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Sample records for ab initio pair

  1. Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Jäger, Benjamin; Bich, Eckard

    2017-06-01

    A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

  2. Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

    PubMed Central

    2017-01-01

    A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac–Coulomb and Dirac–Coulomb–Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved. PMID:28595411

  3. Amino acid anions in organic ionic compounds. An ab initio study of selected ion pairs.

    PubMed

    Benedetto, A; Bodo, E; Gontrani, L; Ballone, P; Caminiti, R

    2014-03-06

    The combination of amino acids in their deprotonated and thus anionic form with a choline cation gives origin to a new and potentially important class of organic ionic compounds. A series of such neutral ion pairs has been investigated by first principle methods. The results reveal intriguing structural motives as well as regular patterns in the charge distribution and predict a number of vibrational and optical properties that could guide the experimental investigation of these compounds. The replacement of choline with its phosphocholine analogue causes the spontaneous reciprocal neutralization of cations and anions, taking place through the transfer of a proton between the two ions. Systems of this kind, therefore, provide a wide and easily accessible playground to probe the ionic/polar transition in organic systems, while the easy transfer of H(+) among neutral and ionic species points to their potential application as proton conductors. The analysis of the ab initio data highlights similarities as well as discrepancies from the rigid-ions force-field picture and suggests directions for the improvement of empirical models.

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

    PubMed

    Petrenko, Y M

    2015-01-01

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

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

    SciTech Connect

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

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

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

    PubMed

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

    2016-05-13

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

  7. 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

  8. 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.

  9. Theory of Magnetic Ordering in the Heavy Rare Earths: Ab Initio Electronic Origin of Pair- and Four-Spin Interactions

    NASA Astrophysics Data System (ADS)

    Mendive-Tapia, Eduardo; Staunton, Julie B.

    2017-05-01

    We describe a disordered local moment theory for long-period magnetic phases and investigate the temperature and magnetic field dependence of the magnetic states in the heavy rare earth elements (HREs), namely, paramagnetic, conical and helical antiferromagnetic (HAFM), fan, and ferromagnetic (FM) states. We obtain a generic HRE magnetic phase diagram which is consequent on the response of the common HRE valence electronic structure to f -electron magnetic moment ordering. The theory directly links the first-order HAFM-FM transition to the loss of Fermi surface nesting, induced by this magnetic ordering, as well as provides a template for analyzing the other phases and exposing where f -electron correlation effects are particularly intricate. Gadolinium, for a range of hexagonal, close-packed lattice constants c and a , is the prototype, described ab initio, and applications to other HREs are made straightforwardly by scaling the effective pair and quartic local moment interactions that emerge naturally from the theory with de Gennes factors and choosing appropriate lanthanide-contracted c and a values.

  10. Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

    PubMed

    Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

    2014-02-01

    The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Collision-induced dipoles and polarizabilities of pairs of hydrogen molecules: Ab initio calculations and results from spherical tensor analysis

    NASA Astrophysics Data System (ADS)

    Li, Xiaoping; Harrison, James F.; Gustafsson, Magnus; Wang, Fei; Abel, Martin; Frommhold, Lothar; Hunt, Katharine L. C.

    2012-12-01

    New ab initio results are reported for the interaction-induced changes in the dipole moments and polarizabilities of pairs of hydrogen molecules, computed using finite-field coupled-cluster methods in MOLPRO 2000 and GAMESS, with an aug-cc-pV5Z (spdf) basis set. Earlier work by X. Li, C. Ahuja, J. F. Harrison, and K. L. C. Hunt, J. Chem. Phys. 126, 214302 (2007), on collision-induced polarizabilities Δα has been extended with 170 additional geometrical configurations of the H2 pairs. In calculations of Δα, we have used a "random field" technique, with up to 120 different field strengths, having components that range from 0.001 to 0.01 a.u. Numerical tests show that the pair dipoles Δμ can be obtained accurately from calculations limited to 6 values of the field in each direction, so this approach has been used to compute Δμ by X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Int. J. Spectroscopy 2010, 371201 (2010). We have evaluated the collision-induced dipoles of H2 pairs for 28 combinations of bond lengths (ranging from 0.942 a.u. to 2.801 a.u.), 7 intermolecular separations R, and 17 different relative orientations. In our work on Δα, the bond lengths are fixed at 1.449 a.u. Our results agree well with the previous ab initio work of W. Meyer, A. Borysow, and L. Frommhold, Phys. Rev. A 40, 6931 (1989), and of Y. Fu, C. G. Zheng and A. Borysow, J. Quant. Spectroscopy and Rad. Transfer, 67, 303 (2000)-where those data exist-for Δμ of H2 pairs. For Δα, our results agree well with the CCSD(T) results obtained by G. Maroulis, J. Phys. Chem. A 104, 4772 (2000) for two pair orientations and fixed R. The pair polarizability anisotropies also agree well with the small-basis self-consistent field results of D. G. Bounds, Mol. Phys. 38, 2099 (1979), although the trace of the polarizability differs by factors of 2 or more from Bounds' results. We have determined the expansion coefficients for Δμ and Δα, expressed as series in the spherical

  12. Ab initio vel ex eventu

    NASA Astrophysics Data System (ADS)

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

    Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

  13. State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

    SciTech Connect

    Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

    2016-03-21

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

  14. State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

    PubMed

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

    2016-03-21

    A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

  15. N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

    2015-03-01

    We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

  16. ns2np4 (n = 4, 5) lone pair triplets whirling in M*F2E3 (M* = Kr, Xe): Stereochemistry and ab initio analyses

    NASA Astrophysics Data System (ADS)

    Galy, Jean; Matar, Samir F.

    2017-02-01

    The stereochemistry of ns2np4 (n = 4, 5) lone pair LP characterizing noble gas Kr and Xe (labeled M*) in M*F2 difluorides is examined within coherent crystal chemistry and ab initio visualizations. M*2+ in such oxidation state brings three lone pairs (E) and difluorides are formulated M*F2E3. The analyses use electron localization function (ELF) obtained within density functional theory calculations showing the development of the LP triplets whirling {E3} quantified in the relevant chemical systems. Detailed ELF data analyses allowed showing that in α KrF2E3 and isostructural XeF2E3 difluorides the three E electronic clouds merge or hybridize into a torus and adopt a perfect gyration circle with an elliptical section, while in β KrF2 the network architecture deforms the whole torus into an ellipsoid shape. Original precise metrics are provided for the torus in the different compounds under study. In KrF2 the geometric changes upon β → α phase transition is schematized and mechanisms for the transformation with temperature or pressure are proposed. The results are further highlighted by electronic band structure calculations which show similar features of equal band gaps of 3 eV in both α and β KrF2 and a reorganization of frontier orbitals due to the different orientations of the F-Kr-F linear molecule in the two tetragonal structures.

  17. Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

    PubMed

    Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel

    2018-04-05

    Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

  18. Topological Semimetals Studied by Ab Initio Calculations

    NASA Astrophysics Data System (ADS)

    Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

    2018-04-01

    In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

  19. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs.

    PubMed

    Marchetti, Barbara; Karsili, Tolga N V; Ashfold, Michael N R; Domcke, Wolfgang

    2016-07-27

    The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.

  20. Separated-pair independent particle model and the generalized Brillouin theorem: ab initio calculations on the dissociation of polyatomic molecules

    SciTech Connect

    Sundberg, Kenneth Randall

    1976-01-01

    A method is developed to optimize the separated-pair independent particle (SPIP) wave function; it is a special case of the separated-pair theory obtained by using two-term natural expansions of the geminals. The orbitals are optimized by a theory based on the generalized Brillouin theorem and iterative configuration interaction (CI) calculations in the space of the SPIP function and its single excitations. The geminal expansion coefficients are optimized by serial 2 x 2 CI calculations. Formulas are derived for the matrix elements. An algorithm to implement the method is presented, and the work needed to evaluate the molecular integrals is discussed.

  1. Ab initio theory and modeling of water

    PubMed Central

    Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

    2017-01-01

    Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

  2. Ab initio theory and modeling of water.

    PubMed

    Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

    2017-10-10

    Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

  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 Dy 4 K 2 ([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 (H 3 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. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Towards ab initio Calculations with the Dynamical Vertex Approximation

    NASA Astrophysics Data System (ADS)

    Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

    2018-04-01

    While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

  5. Ab initio characterization of coupling strength for all types of dangling-bond pairs on the hydrogen-terminated Si(100)-2 × 1 surface

    NASA Astrophysics Data System (ADS)

    Shaterzadeh-Yazdi, Zahra; Sanders, Barry C.; DiLabio, Gino A.

    2018-04-01

    Recent work has suggested that coupled silicon dangling bonds sharing an excess electron may serve as building blocks for quantum-cellular-automata cells and quantum computing schemes when constructed on hydrogen-terminated silicon surfaces. In this work, we employ ab initio density-functional theory to examine the details associated with the coupling between two dangling bonds sharing one excess electron and arranged in various configurations on models of phosphorous-doped hydrogen-terminated silicon (100) surfaces. Our results show that the coupling strength depends strongly on the relative orientation of the dangling bonds on the surface and on the separation between them. The orientation of dangling bonds is determined by the anisotropy of the silicon (100) surface, so this feature of the surface is a significant contributing factor to variations in the strength of coupling between dangling bonds. The results demonstrate that simple models for approximating tunneling, such as the Wentzel-Kramer-Brillouin method, which do not incorporate the details of surface structure, are incapable of providing reasonable estimates of tunneling rates between dangling bonds. The results provide guidance to efforts related to the development of dangling-bond based computing elements.

  6. Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

    DTIC Science & Technology

    2015-07-15

    There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

  7. Ab initio quantum chemistry: methodology and applications.

    PubMed

    Friesner, Richard A

    2005-05-10

    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.

  8. 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.

  9. Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

    NASA Astrophysics Data System (ADS)

    Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

    2015-02-01

    We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7 pairs (Frenkel pairs), in defect-free TiN. This entails that the N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; ˜50% of these processes result in the exchange of two nitrogen lattice atoms (N - NExc) . Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects.

  10. Ab Initio Reactive Computer Aided Molecular Design

    DOE PAGES

    Martínez, Todd J.

    2017-03-21

    Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we arguemore » that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.« less

  11. Ab Initio Reactive Computer Aided Molecular Design

    SciTech Connect

    Martínez, Todd J.

    Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we arguemore » that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.« less

  12. 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.

  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. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

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

    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

  15. Molecular Spectroscopy by Ab Initio Methods

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    Due to recent advances in methods and computers, the accuracy of ab calculations has reached a point where these methods can be used to provide accurate spectroscopic constants for small molecules; this will be illustrated with several examples. We will show how ab initio calculations where used to identify the Hermann infrared system in N2 and two band systems in CO. The identification of all three of these band systems relied on very accurate calculations of quintet states. The analysis of the infrared spectra of cool stars requires knowledge of the intensity of vibrational transitions in SiO for high nu and J levels. While experiment can supply very accurate dipole moments for nu = 0 to 3, this is insufficient to construct a global dipole moment function. We show how theory, combined by the experiment, can be used to generate the line intensities up to nu = 40 and J = 250. The spectroscopy of transition metal containing systems is very difficult for both theory and experiment. We will discuss the identification of the ground state of Ti2 and the spectroscopy of AlCu as examples of how theory can contribute to the understanding of these complex systems.

  16. Ab-initio calculations on melting of thorium

    SciTech Connect

    Mukherjee, D., E-mail: debojyoti@barc.gov.in; Sahoo, B. D.; Joshi, K. D.

    2016-05-23

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

  17. 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)

  18. A note on AB INITIO semiconductor band structures

    NASA Astrophysics Data System (ADS)

    Fiorentini, Vincenzo

    1992-09-01

    We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

  19. Ab initio gene identification in metagenomic sequences

    PubMed Central

    Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark

    2010-01-01

    We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed to bypass this difficulty, one effective method is to estimate parameters from dependencies, formed in evolution, between frequencies of oligonucleotides in protein-coding regions and genome nucleotide composition. Original version of the method was proposed in 1999 and has been used since for (i) reconstructing codon frequency vector needed for gene finding in viral genomes and (ii) initializing parameters of self-training gene finding algorithms. With advent of new prokaryotic genomes en masse it became possible to enhance the original approach by using direct polynomial and logistic approximations of oligonucleotide frequencies, as well as by separating models for bacteria and archaea. These advances have increased the accuracy of model reconstruction and, subsequently, gene prediction. We describe the refined method and assess its accuracy on known prokaryotic genomes split into short sequences. Also, we show that as a result of application of the new method, several thousands of new genes could be added to existing annotations of several human and mouse gut metagenomes. PMID:20403810

  20. Ab initio simulations of molten Ni alloys

    NASA Astrophysics Data System (ADS)

    Woodward, Christopher; Asta, Mark; Trinkle, Dallas R.; Lill, James; Angioletti-Uberti, Stefano

    2010-06-01

    Convective instabilities responsible for misoriented grains in directionally solidified turbine airfoils are produced by variations in liquid-metal density with composition and temperature across the solidification zone. Here, fundamental properties of molten Ni-based alloys, required for modeling these instabilities, are calculated using ab initio molecular dynamics simulations. Equations of state are derived from constant number-volume-temperature ensembles at 1830 and 1750 K for elemental, binary (Ni-X, X=Al, W, Re, and Ta) and ternary (Ni-Al-X, X=W, Re, and Ta) Ni alloys. Calculated molar volumes agree to within 0.6%-1.8% of available measurements. Predictions are used to investigate the range of accuracy of a parameterization of molar volumes with composition and temperature based on measurements of binary alloys. Structural analysis reveals a pronounced tendency for icosahedral short-range order for Ni-W and Ni-Re alloys and the calculations provide estimates of diffusion rates and their dependence on compositions and temperature.

  1. Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

  2. Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

    PubMed

    West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

    2017-11-22

    The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

  3. Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Nomura, Kazuya; Hoshino, Ryota; Hoshiba, Yasuhiro; Danilov, Victor I.; Kurita, Noriyuki

    2013-04-01

    We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

  4. Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe 2 S 3 : Combined ab initio and density matrix renormalization group study

    DOE PAGES

    Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; ...

    2016-08-10

    The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe 2S 3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015)] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe 2S 3. Themore » model is studied with the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only oneWannier orbital receiving the hole carriers while the other remains half-filled. Lastly, these results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.« less

  5. 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.

  6. Visualizing the BEC-BCS crossover in a two-dimensional Fermi gas: Pairing gaps and dynamical response functions from ab initio computations

    NASA Astrophysics Data System (ADS)

    Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei

    2017-12-01

    Experiments with ultracold atoms provide a highly controllable laboratory setting with many unique opportunities for precision exploration of quantum many-body phenomena. The nature of such systems, with strong interaction and quantum entanglement, makes reliable theoretical calculations challenging. Especially difficult are excitation and dynamical properties, which are often the most directly relevant to experiment. We carry out exact numerical calculations, by Monte Carlo sampling of imaginary-time propagation of Slater determinants, to compute the pairing gap in the two-dimensional Fermi gas from first principles. Applying state-of-the-art analytic continuation techniques, we obtain the spectral function and the density and spin structure factors providing unique tools to visualize the BEC-BCS crossover. These quantities will allow for a direct comparison with experiments.

  7. Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

    PubMed

    Alexandrova, Anastassia N; Boldyrev, Alexander I; Li, Xiang; Sarkas, Harry W; Hendricks, Jay H; Arnold, Susan T; Bowen, Kit H

    2011-01-28

    Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.

  8. Ab initio calculation of one-nucleon halo states

    NASA Astrophysics Data System (ADS)

    Rodkin, D. M.; Tchuvil'sky, Yu M.

    2018-02-01

    We develop an approach to microscopic and ab initio description of clustered systems, states with halo nucleon and one-nucleon resonances. For these purposes a basis combining ordinary shell-model components and cluster-channel terms is built up. The transformation of clustered wave functions to the uniform Slater-determinant type is performed using the concept of cluster coefficients. The resulting basis of orthonormalized wave functions is used for calculating the eigenvalues and the eigenvectors of Hamiltonians built in the framework of ab initio approaches. Calculations of resonance and halo states of 5He, 9Be and 9B nuclei demonstrate that the approach is workable and labor-saving.

  9. Multiple time step integrators in ab initio molecular dynamics.

    PubMed

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

    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.

  10. Ab initio interatomic potentials and the thermodynamic properties of fluids

    NASA Astrophysics Data System (ADS)

    Vlasiuk, Maryna; Sadus, Richard J.

    2017-07-01

    Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

  11. A walk through the approximations of ab initio multiple spawning

    NASA Astrophysics Data System (ADS)

    Mignolet, Benoit; Curchod, Basile F. E.

    2018-04-01

    Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

  12. Ab initio calculations of the lattice dynamics of silver halides

    NASA Astrophysics Data System (ADS)

    Gordienko, A. B.; Kravchenko, N. G.; Sedelnikov, A. N.

    2010-12-01

    Based on ab initio pseudopotential calculations, the results of investigations of the lattice dynamics of silver halides AgHal (Hal = Cl, Br, I) are presented. Equilibrium lattice parameters, phonon spectra, frequency densities and effective atomic-charge values are obtained for all types of crystals under study.

  13. 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.

  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. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    PubMed

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  16. A walk through the approximations of ab initio multiple spawning.

    PubMed

    Mignolet, Benoit; Curchod, Basile F E

    2018-04-07

    Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

  17. Ab initio interatomic potentials and the thermodynamic properties of fluids.

    PubMed

    Vlasiuk, Maryna; Sadus, Richard J

    2017-07-14

    Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

  18. Perspective: Ab initio force field methods derived from quantum mechanics

    NASA Astrophysics Data System (ADS)

    Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

    2018-03-01

    It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

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

    NASA Astrophysics Data System (ADS)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

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

  20. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    NASA Astrophysics Data System (ADS)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  1. Ab Initio Infrared and Raman Spectra.

    DTIC Science & Technology

    1982-08-01

    equilibrium and non -equilibrium systems. It b pointed out that a similar ab !ni- te QFC molecular dynamic approach could be used to compute other types of...applied to -2- equilibrium and non -equilibrium system. It is pointed out that a similar oh im- ib QFCT molecular dynamic approach could be used to...desire to be able to experimentally identify and understand transient species or states (such as those existing during the course of chemical

  2. 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).

  3. Ab initio structures and polarizabilities of sodium clusters

    NASA Astrophysics Data System (ADS)

    Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

    2001-09-01

    We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

  4. 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.

  5. 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.

  6. 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.

  7. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    PubMed

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy.

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

    PubMed

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

    2016-09-14

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

  9. 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.

  10. Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

    NASA Astrophysics Data System (ADS)

    Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

    In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

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

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1993-01-01

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

  12. 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.

  13. Characteristics of Raman spectra for graphene oxide from ab initio simulations.

    PubMed

    Wang, Lu; Zhao, Jijun; Sun, Yi-Yang; Zhang, Shengbai B

    2011-11-14

    The Raman spectra of several locally stable structures of the graphene oxide (GO) have been simulated by ab initio calculations. Compared to graphite, the G band of GO is broadened and blueshifted due to the emergence of a series of new Raman peaks. The Raman intensities and positions of the D and G bands depend sensitively on the local atomic configurations. In addition to the normal epoxy and hydroxyl groups, other oxidation groups such as epoxy pairs are also studied. Epoxy pairs induce large blueshift of G band with respect to that of the graphite. © 2011 American Institute of Physics

  14. Ab Initio Calculations of Water Line Strengths

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Partridge, Harry

    1998-01-01

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

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

    SciTech Connect

    Yang, Li; ye, Yeting; Fan, K. M.

    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.more » 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.« less

  16. Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

    PubMed

    Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

    2017-03-14

    Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

  17. 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.

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

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

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

  19. Cooperative effects in spherical spasers: Ab initio analytical model

    NASA Astrophysics Data System (ADS)

    Bordo, V. G.

    2017-06-01

    A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.

  20. Ab initio study of C + H3+ reactions

    NASA Technical Reports Server (NTRS)

    Talbi, D.; DeFrees, D. J.

    1991-01-01

    The reaction C + H3+ --> CH(+) + H2 is frequently used in models of dense interstellar cloud chemistry with the assumption that it is fast, i.e. there are no potential energy barriers inhibiting it. Ab initio molecular orbital study of the triplet CH3+ potential energy surface (triplet because the reactant carbon atom is a ground state triplet) supports this hypothesis. The reaction product is 3 pi CH+; the reaction is to exothermic even though the product is not in its electronic ground state. No path has been found on the potential energy surface for C + H3+ --> CH2(+) + H reaction.

  1. 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.

  2. Graphitic nanofilms of zinc-blende materials: ab initio calculations

    NASA Astrophysics Data System (ADS)

    Hu, San-Lue; Zhao, Li; Li, Yan-Li

    2017-12-01

    Ab initio calculations on ultra-thin nanofilms of 25 kinds of zinc-blende semiconductors demonstrate their stable geometry structures growth along (1 1 1) surface. Our results show that the (1 1 1) surfaces of 9 kinds of zinc-blende semiconductors can transform into a stable graphitelike structure within a certain thickness. The tensile strain effect on the thickness of graphitic films is not obvious. The band gaps of stable graphitic films can be tuned over a wide range by epitaxial tensile strain, which is important for applications in microelectronic devices, solar cells and light-emitting diodes.

  3. Pseudopotential for ab initio calculations of uranium compounds

    NASA Astrophysics Data System (ADS)

    Smirnov, G. S.; Pisarev, V. V.; Stegailov, V. V.

    2018-01-01

    The density functional theory (DFT) is a research tool of the highest importance for electronic structure calculations. It is often the only affordable method for ab initio calculations of complex materials. The pseudopotential approach allows reducing the total number of electrons in the model that speeds up calculations. However, there is a lack of pseudopotentials for heavy elements suitable for condensed matter DFT models. In this work, we present a pseudopotential for uranium developed in the Goedecker-Teter-Hutter form. Its accuracy is illustrated using several molecular and solid-state calculations.

  4. Ab initio molecular dynamics in a finite homogeneous electric field.

    PubMed

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

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

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

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

  6. Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jakse, N.; Pasturel, A.

    2014-05-01

    Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. Quasi-instantaneous jumps separating periods of localized vibrations around a mean position are found to characterize the hydrogen motion at the microscopic scale. The hydrogen motion is furthermore analyzed using the van Hove function. We highlight a non-Fickian behavior for the hydrogen diffusion due to a large spatial distribution of hydrogen jumps. We show that a generalized continuous time random walk (CTRW) model describes the experimental diffusion coefficients in a satisfactory manner. Finally, the impact of impurities and alloying elements on hydrogen diffusion in aluminum is discussed.

  7. Iterative projection algorithms for ab initio phasing in virus crystallography.

    PubMed

    Lo, Victor L; Kingston, Richard L; Millane, Rick P

    2016-12-01

    Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. 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 (A 2Zr 2O 7, A = La, Nd and Sm). It shows that both cations and anions in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are generally more likely to be displaced than those in La 2Zr 2O 7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are lower than those in La 2Zr 2O 7. These results suggest thatmore » the order–disorder structural transition more easily occurs in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 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.« less

  9. 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

  10. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

    PubMed

    Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

    2015-12-08

    Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

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

    PubMed

    Shrestha, Rojan; Zhang, Kam Y J

    2015-02-01

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

  12. Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

    SciTech Connect

    Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

    2006-03-09

    Ab initio calculations at the CCSD(T) level of theory are performed to characterize the Ar + CF ₄ intermolecular potential. Extensive calculations, with and without a correction for basis set superposition error (BSSE), are performed with the cc-pVTZ basis set. Additional calculations are performed with other correlation consistent (cc) basis sets to extrapolate the Ar---CF₄potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF₄ potential. Calculations with the cc-pVTZ basis set and without a BSSE correction, appear to give a good representation ofmore » the potential at the CBS limit and with a BSSE correction. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two analytic potential energy functions were determined for Ar + CF₄by fitting the cc-pVTZ calculations both with and without a BSSE correction. These analytic functions were written as a sum of two body potentials and excellent fits to the ab initio potentials were obtained by representing each two body interaction as a Buckingham potential.« 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. 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. Towards accurate ab initio predictions of the vibrational spectrum of methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.

