectroscopy in combination with ab initio calculations is a powerful technique for the identification of weakly bound intermolecular complexes. Here, weak complexes between formamide and acetylene are studied, and three 1:1 complexes with binding energies of -2.96, -2.46, and -1.79 kcal/mol have been found at the MP2 level of theory (MP2/cc-pVTZ + ZPE + BSSE). The two most stable dimers A and B are identified in argon and nitrogen matrices by comparison between the experimental and calculated infrared frequencies. Both complexes are stabilized by the formamide C=O...HC acetylene and H...pi interactions. Large shifts have been observed experimentally for the C-H stretching vibrations of the acetylene molecule, in very good agreement with the calculated values. Eight 1:2 FMA-acetylene trimers (T-A to T-H) with binding energies between -5.44 and -2.62 kcal/mol (MP2/aug-cc-pVDZ + ZPE + BSSE) were calculated. The two most stable trimers T-A and T-B are very close in energy and have similar infrared spectra. Several weak bands that are in agreement with the calculated frequencies of the trimers T-A and T-B are observed under matrix isolation conditions. However, the differences are too small for a definitive assignment.

  3. Three-dimensional ab initio potential energy surface for H-CO(X̃(2)A').

    PubMed

    Song, Lei; van der Avoird, Ad; Groenenboom, Gerrit C

    2013-08-15

    We present an ab initio potential for the H-CO(X̃(2)A') complex in which the CO bond length is varied and the long-range interactions between H and CO are accurately represented. It was computed using the spin-unrestricted open-shell single and double excitation coupled cluster method with perturbative triples [RHF-UCCSD(T)]. Three doubly augmented correlation-consistent basis sets were utilized to extrapolate the correlation energy to the complete basis set limit. More than 4400 data points were calculated and used for an analytic fit of the potential: long-range terms with inverse power dependence on the H-CO distance R were fit to the data points for large R, the reproducing kernel Hilbert space (RKHS) method was applied to the data at smaller distances. Our potential was compared with previous calculations and with some data extracted from spectroscopy. Furthermore, it was used in three-dimensional discrete variable representation (DVR) calculations of the vibrational frequencies and rotational constants of HCO, which agree very well with the most recently measured data. Also the dissociation energy D0 = 0.623 eV of HCO into H + CO obtained from these calculations agrees well with experimental values. Finally, we made preliminary two-dimensional (2D) calculations of the cross sections for rotationally inelastic H-CO collisions with the CO bond length fixed and obtained good agreement with recently published 2D results.

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C20 clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

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

    DOE PAGES

    Xi, Jianqi; Liu, Bin; Zhang, Yanwen; ...

    2016-07-02

    Interactions between point defects and stacking faults in 3C-SiC are studied using an ab initio method based on density functional theory. The results show that the discontinuity of the stacking sequence considerably affects the configurations and behavior of intrinsic defects, especially in the case of silicon interstitials. The existence of an intrinsic stacking fault (missing a C-Si bilayer) shortens the distance between the tetrahedral-center site and its second-nearest-neighboring silicon layer, making the tetrahedral silicon interstitial unstable. Instead of a tetrahedral configuration with four C neighbors, a pyramid-like interstitial structure with a defect state within the band gap becomes a stablemore » configuration. In addition, orientation rotation occurs in the split interstitials that has diverse effects on the energy landscape of silicon and carbon split interstitials in the stacking fault region. Moreover, our analyses of ionic relaxation and electronic structure of vacancies show that the built-in strain field, owing to the existence of the stacking fault, makes the local environment around vacancies more complex than that in the bulk.« less

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

    PubMed

    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.

  7. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

    Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

  8. Ab initio oscillator strengths and transition probabilities in oxygen-like Cr XVII

    SciTech Connect

    Bogdanovich, P.; Karpuskiene, R.

