Sample records for ab initio post-hartree-fock

  1. Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

    NASA Astrophysics Data System (ADS)

    de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

    2000-09-01

    The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

  2. Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag{sub 2}/graphene

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Mitrushchenkov, Alexander O.; Stoll, Hermann

    2015-09-14

    A combined density functional (DFT) and incremental post-Hartree-Fock (post-HF) approach, proven earlier to calculate He-surface potential energy surfaces [de Lara-Castells et al., J. Chem. Phys. 141, 151102 (2014)], is applied to describe the van der Waals dominated Ag{sub 2}/graphene interaction. It extends the dispersionless density functional theory developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] by including periodic boundary conditions while the dispersion is parametrized via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. Starting with the elementary cluster unit of the target surface (benzene), continuing through the realistic cluster model (coronene), andmore » ending with the periodic model of the extended system, modern ab initio methodologies for intermolecular interactions as well as state-of-the-art van der Waals-corrected density functional-based approaches are put together both to assess the accuracy of the composite scheme and to better characterize the Ag{sub 2}/graphene interaction. The present work illustrates how the combination of DFT and post-HF perspectives may be efficient to design simple and reliable ab initio-based schemes in extended systems for surface science applications.« less

  3. Relativistic Brueckner-Hartree-Fock theory for neutron drops

    NASA Astrophysics Data System (ADS)

    Shen, Shihang; Liang, Haozhao; Meng, Jie; Ring, Peter; Zhang, Shuangquan

    2018-05-01

    Neutron drops confined in an external field are studied in the framework of relativistic Brueckner-Hartree-Fock theory using the bare nucleon-nucleon interaction. The ground-state energies and radii of neutron drops with even numbers from N =4 to N =50 are calculated and compared with results obtained from other nonrelativistic ab initio calculations and from relativistic density functional theory. Special attention has been paid to the magic numbers and to the subshell closures. The single-particle energies are investigated and the monopole effect of the tensor force on the evolutions of the spin-orbit and the pseudospin-orbit splittings is discussed. The results provide interesting insights into neutron-rich systems and can form an important guide for future density functionals.

  4. 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.

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

    PubMed

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

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

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

    PubMed

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

    2015-04-21

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

  7. Optimized norm-conserving Hartree-Fock pseudopotentials

    NASA Astrophysics Data System (ADS)

    Walter, Eric J.; Al-Saidi, Wissam A.

    2006-03-01

    We report soft Hartree-Fock based pseudopotentials obtained using the optimized pseudopotential method. The spurious long range tail due to the non locality of the exchange potential is removed using a self-consistent damping mechanism as employed in exact exchange and recent Hartree-Fock pseudopotentials. The binding energies of several dimers computed using these pseudopotentials within a planewave Hartree-Fock code show good agreement with all-electron results. A. M. Rappe, K. M. Rabe, E. Kaxiras, and J. D. Joannopoulos, Phys. Rev. B 41, 1227 (1990). E. Engel, A. Höck, R. N. Schmid, R. M. Dreizler, and N. Chetty, Phys. Rev. B 64, 125111 (2001). J.R. Trail and R. J. Needs, J. Chem. Phys. 122, 014112 (2005).

  8. Semiempirical evaluation of post-Hartree-Fock diagonal-Born-Oppenheimer corrections for organic molecules.

    PubMed

    Mohallem, José R

    2008-04-14

    Recent post-Hartree-Fock calculations of the diagonal-Born-Oppenheimer correction empirically show that it behaves quite similar to atomic nuclear mass corrections. An almost constant contribution per electron is identified, which converges with system size for specific series of organic molecules. This feature permits pocket-calculator evaluation of the corrections within thermochemical accuracy (10(-1) mhartree or kcal/mol).

  9. 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.

  10. An ab-initio study of the relative stability of the ggg and the gtg conformer in hexane

    NASA Astrophysics Data System (ADS)

    Koglin, Eckhard; Meier, Robert J.

    1999-10-01

    Earlier ab-initio work suggested, on the basis of MP2 level calculations, that the hexane ggg conformer is more stable than the gtg conformer. Because this is unexpected and if true might have a significant impact on force field parametrisations, we have applied Hartree-Fock and post-HF methods to evaluate the relative stability of these conformers. We find that at levels higher than MP2 the gtg conformer is more stable than the ggg conformer, in agreement with the conventional idea that each additional gauche bond causes a further decrease in stability of the conformer. DFT methods were also applied, but although DFT methods including gradient corrections show correct qualitative behaviour, quantitatively the relative energies are far off compared to the post-HF results.

  11. 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.

  12. The any particle molecular orbital grid-based Hartree-Fock (APMO-GBHF) approach

    NASA Astrophysics Data System (ADS)

    Posada, Edwin; Moncada, Félix; Reyes, Andrés

    2018-02-01

    The any particle molecular orbital grid-based Hartree-Fock approach (APMO-GBHF) is proposed as an initial step to perform multi-component post-Hartree-Fock, explicitly correlated, and density functional theory methods without basis set errors. The method has been applied to a number of electronic and multi-species molecular systems. Results of these calculations show that the APMO-GBHF total energies are comparable with those obtained at the APMO-HF complete basis set limit. In addition, results reveal a considerable improvement in the description of the nuclear cusps of electronic and non-electronic densities.

  13. 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.

  14. The fractal geometry of Hartree-Fock

    NASA Astrophysics Data System (ADS)

    Theel, Friethjof; Karamatskou, Antonia; Santra, Robin

    2017-12-01

    The Hartree-Fock method is an important approximation for the ground-state electronic wave function of atoms and molecules so that its usage is widespread in computational chemistry and physics. The Hartree-Fock method is an iterative procedure in which the electronic wave functions of the occupied orbitals are determined. The set of functions found in one step builds the basis for the next iteration step. In this work, we interpret the Hartree-Fock method as a dynamical system since dynamical systems are iterations where iteration steps represent the time development of the system, as encountered in the theory of fractals. The focus is put on the convergence behavior of the dynamical system as a function of a suitable control parameter. In our case, a complex parameter λ controls the strength of the electron-electron interaction. An investigation of the convergence behavior depending on the parameter λ is performed for helium, neon, and argon. We observe fractal structures in the complex λ-plane, which resemble the well-known Mandelbrot set, determine their fractal dimension, and find that with increasing nuclear charge, the fragmentation increases as well.

  15. Vibrational spectroscopic investigation of p-, m- and o-nitrobenzonitrile by using Hartree-Fock and density functional theory

    NASA Astrophysics Data System (ADS)

    Sert, Y.; Ucun, F.

    2013-08-01

    In the present work, the theoretical vibrational spectra of p-, m- and o-nitrobenzonitrile molecules have been analyzed. The harmonic vibrational frequencies and geometric parameters (bond lengths and bond angles) of these molecules have been calculated using ab initio Hartree-Fock and density functional theory methods with 6-311++G(d,p) basis set by Gaussian 03 W, for the first time. Assignments of the vibrational frequencies have been performed by potential energy distribution by using VEDA 4 program. The optimized geometric parameters and harmonic vibrational frequencies have been compared with the corresponding experimental data and seen to be in a good agreement with each other. Also, the highest occupied molecular orbital and lowest unoccupied molecular orbital energies have been obtained.

  16. Existence of Hartree-Fock excited states for atoms and molecules

    NASA Astrophysics Data System (ADS)

    Lewin, Mathieu

    2018-04-01

    For neutral and positively charged atoms and molecules, we prove the existence of infinitely many Hartree-Fock critical points below the first energy threshold (that is, the lowest energy of the same system with one electron removed). This is the equivalent, in Hartree-Fock theory, of the famous Zhislin-Sigalov theorem which states the existence of infinitely many eigenvalues below the bottom of the essential spectrum of the N-particle linear Schrödinger operator. Our result improves a theorem of Lions in 1987 who already constructed infinitely many Hartree-Fock critical points, but with much higher energy. Our main contribution is the proof that the Hartree-Fock functional satisfies the Palais-Smale property below the first energy threshold. We then use minimax methods in the N-particle space, instead of working in the one-particle space.

  17. 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.

  18. Ab initio Hartree-Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one drug molecule.

    PubMed

    Taşal, Erol; Kumalar, Mustafa

    2012-09-01

    In this work, the experimental and theoretical spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one molecule (abbreviated as 5CMOT) are studied. The molecular geometry and vibrational frequencies are calculated in the ground state of molecule using ab initio Hartree-Fock (HF) and Density Function Theory (DFT) methods with 6-311++G(d,p), 6-31G++(d,p), 6-31G(d,p), 6-31G(d) and 6-31G basis sets. Three staggered stable conformers were observed on the torsional potential energy surfaces. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters fairly well agree with the theoretically obtained values for the most stable conformer. The theoretical results showed an excellent agreement with the experimental values. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Computational Nuclear Physics and Post Hartree-Fock Methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lietz, Justin; Sam, Novario; Hjorth-Jensen, M.

    We present a computational approach to infinite nuclear matter employing Hartree-Fock theory, many-body perturbation theory and coupled cluster theory. These lectures are closely linked with those of chapters 9, 10 and 11 and serve as input for the correlation functions employed in Monte Carlo calculations in chapter 9, the in-medium similarity renormalization group theory of dense fermionic systems of chapter 10 and the Green's function approach in chapter 11. We provide extensive code examples and benchmark calculations, allowing thereby an eventual reader to start writing her/his own codes. We start with an object-oriented serial code and end with discussions onmore » strategies for porting the code to present and planned high-performance computing facilities.« less

  20. Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris

    Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less

  1. Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

    DOE PAGES

    Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris; ...

    2018-04-23

    Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less

  2. A finite-temperature Hartree-Fock code for shell-model Hamiltonians

    NASA Astrophysics Data System (ADS)

    Bertsch, G. F.; Mehlhaff, J. M.

    2016-10-01

    The codes HFgradZ.py and HFgradT.py find axially symmetric minima of a Hartree-Fock energy functional for a Hamiltonian supplied in a shell model basis. The functional to be minimized is the Hartree-Fock energy for zero-temperature properties or the Hartree-Fock grand potential for finite-temperature properties (thermal energy, entropy). The minimization may be subjected to additional constraints besides axial symmetry and nucleon numbers. A single-particle operator can be used to constrain the minimization by adding it to the single-particle Hamiltonian with a Lagrange multiplier. One can also constrain its expectation value in the zero-temperature code. Also the orbital filling can be constrained in the zero-temperature code, fixing the number of nucleons having given Kπ quantum numbers. This is particularly useful to resolve near-degeneracies among distinct minima.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

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

  5. Parallel scalability of Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Chow, Edmond; Liu, Xing; Smelyanskiy, Mikhail; Hammond, Jeff R.

    2015-03-01

    Quantum chemistry is increasingly performed using large cluster computers consisting of multiple interconnected nodes. For a fixed molecular problem, the efficiency of a calculation usually decreases as more nodes are used, due to the cost of communication between the nodes. This paper empirically investigates the parallel scalability of Hartree-Fock calculations. The construction of the Fock matrix and the density matrix calculation are analyzed separately. For the former, we use a parallelization of Fock matrix construction based on a static partitioning of work followed by a work stealing phase. For the latter, we use density matrix purification from the linear scaling methods literature, but without using sparsity. When using large numbers of nodes for moderately sized problems, density matrix computations are network-bandwidth bound, making purification methods potentially faster than eigendecomposition methods.

  6. Global solutions of restricted open-shell Hartree-Fock theory from semidefinite programming with applications to strongly correlated quantum systems.

    PubMed

    Veeraraghavan, Srikant; Mazziotti, David A

    2014-03-28

    We present a density matrix approach for computing global solutions of restricted open-shell Hartree-Fock theory, based on semidefinite programming (SDP), that gives upper and lower bounds on the Hartree-Fock energy of quantum systems. While wave function approaches to Hartree-Fock theory yield an upper bound to the Hartree-Fock energy, we derive a semidefinite relaxation of Hartree-Fock theory that yields a rigorous lower bound on the Hartree-Fock energy. We also develop an upper-bound algorithm in which Hartree-Fock theory is cast as a SDP with a nonconvex constraint on the rank of the matrix variable. Equality of the upper- and lower-bound energies guarantees that the computed solution is the globally optimal solution of Hartree-Fock theory. The work extends a previously presented method for closed-shell systems [S. Veeraraghavan and D. A. Mazziotti, Phys. Rev. A 89, 010502-R (2014)]. For strongly correlated systems the SDP approach provides an alternative to the locally optimized Hartree-Fock energies and densities with a certificate of global optimality. Applications are made to the potential energy curves of C2, CN, Cr2, and NO2.

  7. Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

    PubMed

    Zagorac, Jelena; Zagorac, Dejan; Zarubica, Aleksandra; Schön, J Christian; Djuris, Katarina; Matovic, Branko

    2014-10-01

    We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

  8. Hyperfine coupling constants of the nitrogen and phosphorus atoms: A challenge for exact-exchange density-functional and post-Hartree-Fock methods

    NASA Astrophysics Data System (ADS)

    Kaupp, Martin; Arbuznikov, Alexei V.; Heßelmann, Andreas; Görling, Andreas

    2010-05-01

    The isotropic hyperfine coupling constants of the free N(S4) and P(S4) atoms have been evaluated with high-level post-Hartree-Fock and density-functional methods. The phosphorus hyperfine coupling presents a significant challenge to both types of methods. With large basis sets, MP2 and coupled-cluster singles and doubles calculations give much too small values for the phosphorus atom. Triple excitations are needed in coupled-cluster calculations to achieve reasonable agreement with experiment. None of the standard density functionals reproduce even the correct sign of this hyperfine coupling. Similarly, the computed hyperfine couplings depend crucially on the self-consistent treatment in exact-exchange density-functional theory within the optimized effective potential (OEP) method. Well-balanced auxiliary and orbital basis sets are needed for basis-expansion exact-exchange-only OEP approaches to come close to Hartree-Fock or numerical OEP data. Results from the localized Hartree-Fock and Krieger-Li-Iafrate approximations deviate notably from exact OEP data in spite of very similar total energies. Of the functionals tested, only full exact-exchange methods augmented by a correlation functional gave at least the correct sign of the P(S4) hyperfine coupling but with too low absolute values. The subtle interplay between the spin-polarization contributions of the different core shells has been analyzed, and the influence of even very small changes in the exchange-correlation potential could be identified.

  9. Importance of dispersion and electron correlation in ab initio protein folding.

    PubMed

    He, Xiao; Fusti-Molnar, Laszlo; Cui, Guanglei; Merz, Kenneth M

    2009-04-16

    Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

  10. Qualitative breakdown of the unrestricted Hartree-Fock energy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mori-Sánchez, Paula, E-mail: paula.mori@uam.es; Cohen, Aron J., E-mail: ajc54@cam.ac.uk

    2014-10-28

    The stretching of closed-shell molecules is a qualitative problem for restricted Hartree-Fock that is usually circumvented by the use of unrestricted Hartree-Fock (UHF). UHF is well known to break the spin symmetry at the Coulson-Fischer point, leading to a discontinuous derivative in the potential energy surface and incorrect spin density. However, this is generally not considered as a major drawback. In this work, we present a set of two electron molecules which magnify the problem of symmetry breaking and lead to drastically incorrect potential energy surfaces with UHF. These molecules also fail with unrestricted density-functional calculations where a functional suchmore » as B3LYP gives both symmetry breaking and an unphysically low energy due to the delocalization error. The implications for density functional theory are also discussed.« less

  11. Tensor numerical methods in quantum chemistry: from Hartree-Fock to excitation energies.

    PubMed

    Khoromskaia, Venera; Khoromskij, Boris N

    2015-12-21

    We resume the recent successes of the grid-based tensor numerical methods and discuss their prospects in real-space electronic structure calculations. These methods, based on the low-rank representation of the multidimensional functions and integral operators, first appeared as an accurate tensor calculus for the 3D Hartree potential using 1D complexity operations, and have evolved to entirely grid-based tensor-structured 3D Hartree-Fock eigenvalue solver. It benefits from tensor calculation of the core Hamiltonian and two-electron integrals (TEI) in O(n log n) complexity using the rank-structured approximation of basis functions, electron densities and convolution integral operators all represented on 3D n × n × n Cartesian grids. The algorithm for calculating TEI tensor in a form of the Cholesky decomposition is based on multiple factorizations using algebraic 1D "density fitting" scheme, which yield an almost irreducible number of product basis functions involved in the 3D convolution integrals, depending on a threshold ε > 0. The basis functions are not restricted to separable Gaussians, since the analytical integration is substituted by high-precision tensor-structured numerical quadratures. The tensor approaches to post-Hartree-Fock calculations for the MP2 energy correction and for the Bethe-Salpeter excitation energies, based on using low-rank factorizations and the reduced basis method, were recently introduced. Another direction is towards the tensor-based Hartree-Fock numerical scheme for finite lattices, where one of the numerical challenges is the summation of electrostatic potentials of a large number of nuclei. The 3D grid-based tensor method for calculation of a potential sum on a L × L × L lattice manifests the linear in L computational work, O(L), instead of the usual O(L(3) log L) scaling by the Ewald-type approaches.

  12. An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(iii)(HPDO3A)(H2O)

    NASA Astrophysics Data System (ADS)

    Khan, Shehryar; Pollet, Rodolphe; Vuilleumier, Rodolphe; Kowalewski, Jozef; Odelius, Michael

    2017-12-01

    In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field—CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates.

  13. Spatial and Spin Symmetry Breaking in Semidefinite-Programming-Based Hartree-Fock Theory.

    PubMed

    Nascimento, Daniel R; DePrince, A Eugene

    2018-05-08

    The Hartree-Fock problem was recently recast as a semidefinite optimization over the space of rank-constrained two-body reduced-density matrices (RDMs) [ Phys. Rev. A 2014 , 89 , 010502(R) ]. This formulation of the problem transfers the nonconvexity of the Hartree-Fock energy functional to the rank constraint on the two-body RDM. We consider an equivalent optimization over the space of positive semidefinite one-electron RDMs (1-RDMs) that retains the nonconvexity of the Hartree-Fock energy expression. The optimized 1-RDM satisfies ensemble N-representability conditions, and ensemble spin-state conditions may be imposed as well. The spin-state conditions place additional linear and nonlinear constraints on the 1-RDM. We apply this RDM-based approach to several molecular systems and explore its spatial (point group) and spin ( Ŝ 2 and Ŝ 3 ) symmetry breaking properties. When imposing Ŝ 2 and Ŝ 3 symmetry but relaxing point group symmetry, the procedure often locates spatial-symmetry-broken solutions that are difficult to identify using standard algorithms. For example, the RDM-based approach yields a smooth, spatial-symmetry-broken potential energy curve for the well-known Be-H 2 insertion pathway. We also demonstrate numerically that, upon relaxation of Ŝ 2 and Ŝ 3 symmetry constraints, the RDM-based approach is equivalent to real-valued generalized Hartree-Fock theory.

  14. The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

    NASA Astrophysics Data System (ADS)

    Förner, Wolfgang

    1992-03-01

    Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

  15. 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.

  16. Length-dependence of intramolecular electron transfer in σ-bonded rigid molecular rods: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Karna, Shashi P.

    2002-01-01

    The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

  17. Skyrme-Hartree-Fock calculation on He, Li, and Be isotopes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shen, Y.; Ren, Z.

    1996-09-01

    The ground-state properties of He, Li, and Be nuclei are investigated by the Skyrme-Hartree-Fock approach with new force parameters SKI4 of Reinhard and Flocard [Nucl. Phys. A {bold 584}, 467 (1995)] plus a density-dependent pairing correlation. Calculations show that the Skyrme-Hartree-Fock model with above force parameters provides a good description on the binding energy and radii of He, Li, and Be isotopes. It also succeeds in reproducing neutron halos in nuclei {sup 6}He, {sup 8}He, {sup 11}Li, and {sup 14}Be. A detailed discussion on numerical results is provided and an explanation for the above success is given. {copyright} {ital 1996more » The American Physical Society.}« less

  18. Optimized auxiliary basis sets for density fitted post-Hartree-Fock calculations of lanthanide containing molecules

    NASA Astrophysics Data System (ADS)

    Chmela, Jiří; Harding, Michael E.

    2018-06-01

    Optimised auxiliary basis sets for lanthanide atoms (Ce to Lu) for four basis sets of the Karlsruhe error-balanced segmented contracted def2 - series (SVP, TZVP, TZVPP and QZVPP) are reported. These auxiliary basis sets enable the use of the resolution-of-the-identity (RI) approximation in post Hartree-Fock methods - as for example, second-order perturbation theory (MP2) and coupled cluster (CC) theory. The auxiliary basis sets are tested on an enlarged set of about a hundred molecules where the test criterion is the size of the RI error in MP2 calculations. Our tests also show that the same auxiliary basis sets can be used together with different effective core potentials. With these auxiliary basis set calculations of MP2 and CC quality can now be performed efficiently on medium-sized molecules containing lanthanides.

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

    PubMed Central

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

    2015-01-01

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

  20. 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.

  1. 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.

  2. Hartree-Fock studies of hypernuclear properties

    NASA Astrophysics Data System (ADS)

    Lanskoy, D. E.

    1998-08-01

    The Skyrme-Hartree-Fock approach is approved as a powerful tool to reproduce general properties of Λ hypernuclear spectra [1-4] and to relate hypernuclear observables to effective interaction features. In this contribution, we consider briefly some less common hypernuclear systems, which appear to be quite sensitive to details of the relevant interactions. Particularly, we address possible manifestations of the polarization of a hypernuclear core (i.e. core distortion due to hyperon addition), which is driven in terms of the Skyrme force mainly by counterbalance between the two-body ΛN force and the three-body ΛNN (or density-dependent ΛN) one.

  3. Non-plane-wave Hartree-Fock states and nuclear homework potentials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gutierrez, G.; Plastino, A.; de Llano, M.

    1979-12-01

    It is shown that non-plane-wave single-particle Hartree-Fock orbitals giving rise to a ''spin-density-wave-like'' structure give lower energy than plane waves beyond a certain relatively low density in both nuclear and neutron matter with homework pair potentials v/sub 1/ and v/sub 2/.

  4. Advanced ab initio relativistic calculations of transition probabilities for some O I and O III emission lines

    NASA Astrophysics Data System (ADS)

    Nguyen, T. V. B.; Chantler, C. T.; Lowe, J. A.; Grant, I. P.