    2002-01-01

    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.

  16. 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.

  17. 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 NH 3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state spacemore » for which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less

  18. Ab initio elastic properties and tensile strength of crystalline hydroxyapatite.

    PubMed

    Ching, W Y; Rulis, Paul; Misra, A

    2009-10-01

    We report elastic constant calculation and a "theoretical" tensile experiment on stoichiometric hydroxyapatite (HAP) crystal using an ab initio technique. These results compare favorably with a variety of measured data. Theoretical tensile experiments are performed on the orthorhombic cell of HAP for both uniaxial and biaxial loading. The results show considerable anisotropy in the stress-strain behavior. It is shown that the failure behavior of the perfect HAP crystal is brittle for tension along the z-axis with a maximum stress of 9.6 GPa at 10% strain. Biaxial failure envelopes from six "theoretical" loading tests show a highly anisotropic pattern. Structural analysis of the crystal under various stages of tensile strain reveals that the deformation behavior manifests itself mainly in the rotation of the PO(4) tetrahedron with concomitant movements of both the columnar and axial Ca ions. These results are discussed in the context of mechanical properties of bioceramic composites relevant to mineralized tissues.

  19. Reactive Monte Carlo sampling with an ab initio potential

    NASA Astrophysics Data System (ADS)

    Leiding, Jeff; Coe, Joshua D.

    2016-05-01

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

  20. Quantitative verification of ab initio self-consistent laser theory.

    PubMed

    Ge, Li; Tandy, Robert J; Stone, A D; Türeci, Hakan E

    2008-10-13

    We generalize and test the recent "ab initio" self-consistent (AISC) time-independent semiclassical laser theory. This self-consistent formalism generates all the stationary lasing properties in the multimode regime (frequencies, thresholds, internal and external fields, output power and emission pattern) from simple inputs: the dielectric function of the passive cavity, the atomic transition frequency, and the transverse relaxation time of the lasing transition.We find that the theory gives excellent quantitative agreement with full time-dependent simulations of the Maxwell-Bloch equations after it has been generalized to drop the slowly-varying envelope approximation. The theory is infinite order in the non-linear hole-burning interaction; the widely used third order approximation is shown to fail badly.

  1. Molybdenum-titanium phase diagram evaluated from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Barzilai, Shmuel; Toher, Cormac; Curtarolo, Stefano; Levy, Ohad

    2017-07-01

    The design of next generation β -type titanium implants requires detailed knowledge of the relevant stable and metastable phases at temperatures where metallurgical heat treatments can be performed. Recently, a standard specification for surgical implant applications was established for Mo-Ti alloys. However, the thermodynamic properties of this binary system are not well known and two conflicting descriptions of the β -phase stability have been presented in the literature. In this study, we use ab initio calculations to investigate the Mo-Ti phase diagram. These calculations predict that the β phase is stable over a wide concentration range, in qualitative agreement with one of the reported phase diagrams. In addition, they predict stoichiometric compounds, stable at temperatures below 300 ∘C , which have not yet been detected by experiments. The resulting solvus, which defines the transition to the β -phase solid solution, therefore occurs at lower temperatures and is more complex than previously anticipated.

  2. Ab Initio energetics of SiO bond cleavage.

    PubMed

    Hühn, Carolin; Erlebach, Andreas; Mey, Dorothea; Wondraczek, Lothar; Sierka, Marek

    2017-10-15

    A multilevel approach that combines high-level ab initio quantum chemical methods applied to a molecular model of a single, strain-free SiOSi bridge has been used to derive accurate energetics for SiO bond cleavage. The calculated SiO bond dissociation energy and the activation energy for water-assisted SiO bond cleavage of 624 and 163 kJ mol -1 , respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H 2 O-assisted SiO bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero-point vibrational contribution is in the range of -5 to 19 kJ mol -1 . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  3. 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.

  4. Ab initio Eliashberg Theory: Making Genuine Predictions of Superconducting Features

    NASA Astrophysics Data System (ADS)

    Sanna, Antonio; Flores-Livas, José A.; Davydov, Arkadiy; Profeta, Gianni; Dewhurst, Kay; Sharma, Sangeeta; Gross, E. K. U.

    2018-04-01

    We present an application of Eliashberg theory of superconductivity to study a set of novel superconducting systems with a wide range of structural and chemical properties. The set includes three intercalated group-IV honeycomb layered structures, SH3 at 200 GPa (the superconductor with the highest measured critical temperature), the similar system SeH3 at 150 GPa, and a lithium doped mono-layer of black phosphorus. The theoretical approach we adopt is a recently developed, fully ab initio Eliashberg approach that takes into account the Coulomb interaction in a full energy-resolved fashion avoiding any free parameters like μ*. This method provides reasonable estimations of superconducting properties, including TC and the excitation spectra of superconductors.

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

    PubMed Central

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

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

    PubMed

    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)] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. 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.

  7. Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs

    DOE PAGES

    Curchod, Basile F. E.; Sisto, Aaron; Martinez, Todd J.

    2016-12-15

    The ultrafast decay dynamics of 4-( N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S 2 (the initially populated bright state) to S 1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S 1 andmore » acquires locally excited electronic character. Here, our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S 1).« less

  8. Efficient Ab initio Modeling of Random Multicomponent Alloys

    DOE PAGES

    Jiang, Chao; Uberuaga, Blas P.

    2016-03-08

    Here, we present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multi-component alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we also 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. Furthermore, the SSOS methodmore » developed here can be broadly useful for the rapid computational design of multi-component materials, especially those with a large number of alloying elements, a challenging problem for other approaches.« less

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

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

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

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

    PubMed

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

    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.

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

    PubMed

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-19

    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.

  12. Ab Initio Analysis of Auger-Assisted Electron Transfer.

    PubMed

    Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

    2015-01-15

    Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

  13. Fabrication and ab initio study of downscaled graphene nanoelectronic devices

    NASA Astrophysics Data System (ADS)

    Mizuta, Hiroshi; Moktadir, Zakaria; Boden, Stuart A.; Kalhor, Nima; Hang, Shuojin; Schmidt, Marek E.; Cuong, Nguyen Tien; Chi, Dam Hieu; Otsuka, Nobuo; Muruganathan, Manoharan; Tsuchiya, Yoshishige; Chong, Harold; Rutt, Harvey N.; Bagnall, Darren M.

    2012-09-01

    In this paper we first present a new fabrication process of downscaled graphene nanodevices based on direct milling of graphene using an atomic-size helium ion beam. We address the issue of contamination caused by the electron-beam lithography process to pattern the contact metals prior to the ultrafine milling process in the helium ion microscope (HIM). We then present our recent experimental study of the effects of the helium ion exposure on the carrier transport properties. By varying the time of helium ion bombardment onto a bilayer graphene nanoribbon transistor, the change in the transfer characteristics is investigated along with underlying carrier scattering mechanisms. Finally we study the effects of various single defects introduced into extremely-scaled armchair graphene nanoribbons on the carrier transport properties using ab initio simulation.

  14. 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).

  15. 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.

  16. Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

    PubMed

    Kramer, Christian; Gedeck, Peter; Meuwly, Markus

    2013-03-12

    Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

  17. 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

  18. Ab Initio Values of the Thermophysical Properties of Helium as Standards

    PubMed Central

    Hurly, John J.; Moldover, Michael R.

    2000-01-01

    Recent quantum mechanical calculations of the interaction energy of pairs of helium atoms are accurate and some include reliable estimates of their uncertainty. We combined these ab initio results with earlier published results to obtain a helium-helium interatomic potential that includes relativistic retardation effects over all ranges of interaction. From this potential, we calculated the thermophysical properties of helium, i.e., the second virial coefficients, the dilute-gas viscosities, and the dilute-gas thermal conductivities of 3He, 4He, and their equimolar mixture from 1 K to 104 K. We also calculated the diffusion and thermal diffusion coefficients of mixtures of 3He and 4He. For the pure fluids, the uncertainties of the calculated values are dominated by the uncertainties of the potential; for the mixtures, the uncertainties of the transport properties also include contributions from approximations in the transport theory. In all cases, the uncertainties are smaller than the corresponding experimental uncertainties; therefore, we recommend the ab initio results be used as standards for calibrating instruments relying on these thermophysical properties. We present the calculated thermophysical properties in easy-to-use tabular form. PMID:27551630

  19. Ab Initio Protein Structure Prediction Using Chunk-TASSER

    PubMed Central

    Zhou, Hongyi; Skolnick, Jeffrey

    2007-01-01

    We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for obtaining contact potentials and distance restraints. The predicted chunks, selected on the basis of a new fragment comparison method, are folded by a fragment insertion method. Full-length models are built and refined by the TASSER methodology, which searches conformational space via parallel hyperbolic Monte Carlo. We employ an optimized reduced force field that includes knowledge-based statistical potentials and restraints derived from the chunks as well as threading templates. The method is tested on a dataset of 425 hard target proteins ≤250 amino acids in length. The average TM-scores of the best of top five models per target are 0.266, 0.336, and 0.362 by the threading algorithm SP3, original TASSER and chunk-TASSER, respectively. For a subset of 80 proteins with predicted α-helix content ≥50%, these averages are 0.284, 0.356, and 0.403, respectively. The percentages of proteins with the best of top five models having TM-score ≥0.4 (a statistically significant threshold for structural similarity) are 3.76, 20.94, and 28.94% by SP3, TASSER, and chunk-TASSER, respectively, overall, while for the subset of 80 predominantly helical proteins, these percentages are 2.50, 23.75, and 41.25%. Thus, chunk-TASSER shows a significant improvement over TASSER for modeling hard targets where no good template can be identified. We also tested chunk-TASSER on 21 medium/hard targets <200 amino-acids-long from CASP7. Chunk-TASSER is ∼11% (10%) better than TASSER for the total TM-score of the first (best of top five) models. Chunk-TASSER is fully automated and can be used in proteome scale protein structure prediction. PMID:17496016

  20. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

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

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

    PubMed

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

    2014-09-16

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

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  3. Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

    DTIC Science & Technology

    2017-03-24

    NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

  4. Ab initio description of p-shell hypernuclei.

    PubMed

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

    2014-11-07

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

  5. 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.

  6. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Astrophysics Data System (ADS)

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

    1982-04-01

    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.

  7. Ab-Initio Interfacial Studies of Cobalt/Copper Multilayers

    NASA Astrophysics Data System (ADS)

    Villagonzalo, Cristine; Setty, Arun K.; Muratov, Leonid; Cooper, Bernard R.

    2002-03-01

    We present a study of the interface of cobalt/copper (Co/Cu) multilayrs. For its potential in giant magnetoresistance (GMR) device applications,(S.S.Parkin, et al.), Appl. Phys. Lett. 58 (1991) 2710 the Co/Cu system has been studied extensively. The magnitude of GMR is found to depend sensitively on the nature of the interface, however, the underlying mechanism is not well understood. Therefore, we focus on the energy-configuration of Co/Cu multilayers (of 1-4 monolayers for each element) and on the effects of interpenetration. Using an ab-initio full-potential Linear Muffin-Tin Orbital (FP-LMTO) electronic structure method, we seek a stable interfacial structure. Unlike prior studies, our computations are for the experimentally relevant (111) direction. Our preliminary results indicate that Co impurities in bulk Cu are not energetically favorable, in accord with the experimentally observed immiscibility of Co and Cu. Studies in progress of interfacial relaxation in prelude to consideration of interdiffusion and lattice buckling will also be presented.

  8. 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.

  9. 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.

  10. Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

    PubMed

    Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

    2011-06-01

    Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

  11. Domain Wall Formation in Ferromagnetic Layers: An Ab Initio Study

    NASA Astrophysics Data System (ADS)

    Herper, Heike C.

    Domain walls are an inherent feature of ferromagnetic (FM) films consisting of layers with different magnetic orientations. Since FM films are used in electrical devices the question of the influence of domain walls on, e.g., the magnetoresistance has attracted much interest. Besides discussing the resistance contribution of domain walls, it is appropriate to study different types of domain walls and their energy of formation. The behaviour of domain walls is usually discussed within model calculations. In the present paper it is done within an ab initio Green's function technique for layered systems, i.e., the fully relativistic, spin-polarized screened Korringa-Kohn Rostoker method. Results are presented for fcc Co layers covered by two semi-infinite fcc Pt(001) bulk systems or by bulk fcc Co(001), respectively. The resistance, which is caused by the different types of domain walls is discussed within a Kubo-Greenwood approach considering Co(001)/Co24/Co(001) as an example.

  12. Ab Initio Study of KCl and AgCl Clusters.

    NASA Astrophysics Data System (ADS)

    McKeough, James; Hira, Ajit; Cathey, Tommy; Valdez, Alexandra

    This paper presents a theoretical study of molecular clusters that examines the chemical and physical properties of small KnCln and AgnCln clusters (n = 2 - 24). Due to combinations of attractive and repulsive long-range forces, such clusters exhibit structural and dynamical behavior different from that of homogeneous clusters. The potentially important role of these molecular species in biochemical and medicinal processes is widely known. This work applies the hybrid ab initio methods 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 were performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. Potential design of new medicinal drugs is explored. We will also investigate model and material dependence of the results. AMP program of the National Science Foundation.

  13. 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.

  14. Double-walled silicon nanotubes: an ab initio investigation

    NASA Astrophysics Data System (ADS)

    Lima, Matheus P.

    2018-02-01

    The synthesis of silicon nanotubes realized in the last decade demonstrates multi-walled tubular structures consisting of Si atoms in {{sp}}2 and the {{sp}}3 hybridizations. However, most of the theoretical models were elaborated taking as the starting point {{sp}}2 structures analogous to carbon nanotubes. These structures are unfavorable due to the natural tendency of the Si atoms to undergo {{sp}}3. In this work, through ab initio simulations based on density functional theory, we investigated double-walled silicon nanotubes proposing layered tubes possessing most of the Si atoms in an {{sp}}3 hybridization, and with few {{sp}}2 atoms localized at the outer wall. The lowest-energy structures have metallic behavior. Furthermore, the possibility to tune the band structure with the application of a strain was demonstrated, inducing a metal-semiconductor transition. Thus, the behavior of silicon nanotubes differs significantly from carbon nanotubes, and the main source of the differences is the distortions in the lattice associated with the tendency of Si to make four chemical bonds.

  15. 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.

  16. 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.

  17. Experimental and ab initio structure of BrNO2

    NASA Astrophysics Data System (ADS)

    Kwabia Tchana, F.; Orphal, J.; Kleiner, I.; Rudolph, H. D.; Willner, H.; Garcia, P.; Bouba, O.; Demaison, J.; Redlich, B.

    The ν2 fundamental bands of different isotopomers of BrNO2 (79Br15N16O2, 81Br15N16O2, 79Br14N18O2 and 79Br14N16O18O) located around 13 µm were recorded using high-resolution Fourier transform infrared spectrometry. More than 8000 lines of all these isotopomers were reproduced using a Watson-type A-reduced Hamiltonian with a root-mean-square deviation of better than 7 × 10-4 cm-1 for the four isotopomers. Rotational and centrifugal distortion constants for the ν2 = 1 states as well as for the vibrational ground states of these isotopomers were determined. For the first time, an analysis of the ground-state rotational constants obtained in this study combined with the constants obtained in our previous work on the ν2 bands of 79Br14N16O2 and 81Br14N16O2 has allowed us to calculate the rm structure of nitryl bromide. The structural parameters obtained were rm(Br-N) = 2.0118(16) Å, rm(N-O) = 1.1956(12) Å and α(O-N-O) = 131.02(12) Å. A new ab initio structure of nitryl bromide calculated at the CCSD(T)/SDB-aug-cc-pVQZ level of theory is presented and was found to be in fair agreement with the experimental structure.

  18. Ab initio calculations of the absorption spectrum of chalcone

    NASA Astrophysics Data System (ADS)

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

    1999-03-01

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

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

    SciTech Connect

    Donchev, Alexander G.

    2007-10-15

    This paper reports ab initio calculations of rare gas (RG=Kr, Ar, Ne, and He) dimer quadrupoles at the second order of Moeller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG{sub 2} quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG{sub 2}more » quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG{sub 3} quadrupoles is discussed.« less

  20. Ab initio thermodynamic results for warm dense matter

    NASA Astrophysics Data System (ADS)

    Bonitz, Michael

    2016-10-01

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

  1. 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.

  2. Carbene-aerogen bonds: an ab initio study

    NASA Astrophysics Data System (ADS)

    Esrafili, Mehdi D.; Sabouri, Ayda

    2017-04-01

    Through the use of ab initio calculations, the possibility of formation of σ-hole interaction between ZO3 (Z = Ar, Kr and Xe) and carbene species is investigated. Since singlet carbenes show a negative electrostatic potential on their divalent carbon atom, they can favourably interact with the positive electrostatic potential generated by the σ-hole of Z atom of ZO3. The characteristic of this interaction, termed as 'carbene-aerogen' bond, is analysed in terms of geometric, interaction energies and electronic features. The energy decomposition analysis indicates that for all complexes analysed here, the electrostatic energy is more negative than the polarisation or dispersion energy term. According to the electron density analysis, some partial covalent character can be ascribed to XeṡṡṡC interactions. In addition, the carbene-aerogen bond exhibits cooperative effects with the HṡṡṡO hydrogen-bonding interaction in ternary complexes where both interactions coexist. For a given carbene, the amount of these cooperative effects increases with the size of the Z atom. The results obtained in this work may be helpful for the extension and future application of σ-hole intermolecular interactions as well as coordination chemistry.

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

    NASA Astrophysics Data System (ADS)

    Peeters, Anik

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

  4. Physical properties of molybdenum monoboride: Ab-initio study

    NASA Astrophysics Data System (ADS)

    Rajpoot, Priyanka; Rastogi, Anugya; Verma, U. P.

    2018-02-01

    The Ab initio investigations on structural, electronic, optical and thermal properties of MoB have been reported using full potential linearised-augmented plane wave method within the framework of density functional theory. The exchange and correlation potentials were calculated using the Perdew-Burke-Ernzerhof-Sol generalised gradient approximation. The calculated equilibrium lattice constants and cell volume are in excellent agreement with the experimental results as compared to the available theoretical data. Electronic band structure shows that MoB is metallic in nature. From the partial densities of states of MoB it has been found that major contribution on the Fermi level is due to Mo-4d states. Among the reported optical parameters the large value of reflectivity at low energy shows that MoB can be used as a coating material in IR region. Maximum absorption in extreme UV region shows that it can be used in production of electricity through solar power in space vehicles. Various thermal properties have been calculated in a wide temperature range at high pressures. Change in thermal expansion coefficient with respect to temperature shows that anharmonic effect in MoB is very weak at high temperature. The optical and thermal properties of MoB are presented for the first time in this work.

  5. 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.

  6. Ab initio calculations of ionic hydrocarbon compounds with heptacoordinate carbon.

    PubMed

    Wang, George; Rahman, A K Fazlur; Wang, Bin

    2018-04-25

    Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C 6 (CH 3 ) 6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C 7 H 7 ) 3+ , in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C 8 H 8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage. Graphical abstract Possible structural transformations of stable configurations of (C 7 H 7 ) 3+ , which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

  7. Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

    PubMed

    Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay

    2005-12-01

    Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

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

    NASA Technical Reports Server (NTRS)

    Senese, Fredrick; Ake, Robert

    1992-01-01

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

  9. Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

    1997-07-01

    Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

  10. Ab Initio Computation of Dynamical Properties: Pressure Broadening

    NASA Astrophysics Data System (ADS)

    Wiesenfeld, Laurent; Drouin, Brian

    2014-06-01

    Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into

  11. Machine Learning Force Field Parameters from Ab Initio Data

    SciTech Connect

    Li, Ying; Li, Hui; Pickard, Frank C.

    Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor duringmore » the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.« less

  12. Optical properties of highly compressed polystyrene: An ab initio study

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Collins, L. A.; Colgan, J. P.; Goncharov, V. N.; Kilcrease, D. P.

    2017-10-01

    Using all-electron density functional theory, we have performed an ab initio study on x-ray absorption spectra of highly compressed polystyrene (CH). We found that the K -edge shifts in strongly coupled, degenerate polystyrene cannot be explained by existing continuum-lowering models adopted in traditional plasma physics. To gain insights into the K -edge shift in warm, dense CH, we have developed a model designated as "single mixture in a box" (SMIAB), which incorporates both the lowering of the continuum and the rising of the Fermi surface resulting from high compression. This simple SMIAB model correctly predicts the K -edge shift of carbon in highly compressed CH in good agreement with results from quantum molecular dynamics (QMD) calculations. Traditional opacity models failed to give the proper K -edge shifts as the CH density increased. Based on QMD calculations, we have established a first-principles opacity table (FPOT) for CH in a wide range of densities and temperatures [ρ =0.1 -100 g /c m3 and T =2000 -1 000 000 K ]. The FPOT gives much higher Rosseland mean opacity compared to the cold-opacity-patched astrophysics opacity table for warm, dense CH and favorably compares to the newly improved Los Alamos atomic model for moderately compressed CH (ρCH≤10 g /c m3 ), but remains a factor of 2 to 3 higher at extremely high densities (ρCH≥50 g /c m3 ). We anticipate the established FPOT of CH will find important applications to reliable designs of high-energy-density experiments. Moreover, the understanding of K -edge shifting revealed in this study could provide guides for improving the traditional opacity models to properly handle the strongly coupled and degenerate conditions.

  13. Optical properties of highly compressed polystyrene: An ab initio study

    SciTech Connect

    Hu, S. X.; Collins, L. A.; Colgan, J. P.

    Using all-electron density functional theory, we have performed an ab initio study on x ray absorption spectra of highly compressed polystyrene (CH). Here, we found that the K-edge shifts in strongly coupled, degenerate polystyrene cannot be explained by existing continuum-lowering models adopted in traditional plasma physics. To gain insights into the K edge shift in warm, dense CH, we have developed a model designated as “single-mixture-in-a-box” (SMIAB), which incorporates both the lowering of continuum and the rising of Fermi surface resulting from high compression. This simple SMIAB model correctly predicts the K-edge shift of carbon in highly compressed CH inmore » good agreement with results from quantum-molecular-dynamics (QMD) calculations. Traditional opacity models failed to give the proper K-edge shifts as the CH density increased. Based on QMD calculations, we have established a first-principles opacity table (FPOT) for CH in a wide range of densities and temperatures [p = 0.1 to 100 g/cm 3 and T = 2000 to 1,000,000 K]. The FPOT gives much higher Rosseland mean opacity compared to the cold-opacity–patched astrophysics opacity table for warm, dense CH and favorably compares to the newly improved Los Alamos ATOMIC model for moderately compressed CH (pCH ≤10 g/cm 3) but remains a factor of 2 to 3 higher at extremely high densities (pCH ≥ 50 g/cm 3). We anticipate the established FPOT of CH will find important applications to reliable designs of high-energy-density experiments. Moreover, the understanding of K-edge shifting revealed in this study could provide guides for improving the traditional opacity models to properly handle the strongly coupled and degenerate conditions.« less

  14. Optical properties of highly compressed polystyrene: An ab initio study

    DOE PAGES

    Hu, S. X.; Collins, L. A.; Colgan, J. P.; ...