    2008-09-15

    Ab initio energy spectra of the ground configuration 2s{sup 2}2p{sup 4}, the excited configurations 2s2p{sup 5}, 2p{sup 6}, 2s{sup 2}2p{sup 3}3s, 2s{sup 2}2p{sup 3}3p, 2s{sup 2}2p{sup 3}3d, 2s2p{sup 4}3s, 2s2p{sup 4}3p, and 2s2p{sup 4}3d of oxygen-like chromium Cr XVII have been calculated using the configuration interaction method. The wavelengths, oscillator strengths and the emission transition probabilities from configurations 2s{sup 2}2p{sup 3}3l and 2s2p{sup 4}3l are obtained. The radiative lifetimes of excited levels are also presented.0.

  9. PSI3: an open-source Ab Initio electronic structure package.

    PubMed

    Crawford, T Daniel; Sherrill, C David; Valeev, Edward F; Fermann, Justin T; King, Rollin A; Leininger, Matthew L; Brown, Shawn T; Janssen, Curtis L; Seidl, Edward T; Kenny, Joseph P; Allen, Wesley D

    2007-07-15

    PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.

  10. Ab initio calculations of the electronic states of AsH2 including dissociation characteristics.

    PubMed

    Alekseyev, Aleksey B; Buenker, Robert J; Liebermann, Heinz-Peter

    2011-12-28

    Multireference configuration interaction calculations have been carried out for low-lying electronic states of AsH(2). Bending potentials for the ten lowest states of AsH(2) are obtained in C(2v) symmetry for As-H distances fixed at the the ground state equilibrium value of 2.845 a(0), as well as for the minimum energy path constrained to R(1) = R(2). The calculated equilibrium geometries for the X̃(2)B(1) ground state and the Ã(2)A(1) excited state agree very well with the previous experimental and theoretical results, whereas the data for the higher-lying states are obtained for the first time. Asymmetric potential energy surface (PES) cuts (at R(1) = 2.845 a(0), θ = 90.7°) and two-dimensional (2D) PESs for the lowest three states are also new. The calculated ab initio data are used for analysis of possible AsH(2) photodissociation channels and predissociation effects. It is shown that the Ã(2)A(1)-X̃(2)B(1) transition dipole moment decreases with increasing bending angle, which influences the intensity distribution in the Ã(0,0,0)→X̃ emission spectrum (v(2)'' bending series), shifting its maximum to smaller v(2)'' quantum numbers.

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

    PubMed

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

    2011-07-21

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

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

    NASA Astrophysics Data System (ADS)

    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).

  13. Vibrational modes of methane in the structure H clathrate hydrate from ab initio molecular dynamics simulation.

    PubMed

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Yasuoka, Kenji

    2012-10-14

    Vibrational spectra of guest molecules in clathrate hydrates are frequently measured to determine the characteristic signatures of the molecular environment and dynamical properties of guest-host interactions. Here, we present results of our study on the vibrational frequencies of methane molecules in structure H clathrate hydrates, namely, in the 5(12) and 4(3)5(6)6(3) cages, as the frequencies of stretching vibrational modes in these environments are still unclear. The vibrational spectra of methane molecules in structure H clathrate hydrate were obtained from ab initio molecular dynamics simulation and computed from Fourier transform of autocorrelation functions for each distinct vibrational mode. The calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules were found to be lower in the 4(3)5(6)6(3) cages than in the 5(12) cages (3.8 cm(-1) for symmetric stretching and 6.0 cm(-1) for asymmetric stretching). The C-H bond length and average distance between methane molecules and host-water molecules in 4(3)5(6)6(3) cages were slightly longer than those in the 5(12) cages.

  14. An ab initio investigation of some hydrogen-bonded complexes of methanethiol

    NASA Astrophysics Data System (ADS)

    Bricknell, Bradley C.; Ford, Thomas A.