    2014-06-01

    This work presents new ab initio relativistic calculations using the multiconfiguration Dirac-Hartree-Fock method of some O I and O III transition lines detected in B-type and Wolf-Rayet stars. Our results are the first able to be presented in both the length and velocity gauges, with excellent gauge convergence. Compared to previous experimental and theoretical uncertainties of up to 50 per cent, our accuracies appear to be in the range of 0.33-5.60 per cent, with gauge convergence up to 0.6 per cent. Similar impressive convergence of the calculated energies is also shown. Two sets of theoretical computations are compared with earlier tabulated measurements. Excellent agreement is obtained with one set of transitions but an interesting and consistent discrepancy exists between the current work and the prior literature, deserving of future experimental studies.

  5. Restricted Closed Shell Hartree Fock Roothaan Matrix Method Applied to Helium Atom Using Mathematica

    ERIC Educational Resources Information Center

    Acosta, César R.; Tapia, J. Alejandro; Cab, César

    2014-01-01

    Slater type orbitals were used to construct the overlap and the Hamiltonian core matrices; we also found the values of the bi-electron repulsion integrals. The Hartree Fock Roothaan approximation process starts with setting an initial guess value for the elements of the density matrix; with these matrices we constructed the initial Fock matrix.…

  6. CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes.

    PubMed

    Calvello, Simone; Piccardo, Matteo; Rao, Shashank Vittal; Soncini, Alessandro

    2018-03-05

    We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin-orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree-Fock (CAHF) algorithm for the determination of 4f quasi-atomic active orbitals common to all multi-electron spin manifolds contributing to the ground spin-orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi-Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem-specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state-of-the-art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres, represents a more time-efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non-perturbative spin-orbit coupling effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

    NASA Astrophysics Data System (ADS)

    Ylikantola, A.; Linnanto, J.; Knuutinen, J.; Oravilahti, A.; Toivakka, M.

    2013-07-01

    The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree-Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree-Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree-Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

  8. Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

    PubMed

    Kritayakornupong, Chinapong

    2009-12-01

    A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree-Fock level has been performed to investigate structural and dynamical parameters of the V(3+) ion in dilute aqueous solution. A distorted octahedral structure with the average V(3+)-O distance of 1.99 A is evaluated from the QM/MM simulation, which is in good agreement with the X-ray data. Several structural parameters such as angular distribution functions, theta- and tilt-angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V(3+). The Jahn-Teller distortions of the V(3+) ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. (c) 2009 Wiley Periodicals, Inc.

  9. Twist-averaged boundary conditions for nuclear pasta Hartree-Fock calculations

    DOE PAGES

    Schuetrumpf, B.; Nazarewicz, W.

    2015-10-21

    Nuclear pasta phases, present in the inner crust of neutron stars, are associated with nucleonic matter at subsaturation densities arranged in regular shapes. Those complex phases, residing in a layer which is approximately 100-m thick, impact many features of neutron stars. Theoretical quantum-mechanical simulations of nuclear pasta are usually carried out in finite three-dimensional boxes assuming periodic boundary conditions. The resulting solutions are affected by spurious finite-size effects. To remove spurious finite-size effects, it is convenient to employ twist-averaged boundary conditions (TABC) used in condensed matter, nuclear matter, and lattice quantum chromodynamics applications. In this work, we study the effectivenessmore » of TABC in the context of pasta phase simulations within nuclear density functional theory. We demonstrated that by applying TABC reliable results can be obtained from calculations performed in relatively small volumes. By studying various contributions to the total energy, we gain insights into pasta phases in mid-density range. Future applications will include the TABC extension of the adaptive multiresolution 3D Hartree-Fock solver and Hartree-Fock-Bogoliubov TABC applications to superfluid pasta phases and complex nucleonic topologies as in fission.« less

  10. An ab initio study of the electronic structure and relative stability of the halogenated thiophosphorus compounds SPX (X = Cl, F, Br) and their isomers

    NASA Astrophysics Data System (ADS)

    Nowek, Andrzej; Richardson, Rhonda; Babinec, Peter; Leszczyński, Jerzy

    1997-12-01

    The electronic structure and relative stability of the halogenated thiophosphorus compounds SPCl, SPF, and SPBr and their isomers ClSP, FSP, and BrSP were investigated using ab initio post-Hartree-Fock methods. Molecular geometries of all these structures together with the transition states between isomers, have been optimized at the SCF, MP2, and CCSD levels. Single-point CCSD(T) and MP4 calculations have been performed at the optimal CCSD and MP2 geometries. All calculations have been done using the standard 6-311G(2d) basis set. Harmonic vibrational frequencies and IR intensities for all species were calculated at the correlated levels, and they are in good agreement with the available data from matrix-isolated IR spectroscopy. Because the isomers ClSP, FSP, and BrSP have not yet been experimentally observed, we extended our study by calculating of equilibrium constants of isomerization using Eyring transition state theory, and we have found that at sufficiently high temperatures (≈ 1000 K) the equilibrium constants are large enough for the possible detection of these isomers.

  11. The torsional energy profile of 1,2-diphenylethane: an ab initio study

    NASA Astrophysics Data System (ADS)

    Ivanov, Petko M.

    1997-08-01

    Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

  12. Projected Hartree-Fock theory as a polynomial of particle-hole excitations and its combination with variational coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Qiu, Yiheng; Henderson, Thomas M.; Scuseria, Gustavo E.

    2017-05-01

    Projected Hartree-Fock theory provides an accurate description of many kinds of strong correlations but does not properly describe weakly correlated systems. Coupled cluster theory, in contrast, does the opposite. It therefore seems natural to combine the two so as to describe both strong and weak correlations with high accuracy in a relatively black-box manner. Combining the two approaches, however, is made more difficult by the fact that the two techniques are formulated very differently. In earlier work, we showed how to write spin-projected Hartree-Fock in a coupled-cluster-like language. Here, we fill in the gaps in that earlier work. Further, we combine projected Hartree-Fock and coupled cluster theory in a variational formulation and show how the combination performs for the description of the Hubbard Hamiltonian and for several small molecular systems.

  13. An ab initio cluster study of the chemisorption of atomic cesium and hydrogen on reconstructed surfaces of gallium rich gallium arsenide

    NASA Astrophysics Data System (ADS)

    Schailey, Ronald

    1999-11-01

    Chemisorption properties of cesium and hydrogen atoms on the Ga-rich GaAs (100) (2 x 1), (2 x 2), and β(4 x 2) surfaces are investigated using ab initio self-consistent restricted open shell Hartree-Fock (ROHF) total energy calculations with Hay- Wadt effective core potentials. The effects of electron correlation have been included using many-body perturbation theory through second order, with the exception of β(4 x 2) symmetry due to computational limitations. The semiconductor surface is modeled by finite sized hydrogen saturated clusters. The effects of surface relaxation and reconstruction have been investigated in detail. Results are given for the energetics of chemisorption, charge population analysis, HOMO-LUMO gaps, and consequent possibilities of metallization for atomic cesium adsorption. For the chemisorption of atomic hydrogen, the experimentally verified mechanism of surface dimer bond breaking is investigated in detail.

  14. Reconciling phase diffusion and Hartree-Fock approximation in condensate systems

    NASA Astrophysics Data System (ADS)

    Giorgi, Gian Luca; de Pasquale, Ferdinando

    2012-01-01

    Despite the weakly interacting regime, the physics of Bose-Einstein condensates is widely affected by particle-particle interactions. They determine quantum phase diffusion, which is known to be the main cause of loss of coherence. Studying a simple model of two interacting Bose systems, we show how to predict the appearance of phase diffusion beyond the Bogoliubov approximation, providing a self-consistent treatment in the framework of a generalized Hartree-Fock-Bogoliubov perturbation theory.

  15. A finite difference Hartree-Fock program for atoms and diatomic molecules

    NASA Astrophysics Data System (ADS)

    Kobus, Jacek

    2013-03-01

    The newest version of the two-dimensional finite difference Hartree-Fock program for atoms and diatomic molecules is presented. This is an updated and extended version of the program published in this journal in 1996. It can be used to obtain reference, Hartree-Fock limit values of total energies and multipole moments for a wide range of diatomic molecules and their ions in order to calibrate existing and develop new basis sets, calculate (hyper)polarizabilities (αzz, βzzz, γzzzz, Az,zz, Bzz,zz) of atoms, homonuclear and heteronuclear diatomic molecules and their ions via the finite field method, perform DFT-type calculations using LDA or B88 exchange functionals and LYP or VWN correlations ones or the self-consistent multiplicative constant method, perform one-particle calculations with (smooth) Coulomb and Krammers-Henneberger potentials and take account of finite nucleus models. The program is easy to install and compile (tarball+configure+make) and can be used to perform calculations within double- or quadruple-precision arithmetic. Catalogue identifier: ADEB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADEB_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 171196 No. of bytes in distributed program, including test data, etc.: 9481802 Distribution format: tar.gz Programming language: Fortran 77, C. Computer: any 32- or 64-bit platform. Operating system: Unix/Linux. RAM: Case dependent, from few MB to many GB Classification: 16.1. Catalogue identifier of previous version: ADEB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 98(1996)346 Does the new version supersede the previous version?: Yes Nature of problem: The program finds virtually exact solutions of the Hartree-Fock and density functional theory type equations for atoms, diatomic molecules and their ions

  16. Constrained-pairing mean-field theory. IV. Inclusion of corresponding pair constraints and connection to unrestricted Hartree-Fock theory.

    PubMed

    Tsuchimochi, Takashi; Henderson, Thomas M; Scuseria, Gustavo E; Savin, Andreas

    2010-10-07

    Our previously developed constrained-pairing mean-field theory (CPMFT) is shown to map onto an unrestricted Hartree-Fock (UHF) type method if one imposes a corresponding pair constraint to the correlation problem that forces occupation numbers to occur in pairs adding to one. In this new version, CPMFT has all the advantages of standard independent particle models (orbitals and orbital energies, to mention a few), yet unlike UHF, it can dissociate polyatomic molecules to the correct ground-state restricted open-shell Hartree-Fock atoms or fragments.

  17. Ab initio calculation of Ti NMR shieldings for titanium oxides and halides

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.

    Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.

  18. a HARTREE-FOCK Nuclear Mass Table

    NASA Astrophysics Data System (ADS)

    Goriely, S.; Tondeur, F.; Pearson, J. M.

    2001-03-01

    We present the first complete nuclear mass table, HFBCS-1, to be based on the Hartree-Fock-BCS method. The force used, MSk7, is a 10-parameter Skyrme force, along with a 4-parameter δ-function pairing force and a 2-parameter phenomenological Wigner term. Our tabulation presents 9200 nuclei, including all those lying between the drip lines over the range Z, N≥8 and Z≤120. The root-mean-square error of our fit to the 1888 nuclei in this range for which measured masses are given in the 1995 Audi-Wapstra compilation is 0.738 MeV. In addition to the calculated masses, we show the calculated neutron- and proton-separation energies, and beta-decay energies. We also give for each nucleus in the table the calculated values for the deformation parameters and deformation energy (with axial and left-right symmetry assumed), and for the charge radius.

  19. Hartree-Fock mass formulas and extrapolation to new mass data

    NASA Astrophysics Data System (ADS)

    Goriely, S.; Samyn, M.; Heenen, P.-H.; Pearson, J. M.; Tondeur, F.

    2002-08-01

    The two previously published Hartree-Fock (HF) mass formulas, HFBCS-1 and HFB-1 (HF-Bogoliubov), are shown to be in poor agreement with new Audi-Wapstra mass data. The problem lies first with the prescription adopted for the cutoff of the single-particle spectrum used with the δ-function pairing force, and second with the Wigner term. We find an optimal mass fit if the spectrum is cut off both above EF+15 MeV and below EF-15 MeV, EF being the Fermi energy of the nucleus in question. In addition to the Wigner term of the form VW exp(-λ|N-Z|/A) already included in the two earlier HF mass formulas, we find that a second Wigner term linear in |N-Z| leads to a significant improvement in lighter nuclei. These two features are incorporated into our new Hartree-Fock-Bogoliubov model, which leads to much improved extrapolations. The 18 parameters of the model are fitted to the 2135 measured masses for N,Z>=8 with an rms error of 0.674 MeV. With this parameter set a complete mass table, labeled HFB-2, has been constructed, going from one drip line to the other, up to Z=120. The new pairing-cutoff prescription favored by the new mass data leads to weaker neutron-shell gaps in neutron-rich nuclei.

  20. Beyond computational difficulties: Survey of the two decades from the elaboration to the extensive application of the Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Martinez, Jean-Philippe

    2017-11-01

    The Hartree-Fock method, one of the first applications of the new quantum mechanics in the frame of the many-body problem, had been elaborated by Rayner Douglas Hartree in 1928 and Vladimir Fock in 1930. Promptly, the challenge of tedious computations was being discussed and it is well known that the application of the method benefited greatly from the development of computers from the mid-to-late 1950s. However, the years from 1930 to 1950 were by no means years of stagnation, as the method was the object of several considerations related to its mathematical formulation, possible extension, and conceptual understanding. Thus, with a focus on the respective attitudes of Hartree and Fock, in particular with respect to the concept of quantum exchange, the present work puts forward some mathematical and conceptual clarifications, which played an important role for a better understanding of the many-body problem in quantum mechanics.

  1. Antibacterial activity, thermal stability and ab initio study of copolymer containing sulfobetaine and carboxybetaine groups

    NASA Astrophysics Data System (ADS)

    Tarannum, Nazia; Singh, Meenakshi; Yadav, Anil K.

    2017-10-01

    Here, we have explored the antibacterial activity, thermal stability and theoretical study of two copolymers that contain sulfobetaine and carboetaine moiety. Copolymers were synthesized based on Schiff base chemistry with generation of zwitterionic centres by nucleophilic addition of sultone/lactone. To predict and confirm the molecular structure of zwitterionic polyelectrolyte molecule, the theoretical study of structural features and other thermodynamic characteristics of copolymer constituents was obtained by ab initio calculations. Various parameters such as geometry optimization, energy calculations, frequency calculations and intrinsic reaction coefficient (IRC) are simulated using Hartree Fock (HF) method. The geometry optimizations are analyzed at HF/3-21 G default level of theory. The vibrational frequency is calculated via density functional theory (DFT)/B3LYP 6-31G*(d) level whose values are in accord with the experimental observed frequency. Both copolymers have been successfully assessed for antibacterial activity against Staphylococcus aureus and Pseudomonas aeuroginosa bacterial strains by disc diffusion method. The antibacterial study helped in evaluating zone of inhibition, minimum inhibitory concentration and minimum bactericidal concentration. Sulfobetaine copolymer is found to be more effective in curtailing the infection caused by bacteria as compared to carbobetaine.

  2. Influence of the Dirac-Hartree-Fock starting potential on the parity-nonconserving electric-dipole-transition amplitudes in cesium and thallium

    NASA Technical Reports Server (NTRS)

    Perger, W. F.; Das, B. P.

    1987-01-01

    The parity-nonconserving electric-dipole-transition amplitudes for the 6s1/2-7s1/2 transition in cesium and the 6p1/2-7p1/2 transition in thallium have been calculated by the Dirac-Hartree-Fock method. The effects of using different Dirac-Hartree-Fock atomic core potentials are examined and the transition amplitudes for both the length and velocity gauges are given. It is found that the parity-nonconserving transition amplitudes exhibit a greater dependence on the starting potential for thallium than for cesium.

  3. 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.

  4. Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

    PubMed

    Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

    2015-08-05

    Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Conformational study of glyoxal bis(amidinohydrazone) by ab initio methods

    NASA Astrophysics Data System (ADS)

    Mannfors, B.; Koskinen, J. T.; Pietilä, L.-O.

    1997-08-01

    We report the first ab initio molecular orbital study on the ground state of the endiamine tautomer of glyoxal bis(amidinohydrazone) (or glyoxal bis(guanylhydrazone), GBG) free base. The calculations were performed at the following levels of theory: Hartree-Fock, second-order Møller-Plesset perturbation theory and density functional theory (B-LYP and B3-LYP) as implemented in the Gaussian 94 software. The standard basis set 6-31G(d) was found to be sufficient. The default fine grid of Gaussian 94 was used in the density functional calculations. Molecular properties, such as optimized structures, total energies and the electrostatic potential derived (CHELPG) atomic charges, were studied as functions of C-C and N-N conformations. The lowest energy conformation was found to be all- trans, in agreement with the experimental solid-state structure. The second conformer with respect to rotation around the central C-C bond was found to be the cis conformer with an MP2//HF energy of 4.67 kcal mol -1. For rotation around the N-N bond the energy increased monotonically from the trans conformation to the cis conformation, the cis energy being very high, 22.01 kcal mol -1 (MP2//HF). The atomic charges were shown to be conformation dependent, and the bond charge increments and especially the conformational changes of the bond charge increments were found to be easily transferable between structurally related systems.

  6. Generalization of the Hartree-Fock approach to collision processes

    NASA Astrophysics Data System (ADS)

    Hahn, Yukap

    1997-06-01

    The conventional Hartree and Hartree-Fock approaches for bound states are generalized to treat atomic collision processes. All the single-particle orbitals, for both bound and scattering states, are determined simultaneously by requiring full self-consistency. This generalization is achieved by introducing two Ansäauttze: (a) the weak asymptotic boundary condition, which maintains the correct scattering energy and target orbitals with correct number of nodes, and (b) square integrable amputated scattering functions to generate self-consistent field (SCF) potentials for the target orbitals. The exact initial target and final-state asymptotic wave functions are not required and thus need not be specified a priori, as they are determined simultaneously by the SCF iterations. To check the asymptotic behavior of the solution, the theory is applied to elastic electron-hydrogen scattering at low energies. The solution is found to be stable and the weak asymptotic condition is sufficient to produce the correct scattering amplitudes. The SCF potential for the target orbital shows the strong penetration by the projectile electron during the collision, but the exchange term tends to restore the original form. Potential applicabilities of this extension are discussed, including the treatment of ionization and shake-off processes.

  7. Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

    NASA Astrophysics Data System (ADS)

    Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

    2013-06-01

    The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

  8. An ab initio time-dependent Hartree Fock study of solvent effects on the polarizability and second hyperpolarizability of polyacetylene chains within the polarizable continuum model

    NASA Astrophysics Data System (ADS)

    Champagne, Benoı̂t; Mennucci, Benedetta; Cossi, Maurizio; Cammi, Roberto; Tomasi, Jacopo

    1998-11-01

    The solvent effects upon the longitudinal polarizability ( αL) and second hyperpolarizability ( γL) of small all-trans polyacetylene (PA) chains ranging from C 2H 4 to C 10H 12 have been evaluated at the time-dependent Hartree-Fock (TDHF) level within the framework of the polarizable continuum model. The solvent effects, which correspond to the solvent-induced modifications of the solute properties, result in large increases of the linear and nonlinear responses even for solvents with low dielectric constants. When the dielectric constant is increased, the αL values tend to saturate at values 30%-40% larger than in vacuo, whereas for γL it ranges from 100% to 400% depending upon the nonlinear optical process and the length of the PA chain. These solvent-induced αL and γL enhancements can partially be accounted for by the corresponding decrease of the energy of the lowest optically-allowed electronic excitation. The geometrical parameters of the ground state of the PA chains are almost unaffected by the solvent. This shows that the solvent effects are mainly of electronic nature. In addition, the local field factors, which relate the macroscopic or Maxwell field to the field experienced by the solute, tend towards unity with increasing chain length for the longitudinal PA axis.

  9. Positron and electron energy bands in several ionic crystals using restricted Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Kunz, A. B.; Waber, J. T.

    1981-08-01

    Using a restricted Hartree-Fock formalism and suitably localized and symmetrized wave functions, both the positron and electron energy bands were calculated for NaF, MgO and NiO. The lowest positron state at Γ 1 lies above the vacuum level and negative work functions are predicted. Positron annihilation rates were calculated and found to be in good agreement with measured lifetimes.

  10. Near Hartree-Fock quality GTO basis sets for the first- and third-row atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry

    1989-01-01

    Energy-optimized Gaussian-type-orbital (GTO) basis sets of accuracy approaching that of numerical Hartree-Fock computations are compiled for the elements of the first and third rows of the periodic table. The methods employed in calculating the sets are explained; the applicability of the sets to electronic-structure calculations is discussed; and the results are presented in tables and briefly characterized.

  11. Uniform in N global well-posedness of the time-dependent Hartree-Fock-Bogoliubov equations in R^{1+1}

    NASA Astrophysics Data System (ADS)

    Chong, Jacky Jia Wei

    2018-04-01

    We prove the global well-posedness of the time-dependent Hartree-Fock-Bogoliubov (TDHFB) equations in R^{1+1} with two-body interaction potential of the form N^{-1}v_N(x) = N^{β -1} v(N^β x) where v≥0 is a sufficiently regular radial function, i.e., v \\in L^1(R)\\cap C^∞ (R) . In particular, using methods of dispersive PDEs similar to the ones used in Grillakis and Machedon (Commun Partial Differ Equ 42:24-67, 2017), we are able to show for any scaling parameter β >0 the TDHFB equations are globally well-posed in some Strichartz-type spaces independent of N, cf. (Bach et al. in The time-dependent Hartree-Fock-Bogoliubov equations for Bosons, 2016. arXiv:1602.05171).

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

    NASA Astrophysics Data System (ADS)

    Arslan, Hakan; Algül, Öztekin

    2008-06-01

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

  13. Studies of the electron density in the highest occupied molecular orbitals of PH 3, PF 3 and P(CH 3) 3 by electron momentum spectroscopy and Hartree-Fock, MRSD-CI and DFT calculations

    NASA Astrophysics Data System (ADS)

    Rolke, J.; Brion, C. E.