    2017-10-16

    Using all-electron density functional theory, we have performed an ab initio study on x ray absorption spectra of highly compressed polystyrene (CH). Here, we found that the K-edge shifts in strongly coupled, degenerate polystyrene cannot be explained by existing continuum-lowering models adopted in traditional plasma physics. To gain insights into the K edge shift in warm, dense CH, we have developed a model designated as “single-mixture-in-a-box” (SMIAB), which incorporates both the lowering of continuum and the rising of Fermi surface resulting from high compression. This simple SMIAB model correctly predicts the K-edge shift of carbon in highly compressed CH inmore » good agreement with results from quantum-molecular-dynamics (QMD) calculations. Traditional opacity models failed to give the proper K-edge shifts as the CH density increased. Based on QMD calculations, we have established a first-principles opacity table (FPOT) for CH in a wide range of densities and temperatures [p = 0.1 to 100 g/cm 3 and T = 2000 to 1,000,000 K]. The FPOT gives much higher Rosseland mean opacity compared to the cold-opacity–patched astrophysics opacity table for warm, dense CH and favorably compares to the newly improved Los Alamos ATOMIC model for moderately compressed CH (pCH ≤10 g/cm 3) but remains a factor of 2 to 3 higher at extremely high densities (pCH ≥ 50 g/cm 3). We anticipate the established FPOT of CH will find important applications to reliable designs of high-energy-density experiments. Moreover, the understanding of K-edge shifting revealed in this study could provide guides for improving the traditional opacity models to properly handle the strongly coupled and degenerate conditions.« less

  15. 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.

  16. Ab initio kinetics of gas phase decomposition reactions.

    PubMed

    Sharia, Onise; Kuklja, Maija M

    2010-12-09

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

  17. Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

    PubMed

    Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

    2015-12-14

    The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

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

    PubMed

    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 CF3X-B that involve one trifluorohalomethane CF3X (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 (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). 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.

  19. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

    PubMed

    Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

    2018-01-01

    A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  20. Ab initio molecular dynamics simulation of LiBr association in water

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei; Philpott, Michael R.

    2000-12-01

    A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

  1. 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

  2. Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

    NASA Astrophysics Data System (ADS)

    Mishra, S. B.; Nanda, B. R. K.

    2017-05-01

    Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

  3. Many-body optimization using an ab initio monte carlo method.

    PubMed

    Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

    2003-01-01

    Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

  4. 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.

  5. An ab initio study of the conformational energy map of acetylcholine

    NASA Astrophysics Data System (ADS)

    Segall, M. D.; Payne, M. C.; Boyes, R. N.

    An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

  6. Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.

    PubMed

    Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

    2013-07-30

    This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. Copyright © 2013 Wiley Periodicals, Inc.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  8. AB INITIO Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

    NASA Astrophysics Data System (ADS)

    Goldman, Nir; Fried, Laurence E.; Mundy, Christopher J.; Kuo, I.-F. William; Curioni, Alessandro; Reed, Evan J.

    2007-12-01

    We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

  9. 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.

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

    PubMed Central

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

    2015-01-01

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

  11. 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.

  12. Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

    NASA Astrophysics Data System (ADS)

    Saieswari, A.; Kumar, Sanjay

    2007-12-01

    An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

  13. 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.

  14. Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

    NASA Astrophysics Data System (ADS)

    Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

    2017-10-01

    We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

  15. Light focusing through a multiple scattering medium: ab initio computer simulation

    NASA Astrophysics Data System (ADS)

    Danko, Oleksandr; Danko, Volodymyr; Kovalenko, Andrey

    2018-01-01

    The present study considers ab initio computer simulation of the light focusing through a complex scattering medium. The focusing is performed by shaping the incident light beam in order to obtain a small focused spot on the opposite side of the scattering layer. MSTM software (Auburn University) is used to simulate the propagation of an arbitrary monochromatic Gaussian beam and obtain 2D distribution of the optical field in the selected plane of the investigated volume. Based on the set of incident and scattered fields, the pair of right and left eigen bases and corresponding singular values were calculated. The pair of right and left eigen modes together with the corresponding singular value constitute the transmittance eigen channel of the disordered media. Thus, the scattering process is described in three steps: 1) initial field decomposition in the right eigen basis; 2) scaling of decomposition coefficients for the corresponding singular values; 3) assembling of the scattered field as the composition of the weighted left eigen modes. Basis fields are represented as a linear combination of the original Gaussian beams and scattered fields. It was demonstrated that 60 independent control channels provide focusing the light into a spot with the minimal radius of approximately 0.4 μm at half maximum. The intensity enhancement in the focal plane was equal to 68 that coincided with theoretical prediction.

  16. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

    PubMed Central

    Hu, Hao; Yang, Weitao

    2013-01-01

    Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

  17. Intermolecular Potentials of Methane Assessed by Second Virial Coefficients, ab Initio Dimer Interaction Energies, and Aggregate Cohesive Energies.

    PubMed

    Ribeiro, Douglas S

    2017-06-01

    This study presents computations of three energy related properties for 26 previously published multisite intermolecular potentials of methane: MM2, MM3, MM2en, MM3en, MM2mc, MM3mc, MM3envir, RMK, OPLS all-atom, MUB-2, AMBER, BOYD, Williams, Sheikh, MG, Tsuzuki, E2-Gay, E4-Gay, MP4exp-6(iii), MP4exp-6(iv), Rowley-A, Rowley-B, TraPPE-EH, Ouyang, CLC, and Chao and three united atom potentials: Saager-Fischer (SF), OPLS united atom, and HFD. The three properties analyzed are the second virial coefficients for 14 temperature points in the range of 110 to 623.15 K, the interaction energies for 12 orientations of the methane dimer as a function of distance followed by a comparison to three ab initio data sets and the cohesive energy of the aggregate of 512 methane molecules. The latter computed energies are correlated to latent heat of evaporation of 11 potentials and are proposed as surrogate approximate parameters for ΔH vap for the studied potentials. The 10 best performing potentials are selected by rms order in each one of the properties and three of them are found to be present simultaneously in the three sets: Tsuzuki, MM3mc, and MM2mc. On the basis of the cohesive energy of the aggregate, a quantitative measure of the anisotropy of the potentials is proposed. The results are discussed on the basis of anisotropy, nonadditivity and ability of the potentials to reproduce ab initio data. It is concluded that the nonadditivity of the pair potentials holds and the available ab initio data did not lead to pair potentials that are cohesive enough to reproduce accurately the second virial coefficients.

  18. 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

  19. Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

    NASA Astrophysics Data System (ADS)

    Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

    This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

  20. Vibrational modes in thymine molecule from an ab initio MO calculation

    NASA Astrophysics Data System (ADS)

    Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ueda, Toyotoshi; Ushizawa, Koichi; Ito, Gen; Kumakura, Akiko; Tsuboi, Masamichi

    1997-03-01

    Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

  1. Ab initio theory of noble gas atoms in bcc transition metals

    DOE PAGES

    Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; ...

    2018-01-01

    Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe).

  2. 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.

  3. Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

    NASA Astrophysics Data System (ADS)

    Vlasiuk, Maryna; Sadus, Richard J.

    2017-06-01

    The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

  4. One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

    ERIC Educational Resources Information Center

    Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

    2016-01-01

    The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…

  5. 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…

  6. Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

    PubMed Central

    Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

    2017-01-01

    Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

  7. Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

    PubMed

    Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

    2017-05-01

    Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  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. Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

    PubMed

    Vlasiuk, Maryna; Sadus, Richard J

    2017-06-28

    The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

  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. 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.

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

    PubMed

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

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

  13. Understanding ionic conductivity trends in polyborane solid electrolytes from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Varley, Joel; Kweon, Kyoung; Mehta, Prateek; Shea, Patrick; Heo, Tae Wook; Stavila, Vitalie; Udovic, Terrence; Wood, Brandon

    Polyborane salts based on B12H122- , B10H102- , and their carboborane counterparts CB11H12- and CB9H10- demonstrate extraordinary Li and Na superionic conductivity that make them attractive as electrolytes in all-solid-state batteries. Their rich chemical and structural diversity creates a versatile design space that could be used to optimize materials with even higher conductivity at lower temperatures; however, many mechanistic details remain enigmatic, including reasons why certain modifications lead to improved performance. Here, we use extensive ab initio molecular dynamics simulations to broadly explore the dependence of ionic conductivity on cation/anion pair combinations for Li and Na polyborane salts. Further simulations based on Li2B12H12 as a model system are used to probe the additional influence of local perturbations, including modifications to chemistry, stoichiometry, and composition. Carbon doping, anion alloying, and cation off-stoichiometry are found to be favorable because they introduce intrinsic disorder, which facilitates local deviations from the expected cation population. Anion reorientations are also discovered to be critical for conduction, with benefits associated with lattice expansion traceable to the facilitation of anion rotation at larger volumes. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  14. Initial hydration processes of magnesium chloride: size-selected anion photoelectron spectroscopy and ab initio calculations.

    PubMed

    Feng, Gang; Liu, Cheng-Wen; Zeng, Zhen; Hou, Gao-Lei; Xu, Hong-Guang; Zheng, Wei-Jun

    2017-06-14

    To understand the initial hydration processes of MgCl 2 , we measured photoelectron spectra of MgCl 2 (H 2 O) n - (n = 0-6) and conducted ab initio calculations on MgCl 2 (H 2 O) n - and their neutral counterparts up to n = 7. A dramatic drop in the vertical detachment energy (VDE) was observed upon addition of the first water molecule to bare MgCl 2 - . This large variation in VDE can be associated with the charge-transfer-to-solvent (CTTS) effect occurring in the MgCl 2 (H 2 O) n - clusters, as hydration induces transfer of the excess electron of MgCl 2 - to the water molecules. Investigation of the separation of Cl - -Mg 2+ ion pair shows that, in MgCl 2 (H 2 O) n - anions, breaking of the first Mg-Cl bond occurs at n = 4, while breaking of the second Mg-Cl bond takes place at n = 6. For neutral MgCl 2 (H 2 O) n clusters, breaking of the first Mg-Cl bond starts at n = 7.

  15. Design of two-photon molecular tandem architectures for solar cells by ab initio theory

    DOE PAGES

    Ornso, Kristian B.; Garcia-Lastra, Juan M.; De La Torre, Gema; ...

    2015-03-04

    An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range. Three different architectures are considered: the first two involve a complex consisting of two dye molecules with appropriately matched frontier orbitals, connected by a molecular diode. Optimized combinations of dye molecules are determined by taking advantage of our computational database of the structural and energetic properties of several thousand porphyrin dyes. The third design is amore » molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices, such as the synthesis of the tandem molecules and potential loss mechanisms, are addressed.« less

  16. Water trimer torsional spectrum from accurate ab initio and semiempirical potentials

    NASA Astrophysics Data System (ADS)

    van der Avoird, Ad; Szalewicz, Krzysztof

    2008-01-01

    The torsional levels of (H2O)3 and (D2O)3 were calculated in a restricted dimensionality (three-dimensional) model with several recently proposed water potentials. Comparison with the experimental data provides a critical test, not only of the pair interactions that have already been probed on the water dimer spectra, but also of the nonadditive three-body contributions to the potential. The purely ab initio CC-pol and HBB potentials that were previously shown to yield very accurate water dimer levels, also reproduce the trimer levels well when supplemented with an appropriate three-body interaction potential. The TTM2.1 potential gives considerably less good agreement with experiment. Also the semiempirical VRT(ASP-W)III potential, fitted to the water dimer vibration-rotation-tunneling levels, gives substantial disagreement with the measured water trimer levels, which shows that the latter probe the potential for geometries other than those probed by the dimer spectrum. Although the three-body nonadditive interactions significantly increase the stability of the water trimer, their effect on the torsional energy barriers and vibration-tunneling frequencies is less significant.

  17. Ionization dynamics of the water trimer: A direct ab initio MD study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Takada, Tomoya

    2013-03-01

    Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ˜15 fs after the ionization). In complex channel, an ion-radical contact pair (H3O+-OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50-100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.

  18. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.

    2016-07-01

    Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and

  19. 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., E-mail: sdchao@spring.iam.ntu.edu.tw

    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-pairmore » (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.« less

  20. AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

    NASA Astrophysics Data System (ADS)

    Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

    2013-03-01

    The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

  1. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA.

    PubMed

    Orimoto, Yuuichi; Aoki, Yuriko

    2016-07-14

    An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between "choose-maximum" (choose a base pair giving the maximum β for each step) and "choose-minimum" (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

  2. Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA

    SciTech Connect

    Orimoto, Yuuichi, E-mail: orimoto.yuuichi.888@m.kyushu-u.ac.jp; Aoki, Yuriko; Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012

    An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method,more » and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (β) in DNA, a substantial difference was observed depending on optimization conditions between “choose-maximum” (choose a base pair giving the maximum β for each step) and “choose-minimum” (choose a base pair giving the minimum β). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.« less

  3. 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

  4. 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.

  5. Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

    NASA Astrophysics Data System (ADS)

    Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

    2018-05-01

    Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

  6. Crossover of cation partitioning in olivines: a combination of ab initio and Monte Carlo study

    NASA Astrophysics Data System (ADS)

    Chatterjee, Swastika; Bhattacharyya, Sirshendu; Sengupta, Surajit; Saha-Dasgupta, Tanusri

    2011-04-01

    We report studies based on a combination of ab initio electronic structure and Monte Carlo (MC) technique on the problem of cation partitioning among inequivalent octahedral sites, M1 and M2 in mixed olivines containing Mg2+ and Fe2+ ions. Our MC scheme uses interactions derived out of ab initio, density functional calculations carried out on measured crystal structure data. Our results show that there is no reversal of the preference of Fe for M1 over M2 as a function of temperature. Our findings do not agree with the experimental findings of Redfern et al. (Phys Chem Miner 27:630-637, 2000), but are in agreement with those of Heinemann et al. (Eur J Mineral 18:673-689, 2006) and Morozov et al. (Eur J Mineral 17:495-500, 2005).

  7. A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

    An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

  8. 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.

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

    SciTech Connect

    Sharma, Nalini, E-mail: nalini-2808@yahoo.co.in; Ahluwalia, P. K.; Thakur, Anil

    2016-05-23

    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 (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}Pb{sub 10}) 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 localmore » arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.« less

  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. 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.

  12. {bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

    SciTech Connect

    Richardson, S.L.; Martins, J.L.

    1998-12-01

    In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

  13. 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 factormore » shows the presence of liquid state in the considered alloys.« less

  14. 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.

  15. Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

    PubMed

    Aalbergsjø, Siv G; Pauwels, Ewald; Van Yperen-De Deyne, Andy; Van Speybroeck, Veronique; Sagstuen, Einar

    2014-08-28

    As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  17. Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

    PubMed

    Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

    2011-12-14

    A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

  18. Ab initio simulations of iron-nickel alloys at Earth's core conditions

    NASA Astrophysics Data System (ADS)

    Côté, Alexander S.; Vočadlo, Lidunka; Brodholt, John P.

    2012-09-01

    We report ab initio density functional theory calculations on iron-nickel (FeNi) alloys at conditions representative of the Earth's inner core. We test different concentrations of Ni, up to ∼39 wt% using ab initio lattice dynamics, and investigate the thermodynamic and vibrational stability of the three candidate crystal structures (bcc, hcp and fcc). First of all, at inner core pressures, we find that pure Fe transforms from the hcp to the fcc phase at around 6000 K. Secondly, in agreement with low pressure experiments on Fe-Ni alloys, we find the fcc structure is stabilised by the incorporation of Ni under core pressures and temperatures. Our results show that the fcc structure may, therefore, be stable under core conditions depending on the temperature in the inner core and the Ni content. Lastly, we find that within the quasi-harmonic approximation, there is no stability field for FeNi alloys in the bcc structure under core conditions.

  19. 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.

  20. Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

    NASA Astrophysics Data System (ADS)

    Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

    2018-04-01

    The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

  1. An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

    NASA Astrophysics Data System (ADS)

    Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

    2018-04-01

    The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

  2. Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

    PubMed

    Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

    2017-12-01

    α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

  3. Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

    PubMed

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

    2009-10-29

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

  4. An Automated Ab Initio Framework for Identifying New Ferroelectrics

    NASA Astrophysics Data System (ADS)

    Smidt, Tess; Reyes-Lillo, Sebastian E.; Jain, Anubhav; Neaton, Jeffrey B.

    Ferroelectric materials have a wide-range of technological applications including non-volatile RAM and optoelectronics. In this work, we present an automated first-principles search for ferroelectrics. We integrate density functional theory, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known and proposed ferroelectrics. We screen thousands of candidates using symmetry relations between nonpolar and polar structure pairs. We use two search strategies 1) polar-nonpolar pairs with the same composition and 2) polar-nonpolar structure type pairs. Results are automatically parsed, stored in a database, and accessible via a web interface showing distortion animations and plots of polarization and total energy as a function of distortion. We benchmark our results against experimental data, present new ferroelectric candidates found through our search, and discuss future work on expanding this search methodology to other material classes such as anti-ferroelectrics and multiferroics.

  5. Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

    PubMed

    Exner, Kai S; Over, Herbert

    2017-05-16

    Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a

  6. Ab initio theory of the N2V defect in diamond for quantum memory implementation

    NASA Astrophysics Data System (ADS)

    Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam

    2017-10-01

    The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.

  7. Atomistic and Ab Initio Calculations or Ternary II-IV-V2 Semiconductors

    DTIC Science & Technology

    1999-12-07

    consisting of two- and three-body terms is developed reproducing crystal lattice constants, elastic and dielectric constants very well. The calculated...the lattice . This difference may well be due to defect-induced lattice distortion which plays a key role in stabilizing the hole states in the... lattice . 15. SUBJECT TERMS Chalcopyrites, Defects, Atomistic and AB Initio Calculations 16. SECURITY CLASSIFICATION OF: a. REPORT u b. ABSTRACT U

  8. Ab initio calculations of potential energy curves of Hg/sub 2/ and TlHg

    SciTech Connect

    Celestino, K.C.; Ermler, W.C.

    1984-08-15

    Potential energy curves for electronic states of Hg/sub 2/ and TlHg are presented and analyzed. They are derived using large scale configuration interaction procedures for the valence electrons, with the core electrons represented by ab initio relativistic effective potentials. The effect of spin-orbit coupling are investigated for the low-lying excimer states. It is determined that neither system possesses strongly bound electronic states for which transitions to the repulsive ground states are optically allowed.

  9. Ab initio SCF calculations on the potential energy surface of potassium cyanide (KCN)

    NASA Astrophysics Data System (ADS)

    Wormer, Paul E. S.; Tennyson, Jonathan

    1981-08-01

    The potential energy surface of KCN has been generated by ab initio SCF calculations in the region of equilibrium bond distances. An analytic representation of the surface is presented. The calculations show that the bonding between K and CN is ionic, and that the structure of KCN is triangular, which confirms recent experimental findings. The computed geometry is &KCN = 62.4°, rCK = 5.492a0, and rCN = 2.186a0.

  10. Ab initio optical potentials and nucleon scattering on medium mass nuclei

    NASA Astrophysics Data System (ADS)

    Idini, A.; Barbieri, C.; Navrátil, P.

    2018-03-01

    We show first results for the elastic scattering of neutrons off oxygen and calcium isotopes obtained from ab initio optical potentials. The potential is derived using self-consistent Green’s function theory (SCGF) with the saturating chiral interaction NNLOsat. Calculations are compared to available scattering data and show that it is possible to reproduce low energy scattering observables in medium mass nuclei from first principles.

  11. Ab initio calculations for the elastic properties of magnesium under pressure

    NASA Astrophysics Data System (ADS)

    Sin'Ko, G. V.; Smirnov, N. A.

    2009-09-01

    Results of ab initio calculations of the elastic constants for the hcp, bcc, double hcp (dhcp), and fcc magnesium in a wide range of pressures are presented. The calculated elastic constants are compared with available experimental and theoretical data. We discuss the effect of the electron topological transition that occurs when the hcp structure is compressed on results of calculations and consider possibility of observing the hcp→dhcp transition on the magnesium Hugoniot.

  12. Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

    PubMed

    Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

    2018-01-01

    Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

  13. Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

    PubMed Central

    Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

    2018-01-01

    Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

  14. Decohesion models informed by first-principles calculations: The ab initio tensile test

    NASA Astrophysics Data System (ADS)

    Enrique, Raúl A.; Van der Ven, Anton

    2017-10-01

    Extreme deformation and homogeneous fracture can be readily studied via ab initio methods by subjecting crystals to numerical "tensile tests", where the energy of locally stable crystal configurations corresponding to elongated and fractured states are evaluated by means of density functional method calculations. The information obtained can then be used to construct traction curves of cohesive zone models in order to address fracture at the macroscopic scale. In this work, we perform an in depth analysis of traction curves and how ab initio calculations must be interpreted to rigorously parameterize an atomic scale cohesive zone model, using crystalline Ag as an example. Our analysis of traction curves reveal the existence of two qualitatively distinct decohesion criteria: (i) an energy criterion whereby the released elastic energy equals the energy cost of creating two new surfaces and (ii) an instability criterion that occurs at a higher and size independent stress than that of the energy criterion. We find that increasing the size of the simulation cell renders parts of the traction curve inaccessible to ab initio calculations involving the uniform decohesion of the crystal. We also find that the separation distance below which a crack heals is not a material parameter as has been proposed in the past. Finally, we show that a large energy barrier separates the uniformly stressed crystal from the decohered crystal, resolving a paradox predicted by a scaling law based on the energy criterion that implies that large crystals will decohere under vanishingly small stresses. This work clarifies confusion in the literature as to how a cohesive zone model is to be parameterized with ab initio "tensile tests" in the presence of internal relaxations.

  15. Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

    SciTech Connect

    Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

    2017-10-27

    Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the numbermore » of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.« less

  16. Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

    PubMed

    Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

    2016-10-26

    For CO and N 2 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.

  17. 7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

    SciTech Connect

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

    2006-10-12

    There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) predicts low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. We present here a brief overview of the first steps taken toward nuclear reaction applications. In particular, we discuss our calculation of the {sup 7}Be(p,{gamma}){sup 8}B S-factor. We also present our first results of the {sup 3}He({alpha},{gamma}){sup 7}Be S-factor and of the S-factor of the mirror reaction {sup 3}H({alpha},{gamma}){sup 7}Li.more » The {sup 7}Be(p,{gamma}){sup 8}B and {sup 3}He({alpha},{gamma}){sup 7}Be reactions correspond to the most important uncertainties in solar model predictions of neutrino fluxes.« less

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

    SciTech Connect

    Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

    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 ismore » 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.« less

  19. Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

    NASA Astrophysics Data System (ADS)

    Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

    2015-09-01

    The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

  20. Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

    PubMed

    Greenberg, Ido; Shkolnisky, Yoel

    2017-11-01

    We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

    PubMed

    Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

    2018-01-18

    Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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 tomore » 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.« less

  7. Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

    PubMed

    Neelamraju, S; Schön, J C; Doll, K; Jansen, M

    2012-01-21

    We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential.

  8. Collisional Dissociation of CO: ab initio Potential Energy Surfaces and Quasiclassical Trajectory Rate Coefficients

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Jaffe, Richard L.; Chaban, Galina M.

    2016-01-01

    We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.

  9. Ab initio Study of Naptho-Homologated DNA Bases

    SciTech Connect

    Sumpter, Bobby G; Vazquez-Mayagoitia, Alvaro; Huertas, Oscar

    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-Crickmore » 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.« less

  10. Ab initio study of naphtho-homologated DNA bases.

    PubMed

    Vazquez-Mayagoita, Alvaro; Huertas, Oscar; Fuentes-Cabrera, Miguel; Sumpter, Bobby G; Orozco, Modesto; Luque, F Javier

    2008-02-21

    Naphtho-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 naphtho-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 forms of naphtho-thymine (yyT) and naphtho-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 naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-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 naphtho-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.

  11. An Ab Initio Study of CuCO

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1994-01-01

    Modified coupled-pair functional (MCPF) calculations and coupled cluster singles and doubles calculations, which include a perturbational estimate of the connected triples [CCSD(T)], yield a bent structure for CuCO, thus, supporting the prediction of a nonlinear structure based on density functional (DF) calculations. Our best estimate for the binding energy is 4.9 +/- 1.4 kcal/mol; this is in better agreement with experiment (6.0 +/- 1.2 kcal/mol) than the DF approach which yields a value (19.6 kcal/mol) significantly larger than experiment.