    2010-07-01

    The hydrogen-bonded complexes formed between methanethiol, as proton donor, and trimethyl amine, dimethyl ether, methyl fluoride, trimethyl phosphine, dimethyl sulphide and methyl chloride, as proton acceptors, have been studied by means of ab initio calculations at the second order level of Møller-Plesset perturbation theory and using the 6-311++G(d,p) basis set. The hydrogen bond energies were found to correlate with the gas phase basicities of the proton acceptors. The increases of the SH bond lengths, the shifts of the wavenumbers of the SH stretching modes and the increases of their infrared intensities were also found to be dependent on the interaction energies. The results for the CH 3SH·S(CH 3) 2 complex are anomalous, and this is attributed to deficiencies with the basis set used for sulphur. The data for the CH 3SH complex closely mirror the behaviour of the corresponding complexes of CH 3OH and (CH 3) 2NH, with the perturbations of the various properties varying consistently in the order CH 3OH > (CH 3) 2NH > CH 3SH.

  15. Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs.

    PubMed

    Quarti, Claudio; Milani, Alberto; Civalleri, Bartolomeo; Orlando, Roberto; Castiglioni, Chiara

    2012-07-19

    State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

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

    SciTech Connect

    Yamaji, Youhei

    2015-12-31

    Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.

  18. 4He+n+n continuum within an ab initio framework

    SciTech Connect

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

    2014-07-16

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

  19. Carbonate-Bridged Lanthanoid Triangles: Single-Molecule Magnet Behavior, Inelastic Neutron Scattering, and Ab Initio Studies.

    PubMed

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

    2016-06-06

    comprised of contributions from large MJ, giving rise to slow magnetic relaxation. Although no direct evidence for intramolecular RE···RE magnetic coupling is observed in either magnetic or INS studies, on the basis of the ab initio calculations, we find noncollinear magnetic axes in 1-Er that are coplanar with the erbium triangle and radially arranged with respect to the triangle's centroid; thus, we argue that the absence of magnetic coupling in this system arises from dipolar and antiferromagnetic superexchange interactions that cancel each other out.

  20. Vicinal fluorine-proton coupling constants. Ab initio calculations of angular dependence and substituent effects

    NASA Astrophysics Data System (ADS)

    San Fabián, J.; Guilleme, J.

    1996-06-01

    A data set of vicinal fluorine-proton coupling constants has been calculated by means of the SCF ab initio and semiempirical INDO/FPT methods. The angular dependence, the effect of individual substituents, and the effect of interaction between two substituents upon the 3JFH couplings have been studied for the molecules CH 2FCH 3, CHF 2CH 3, CH 2FCH 2F, CF 3CH 3, and CHF 2CH 2F. The four contributions to 3JFH ( JFC, JSD, JOD and JOP) have been computed using the standard basis sets 6-31G, 6-31G ∗, 6-31G ∗∗ and 6-311G ∗∗ and a double zeta basis set [4s2p1d/2s1p] with additional tight s functions on the H and F. The agreement with the experimental data is better for the last basis set but the trends of the angular dependence and substituent effects are also reproduced by the remaining basis sets. The major contribution arises from the FC term and the remaining contributions are much smaller being the OP the most important. The individual effect of an electronegative substituent depends on the carbon to which is bonded, being more important when the substituent is bonded to the carbon with the coupled hydrogen. The effect of interaction between two substituents seems to be not negligible, reaching values up to 6 Hz. The most important calculated interaction effects are the geminal δC012FF, δC034FF and δC134FF as well as the vicinal δC213FF and δC214FF.

  1. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

    SciTech Connect

    Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

    2014-07-03

    Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is

  2. Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

    1991-01-01

    The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

  3. Phosphorous bonding in PCl3:H2O adducts: A matrix isolation infrared and ab initio computational studies

    NASA Astrophysics Data System (ADS)

    Joshi, Prasad Ramesh; Ramanathan, N.; Sundararajan, K.; Sankaran, K.