    1996-06-01

    The spherically averaged momentum profiles for the highest occupied molecular orbitals of PF 3 and P(CH 3) 3 have been obtained by electron momentum spectroscopy. The measurements provide a stringent test of basis set effects and the quality of ab-initio methods in the description of these larger molecular systems. As in previous work on the methyl-substituted amines, intuitive arguments fail to predict the correct amount of s- and p-type contributions to the momentum profile while delocalized molecular orbital concepts provide a more adequate description of the HOMOs. The experimental momentum profiles have been compared with theoretical momentum profiles calculated at the level of the target Hartree-Fock approximation with a range of basis sets. New Hartree-Fock calculations are also presented for the HOMO of PH 3 and compared to previously published experimental and theoretical momentum profiles. The experimental momentum profiles have further been compared to calculations at the level of the target Kohn-Sham approximation using density functional theory with the local density approximation and also with gradient corrected (non-local) exchange correlation potentials. In addition, total energies and dipole moments have been calculated for all three molecules by the various theoretical methods and compared to experimental values. Calculated 'density difference maps' show the regions where the HOMO momentum and position electron densities of PF 3 and P(CH 3) 3 change relative to the corresponding HOMO density of PH 3. The results suggest that methyl groups have an electron-attracting effect (relative to H) on the HOMO charge density in trimethyl phosphines. These conclusions are supported by a consideration of dipole moments and the 31P NMR chemical shifts for PH 3, PF 3 and P(CH 3) 3.

  14. Investigation of nuclear structure of 30-44S isotopes using spherical and deformed Skyrme-Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Alzubadi, A. A.

    2015-06-01

    Nuclear many-body system is usually described by a mean-field built upon a nucleon-nucleon effective interaction. In this work, we investigate ground state properties of the sulfur isotopes covering a wide range from the line of stability up to the dripline region (30-44S). For this purpose the Hartree-Fock mean field theory in coordinate space with a Skyrme parameterization SkM* has been utilized. In particular, we calculate the nuclear charge, neutrons, protons, mass densities, the associated radii, neutron skin thickness and binding energy. The charge form factors have been also investigated using SkM*, SkO, SkE, SLy4 and Skxs15 Skyrme parameterizations and the results obtained using the theoretical approach are compared with the available experimental data. To investigate the potential energy surface as a function of the quadrupole deformation for isotopic sulfur chains, Skyrme-Hartree-Fock-Bogoliubov theory has been adopted with SLy4 parameterization.

  15. Equilibration in the time-dependent Hartree-Fock approach probed with the Wigner distribution function

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Loebl, N.; Maruhn, J. A.; Reinhard, P.-G.

    2011-09-15

    By calculating the Wigner distribution function in the reaction plane, we are able to probe the phase-space behavior in the time-dependent Hartree-Fock scheme during a heavy-ion collision in a consistent framework. Various expectation values of operators are calculated by evaluating the corresponding integrals over the Wigner function. In this approach, it is straightforward to define and analyze quantities even locally. We compare the Wigner distribution function with the smoothed Husimi distribution function. Different reaction scenarios are presented by analyzing central and noncentral {sup 16}O +{sup 16}O and {sup 96}Zr +{sup 132}Sn collisions. Although we observe strong dissipation in the timemore » evolution of global observables, there is no evidence for complete equilibration in the local analysis of the Wigner function. Because the initial phase-space volumes of the fragments barely merge and mean values of the observables are conserved in fusion reactions over thousands of fm/c, we conclude that the time-dependent Hartree-Fock method provides a good description of the early stage of a heavy-ion collision but does not provide a mechanism to change the phase-space structure in a dramatic way necessary to obtain complete equilibration.« less

  16. Hartree-Fock limit values of multipole moments, polarizabilities, and hyperpolarizabilities for atoms and diatomic molecules

    NASA Astrophysics Data System (ADS)

    Kobus, Jacek

    2015-02-01

    Recently it has been demonstrated that the finite difference Hartree-Fock method can be used to deliver highly accurate values of electric multipole moments together with polarizabilities αz z,Az ,z z , and hyperpolarizabilities βz z z, γz z z,Bz z ,z z , for the ground states of various atomic and diatomic systems. Since these results can be regarded as de facto Hartree-Fock limit values their quality is of the utmost importance. This paper reexamines the use of the finite field method to calculate these electric properties, discusses its accuracy, and presents an updated list of the properties for the following atoms and diatomic molecules: H-, He, Li, Li+,Li2 +,Li-,Be2 + , Be, B+,C2 + , Ne, Mg2 +, Mg, Al+,Si2 + , Ar, K+,Ca2 +,Rb+,Sr2 +,Zr4 +,He2 , Be2,N2,F2,O2 , HeNe, LiH2 +, LiCl, LiBr, BH, CO, FH, NaCl, and KF. The potential energy curves and the dependence of the electric properties on the internuclear distance is also studied for He2,LiH+,Be2 , and HeNe systems.

  17. Superdeformed bands in neutron-rich sulfur isotopes suggested by cranked Skyrme-Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Inakura, T.; Mizutori, S.; Yamagami, M.; Matsuyanagi, K.

    2003-12-01

    On the basis of the cranked Skyrme-Hartree-Fock calculations in the three-dimensional coordinate-mesh representation, we suggest that, in addition to the well-known candidate 32S, the neutron-rich nucleus 36S and the drip-line nuclei, 48S and 50S, are also good candidates for finding superdeformed rotational bands in sulfur isotopes. Calculated density distributions for the superdeformed states in 48S and 50S exhibit superdeformed neutron skins.

  18. Self-consistent Hartree-Fock RPA calculations in 208Pb

    NASA Astrophysics Data System (ADS)

    Taqi, Ali H.; Ali, Mohammed S.

    2018-01-01

    The nuclear structure of 208Pb is studied in the framework of the self-consistent random phase approximation (SCRPA). The Hartree-Fock mean field and single particle states are used to implement a completely SCRPA with Skyrme-type interactions. The Hamiltonian is diagonalised within a model space using five Skyrme parameter sets, namely LNS, SkI3, SkO, SkP and SLy4. In view of the huge number of the existing Skyrme-force parameterizations, the question remains which of them provide the best description of data. The approach attempts to accurately describe the structure of the spherical even-even nucleus 208Pb. To illustrate our approach, we compared the binding energy, charge density distribution, excitation energy levels scheme with the available experimental data. Moreover, we calculated isoscalar and isovector monopole, dipole, and quadrupole transition densities and strength functions.

  19. Second-Order Moller-Plesset Perturbation Theory for Molecular Dirac-Hartree-Fock Wave Functions

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Arnold, James O. (Technical Monitor)

    1994-01-01

    Moller-Plesset perturbation theory is developed to second order for a selection of Kramers restricted Dirac-Hartree-Fock closed and open-shell reference wave functions. The open-shell wave functions considered are limited to those with no more than two electrons in open shells, but include the case of a two-configuration SCF reference. Denominator shifts are included in the style of Davidson's OPT2 method. An implementation which uses unordered integrals with labels is presented, and results are given for a few test cases.

  20. Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

    2015-12-07

    We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

  1. 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

  2. The properties of nuclear matter with lattice NN potential in relativistic Brueckner-Hartree-Fock theory

    PubMed Central

    Hu, Jinniu; Toki, Hiroshi; Shen, Hong

    2016-01-01

    We study the properties of nuclear matter with lattice nucleon-nucleon (NN) potential in the relativistic Brueckner-Hartree-Fock (RBHF) theory. To use this potential in such a microscopic many-body theory, we firstly have to construct a one-boson-exchange potential (OBEP) based on the latest lattice NN potential. Three mesons, pion, σ meson, and ω meson, are considered. Their coupling constants and cut-off momenta are determined by fitting the on-shell behaviors and phase shifts of the lattice force, respectively. Therefore, we obtain two parameter sets of the OBEP potential (named as LOBEP1 and LOBEP2) with these two fitting ways. We calculate the properties of symmetric and pure neutron matter with LOBEP1 and LOBEP2. In non-relativistic Brueckner-Hartree-Fock case, the binding energies of symmetric nuclear matter are around −3 and −5 MeV at saturation density, while it becomes −8 and −12 MeV in relativistic framework with 1S0, 3S1, and 3D1 channels using our two parameter sets. For the pure neutron matter, the equations of state in non-relativistic and relativistic cases are very similar due to only consideration 1S0 channel with isospin T = 1 case. PMID:27752124

  3. The properties of nuclear matter with lattice NN potential in relativistic Brueckner-Hartree-Fock theory.

    PubMed

    Hu, Jinniu; Toki, Hiroshi; Shen, Hong

    2016-10-18

    We study the properties of nuclear matter with lattice nucleon-nucleon (NN) potential in the relativistic Brueckner-Hartree-Fock (RBHF) theory. To use this potential in such a microscopic many-body theory, we firstly have to construct a one-boson-exchange potential (OBEP) based on the latest lattice NN potential. Three mesons, pion, σ meson, and ω meson, are considered. Their coupling constants and cut-off momenta are determined by fitting the on-shell behaviors and phase shifts of the lattice force, respectively. Therefore, we obtain two parameter sets of the OBEP potential (named as LOBEP1 and LOBEP2) with these two fitting ways. We calculate the properties of symmetric and pure neutron matter with LOBEP1 and LOBEP2. In non-relativistic Brueckner-Hartree-Fock case, the binding energies of symmetric nuclear matter are around -3 and -5 MeV at saturation density, while it becomes -8 and -12 MeV in relativistic framework with 1 S 0 , 3 S 1 , and 3 D 1 channels using our two parameter sets. For the pure neutron matter, the equations of state in non-relativistic and relativistic cases are very similar due to only consideration 1 S 0 channel with isospin T = 1 case.

  4. 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

  5. Modified Hartree-Fock-Bogoliubov theory at finite temperature

    NASA Astrophysics Data System (ADS)

    Dinh Dang, Nguyen; Arima, Akito

    2003-07-01

    The modified Hartree-Fock-Bogoliubov (MHFB) theory at finite temperature is derived, which conserves the unitarity relation of the particle-density matrix. This is achieved by constructing a modified-quasiparticle-density matrix, where the fluctuation of the quasiparticle number is microscopically built in. This matrix can be directly obtained from the usual quasiparticle-density matrix by applying the secondary Bogoliubov transformation, which includes the quasiparticle-occupation number. It is shown that, in the limit of constant pairing parameter, the MHFB theory yields the previously obtained modified BCS (MBCS) equations. It is also proved that the modified quasiparticle-random-phase approximation, which is based on the MBCS quasiparticle excitations, conserves the Ikeda sum rule. The numerical calculations of the pairing gap, heat capacity, level density, and level-density parameter within the MBCS theory are carried out for 120Sn. The results show that the superfluid-normal phase transition is completely washed out. The applicability of the MBCS up to a temperature as high as T˜5 MeV is analyzed in detail.

  6. 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.

  7. Straightening the Hierarchical Staircase for Basis Set Extrapolations: A Low-Cost Approach to High-Accuracy Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Varandas, António J. C.

    2018-04-01

    Because the one-electron basis set limit is difficult to reach in correlated post-Hartree-Fock ab initio calculations, the low-cost route of using methods that extrapolate to the estimated basis set limit attracts immediate interest. The situation is somewhat more satisfactory at the Hartree-Fock level because numerical calculation of the energy is often affordable at nearly converged basis set levels. Still, extrapolation schemes for the Hartree-Fock energy are addressed here, although the focus is on the more slowly convergent and computationally demanding correlation energy. Because they are frequently based on the gold-standard coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)], correlated calculations are often affordable only with the smallest basis sets, and hence single-level extrapolations from one raw energy could attain maximum usefulness. This possibility is examined. Whenever possible, this review uses raw data from second-order Møller-Plesset perturbation theory, as well as CCSD, CCSD(T), and multireference configuration interaction methods. Inescapably, the emphasis is on work done by the author's research group. Certain issues in need of further research or review are pinpointed.

  8. 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.

  9. Time-Dependent Hartree-Fock Approach to Nuclear Pasta at Finite Temperature

    NASA Astrophysics Data System (ADS)

    Schuetrumpf, B.; Klatt, M. A.; Iida, K.; Maruhn, J. A.; Mecke, K.; Reinhard, P.-G.

    2013-03-01

    We present simulations of neutron-rich matter at subnuclear densities, like supernova matter, with the time-dependent Hartree-Fock approximation at temperatures of several MeV. The initial state consists of α particles randomly distributed in space that have a Maxwell-Boltzmann distribution in momentum space. Adding a neutron background initialized with Fermi distributed plane waves the calculations reflect a reasonable approximation of astrophysical matter. This matter evolves into spherical, rod-like, and slab-like shapes and mixtures thereof. The simulations employ a full Skyrme interaction in a periodic three-dimensional grid. By an improved morphological analysis based on Minkowski functionals, all eight pasta shapes can be uniquely identified by the sign of only two valuations, namely the Euler characteristic and the integral mean curvature.

  10. 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

  11. Theoretical dissociation energies for the alkali and alkaline-earth monofluorides and monochlorides

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

    1986-01-01

    Spectroscopic parameters are accurately determined for the alkali and alkaline-earth monofluorides and monochlorides by means of ab initio self-consistent field and correlated wave function calculations. Numerical Hartree-Fock calculations are performed on selected systems to ensure that the extended Slater basis sets employed are near the Hartree-Fock limit. Since the bonding is predominantly electrostatic in origin, a strong correlation exists between the dissociation energy (to ions) and the spectroscopic parameter r(e). By dissociating to the ionic limits, most of the differential correlation effects can be embedded in the accurate experimental electron affinities and ionization potentials.

  12. Parallel implementation of Hartree-Fock and density functional theory analytical second derivatives

    NASA Astrophysics Data System (ADS)

    Baker, Jon; Wolinski, Krzysztof; Malagoli, Massimo; Pulay, Peter

    2004-01-01

    We present an efficient, parallel implementation for the calculation of Hartree-Fock and density functional theory analytical Hessian (force constant, nuclear second derivative) matrices. These are important for the determination of harmonic vibrational frequencies, and to classify stationary points on potential energy surfaces. Our program is designed for modest parallelism (4-16 CPUs) as exemplified by our standard eight-processor QuantumCube™. We can routinely handle systems with up to 100+ atoms and 1000+ basis functions using under 0.5 GB of RAM memory per CPU. Timings are presented for several systems, ranging in size from aspirin (C9H8O4) to nickel octaethylporphyrin (C36H44N4Ni).

  13. Configuration-constrained cranking Hartree-Fock pairing calculations for sidebands of nuclei

    NASA Astrophysics Data System (ADS)

    Liang, W. Y.; Jiao, C. F.; Wu, Q.; Fu, X. M.; Xu, F. R.

    2015-12-01

    Background: Nuclear collective rotations have been successfully described by the cranking Hartree-Fock-Bogoliubov (HFB) model. However, for rotational sidebands which are built on intrinsic excited configurations, it may not be easy to find converged cranking HFB solutions. The nonconservation of the particle number in the BCS pairing is another shortcoming. To improve the pairing treatment, a particle-number-conserving (PNC) pairing method was suggested. But the existing PNC calculations were performed within a phenomenological one-body potential (e.g., Nilsson or Woods-Saxon) in which one has to deal the double-counting problem. Purpose: The present work aims at an improved description of nuclear rotations, particularly for the rotations of excited configurations, i.e., sidebands. Methods: We developed a configuration-constrained cranking Skyrme Hartree-Fock (SHF) calculation with the pairing correlation treated by the PNC method. The PNC pairing takes the philosophy of the shell model which diagonalizes the Hamiltonian in a truncated model space. The cranked deformed SHF basis provides a small but efficient model space for the PNC diagonalization. Results: We have applied the present method to the calculations of collective rotations of hafnium isotopes for both ground-state bands and sidebands, reproducing well experimental observations. The first up-bendings observed in the yrast bands of the hafnium isotopes are reproduced, and the second up-bendings are predicted. Calculations for rotational bands built on broken-pair excited configurations agree well with experimental data. The band-mixing between two Kπ=6+ bands observed in 176Hf and the K purity of the 178Hf rotational state built on the famous 31 yr Kπ=16+ isomer are discussed. Conclusions: The developed configuration-constrained cranking calculation has been proved to be a powerful tool to describe both the yrast bands and sidebands of deformed nuclei. The analyses of rotational moments of inertia

  14. Optimal plane-wave Hartree-Fock states for many-fermion systems

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    de Llano, M.; Plastino, A.; Zabolitzky, J.G.

    1979-12-01

    The possibility of taking plane-wave orbitals of a Hartree-Fock determinant to fill k space differently from the ''normal'' Fermi sphere is investigated for several two-body potentials including the ''homework'' v/sub 0/, v/sub 1/, and v/sub 2/ - aken from the Reid nucleon-nucleon force - as well as a sum-of-Gaussians potential chosen to fit the deuteron binding and size. A random-search and random-walk numerical algorithm shows that, provided the potential strengths are made large enough, a single-shell ''abnormal'' occupation is always found to be lower in energy than the normal one if sufficient attraction is present in the two-body interaction. Nomore » abnormal occupation is possible for, among other pair interactions, the electron or charged-boson fluid, the repulsive square barrier, and a common form of the He-He interaction.« less

  15. Hartree-Fock investigation of muon trapping in the chemical ferromagnet 4-(/p-chlorobenzylideneamino)-TEMPO

    NASA Astrophysics Data System (ADS)

    Jeong, Junho; Briere, Tina M.; Sahoo, N.; Das, T. P.; Ohira, Seiko; Nishiyama, K.; Nagamine, K.

    2000-08-01

    First-principles unrestricted Hartree-Fock theory is used to obtain the trapping sites for muon and muonium in ferromagnetic p-Cl-Ph-CHN-TEMPO (4-( p-chlorobenzylideneamino)- 2,2,6,6-tetramethylpiperidin-1-yloxyl) and the hyperfine interaction tensors for these sites. Using the calculated hyperfine interactions to fit the two experimentally observed muon spin rotation frequencies, it has been concluded that the two most likely candidates for explaining the experimental data are a muon trapped at the chlorine site and a singlet muonium state at the radical oxygen. The direction of the easy axis is also determined.

  16. Conserving and gapless Hartree-Fock-Bogoliubov theory for the three-dimensional dilute Bose gas

    NASA Astrophysics Data System (ADS)

    Zhang, Ya-Hui; Li, Dingping

    2013-11-01

    The excitation spectrum for the three-dimensional Bose gas in the Bose-Einstein condensation phase is calculated nonperturbatively with the modified Hartree-Fock-Bogoliubov theory, which is both conserving and gapless. From improved Φ-derivable theory, the diagrams needed to preserve the Ward-Takahashi identity are re-summed in a systematic and nonperturbative way. It is valid up to the critical temperature where the dispersion relation of the low-energy excitation spectrum changes from linear to quadratic. Because including the higher-order fluctuation, the results show significant improvement on the calculation of the shift of critical temperature with other conserving and gapless theories.

  17. Near Hartree-Fock quality GTO basis sets for the second-row atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry

    1987-01-01

    Energy optimized, near Hartree-Fock quality Gaussian basis sets ranging in size from (17s12p) to (20s15p) are presented for the ground states of the second-row atoms for Na(2P), Na(+), Na(-), Mg(3P), P(-), S(-), and Cl(-). In addition, optimized supplementary functions are given for the ground state basis sets to describe the negative ions, and the excited Na(2P) and Mg(3P) atomic states. The ratios of successive orbital exponents describing the inner part of the 1s and 2p orbitals are found to be nearly independent of both nuclear charge and basis set size. This provides a method of obtaining good starting estimates for other basis set optimizations.

  18. Proper and improper zero energy modes in Hartree-Fock theory and their relevance for symmetry breaking and restoration.

    PubMed

    Cui, Yao; Bulik, Ireneusz W; Jiménez-Hoyos, Carlos A; Henderson, Thomas M; Scuseria, Gustavo E

    2013-10-21

    We study the spectra of the molecular orbital Hessian (stability matrix) and random-phase approximation (RPA) Hamiltonian of broken-symmetry Hartree-Fock solutions, focusing on zero eigenvalue modes. After all negative eigenvalues are removed from the Hessian by following their eigenvectors downhill, one is left with only positive and zero eigenvalues. Zero modes correspond to orbital rotations with no restoring force. These rotations determine states in the Goldstone manifold, which originates from a spontaneously broken continuous symmetry in the wave function. Zero modes can be classified as improper or proper according to their different mathematical and physical properties. Improper modes arise from symmetry breaking and their restoration always lowers the energy. Proper modes, on the other hand, correspond to degeneracies of the wave function, and their symmetry restoration does not necessarily lower the energy. We discuss how the RPA Hamiltonian distinguishes between proper and improper modes by doubling the number of zero eigenvalues associated with the latter. Proper modes in the Hessian always appear in pairs which do not double in RPA. We present several pedagogical cases exemplifying the above statements. The relevance of these results for projected Hartree-Fock methods is also addressed.

  19. 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.

  20. Quantum supercharger library: hyper-parallelism of the Hartree-Fock method.

    PubMed

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

    2015-07-05

    We present here a set of algorithms that completely rewrites the Hartree-Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS-US, GAMESS-UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6-31G Self-Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one- and two-electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  1. Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Faegri, Knut, Jr.; Taylor, Peter R.

    1990-01-01

    Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.

  2. Restricted Hartree Fock using complex-valued orbitals: A long-known but neglected tool in electronic structure theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Small, David W.; Sundstrom, Eric J.; Head-Gordon, Martin

    2015-01-14

    Restricted Hartree Fock using complex-valued orbitals (cRHF) is studied. We introduce an orbital pairing theorem, with which we obtain a concise connection between cRHF and real-valued RHF, and use it to uncover the close relationship between cRHF, unrestricted Hartree Fock, and generalized valence bond perfect pairing. This enables an intuition for cRHF, contrasting with the generally unintuitive nature of complex orbitals. We also describe an efficient computer implementation of cRHF and its corresponding stability analysis. By applying cRHF to the Be + H{sub 2} insertion reaction, a Woodward-Hoffmann violating reaction, and a symmetry-driven conical intersection, we demonstrate in genuine molecularmore » systems that cRHF is capable of removing certain potential energy surface singularities that plague real-valued RHF and related methods. This complements earlier work that showed this capability in a model system. We also describe how cRHF is the preferred RHF method for certain radicaloid systems like singlet oxygen and antiaromatic molecules. For singlet O{sub 2}, we show that standard methods fail even at the equilibrium geometry. An implication of this work is that, regardless of their individual efficacies, cRHF solutions to the HF equations are fairly commonplace.« less

  3. 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

  4. Constrained Hartree-Fock Theory and Study of Deformed Structures of Closed Shell Nuclei

    NASA Astrophysics Data System (ADS)

    Praharaj, Choudhury

    2016-03-01

    We have studied some N or Z = 50 nuclei in a microscopic model with effective interaction in a reasonably large shell model space. Excitation of particles across 50 shell closure leads to well-deformed excited prolate configurations. The potential energy surfaces of nuclei are studied using Hartree-Fock theory with quadrupole constraint to explore the various deformed configurations of N = 50 nuclei 82Ge , 84Se and 86Kr . Energy spectra are calculated from various intrinsic states using Peierls-Yoccoz angular momentum projection technique. Results of spectra and electromagnetic moments and transitions will be presented for N = 50 nuclei and for Z = 50 114Sn nucleus. Supported by Grant No SB/S2/HEP-06/2013 of DST.