  12. An ab initio study on the effect of iron atom junction on transport characteristics of carbon-silicon mixed chain

    NASA Astrophysics Data System (ADS)

    Hu, Wei; Zhou, Qinghua; Liu, Wenhua; Liang, Yan; Wang, Tao; Wan, Haiqing

    2018-04-01

    The effect of iron atom junction on transport characteristics of carbon-silicon mixed chain has been studied from an ab initio study. At zero bias, the Fe(CSi)n system appears to be the decrease of the conductance as the number of the Si-C pairs in the chain increases (n changes). When n > 5, the conductance tends to zero. These changes are independent of the transferring charge of the system, depending on the coupling of the electrodes and the central region. Under bias, the higher the bias voltage, the bigger the transmission coefficient of the system, and the transmission peak moves closer to the Fermi level. The I-V curves of Fe(CSi)2 and Fe (CSi)3 are linear, showing the behavior of metal resistance.

  13. AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid Sb from 913 K to 1193 K

    NASA Astrophysics Data System (ADS)

    Hao, Qing-Hai; Li, Y. D.; Kong, Xiang-Shan; Liu, C. S.

    2013-02-01

    Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4 and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb. There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973-1023 K.

  14. Structural and electronic transport properties of compound forming HgPb liquid alloy using ab-initio pseudopotential

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    The electrical resistivity of compound forming liquid alloy HgPb is studied as a function of concentration. Hard sphere diameters of Hg and Pb are obtained through the inter-ionic pair potential evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. The concentration dependence in resistivity occurs due to preferential ordering of unlike atoms as nearest neighbours with help of complex formation model. Though the compound HgiPbi as per structure peaks is found to be less stable. However it contributes significantly to resistivity as compared to bare ions.

  15. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    NASA Astrophysics Data System (ADS)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  16. Ab initio molecular dynamics of the reactivity of vitamin C toward hydroxyl and HO₂/O⁻₂ radicals.

    PubMed

    Lespade, Laure

    2017-11-21

    Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and [Formula: see text] radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of [Formula: see text] radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton. Graphical Abstract Reactivity of vitamin C toward hydroxyl and [Formula: see text] radicals.

  17. Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava; Hanagud, Sathya

    2009-06-01

    Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

  18. 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.

  19. Stereoelectronic control in peptide bond formation. Ab initio calculations and speculations on the mechanism of action of serine proteases.

    PubMed Central

    Gorenstein, D G; Taira, K

    1984-01-01

    Ab initio molecular orbital calculations have been performed on the reaction profile for the addition/elimination reaction between ammonia and formic acid, proceeding via a tetrahedral intermediate: NH3 + HCO2H----H2NCH(OH)2----NH2CHO + H2O. Calculated transition state energies for the first addition step of the reaction revealed that a lone pair on the oxygen of the OH group, which is antiperiplanar to the attacking nitrogen, stabilized the transition state by 3.9 kcal/mol, thus supporting the hypothesis of stereoelectronic control for this reaction. In addition, a secondary, counterbalancing stereoelectronic effect stabilizes the second step, water elimination, transition state by 3.1 kcal/mol if the lone pair on the leaving water oxygen is not antiperiplanar to the C-N bond. The best conformation for the transition states was thus one with a lone pair antiperiplanar to the adjacent scissile bond and also one without a lone-pair orbital on the scissile bond oxygen or nitrogen antiperiplanar to the adjacent polar bond. The significance of these stereoelectronic effects for the mechanism of action of serine proteases is discussed. PMID:6394065

  20. Ab initio studies of isolated boron substitutional defects in graphane

    NASA Astrophysics Data System (ADS)

    Mapasha, R. E.; Chetty, N.

    2017-10-01

    We have systematically studied energetics, structural and electronic properties of different configurations of the B atoms substituting C-H pairs located on a single hexagonal ring in a graphane system using the first-principles density functional theory (DFT). A total number of 12 distinct B dopants configurations were identified and characterized. Based on the formation energy analysis, we found that relative stability of B dopants depends greatly on the defect configurations. Our results suggest that the B substitutions prefer to be distributed randomly but avoiding the formation of homo-elemental B-B bonds in a graphane system, at any concentration. Generally, the values of band gap decrease as the number of B dopants increases, but the low energy configurations have large band gaps compared to those that have homo-elemental bonds. As a result, the band gap of graphane can be fine tuned through the change in the structural arrangement of B atoms. The adequate control of the electronic structure of graphane through doping should be essential for technological device applications.

  1. Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path.

    PubMed

    Varandas, A J C

    2011-05-28

    The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative

  2. Ab initio study of the ground and excited electronic states of the methyl radical

    PubMed Central

    Zanchet, A.; Bañares, L.; Senent, M. L.; García-Vela, A.

    2016-01-01

    The ground and some excited electronic states of the methyl radical have been characterized by means of highly correlated ab intio techniques. The specific excited states investigated are those involved in the dissociation of the radical, namely the 3s and 3pz Rydberg states, and the A1 and B1 valence states crossing them, respectively. The C-H dissociative coordinate and the HCH bending angle were considered in order to generate the first two-dimensional ab initio representation of the potential surfaces of the above electronic states of CH3, along with the nonadiabatic couplings between them. Spectroscopic constants and frequencies calculated for the ground and bound excited states agree well with most of the available experimental data. Implications of the shape of the excited potential surfaces and couplings for the dissociation pathways of CH3 are discussed in the light of recent experimental results for dissociation from low-lying vibrational states of CH3. Based on the ab initio data some predictions are made regarding methyl photodissociation from higher initial vibrational states. PMID:27892569

  3. Conformational and Structural Studies of Isopropylamine from Temperature Dependent Raman Spectra of Xenon Solutions and {AB INITIO} Calculations

    NASA Astrophysics Data System (ADS)

    Klaassen, Joshua J.; Darkhalil, Ikhlas D.; Durig, James R.

    2012-06-01

    The Raman and infrared spectra (4000 to 50 cm-1) of the gas, liquid or solution, and solid have been recorded of isopropylamine, (CH3)2CHNH2. Variable temperature (-50 to -100oC) studies of the Raman spectra (3500 to 100 cm-1) dissolved in liquid xenon have been carried out. From these data, both the {trans} and {gauche} conformers have been identified and their relative stability obtained. The enthalpy difference has been determined from 20 band pairs at 6 temperatures to be 113 +/- 11 cm-1 (1.35 +/- 0.13 kJ mol-1) with the {trans} conformer the more stable form. The percentage of the {gauche} conformer is estimated to be 54 +/- 1 percent at ambient temperature. The conformational stabilities have been predicted from {ab initio} calculations utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. By utilizing previously reported microwave rotational constants along with {ab initio} MP2(full)/6-311+G(d,p) predicted structural values, adjusted r0 parameters have been obtained for the {trans} conformer. The determined heavy atom and NH2 distances in angstroms are C-C = 1.530(3), C-N = 1.465(3), N-H = 1.019(3) and angles in degrees NCC = 108.9(5), CCC = 111.0(5), HNC = 110.3(5). The structural parameters for the {gauche} conformer were estimated by using the same adjustment differences to the {gauche} form as those obtained for the corresponding {trans} parameters. Vibrational assignments have been provided for the observed bands for both conformers which are supported by MP2(full)/6-31G(d) {ab initio} calculations to predict harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are discussed and compared to the corresponding properties of some related molecules.

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

    PubMed

    Zhang, Dawei; Liu, Chungen

    2016-04-12

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  6. Using Ab-Initio Calculations to Appraise Stm-Based - and Kink-Formation Energies

    NASA Astrophysics Data System (ADS)

    Feibelman, Peter J.

    2001-03-01

    Ab-initio total energies can and should be used to test the typically model-dependent results of interpreting STM morphologies. The benefits of such tests are illustrated here by ab-initio energies of step- and kink-formation on Pb and Pt(111) which show that the STM-based values of the kink energies must be revised. On Pt(111), the computed kink-energies for (100)- and (111)-microfacet steps are about 0.25 and 0.18 eV. These results imply a specific ratio of formation energies for the two step types, namely 1.14, in excellent agreement with experiment. If kink-formation actually cost the same energy on the two step types, an inference drawn from scanning probe observations of step wandering,(M. Giesen et al., Surf. Sci. 366, 229(1996).) this ratio ought to be 1. In the case of Pb(111), though computed energies to form (100)- and (111)-microfacet steps agree with measurement, the ab-initio kink-formation energies for the two step types, 41 and 60 meV, are 40-50% below experimental values drawn from STM images.(K. Arenhold et al., Surf. Sci. 424, 271(1999).) The discrepancy results from interpreting the images with a step-stiffness vs. kink-energy relation appropriate to (100) but not (111) surfaces. Good agreement is found when proper account of the trigonal symmetry of Pb(111) is taken in reinterpreting the step-stiffness data.

  7. Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.

    PubMed

    Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

    2009-09-01

    Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. Copyright 2008 Wiley Periodicals, Inc.

  8. A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

    A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easilymore » extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}« less

  9. New insights into mechanistic photoisomerization of ethylene-bridged azobenzene from ab initio multiple spawning simulation.

    PubMed

    Liu, Lihong; Wang, Yating; Fang, Qiu

    2017-02-14

    Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S 1 ), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S 1 relaxation processes, the nonadiabatic transition from S 1 to the ground state (S 0 ) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S 1 → S 0 transition are not distributed in the MECI regions. Once decaying to the S 0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S 0 state. It is the nonergodic behavior of the S 1 and S 0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.

  10. Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

    PubMed Central

    Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

    2012-01-01

    Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

  11. Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

    SciTech Connect

    Holst, Bastian; French, Martin; Redmer, Ronald

    2011-06-15

    Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

  12. Ab initio simulation of particle momentum distributions in high-pressure water

    NASA Astrophysics Data System (ADS)

    Ceriotti, M.

    2014-12-01

    Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.

  13. 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.

  14. 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.

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

    SciTech Connect

    Pal, Soumyadipta, E-mail: soumyadipta.pal@gmail.com; Mahadevan, Priya; Biswas, C.

    2015-06-24

    The trend of site occupation of Co at Ni sites of Ni{sub 2}MnIn system is studied in austenitic phase having L2{sub 1} structure by ab initio density functional theory (DFT) calculation. The Co atoms prefer to be at Ni sites rather than Mn site and are ferromagetically coupled with Ni and Mn. The ground state has tetragonal structure for Ni{sub 1.5}Co{sub 0.5}MnIn and Ni{sub 1.25}Co{sub 0.75}MnIn. The Co tends to form cluster.

  16. The molecular structure and conformation of tetrabromoformaldazine: ab initio and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jeong, Myongho; Kwon, Younghi

    2000-06-01

    Ab initio and density functional theory methods are applied to investigate the molecular structure and conformational nature of tetrabromoformaldazine. The calculations including the effects of the electron correlation at the B3LYP and MP2 levels with the basis set 6-311+G(d) can reproduce the experimental geometrical parameters at the skew conformation. The N-N bond torsional angle φ calculated at the MP2/6-311+G(d) level is found to be closest to the observed angle. The scanning of the potential energy surface suggests that the anti-conformation is at a saddle point corresponding to the transition state.

  17. Ab initio study of energy transfer rates and impact sensitivities of crystalline explosives.

    PubMed

    Bernstein, Jonathan

    2018-02-28

    Impact sensitivities of various crystalline explosives were predicted by means of plane wave-density functional theory calculations. Crystal structures and complete vibrational spectra of TATB, PETN, FOX7, TEX, 14DNI, and β-HMX molecular crystals were calculated. A correlation between the phonon-vibron coupling (which is proportionally related to the energy transfer rate between the phonon manifold and the intramolecular vibrational modes) and impact sensitivities of secondary explosives was found. We propose a method, based on ab initio calculations, for the evaluation of impact sensitivities, which consequently can assist in screening candidates for chemical synthesis of high energetic materials.

  18. Ab initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5-Dinitrobiuret

    DTIC Science & Technology

    2016-03-14

    Journal Article 3. DATES COVERED (From - To) Feb 2015-May 2015 4. TITLE AND SUBTITLE Ab initio Kinetics and Thermal Decomposition Mechanism of 5a...tetrazole-free, nitrogen-rich, energetic compounds. For the first time, the thermal decomposition mechanisms of MNB and DNB have been investigated...potential energy surfaces for thermal decomposition of MNB and DNB were characterized at the RCCSD(T)/cc-pV∞Z//M06-2X/aug- cc-pVTZ level of theory

  19. FTIR cryospectroscopic and ab initio studies of desflurane-dimethyl ether H-bonded complexes.

    PubMed

    Melikova, S M; Rutkowski, K S; Rospenk, M

    2017-09-05

    The IR spectra of mixtures of desflurane and dimethyl ether are studied with the help of FTIR cryospectroscopy in liquefied Kr at T~118-158K. Comparative analysis of the experimental data and results of ab initio calculations show that either of the two C-H groups of desflurane is involved in heterodimer formation of comparable strengths. The blue frequency shift is found for stretching vibrations of those C-H donors which directly participate in H-bond formation. Additionally the complexes are stabilized by weaker contacts between hydrogen atoms of dimethyl ether and fluorine atoms of desflurane. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Ab Initio Calculations of Singlet and Triplet Excited States of Chlorine Nitrate and Nitric Acid

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    Ab initio calculations of vertical excitations to singlet and triplet excited states of chlorine nitrate and nitric acid are reported. The nature of the electronic transitions are examined by decomposing the difference density into the sum of detachment and attachment densities. Counterparts for the three lowest singlet excited states of nitric acid survive relatively unperturbed in chlorine nitrate, while other low-lying singlet states of chlorine nitrate appear to be directly dissociative in the ClO chromophore. These results suggest an assignment of the two main peaks in the experimental chlorine nitrate absorption spectrum. In addition, triplet vertical excitations and the lowest optimized triplet geometries of both molecules are studied.

  1. Stabilization of flat aromatic Si6 rings analogous to benzene: ab initio theoretical prediction.

    PubMed

    Zdetsis, Aristides D

    2007-12-07

    It is shown by ab initio calculations, based on density functional (DFT/B3LYP), and high level coupled-cluster [CCSD(T)] and quadratic CI [QCISD(T)] methods, that flat aromatic silicon structures analogous to benzene (C6H6) can be stabilized in the presence of lithium. The resulting planar Si6Li6 structure is both stable and aromatic, sharing many key characteristics with benzene. To facilitate possible synthesis and characterization of these species, routes of formation with high exothermicity are suggested and several spectral properties (including optical absorption, infrared, and Raman) are calculated.

  2. Ab-initio study of several static and dynamic properties of liquid palladium and platinum

    NASA Astrophysics Data System (ADS)

    González, L. E.; González, D. J.; Molla, Mohammad Riazuddin; Ahmed, A. Z. Ziauddin; Bhuiyan, G. M.

    2017-08-01

    We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.

  3. Ab initio predictions on the rotational spectra of carbon-chain carbene molecules.

    PubMed

    Maluendes, S A; McLean, A D

    1992-12-18

    We predict rotational constants for the carbon-chain molecules H2C=(C=)nC, n=3-8, using ab initio computations, observed values for the earlier members in the series, H2CCC and H2CCCC with n=1 and 2, and empirical geometry corrections derived from comparison of computation and experiment on related molecules. H2CCC and H2CCCC have already been observed by radioastronomy; higher members in the series, because of their large dipole moments, which we have calculated, are candidates for astronomical searches. Our predictions can guide searches and assist in both astronomical and laboratory detection.

  4. Ab initio predictions on the rotational spectra of carbon-chain carbene molecules

    NASA Technical Reports Server (NTRS)

    Maluendes, S. A.; McLean, A. D.; Loew, G. H. (Principal Investigator)

    1992-01-01

    We predict rotational constants for the carbon-chain molecules H2C=(C=)nC, n=3-8, using ab initio computations, observed values for the earlier members in the series, H2CCC and H2CCCC with n=1 and 2, and empirical geometry corrections derived from comparison of computation and experiment on related molecules. H2CCC and H2CCCC have already been observed by radioastronomy; higher members in the series, because of their large dipole moments, which we have calculated, are candidates for astronomical searches. Our predictions can guide searches and assist in both astronomical and laboratory detection.

  5. Photodissociation of phenol via nonadiabatic tunneling: Comparison of two ab initio based potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Xie, Changjian; Guo, Hua

    2017-09-01

    The nonadiabatic tunneling-facilitated photodissociation of phenol is investigated using a reduced-dimensional quantum model on two ab initio-based coupled potential energy surfaces (PESs). Although dynamics occurs largely on the lower adiabat, the proximity to a conical intersection between the S1 and S2 states requires the inclusion of both the geometric phase (GP) and diagonal Born-Oppenheimer correction (DBOC). The lifetime of the lowest-lying vibronic state is computed using the diabatic and various adiabatic models. The GP and DBOC terms are found to be essential on one set of PESs, but have a small impact on the other.

  6. Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

    PubMed Central

    Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.

    2015-01-01

    The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219

  7. Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study.

    PubMed

    Xiao, H Y; Weber, W J; Zhang, Y; Zu, X T; Li, S

    2015-02-09

    The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.

  8. Ab initio molecular dynamics simulation of aqueous solution of nitric oxide in different formal oxidation states

    NASA Astrophysics Data System (ADS)

    Venâncio, Mateus F.; Rocha, Willian R.

    2015-10-01

    Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.

  9. Exploring Partonic Structure of Hadrons Using ab initio Lattice QCD Calculations.

    PubMed

    Ma, Yan-Qing; Qiu, Jian-Wei

    2018-01-12

    Following our previous proposal, we construct a class of good "lattice cross sections" (LCSs), from which we can study the partonic structure of hadrons from ab initio lattice QCD calculations. These good LCSs, on the one hand, can be calculated directly in lattice QCD, and on the other hand, can be factorized into parton distribution functions (PDFs) with calculable coefficients, in the same way as QCD factorization for factorizable hadronic cross sections. PDFs could be extracted from QCD global analysis of the lattice QCD generated data of LCSs. We also show that the proposed functions for lattice QCD calculation of PDFs in the literature are special cases of these good LCSs.

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

    NASA Astrophysics Data System (ADS)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

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

  11. Curved-line search algorithm for ab initio atomic structure relaxation

    NASA Astrophysics Data System (ADS)

    Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

    2017-09-01

    Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

  12. Analysis of Borderline Substitution/Electron Transfer Pathways from Direct ab initio MD Simulations

    SciTech Connect

    Yamataka, H; Aida, M A.; Dupuis, Michel

    Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH2O?- with CH3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the SN2-like transition state (TS): (i) a direct formation of SN2 products, (ii) a direct formation of ET products, and (iii) a 2-step formation of ET products via the SN2 valley. The direct formation of the ET product through the SN2-like TS appears to be more favorable at higher temperatures. The 2-step process depends on the amount of energy that goes into the C-C stretching mode.

  13. Ab initio study of the alkaline hydrolysis of a thio-β-lactam structure

    NASA Astrophysics Data System (ADS)

    Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

    2000-08-01

    The alkaline hydrolysis of a thio-β-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-β-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-β-lactam might be an effective inhibitor for β-lactamases.

  14. Ab initio R-matrix calculations of e+-molecule scattering

    NASA Technical Reports Server (NTRS)

    Danby, Grahame; Tennyson, Jonathan

    1990-01-01

    The adaptation of the molecular R-matrix method, originally developed for electron-molecule collision studies, to positron scattering is discussed. Ab initio R-matrix calculations are presented for collisions of low energy positrons with a number of diatomic systems including H2, HF and N2. Differential elastic cross sections for positron-H2 show a minimum at about 45 deg for collision energies between 0.3 and 0.5 Ryd. The calculations predict a bound state of positronHF. Calculations on inelastic processes in N2 and O2 are also discussed.

  15. Cobalt-doped ZnO nanocrystals: quantum confinement and surface effects from ab initio methods.

    PubMed

    Schoenhalz, Aline L; Dalpian, Gustavo M

    2013-10-14

    Cobalt-doped ZnO nanocrystals were studied through ab initio methods based on the Density Functional Theory. Both quantum confinement and surface effects were explicitly taken into account. When only quantum confinement effects are considered, Co atoms interact through a superexchange mechanism, stabilizing an antiferromagnetic ground state. Usually, this is the case for high quality nanoparticles with perfect surface saturation. When the surfaces were considered, a strong hybridization between the Co atoms and surfaces was observed, strongly changing their electronic and magnetic properties. Our results indicated that the surfaces might qualitatively change the properties of impurities in semiconductor nanocrystals.

  16. High order discretization techniques for real-space ab initio simulations

    NASA Astrophysics Data System (ADS)

    Anderson, Christopher R.

    2018-03-01

    In this paper, we present discretization techniques to address numerical problems that arise when constructing ab initio approximations that use real-space computational grids. We present techniques to accommodate the singular nature of idealized nuclear and idealized electronic potentials, and we demonstrate the utility of using high order accurate grid based approximations to Poisson's equation in unbounded domains. To demonstrate the accuracy of these techniques, we present results for a Full Configuration Interaction computation of the dissociation of H2 using a computed, configuration dependent, orbital basis set.

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

    NASA Astrophysics Data System (ADS)

    Li, Ailin; Yan, Tianying; Shen, Panwen

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

  18. Electronic states of Zn2 - Ab initio calculations of a prototype for Hg2

    NASA Technical Reports Server (NTRS)

    Hay, P. J.; Dunning, T. H., Jr.; Raffenetti, R. C.

    1976-01-01

    The electronic states of Zn2 are investigated by ab initio polarization configuration-interaction calculations. Molecular states dissociating to Zn(1S) + Zn(1S, 3P, 1P) and Zn(3P) + Zn(3P) are treated. Important effects from states arising from Zn(+)(25) + Zn(-)(2P) are found in the potential-energy curves and electronic-transition moments. A model calculation for Hg2 based on the Zn2 curves and including spin-orbit coupling leads to a new interpretation of the emission bands in Hg vapor.

  19. The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jakse, N.; Pasturel, A.

    2014-09-01

    We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.

  20. Ab initio study of energy transfer rates and impact sensitivities of crystalline explosives

    NASA Astrophysics Data System (ADS)

    Bernstein, Jonathan

    2018-02-01

    Impact sensitivities of various crystalline explosives were predicted by means of plane wave-density functional theory calculations. Crystal structures and complete vibrational spectra of TATB, PETN, FOX7, TEX, 14DNI, and β-HMX molecular crystals were calculated. A correlation between the phonon-vibron coupling (which is proportionally related to the energy transfer rate between the phonon manifold and the intramolecular vibrational modes) and impact sensitivities of secondary explosives was found. We propose a method, based on ab initio calculations, for the evaluation of impact sensitivities, which consequently can assist in screening candidates for chemical synthesis of high energetic materials.

  1. Electronic structure and magnetism of titanium substituted Cd3P2: An ab-initio study

    NASA Astrophysics Data System (ADS)

    Jaiganesh, G.; Jaya, S. Mathi

    2018-05-01

    Using the ab-initio computations that are based on the density functional theory, we have investigated the magnetism and electronic properties of one and two Ti atom substituted Cd3P2 compound. The magnetic stability of the substituted compounds was obtained by analyzing the minimum total energies in nonmagnetic, ferromagnetic and antiferromagnetic phases. Our results indicated the formation of magnetic order in one and two Ti atom substituted Cd3P2 as well as metallic characteristics in these systems. A significant value of the magnetic moment of Ti atom is observed from our calculations. We further find that the neighboring Cd and P atoms too acquire a small magnetic moment.

  2. Vibrational energy levels for CH4 from an ab initio potential

    NASA Technical Reports Server (NTRS)

    Schwenke, D. W.; Partridge, H.

    2001-01-01

    Many areas of astronomy and astrophysics require an accurate high temperature spectrum of methane (CH4). The goal of the present research is to determine an accurate ab initio potential energy surface (PES) for CH4. As a first step towards this goal, we have determined a PES including up to octic terms. We compare our results with experiment and to a PES based on a quartic expansion. Our octic PES gives good agreement with experiment for all levels, while the quartic PES only for the lower levels.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  4. Elimination of the azeotropic point of acetone and methanol by 1,3-dimethylimidazolium dimethylphosphate: an ab initio calculation study.