    2017-01-01

    Non-covalent interaction between PCl3 and H2O was studied using matrix isolation infrared spectroscopy and ab initio computations. Computations indicated that the adducts are stabilized through novel P⋯O type phosphorus bonding and conventional Psbnd Cl⋯H type hydrogen bonding interactions, where the former adduct is the global minimum. Experimentally, the P⋯O phosphorus bonded adduct was identified in N2 matrix, which was evidenced from the shifts in the vibrational wavenumbers of the modes involving PCl3 and H2O sub-molecules. Atoms in Molecules and Natural Bond Orbital analyses have been performed to understand the nature of interactions in the phosphorus and hydrogen bonded adducts. Interestingly, experimental evidence for the formation of higher PCl3sbnd H2O adduct was also observed in N2 matrix.

  4. Ab initio shell model with a chiral-symmetry-based three-nucleon force for the p-shell nuclei

    SciTech Connect

    Navratil, P; Hayes, A C; Vary, J P; Ormand, W E

    2003-10-14

    The ab initio no-core shell model (NCSM) is extended to include a realistic three-body interaction in calculations for p-shell nuclei. They present results of first applications using the Argonne V8' nucleon-nucleon (NN) potential and the Tucson-Melbourne TM'(99) three-nucleon interaction (TNI). In addition to increase of binding energy, they observe a trend toward level-ordering and level-spacing improvement in comparison to experiment. With the TNI they obtain a correct ground-state spin for {sup 10}B contrary to calculations with NN potentials only. They also investigate neutrino-{sup 12}C exclusive cross sections and muon capture on {sup 12}C. They show that realistic nucleon-nucleon interactions underpredict the experimental cross sections by a factor of two or more. By including the TNI a much better agreement with experiment is achieved along with an encouraging trend.

  5. Coordination properties of a metal chelator clioquinol to Zn(2+) studied by static DFT and ab initio molecular dynamics.

    PubMed

    Rodríguez-Santiago, Luis; Alí-Torres, Jorge; Vidossich, Pietro; Sodupe, Mariona

    2015-05-28

    Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(ii) to lead to a binary metal/ligand 1 : 2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)2 neutral complexes, to which additional water molecules may coordinate. In the present work, the coordinative properties of clioquinol in aqueous solution have been analyzed by means of static, minimal cluster based DFT calculations and explicit solvent ab initio molecular dynamics simulations. Results from static calculations accounting for solvent effects by means of polarized continuum models suggest that the preferred metal coordination environment is tetrahedral Zn(CQ)2, whereas ab initio molecular dynamics simulations point to quasi degenerate penta Zn(CQ)2(H2O) and hexa Zn(CQ)2(H2O)2 coordinated complexes. The possible reasons for these discrepant results are discussed.

  6. Thermodynamics of mixing in MgSiO 3-Al 2O 3 perovskite and ilmenite from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Jung, D. Y.; Vinograd, V. L.; Fabrichnaya, O. B.; Oganov, A. R.; Schmidt, M. W.; Winkler, B.

    2010-07-01

    The thermodynamic mixing functions of MgSiO 3-Al 2O 3 solid solutions in perovskite and ilmenite structures were modeled based on the results of ab initio calculations applied to a set of supercell structures containing 64 and 48 exchangeable sites, respectively. The sampled structures were constructed from the supercells of the end-members MgSiO 3 perovskite and Al 2O 3 corundum by inserting double AlAl and MgSi defects, respectively, at all possible distances. From these calculations the pairwise effective interactions were derived and used to calculate enthalpy differences between successive configurations produced in Monte Carlo simulation runs. The temperature dependent enthalpies of mixing of the solid solutions were evaluated as averages over the Monte Carlo runs while the free energies of mixing were calculated with the method of thermodynamic integration. The phase equilibria of perovskite, ilmenite and garnet in the Mg-Si-Al-O system were calculated using the computed models of mixing and the standard thermodynamic properties of the end-members from the data base of Fabrichnaya (1999). The obtained activity-composition models are in good agreement with available experimental constraints, thereby showing that the thermodynamic effects of mixing in silicate solid solutions with coupled substitutions can be reliably predicted based on ab initio calculated total energies of a small set of supercell structures.