  5. Accuracy of Hartree-Fock wave functions for electron-H/sub 2/ scattering calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Feldt, A.N.

    1988-05-01

    Recent papers on electron-N/sub 2/ scattering by Rumble, Stevens, and Truhlar (J. Phys. B 17, 3151 (1984)) and Weatherford, Brown, and Temkin (Phys. Rev. A 35, 4561 (1987)) have suggested that Hartree-Fock (HF) wave functions may not be accurate for calculating potentials for use in studying electron-molecule collisions. A comparison of results for electron-H/sub 2/ scattering using both correlated and HF wave functions is presented. It is found that for both elastic and inelastic collisions and for all energies considered (up to 10 eV) the HF wave functions yield results in excellent agreement with those obtained from the more accuratemore » wave functions.« less

  6. 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.

  7. A Hartree-Fock-Bogoliubov mass formula

    NASA Astrophysics Data System (ADS)

    Samyn, M.; Goriely, S.; Heenen, P.-H.; Pearson, J. M.; Tondeur, F.

    2002-03-01

    In order to have more reliable predictions of nuclear masses at the neutron drip line, we here go beyond the recent mass formula HFBCS-1 and present a new mass formula, HFB-1, based on the Hartree-Fock-Bogoliubov method. As with the HFBCS-1 mass formula, we use a 10-parameter Skyrme force along with a 4-parameter δ-function pairing force and a 2-parameter phenomenological Wigner term. However, with the original HFBCS-1 Skyrme force (MSk7), the rms error becomes unacceptably large and a new force fit is required. With the isoscalar and isovector effective masses constrained to be equal, the remaining 15 degrees of freedom are fitted to the masses of all the 1754 measured nuclei with A⩾16, | N- Z|>2 given in the 1995 Audi-Wapstra compilation. The rms error with respect to the masses of all the 1888 measured nuclei with Z, N⩾8 is 0.764 MeV. A complete mass table, HFB-1 (available on the Web), has been constructed, giving all nuclei lying between the two drip lines over the range Z, N⩾8 and Z⩽120. A comparison between HFB-1 and HFBCS-1 mass tables shows that the HFBCS model is a very good approximation of the HFB theory, in particular for masses, the extrapolated masses never differing by more than 2 MeV below Z⩽110. We also find that the behaviour of shell gaps far away from the region of beta stability does not depend on whether the HFBCS or HFB methods are used, in particular, no quenching of astrophysical interest arises from replacing the BCS method by the Bogoliubov method.

  8. Electronic Structure and Absorption Spectra of Sodium 2-Hydroxy-5-({2-Methoxy-4[(4-Sulfophenyl)Diazenyl]Phenyl}Diazenyl)Benzoate

    NASA Astrophysics Data System (ADS)

    Almodarresiyeh, H. A.; Shahab, S. N.; Zelenkovsky, V. M.; Agabekov, V. E.

    2014-03-01

    The electronic structure and geometry of the synthesized azodye sodium 2-hydroxy-5-({2-methoxy-4[(4-sulfophenyl) diazenyl]phenyl}diazenyl)benzoate (M12) were calculated theoretically by an ab initio Hartree-Fock method in basis set 6-31G. The nature of absorption bands in the visible and near-UV spectral regions was interpreted.

  9. Charge and Spin Currents in Open-Shell Molecules:  A Unified Description of NMR and EPR Observables.

    PubMed

    Soncini, Alessandro

    2007-11-01

    The theory of EPR hyperfine coupling tensors and NMR nuclear magnetic shielding tensors of open-shell molecules in the limit of vanishing spin-orbit coupling (e.g., for organic radicals) is analyzed in terms of spin and charge current density vector fields. The ab initio calculation of the spin and charge current density response has been implemented at the Restricted Open-Shell Hartree-Fock, Unrestricted Hartree-Fock, and unrestricted GGA-DFT level of theory. On the basis of this formalism, we introduce the definition of nuclear hyperfine coupling density, a scalar function of position providing a partition of the EPR observable over the molecular domain. Ab initio maps of spin and charge current density and hyperfine coupling density for small radicals are presented and discussed in order to illustrate the interpretative advantages of the newly introduced approach. Recent NMR experiments providing evidence for the existence of diatropic ring currents in the open-shell singlet pancake-bonded dimer of the neutral phenalenyl radical are directly assessed via the visualization of the induced current density.

  10. Multiconfiguration Dirac-Hartree-Fock calculations of energy levels and radiative rates of Fe VII

    NASA Astrophysics Data System (ADS)

    Li, Yang; Xu, Xiaokai; Li, Bowen; Jönsson, Per; Chen, Ximeng

    2018-06-01

    Detailed calculations are performed for 134 fine-structure levels of the 3p63d2, 3p63d4s, 3p53d3 and 3p63d4p configurations in Fe VII using the multiconfiguration Dirac-Hartree-Fock (MCDHF) and relativistic configuration interaction (RCI) methods. Important electron correlation effects are systematically accounted for through active space (AS) expansions. Our results compare well with experimental measurements, emphasizing the importance of a careful treatment of electron correlation, and provide some missing data in the NIST atomic database. The data obtained are expected to be useful in astrophysical applications, particularly for the research of the solar coronal plasma.

  11. Time-dependent Hartree-Fock approach to nuclear ``pasta'' at finite temperature

    NASA Astrophysics Data System (ADS)

    Schuetrumpf, B.; Klatt, M. A.; Iida, K.; Maruhn, J. A.; Mecke, K.; Reinhard, P.-G.

    2013-05-01

    We present simulations of neutron-rich matter at subnuclear densities, like supernova matter, with the time-dependent Hartree-Fock approximation at temperatures of several MeV. The initial state consists of α particles randomly distributed in space that have a Maxwell-Boltzmann distribution in momentum space. Adding a neutron background initialized with Fermi distributed plane waves the calculations reflect a reasonable approximation of astrophysical matter. This matter evolves into spherical, rod-like, and slab-like shapes and mixtures thereof. The simulations employ a full Skyrme interaction in a periodic three-dimensional grid. By an improved morphological analysis based on Minkowski functionals, all eight pasta shapes can be uniquely identified by the sign of only two valuations, namely the Euler characteristic and the integral mean curvature. In addition, we propose the variance in the cell density distribution as a measure to distinguish pasta matter from uniform matter.

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

    DOE PAGES

    Signoracci, Angelo J.; Duguet, Thomas; Hagen, Gaute; ...

    2015-06-29

    relatively constant for all five nuclei, in both the Hartree-Fock-Bogoliubov and BCCD approximations. Conclusions: The newly developed many-body formalism increases the potential span of ab initio calculations based on single-reference coupled cluster techniques tremendously, i.e., potentially to reach several hundred additional midmass nuclei. The new formalism offers a wealth of potential applications and further extensions dedicated to the description of ground and excited states of open-shell nuclei. Short-term goals include the implementation of three-nucleon forces at the normal-ordered two-body level. Midterm extensions include the approximate treatment of triples corrections and the development of the equation-of-motion methodology to treat both excited states and odd nuclei. Long-term extensions include exact restoration of U(1) and SU(2) symmetries.« less

  13. Hartree-Fock theory of the inhomogeneous electron gas at a jellium metal surface: Rigorous upper bounds to the surface energy and accurate work functions

    NASA Astrophysics Data System (ADS)

    Sahni, V.; Ma, C. Q.

    1980-12-01

    The inhomogeneous electron gas at a jellium metal surface is studied in the Hartree-Fock approximation by Kohn-Sham density functional theory. Rigorous upper bounds to the surface energy are derived by application of the Rayleigh-Ritz variational principle for the energy, the surface kinetic, electrostatic, and nonlocal exchange energy functionals being determined exactly for the accurate linear-potential model electronic wave functions. The densities obtained by the energy minimization constraint are then employed to determine work-function results via the variationally accurate "displaced-profile change-in-self-consistent-field" expression. The theoretical basis of this non-self-consistent procedure and its demonstrated accuracy for the fully correlated system (as treated within the local-density approximation for exchange and correlation) leads us to conclude these results for the surface energies and work functions to be essentially exact. Work-function values are also determined by the Koopmans'-theorem expression, both for these densities as well as for those obtained by satisfaction of the constraint set on the electrostatic potential by the Budd-Vannimenus theorem. The use of the Hartree-Fock results in the accurate estimation of correlation-effect contributions to these surface properties of the nonuniform electron gas is also indicated. In addition, the original work and approximations made by Bardeen in this attempt at a solution of the Hartree-Fock problem are briefly reviewed in order to contrast with the present work.

  14. Optimized norm-conserving Hartree-Fock pseudopotentials for plane-wave calculations

    NASA Astrophysics Data System (ADS)

    Al-Saidi, W. A.; Walter, E. J.; Rappe, A. M.

    2008-02-01

    We report Hartree-Fock (HF)-based pseudopotentials suitable for plane-wave calculations. Unlike typical effective core potentials, the present pseudopotentials are finite at the origin and exhibit rapid convergence in a plane-wave basis; the optimized pseudopotential method [A. M. Rappe , Phys. Rev. B 41, 1227 (1990)] improves plane-wave convergence. Norm-conserving HF pseudopotentials are found to develop long-range non-Coulombic behavior which does not decay faster than 1/r , and is nonlocal. This behavior, which stems from the nonlocality of the exchange potential, is remedied using a recently developed self-consistent procedure [J. R. Trail and R. J. Needs, J. Chem. Phys. 122, 014112 (2005)]. The resulting pseudopotentials slightly violate the norm conservation of the core charge. We calculated several atomic properties using these pseudopotentials, and the results are in good agreement with all-electron HF values. The dissociation energies, equilibrium bond lengths, and frequencies of vibration of several dimers obtained with these HF pseudopotentials and plane waves are also in good agreement with all-electron results.

  15. Holomorphic Hartree-Fock Theory: The Nature of Two-Electron Problems.

    PubMed

    Burton, Hugh G A; Gross, Mark; Thom, Alex J W

    2018-02-13

    We explore the existence and behavior of holomorphic restricted Hartree-Fock (h-RHF) solutions for two-electron problems. Through algebraic geometry, the exact number of solutions with n basis functions is rigorously identified as 1 / 2 (3 n - 1), proving that states must exist for all molecular geometries. A detailed study on the h-RHF states of HZ (STO-3G) then demonstrates both the conservation of holomorphic solutions as geometry or atomic charges are varied and the emergence of complex h-RHF solutions at coalescence points. Using catastrophe theory, the nature of these coalescence points is described, highlighting the influence of molecular symmetry. The h-RHF states of HHeH 2+ and HHeH (STO-3G) are then compared, illustrating the isomorphism between systems with two electrons and two electron holes. Finally, we explore the h-RHF states of ethene (STO-3G) by considering the π electrons as a two-electron problem and employ NOCI to identify a crossing of the lowest energy singlet and triplet states at the perpendicular geometry.

  16. 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.

  17. Exact exchange potential evaluated from occupied Kohn-Sham and Hartree-Fock solutions

    NASA Astrophysics Data System (ADS)

    Cinal, M.; Holas, A.

    2011-06-01

    The reported algorithm determines the exact exchange potential vx in an iterative way using energy shifts (ESs) and orbital shifts (OSs) obtained with finite-difference formulas from the solutions (occupied orbitals and their energies) of the Hartree-Fock-like equation and the Kohn-Sham-like equation, the former used for the initial approximation to vx and the latter for increments of ES and OS due to subsequent changes of vx. Thus, the need for solution of the differential equations for OSs, used by Kümmel and Perdew [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.90.043004 90, 043004 (2003)], is bypassed. The iterated exchange potential, expressed in terms of ESs and OSs, is improved by modifying ESs at odd iteration steps and OSs at even steps. The modification formulas are related to the optimized-effective-potential equation (satisfied at convergence) written as the condition of vanishing density shift (DS). They are obtained, respectively, by enforcing its satisfaction through corrections to approximate OSs and by determining the optimal ESs that minimize the DS norm. The proposed method, successfully tested for several closed-(sub)shell atoms, from Be to Kr, within the density functional theory exchange-only approximation, proves highly efficient. The calculations using the pseudospectral method for representing orbitals give iterative sequences of approximate exchange potentials (starting with the Krieger-Li-Iafrate approximation) that rapidly approach the exact vx so that, for Ne, Ar, and Zn, the corresponding DS norm becomes less than 10-6 after 13, 13, and 9 iteration steps for a given electron density. In self-consistent density calculations, orbital energies of 10-4 hartree accuracy are obtained for these atoms after, respectively, 9, 12, and 12 density iteration steps, each involving just two steps of vx iteration, while the accuracy limit of 10-6 to 10-7 hartree is reached after 20 density iterations.

  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. Toward a muon-specific electronic structure theory: effective electronic Hartree-Fock equations for muonic molecules.

    PubMed

    Rayka, Milad; Goli, Mohammad; Shahbazian, Shant

    2018-02-07

    An effective set of Hartree-Fock (HF) equations are derived for electrons of muonic systems, i.e., molecules containing a positively charged muon, conceiving the muon as a quantum oscillator, which are completely equivalent to the usual two-component HF equations used to derive stationary states of the muonic molecules. In these effective equations, a non-Coulombic potential is added to the orthodox coulomb and exchange potential energy terms, which describes the interaction of the muon and the electrons effectively and is optimized during the self-consistent field cycles. While in the two-component HF equations a muon is treated as a quantum particle, in the effective HF equations it is absorbed into the effective potential and practically transformed into an effective potential field experienced by electrons. The explicit form of the effective potential depends on the nature of muon's vibrations and is derivable from the basis set used to expand the muonic spatial orbital. The resulting effective Hartree-Fock equations are implemented computationally and used successfully, as a proof of concept, in a series of muonic molecules containing all atoms from the second and third rows of the Periodic Table. To solve the algebraic version of the equations muon-specific Gaussian basis sets are designed for both muon and surrounding electrons and it is demonstrated that the optimized exponents are quite distinct from those derived for the hydrogen isotopes. The developed effective HF theory is quite general and in principle can be used for any muonic system while it is the starting point for a general effective electronic structure theory that incorporates various types of quantum correlations into the muonic systems beyond the HF equations.

  20. Non-expanded dispersion energies and damping functions for Ar 2 and Li 2

    NASA Astrophysics Data System (ADS)

    Knowles, Peter J.; Meath, William J.

    1986-02-01

    The non-expanded second-order dispersion energies and damping functions associated with the long-range dispersion energies varying as R-6, R-8and R-10 have been calculated for Ar 2 and Li 2 with the time-dependent Hartree-Fock method, using extended Gaussian basis sets. These results are used to discuss the difficulties associated with ab initio computations of these quantities.

  1. 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.

  2. Ab-initio and DFT methodologies for computing hyperpolarizabilities and susceptibilities of highly conjugated organic compounds for nonlinear optical applications

    NASA Astrophysics Data System (ADS)

    Karakas, A.; Karakaya, M.; Ceylan, Y.; El Kouari, Y.; Taboukhat, S.; Boughaleb, Y.; Sofiani, Z.

    2016-06-01

    In this talk, after a short introduction on the methodologies used for computing dipole polarizability (α), second and third-order hyperpolarizability and susceptibility; the results of theoretical studies performed on density functional theory (DFT) and ab-initio quantum mechanical calculations of nonlinear optical (NLO) properties for a few selected organic compounds and polymers will be explained. The electric dipole moments (μ) and dispersion-free first hyperpolarizabilities (β) for a family of azo-azulenes and a styrylquinolinium dye have been determined by DFT at B3LYP level. To reveal the frequency-dependent NLO behavior, the dynamic α, second hyperpolarizabilities (γ), second (χ(2)) and third-order (χ(3)) susceptibilites have been evaluated using time-dependent HartreeFock (TDHF) procedure. To provide an insight into the third-order NLO phenomena of a series of pyrrolo-tetrathiafulvalene-based molecules and pushpull azobenzene polymers, two-photon absorption (TPA) characterizations have been also investigated by means of TDHF. All computed results of the examined compounds are compared with their previous experimental findings and the measured data for similar structures in the literature. The one-photon absorption (OPA) characterizations of the title molecules have been theoretically obtained by configuration interaction (CI) method. The highest occupied molecular orbitals (HOMO), the lowest unoccupied molecular orbitals (LUMO) and the HOMO-LUMO band gaps have been revealed by DFT at B3LYP level for azo-azulenes, styrylquinolinium dye, push-pull azobenzene polymers and by parametrization method 6 (PM6) for pyrrolo-tetrathiafulvalene-based molecules.

  3. 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.

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  5. 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.

  6. Hartree-Fock calculation of the differential photoionization cross sections of small Li clusters

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Galitskiy, S. A.; Artemyev, A. N.; Jänkälä, K.

    2015-01-21

    Cross sections and angular distribution parameters for the single-photon ionization of all electron orbitals of Li{sub 2−8} are systematically computed in a broad interval of the photoelectron kinetic energies for the energetically most stable geometry of each cluster. Calculations of the partial photoelectron continuum waves in clusters are carried out by the single center method within the Hartree-Fock approximation. We study photoionization cross sections per one electron and analyze in some details general trends in the photoionization of inner and outer shells with respect to the size and geometry of a cluster. The present differential cross sections computed for Li{submore » 2} are in a good agreement with the available theoretical data, whereas those computed for Li{sub 3−8} clusters can be considered as theoretical predictions.« less

  7. Analytic energy gradient of projected Hartree-Fock within projection after variation

    NASA Astrophysics Data System (ADS)

    Uejima, Motoyuki; Ten-no, Seiichiro

    2017-03-01

    We develop a geometrical optimization technique for the projection-after-variation (PAV) scheme of the recently refined projected Hartree-Fock (PHF) as a fast alternative to the variation-after-projection (VAP) approach for optimizing the structures of molecules/clusters in symmetry-adapted electronic states at the mean-field computational cost. PHF handles the nondynamic correlation effects by restoring the symmetry of a broken-symmetry single reference wavefunction and moreover enables a black-box treatment of orbital selections. Using HF orbitals instead of PHF orbitals, our approach saves the computational cost for the orbital optimization, avoiding the convergence problem that sometimes emerges in the VAP scheme. We show that PAV-PHF provides geometries comparable to those of the complete active space self-consistent field and VAP-PHF for the tested systems, namely, CH2, O3, and the [Cu2O2 ] 2 + core, where nondynamic correlation is abundant. The proposed approach is useful for large systems mainly dominated by nondynamic correlation to find stable structures in many symmetry-adapted states.

  8. Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock.

    PubMed

    Tamayo-Mendoza, Teresa; Kreisbeck, Christoph; Lindh, Roland; Aspuru-Guzik, Alán

    2018-05-23

    Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult , a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

  9. Spin Hartree-Fock approach to studying quantum Heisenberg antiferromagnets in low dimensions

    NASA Astrophysics Data System (ADS)

    Werth, A.; Kopietz, P.; Tsyplyatyev, O.

    2018-05-01

    We construct a new mean-field theory for a quantum (spin-1/2) Heisenberg antiferromagnet in one (1D) and two (2D) dimensions using a Hartree-Fock decoupling of the four-point correlation functions. We show that the solution to the self-consistency equations based on two-point correlation functions does not produce any unphysical finite-temperature phase transition, in accord with the Mermin-Wagner theorem, unlike the common approach based on the mean-field equation for the order parameter. The next-neighbor spin-spin correlation functions, calculated within this approach, reproduce closely the strong renormalization by quantum fluctuations obtained via a Bethe ansatz in 1D and a small renormalization of the classical antiferromagnetic state in 2D. The heat capacity approximates with reasonable accuracy the full Bethe ansatz result at all temperatures in 1D. In 2D, we obtain a reduction of the peak height in the heat capacity at a finite temperature that is accessible by high-order 1 /T expansions.

  10. Exact exchange potential evaluated from occupied Kohn-Sham and Hartree-Fock solutions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cinal, M.; Holas, A.

    2011-06-15

    The reported algorithm determines the exact exchange potential v{sub x} in an iterative way using energy shifts (ESs) and orbital shifts (OSs) obtained with finite-difference formulas from the solutions (occupied orbitals and their energies) of the Hartree-Fock-like equation and the Kohn-Sham-like equation, the former used for the initial approximation to v{sub x} and the latter for increments of ES and OS due to subsequent changes of v{sub x}. Thus, the need for solution of the differential equations for OSs, used by Kuemmel and Perdew [Phys. Rev. Lett. 90, 043004 (2003)], is bypassed. The iterated exchange potential, expressed in terms ofmore » ESs and OSs, is improved by modifying ESs at odd iteration steps and OSs at even steps. The modification formulas are related to the optimized-effective-potential equation (satisfied at convergence) written as the condition of vanishing density shift (DS). They are obtained, respectively, by enforcing its satisfaction through corrections to approximate OSs and by determining the optimal ESs that minimize the DS norm. The proposed method, successfully tested for several closed-(sub)shell atoms, from Be to Kr, within the density functional theory exchange-only approximation, proves highly efficient. The calculations using the pseudospectral method for representing orbitals give iterative sequences of approximate exchange potentials (starting with the Krieger-Li-Iafrate approximation) that rapidly approach the exact v{sub x} so that, for Ne, Ar, and Zn, the corresponding DS norm becomes less than 10{sup -6} after 13, 13, and 9 iteration steps for a given electron density. In self-consistent density calculations, orbital energies of 10{sup -4} hartree accuracy are obtained for these atoms after, respectively, 9, 12, and 12 density iteration steps, each involving just two steps of v{sub x} iteration, while the accuracy limit of 10{sup -6} to 10{sup -7} hartree is reached after 20 density iterations.« less

  11. Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

    PubMed

    Guidez, Emilie B; Gordon, Mark S

    2015-03-12

    The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

  12. Adaptive multi-resolution 3D Hartree-Fock-Bogoliubov solver for nuclear structure

    NASA Astrophysics Data System (ADS)

    Pei, J. C.; Fann, G. I.; Harrison, R. J.; Nazarewicz, W.; Shi, Yue; Thornton, S.