    PubMed

    Yu, Guangren; Liu, Xiaomin; Zhang, Xiaochun; Chen, Xiaochun; Liu, Zhiping; Abdeltawab, Ahmed A

    2017-03-01

    1,3-Dimethylimidazolium dimethylphosphate ([C 1 mim][DMP]) was observed experimentally to be able to eliminate the atmospheric azeotropic point of acetone and methanol, which is an important azeotrope generally encountered in furfural production and the Fischer-Tropsch process. Here, we employed ab initio calculation to understand the underlying mechanism of [C 1 mim][DMP] in eliminating the azeotropic point of acetone and methanol. Structure, energy and interaction in binary-, ternary- and quaternary-clusters composed of methanol, acetone, [C 1 mim] + or/and [DMP]‾ were calculated. The σ-hole, AIM and NBO analyses were performed to understand intermolecular interaction with electron density, electron occupancy, charge transfer and molecular orbital interaction. Hydrogen bond interaction plays a key role in azeotropic point elimination; due to the much stronger hydrogen bond interaction between methanol and [C 1 mim][DMP] than that between acetone and [C 1 mim][DMP], [C 1 mim][DMP] prefers to interact with methanol rather than acetone, and the original interaction between methanol and acetone is separated by [C 1 mim][DMP]. The hydrogen bond is from the orbital interaction between O lone-pair-electron orbitals of the hydrogen bond acceptor and σ * (C-H) or σ * (O-H) anti-bonding orbitals of the hydrogen bond donor, where remarkable electron or charge transfer occurs. These theoretical calculation results are in agreement with the experimental observation that [C 1 mim][DMP] eliminates the azeotropic point of methanol and acetone. This work shows that ab initio calculation may be employed to rationalize the design or synthesis of ionic liquids for separating azeotropes. Graphical Abstract Elimination of azeotropic point of acetone and methanol by [C 1 mim][DMP].

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

    DOE PAGES

    Binosi, Daniele; Chang, Lei; Papavassiliou, Joannis; ...

    2015-03-01

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

  6. The electron affinity of Al13H cluster: high level ab initio study

    NASA Astrophysics Data System (ADS)

    Moc, Jerzy

    2014-11-01

    Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the

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

    PubMed

    Ran, Shi-Ju

    2016-05-01

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

  8. On the Interaction between Carbon Dioxide and Nanomaterials with High Accuracy ab initio and DFT Calculations

    NASA Astrophysics Data System (ADS)

    Vogiatzis, Konstantinos D.; Mavrandonakis, Antreas; Klopper, Wim; Froudakis, George

    2009-08-01

    The separation, capture and storage of carbon dioxide from the flue gas is an environmental and economical problem of significant importance. Zeolites and activated carbons have been used from the industries in order to reduce the emissions of CO2. A new family of materials, the metal-organic frameworks (MOFs), has been recently proposed as an efficient substitute of the abovementioned materials. In particular, materials based on zinc complexes with imidazo-like aromatic compounds which builds frameworks similar with those of Zeolites (Zeolite-Imidazolium Frameworks, ZIFs), have the potential for efficient separation of CO2 from CO and CH4. [1]. Weak interactions between carbon dioxide and heterocyclic aromatic compounds are being examined with high accuracy ab initio methods. CO2 has zero dipole moment but a significant quadrupole moment enables it to operate as a weak acid or weak base, according to his environment. Nitrogen-containing aromatic compounds act as electron donors, while CO2 acts as an electron acceptor. Electrostatic interactions induce a non-permanent dipole moment on CO2 and the complex is stabilized by in-plane hydrogen bonds between the charged oxygens of CO2 and nearby hydrogen of the aromatic molecule. In addition, dispersion forces from the electron correlation contribute to the interaction energy. By using explicitly correlated methods (MP2-F12/aug-cc-pVTZ) [2] and by adding the contribution from the triples excitations, calculated with a smaller basis (6-311++G**), we reach to an approximate CCSD(T) complete basis set result. [3] Extrapolation schemes were used in order to reach the MP2 basis set limit and compare it with the CCSD(T)/CBS result. Those results are in excellent agreement with the explicitly correlated MP2-F12. In addition, our complexes are being investigated with DFT methods that calculate separately the dispersion energy (DFT-D) [4] and modified MP2 which scaling of spin pair correlation [5]. DFT-D results are in good

  9. A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

    NASA Technical Reports Server (NTRS)

    Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

    1991-01-01

    The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

  10. 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.

  11. Ab initio calculation of the rotational spectrum of methane vibrational ground state

    NASA Astrophysics Data System (ADS)

    Cassam-Chenaï, P.; Liévin, J.

    2012-05-01

    In a previous article we have introduced an alternative perturbation scheme to the traditional one starting from the harmonic oscillator, rigid rotator Hamiltonian, to find approximate solutions of the spectral problem for rotation-vibration molecular Hamiltonians. The convergence of our method for the methane vibrational ground state rotational energy levels was quicker than that of the traditional method, as expected, and our predictions were quantitative. In this second article, we study the convergence of the ab initio calculation of effective dipole moments for methane within the same theoretical frame. The first order of perturbation when applied to the electric dipole moment operator of a spherical top gives the expression used in previous spectroscopic studies. Higher orders of perturbation give corrections corresponding to higher centrifugal distortion contributions and are calculated accurately for the first time. Two potential energy surfaces of the literature have been used for solving the anharmonic vibrational problem by means of the vibrational mean field configuration interaction approach. Two corresponding dipole moment surfaces were calculated in this work at a high level of theory. The predicted intensities agree better with recent experimental values than their empirical fit. This suggests that our ab initio dipole moment surface and effective dipole moment operator are both highly accurate.

  12. Ab initio many-body calculations of nucleon scattering on ^16O

    NASA Astrophysics Data System (ADS)

    Navratil, Petr; Quaglioni, Sofia; Roth, Robert

    2008-10-01

    We develop a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, Plenum, New York, 1987. with the ab initio no-core shell model (NCSM).ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000). In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. We will present results for low-energy nucleon scattering on ^16O and for A=17 bound states obtained using realistic nucleon-nucleon potentials. The ^16O wave functions are calculated within the importance-truncated NCSMootnotetextR. Roth and P. Navratil, Phys. Rev. Lett. 99, 092501 (2007). that allows the use of model spaces up to 18φ and ultimately enables to reach convergence of phase-shifts and other observables. Prepared by LLNL under Contract DE-AC52-07NA27344. Support from the U.S. DOE/SC/NP (Work Proposal No. SCW0498), and from the U. S. Department of Energy Grant DE-FC02-07ER41457 is acknowledged.

  13. Estudio ab initio del mecanismo de la reacción HSO + O3

    NASA Astrophysics Data System (ADS)

    Nebot Gil, I.

    La reacción entre el radical HSO y el ozono ha sido ampliamente estudiada desde el punto de vista experimental debido a la importancia que tiene el radical HSO en la oxidación de los compuestos de azufre reductores y a que puede contribuir a la producción de H2SO4 [1-4]. Se realizaron diversos estudios teóricos sobre la cinética de la reacción entre el radical HSO y el ozono. La reacción del HSO con el ozono presenta tres canales diferentes : HSO + O3 &rightarrow &HSO2 + O2 &rightarrow &HS + 2 O2 &rightarrow &SO + OH + O2 La controversia existente entre los grupos experimentales sobre cuál de las tres vías es la predominante, se ha resuelto mediante un estudio teórico de todas ellas utilizando métodos ab initio. La estructura de todos los reactivos, productos, intermedios y estados de transición ha sido optimizada a nivel ab initio utilizando los métodos UMP2 /6-31G** y QCISD/6-31G**.

  14. Ab initio phonon point defect scattering and thermal transport in graphene

    DOE PAGES

    Polanco, Carlos A.; Lindsay, Lucas R.

    2018-01-04

    Here, we study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitudemore » smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (~ω 0) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. In conclusion, this work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.« less

  15. Comparative study of ab initio nonradiative recombination rate calculations under different formalisms

    NASA Astrophysics Data System (ADS)

    Shi, Lin; Xu, Ke; Wang, Lin-Wang

    2015-05-01

    Nonradiative carrier recombination is of both great applied and fundamental importance, but the correct ab initio approaches to calculate it remain to be inconclusive. Here we used five different approximations to calculate the nonradiative carrier recombinations of two complex defect structures GaP :Z nGa-OP and GaN :Z nGa-VN , and compared the results with experiments. In order to apply different multiphonon assisted electron transition formalisms, we have calculated the electron-phonon coupling constants by ab initio density functional theory for all phonon modes. Compared with different methods, the capture coefficients calculated by the static coupling theory are 4.30 ×10-8 and 1.46 ×10-7c m3/s for GaP :Z nGa-OP and GaN :Z nGa-VN , which are in good agreement with the experiment results, (4-1+2) ×10-8 and 3.0 ×10-7c m3/s , respectively. We also provided arguments for why the static coupling theory should be used to calculate the nonradiative decays of semiconductors.

  16. Ab Initio Design of Potent Anti-MRSA Peptides based on Database Filtering Technology

    PubMed Central

    Mishra, Biswajit; Wang, Guangshun

    2012-01-01

    To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed.1 This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g. amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database2 by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 minutes. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. A combination of our ab initio design with database screening3 led to yet another peptide with enhanced potency. Because of simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well. PMID:22803960

  17. Ab initio design of potent anti-MRSA peptides based on database filtering technology.

    PubMed

    Mishra, Biswajit; Wang, Guangshun

    2012-08-01

    To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.

  18. Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi

    NASA Technical Reports Server (NTRS)

    Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.

    2016-01-01

    For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.

  19. Ab initio study of intrinsic profiles of liquid metals and their reflectivity

    NASA Astrophysics Data System (ADS)

    del Rio, B. G.; Souto, J.; Alemany, M. M. G.; González, L. E.

    2017-08-01

    The free surfaces of liquid metals are known to exhibit a stratified profile that, in favourable cases, shows up in experiments as a peak in the ratio between the reflectivity function and that of an ideal step-like profile. This peak is located at a wave-vector related to the distance between the layers of the profile. In fact the surface roughness produced by thermally induced capillary waves causes a depletion of the previous so called intrinsic reflectivity by a damping factor that may hinder the observation of the peak. The behaviour of the intrinsic reflectivity below the layering peak is however far from being universal, with systems as Ga or In where the reflectiviy falls uniformly towards the q → 0 value, others like Sn or Bi where a shoulder appears at intermediate wavevectors, and others like Hg which show a minimum. We have performed extensive ab initio simulations of the free liquid surfaces of Bi, Pb and Hg, that yield direct information on the structure of the profiles and found that the macroscopic capillary wave theory usually employed in order to remove the capillary wave components fails badly in some cases for the typical sample sizes affordable in ab initio simulations. However, a microscopic method for the determination of the intrinsic profile is shown to be succesful in obtaining meaningful intrinsic profiles and corresponding reflectivities which reproduce correctly the qualitative behaviour observed experimentally.

  20. Ab initio calculations of the concentration dependent band gap reduction in dilute nitrides

    NASA Astrophysics Data System (ADS)

    Rosenow, Phil; Bannow, Lars C.; Fischer, Eric W.; Stolz, Wolfgang; Volz, Kerstin; Koch, Stephan W.; Tonner, Ralf

    2018-02-01

    While being of persistent interest for the integration of lattice-matched laser devices with silicon circuits, the electronic structure of dilute nitride III/V-semiconductors has presented a challenge to ab initio computational approaches. The origin of the computational problems is the strong distortion exerted by the N atoms on most host materials. Here, these issues are resolved by combining density functional theory calculations based on the meta-GGA functional presented by Tran and Blaha (TB09) with a supercell approach for the dilute nitride Ga(NAs). Exploring the requirements posed to supercells, it is shown that the distortion field of a single N atom must be allowed to decrease so far that it does not overlap with its periodic images. This also prevents spurious electronic interactions between translational symmetric atoms, allowing us to compute band gaps in very good agreement with experimentally derived reference values. In addition to existing approaches, these results offer a promising ab initio avenue to the electronic structure of dilute nitride semiconductor compounds.

  1. Unification of the phonon mode behavior in semiconductor alloys: Theory and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Pagès, O.; Postnikov, A. V.; Kassem, M.; Chafi, A.; Nassour, A.; Doyen, S.

    2008-03-01

    We demonstrate how to overcome serious problems in understanding and classification of vibration spectra in semiconductor alloys, following from traditional use of the virtual crystal approximation (VCA). We show that such different systems as InGaAs (1- bond→1 -mode behavior), InGaP (modified 2-mode), and ZnTeSe (2- bond→1 -mode) obey, in fact, the same phonon mode behavior—hence probably a universal one—of a percolation type (1- bond→2 -mode). The change of paradigm from the “VCA insight” (an averaged microscopic one) to the “percolation insight” (a mesoscopic one) offers a promising link toward the understanding of alloy disorder. The discussion is supported by ab initio simulation of the phonon density of states at the zone center of representative supercells at intermediary composition (ZnTeSe) and at the impurity-dilute limits (all systems). In particular, we propose a simple ab initio “protocol” to estimate the basic input parameters of our semiempirical “percolation” model for the calculation of the 1- bond→2 -mode vibration spectra of zinc blende alloys. With this, the model turns self-sufficient.

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

    PubMed

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

    2015-07-01

    Hydroxyapatite (HAP) is an important bioceramic which constitutes the mineral components of bones and hard tissues in mammals. It is bioactive and used as bioceramic coatings for metallic implants and bone fillers. HAP readily absorbs a large amount of impurities. Knowledge on the elastic and mechanical properties of impurity-doped HAP is a subject of great importance to its potential for biomedical applications. Zn and Mg are the most common divalent cations HAP absorbs. Using density function theory based ab initio methods, we have carried out a large number of ab initio calculations to obtain the bulk elastic and mechanical properties of HAP with Zn or Mg doped in different concentration at the Ca1 and Ca2 sites using large 352-atom supercells. Detailed information on their dependece on the concetraion of the substitued impurity is obtained. Our results show that Mg enhances overall elastic and bulk mechanical properties whereas Zn tends to degrade except at low concentrations. At a higher concentration, the mechanical properties of Zn and Mg doped HAP also depend significantly on impurity distribution between the Ca1 and Ca2 sites. There is a strong evidence that Zn prefers Ca2 site for substituion whereas Mg has no such preference. These results imply that proper control of dopant concentration and their site preference must carefully considered in using doped HAP for specific biomedical applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Conformational stability, r(0) structural parameters, vibrational assignments and ab initio calculations of ethyldichlorophosphine.

    PubMed

    Darkhalil, Ikhlas D; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K; Durig, James R

    2015-02-05

    Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm(-1)) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88±9 cm(-1) (1.04±0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. 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 J π = 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

  5. Ab initio study of the structure and dynamics of bulk liquid Fe

    NASA Astrophysics Data System (ADS)

    Marqués, M.; González, L. E.; González, D. J.

    2015-10-01

    Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

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

    DOE PAGES

    Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...

    2015-07-24

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

  7. Ab initio phonon point defect scattering and thermal transport in graphene

    SciTech Connect

    Polanco, Carlos A.; Lindsay, Lucas R.

    Here, we study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitudemore » smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (~ω 0) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. In conclusion, this work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.« less

  8. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

    PubMed

    Xu, Dong; Zhang, Yang

    2012-07-01

    Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

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

    NASA Astrophysics Data System (ADS)

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

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

  10. Consistent integration of experimental and ab initio data into molecular and coarse-grained models

    NASA Astrophysics Data System (ADS)

    Vlcek, Lukas

    As computer simulations are increasingly used to complement or replace experiments, highly accurate descriptions of physical systems at different time and length scales are required to achieve realistic predictions. The questions of how to objectively measure model quality in relation to reference experimental or ab initio data, and how to transition seamlessly between different levels of resolution are therefore of prime interest. To address these issues, we use the concept of statistical distance to define a measure of similarity between statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the systems' measurable properties. Through systematic coarse-graining, we arrive at appropriate expressions for optimization loss functions consistently incorporating microscopic ab initio data as well as macroscopic experimental data. The design of coarse-grained and multiscale models is then based on factoring the model system partition function into terms describing the system at different resolution levels. The optimization algorithm takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space, enabling us to scan millions of parameter combinations per hour on a single CPU. The robustness and generality of the new model optimization framework and its efficient implementation are illustrated on selected examples including aqueous solutions, magnetic systems, and metal alloys.

  11. A new ab initio potential energy surface for the Ne-H 2 interaction

    NASA Astrophysics Data System (ADS)

    Lique, François

    2009-03-01

    A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

  12. Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

    NASA Astrophysics Data System (ADS)

    Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

    2001-06-01

    The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

  13. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    SciTech Connect

    Han, Huixian; School of Physics, Northwest University, Xi’an, Shaanxi 710069; Li, Anyang

    2014-12-28

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S{sub 0}) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm{sup −1}. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies upmore » to 12 700 cm{sup −1} above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.« less

  14. 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. ).

  15. Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

    NASA Astrophysics Data System (ADS)

    Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.

    2017-08-01

    The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.

  16. Fourier transform microwave spectra and ab initio calculation of N-ethylformamide

    NASA Astrophysics Data System (ADS)

    Ohba, Keisuke; Usami, Tsuyoshi; Kawashima, Yoshiyuki; Hirota, Eizi

    2005-06-01

    A peptide molecule: N-ethylformamide HCONHCH 2CH 3 (NEFA) was investigated by Fourier transform microwave spectroscopy in order to determine molecular structure, potential barrier to methyl internal rotation, and nuclear quadrupole coupling constant of the nitrogen atom. All the three ( a, b and c) types of transitions were observed; they were split into hyperfine structure components due to nitrogen nuclear quadrupole coupling. The rotational constants of NEFA were determined to be A=9904.8373(6), B=3521.0995(2) and C=2984.9808(2) MHz, with three standard deviations in parentheses. The inertial defect Δ= Icc- Iaa- Ibb was calculated from the rotational constants to be -25.24492(2) uÅ 2, which indicates the ethyl group to be bent out of the peptide linkage plane. A comparison of the observed rotational constants with those calculated by an ab initio molecular orbital method also led us to conclude that the most stable form of NEFA is trans- sc, a conformer with a nonplanar heavy atom skeleton. No evidence has so far been obtained for the existence of other conformers, as was the case for a related molecule: N-ethylacetamide. We have also observed spectra of five singly substituted isotopomers, three 13C and one for each of 15N and 18O, from which we derived a partial rs structure, in fair agreement with an ab initio result.

  17. 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

    2017-04-06

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

  18. Novel high-pressure phase of ZrO{sub 2}: An ab initio prediction

    SciTech Connect

    Durandurdu, Murat, E-mail: murat.durandurdu@agu.edu.tr

    2015-10-15

    The high-pressure behavior of the orthorhombic cotunnite type ZrO{sub 2} is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni{sub 2}In type) within P6{sub 3}/mmc symmetry is predicted through the simulation. The Ni{sub 2}In type crystal is the densest high-pressure phase of ZrO{sub 2} proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni{sub 2}In type hexagonal phase forms in zirconia atmore » high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO{sub 2} through an ab initio simulation. • Cotunnite ZrO{sub 2} adopts the Ni{sub 2}In type structure at high pressure. • The Ni{sub 2}In type structure is the densest high-pressure phase of ZrO{sub 2} proposed so far. • The preferred mechanism in ZrO{sub 2} differs from the other metal dioxides.« less

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

    DOE PAGES

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

    2016-08-08

    Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrainedmore » ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though the effect is more pronounced for C-H bond activation due to less disruption of the hydrogen-bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased, or uncharged Pt(111). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

  20. Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

    NASA Astrophysics Data System (ADS)

    Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

    2013-06-01

    Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  2. Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

    PubMed Central

    Li, Jun; Riehle, Michelle M; Zhang, Yan; Xu, Jiannong; Oduol, Frederick; Gomez, Shawn M; Eiglmeier, Karin; Ueberheide, Beatrix M; Shabanowitz, Jeffrey; Hunt, Donald F; Ribeiro, José MC; Vernick, Kenneth D

    2006-01-01

    Background Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. Results We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. Conclusion Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms. PMID:16569258

  3. 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.

  4. 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%).

  5. Ab initio phonon point defect scattering and thermal transport in graphene

    NASA Astrophysics Data System (ADS)

    Polanco, Carlos A.; Lindsay, Lucas

    2018-01-01

    We study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitude smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (˜ω0 ) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. This work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.

  6. Nonconventional screening of the Coulomb interaction in FexOy clusters: An ab initio study

    NASA Astrophysics Data System (ADS)

    Peters, L.; Şaşıoǧlu, E.; Rossen, S.; Friedrich, C.; Blügel, S.; Katsnelson, M. I.

    2017-04-01

    From microscopic point-dipole model calculations of the screening of the Coulomb interaction in nonpolar systems by polarizable atoms, it is known that screening strongly depends on dimensionality. For example, in one-dimensional systems, the short-range interaction is screened, while the long-range interaction is antiscreened. This antiscreening is also observed in some zero-dimensional structures, i.e., molecular systems. By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the FLAPW method, we study screening of the Coulomb interaction in FexOy clusters. For completeness, these results are compared with their bulk counterpart magnetite. It appears that the on-site Coulomb interaction is very well screened both in the clusters and bulk. On the other hand, for the intersite Coulomb interaction, the important observation is made that it is almost constant throughout the clusters, while for the bulk it is almost completely screened. More precisely and interestingly, in the clusters antiscreening is observed by means of ab initio calculations.

  7. Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

    NASA Astrophysics Data System (ADS)

    Amaran, Saieswari; Kumar, Sanjay

    2007-12-01

    State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

  8. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    NASA Astrophysics Data System (ADS)

    Han, Huixian; Li, Anyang; Guo, Hua

    2014-12-01

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

  9. A Toolbox for Ab Initio 3-D Reconstructions in Single-particle Electron Microscopy

    PubMed Central

    Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S

    2010-01-01

    Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a “toolbox” of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map. PMID:20018246

  10. Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  11. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins

    PubMed Central

    Yang, Jing; He, Bao-Ji; Jang, Richard; Zhang, Yang; Shen, Hong-Bin

    2015-01-01

    Abstract Motivation: Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g. >3 bonds, is too low to effectively assist structure assembly simulations. Results: We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins. Availability and implementation: http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/ Contact: zhng@umich.edu or hbshen@sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26254435

  12. Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  13. High pressure stability of lithium metatitanate and metazirconate: Insight from experiments & ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Chitnis, Abhishek; Chakraborty, B.; Tripathi, B. M.; Tyagi, A. K.; Garg, Nandini

    2018-02-01

    Lithium metatitanate (LTO) and lithium metazirconate (LZO) are lithium rich ceramics which can be used as tritium breeder materials for thermonuclear reactors. In-situ x-ray diffraction and ab-initio studies at high pressure show that LTO has a higher bulk modulus than that of LZO. In fact these studies indicate that they are the least compressible of the known lithium rich ceramics like Li2O or Li4SiO4, which are potential candidates for blanket materials. These studies show that the TiO6 octahedra are responsible for the higher bulk modulus of LTO when compared to that of LZO. It has also been shown that the compressibility and distortion of the softer LiO6 octahedra can be controlled by altering the stacking sequence of the more rigid covalently bonded octahedra. This knowledge can be used by chemists to design new lithium based ceramics with higher bulk modulus. It was observed that LTO was stable upto 34 GPa. Ab initio DFT calculations helped to understand the anisotropy in compressibility of both LZO and LTO. This study also shows, that even though the empirical potentials developed by Vijaykumar et al. successfully determine the ambient pressure structure of lithium metatitanate, they cannot be used at non ambient conditions like high pressure [1].

  14. Structural phase transition of BeTe: an ab initio molecular dynamics study.

    PubMed

    Alptekin, Sebahaddin

    2017-08-11

    Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results. Graphical abstract The energy-volume relation and ZB phase for the BeTe.