  7. Methane adsorption on porous nano-silica in the presence of water: An experimental and ab initio study.

    PubMed

    Wang, Lu; Yu, Qingchun

    2016-04-01

    This study investigated the effects of silanol groups and water content on methane adsorption on hydrophilic nano-silica H-380 through experiments and ab initio calculations. Fourier transform infrared (FTIR) spectroscopy was used to confirm the presence of silanol groups on the solid surface, and the pore size distribution between 0 and 40nm was determined using CO2 and N2 sorption experiments. Ab initio MP2 and complete basis set model (CBS-4) calculations were performed to optimize four different silica surfaces with and without silanol groups using different basis sets. The theoretical calculations and experiments indicated that the adsorption of methane slightly decreased when the water content was low. As the water content increased from 29.03wt% to 40.54wt%, the confined water molecules (water within the pores) promoted the adsorption of CH4 by forming deeper adsorption potential energy wells, thus rendering the system more stable. The experimental isotherms at 308.15-318.15K were obtained over a wide range of water contents up to 75.05wt%. The experimental data are consistent with the theoretical analysis, indicating an increase in the adsorption of CH4 as the water content increased from 39.75wt% to 50.35wt%. Additionally, the adsorption of CH4 sharply decreased when the water content was greater than 63.12wt%. This study contributes essential data on methane-confined H2O interactions on nano-silica surfaces to the scientific literature.

  8. The many-body Wigner Monte Carlo method for time-dependent ab-initio quantum simulations

    SciTech Connect

    Sellier, J.M. Dimov, I.

    2014-09-15

    The aim of ab-initio approaches is the simulation of many-body quantum systems from the first principles of quantum mechanics. These methods are traditionally based on the many-body Schrödinger equation which represents an incredible mathematical challenge. In this paper, we introduce the many-body Wigner Monte Carlo method in the context of distinguishable particles and in the absence of spin-dependent effects. Despite these restrictions, the method has several advantages. First of all, the Wigner formalism is intuitive, as it is based on the concept of a quasi-distribution function. Secondly, the Monte Carlo numerical approach allows scalability on parallel machines that is practically unachievable by means of other techniques based on finite difference or finite element methods. Finally, this method allows time-dependent ab-initio simulations of strongly correlated quantum systems. In order to validate our many-body Wigner Monte Carlo method, as a case study we simulate a relatively simple system consisting of two particles in several different situations. We first start from two non-interacting free Gaussian wave packets. We, then, proceed with the inclusion of an external potential barrier, and we conclude by simulating two entangled (i.e. correlated) particles. The results show how, in the case of negligible spin-dependent effects, the many-body Wigner Monte Carlo method provides an efficient and reliable tool to study the time-dependent evolution of quantum systems composed of distinguishable particles.

  9. Theoretical study of the dynamics of Cl + O3 reaction I. Ab initio potential energy surface and quasiclassical trajectory results.

    PubMed

    Castillo, J F; Aoiz, F J; Martínez-Haya, B

    2011-05-14

    We present a global full dimensional potential energy surface (PES) for the Cl + O(3)→ ClO + O(2) reaction, which is an elementary step in a catalytic cycle that leads to the destruction of ozone in the stratosphere. The PES is constructed by interpolation of quantum chemistry data using the method developed by Collins and co-workers. Ab initio data points (energy, gradients and Hessian matrix elements) have been calculated at the UQCISD/aug-cc-pVDZ (unrestricted quadratic configuration interaction with single and double excitations) level of theory. The ab initio calculations predict a markedly non-coplanar (dihedral angle of 80°) transition state for the reaction, located very early in the reactant valley and slightly below the energy of the reactants as long as the spin-orbit splitting is neglected. Quasiclassical trajectory (QCT) calculations have been carried out at several collision energies to investigate the reaction dynamics. The QCT excitation function shows no threshold, displays a minimum at a collision energy of 2.5 kcal mol(-1), and then increases monotonically at larger collision energies. This behaviour is consistent with a barrierless reaction dominated by an oxygen-abstraction mechanism. The calculated product vibrational distributions (strongly inverted for ClO) and rate constants are compared with experimental determinations. Differential cross sections (DCS) summed over all final states are found to be in fairly good agreement with those derived from crossed molecular beam experiments.