    2014-08-01

    Background: Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, are all characterized by large sizes and complex topologies in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. Purpose: To describe complex superfluid many-fermion systems, we introduce an adaptive pseudospectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. Methods: The numerical method is based on the multi-resolution and computational harmonic analysis techniques with a multi-wavelet basis. The application of state-of-the-art parallel programming techniques include sophisticated object-oriented templates which parse the high-level code into distributed parallel tasks with a multi-thread task queue scheduler for each multi-core node. The internode communications are asynchronous. The algorithm is variational and is capable of solving coupled complex-geometric systems of equations adaptively, with functional and boundary constraints, in a finite spatial domain of very large size, limited by existing parallel computer memory. For smooth functions, user-defined finite precision is guaranteed. Results: The new adaptive multi-resolution Hartree-Fock-Bogoliubov (HFB) solver madness-hfb is benchmarked against a two-dimensional coordinate-space solver hfb-ax that is based on the B-spline technique and a three-dimensional solver

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Multi-configuration Dirac-Hartree-Fock (MCDHF) calculations for Ni XXV

    NASA Astrophysics Data System (ADS)

    Singh, Narendra; Aggarwal, Sunny

    2018-03-01

    We present accurate 165 fine-structure energy levels related to the configurations 1s22s2, 1s22p2, 1s2nƖn‧l‧ (n = 2, n‧ = 2, 3, 4, 5, Ɩ = s,p Ɩ‧ = s, p, d, f, g) of Ni XXV which may be useful ion for astrophysical and fusion plasma. For the calculations of energy levels and radiative rates, we have used the multiconfiguration Dirac-Hartree-Fock (MCDHF) method employed in GRASP2K code. The calculations are carried out in the active space approximation with the inclusion of the Breit interaction, the finite nuclear size effect, and quantum electrodynamic corrections. The transition wavelengths, transition probabilities, line strengths, and absorption oscillator strengths are reported for electric dipole (E1), electric quadrupole (E2), magnetic dipole (M1), magnetic quadrupole (M2) transitions from the ground state. We have compared our calculated results with available theoretical and experimental data and good agreement is achieved. We predict new energy levels, oscillator strengths, line strengths and transition probabilities, where no other experimental or theoretical results are available. The present complete set of results should be of great help in line identification and the interpretation of spectra, as well as in the modelling and diagnostics of astrophysical and fusion plasmas.

  18. 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.

  19. A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. I. General formalism and application to open-shell states.

    PubMed

    Miranda, R P; Fisher, A J; Stella, L; Horsfield, A P

    2011-06-28

    The solution of the time-dependent Schrödinger equation for systems of interacting electrons is generally a prohibitive task, for which approximate methods are necessary. Popular approaches, such as the time-dependent Hartree-Fock (TDHF) approximation and time-dependent density functional theory (TDDFT), are essentially single-configurational schemes. TDHF is by construction incapable of fully accounting for the excited character of the electronic states involved in many physical processes of interest; TDDFT, although exact in principle, is limited by the currently available exchange-correlation functionals. On the other hand, multiconfigurational methods, such as the multiconfigurational time-dependent Hartree-Fock (MCTDHF) approach, provide an accurate description of the excited states and can be systematically improved. However, the computational cost becomes prohibitive as the number of degrees of freedom increases, and thus, at present, the MCTDHF method is only practical for few-electron systems. In this work, we propose an alternative approach which effectively establishes a compromise between efficiency and accuracy, by retaining the smallest possible number of configurations that catches the essential features of the electronic wavefunction. Based on a time-dependent variational principle, we derive the MCTDHF working equation for a multiconfigurational expansion with fixed coefficients and specialise to the case of general open-shell states, which are relevant for many physical processes of interest.

  20. 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.

  1. 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.

  2. An efficient implementation of semi-numerical computation of the Hartree-Fock exchange on the Intel Phi processor

    NASA Astrophysics Data System (ADS)

    Liu, Fenglai; Kong, Jing

    2018-07-01

    Unique technical challenges and their solutions for implementing semi-numerical Hartree-Fock exchange on the Phil Processor are discussed, especially concerning the single- instruction-multiple-data type of processing and small cache size. Benchmark calculations on a series of buckyball molecules with various Gaussian basis sets on a Phi processor and a six-core CPU show that the Phi processor provides as much as 12 times of speedup with large basis sets compared with the conventional four-center electron repulsion integration approach performed on the CPU. The accuracy of the semi-numerical scheme is also evaluated and found to be comparable to that of the resolution-of-identity approach.

  3. 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.

  4. Theoretical description of the 2A/double prime/ and 2A/prime/ states of the peroxyformyl radical. [for air pollution and Mars atmospheric studies

    NASA Technical Reports Server (NTRS)

    Winter, N. W.; Goddard, W. A., III; Bender, C. F.

    1975-01-01

    Simple orbital ideas are used to describe the lowest two states of the peroxyformyl radical, and ab initio Hartree-Fock calculations in these states are reported. It is found that both states may be formed exothermically by association of O2 and HCO in their ground states; however, the excited state may decompose readily to OH and CO2. The possible role of such processes in oxidation of aldelydes is discussed.

  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. 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.

  7. 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.

  8. 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.

  9. Linear scaling computation of the Fock matrix. II. Rigorous bounds on exchange integrals and incremental Fock build

    NASA Astrophysics Data System (ADS)

    Schwegler, Eric; Challacombe, Matt; Head-Gordon, Martin

    1997-06-01

    A new linear scaling method for computation of the Cartesian Gaussian-based Hartree-Fock exchange matrix is described, which employs a method numerically equivalent to standard direct SCF, and which does not enforce locality of the density matrix. With a previously described method for computing the Coulomb matrix [J. Chem. Phys. 106, 5526 (1997)], linear scaling incremental Fock builds are demonstrated for the first time. Microhartree accuracy and linear scaling are achieved for restricted Hartree-Fock calculations on sequences of water clusters and polyglycine α-helices with the 3-21G and 6-31G basis sets. Eightfold speedups are found relative to our previous method. For systems with a small ionization potential, such as graphitic sheets, the method naturally reverts to the expected quadratic behavior. Also, benchmark 3-21G calculations attaining microhartree accuracy are reported for the P53 tetramerization monomer involving 698 atoms and 3836 basis functions.

  10. 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.

  11. 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

  12. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  14. Ab initio electronic structure of the progestogen norethisterone and its 5 alpha-derivatives.

    PubMed

    Kubli-Garfias, Carlos; Vázquez, Ricardo; Cooney, Austin J; Larrea, Fernando

    2002-11-01

    The steroid 17 alpha-ethynyl-19-nor-4-androsten-17 beta-ol, 3-one (Norethisterone; NET) and its 5 alpha-dihydro (5 alpha-NET), 3 alpha- and 3 beta-tetrahydro derivatives (3 alpha,5 alpha- and 3 beta,5 alpha-NET), were comparatively studied by the ab initio quantum mechanics theory. Additionally, 5 alpha-androstan-3 beta,17 beta-diol (ADIOL) was also studied. The Hartree-Fock method and the 6-31G(*) basis set were used to obtain the lowest energy conformation, geometries, electronic structure and physicochemical properties of the steroids. The results showed bond distances and valence angles similar among all steroids, but some differences in dihedral angles in the A-B-ring system were observed. The electronic structure analysis showed that NET has both frontier orbitals that is, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) located at the C4-C5 pi-bond. In A-ring reduced derivatives, the HOMO was found at the 17 beta-OH and ethynyl groups. In the case of 5 alpha-NET, the LUMO was confined to the A-ring and its C3 carbonyl group while the two NET tetrahydro-reduced derivatives showed the LUMO at the 17 beta-OH and ethynyl groups. The energy changes of the rotational barrier of the 17 beta-OH group suggest that its movement is somewhat restricted by the 17 alpha-ethynyl group. Interestingly both groups at C17 form a single electrostatic potential with high electronic density. On the other side, the 19-nor condition increases the A-ring mobility. However, the 3 beta-OH group of 3 beta,5 alpha-NET may rotate without significant energy differences as compared to the same group in ADIOL. The electronic structure of NET and its A-ring reduced derivatives explains in some extent their interaction with androgen and progesterone receptors as well as their selectivity for the estrogen alpha-receptor.

  15. 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.

  16. Covariant density functional theory: predictive power and first attempts of a microscopic derivation

    NASA Astrophysics Data System (ADS)

    Ring, Peter

    2018-05-01

    We discuss systematic global investigations with modern covariant density functionals. The number of their phenomenological parameters can be reduced considerable by using microscopic input from ab-initio calculations in nuclear matter. The size of the tensor force is still an open problem. Therefore we use the first full relativistic Brueckner-Hartree-Fock calculations in finite nuclear systems in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

  17. Assessing the role of Hartree-Fock exchange, correlation energy and long range corrections in evaluating ionization potential, and electron affinity in density functional theory.

    PubMed

    Vikramaditya, Talapunur; Lin, Shiang-Tai

    2017-06-05

    Accurate determination of ionization potentials (IPs), electron affinities (EAs), fundamental gaps (FGs), and HOMO, LUMO energy levels of organic molecules play an important role in modeling and predicting the efficiencies of organic photovoltaics, OLEDs etc. In this work, we investigate the effects of Hartree Fock (HF) Exchange, correlation energy, and long range corrections in predicting IP and EA in Hybrid Functionals. We observe increase in percentage of HF exchange results in increase of IPs and decrease in EAs. Contrary to the general expectations inclusion of both HF exchange and correlation energy (from the second order perturbation theory MP2) leads to poor prediction. Range separated Hybrid Functionals are found to be more reliable among various DFT Functionals investigated. DFT Functionals predict accurate IPs whereas post HF methods predict accurate EAs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. 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.

  19. 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

  20. 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.

  1. The Application of Some Hartree-Fock Model Calculation to the Analysis of Atomic and Free-Ion Optical Spectra

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hayhurst, Thomas Laine

    1980-08-06

    Techniques for applying ab-initio calculations to the is of atomic spectra are investigated, along with the relationship between the semi-empirical and ab-initio forms of Slater-Condon theory. Slater-Condon theory is reviewed with a focus on the essential features that lead to the effective Hamiltonians associated with the semi-empirical form of the theory. Ab-initio spectroscopic parameters are calculated from wavefunctions obtained via self-consistent field methods, while multi-configuration Hamiltonian matrices are constructed and diagonalized with computer codes written by Robert Cowan of Los Alamos Scientific Laboratory. Group theoretical analysis demonstrates that wavefunctions more general than Slater determinants (i.e. wavefunctions with radial correlations betweenmore » electrons) lead to essentially the same parameterization of effective Hamiltonians. In the spirit of this analysis, a strategy is developed for adjusting ab-initio values of the spectroscopic parameters, reproducing parameters obtained by fitting the corresponding effective Hamiltonian. Secondary parameters are used to "screen" the calculated (primary) spectroscopic parameters, their values determined by least squares. Extrapolations of the secondary parameters determined from analyzed spectra are attempted to correct calculations of atoms and ions without experimental levels. The adjustment strategy and extrapolations are tested on the K I sequence from K 0+ through Fe 7+, fitting to experimental levels for V 4+, and Cr 5+; unobserved levels and spectra are predicted for several members of the sequence. A related problem is also discussed: Energy levels of the Uranium hexahalide complexes, (UX 6) 2- for X= F, Cl, Br, and I, are fit to an effective Hamiltonian (the f 2 configuration in O h symmetry) with corrections proposed by Brian Judd.« less

  2. Nuclear Pasta at Finite Temperature with the Time-Dependent Hartree-Fock Approach

    NASA Astrophysics Data System (ADS)

    Schuetrumpf, B.; Klatt, M. A.; Iida, K.; Maruhn, J. A.; Mecke, K.; Reinhard, P.-G.

    2016-01-01

    We present simulations of neutron-rich matter at sub-nuclear densities, like supernova matter. With the time-dependent Hartree-Fock approximation we can study the evolution of the system at temperatures of several MeV employing a full Skyrme interaction in a periodic three-dimensional grid [1]. The initial state consists of α particles randomly distributed in space that have a Maxwell-Boltzmann distribution in momentum space. Adding a neutron background initialized with Fermi distributed plane waves the calculations reflect a reasonable approximation of astrophysical matter. The matter evolves into spherical, rod-like, connected rod-like and slab-like shapes. Further we observe gyroid-like structures, discussed e.g. in [2], which are formed spontaneously choosing a certain value of the simulation box length. The ρ-T-map of pasta shapes is basically consistent with the phase diagrams obtained from QMD calculations [3]. By an improved topological analysis based on Minkowski functionals [4], all observed pasta shapes can be uniquely identified by only two valuations, namely the Euler characteristic and the integral mean curvature. In addition we propose the variance in the cell-density distribution as a measure to distinguish pasta matter from uniform matter.

  3. The spectroscopic (FTIR, FT-IR gas phase and FT-Raman), first order hyperpolarizabilities, NMR analysis of 2,4-dichloroaniline by ab initio HF and density functional methods.

    PubMed

    Sundaraganesan, N; Karpagam, J; Sebastian, S; Cornard, J P

    2009-07-01

    In this work, the experimental and theoretical study on molecular structure and vibrational spectra of 2,4-dichloroaniline (2,4-DCA) were studied. The Fourier transform infrared (gas phase) and Fourier transform Raman spectra of 2,4-DCA were recorded. The molecular geometry and vibrational frequencies of 2,4-DCA in the ground state were calculated by using the Hartree-Fock (HF) and density functional (DF) methods (BLYP, B3LYP and SVWN) with 6-31G(d,p) as basis set. Comparison of the observed fundamental vibrational frequencies of 2,4-DCA with calculated results by HF and density functional methods indicates that BLYP is superior to other methods for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. The electric dipole moment (micro) and the first hyperpolarizability (beta) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4-DCA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Natural atomic charges of 2,4-DCA and 4-chloroaniline was calculated and compared. The isotropic chemical shift computed by (13)C NMR analyses also shows good agreement with experimental observations. The theoretically predicted FTIR and FT-Raman spectra of the title molecule have been constructed.

  4. Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

    NASA Astrophysics Data System (ADS)

    Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

    1981-09-01

    Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

  5. 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.

  6. 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.

  7. 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.

  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 on melting of thorium

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  10. 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).

  11. 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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  13. 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.

  14. Hartree-Fock treatment of Fermi polarons using the Lee-Low-Pine transformation

    NASA Astrophysics Data System (ADS)

    Kain, Ben; Ling, Hong Y.

    2017-09-01

    We consider the Fermi polaron problem at zero temperature, where a single impurity interacts with noninteracting host fermions. We approach the problem starting with a Fröhlich-like Hamiltonian where the impurity is described with canonical position and momentum operators. We apply the Lee-Low-Pine (LLP) transformation to change the fermionic Fröhlich Hamiltonian into the fermionic LLP Hamiltonian, which describes a many-body system containing host fermions only. We adapt the self-consistent Hartree-Fock (HF) approach, first proposed by Edwards, to the fermionic LLP Hamiltonian in which a pair of host fermions with momenta k and k' interact with a potential proportional to k .k' . We apply the HF theory, which has the advantage of not restricting the number of particle-hole pairs, to repulsive Fermi polarons in one dimension. When the impurity and host fermion masses are equal our variational ansatz, where HF orbitals are expanded in terms of free-particle states, produces results in excellent agreement with McGuire's exact analytical results based on the Bethe ansatz. This work raises the prospect of using the HF ansatz and its time-dependent generalization as building blocks for developing all-coupling theories for both equilibrium and nonequilibrium Fermi polarons in higher dimensions.

  15. Spiral magnetism in the single-band Hubbard model: the Hartree-Fock and slave-boson approaches.

    PubMed

    Igoshev, P A; Timirgazin, M A; Gilmutdinov, V F; Arzhnikov, A K; Irkhin, V Yu

    2015-11-11

    The ground-state magnetic phase diagram is investigated within the single-band Hubbard model for square and different cubic lattices. The results of employing the generalized non-correlated mean-field (Hartree-Fock) approximation and generalized slave-boson approach by Kotliar and Ruckenstein with correlation effects included are compared. We take into account commensurate ferromagnetic, antiferromagnetic, and incommensurate (spiral) magnetic phases, as well as phase separation into magnetic phases of different types, which was often lacking in previous investigations. It is found that the spiral states and especially ferromagnetism are generally strongly suppressed up to non-realistically large Hubbard U by the correlation effects if nesting is absent and van Hove singularities are well away from the paramagnetic phase Fermi level. The magnetic phase separation plays an important role in the formation of magnetic states, the corresponding phase regions being especially wide in the vicinity of half-filling. The details of non-collinear and collinear magnetic ordering for different cubic lattices are discussed.

  16. Insufficient Hartree–Fock Exchange in Hybrid DFT Functionals Produces Bent Alkynyl Radical Structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oyeyemi, Victor B.; Keith, John A.; Pavone, Michele

    2012-01-11

    Density functional theory (DFT) is often used to determine the electronic and geometric structures of molecules. While studying alkynyl radicals, we discovered that DFT exchange-correlation (XC) functionals containing less than ~22% Hartree–Fock (HF) exchange led to qualitatively different structures than those predicted from ab initio HF and post-HF calculations or DFT XCs containing 25% or more HF exchange. We attribute this discrepancy to rehybridization at the radical center due to electron delocalization across the triple bonds of the alkynyl groups, which itself is an artifact of self-interaction and delocalization errors. Inclusion of sufficient exact exchange reduces these errors and suppressesmore » this erroneous delocalization; we find that a threshold amount is needed for accurate structure determinations. Finally, below this threshold, significant errors in predicted alkyne thermochemistry emerge as a consequence.« less

  17. Bubble nuclei within the self-consistent Hartree-Fock mean field plus pairing approach

    NASA Astrophysics Data System (ADS)

    Phuc, L. Tan; Hung, N. Quang; Dang, N. Dinh

    2018-02-01

    The depletion of the nuclear density at its center, called the nuclear bubble, is studied within the Skyrme Hartree-Fock mean field consistently incorporating the superfluid pairing. The latter is obtained within the finite-temperature Bardeen-Cooper-Schrieffer theory and within the approach using the exact pairing. The numerical calculations are carried out for 22O and 34Si nuclei, whose bubble structures, caused by a very low occupancy of the 2 s1 /2 level, were previously predicted at T =0 . Among 24 Skyrme interactions under consideration, the MSk3 is the only one which reproduces the experimentally measured occupancy of the 2 s1 /2 proton level as well as the binding energy, and consequently produces the most pronounced bubble structure in 34Si. As compared to the approaches employing the same BSk14 interaction, our approach with exact pairing predicts a pairing effect which is stronger in 22O and weaker in 34Si. The increase in temperature depletes the bubble structure and completely washes it out when the temperature reaches a critical value, at which the factor measuring the depletion of the nucleon density vanishes.

  18. Theoretical dissociation energies for ionic molecules

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

    1986-01-01

    Ab initio calculations at the self-consistent-field and singles plus doubles configuration-interaction level are used to determine accurate spectroscopic parameters for most of the alkali and alkaline-earth fluorides, chlorides, oxides, sulfides, hydroxides, and isocyanides. Numerical Hartree-Fock (NHF) calculations are performed on selected systems to ensure that the extended Slater basis sets employed for the diatomic systems are near the Hartree-Fock limit. Extended Gaussian basis sets of at least triple-zeta plus double polarization equality are employed for the triatomic system. With this model, correlation effects are relatively small, but invariably increase the theoretical dissociation energies. The importance of correlating the electrons on both the anion and the metal is discussed. The theoretical dissociation energies are critically compared with the literature to rule out disparate experimental values. Theoretical (sup 2)Pi - (sup 2)Sigma (sup +) energy separations are presented for the alkali oxides and sulfides.

  19. Koopmans' theorem in the Hartree-Fock method. General formulation

    NASA Astrophysics Data System (ADS)

    Plakhutin, Boris N.

    2018-03-01

    This work presents a general formulation of Koopmans' theorem (KT) in the Hartree-Fock (HF) method which is applicable to molecular and atomic systems with arbitrary orbital occupancies and total electronic spin including orbitally degenerate (OD) systems. The new formulation is based on the full set of variational conditions imposed upon the HF orbitals by the variational principle for the total energy and the conditions imposed by KT on the orbitals of an ionized electronic shell [B. N. Plakhutin and E. R. Davidson, J. Chem. Phys. 140, 014102 (2014)]. Based on these conditions, a general form of the restricted open-shell HF method is developed, whose eigenvalues (orbital energies) obey KT for the whole energy spectrum. Particular attention is paid to the treatment of OD systems, for which the new method gives a number of unexpected results. For example, the present method gives four different orbital energies for the triply degenerate atomic level 2p in the second row atoms B to F. Based on both KT conditions and a parallel treatment of atoms B to F within a limited configuration interaction approach, we prove that these four orbital energies, each of which is triply degenerate, are related via KT to the energies of different spin-dependent ionization and electron attachment processes (2p)N → (2p ) N ±1. A discussion is also presented of specific limitations of the validity of KT in the HF method which arise in OD systems. The practical applicability of the theory is verified by comparing KT estimates of the ionization potentials I2s and I2p for the second row open-shell atoms Li to F with the relevant experimental data.

  20. 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.

  1. Two-parameter partially correlated ground-state electron density of some light spherical atoms from Hartree-Fock theory with nonintegral nuclear charge

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cordero, Nicolas A.; March, Norman H.; Alonso, Julio A.

    2007-05-15

    Partially correlated ground-state electron densities for some spherical light atoms are calculated, into which nonrelativistic ionization potentials represent essential input data. The nuclear cusp condition of Kato is satisfied precisely. The basic theoretical starting point, however, is Hartree-Fock (HF) theory for the N electrons under consideration but with nonintegral nuclear charge Z{sup '} slightly different from the atomic number Z (=N). This HF density is scaled with a parameter {lambda}, near to unity, to preserve normalization. Finally, some tests are performed on the densities for the atoms Ne and Ar, as well as for Be and Mg.

  2. Roothaan-Hartree-Fock ground-state atomic wave functions: Slater-type orbital expansions and expectation values for Z = 2-54

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bunge, C.F.; Barrientos, J.A.; Bunge, A.V.