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

    PubMed

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

    2015-04-01

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

  16. Ab initio study of the structural properties of acetonitrile-water mixtures

    NASA Astrophysics Data System (ADS)

    Chen, Jinfan; Sit, Patrick H.-L.

    2015-08-01

    Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

  17. Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

    PubMed

    Szabó, István; Czakó, Gábor

    2017-11-30

    We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

  18. Ab initio study of Pd carbonyls and CO/Pd(110)

    SciTech Connect

    Ramprasad, R.; Glassford, K.M.; Adams, J.B.

    1994-12-31

    Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

  19. 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.

  20. Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

    PubMed

    Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

    2017-09-05

    Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

  1. Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

    PubMed

    Martí-Rujas, Javier; Kawano, Masaki

    2013-02-19

    Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  3. Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

    NASA Astrophysics Data System (ADS)

    Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

    2018-01-01

    Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

  4. The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

    2018-06-01

    Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

  5. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    PubMed

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    the pairwise-atomic Hamiltonian matrices required for practical applications. These matrices can be retained as functions of scalar atomic-pair separations and employed in assembling aggregate Hamiltonian matrices, with Wigner rotation matrices providing analytical representations of their angular degrees of freedom. In this way, ab initio potential energy surfaces are obtained in the complete absence of repeated evaluations and transformations of the one- and two-electron integrals at different molecular geometries required in most ab inito molecular calculations, with large Hamiltonian matrix assembly simplified and explicit diagonalizations avoided employing partitioning and Brillouin-Wigner or Rayleigh-Schrödinger perturbation theory. Illustrative applications of the important components of the formalism, selected aspects of the scaling of the approach, and aspects of "on-the-fly" interfaces with Monte Carlo and molecular-dynamics methods are described in anticipation of subsequent applications to biomolecules and other large aggregates.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

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

    SciTech Connect

    Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy

    2006-09-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

  10. 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

  11. Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

    NASA Astrophysics Data System (ADS)

    Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

    2000-08-01

    The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

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

    PubMed

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

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

  13. Strategic L2 Lexical Innovation: Case Study of a University-Level Ab Initio Learner of German.

    ERIC Educational Resources Information Center

    Ridley, Jennifer; Singleton, David

    1995-01-01

    This article presents a case study of one English-speaking ab initio learner of German. It found that in target language production tasks performed over a two-year period, the subject exhibited a particular tendency toward lexical innovation as a strategy to cope with the lack of target language lexical knowledge. (38 references) (MDM)

  14. The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Huo, Winifred (Technical Monitor)

    1998-01-01

    We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions,

  15. Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

    PubMed

    Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

    2016-09-21

    Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

  16. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

    PubMed Central

    Zhang, Yang

    2014-01-01

    We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

  17. The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Huo, Winifred (Technical Monitor)

    1998-01-01

    We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions.

  18. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

    PubMed

    Zhang, Yang

    2014-02-01

    We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

  19. Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

    SciTech Connect

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

    2015-02-09

    In this study, the response of titanate pyrochlores (A 2Ti 2O 7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O 2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization inmore » titanate pyrochlores under laser, electron and ion irradiations.« less

  20. Ab Initio Effective Rovibrational Hamiltonians for Non-Rigid Molecules via Curvilinear VMP2

    NASA Astrophysics Data System (ADS)

    Changala, Bryan; Baraban, Joshua H.

    2017-06-01

    Accurate predictions of spectroscopic constants for non-rigid molecules are particularly challenging for ab initio theory. For all but the smallest systems, ``brute force'' diagonalization of the full rovibrational Hamiltonian is computationally prohibitive, leaving us at the mercy of perturbative approaches. However, standard perturbative techniques, such as second order vibrational perturbation theory (VPT2), are based on the approximation that a molecule makes small amplitude vibrations about a well defined equilibrium structure. Such assumptions are physically inappropriate for non-rigid systems. In this talk, we will describe extensions to curvilinear vibrational Møller-Plesset perturbation theory (VMP2) that account for rotational and rovibrational effects in the molecular Hamiltonian. Through several examples, we will show that this approach provides predictions to nearly microwave accuracy of molecular constants including rotational and centrifugal distortion parameters, Coriolis coupling constants, and anharmonic vibrational and tunneling frequencies.

  1. An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence.

    PubMed

    Cupellini, Lorenzo; Jurinovich, Sandro; Campetella, Marco; Caprasecca, Stefano; Guido, Ciro A; Kelly, Sharon M; Gardiner, Alastair T; Cogdell, Richard; Mennucci, Benedetta

    2016-11-10

    The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.

  2. Ab Initio Potential Energy Surfaces and Quantum Dynamics for Polyatomic Bimolecular Reactions.

    PubMed

    Fu, Bina; Zhang, Dong H

    2018-05-08

    There has been great progress in the development of potential energy surfaces (PESs) and quantum dynamics calculations in the gas phase. The establishment of a fitting procedure for highly accurate PESs and new developments in quantum reactive scattering on reliable PESs allow accurate characterization of reaction dynamics beyond triatomic systems. This review will give the recent development in our group in constructing ab initio PESs based on neural networks and the time-dependent wave packet calculations for bimolecular reactions beyond three atoms. Bimolecular reactions of current interest to the community, namely, OH + H 2 , H + H 2 O, OH + CO, H + CH 4 , and Cl + CH 4 , are focused on. Quantum mechanical characterization of these reactions uncovers interesting dynamical phenomena with an unprecedented level of sophistication and has greatly advanced our understanding of polyatomic reaction dynamics.

  3. Ab initio Study on Ionization Energies of 3-Amino-1-propanol

    NASA Astrophysics Data System (ADS)

    Wang, Ke-dong; Jia, Ying-bin; Lai, Zhen-jiang; Liu, Yu-fang

    2011-06-01

    Fourteen conformers of 3-amino-1-propanol as the minima on the potential energy surface are examined at the MP2/6-311++G** level. Their relative energies calculated at B3LYP, MP3 and MP4 levels of theory indicated that two most stable conformers display the intramolecular OH···N hydrogen bonds. The vertical ionization energies of these conformers calculated with ab initio electron propagator theory in the P3/aug-cc-pVTZ approximation are in agreement with experimental data from photoelectron spectroscopy. Natural bond orbital analyses were used to explain the differences of IEs of the highest occupied molecular ortibal of conformers. Combined with statistical mechanics principles, conformational distributions at various temperatures are obtained and the temperature dependence of photoelectron spectra is interpreted.

  4. Ab initio thermodynamics and kinetics for coalescence on nanoislands and nanopits on metal(100) surfaces

    NASA Astrophysics Data System (ADS)

    Evans, Jim; Han, Yong; Stoldt, Conrad; Thiel, Patricia

    Coalescence or sintering of nanoscale features on metal(100) surfaces is mediated by periphery or edge diffusion. These processes are highly sensitive to the multiple diffusion barriers for various local edge environments. We provide an optimal strategy to determine both thermodynamics and kinetics for these systems at the ab initio level. The former requires assessing conventional interactions between adatoms at adsorption sites. The latter requires assessing unconventional interactions between the hopping atom at a bridge site transition state and other nearby atoms. KMC simulation reveals that this formulation recovers observed sintering times for Ag nanoislands on Ag(100), including a novel size dependence. The formulation also applies for nanopits where there are additional challenges to capture kinetics. Work supported by NSF Grant CHE-1507223.

  5. Linear electro-optic effect in semiconductors: Ab initio description of the electronic contribution

    NASA Astrophysics Data System (ADS)

    Prussel, Lucie; Véniard, Valérie

    2018-05-01

    We propose an ab initio framework to derive the electronic part of the second-order susceptibility tensor for the electro-optic effect in bulk semiconductors. We find a general expression for χ(2 ) evaluated within time-dependent density-functional theory, including explicitly the band-gap corrections at the level of the scissors approximation. Excitonic effects are accounted for, on the basis of a simple scalar approximation. We apply our formalism to the computation of the electro-optic susceptibilities for several semiconductors, such as GaAs, GaN, and SiC. Taking into account the ionic contribution according to the Faust-Henry coefficient, we obtain a good agreement with experimental results. Finally, using different types of strain to break centrosymmetry, we show that high electro-optic coefficients can be obtained in bulk silicon for a large range of frequencies.

  6. Ab Initio Study of Polarizabilities of Oligothiophene, Oligocyclopentadiene and Oligofulvene and their Cyano Substituted Oligomers

    NASA Astrophysics Data System (ADS)

    Lagowski, Jolanta; Ferdous, Sultana

    2005-03-01

    Ab Initio polarizabilities of thiophene, fulvene and cyclopentadiene based conducting oligomers and polymers and their cyano derivatives have been calculated using the Hartree-Fock (HF), configuration interaction (singles) (CIS ) and density functional (DF) theories with 3-21G* basis using Gaussian software. The main motivation of this investigation is to determine the correlation between the excitation energies and polarizabilities for the conjugated systems studied. It has been found that HF and DF approaches give similar magnitudes for polarizabilities whereas CIS theory provides results that are considerably different. All three methods predict similar trends in polarizabilities as a function of oligomer length and bond alternation along the backbone of the oligomers. It has also been observed that the end groups and the number of `double' bonds have a significant effect on the magnitude of polarizability per C-C bond. Comparison with experimental results will be made where possible.

  7. Ab initio approach to the ion stopping power at the plasma-solid interface

    NASA Astrophysics Data System (ADS)

    Bonitz, Michael; Schlünzen, Niclas; Wulff, Lasse; Joost, Jan-Philip; Balzer, Karsten

    2016-10-01

    The energy loss of ions in solids is of key relevance for many applications of plasmas, ranging from plasma technology to fusion. Standard approaches are based on density functional theory or SRIM simulations, however, the applicability range and accuracy of these results are difficult to assess, in particular, for low energies. Here we present an independent approach that is based on ab initio nonequilibrium Green functions theory, e.g. that allows to incorporate electronic correlations effects of the solid. We present the first application of this method to low-temperature plasmas, concentrating on proton and alpha-particle stopping in a graphene layer. In addition to the stopping power we present time-dependent results for the local electron density, the spectral function and the photoemission spectrum that is directly accessible in optical, UV or x-ray diagnostics. http://www.itap.uni-kiel.de/theo-physik/bonitz/.

  8. The large amplitude motions of methylamine from the perspective of the highly correlated ab initio methods

    NASA Astrophysics Data System (ADS)

    Senent, M. L.

    2018-01-01

    CCSD(T)-F12 theory in connection with extended basis sets is employed to determine the electronic ground state spectroscopic parameters of methylamine at low temperatures. The geometry, the rotational constants, all the fundamental frequencies, the dipole moment and its components, and the centrifugal distortion constants, are provided. The ground vibrational state rotational constants were found to be A0 = 103067.15 MHz, B0 = 22588.29 MHz, and C0 = 21710.50 MHz and the dipole moment to be 1.4071D. Fermi displacements of the vibrational bands are predicted. The low vibrational energy levels corresponding to the large amplitude motions are determine variationally using a flexible three-dimensional model depending on three variables: the HNH bending, the NH2 wagging and the CH3 torsional coordinates. The computed levels are compared with previous experimental and calculated energies. Methylamine parameters are very sensitive to the level of ab initio calculations.

  9. Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase.

    PubMed

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2007-08-23

    We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determining step is the release of the NH3 molecule.

  10. Spectroscopy of 50Sc and ab initio calculations of B (M 3 ) strengths

    NASA Astrophysics Data System (ADS)

    Garnsworthy, A. B.; Bowry, M.; Olaizola, B.; Holt, J. D.; Stroberg, S. R.; Cruz, S.; Georges, S.; Hackman, G.; MacLean, A. D.; Measures, J.; Patel, H. P.; Pearson, C. J.; Svensson, C. E.

    2017-10-01

    The GRIFFIN spectrometer at TRIUMF-ISAC has been used to study excited states and transitions in 50Sc following the β decay of 50Ca. Branching ratios were determined from the measured γ -ray intensities, and angular correlations of γ rays have been used to firmly assign the spins of excited states. The presence of an isomeric state that decays by an M 3 transition with a B (M 3 ) strength of 13.6(7) W.u. has been confirmed. We compare the first ab initio calculations of B (M 3 ) strengths in light- and medium-mass nuclei from the valence-space in-medium similarity renormalization group approach, using consistently derived effective Hamiltonians and effective M 3 operator. The experimental data are well reproduced for isoscalar M 3 transitions when using bare g factors, but the strength of isovector M 3 transitions are found to be underestimated by an order of magnitude.

  11. Ammonia-hydrogen bromide and ammonia-hydrogen iodide complexes: anion photoelectron and ab initio studies.

    PubMed

    Eustis, S N; Whiteside, A; Wang, D; Gutowski, M; Bowen, K H

    2010-01-28

    The ammonia-hydrogen bromide and ammonia-hydrogen iodide, anionic heterodimers were studied by anion photoelectron spectroscopy. In complementary studies, these anions and their neutral counterparts were also investigated via ab initio theory at the coupled cluster level. In both systems, neutral NH(3)...HX dimers were predicted to be linear, hydrogen-bonded complexes, whereas their anionic dimers were found to be proton-transferred species of the form, (NH(4)(+)X(-))(-). Both experimentally measured and theoretically predicted vertical detachment energies (VDE) are in excellent agreement for both systems, with values for (NH(4)(+)Br(-))(-) being 0.65 and 0.67 eV, respectively, and values for (NH(4)(+)I(-))(-) being 0.77 and 0.81 eV, respectively. These systems are discussed in terms of our previous study of (NH(4)(+)Cl(-))(-).

  12. The C4H radical and the diffuse interstellar bands. An ab initio study

    NASA Technical Reports Server (NTRS)

    Kolbuszewski, Marcin

    1994-01-01

    An ab initio study of the low-lying electronic states of C4H has been presented where the species studied has a chi(2)sigma(+) ground state and two low lying pi states. Based on the vertical and adiabatic excitation energies between those states it is suggested that the 4428 A diffuse interstellar band is not carried by C4H. The application of the particle in a box model shows strong coincidences between the strong DIB's and predicted wavelengths of pi-pi transitions in C(2n)H series. Based on those coincidences, it is suggested the C(2n)H species as good candidates for carriers of diffuse interstellar bands.

  13. Raman scattering tensors in thymine molecule from an ab initio MO calculation

    NASA Astrophysics Data System (ADS)

    Tsuboi, Masamichi; Kumakura, Akiko; Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ushizawa, Koichi; Ueda, Toyotoshi

    1997-03-01

    Ab initio SCF MO calculations have been made of the thymine molecule for the permanent polarizability and the polarizability derivatives with respect to the normal coordinates. The latter correspond to the components of the Raman tensors, and each of these tensors was brought into a visualized form by a transformation of the tensor axes into the principal system. For a comparison with such computational findings, a polarized Raman spectroscopic measurement has been made of a single crystal of thymine with 488.0 nm excitation. For most of the in-plane vibrations, calculated tensors were found to be well correlated with the observed Raman scattering anisotropy. On the basis of such correlations, discussions are given as for the polarizability oscillations caused by the atomic displacements in the molecule.

  14. Comparison between phenomenological and ab-initio reaction and relaxation models in DSMC

    NASA Astrophysics Data System (ADS)

    Sebastião, Israel B.; Kulakhmetov, Marat; Alexeenko, Alina

    2016-11-01

    New state-specific vibrational-translational energy exchange and dissociation models, based on ab-initio data, are implemented in direct simulation Monte Carlo (DSMC) method and compared to the established Larsen-Borgnakke (LB) and total collision energy (TCE) phenomenological models. For consistency, both the LB and TCE models are calibrated with QCT-calculated O2+O data. The model comparison test cases include 0-D thermochemical relaxation under adiabatic conditions and 1-D normal shockwave calculations. The results show that both the ME-QCT-VT and LB models can reproduce vibrational relaxation accurately but the TCE model is unable to reproduce nonequilibrium rates even when it is calibrated to accurate equilibrium rates. The new reaction model does capture QCT-calculated nonequilibrium rates. For all investigated cases, we discuss the prediction differences based on the new model features.

  15. Ab initio calculations of deep-level carrier nonradiative recombination rates in bulk semiconductors.

    PubMed

    Shi, Lin; Wang, Lin-Wang

    2012-12-14

    Nonradiative carrier recombination is of both applied and fundamental interest. Here a novel algorithm is introduced to calculate such a deep level nonradiative recombination rate using the ab initio density functional theory. This algorithm can calculate the electron-phonon coupling constants all at once. An approximation is presented to calculate the phonon modes for one impurity in a large supercell. The neutral Zn impurity site together with a N vacancy is considered as the carrier-capturing deep impurity level in bulk GaN. Its capture coefficient is calculated as 5.57 × 10(-10)cm(3)/s at 300 K. We found that there is no apparent onset of such a nonradiative process as a function of temperature.

  16. Ab initio density functional theory investigation of structural and electronic properties of silicon carbide nanotube bundles

    NASA Astrophysics Data System (ADS)

    Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

    2008-10-01

    By using ab initio density functional theory the structural and electronic properties of isolated and bundled (8,0) and (6,6) silicon carbide nanotubes (SiCNTs) are investigated. Our results show that for such small diameter nanotubes the inter-tube interaction causes a very small radial deformation, while band splitting and reduction of the semiconducting energy band gap are significant. We compared the equilibrium interaction energy and inter-tube separation distance of (8,0) SiCNT bundle with (10,0) carbon nanotube (CNT) bundle where they have the same radius. We found that there is a larger inter-tube separation and weaker inter-tube interaction in the (8,0) SiCNT bundle with respect to (10,0) CNT bundle, although they have the same radius.

  17. Ab initio density functional theory investigation of Li-intercalated silicon carbide nanotube bundles

    NASA Astrophysics Data System (ADS)

    Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

    2009-06-01

    We present the results of ab initio density functional theory calculations on the energetic, and geometric and electronic structure of Li-intercalated ( 6,6) silicon carbide nanotube (SiCNT) bundles. Our results show that intercalation of lithium leads to the significant changes in the geometrical structure. The most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the SiCNTs. All the Li-intercalated ( 6,6) SiCNT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial space are susceptible for intercalation. The present calculations suggest that the SiCNT bundle is a promising candidate for the anode material in battery applications.

  18. An ab initio variationally computed room-temperature line list for (32)S(16)O3.

    PubMed

    Underwood, Daniel S; Tennyson, Jonathan; Yurchenko, Sergei N

    2013-07-07

    Ab initio potential energy and dipole moment surfaces are computed for sulfur trioxide (SO3) at the CCSD(T)-F12b level of theory with appropriate triple-zeta basis sets. The analytical representations of these surfaces are used, with a slight correction, to compute pure rotational and rotation-vibration spectra of (32)S(16)O3 using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0-4000 cm(-1) with rotational states up to J = 85. The resulting line list of 174,674,257 transitions is appropriate for modelling room temperature (32)S(16)O3 spectra. Good agreement is found with the observed infrared absorption spectra and the calculations are used to place the measured relative intensities on an absolute scale. A list of 10,878 experimental transitions is provided in a form suitable for inclusion in standard atmospheric and planetary spectroscopic databases.

  19. Hydrogen Recombination and Dimer Formation on Graphite from Ab Initio Molecular Dynamics Simulations.

    PubMed

    Casolo, S; Tantardini, G F; Martinazzo, R

    2016-07-14

    We studied Eley-Rideal molecular hydrogen formation on graphite using ab initio molecular dynamics, in the energy range relevant for the chemistry of the interstellar medium and for terrestrial experiments employing cold plasma (0.02-1 eV). We found substantial projectile steering effects that prevent dimer formation at low energies, thereby ruling out any catalytic synthetic pathways that form hydrogen molecules. Ortho and para dimers do form efficiently thanks to preferential sticking, but only at energies that are too high to be relevant for the chemistry of the interstellar medium. Computed reaction cross sections and ro-vibrational product populations are in good agreement with available experimental data and capable of generating adsorbate configurations similar to those observed with scanning tunneling microscopy techniques.

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

    SciTech Connect

    Curchod, Basile F. E.; Martínez, Todd J., E-mail: toddjmartinez@gmail.com; SLAC National Accelerator Laboratory, Menlo Park, California 94025

    2016-03-14

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

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

    SciTech Connect

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

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

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

    PubMed

    Müller, Julian; Hartke, Bernd

    2016-08-09

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

  3. 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.

  4. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Amorphous Ge quantum dots embedded in crystalline Si: ab initio results.

    PubMed

    Laubscher, M; Küfner, S; Kroll, P; Bechstedt, F

    2015-10-14

    We study amorphous Ge quantum dots embedded in a crystalline Si matrix through structure modeling and simulation using ab initio density functional theory including spin-orbit interaction and quasiparticle effects. Three models are generated by replacing a spherical region within diamond Si by Ge atoms and creating a disordered bond network with appropriate density inside the Ge quantum dot. After total-energy optimisations of the atomic geometry we compute the electronic and optical properties. We find three major effects: (i) the resulting nanostructures adopt a type-I heterostructure character; (ii) the lowest optical transitions occur only within the Ge quantum dots, and do not involve or cross the Ge-Si interface. (iii) for larger amorphous Ge quantum dots, with diameters of about 2.0 and 2.7 nm, absorption peaks appear in the mid-infrared spectral region. These are promising candidates for intense luminescence at photon energies below the gap energy of bulk Ge.

  6. Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate

    PubMed Central

    Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian

    2016-01-01

    High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation. PMID:26754622

  7. Ab initio study on the dynamics of furfural at the liquid-solid interfaces

    NASA Astrophysics Data System (ADS)

    Dang, Hongli; Xue, Wenhua; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2013-03-01

    Catalytic biomass conversion sometimes occurs at the liquid-solid interfaces. We report ab initio molecular dynamics simulations at finite temperatures for the catalytic reactions involving furfural at the water-Pd and water-Cu interfaces. We found that, during the dynamic process, the furan ring of furfural prefers to be parallel to the Pd surface and the aldehyde group tends to be away from the Pd surface. On the other hand, at the water-Cu(111) interface, furfural prefers to be tilted to the Cu surface while the aldehyde group is bonded to the surface. In both cases, interaction of liquid water and furfural is identified. The difference of dynamic process of furfural at the two interfaces suggests different catalytic reaction mechanisms for the conversion of furfural, consistent with the experimental investigations. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSED's and NERSC's supercomputers

  8. Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2013-03-01

    Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

  9. Lattice dynamics of solid N2 with an ab initio intermolecular potential

    NASA Astrophysics Data System (ADS)

    Luty, T.; van der Avoird, A.; Berns, R. M.

    1980-11-01

    We have performed harmonic and self-consistent phonon lattice dynamics calculations for α and γ N2 crystals using an intermolecular potential from ab initio calculations. This potential contains electrostatic (multipole) interactions, up to all R-9 terms inclusive, anisotropic dispersion interactions up to all R-10 terms inclusive, and anisotropic overlap interactions caused by charge penetration and exchange between the molecules. The lattice constants, cohesion energy, the frequencies of the translational phonon modes and the Grüneisen parameters for the librational modes are in good agreement with experimental values, confirming the quality of the potential. The frequencies of the librational modes and those of the mixed modes are less well reproduced, especially at temperatures near the α-β phase transition. Probably, the self-consistent phonon method used does not fully account for the anharmonicity in the librations.

  10. 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.

  11. Insights into H2 formation in space from ab initio molecular dynamics

    PubMed Central

    Casolo, Simone; Tantardini, Gian Franco; Martinazzo, Rocco

    2013-01-01

    Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley–Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley–Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account. PMID:23572584

  12. Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

    2016-05-01

    The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

  13. Ab initio study of the Jπ=0± continuum structures in 4He

    NASA Astrophysics Data System (ADS)

    Aoyama, S.; Baye, D.