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

    PubMed

    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.

  11. Investigation on electronic and magnetic properties of Mn2NiAl by ab initio calculations and Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Masrour, R.; Jabar, A.; Hlil, E. K.; Hamedoun, M.; Benyoussef, A.; Hourmatallah, A.; Rezzouk, A.; Bouslykhane, K.; Benzakour, N.

    2017-04-01

    Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Mn2NiAl. Magnetic moment considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for Monte Carlo simulations to compute other magnetic parameters. Also, the magnetic properties of Mn2NiAl are studied using the Monte Carlo simulations. The variation of magnetization and magnetic susceptibility with the reduced temperature of Mn2NiAl are investigated. The transition temperature of this system is deduced for different values exchange interaction and crystal field. The thermal total magnetization has been obtained, and the magnetic hysteresis cycle is established. The total magnetic moment is superior to those obtained by the other method and is mainly determined by the antiparallel aligned MnI, MnII and Ni spin moments. The superparamagnetic phase is found at the neighborhood of transition temperature.

  12. Ab initio electronic structure of quasi-two-dimensional materials: A "native" Gaussian-plane wave approach.

    PubMed

    Trevisanutto, Paolo E; Vignale, Giovanni

    2016-05-28

    Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is "native" to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory - density functional theory, GW approximation and Bethe-Salpeter equation - are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.

  13. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH2(+).

    PubMed

    Li, Y Q; Zhang, P Y; Han, K L

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.

  14. Conformational Characteristics of Poly(tetrafluoroethylene) (PTFE) Based Upon Ab Initio Electronic Structure Calculations on Model Molecules

    NASA Technical Reports Server (NTRS)

    Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

    1994-01-01

    Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.

  15. Ab initio investigation of benzene clusters: Molecular tailoring approach

    NASA Astrophysics Data System (ADS)

    Mahadevi, A. Subha; Rahalkar, Anuja P.; Gadre, Shridhar R.; Sastry, G. Narahari

    2010-10-01

    An exhaustive study on the clusters of benzene (Bz)n, n =2-8, at MP2/6-31++G∗∗ level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (˜0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n -1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.

  16. Ab initio study of the KrH+ photodissociation.

    PubMed

    Alekseyev, Aleksey B; Buenker, Robert J; Liebermann, Heinz-Peter

    2008-06-21

    The multireference spin-orbit configuration interaction method is employed to calculate potential energy curves for the ground and low-lying excited states of the KrH(+) cation. For the first time, the spin-orbit interaction is taken into account and electric dipole moments are computed for transitions to the states responsible for the first absorption continuum (A band) of KrH(+). On this basis, the partial and total absorption spectra in this energy range are obtained. It is shown that the A-band absorption is dominated by the parallel A (1)Sigma(+)<--X (1)Sigma(+) transition. In the low-energy part of the band (<83x10(3) cm(-1)) the absorption is mainly caused by the spin-forbidden b (3)Pi(0(+) )<--X (1)Sigma(+) excitation, while perpendicular transitions to the B (1)Pi and b (3)Pi(1) states are significantly weaker. The branching ratio Gamma for the photodissociation products is calculated and it is shown to increase smoothly from 0 in the red tail of the band to 1 at E>or=90x10(3) cm(-1). The latter value corresponds to the exclusive formation of the spin-excited Kr(+)((2)P(12)) ions, which may be used to obtain laser generation on the Kr(+)((2)P(12)-(2)P(32)) transition.