    1993-01-01

    Roothaan-Hartree-Fock orbitals expressed in a Slater-type basis are reported for the ground states of He through Xe. Energy accuracy ranges between 8 and 10 significant figures, reducing by between 21 and 2,770 times the energy errors of the previous such compilation (E. Clementi and C. Roetti, Atomic Data and Nuclear Data Tables 14, 177, 1974). For each atom, the total energy, kinetic energy, potential energy, virial ratio, electron density at the nucleus, and the Kato cusp are given together with radial expectation values [l angle]r[sup n][r angle] with n from [minus]3 to 2 for each orbital, orbital energies, and orbitalmore » expansion coefficients. 29 refs., 1 tab.« less

  3. 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.

  4. Axial deformed solution of the Skyrme-Hartree-Fock-Bogolyubov equations using the transformed harmonic oscillator Basis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Perez, R. Navarro; Schunck, N.; Lasseri, R.

    2017-03-09

    HFBTHO is a physics computer code that is used to model the structure of the nucleus. It is an implementation of the nuclear energy Density Functional Theory (DFT), where the energy of the nucleus is obtained by integration over space of some phenomenological energy density, which is itself a functional of the neutron and proton densities. In HFBTHO, the energy density derives either from the zero-range Dkyrme or the finite-range Gogny effective two-body interaction between nucleons. Nuclear superfluidity is treated at the Hartree-Fock-Bogoliubov (HFB) approximation, and axial-symmetry of the nuclear shape is assumed. This version is the 3rd release ofmore » the program; the two previous versions were published in Computer Physics Communications [1,2]. The previous version was released at LLNL under GPL 3 Open Source License and was given release code LLNL-CODE-573953.« less

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Immediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule

    NASA Astrophysics Data System (ADS)

    Kristyán, Sándor

    1997-11-01

    In the author's previous work (Chem. Phys. Lett. 247 (1995) 101 and Chem. Phys. Lett. 256 (1996) 229) a simple quasi-linear relationship was introduced between the number of electrons, N, participating in any molecular system and the correlation energy: -0.035 ( N - 1) > Ecorr[hartree] > - 0.045( N -1). This relationship was developed to estimate more accurately correlation energy immediately in ab initio calculations by using the partial charges of atoms in the molecule, easily obtained after Hartree-Fock self-consistent field (HF-SCF) calculations. The method is compared to the well-known B3LYP, MP2, CCSD and G2M methods. Correlation energy estimations for negatively (-1) charged atomic ions are also reported.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. A multireference perturbation method using non-orthogonal Hartree-Fock determinants for ground and excited states

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yost, Shane R.; Kowalczyk, Tim; Van Voorhis, Troy, E-mail: tvan@mit.edu

    2013-11-07

    In this article we propose the ΔSCF(2) framework, a multireference strategy based on second-order perturbation theory, for ground and excited electronic states. Unlike the complete active space family of methods, ΔSCF(2) employs a set of self-consistent Hartree-Fock determinants, also known as ΔSCF states. Each ΔSCF electronic state is modified by a first-order correction from Møller-Plesset perturbation theory and used to construct a Hamiltonian in a configuration interactions like framework. We present formulas for the resulting matrix elements between nonorthogonal states that scale as N{sub occ}{sup 2}N{sub virt}{sup 3}. Unlike most active space methods, ΔSCF(2) treats the ground and excited statemore » determinants even-handedly. We apply ΔSCF(2) to the H{sub 2}, hydrogen fluoride, and H{sub 4} systems and show that the method provides accurate descriptions of ground- and excited-state potential energy surfaces with no single active space containing more than 10 ΔSCF states.« less

  17. Efficient method of evaluation for Gaussian Hartree-Fock exchange operator for Gau-PBE functional

    NASA Astrophysics Data System (ADS)

    Song, Jong-Won; Hirao, Kimihiko

    2015-07-01

    We previously developed an efficient screened hybrid functional called Gaussian-Perdew-Burke-Ernzerhof (Gau-PBE) [Song et al., J. Chem. Phys. 135, 071103 (2011)] for large molecules and extended systems, which is characterized by the usage of a Gaussian function as a modified Coulomb potential for the Hartree-Fock (HF) exchange. We found that the adoption of a Gaussian HF exchange operator considerably decreases the calculation time cost of periodic systems while improving the reproducibility of the bandgaps of semiconductors. We present a distance-based screening scheme here that is tailored for the Gaussian HF exchange integral that utilizes multipole expansion for the Gaussian two-electron integrals. We found a new multipole screening scheme helps to save the time cost for the HF exchange integration by efficiently decreasing the number of integrals of, specifically, the near field region without incurring substantial changes in total energy. In our assessment on the periodic systems of seven semiconductors, the Gau-PBE hybrid functional with a new screening scheme has 1.56 times the time cost of a pure functional while the previous Gau-PBE was 1.84 times and HSE06 was 3.34 times.

  18. Efficient method of evaluation for Gaussian Hartree-Fock exchange operator for Gau-PBE functional

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Song, Jong-Won; Hirao, Kimihiko, E-mail: hirao@riken.jp

    2015-07-14

    We previously developed an efficient screened hybrid functional called Gaussian-Perdew–Burke–Ernzerhof (Gau-PBE) [Song et al., J. Chem. Phys. 135, 071103 (2011)] for large molecules and extended systems, which is characterized by the usage of a Gaussian function as a modified Coulomb potential for the Hartree-Fock (HF) exchange. We found that the adoption of a Gaussian HF exchange operator considerably decreases the calculation time cost of periodic systems while improving the reproducibility of the bandgaps of semiconductors. We present a distance-based screening scheme here that is tailored for the Gaussian HF exchange integral that utilizes multipole expansion for the Gaussian two-electron integrals.more » We found a new multipole screening scheme helps to save the time cost for the HF exchange integration by efficiently decreasing the number of integrals of, specifically, the near field region without incurring substantial changes in total energy. In our assessment on the periodic systems of seven semiconductors, the Gau-PBE hybrid functional with a new screening scheme has 1.56 times the time cost of a pure functional while the previous Gau-PBE was 1.84 times and HSE06 was 3.34 times.« less

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  5. Direct mapping between exchange potentials of Hartree-Fock and Kohn-Sham schemes as origin of orbital proximity

    NASA Astrophysics Data System (ADS)

    Cinal, M.

    2010-01-01

    It is found that for closed-l-shell atoms, the exact local exchange potential vx(r) calculated in the exchange-only Kohn-Sham (KS) scheme of the density functional theory (DFT) is very well represented within the region of every atomic shell by each of the suitably shifted potentials obtained with the nonlocal Fock exchange operator for the individual Hartree-Fock (HF) orbitals belonging to this shell. This newly revealed property is not related to the well-known steplike shell structure in the response part of vx(r), but it results from specific relations satisfied by the HF orbital exchange potentials. These relations explain the outstanding proximity of the occupied HF and exchange-only KS orbitals as well as the high quality of the Krieger-Li-Iafrate and localized HF (or, equivalently, common-energy-denominator) approximations to the DFT exchange potential vx(r). Another highly accurate representation of vx(r) is given by the continuous piecewise function built of shell-specific exchange potentials, each defined as the weighted average of the shifted orbital exchange potentials corresponding to a given shell. The constant shifts added to the HF orbital exchange potentials, to map them onto vx(r), are nearly equal to the differences between the energies of the corresponding KS and HF orbitals. It is discussed why these differences are positive and grow when the respective orbital energies become lower for inner orbitals.

  6. Structure and gas phase stability of complexes L . .. M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

    NASA Astrophysics Data System (ADS)

    Remko, Milan

    Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+ , Na+ and Mg2+ . Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li+ > Na+ . The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

  7. Ab initio effective core potentials including relativistic effects and their application to the electronic structure calculations of heavy atoms and molecules

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, Y.S.

    1977-11-01

    The effects of the 4f shell of electrons and the relativity of valence electrons are compared. The effect of 4f shell (lanthanide contraction) is estimated from the numerical Hartree-Fock (HF) calculations of pseudo-atoms corresponding to Hf, Re, Au, Hg, Tl, Pb and Bi without 4f electrons and with atomic numbers reduced by 14. The relativistic effect estimated from the numerical Dirac-Hartree-Fock (DHF) calculations of those atoms is comparable in the magnitude with that of the 4f shell of electrons. Both are larger for 6s than for 5d or 6p electrons. The various relativistic effects on valence electrons are discussed inmore » detail to determine the proper level of the approximation for the valence electron calculations of systems with heavy elements. An effective core potential system has been developed for heavy atoms in which relativistic effects are included in the effective potentials.« less

  8. 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.

  9. 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.

  10. 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.

  11. All-electron molecular Dirac-Hartree-Fock calculations - Properties of the group IV monoxides GeO, SnO, and PbO

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.

    1993-01-01

    Dirac-Hartree-Fock calculations have been carried out on the ground states of the group IV monoxides GeO, SnO and PbO. Geometries, dipole moments and infrared data are presented. For comparison, nonrelativistic, first-order perturbation and relativistic effective core potential calculations have also been carried out. Where appropriate the results are compared with the experimental data and previous calculations. Spin-orbit effects are of great importance for PbO, where first-order perturbation theory including only the mass-velocity and Darwin terms is inadequate to predict the relativistic corrections to the properties. The relativistic effective core potential results show a larger deviation from the all-electron values than for the hydrides, and confirm the conclusions drawn on the basis of the hydride calculations.

  12. All-electron molecular Dirac-Hartree-Fock calculations: Properties of the group IV monoxides GeO, SnO and PbO

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.

    1991-01-01

    Dirac-Hartree-Fock calculations have been carried out on the ground states of the group IV monoxides GeO, SnO and PbO. Geometries, dipole moments and infrared data are presented. For comparison, nonrelativistic, first-order perturbation and relativistic effective core potential calculations have also been carried out. Where appropriate the results are compared with the experimental data and previous calculations. Spin-orbit effects are of great importance for PbO, where first-order perturbation theory including only the mass-velocity and Darwin terms is inadequate to predict the relativistic corrections to the properties. The relativistic effective core potential results show a larger deviation from the all-electron values than for the hydrides, and confirm the conclusions drawn on the basis of the hydride calculations.

  13. A Fortran 90 Hartree-Fock program for one-dimensional periodic π-conjugated systems using Pariser-Parr-Pople model

    NASA Astrophysics Data System (ADS)

    Kondayya, Gundra; Shukla, Alok

    2012-03-01

    Pariser-Parr-Pople (P-P-P) model Hamiltonian is employed frequently to study the electronic structure and optical properties of π-conjugated systems. In this paper we describe a Fortran 90 computer program which uses the P-P-P model Hamiltonian to solve the Hartree-Fock (HF) equation for infinitely long, one-dimensional, periodic, π-electron systems. The code is capable of computing the band structure, as also the linear optical absorption spectrum, by using the tight-binding and the HF methods. Furthermore, using our program the user can solve the HF equation in the presence of a finite external electric field, thereby, allowing the simulation of gated systems. We apply our code to compute various properties of polymers such as trans-polyacetylene, poly- para-phenylene, and armchair and zigzag graphene nanoribbons, in the infinite length limit. Program summaryProgram title: ppp_bulk.x Catalogue identifier: AEKW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 87 464 No. of bytes in distributed program, including test data, etc.: 2 046 933 Distribution format: tar.gz Programming language: Fortran 90 Computer: PCs and workstations Operating system: Linux, Code was developed and tested on various recent versions of 64-bit Fedora including Fedora 14 (kernel version 2.6.35.12-90). Classification: 7.3 External routines: This program needs to link with LAPACK/BLAS libraries compiled with the same compiler as the program. For the Intel Fortran Compiler we used the ACML library version 4.4.0, while for the gfortran compiler we used the libraries supplied with the Fedora distribution. Nature of problem: The electronic structure of one-dimensional periodic π-conjugated systems is an intense area of research at

  14. Quantum treatment of protons with the reduced explicitly correlated Hartree-Fock approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sirjoosingh, Andrew; Pak, Michael V.; Brorsen, Kurt R.

    2015-06-07

    The nuclear-electronic orbital (NEO) approach treats select nuclei quantum mechanically on the same level as the electrons and includes nonadiabatic effects between the electrons and the quantum nuclei. The practical implementation of this approach is challenging due to the significance of electron-nucleus dynamical correlation. Herein, we present a general extension of the previously developed reduced NEO explicitly correlated Hartree-Fock (RXCHF) approach, in which only select electronic orbitals are explicitly correlated to each quantum nuclear orbital via Gaussian-type geminal functions. Approximations of the electronic exchange between the geminal-coupled electronic orbitals and the other electronic orbitals are also explored. This general approachmore » enables computationally tractable yet accurate calculations on molecular systems with quantum protons. The RXCHF method is applied to the hydrogen cyanide (HCN) and FHF{sup −} systems, where the proton and all electrons are treated quantum mechanically. For the HCN system, only the two electronic orbitals associated with the CH covalent bond are geminal-coupled to the proton orbital. For the FHF{sup −} system, only the four electronic orbitals associated with the two FH covalent bonds are geminal-coupled to the proton orbital. For both systems, the RXCHF method produces qualitatively accurate nuclear densities, in contrast to mean field-based NEO approaches. The development and implementation of the RXCHF method provide the framework to perform calculations on systems such as proton-coupled electron transfer reactions, where electron-proton nonadiabatic effects are important.« less

  15. Rotational and vibrational transitions for Li + H2 collisions

    NASA Technical Reports Server (NTRS)

    Choi, B. H.; Poe, R. T.; Tang, K. T.

    1977-01-01

    Close coupling calculations for integral and differential cross sections have been carried out for Li + H2 collisions with an ab initio Hartree-Fock potential energy surface. Rotational, vibrational, and vib-rotational excitation cross sections are reported at 0.4336 eV, 0.7 eV, and 0.8673 eV in the center of mass system. For pure rotational excitations, which dominate the inelastic scattering, coupling with vibrational states is not very important. For vibrational transitions, the influence of large multiquantum rotational transitions is far less than that found for Li(+) + H2 collisions.

  16. Level Energies, Oscillator Strengths and Lifetimes for Transitions in Pb IV

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colon, C.; Alonso-Medina, A.; Zanon, A.

    2008-10-22

    Oscillator strengths for several lines of astrophysical interest arising from some configurations and some levels radiative lifetimes of Pb IV have been calculated. These values were obtained in intermediate coupling (IC) and using ab initio relativistic Hartree-Fock calculations. We use for the IC calculations the standard method of least square fitting of experimental energy levels by means of computer codes from Cowan. Transition Probabilities and oscillator strengths obtained, although in general agreement with the rare experimental data, do present some noticeable discrepancies that are studied in the text.

  17. On the way to a microscopic derivation of covariant density functionals in nuclei

    NASA Astrophysics Data System (ADS)

    Ring, Peter

    2018-02-01

    Several methods are discussed to derive covariant density functionals from the microscopic input of bare nuclear forces. In a first step there are semi-microscopic functionals, which are fitted to ab-initio calculations of nuclear matter and depend in addition on very few phenomenological parameters. They are able to describe nuclear properties with the same precision as fully phenomenological functionals. In a second step we present first relativistic Brueckner-Hartree-Fock calculations in finite nuclei in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

  18. 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.

  19. Microscopic optical model potential based on a Dirac Brueckner Hartree Fock approach and the relevant uncertainty analysis

    NASA Astrophysics Data System (ADS)

    Xu, Ruirui; Ma, Zhongyu; Muether, Herbert; van Dalen, E. N. E.; Liu, Tinjin; Zhang, Yue; Zhang, Zhi; Tian, Yuan

    2017-09-01

    A relativistic microscopic optical model potential, named CTOM, for nucleon-nucleus scattering is investigated in the framework of Dirac-Brueckner-Hartree-Fock approach. The microscopic feature of CTOM is guaranteed through rigorously adopting the isospin dependent DBHF calculation within the subtracted T matrix scheme. In order to verify its prediction power, a global study n, p+ A scattering are carried out. The predicted scattering observables coincide with experimental data within a good accuracy over a broad range of targets and a large region of energies only with two free items, namely the free-range factor t in the applied improved local density approximation and minor adjustments of the scalar and vector potentials in the low-density region. In addition, to estimate the uncertainty of the theoretical results, the deterministic simple least square approach is preliminarily employed to derive the covariance of predicted angular distributions, which is also briefly contained in this paper.

  20. 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.

  1. 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.

  2. 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)

  3. 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.

  4. 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.

  5. A Hartree-Fock Application Using UPC++ and the New DArray Library

    DOE PAGES

    Ozog, David; Kamil, Amir; Zheng, Yili; ...

    2016-07-21

    The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming modelsmore » and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.« less

  6. A Hartree-Fock Application Using UPC++ and the New DArray Library

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ozog, David; Kamil, Amir; Zheng, Yili

    The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming modelsmore » and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.« less

  7. Effect of Hartree-Fock exact exchange on intramolecular magnetic coupling constants of organic diradicals

    NASA Astrophysics Data System (ADS)

    Cho, Daeheum; Ko, Kyoung Chul; Ikabata, Yasuhiro; Wakayama, Kazufumi; Yoshikawa, Takeshi; Nakai, Hiromi; Lee, Jin Yong

    2015-01-01

    The intramolecular magnetic coupling constant (J) of diradical systems linked with five- or six-membered aromatic rings was calculated to obtain the scaling factor (experimental J/calculated J ratio) for various density functional theory (DFT) functionals. Scaling factors of group A (PBE, TPSSh, B3LYP, B97-1, X3LYP, PBE0, and BH&HLYP) and B (M06-L, M06, M06-2X, and M06-HF) were shown to decrease as the amount of Hartree-Fock exact exchange (HFx) increases, in other words, overestimation of calculated J becomes more severe as the HFx increases. We further investigated the effect of HFx fraction of DFT functional on J value, spin contamination, and spin density distributions by comparing the B3LYP analogues containing different amount of HFx. It was revealed that spin contamination and spin densities at each atom increases as the HFx increases. Above all, newly developed BLYP-5 functional, which has 5% of HFx, was found to have the scaling factor of 1.029, indicating that calculated J values are very close to that of experimental values without scaling. BLYP-5 has potential to be utilized for accurate evaluation of intramolecular magnetic coupling constant (J) of diradicals linked by five- or six-membered aromatic ring couplers.

  8. Effect of Hartree-Fock exact exchange on intramolecular magnetic coupling constants of organic diradicals.

    PubMed

    Cho, Daeheum; Ko, Kyoung Chul; Ikabata, Yasuhiro; Wakayama, Kazufumi; Yoshikawa, Takeshi; Nakai, Hiromi; Lee, Jin Yong

    2015-01-14

    The intramolecular magnetic coupling constant (J) of diradical systems linked with five- or six-membered aromatic rings was calculated to obtain the scaling factor (experimental J/calculated J ratio) for various density functional theory (DFT) functionals. Scaling factors of group A (PBE, TPSSh, B3LYP, B97-1, X3LYP, PBE0, and BH&HLYP) and B (M06-L, M06, M06-2X, and M06-HF) were shown to decrease as the amount of Hartree-Fock exact exchange (HFx) increases, in other words, overestimation of calculated J becomes more severe as the HFx increases. We further investigated the effect of HFx fraction of DFT functional on J value, spin contamination, and spin density distributions by comparing the B3LYP analogues containing different amount of HFx. It was revealed that spin contamination and spin densities at each atom increases as the HFx increases. Above all, newly developed BLYP-5 functional, which has 5% of HFx, was found to have the scaling factor of 1.029, indicating that calculated J values are very close to that of experimental values without scaling. BLYP-5 has potential to be utilized for accurate evaluation of intramolecular magnetic coupling constant (J) of diradicals linked by five- or six-membered aromatic ring couplers.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Transport model of controlled molecular rectifier showing unusual negative differential resistance effect.

    PubMed

    Granhen, Ewerton Ramos; Reis, Marcos Allan Leite; Souza, Fabrício M; Del Nero, Jordan

    2010-12-01

    We investigate theoretically the charge accumulated Q in a three-terminal molecular device in the presence of an external electric field. Our approach is based on ab initio Hartree-Fock and density functional theory methodology contained in Gaussian package. Our main finding is a negative differential resistance (NDR) in the charge Q as a function of an external electric field. To explain this NDR effect we apply a phenomenological capacitive model based on a quite general system composed of many localized levels (that can be LUMOs of a molecule) coupled to source and drain. The capacitance accounts for charging effects that can result in Coulomb blockade (CB) in the transport. We show that this CB effect gives rise to a NDR for a suitable set of phenomenological parameters, like tunneling rates and charging energies. The NDR profile obtained in both ab initio and phenomenological methodologies are in close agreement.

  15. 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.

  16. On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

    PubMed

    Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

    2010-03-01

    Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

  17. 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.

  18. 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.

  19. Methods and Strategies for the Ab Initio Design of Novel Manganese Oxide- Based Water Splitting Photocatalyst Materials

    NASA Astrophysics Data System (ADS)

    Kanan, Dalal K.