    2018-05-01

    The Jπ=0± continuum structures in 4He are investigated by using an ab initio reaction theory with the microscopic R -matrix method. In the Ex≥˜20 MeV excitation energy region of 4He, the continuum states are mainly described by the t +p , h +n , and d +d channels. The Jπ=0± elastic phase shifts of the t +p and h +n channels show an apparently resonant behavior which might indicate the existence of excited 03+ and 02- resonance states of 4He above the known 02+ and 01- ones. However, the corresponding 03+ and 02- resonances have not been observed yet, although an experimental candidate with a large decay width is reported for 02-. In this paper, by analyzing the Jπ=0± S matrices, we discuss why the observation of these states is unlikely.

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  15. Ab initio study of the ground state surface of Cu3

    NASA Technical Reports Server (NTRS)

    Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.; Walch, Stephen P.; Laskowski, Bernard C.

    1986-01-01

    The ground state surface of the metallic trimer Cu3 is investigated theoretically. Relativistic and correlation effects are taken into account in ab initio computations, which are calibrated against analogous computations for the 1Sigma(g)+ state of Cu2; the results are presented in tables and analyzed. The Cu3 ground state is found to have a 2B2 C(2v) structure with angle greater than 60 deg, lying 59/cm below a 2A1 C(2v) geometry and 280/cm below the D(3h) equilateral geometry. These findings are shown to be in good agreement with the experimental measurements of Rohlfing and Valentini (1986) and their analysis (in terms of a Jahn-Teller distortion of 2E-prime equilateral-triangle geometry) by Truhlar et al. (1986).

  16. Classical trajectory studies of gas phase reaction dynamics and kinetics using ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.

    1989-01-01

    Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  18. Ultrafast transformation of graphite to diamond: an ab initio study of graphite under shock compression.

    PubMed

    Mundy, Christopher J; Curioni, Alessandro; Goldman, Nir; Will Kuo, I-F; Reed, Evan J; Fried, Laurence E; Ianuzzi, Marcella

    2008-05-14

    We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12 kms (longitudinal stress>130 GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.

  19. Ab initio study on the 1:2 reaction of CO 2 with dimethylamine

    NASA Astrophysics Data System (ADS)

    Jamróz, MichałH.; Dobrowolski, Jan Cz.; Borowiak, Marek A.

    1997-02-01

    The reaction between CO 2 and the dimethylamine molecule in the presence of a second dimethylamine molecule is modeled by the ab initio RHF/3-21G method. Starting from the most stable 1:2 complex, the most effective reaction pathway turned out to be proton transfer between amine molecules followed by immediate proton transfer from one of the amine molecules to the CO 2 moiety. The activation barrier for this pathway (9.54 kcal mol -1 with respect to the 1:2 complex) is within the range of activation energy values found in kinetic studies for similar reactions with different hydroxylamines (from 9.2 to 13.0 kcal mol -1). The reaction product is the cyclic hydrogen bonded complex of dimethylcarbamic acid with dimethylamine.

  20. Formation Dynamics of Potassium-Based Graphite Intercalation Compounds: An Ab Initio Study

    NASA Astrophysics Data System (ADS)

    Jiang, Xiankai; Song, Bo; Tománek, David

    2018-04-01

    This paper is a contribution to the Physical Review Applied collection in memory of Mildred S. Dresselhaus. We use ab initio molecular dynamics simulations to study the microscopic dynamics of potassium intercalation in graphite. Upon adsorbing on graphite from the vapor phase, K atoms transfer their valence charge to the substrate. K atoms adsorbed on the surface diffuse rapidly along the graphene basal plane and eventually enter the interlayer region following a "U -turn" across the edge, gaining additional energy. This process is promoted at higher coverages associated with higher K pressure, leading to the formation of a stable intercalation compound. We find that the functionalization of graphene edges is an essential prerequisite for intercalation since bare edges reconstruct and reconnect, closing off the entry channels for the atoms.

  1. Analysis of borderline substitution/electron transfer pathways from direct ab initio MD simulations

    NASA Astrophysics Data System (ADS)

    Yamataka, Hiroshi; Aida, Misako; Dupuis, Michel

    2002-02-01

    Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH 2O rad - with CH 3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the S N2-like transition state (TS): (i) a direct formation of S N2 products, (ii) a direct formation of ET products, and (iii) a two-step formation of ET products via the S N2 valley. The direct formation of the ET product through the S N2-like TS appears to be more favorable at higher temperatures. The two-step process depends on the amount of energy that goes into the C-C stretching mode.

  2. Carbon diffusion in molten uranium: an ab initio molecular dynamics study

    SciTech Connect

    Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.

    In this work we used ab initio molecular dynamics (AIMD) within the framework of density functional theory (DFT) and the projector-augmented wave (PAW) method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activationmore » energy for carbon was nearly twice that of uranium: 0.55±0.03 eV for carbon compared to 0.32±0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.« less

  3. Structural phase transition of gold under uniaxial, tensile, and triaxial stresses: An ab initio study

    NASA Astrophysics Data System (ADS)

    Durandurdu, Murat

    2007-07-01

    The behavior of gold crystal under uniaxial, tensile, and three different triaxial stresses is studied using an ab initio constant pressure technique within a generalized gradient approximation. Gold undergoes a phase transformation from the face-centered-cubic structure (fcc) to a body-centered-tetragonal (bct) structure having the space group of I4/mmm with the application of uniaxial stress, while it transforms to a face-centered-tetragonal (fct) phase within I4/mmm symmetry under uniaxial tensile loading. Further uniaxial compression of the bct phase results in a symmetry change from I4/mmm to P1 at high stresses and ultimately structural failure around 200.0GPa . For the case of triaxial stresses, gold also converts into a bct state. The critical stress for the fcc-to-bct transformation increases as the ratio of the triaxial stress increases. Both fct and bct phases are elastically unstable.

  4. Carbon diffusion in molten uranium: an ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.; Henson, Neil J.; Devanathan, Ram; Schwantes, Jon M.; Reilly, Dallas D.

    2018-04-01

    In this work we used ab initio molecular dynamics within the framework of density functional theory and the projector-augmented wave method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activation energy for carbon was nearly twice that of uranium: 0.55 ± 0.03 eV for carbon compared to 0.32 ± 0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.

  5. Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging

    DOE PAGES

    Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.; ...

    2014-12-11

    In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropicmore » component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.« less

  6. Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging

    SciTech Connect

    Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.

    In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropicmore » component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.« less

  7. Communication: GAIMS—generalized ab initio multiple spawning for both internal conversion and intersystem crossing processes

    DOE PAGES

    Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; ...

    2016-03-11

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

  8. Ab initio structure prediction of silicon and germanium sulfides for lithium-ion battery materials

    NASA Astrophysics Data System (ADS)

    Hsueh, Connie; Mayo, Martin; Morris, Andrew J.

    Conventional experimental-based approaches to materials discovery, which can rely heavily on trial and error, are time-intensive and costly. We discuss approaches to coupling experimental and computational techniques in order to systematize, automate, and accelerate the process of materials discovery, which is of particular relevance to developing new battery materials. We use the ab initio random structure searching (AIRSS) method to conduct a systematic investigation of Si-S and Ge-S binary compounds in order to search for novel materials for lithium-ion battery (LIB) anodes. AIRSS is a high-throughput, density functional theory-based approach to structure prediction which has been successful at predicting the structures of LIBs containing sulfur and silicon and germanium. We propose a lithiation mechanism for Li-GeS2 anodes as well as report new, theoretically stable, layered and porous structures in the Si-S and Ge-S systems that pique experimental interest.

  9. Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.

    PubMed

    Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R

    2015-07-08

    We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.

  10. Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters

    NASA Astrophysics Data System (ADS)

    Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian

    2017-10-01

    Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).

  11. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data

    NASA Astrophysics Data System (ADS)

    White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.

    2017-01-01

    Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.

  12. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data.

    PubMed

    White, Andrew D; Knight, Chris; Hocky, Glen M; Voth, Gregory A

    2017-01-28

    Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.

  13. Ab initio Prediction of Martensitic and Intermartensitic Phase Boundaries in Ni-Mn-Ga

    NASA Astrophysics Data System (ADS)

    Dutta, B.; ćakır, A.; Giacobbe, C.; Al-Zubi, A.; Hickel, T.; Acet, M.; Neugebauer, J.

    2016-01-01

    Despite the importance of martensitic transformations of Ni-Mn-Ga Heusler alloys for their magnetocaloric and shape-memory properties, the martensitic part of their phase diagrams is not well determined. Using an ab initio approach that includes the interplay of lattice and vibrational degrees of freedom we identify an intermartensitic transformation between a modulated and a nonmodulated phase as a function of excess Ni and Mn content. Based on an evaluation of the theoretical findings and experimental x-ray diffraction data for Mn-rich alloys, we are able to predict the phase diagram for Ni-rich alloys. In contrast to other mechanisms discussed for various material systems in the literature, we herewith show that the intermartensitic transformation can be understood solely using thermodynamic concepts.

  14. Ab Initio Vibrational Levels For HO2 and Vibrational Splittings for Hydrogen Atom Transfer

    NASA Technical Reports Server (NTRS)

    Barclay, V. J.; Dateo, Christopher E.; Hamilton, I. P.; Arnold, James O. (Technical Monitor)

    1994-01-01

    We calculate vibrational levels and wave functions for HO2 using the recently reported ab initio potential energy surface of Walch and Duchovic. There is intramolecular hydrogen atom transfer when the hydrogen atom tunnels through a T-shaped saddle point separating two equivalent equilibrium geometries, and correspondingly, the energy levels are split. We focus on vibrational levels and wave functions with significant splitting. The first three vibrational levels with splitting greater than 2/cm are (15 0), (0 7 1) and (0 8 0) where V(sub 2) is the O-O-H bend quantum number. We discuss the dynamics of hydrogen atom transfer; in particular, the O-O distances at which hydrogen atom transfer is most probable for these vibrational levels. The material of the proposed presentation was reviewed and the technical content will not reveal any information not already in the public domain and will not give any foreign industry or government a competitive advantage.

  15. FTIR, FT-Raman spectra and ab initio, DFT vibrational analysis of 2,4-dinitrophenylhydrazine.

    PubMed

    Sundaraganesan, N; Ayyappan, S; Umamaheswari, H; Joshua, B Dominic

    2007-01-01

    The FTIR and FT-Raman spectra of 2,4-dinitrophenylhydrazine (2,4-DNPH) has been recorded in the region 4000-400 and 3500-50cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,4-DNPH were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

  16. FTIR, FT-Raman spectra and ab initio, DFT vibrational analysis of 2,4-dinitrophenylhydrazine

    NASA Astrophysics Data System (ADS)

    Sundaraganesan, N.; Ayyappan, S.; Umamaheswari, H.; Dominic Joshua, B.

    2007-01-01

    The FTIR and FT-Raman spectra of 2,4-dinitrophenylhydrazine (2,4-DNPH) has been recorded in the region 4000-400 and 3500-50 cm -1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,4-DNPH were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

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

    NASA Astrophysics Data System (ADS)

    Ji, Pengfei; Zhang, Yuwen

    2016-04-01

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

  18. A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

    PubMed

    Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

    2009-07-28

    Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

  19. Ab initio study of structural and mechanical property of solid molecular hydrogens

    NASA Astrophysics Data System (ADS)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  20. Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

    NASA Astrophysics Data System (ADS)

    VandeVondele, Joost; Rothlisberger, Ursula

    2000-09-01

    We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

  1. Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures

    NASA Astrophysics Data System (ADS)

    Clay, Raymond; Morales, Miguel

    2017-06-01

    In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  2. Progress towards an ab initio real-time treatment of warm dense matter

    NASA Astrophysics Data System (ADS)

    Baczewski, Andrew; Cangi, Attila; Hansen, Stephanie; Jensen, Daniel

    2017-10-01

    Time-dependent density functional theory (TDDFT) provides an accurate description of equilibrium properties of warm dense matter, such as the dynamic structure factor (Baczewski et al., Phys. Rev. Lett., 116(11), 2016). While non-equilibrium properties, such as stopping power, have also been demonstrated to be within the grasp of TDDFT, the ultrafast isochoric heating of condensed matter into the warm dense state, enabled by recent advances in XFELs, remains beyond its capabilities. In this talk, we will describe the successes of and continuing challenges for TDDFT for warm dense matter, and present progress towards a more complete ab initio treatment of isochoric x-ray heating. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International, Inc., for the DOE's National Nuclear Security Administration under contract DE-NA0003525.

  3. AFLOWLIB.ORG: a Distributed Materials Properties Repository from High-throughput Ab initio Calculations

    DTIC Science & Technology

    2011-11-15

    uncle) fcc (uncle) hcp (uncle) phase-diagram Ag Al Al Au Au Bi Bi Ca Ca Cd Cd Ce Ce Co Co Cr Cr Cu Cu Fe Fe Ga Ga Gd Gd Ge Ge Hf...Hf Hg Hg In In Ir Ir La La Li Li Mg Mg Mn Mn Mo Mo Na Na Nb Nb Ni Ni Os Os Pb Pb Pd Pd Pt Pt Rb Rb Re Re Rh Rh Ru Ru Sb Sb Sc...2 S. Curtarolo, A. N. Kolmogorov, and F. H. Cocks, High-throughput ab initio analysis of the Bi-In, Bi- Mg , Bi-Sb, In- Mg , In-Sb, and Mg -Sb systems

  4. Formation of superconducting platinum hydride under pressure: an ab initio approach

    NASA Astrophysics Data System (ADS)

    Kim, Duck Young; Scheicher, Ralph; Pickard, Chris; Needs, Richard; Ahuja, Rajeev

    2012-02-01

    Noble metals such as Pt, Au, or Re are commonly used for electrodes and gaskets in diamond anvil cells for high-pressure research because they are expected to rarely undergo structural transformation and possess simple equation of states. Specifically Pt has been used widely for high-pressure experiments and has been considered to resist hydride formation under pressure. Pressure-induced reactions of metals with hydrogen are in fact quite likely because hydrogen atoms can occupy interstitial positions in the metal lattice, which can lead to unexpected effects in experiments. In our study, PRL 107 117002 (2011), we investigated crystal structures using ab initio random structure searching (AIRSS) and predicted the formation of platinum mono-hydride above 22 GPa and superconductivity Tc was estimated to be 10 -- 25 K above around 80 GPa. Furthermore, we showed that the formation of fcc noble metal hydrides under pressure is common and examined the possibility of superconductivity in these materials.

  5. Ab initio study on the molecular recognition by metalloporphyrins: CO interaction with iron porphyrin

    NASA Astrophysics Data System (ADS)

    Han, Seungwu; Cho, Kyeongjae; Ihm, Jisoon

    1999-02-01

    We have performed ab initio pseudopotential calculations to study the effects of structural deformations of iron porphyrin on the configuration of a carbon monoxide (CO) attached to it. We have considered two proximal deformations around the heme group: (i) rotation of a pyrrole ring in the iron porphyrin, and (ii) rotation of the imidazole side chain bound to the iron atom. We have identified induced changes of the atomic geometry and the electronic structure of the iron porphyrin-CO complex, and the results elucidate the microscopic nature of the CO interaction with the iron porphyrin. Implications on the controversies over the binding angle of the CO molecule on the iron porphyrin under different circumstances are discussed. A potential application to the simulation-based chemical sensor design is also discussed.

  6. Ab initio perspective on the Mollwo-Ivey relation for F centers in alkali halides

    NASA Astrophysics Data System (ADS)

    Tiwald, Paul; Karsai, Ferenc; Laskowski, Robert; Gräfe, Stefanie; Blaha, Peter; Burgdörfer, Joachim; Wirtz, Ludger

    2015-10-01

    We revisit the well-known Mollwo-Ivey relation that describes the "universal" dependence of the absorption energies of F-type color centers on the lattice constant a of alkali-halide crystals, Eabs∝a-n. We perform both state-of-the-art ab initio quantum chemistry and post-DFT calculations of F-center absorption spectra. By "tuning" independently the lattice constant and the atomic species we show that the scaling with the lattice constant alone (keeping the elements fixed) would yield n =2 in agreement with the "particle-in-the-box" model. Keeping the lattice constant fixed and changing the atomic species enables us to quantify the ion-size effects which are shown to be responsible for the exponent n ≈1.8 .

  7. Fully ab initio calculation of the resonant one-phonon Raman intensity of graphene

    NASA Astrophysics Data System (ADS)

    Reichardt, Sven; Wirtz, Ludger

    We developed a fully ab initio, many-body perturbation theory approach for the calculation of resonant, one-phonon Raman spectra. Our general approach is applicable to any material and here we present its application to the case of graphene. Our diagrammatic, first-principles approach allows us to go beyond and improve on an earlier theoretical study by Basko, which relied on an analytical calculation in certain limits. We investigate the dependence of the G peak intensity on both the excitation energy and Fermi level. Furthermore, our method allows us to identify the relevant electronic quantum pathways and to demonstrate the importance of the contributions from non-resonant electronic transitions. We also applied our approach to the calculation of the resonant one-phonon Raman spectrum of MoS2, with our results being in good agreement with experimental data. SR acknowledges financial support from the National Research Fund (FNR) Luxembourg.

  8. Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy

    NASA Astrophysics Data System (ADS)

    Wang, S. Y.; Kramer, M. J.; Xu, M.; Wu, S.; Hao, S. G.; Sordelet, D. J.; Ho, K. M.; Wang, C. Z.

    2009-04-01

    X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al60Cu40 have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.

  9. Ab initio Prediction of Martensitic and Intermartensitic Phase Boundaries in Ni-Mn-Ga.

    PubMed

    Dutta, B; Çakır, A; Giacobbe, C; Al-Zubi, A; Hickel, T; Acet, M; Neugebauer, J

    2016-01-15

    Despite the importance of martensitic transformations of Ni-Mn-Ga Heusler alloys for their magnetocaloric and shape-memory properties, the martensitic part of their phase diagrams is not well determined. Using an ab initio approach that includes the interplay of lattice and vibrational degrees of freedom we identify an intermartensitic transformation between a modulated and a nonmodulated phase as a function of excess Ni and Mn content. Based on an evaluation of the theoretical findings and experimental x-ray diffraction data for Mn-rich alloys, we are able to predict the phase diagram for Ni-rich alloys. In contrast to other mechanisms discussed for various material systems in the literature, we herewith show that the intermartensitic transformation can be understood solely using thermodynamic concepts.

  10. Ab initio calculations, structure, NBO and NCI analyses of Xsbnd H⋯π interactions

    NASA Astrophysics Data System (ADS)

    Wu, Qiyang; Su, He; Wang, Hongyan; Wang, Hui

    2018-02-01

    The performance of ab initio methods (MP2, DFT/B3LYP, random-phase approximation (RPA), CCSD(T) and QCISD(T)) in predicting interaction energy of Xsbnd H⋯π (Xsbnd H = HCCH, HCl, HF; π = C2H2, C2H4, C6H6) hydrogen complexes are assessed systematically. The CCSD(T)/CBS benchmarks of interaction energy are reported. It is found that RPA agrees well with CCSD(T)/CBS benchmarks and experimental results. CCSD(T) and QCISD(T) perform the best only when compared with CCSD(T)/CBS benchmarks, MP2 performs well only for experimental data. B3LYP provides the worst accuracy. Additionally, the equilibrium structure, interaction type of Xsbnd H⋯π hydrogen complexes are investigated by the natural bond orbital (NBO) and the non-covalent interaction index (NCI).

  11. Ab initio calculation of the ion feature in x-ray Thomson scattering.

    PubMed

    Plagemann, Kai-Uwe; Rüter, Hannes R; Bornath, Thomas; Shihab, Mohammed; Desjarlais, Michael P; Fortmann, Carsten; Glenzer, Siegfried H; Redmer, Ronald

    2015-07-01

    The spectrum of x-ray Thomson scattering is proportional to the dynamic structure factor. An important contribution is the ion feature which describes elastic scattering of x rays off electrons. We apply an ab initio method for the calculation of the form factor of bound electrons, the slope of the screening cloud of free electrons, and the ion-ion structure factor in warm dense beryllium. With the presented method we can calculate the ion feature from first principles. These results will facilitate a better understanding of x-ray scattering in warm dense matter and an accurate measurement of ion temperatures which would allow determining nonequilibrium conditions, e.g., along shock propagation.

  12. Ab initio surface properties of Ag-Sn alloys: implications for lead-free soldering.

    PubMed

    Saleh, Gabriele; Xu, Chen; Sanvito, Stefano

    2018-02-07

    Ag and Sn are the major components of solder alloys adopted to assemble printed circuit boards. The qualities that make them the alloys of choice for the modern electronic industry are related to their physical and chemical properties. For corrosion resistance and solderability, surface properties are particularly important. Yet, atomic-level information about the surfaces of these alloys is not known. Here we fill this gap by presenting an extensive ab initio investigation of composition, energetics, structure and reactivity of Ag-Sn alloy surfaces. The structure and stability of various surfaces is evaluated, and the main factors determining the energetics of surface formation are uncovered. Oxygen and sulphur chemisorptions are studied and discussed in the framework of corrosion tendency, an important issue for printed circuit boards. Adsorption energy trends are rationalized based on the analysis of structural and electronic features.

  13. Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

    PubMed Central

    2017-01-01

    Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

  14. Exploration of phase transition in Th2C under pressure: An Ab-initio investigation

    NASA Astrophysics Data System (ADS)

    Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.

    2018-05-01

    With the motivation of searching for new compounds in the Th-C system, we have performed ab initio evolutionary searches for all the stable compounds in this binary system in the pressure range of 0-100 GPa. We have found previously unknown, thermodynamically stable, composition Th2C along with experimentally known ThC, ThC2 and Th2C3 phases at 0 GPa. Interestingly at pressure of 13 GPa the predicted ground state orthorhombic (SG no. 59, Pmmn) phase of Th2C transforms to trigonal (SG no. 164, P-3m1) phase. We also find the mechanical and dynamical stability of both the phases. Further, the theoretically determined equation of state has been utilized to derive various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus of Pmmn phase at ambient conditions.

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

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  16. Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

    PubMed

    Šipr, O; Ebert, H; Minár, J

    2015-02-11

    A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

  17. Exploration of phase transition in ThS under pressure: An ab-initio investigation

    NASA Astrophysics Data System (ADS)

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

    2018-04-01

    The ab-initio total energy calculations have been performed in thorium sulphide (ThS) to explore its high pressure phase stability. Our calculations predict a phase transformation from ambient rocksalt type structure (B1 phase) to a rhombohedral structure (R-3m phase) at ˜ 15 GPa and subsequently R-3m phase transforms to CsCl type structure (B2 phase) at ˜ 45 GPa. The first phase transition has been identified as second order type; whereas, the second transition is of first order type with volume discontinuity of 6.5%. The predicted high pressure R-3m phase is analogous to the experimentally observed hexagonal (distorted fcc) phase (Benedict et al., J. Less-Common Met., 1984) above 20 GPa. Further, using these calculations we have derived the equation of state which has been utilized to determine various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus at ambient conditions.

  18. Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

    PubMed

    Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

    2014-04-23

    We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

  19. Organic carbonates: experiment and ab initio calculations for prediction of thermochemical properties.

    PubMed

    Verevkin, Sergey P; Emel'yanenko, Vladimir N; Kozlova, Svetlana A

    2008-10-23

    This work has been undertaken in order to obtain data on thermodynamic properties of organic carbonates and to revise the group-additivity values necessary for predicting their standard enthalpies of formation and enthalpies of vaporization. The standard molar enthalpies of formation of dibenzyl carbonate, tert-butyl phenyl carbonate, and diphenyl carbonate were measured using combustion calorimetry. Molar enthalpies of vaporization of these compounds were obtained from the temperature dependence of the vapor pressure measured by the transpiration method. Molar enthalpy of sublimation of diphenyl carbonate was measured in the same way. Ab initio calculations of molar enthalpies of formation of organic carbonates have been performed using the G3MP2 method, and results are in excellent agreement with the available experiment. Then the group-contribution method has been developed to predict values of the enthalpies of formation and enthalpies of vaporization of organic carbonates.