  17. Ab initio multireference study of the BN molecule

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.; Lee, Timothy J.; Scuseria, Gustavo E.; Taylor, Peter R.

    1992-01-01

    The lowest 1Sigma(+) and 3Pi states of the BN molecule are studied using multireference configuration interaction (MRCI) and averaged coupled-pair functional (ACPF) methods and large atomic natural orbital (ANO) basis sets, as well as several coupled cluster methods. Our calculations strongly support a 3Pi ground state, but the a1Sigma(+) state lies only 381 +/- 100/cm higher. The a1Sigma(+) state wave function exhibits strong multireference character and, consequently, the predictions of the perturbationally-based single-reference CCSD(T) coupled cluster method are not as reliable in this case as the multireference results. The theoretical predictions for the spectroscopic constants of BN are in good agreement with experiment for the Chi3Pi state, but strongly suggest a misassignment of the fundamental vibrational frequency for the a1Sigma(+) state.

  18. Ab-initio study of polypyrrole as a pervaporation membrane

    NASA Astrophysics Data System (ADS)

    Botelho, Andre; Lin, Xi

    2010-03-01

    The affinities between polypyrrole, water, ethanol and a sulfonate-carrying ion were calculated from first principles. All interactions were demonstrably hydrogen bonds between the oxygen from the sulfonate groups and the hydrogen in the hydroxyl (for water and ethanol) and amine groups (for polypyrrole). Each sulfonate group was shown to form three hydrogen bonds, with any of the three other types of molecules, allowing the ion complex to bind to multiple polypyrrole chains, water, and ethanol molecules simultaneously. The energies indicated a higher affinity between the ion and poypyrrole, second highest between water and the ion, and the lowest for ethanol and the ion. A high affinity of the ion to the polymer backbone is desirable to prevent leeching. The ion was found to have a higher affinity to water molecules than to ethanol, confirming the system's selectivity in separating water from ethanol.

  19. Ab initio Study of Naptho-Homologated DNA Bases

    SciTech Connect

    Sumpter, Bobby G; Vazquez-Mayagoitia, Alvaro; Huertas, Oscar; Fuentes-Cabrera, Miguel A; Orozco, Modesto; Luque, Javier

    2008-01-01

    Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

  20. Treatment of dilute clusters of methanol and water by ab initio quantum mechanical calculations.

    PubMed

    Ruckenstein, Eli; Shulgin, Ivan L; Tilson, Jeffrey L

    2005-02-10

    Large molecular clusters can be considered as intermediate states between gas and condensed phases, and information about them can help us understand condensed phases. In this paper, ab initio quantum mechanical methods have been used to examine clusters formed of methanol and water molecules. The main goal was to obtain information about the intermolecular interactions and the structure of methanol/water clusters at the molecular level. The large clusters (CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10)) containing one molecule of one component (methanol or water) and many (12, 10) molecules of the other component were considered. Møller-Plesset perturbation theory (MP2) was used in the calculations. Several representative cluster geometries were optimized, and nearest-neighbor interaction energies were calculated for the geometries obtained in the first step. The results of the calculations were compared to the available experimental information regarding the liquid methanol/water mixtures and to the molecular dynamics and Monte Carlo simulations, and good agreement was found. For the CH(4)O...(H(2)O)(12) cluster, it was shown that the molecules of water can be subdivided into two classes: (i) H bonded to the central methanol molecule and (ii) not H bonded to the central methanol molecule. As expected, these two classes exhibited striking energy differences. Although they are located almost the same distance from the carbon atom of the central methanol molecule, they possess very different intermolecular interaction energies with the central molecule. The H bonding constitutes a dominant factor in the hydration of methanol in dilute aqueous solutions. For the H(2)O...(CH(4)O)(10) cluster, it was shown that the central molecule of water has almost three H bonds with the methanol molecules; this result differs from those in the literature that concluded that the average number of H bonds between a central water molecule and methanol molecules in dilute solutions of