    Photoelectrochemical cells (PECs) use sunlight to drive endoergic reactions such as carbon dioxide reduction to fuels or water-splitting for renewable hydrogen production. However, materials that combine both the efficiency and low cost needed to make solar-powered catalysis a practical reality have yet to be discovered. This thesis presents methods and new design strategies for developing novel, efficient, robust, and inexpensive photocatalysts based on transition metal oxides (TMOs). Quantum mechanics methodologies are developed and tested for their ability to predict the properties of known materials and then used to predict how altering the composition by alloying and doping with abundant elements affects optical, electronic, transport, and catalytic properties. The first material considered for photocatalysis is MnO, the bio-inspired solid state analogue of the photosystem II active site. GW theory with input from hybrid DFT and ab initio DFT+U capably predicts the photoemission/inverse photoemission (PE/IPE) band gap and dielectric properties. An ab initio value of U-J = 3.5 eV for Mn2+ was determined using unrestricted Hartree-Fock theory on cluster-size-converged electrostatically embedded clusters. The lowest-lying excitations in MnO, studied using ECW theory, are found to be single Mn d → d ligand field excitations (~2.5 eV, ~108 s lifetime), followed by double d → d excitations (~5.2 eV, ~106 s lifetime), Mn 3d-4s excitations (~6.3 eV, ~10-3 s lifetime), and higher-lying O 2p → Mn 3d ligand-to-metal charge-transfer (LMCT) excitations (~10.1 eV, ~10-4 s lifetime). The longer-lived transitions should exhibit better electron-hole pair separation and enhance photoconductivity depending on ease of carrier transport. While MnO possesses suitable band edge energies, its band gap is too large for efficient sunlight absorption. We predict alloying MnO with ZnO in varying amounts reduces the PE/IPE band gap (to 2.6 eV for the 1:1 alloy) while preserving

  20. The Dielectric Permittivity of Crystals in the Reduced Hartree-Fock Approximation

    NASA Astrophysics Data System (ADS)

    Cancès, Éric; Lewin, Mathieu

    2010-07-01

    In a recent article (Cancès et al. in Commun Math Phys 281:129-177, 2008), we have rigorously derived, by means of bulk limit arguments, a new variational model to describe the electronic ground state of insulating or semiconducting crystals in the presence of local defects. In this so-called reduced Hartree-Fock model, the ground state electronic density matrix is decomposed as {γ = γ^0_per + Q_{ν,\\varepsilon_F}}, where {γ^0_per} is the ground state density matrix of the host crystal and {Q_{ν,\\varepsilon_F}} the modification of the electronic density matrix generated by a modification ν of the nuclear charge of the host crystal, the Fermi level ɛ F being kept fixed. The purpose of the present article is twofold. First, we study in more detail the mathematical properties of the density matrix {Q_{ν,\\varepsilon_F}} (which is known to be a self-adjoint Hilbert-Schmidt operator on {L^2(mathbb{R}^3)}). We show in particular that if {int_{mathbb{R}^3} ν neq 0, Q_{ν,\\varepsilon_F}} is not trace-class. Moreover, the associated density of charge is not in {L^1(mathbb{R}^3)} if the crystal exhibits anisotropic dielectric properties. These results are obtained by analyzing, for a small defect ν, the linear and nonlinear terms of the resolvent expansion of {Q_{ν,\\varepsilon_F}}. Second, we show that, after an appropriate rescaling, the potential generated by the microscopic total charge (nuclear plus electronic contributions) of the crystal in the presence of the defect converges to a homogenized electrostatic potential solution to a Poisson equation involving the macroscopic dielectric permittivity of the crystal. This provides an alternative (and rigorous) derivation of the Adler-Wiser formula.

  1. 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.

  2. 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.

  3. 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.

  4. Neutral-atom electron binding energies from relaxed-orbital relativistic Hartree-Fock-Slater calculations for Z between 2 and 106

    NASA Technical Reports Server (NTRS)

    Huang, K.-N.; Aoyagi, M.; Mark, H.; Chen, M. H.; Crasemann, B.

    1976-01-01

    Electron binding energies in neutral atoms have been calculated relativistically, with the requirement of complete relaxation. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first-order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all elements with atomic numbers ranging from 2 to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. Binding energies including relaxation are listed for all electrons in all atoms over the indicated range of atomic numbers. A self-energy correction is included for the 1s, 2s, and 2p(1/2) levels. Results for selected atoms are compared with energies calculated by other methods and with experimental values.

  5. The unrestricted Hartree-Fock self consistent field calculation for spin density wave state in metallic carbon nanotube

    NASA Astrophysics Data System (ADS)

    Kobayashi, Katsushi

    1997-06-01

    The possibility of a spin density wave (SDW) state in a metallic carbon nanotube (CN) and its electronic properties are investigated within the Hartree-Fock self consistent field (SCF) energy-band calculation. Two kinds of spatial SDW states are assumed in this study. Each assumed SDW on the wave function is constructed with the degenerate π orbital in the metallic CN system. The results calculated for the one SDW model of CN always have a relative stability (˜ 0.1 eV/cell) in SCF total energy compared with the original model in which no SDW is assumed. All the results calculated for another SDW model are completely equal to the original one. Moreover, in the energy dispersion of the former stable SDW model, the degenerate π level found in the original model disappears and the band gap (3-5 eV) occurs around at the Fermi level. The energetic stability and the band gap are also found in the π-electron band calculation within the Hubbard Hamiltonian.

  6. 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.

  7. Effects of nitrogenous substituent groups on the benzene dication

    NASA Astrophysics Data System (ADS)

    Forgy, C. C.; Schlimgen, A. W.; Mazziotti, D. A.

    2018-05-01

    The benzene dication possesses a pentagonal-pyramidal structure with a hexacoordinated carbon. In contrast, halogenated benzene dications retain a similar structure to their parent molecules. In this work, we report on theoretical studies of the structures of the dications of benzene with nitrogenous substituents. We find that the nitrobenzene dication favours a near ideal pentagonal-pyramidal structure, while the aniline dication favours a flat, hexagonal structure. Reduced-density-matrices methods give predictions in agreement with available ab initio calculations and experiment. These results are also compared with those from the Hartree-Fock method and density functional theory.

  8. 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.

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

    NASA Technical Reports Server (NTRS)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

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

  10. Ab initio 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.

  11. 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.

  12. 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.

  13. Theoretical and experimental studies of the structure and vibrational spectra of NTO

    NASA Astrophysics Data System (ADS)

    Sorescu, Dan C.; Sutton, Teressa R. L.; Thompson, Donald L.; Beardall, David; Wight, Charles A.

    1996-10-01

    The structure and vibrational spectra of the high explosive 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) have been determined by ab initio molecular orbital calculations at the Hartree-Fock and second-order Møller-Plesset levels and by density functional theory (B3LYP). Experimental frequencies for the molecule have been determined from infrared spectra of pure NTO films and NTO molecules isolated in an argon matrix at 21 K. A force field for gas phase NTO has been obtained based on calculated results at the MP2/6-311G∗∗ level. In addition, a force field for solid state NTO has been constructed using the experimental vibrational frequencies for NTO films and scaled ab initio vibrational frequencies. Differences between the solid state and gas phase results indicate that the environment and preparation procedure exert a marked influence on the spectral characteristics of the NTO molecule.

  14. Analytic second derivatives of the energy in the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

    2013-04-01

    We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm-1 in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.

  15. A single molecule rectifier with strong push-pull coupling

    NASA Astrophysics Data System (ADS)

    Saraiva-Souza, Aldilene; Macedo de Souza, Fabricio; Aleixo, Vicente F. P.; Girão, Eduardo Costa; Filho, Josué Mendes; Meunier, Vincent; Sumpter, Bobby G.; Souza Filho, Antônio Gomes; Del Nero, Jordan

    2008-11-01

    We theoretically investigate the electronic charge transport in a molecular system composed of a donor group (dinitrobenzene) coupled to an acceptor group (dihydrophenazine) via a polyenic chain (unsaturated carbon bridge). Ab initio calculations based on the Hartree-Fock approximations are performed to investigate the distribution of electron states over the molecule in the presence of an external electric field. For small bridge lengths (n =0-3) we find a homogeneous distribution of the frontier molecular orbitals, while for n >3 a strong localization of the lowest unoccupied molecular orbital is found. The localized orbitals in between the donor and acceptor groups act as conduction channels when an external electric field is applied. We also calculate the rectification behavior of this system by evaluating the charge accumulated in the donor and acceptor groups as a function of the external electric field. Finally, we propose a phenomenological model based on nonequilibrium Green's function to rationalize the ab initio findings.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    2015-05-21

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

    PubMed

    Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R

    2016-12-21

    For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H d (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H d by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H d determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Structure factors for tunneling ionization rates of molecules: General Hartree-Fock-based integral representation

    NASA Astrophysics Data System (ADS)

    Madsen, Lars Bojer; Jensen, Frank; Dnestryan, Andrey I.; Tolstikhin, Oleg I.

    2017-07-01

    In the leading-order approximation of the weak-field asymptotic theory (WFAT), the dependence of the tunneling ionization rate of a molecule in an electric field on its orientation with respect to the field is determined by the structure factor of the ionizing molecular orbital. The WFAT yields an expression for the structure factor in terms of a local property of the orbital in the asymptotic region. However, in general quantum chemistry approaches molecular orbitals are expanded in a Gaussian basis which does not reproduce their asymptotic behavior correctly. This hinders the application of the WFAT to polyatomic molecules, which are attracting increasing interest in strong-field physics. Recently, an integral-equation approach to the WFAT for tunneling ionization of one electron from an arbitrary potential has been developed. The structure factor is expressed in an integral form as a matrix element involving the ionizing orbital. The integral is not sensitive to the asymptotic behavior of the orbital, which resolves the difficulty mentioned above. Here, we extend the integral representation for the structure factor to many-electron systems treated within the Hartree-Fock method and show how it can be implemented on the basis of standard quantum chemistry software packages. We validate the methodology by considering noble-gas atoms and the CO molecule, for which accurate structure factors exist in the literature. We also present benchmark results for CO2 and for NH3 in the pyramidal and planar geometries.

  9. 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.

  10. Molecular wave function and effective adiabatic potentials calculated by extended multi-configuration time-dependent Hartree-Fock method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru

    We first calculate the ground-state molecular wave function of 1D model H{sub 2} molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understandmore » dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.« less

  11. Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions.

    PubMed

    Boström, Jonas; Aquilante, Francesco; Pedersen, Thomas Bondo; Lindh, Roland

    2009-06-09

    The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Møller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.

  12. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  15. A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-11-28

    A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.

  16. Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

    PubMed

    Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

    2011-09-21

    The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of

  17. 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).

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  19. All-electron molecular Dirac-Hartree-Fock calculations - The group IV tetrahydrides CH4, SiH4, GeH4, SnH4, and PbH4

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Taylor, Peter R.; Faegri, Knut, Jr.; Partridge, Harry

    1991-01-01

    A basis-set-expansion Dirac-Hartree-Fock program for molecules is described. Bond lengths and harmonic frequencies are presented for the ground states of the group 4 tetrahydrides, CH4, SiH4, GeH4, SnH4, and PbH4. The results are compared with relativistic effective core potential (RECP) calculations, first-order perturbation theory (PT) calculations and with experimental data. The bond lengths are well predicted by first-order perturbation theory for all molecules, but none of the RECP's considered provides a consistent prediction. Perturbation theory overestimates the relativistic correction to the harmonic frequencies; the RECP calculations underestimate the correction.

  20. All-electron molecular Dirac-Hartree-Fock calculations: The group 4 tetrahydrides CH4, SiH4, GeH4, SnH4 and PbH4

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Taylor, Peter R.; Faegri, Knut, Jr.; Partridge, Harry

    1990-01-01

    A basis-set-expansion Dirac-Hartree-Fock program for molecules is described. Bond lengths and harmonic frequencies are presented for the ground states of the group 4 tetrahydrides, CH4, SiH4, GeH4, SnH4, and PbH4. The results are compared with relativistic effective core potential (RECP) calculations, first-order perturbation theory (PT) calculations and with experimental data. The bond lengths are well predicted by first-order perturbation theory for all molecules, but non of the RECP's considered provides a consistent prediction. Perturbation theory overestimates the relativistic correction to the harmonic frequencies; the RECP calculations underestimate the correction.

  1. 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.

  2. 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.

  3. Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis.. (VI) HFODD (v2.40h): A new version of the program

    NASA Astrophysics Data System (ADS)

    Dobaczewski, J.; Satuła, W.; Carlsson, B. G.; Engel, J.; Olbratowski, P.; Powałowski, P.; Sadziak, M.; Sarich, J.; Schunck, N.; Staszczak, A.; Stoitsov, M.; Zalewski, M.; Zduńczuk, H.

    2009-11-01

    We describe the new version (v2.40h) of the code HFODD which solves the nuclear Skyrme-Hartree-Fock or Skyrme-Hartree-Fock-Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented: (i) projection on good angular momentum (for the Hartree-Fock states), (ii) calculation of the GCM kernels, (iii) calculation of matrix elements of the Yukawa interaction, (iv) the BCS solutions for state-dependent pairing gaps, (v) the HFB solutions for broken simplex symmetry, (vi) calculation of Bohr deformation parameters, (vii) constraints on the Schiff moments and scalar multipole moments, (viii) the DT2h transformations and rotations of wave functions, (ix) quasiparticle blocking for the HFB solutions in odd and odd-odd nuclei, (x) the Broyden method to accelerate the convergence, (xi) the Lipkin-Nogami method to treat pairing correlations, (xii) the exact Coulomb exchange term, (xiii) several utility options, and we have corrected three insignificant errors. New version program summaryProgram title: HFODD (v2.40h) Catalogue identifier: ADFL_v2_2 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADFL_v2_2.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 79 618 No. of bytes in distributed program, including test data, etc.: 372 548 Distribution format: tar.gz Programming language: FORTRAN-77 and Fortran-90 Computer: Pentium-III, AMD-Athlon, AMD-Opteron Operating system: UNIX, LINUX, Windows XP Has the code been

  4. Hartree-Fock implementation using a Laguerre-based wave function for the ground state and correlation energies of two-electron atoms.

    PubMed

    King, Andrew W; Baskerville, Adam L; Cox, Hazel

    2018-03-13

    An implementation of the Hartree-Fock (HF) method using a Laguerre-based wave function is described and used to accurately study the ground state of two-electron atoms in the fixed nucleus approximation, and by comparison with fully correlated (FC) energies, used to determine accurate electron correlation energies. A variational parameter A is included in the wave function and is shown to rapidly increase the convergence of the energy. The one-electron integrals are solved by series solution and an analytical form is found for the two-electron integrals. This methodology is used to produce accurate wave functions, energies and expectation values for the helium isoelectronic sequence, including at low nuclear charge just prior to electron detachment. Additionally, the critical nuclear charge for binding two electrons within the HF approach is calculated and determined to be Z HF C =1.031 177 528.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  7. 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).

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

    NASA Astrophysics Data System (ADS)

    Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

    2015-03-01

    Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Ng, T. Y.; Yeak, S. H.; Liew, K. M.

    2008-02-01

    A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

  20. 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.

  1. Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

    PubMed Central

    Xu, Dong; Zhang, Yang

    2013-01-01

    Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

  2. Microwave spectrum and structure of bicyclo /1.1.1/ pentanone and comparison with several theoretical structures

    NASA Technical Reports Server (NTRS)

    Mcrae, Glenn A.; Cohen, Edward A.; Sponsler, Michael B.; Dougherty, Dennis A.

    1986-01-01

    The microwave spectra of five isotopic species of bicyclo (1.1.1) pentanone have been investigated. The rotational constants along with various centrifugal distortion constants for each species have been determined. From the rotational constants, a complete r(s) structure has been determined for the heavy atoms. Analysis of Stark effect measurements has shown the dipole moment to be along the a principal inertial axis with a magnitude of 3.164 (5) D. These results are compared with those obtained by four current theoretical methods: molecular mechanics (MM2), MNDO, and Hartree-Fock ab initio theory with STO-3G and 3-21G basis sets.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

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

    PubMed

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

    2015-02-01

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

  8. 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.

  9. 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

  10. 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.

  11. Solution of the Skyrme Hartree Fock Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (V) HFODD(v2.08k)

    NASA Astrophysics Data System (ADS)

    Dobaczewski, J.; Olbratowski, P.

    2005-05-01

    We describe the new version (v2.08k) of the code HFODD which solves the nuclear Skyrme-Hartree-Fock or Skyrme-Hartree-Fock-Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. Similarly as in the previous version (v2.08i), all symmetries can be broken, which allows for calculations with angular frequency and angular momentum tilted with respect to the mass distribution. In the new version, three minor errors have been corrected. New Version Program SummaryTitle of program: HFODD; version: 2.08k Catalogue number: ADVA Catalogue number of previous version: ADTO (Comput. Phys. Comm. 158 (2004) 158) Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVA Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Does the new version supersede the previous one: yes Computers on which this or another recent version has been tested: SG Power Challenge L, Pentium-II, Pentium-III, AMD-Athlon Operating systems under which the program has been tested: UNIX, LINUX, Windows-2000 Programming language used: Fortran Memory required to execute with typical data: 10M words No. of bits in a word: 64 No. of lines in distributed program, including test data, etc.: 52 631 No. of bytes in distributed program, including test data, etc.: 266 885 Distribution format:tar.gz Nature of physical problem: The nuclear mean-field and an analysis of its symmetries in realistic cases are the main ingredients of a description of nuclear states. Within the Local Density Approximation, or for a zero-range velocity-dependent Skyrme interaction, the nuclear mean-field is local and velocity dependent. The locality allows for an effective and fast solution of the self-consistent Hartree-Fock equations, even for heavy nuclei, and for various nucleonic ( n-particle n-hole) configurations, deformations, excitation energies, or angular momenta. Similar Local Density Approximation in the particle-particle channel, which is equivalent to using a zero

  12. Axially deformed solution of the Skyrme-Hartree-Fock-Bogolyubov equations using the transformed harmonic oscillator basis (III) HFBTHO (v3.00): A new version of the program

    NASA Astrophysics Data System (ADS)

    Perez, R. Navarro; Schunck, N.; Lasseri, R.-D.; Zhang, C.; Sarich, J.

    2017-11-01

    We describe the new version 3.00 of the code HFBTHO that solves the nuclear Hartree-Fock (HF) or Hartree-Fock-Bogolyubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis. In the new version, we have implemented the following features: (i) the full Gogny force in both particle-hole and particle-particle channels, (ii) the calculation of the nuclear collective inertia at the perturbative cranking approximation, (iii) the calculation of fission fragment charge, mass and deformations based on the determination of the neck, (iv) the regularization of zero-range pairing forces, (v) the calculation of localization functions, (vi) a MPI interface for large-scale mass table calculations. Program Files doi:http://dx.doi.org/10.17632/c5g2f92by3.1 Licensing provisions: GPL v3 Programming language: FORTRAN-95 Journal reference of previous version: M.V. Stoitsov, N. Schunck, M. Kortelainen, N. Michel, H. Nam, E. Olsen, J. Sarich, and S. Wild, Comput. Phys. Commun. 184 (2013). Does the new version supersede the previous one: Yes Summary of revisions: 1. the Gogny force in both particle-hole and particle-particle channels was implemented; 2. the nuclear collective inertia at the perturbative cranking approximation was implemented; 3. fission fragment charge, mass and deformations were implemented based on the determination of the position of the neck between nascent fragments; 4. the regularization method of zero-range pairing forces was implemented; 5. the localization functions of the HFB solution were implemented; 6. a MPI interface for large-scale mass table calculations was implemented. Nature of problem:HFBTHO is a physics computer code that is used to model the structure of the nucleus. It is an implementation of the energy density functional (EDF) approach to atomic nuclei, where the energy of the nucleus is obtained by integration over space of some phenomenological energy density, which is itself a functional of the neutron and proton

  13. 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.

  14. 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.

  15. Stopping power and range calculations in human tissues by using the Hartree-Fock-Roothaan wave functions

    NASA Astrophysics Data System (ADS)

    Usta, Metin; Tufan, Mustafa Çağatay

    2017-11-01

    The object of this work is to present the consequences for the stopping power and range values of some human tissues at energies ranging from 1 MeV to 1 GeV and 1-500 MeV, respectively. The considered human tissues are lung, intestine, skin, larynx, breast, bladder, prostate and ovary. In this work, the stopping power is calculated by considering the number of velocity-dependent effective charge and effective mean excitation energies of the target material. We used the Hartree-Fock-Roothaan (HFR) atomic wave function to determine the charge density and the continuous slowing down approximation (CSDA) method for the calculation of the proton range. Electronic stopping power values of tissues results have been compared with the ICRU 44, 46 reports, SRIM, Janni and CasP data over the percent error rate. Range values relate to tissues have compared the range results with the SRIM, FLUKA and Geant4 data. For electronic stopping power results, ICRU, SRIM and Janni's data indicated the best fit with our values at 1-50, 50-250 MeV and 250 MeV-1 GeV, respectively. For range results, the best accordance with the calculated values have been found the SRIM data and the error level is less than 10% in proton therapy. However, greater 30% errors were observed in the 250 MeV and over energies.

  16. 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.

  17. Hartree-Fock and density functional theory study of alpha-cyclodextrin conformers.

    PubMed

    Jiménez, Verónica; Alderete, Joel B

    2008-01-31

    Herein, we report the geometry optimization of four conformers of alpha-cyclodextrin (alpha-CD) by means of PM3, HF/STO-3G, HF/3-21G, HF/6-31G(d), B3LYP/6-31G(d), and X3LYP/6-31G(d) calculations. The analysis of several geometrical parameters indicates that all conformers possess bond lengths, angles, and dihedrals that agree fairly well with the crystalline structure of alpha-CD. However, only three of them (1-3) resemble the polar character of CDs and show intramolecular hydrogen-bonding patterns that agree with experimental NMR data. Among them, conformer 3 appears to be the most stable species both in the gas phase and in solution; therefore, it is expected to be the most suitable representative structure for alpha-CD conformation. The purpose of selecting such a species is to identify an appropriate structure to be employed as a starting point for reliable computational studies on complexation phenomena. Our results indicate that the choice of a particular alpha-CD conformer should affect the results of ab initio computational studies on the inclusion complexation with this cyclodextrin since both the direction and the magnitude of the dipole moment depend strongly on the conformation of alpha-CD.

  18. 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 .

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  20. Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-01-01

    We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

  1. 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.

  2. 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.

  3. Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

    NASA Technical Reports Server (NTRS)

    Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

    2002-01-01

    The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  11. 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.

  12. 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.

  13. 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.

  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. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  17. 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.

  18. 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.

  19. 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

  20. Ab initio study of the electron energy loss function in a graphene-sapphire-graphene composite system

    NASA Astrophysics Data System (ADS)

    Despoja, Vito; Djordjević, Tijana; Karbunar, Lazar; Radović, Ivan; Mišković, Zoran L.

    2017-08-01

    The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3 . The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm-1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm-1 for doped graphene layers with the Fermi energy of 0.2 eV.