  20. Modeling and Ab initio Calculations of Thermal Transport in Si-Based Clathrates and Solar Perovskites

    NASA Astrophysics Data System (ADS)

    He, Yuping

    2015-03-01

    We present calculations of the thermal transport coefficients of Si-based clathrates and solar perovskites, as obtained from ab initio calculations and models, where all input parameters derived from first principles. We elucidated the physical mechanisms responsible for the measured low thermal conductivity in Si-based clatherates and predicted their electronic properties and mobilities, which were later confirmed experimentally. We also predicted that by appropriately tuning the carrier concentration, the thermoelectric figure of merit of Sn and Pb based perovskites may reach values ranging between 1 and 2, which could possibly be further increased by optimizing the lattice thermal conductivity through engineering perovskite superlattices. Work done in collaboration with Prof. G. Galli, and supported by DOE/BES Grant No. DE-FG0206ER46262.

  1. Berry curvature dipole in Weyl semimetal materials: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Sun, Yan; Yan, Binghai

    2018-01-01

    Noncentrosymmetric metals are anticipated to exhibit a dc photocurrent in the nonlinear optical response caused by the Berry curvature dipole in momentum space. Weyl semimetals (WSMs) are expected to be excellent candidates for observing these nonlinear effects because they carry a large Berry curvature concentrated in small regions, i.e., near the Weyl points. We have implemented the semiclassical Berry curvature dipole formalism into an ab initio scheme and investigated the second-order nonlinear response for two representative groups of materials: the TaAs-family type-I WSMs and the MoTe2-family type-II WSMs. Both types of WSMs exhibited a Berry curvature dipole in which type-II Weyl points are usually superior to the type-I WSM because of the strong tilt. Corresponding nonlinear susceptibilities in several materials promise a nonlinear Hall effect in the dc field limit, which is within the experimentally detectable range.

  2. Exploring Partonic Structure of Hadrons Using ab initio Lattice QCD Calculations

    DOE PAGES

    Ma, Yan-Qing; Qiu, Jian-Wei

    2018-01-10

    Following our previous proposal, we construct a class of good "lattice cross sections" (LCSs), from which we can study the partonic structure of hadrons from ab initio lattice QCD calculations. These good LCSs, on the one hand, can be calculated directly in lattice QCD, and on the other hand, can be factorized into parton distribution functions (PDFs) with calculable coefficients, in the same way as QCD factorization for factorizable hadronic cross sections. PDFs could be extracted from QCD global analysis of the lattice QCD generated data of LCSs. In conclusion, we also show that the proposed functions for lattice QCDmore » calculation of PDFs in the literature are special cases of these good LCSs.« less

  3. Doppler broadening of neutron-induced resonances using ab initio phonon spectrum

    NASA Astrophysics Data System (ADS)

    Noguere, G.; Maldonado, P.; De Saint Jean, C.

    2018-05-01

    Neutron resonances observed in neutron cross section data can only be compared with their theoretical analogues after a correct broadening of the resonance widths. This broadening is usually carried out by two different theoretical models, namely the Free Gas Model and the Crystal Lattice Model, which, however, are only applicable under certain assumptions. Here, we use neutron transmission experiments on UO2 samples at T=23.7 K and T=293.7 K, to investigate the limitations of these models when an ab initio phonon spectrum is introduced in the calculations. Comparisons of the experimental and theoretical transmissions highlight the underestimation of the energy transferred at low temperature and its impact on the accurate determination of the radiation widths Γ_{γ_{λ}} of the 238U resonances λ. The observed deficiency of the model represents an experimental evidence that the Debye-Waller factor is not correctly calculated at low temperature near the Neel temperature ( TN=30.8 K).

  4. The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2011-10-01

    High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC = CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98 ± 0.17, -1.67 ± 0.82, 7.64 ± 0.21, 8.39 ± 0.31, 2.82 ± 0.52, 10.27 ± 0.39, 9.12 ± 0.18, 5.47 ± 0.53, 7.50 ± 0.43, 10.12 ± 0.51, 8.49 ± 0.33, and 6.19 ± 0.18 kcal mol-1 for X = BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD = 1.04 kcal mol-1).

  5. Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

    PubMed Central

    Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

    2015-01-01

    We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score=0.736 and RMSD=2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. PMID:26370505

  6. 14N NQR lineshape in nanocrystals: An ab initio investigation of urea

    PubMed Central

    Gregorovič, Alan

    2017-01-01

    14N nuclear quadrupole resonance (NQR) lineshapes mostly contain information of low interest, although in nanocrystals they may display some unexpected behaviour. In this work, we present an ab initio computational study of the 14N NQR lineshapes in urea nanocrystals as a function of the nanocrystal size and geometry, focusing on the surface induced broadening of the lineshapes. The lineshapes were obtained through a calculation of the electric field gradient for each nitrogen site in the nanocrystal separately, taking into account the individual crystal field by embedding the molecule of interest in a suitable lattice of point multipoles representing other urea molecules in the nanocrystal. The small influence of distant molecules is found with a series expansion, using the in-crystal Sternheimer shieldings which we also calculated ab initio. We have considered nanocrystals with two geometries: a sphere and a cube, with characteristic sizes between 5 and 100 nm. Our calculations suggest that there is a dramatic difference between the linewidths for the two geometries. For spheres, we find a steep drop in linewidths at ∼10 nm; at 5 nm the linewidth is ∼11 kHz, whereas for sizes above 20 nm the linewidth is practically negligible (<100 Hz). For cubes, on the other hand, we find a steady 1/size decrease, from 12 kHz at 10 nm to 1.2 kHz at 100 nm. This analysis is important for 14N NQR spectroscopy of crystalline pharmaceuticals, where nanoparticles are increasingly more often embedded in some sort of matrix. Although this is only a theoretical analysis, we believe that this work can serve as a guidance for the forthcoming experimental analysis. PMID:28527464

  7. On the photoisomerization of 5-hydroxytropolone: An ab initio and nuclear wave function study

    NASA Astrophysics Data System (ADS)

    Paz, Juan J.; Moreno, Miquel; Lluch, José M.

    1997-10-01

    In this paper we perform ab initio calculations for the stable conformations and the transition states for the isomerization processes in 5-hydroxytropolone in both the ground (S0) and first excited (S1) singlet electronic states. The Hartree-Fock self-consistent field (SCF) level and a complete active space SCF (CASSCF) level for S0 are considered, whereas the configuration interaction all single excitation method (CIS) and the CASSCF levels are used to deal with the S1 state. Energies are reevaluated at all levels through perturbation theory up to second order: Møller-Plesset for the Hartree-Fock and CIS methods, and the CASPT2 method for CAS results. The ab initio results are then used to perform different monodimensional fits to the potential energy surfaces in order to analyze the wave functions for the nuclear motions in both electronic states. Our best results predict that for the S0 state two stable conformers, syn and anti, can exist in thermal equilibrium. In accordance with experimental expectations the syn isomer is the most stable. As for the S1 state, and again in accord with experimental spectroscopical data, the order of stability reverses, the anti being the most stable. A more interesting result is that analysis of the nuclear wave functions shows an important syn-anti mixing in the S1 state that does not appear in S0. This result explains the appearance of syn-anti and anti-syn crossover transitions observed in the electronic spectra of 5-hydroxytropolone so that syn-anti reaction may take place through photoisomerization.

  8. Lanthanide complex coordination polyhedron geometry prediction accuracies of ab initio effective core potential calculations.

    PubMed

    Freire, Ricardo O; Rocha, Gerd B; Simas, Alfredo M

    2006-03-01

    lanthanide coordination compounds efficiently and accurately is central for the design of new ligands capable of forming stable and highly luminescent complexes. Accordingly, we present in this paper a report on the capability of various ab initio effective core potential calculations in reproducing the coordination polyhedron geometries of lanthanide complexes. Starting with all combinations of HF, B3LYP and MP2(Full) with STO-3G, 3-21G, 6-31G, 6-31G* and 6-31+G basis sets for [Eu(H2O)9]3+ and closing with more manageable calculations for the larger complexes, we computed the fully predicted ab initio geometries for a total of 80 calculations on 52 complexes of Sm(III), Eu(III), Gd(III), Tb(III), Dy(III), Ho(III), Er(III) and Tm(III), the largest containing 164 atoms. Our results indicate that RHF/STO-3G/ECP appears to be the most efficient model chemistry in terms of coordination polyhedron crystallographic geometry predictions from isolated lanthanide complex ion calculations. Moreover, both augmenting the basis set and/or including electron correlation generally enlarged the deviations and aggravated the quality of the predicted coordination polyhedron crystallographic geometry. Our results further indicate that Cosentino et al.'s suggestion of using RHF/3-21G/ECP geometries appears to be indeed a more robust, but not necessarily, more accurate recommendation to be adopted for the general lanthanide complex case. [Figure: see text].

  9. Ab initio study of thermoelectric properties of doped SnO{sub 2} superlattices

    SciTech Connect

    Borges, P.D., E-mail: pdborges@gmail.com; Silva, D.E.S.; Castro, N.S.

    2015-11-15

    Transparent conductive oxides, such as tin dioxide (SnO{sub 2}), have recently shown to be promising materials for thermoelectric applications. In this work we studied the thermoelectric properties of Fe-, Sb- and Zn-uniformly doping and co-doping SnO{sub 2}, as well as of Sb and Zn planar (or delta)-doped layers in SnO{sub 2} forming oxide superlattices (SLs). Based on the semiclassical Boltzmann transport equations (BTE) in conjunction with ab initio electronic structure calculations, the Seebeck coefficient (S) and figure of merit (ZT) are obtained for these systems, and are compared with available experimental data. The delta doping approach introduces a remarkable modificationmore » in the electronic structure of tin dioxide, when compared with the uniform doping, and colossal values for ZT are predicted for the delta-doped oxide SLs. This result is a consequence of the two-dimensional electronic confinement and the strong anisotropy introduced by the doped planes. In comparison with the uniformly doped systems, our predictions reveal a promising use of delta-doped SnO{sub 2} SLs for enhanced S and ZT, which emerge as potential candidates for thermoelectric applications. - Graphical abstract: Band structure and Figure of merit for SnO2:Sb superlattice along Z direction, P. D. Borges, D. E. S. Silva, N. S. Castro, C. R. Ferreira, F. G. Pinto, J. Tronto and L. Scolfaro, Ab initio study of thermoelectric properties of doped SnO2 superlattices. - Highlights: • Thermoelectric properties of SnO{sub 2}-based alloys and superlattices. • High figure of merit is predicted for planar-doped SnO{sub 2} superlattices. • Nanotechnology has an important role for the development of thermoelectric devices.« less

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

    SciTech Connect

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

    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

  11. 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

  12. Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

    PubMed Central

    Xu, Dong; Zhang, Yang

    2012-01-01

    Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

  13. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

    PubMed

    Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

    2016-09-01

    We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  14. 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., E-mail: tmarkland@stanford.edu

    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 asmore » 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.« less

  15. 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.

  16. Ab Initio Kinetics of Hydrogen Abstraction from Methyl Acetate by Hydrogen, Methyl, Oxygen, Hydroxyl, and Hydroperoxy Radicals.

    PubMed

    Tan, Ting; Yang, Xueliang; Krauter, Caroline M; Ju, Yiguang; Carter, Emily A

    2015-06-18

    The kinetics of hydrogen abstraction by five radicals (H, O((3)P), OH, CH3, and HO2) from methyl acetate (MA) is investigated theoretically in order to gain further understanding of certain aspects of the combustion chemistry of biodiesels, such as the effect of the ester moiety. We employ ab initio quantum chemistry methods, coupled cluster singles and doubles with perturbative triples correction (CCSD(T)) and multireference averaged coupled pair functional theory (MRACPF2), to predict chemically accurate reaction energetics. Overall, MRACPF2 predicts slightly higher barrier heights than CCSD(T) for MA + H/CH3/O/OH, but slightly lower barrier heights for hydrogen abstraction by HO2. Based on the obtained reaction energies, we also report high-pressure-limit rate constants using transition state theory (TST) in conjunction with the separable-hindered-rotor approximation, the variable reaction coordinate TST, and the multi-structure all-structure approach. The fitted modified Arrhenius expressions are provided over a temperature range of 250 to 2000 K. The predictions are in good agreement with available experimental results. Abstractions from both of the methyl groups in MA are expected to contribute to consumption of the fuel as they exhibit similar rate coefficients. The reactions involving the OH radical are predicted to have the highest rates among the five abstracting radicals, while those initiated by HO2 are expected to be the lowest.

  17. An ab initio study of Fe(CO)n, n = 1,5, and Cr(CO)6

    NASA Technical Reports Server (NTRS)

    Barnes, Leslie A.; Rosi, Marzio; Bauschlicher, Charles W., Jr.

    1991-01-01

    Ab initio calculations have been performed for Cr(CO)6 and Fe(CO)n, n = 1,5. Basis sets of better than double zeta quality are used, and correlation is included using the modified coupler-pair functional method. The computed geometries and force constants are in reasonable agreement with experiment. The sequential bond dissociation energies of CO from Fe(CO)5 are estimated to be: 39, 31, 25, 22, and greater than 5 kcal/mol. It is noted that the first bond dissociation energy is relative to the singlet ground state of Fe(CO)5 and the lowest singlet state of Fe(CO)4, whereas the second is relative to the ground triplet states of Fe(CO)4 and Fe(CO)3. In addition, the binding energy for Fe-CO would be modified to 18 kcal/mol if dissociation occurred to the Fe(5F) excited state asymptote. The CO binding energies for Fe and Cr are found to be in poorer agreement with experiment than those found in a previous study on Ni(CO)4. The origins of this difference are discussed.

  18. 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.

  19. Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations.

    PubMed

    Yoshioka, Akio; Fukuzawa, Kaori; Mochizuki, Yuji; Yamashita, Katsumi; Nakano, Tatsuya; Okiyama, Yoshio; Nobusawa, Eri; Nakajima, Katsuhisa; Tanaka, Shigenori

    2011-09-01

    Ab initio electronic-state calculations for influenza virus hemagglutinin (HA) trimer complexed with Fab antibody were performed on the basis of the fragment molecular orbital (FMO) method at the second and third-order Møller-Plesset (MP2 and MP3) perturbation levels. For the protein complex containing 2351 residues and 36,160 atoms, the inter-fragment interaction energies (IFIEs) were evaluated to illustrate the effective interactions between all the pairs of amino acid residues. By analyzing the calculated data on the IFIEs, we first discussed the interactions and their fluctuations between multiple domains contained in the trimer complex. Next, by combining the IFIE data between the Fab antibody and each residue in the HA antigen with experimental data on the hemadsorption activity of HA mutants, we proposed a protocol to predict probable mutations in HA. The proposed protocol based on the FMO-MP2.5 calculation can explain the historical facts concerning the actual mutations after the emergence of A/Hong Kong/1/68 influenza virus with subtype H3N2, and thus provides a useful methodology to enumerate those residue sites likely to mutate in the future. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Ab Initio Cluster Calculations for the Adsorption of Small Molecules on Oxide Surfaces - from Single Molecules to Monolayers

    NASA Astrophysics Data System (ADS)

    Pykavy, M.; Staemmler, V.; Rittner, F.

    2000-04-01

    Quantum chemical ab initio cluster calculations were performed for the adsorption of small molecules on metal oxide surfaces. Two systems were studied in detail: The adsorption of N2 on the (110) surface plane of TiO2 (rutile) and the adsorption of CO on the polar (0001) surface of Cr2O3. In both cases a full five-dimensional potential for the interaction of a single molecule with the respective surface was calculated. For N2/TiO2 (110) the minimum was found for the end-on adsorption of N2 atop a coordinately unsaturated surface Ti atom, with an adsorption energy of (35 ± 5) kJ/mol. In the case of CO/Cr2O3 (0001) the CO molecule is adsorbed strongly tilted (almost side-on) along a line connecting two Cr3+ ions at the surface; the calculated adsorption energy is 22 kJ/mol. In conjunction with empirical pair potentials for the N2/N2 and CO/CO interaction in the gas phase, Monte Carlo simulations were carried out to determine adsorption isotherms and the geometric structure of adsorbed monolayers.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed

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

    2015-05-21

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

  3. Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

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

    DOE PAGES

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

    2014-05-05

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

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

    SciTech Connect

    Orimoto, Yuuichi; Xie, Peng; Liu, Kai

    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 negligiblymore » 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

  6. Mechanical properties of Fe rich Fe-Si alloys: ab initio local bulk-modulus viewpoint

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Somesh Kr; Kohyama, Masanori; Tanaka, Shingo; Shiihara, Yoshinori; Saengdeejing, Arkapol; Chen, Ying; Mohri, Tetsuo

    2017-11-01

    Fe-rich Fe-Si alloys show peculiar bulk-modulus changes depending on the Si concentration in the range of 0-15 at.%Si. In order to clarify the origin of this phenomenon, we have performed density-functional theory calculations of supercells of Fe-Si alloy models with various Si concentrations. We have applied our recent techniques of ab initio local energy and local stress, by which we can obtain a local bulk modulus of each atom or atomic group as a local constituent of the cell-averaged bulk modulus. A2-phase alloy models are constructed by introducing Si substitution into bcc Fe as uniformly as possible so as to prevent mutual neighboring, while higher Si concentrations over 6.25 at.%Si lead to contacts between SiFe8 cubic clusters via sharing corner Fe atoms. For 12.5 at.%Si, in addition to an A2 model, we deal with partial D03 models containing local D03-like layers consisting of edge-shared SiFe8 cubic clusters. For the cell-averaged bulk modulus, we have successfully reproduced the Si-concentration dependence as a monotonic decrease until 11.11 at.%Si and a recovery at 12.5 at.%Si. The analysis of local bulk moduli of SiFe8 cubic clusters and Fe regions is effective to understand the variations of the cell-averaged bulk modulus. The local bulk moduli of Fe regions become lower for increasing Si concentration, due to the suppression of bulk-like d-d bonding states in narrow Fe regions. For higher Si concentrations till 11.11 at.%Si, corner-shared contacts or 1D chains of SiFe8 clusters lead to remarkable reduction of local bulk moduli of the clusters. At 12 at.%Si, on the other hand, two- or three-dimensional arrangements of corner- or edge-shared SiFe8 cubic clusters show greatly enhanced local bulk moduli, due to quite different bonding nature with much stronger p-d hybridization. The relation among the local bulk moduli, local electronic and magnetic structures, and local configurations such as connectivity of SiFe8 clusters and Fe-region sizes has been

  7. High pressure behaviour of uranium dicarbide (UC{sub 2}): Ab-initio study

    SciTech Connect

    Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Mukherjee, D.; Joshi, K. D.

    2016-08-28

    The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ∼8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressuresmore » placed at ∼24 GPa and ∼50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ∼17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC{sub 2} sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such

  8. Inner Core Anisotropy: Can Seismic Observations be Reconciled with Ab Initio Calculations of Elasticity?

    NASA Astrophysics Data System (ADS)

    Song, X.; Jordan, T. H.

    2016-12-01

    Body-wave and normal-mode observations have revealed an inner-core structure that is radially layered, axially anisotropic, and hemispherically asymmetric. Previous theoretical studies have examined the consistency of these features with the elasticity of iron crystals thought to dominate inner-core composition, but a fully consistent model has been elusive. Here we compare the seismic observation with effective-medium models derived from ab initio calculations of the elasticity tensors for hcp-Fe and bcc-Fe. Our estimates are based on Jordan's (GJI, 2015) effective medium theory, which is derived from a self-consistent, second-order Born approximation. The theory provides closed-form expressions for the effective elastic parameters of 3D anisotropic, heterogeneous media in which the local anisotropy is a constant hexagonal stiffness tensor C stochastically oriented about a constant symmetry axis \\hat{s} and the statistics of the small-scale heterogeneities are transversely isotropic in the plane perpendicular to \\hat{s}. The stochastic model is then described by a dimensionless "aspect ratio of the heterogeneity", 0 ≤ η < ∞, and a dimensionless "orientation ratio of the anisotropy", 0 ≤ ξ < ∞. The latter determines the degree to which the axis of C is aligned with \\hat{s}. We compute the loci of models with \\hat{s} oriented along the Earth's rotational axis ( \\hat{s} = north) by varying ξ and η for various ab initio estimates of C. We show that a lot of widely used estimates of C are inconsistent with most published normal-mode models of inner-core anisotropy. In particular, if the P-wave fast axis aligns with the rotational axis, which is required to satisfy the body-wave observations, then these hcp-Fe models predict that the fast polarization of the S waves is in the plane perpendicular to \\hat{s}, which disagrees with most normal-mode models. We have attempted to resolve this discrepancy by examining alternative hcp-Fe models, including

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  10. Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

    PubMed

    Opletal, George; Drumm, Daniel W; Wang, Rong P; Russo, Salvy P

    2014-07-03

    Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

  11. Ab initio NMR parameters of BrCH3 and ICH3 with relativistic and vibrational corrections

    NASA Astrophysics Data System (ADS)

    Uhlíková, Tereza; Urban, Štěpán

    2018-05-01

    This study is focused on two effects identified when NMR parameters are calculated based on first principles. These effects are 1. vibrational correction of properties when using ab initio optimized equilibrium geometry; 2. relativistic effects and limits of using the Flygare equation. These effects have been investigated and determined for nuclear spin-rotation constants and nuclear magnetic shieldings for the CH3Br and CH3I molecules. The most significant result is the difference between chemical shieldings determined based on the ab initio relativistic four-component Dirac-Coulomb Hamiltonian and chemical shieldings calculated using experimental values and the Flygare equation. This difference is approximately 320 ppm and 1290 ppm for 79Br and 127I in the CH3X molecule, respectively.

  12. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    DOE PAGES

    Dytrych, T.; Maris, P.; Launey, K. D.; ...

    2016-06-22

    We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU3-selected subspaces. We demonstrate LSU3shell’s strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states withmore » a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

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

    NASA Astrophysics Data System (ADS)

    Autrey, Daniel; Choo, Jaebum; Laane, Jaan

    2000-10-01

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

  14. Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

    NASA Astrophysics Data System (ADS)

    Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

    2017-09-01

    Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

  15. General Rule of Negative Effective Ueff System & Materials Design of High-Tc Superconductors by ab initio Calculations

    NASA Astrophysics Data System (ADS)

    Katayama-Yoshida, Hiroshi; Nakanishi, Akitaka; Uede, Hiroki; Takawashi, Yuki; Fukushima, Tetsuya; Sato, Kazunori

    2014-03-01

    Based upon ab initio electronic structure calculation, I will discuss the general rule of negative effective U system by (1) exchange-correlation-induced negative effective U caused by the stability of the exchange-correlation energy in Hund's rule with high-spin ground states of d5 configuration, and (2) charge-excitation-induced negative effective U caused by the stability of chemical bond in the closed-shell of s2, p6, and d10 configurations. I will show the calculated results of negative effective U systems such as hole-doped CuAlO2 and CuFeS2. Based on the total energy calculations of antiferromagnetic and ferromagnetic states, I will discuss the magnetic phase diagram and superconductivity upon hole doping. I also discuss the computational materials design method of high-Tc superconductors by ab initio calculation to go beyond LDA and multi-scale simulations.

  16. Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

    PubMed

    Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

    2016-07-15

    The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    SciTech Connect

    Dytrych, T.; Maris, Pieter; Launey, K. D.

    2016-06-09

    We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations ofmore » states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

  18. Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

    PubMed

    Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

    2010-01-21

    Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

  19. Ab initio density functional theory investigation of structural and electronic properties of double-walled silicon carbide nanotubes

    NASA Astrophysics Data System (ADS)

    Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

    2009-12-01

    By using ab initio density functional theory, the structural and electronic properties of (n,n)@(11,11) double-walled silicon carbide nanotubes (SiCNTs) are investigated. Our calculations reveal the existence of an energetically favorable double-walled nanotube whose interwall distance is about 4.3 Å. Interwall spacing and curvature difference are found to be essential for the electronic states around the Fermi level.

  20. Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

    DOE PAGES

    Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr; ...

    2016-05-10

    Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less