  1. Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr

    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

  2. Hartree-Fock study of the Anderson metal-insulator transition in the presence of Coulomb interaction: Two types of mobility edges and their multifractal scaling exponents

    NASA Astrophysics Data System (ADS)

    Lee, Hyun-Jung; Kim, Ki-Seok

    2018-04-01

    We investigate the role of Coulomb interaction in the multifractality of Anderson metal-insulator transition, where the Coulomb interaction is treated within the Hartree-Fock approximation, but disorder effects are taken into account exactly. An innovative technical aspect in our simulation is to utilize the Ewald-sum technique, which allows us to introduce the long-range nature of the Coulomb interaction into Hartree-Fock self-consistent equations of order parameters more accurately. This numerical simulation reproduces the Altshuler-Aronov correction in a metallic state and the Efros-Shklovskii pseudogap in an insulating phase, where the density of states ρ (ω ) is evaluated in three dimensions. Approaching the quantum critical point of a metal-insulator transition from either the metallic or insulting phase, we find that the density of states is given by ρ (ω ) ˜|ω| 1 /2 , which determines one critical exponent of the McMillan-Shklovskii scaling theory. Our main result is to evaluate the eigenfunction multifractal scaling exponent αq, given by the Legendre transformation of the fractal dimension τq, which characterizes the scaling behavior of the inverse participation ratio with respect to the system size L . Our multifractal analysis leads us to identify two kinds of mobility edges, one of which occurs near the Fermi energy and the other of which appears at a high energy, where the density of states at the Fermi energy shows the Coulomb-gap feature. We observe that the multifractal exponent at the high-energy mobility edge remains to be almost identical to that of the Anderson localization transition in the absence of Coulomb interactions. On the other hand, we find that the multifractal exponent near the Fermi energy is more enhanced than that at the high-energy mobility edge, suspected to result from interaction effects. However, both the multifractal exponents do not change even if the strength of the Coulomb interaction varies. We also show that the

  3. 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.

  4. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-08-07

    Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

  5. Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (IV) HFODD (v2.08i): a new version of the program

    NASA Astrophysics Data System (ADS)

    Dobaczewski, J.; Olbratowski, P.

    2004-04-01

    We describe the new version (v2.08i) of the code HFODD which solves the nuclear Skyrme-Hartree-Fock or Skyrme-Hartree-Fock-Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, all symmetries can be broken, which allows for calculations with angular frequency and angular momentum tilted with respect to the mass distribution. The new version contains an interface to the LAPACK subroutine ZHPEVX. Program summaryTitle of the program:HFODD (v2.08i) Catalogue number: ADTO Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTO Reference in CPC for earlier version of program: J. Dobaczewski and J. Dudek, Comput. Phys. Commun. 131 (2000) 164 (v1.75r) Catalogue number of previous version: ADML Licensing provisions: none Does the new version supersede the previous one: yes Computers on which the program has been tested: SG Power Challenge L, Pentium-II, Pentium-III, AMD-Athlon Operating systems: UNIX, LINUX, Windows-2000 Programming language used: FORTRAN-77 and FORTRAN-90 Memory required to execute with typical data: 10 Mwords No. of bits in a word: The code is written in single-precision for the use on a 64-bit processor. The compiler option -r8 or +autodblpad (or equivalent) has to be used to promote all real and complex single-precision floating-point items to double precision when the code is used on a 32-bit machine. Has the code been vectorised?: Yes No. of bytes in distributed program, including test data, etc.: 265352 No. of lines in distributed program: 52656 Distribution format: tar gzip file Nature of physical problem: The nuclear mean-field and an analysis of its symmetries in realistic cases are the main ingredients of a description of nuclear states. Within the Local Density Approximation, or for a zero-range velocity-dependent Skyrme interaction, the nuclear mean-field is local and velocity dependent. The locality allows for

  6. 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. ).

  7. Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

    NASA Astrophysics Data System (ADS)

    Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.

    2005-02-01

    A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

  8. Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

    NASA Astrophysics Data System (ADS)

    Kubas, Adam; Hoffmann, Felix; Heck, Alexander; Oberhofer, Harald; Elstner, Marcus; Blumberger, Jochen

    2014-03-01

    We introduce a database (HAB11) of electronic coupling matrix elements (Hab) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute Hab values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

  9. 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).

  10. 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.

  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. Ab initio many-body perturbation theory and no-core shell model

    NASA Astrophysics Data System (ADS)

    Hu, B. S.; Wu, Q.; Xu, F. R.

    2017-10-01

    In many-body perturbation theory (MBPT) we always introduce a parameter N shell to measure the maximal allowed major harmonic-oscillator (HO) shells for the single-particle basis, while the no-core shell model (NCSM) uses N maxℏΩ HO excitation truncation above the lowest HO configuration for the many-body basis. It is worth comparing the two different methods. Starting from “bare” and Okubo-Lee-Suzuki renormalized modern nucleon-nucleon interactions, NNLOopt and JISP16, we show that MBPT within Hartree-Fock bases is in reasonable agreement with NCSM within harmonic oscillator bases for 4He and 16O in “close” model space. In addition, we compare the results using “bare” force with the Okubo-Lee-Suzuki renormalized force. Supported by National Key Basic Research Program of China (2013CB834402), National Natural Science Foundation of China (11235001, 11320101004, 11575007) and the CUSTIPEN (China-U.S. Theory Institute for Physics with Exotic Nuclei) funded by the U.S. Department of Energy, Office of Science (DE-SC0009971)

  13. 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.

  14. 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.

  15. 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

  16. Ab Initio Reactive Computer Aided Molecular Design

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  17. 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%).

  18. 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.

  19. 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.

  20. 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.

  1. Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

    Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

  2. 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

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

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

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

  4. 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.

  5. 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.

  6. 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.

  7. 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…

  8. Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled?

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sylvetsky, Nitai, E-mail: gershom@weizmann.ac.il; Martin, Jan M. L., E-mail: gershom@weizmann.ac.il; Peterson, Kirk A., E-mail: kipeters@wsu.edu

    2016-06-07

    In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H–He, B–Ne, and Al–Ar, is shown to be very close to the basis setmore » limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl{sub 4}) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than “valence limit + CV correction” approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xie, Binbin; Liu, Lihong; Cui, Ganglong

    2015-11-21

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  16. 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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  18. 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.

  19. Construction of the Fock Matrix on a Grid-Based Molecular Orbital Basis Using GPGPUs.

    PubMed

    Losilla, Sergio A; Watson, Mark A; Aspuru-Guzik, Alán; Sundholm, Dage

    2015-05-12

    We present a GPGPU implementation of the construction of the Fock matrix in the molecular orbital basis using the fully numerical, grid-based bubbles representation. For a test set of molecules containing up to 90 electrons, the total Hartree-Fock energies obtained from reference GTO-based calculations are reproduced within 10(-4) Eh to 10(-8) Eh for most of the molecules studied. Despite the very large number of arithmetic operations involved, the high performance obtained made the calculations possible on a single Nvidia Tesla K40 GPGPU card.

  20. 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.

  1. Structure of Be9Λ and 10Be Λ Λ using the beyond-mean-field Skyrme-Hartree-Fock approach

    NASA Astrophysics Data System (ADS)

    Li, Wen-Ying; Cui, Ji-Wei; Zhou, Xian-Rong

    2018-03-01

    Based on the beyond-mean-field Skyrme-Hartree-Fock model, the up-to-date Skyrme-type N Λ interaction, SLL4, is used to investigate the properties of Be9Λ comprehensively. Energies of different configurations, such as 8Be⊗Λ [000 ] 1 /2+ , 8Be⊗Λ [110 ] 1 /2- , 8Be⊗Λ [101 ] 3 /2- , and 8Be⊗Λ [101 ] 1 /2- are given and used to study the effects of Λ occupying different orbitals. The calculated energy spectra, including both positive- and negative-parity levels, are given and compared to the experimental data. The observed positive-parity spin doublets (3 /2+,5 /2+ ) are successfully reproduced, but the energy difference needs further investigation. The two well-known band structures corresponding to the genuine hypernuclear states and the 9Be-analog states are also obtained and compared with the observed ones. The shrinkage effect of Λ occupying Λ [000 ] 1 /2+ is investigated through the density distributions of nuclear core. And finally, the E 2 transition rates are given and compared with the observed data and with the results of the hypernuclear particle-rotor model. Properties of 10Be Λ Λ are also studied to show the completeness of this current model.

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

    PubMed

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

    2014-07-14

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

  3. 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.

  4. 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.

  5. 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.

  6. Efficient exact-exchange time-dependent density-functional theory methods and their relation to time-dependent Hartree-Fock.

    PubMed

    Hesselmann, Andreas; Görling, Andreas

    2011-01-21

    A recently introduced time-dependent exact-exchange (TDEXX) method, i.e., a response method based on time-dependent density-functional theory that treats the frequency-dependent exchange kernel exactly, is reformulated. In the reformulated version of the TDEXX method electronic excitation energies can be calculated by solving a linear generalized eigenvalue problem while in the original version of the TDEXX method a laborious frequency iteration is required in the calculation of each excitation energy. The lowest eigenvalues of the new TDEXX eigenvalue equation corresponding to the lowest excitation energies can be efficiently obtained by, e.g., a version of the Davidson algorithm appropriate for generalized eigenvalue problems. Alternatively, with the help of a series expansion of the new TDEXX eigenvalue equation, standard eigensolvers for large regular eigenvalue problems, e.g., the standard Davidson algorithm, can be used to efficiently calculate the lowest excitation energies. With the help of the series expansion as well, the relation between the TDEXX method and time-dependent Hartree-Fock is analyzed. Several ways to take into account correlation in addition to the exact treatment of exchange in the TDEXX method are discussed, e.g., a scaling of the Kohn-Sham eigenvalues, the inclusion of (semi)local approximate correlation potentials, or hybrids of the exact-exchange kernel with kernels within the adiabatic local density approximation. The lowest lying excitations of the molecules ethylene, acetaldehyde, and pyridine are considered as examples.

  7. Ab initio Hartree-Fock investigation of 1- H-pyrrolo[3,2- b]pyridine-3-yl acetic acid

    NASA Astrophysics Data System (ADS)

    Ramek, Michael; Tomić, Sanja

    2001-09-01

    The potential energy surface of 1- H-pyrrolo[3,2- b]pyridine-3-yl acetic acid has been investigated via RIIF/6-31G* calculations. The stationary points and reaction paths for syn orientation of the COOH group were determined and are compared with those of the derivatives of 3-indole acetic acid, which act as plant growth hormones. 1- H-pyrrolo[3,2- b]pyridine-3-yl acetic acid forms a kinetically stable conformer with a strong intramolecular hydrogen bond, in which the COOH group is in anti orientation. The influence of this hydrogen bond on bond lengths and vibration frequencies is described.

  8. Ab initio study on the formation of triiodide CT complex from the reaction of iodine with 2,3-diaminopyridine.

    PubMed

    Al-Hashimi, Nessreen A; Hussein, Yasser H A

    2010-01-01

    The charge transfer (CT) interaction between iodine and 2,3-diaminopyridine (DAPY) has been thoroughly investigated via theoretical calculations. A Hartree-Fock, 3-21G level of theory was used to optimize and calculate the Mullican charge distribution scheme as well as the vibrational frequencies of DAPY alone and both its CT complexes with one and two iodine molecules. A very good agreement was found between experiment and theory. New illustrations were concluded with a deep analysis and description for the vibrational frequencies of the formed CT complexes. The two-step CT complex formation mechanism published earlier was supported. Copyright 2009 Elsevier B.V. All rights reserved.

  9. 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.

  10. Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

    PubMed

    Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

    2016-12-15

    MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

  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. Potential energy curves of the Na2+ molecular ion from all-electron ab initio relativistic calculations

    NASA Astrophysics Data System (ADS)

    Bewicz, Anna; Musiał, Monika; Kucharski, Stanisław A.

    2017-11-01

    The equation-of-motion coupled-cluster method for electron affinity calculations has been used to study potential energy curves (PECs) for the Na+2 molecular ion. Although the studied molecule represents the open shell system the applied approach employs the closed shell Na+ 22 ion as the reference. In addition the Na+ 22 system dissociates into the closed shell fragments; hence, the restricted Hartree-Fock scheme can be used within the whole range of interatomic distances, from 2 to 45 Å. We used large basis set engaging 268 basis functions with all 21 electrons correlated. The relativistic effects are included via second-order Douglas-Kroll method. The computed PECs, spectroscopic molecular constants and vibrational energy levels agree well with experimental values if the latter are available or with other theoretical data.

  13. 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.

  14. 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

  15. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  16. 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

  17. Discovering chemistry with an ab initio nanoreactor

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  18. Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

    PubMed

    Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

    2017-01-03

    Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

  19. Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

    PubMed

    Kawashima, Yukio; Tachikawa, Masanori

    2014-01-14

    Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

  20. Lifetimes and oscillator strengths for the 5s5p6s, 5s5p5d and 5p3 levels in single-ionized tin

    NASA Astrophysics Data System (ADS)

    Colón, C.; Alonso-Medina, A.

    2004-08-01

    Radiative oscillator strengths for 103 lines arising from 5s5p6s, 5s5p5d and 5p3 configurations of Sn II and lifetimes corresponding to several levels of these configurations have been calculated. These values were obtained in intermediate coupling (IC) and using ab initio relativistic Hartree-Fock (HFR) calculations. We use the standard method of least square fitting of experimental energy levels for the IC calculations by means of computer codes from Cowan. Tables 1 and 2 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/422/1109

  1. On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

    NASA Astrophysics Data System (ADS)

    Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

    Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

  2. Electronic and magnetic structure of KNiF3 perovskite

    NASA Astrophysics Data System (ADS)

    Ricart, J. M.; Dovesi, R.; Roetti, C.; Saunders, V. R.

    1995-07-01

    The ground-state electronic structure of the ferromagnetic and antiferromagnetic phases of KNiF3 has been investigated using the ab initio periodic Hartree-Fock approach. The system is a wide-gap insulator. The antiferromagnetic phase is correctly predicted to be more stable than the ferromagnetic phase (0.031 eV per Ni pair at the experimental geometry). The energy difference between these phases is shown to obey a d-12 (d is the shortest Ni-Ni distance) power law, as suggested in the literature. The superexchange interaction turns out to be additive with respect to the number of Ni-Ni neighbors, as assumed in model spin Hamiltonians. Elastic properties, charge, and spin-density maps, and density of states plots are reported.

  3. Correlation study of sodium-atom chemisorption on the GaAs(110) surface

    NASA Astrophysics Data System (ADS)

    Song, K. M.; Khan, D. C.; Ray, A. K.

    1994-01-01

    Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

  4. GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

    PubMed

    Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

    2018-06-07

    The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

  5. 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.

  6. 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**.

  7. 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.

  8. 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

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

    PubMed

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

    2016-03-21

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

  10. 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.

  11. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

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

  12. 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

  13. Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

    PubMed

    Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

    2014-08-01

    In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. 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.

  20. 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.

  1. 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…

  2. 5Beta,6beta-epoxy-17-oxoandrostan-3beta-yl acetate and 5beta,6beta-epoxy-20-oxopregnan-3beta-yl acetate.

    PubMed

    Pinto, Rui M A; Salvador, Jorge A R; Paixão, José A

    2008-05-01

    In the title compounds, C(21)H(30)O(4), (I), and C(23)H(34)O(4), (II), respectively, which are valuable intermediates in the synthesis of important steroid derivatives, rings A and B are cis-(5beta,10beta)-fused. The two molecules have similar conformations of rings A, B and C. The presence of the 5beta,6beta-epoxide group induces a significant twist of the steroid nucleus and a strong flattening of the B ring. The different C17 substituents result in different conformations for ring D. Cohesion of the molecular packing is achieved in both compounds only by weak intermolecular interactions. The geometries of the molecules in the crystalline environment are compared with those of the free molecules as given by ab initio Roothan Hartree-Fock calculations. We show in this work that quantum mechanical ab initio methods reproduce well the details of the conformation of these molecules, including a large twist of the steroid nucleus. The calculated twist values are comparable, but are larger than the observed values, indicating a possible small effect of the crystal packing on the twist angles.

  3. Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

    PubMed

    Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

    2018-06-12

    We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

  4. 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.

  5. Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling of N-Methylacetamide

    NASA Technical Reports Server (NTRS)

    Gregurick, Susan K.; Chaban, Galina M.; Gerber, R. Benny; Kwak, Dochou (Technical Monitor)

    2001-01-01

    The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans(sub ct) configuration, including all degrees of freedom. The vibrational states and the spectroscopy are directly computed from this potential surface using the Correlation Corrected Vibrational Self-Consistent Field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low temperature experimental matrix data. Analysis of our calculated spectroscopic results show that: (1) The excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality; (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field; (3) The empirical force field in particular overestimates anharmonic couplings for the amide-2 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions; (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution;and (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide-1 and other internal modes. The implication of this is that the intramolecular energy flow between the amide-1 and the other internal modes may be smaller than anticipated. These results may have

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  7. 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.

  8. 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

  9. 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.

  10. Tensor force effect on the evolution of single-particle energies in some isotopic chains in the relativistic Hartree-Fock approximation

    NASA Astrophysics Data System (ADS)

    López-Quelle, M.; Marcos, S.; Niembro, R.; Savushkin, L. N.

    2018-03-01

    Within a nonlinear relativistic Hartree-Fock approximation combined with the BCS method, we study the effect of the nucleon-nucleon tensor force of the π-exchange potential on the spin- and pseudospin-orbit doublets along the Ca and Sn isotopic chains. We show how the self-consistent tensor force effect modifies the splitting of both kinds of doublets in an interdependent form, leading, quite generally, to opposite effects in the accomplishment of the spin and pseudospin symmetries (the one is restored, the other one deteriorates and vice versa). The ordering of the single-particle energy levels is crucial to this respect. Also, we observe a mutual dependence on the evolution of the shell closure gap Z = 50 and the energy band outside the core, along the Sn chain, as due to the tensor force. In fact, when the shell gap is quenched the outside energy band is enlarged, and vice versa. A reduction of the strength of the pion tensor force with respect to its experimental value from the nucleon-nucleon scattering is needed to get results closer to the experiment. Pairing correlations act to some extent in the opposite direction of the tensor term of the one-pion-exchange force.

  11. 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.

  12. Ab initio study of the neutral and anionic alkali and alkaline earth hydroxides: Electronic structure and prospects for sympathetic cooling of OH−

    PubMed Central

    2017-01-01

    We have performed a systematic ab initio study on alkali and alkaline earth hydroxide neutral (MOH) and anionic (MOH−) species where M = Li, Na, K, Rb, Cs or Be, Mg, Ca, Sr, Ba. The CCSD(T) method with extended basis sets and Dirac-Fock relativistic effective core potentials for the heavier atoms has been used to study their equilibrium geometries, interaction energies, electron affinities, electric dipole moment, and potential energy surfaces. All neutral and anionic species exhibit a linear shape with the exception of BeOH, BeOH−, and MgOH−, for which the equilibrium structure is found to be bent. Our analysis shows that the alkaline earth hydroxide anions are valence-bound whereas the alkali hydroxide anions are dipole bound. In the context of sympathetic cooling of OH− by collision with ultracold alkali and alkaline earth atoms, we investigate the 2D MOH− potential energy surfaces and the associative detachment reaction M + OH→− MOH + e−, which is the only energetically allowed reactive channel in the cold regime. We discuss the implication for the sympathetic cooling of OH− and conclude that Li and K are the best candidates for an ultracold buffer gas. PMID:28527437

  13. 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.

  14. 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.

  15. 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.

  16. Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.

    PubMed

    France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

    2016-03-14

    In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

  17. Wave-function-based approach to quasiparticle bands: Insight into the electronic structure of c-ZnS

    NASA Astrophysics Data System (ADS)

    Stoyanova, A.; Hozoi, L.; Fulde, P.; Stoll, H.

    2011-05-01

    Ab initio wave-function-based methods are employed for the study of quasiparticle energy bands of zinc-blende ZnS, with focus on the Zn 3d “semicore” states. The relative energies of these states with respect to the top of the S 3p valence bands appear to be poorly described as compared to experimental values not only within the local density approximation (LDA), but also when many-body corrections within the GW approximation are applied to the LDA or LDA + U mean-field solutions [T. Miyake, P. Zhang, M. L. Cohen, and S. G. Louie, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.74.245213 74, 245213 (2006)]. In the present study, we show that for the accurate description of the Zn 3d states a correlation treatment based on wave-function methods is needed. Our study rests on a local Hamiltonian approach which rigorously describes the short-range polarization and charge redistribution effects around an extra hole or electron placed into the valence respective conduction bands of semiconductors and insulators. The method also facilitates the computation of electron correlation effects beyond relaxation and polarization. The electron correlation treatment is performed on finite clusters cut off the infinite system. The formalism makes use of localized Wannier functions and embedding potentials derived explicitly from prior periodic Hartree-Fock calculations. The on-site and nearest-neighbor charge relaxation lead to corrections of several eV to the Hartree-Fock band energies and gap. Corrections due to long-range polarization are of the order of 1.0 eV. The dispersion of the Hartree-Fock bands is only slightly affected by electron correlations. We find the Zn 3d “semicore” states to lie ~9.0 eV below the top of the S 3p valence bands, in very good agreement with values from valence-band x-ray photoemission.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu; Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000more » coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.« less

  19. 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.

  20. 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

  1. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

    PubMed

    Simkovic, Felix; Thomas, Jens M H; Keegan, Ronan M; Winn, Martyn D; Mayans, Olga; Rigden, Daniel J

    2016-07-01

    For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

  2. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

    PubMed Central

    Simkovic, Felix; Thomas, Jens M. H.; Keegan, Ronan M.; Winn, Martyn D.; Mayans, Olga; Rigden, Daniel J.

    2016-01-01

    For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (‘decoys’), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing. PMID:27437113

  3. Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

    NASA Technical Reports Server (NTRS)

    Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

    2000-01-01

    The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

  4. 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).

  5. 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.

  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. 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.

  8. 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

  9. Multiscale modeling of current-induced switching in magnetic tunnel junctions using ab initio spin-transfer torques

    NASA Astrophysics Data System (ADS)

    Ellis, Matthew O. A.; Stamenova, Maria; Sanvito, Stefano

    2017-12-01

    There exists a significant challenge in developing efficient magnetic tunnel junctions with low write currents for nonvolatile memory devices. With the aim of analyzing potential materials for efficient current-operated magnetic junctions, we have developed a multi-scale methodology combining ab initio calculations of spin-transfer torque with large-scale time-dependent simulations using atomistic spin dynamics. In this work we introduce our multiscale approach, including a discussion on a number of possible schemes for mapping the ab initio spin torques into the spin dynamics. We demonstrate this methodology on a prototype Co/MgO/Co/Cu tunnel junction showing that the spin torques are primarily acting at the interface between the Co free layer and MgO. Using spin dynamics we then calculate the reversal switching times for the free layer and the critical voltages and currents required for such switching. Our work provides an efficient, accurate, and versatile framework for designing novel current-operated magnetic devices, where all the materials details are taken into account.

  10. Long-range corrected density functional theory with accelerated Hartree-Fock exchange integration using a two-Gaussian operator [LC-ωPBE(2Gau)].

    PubMed

    Song, Jong-Won; Hirao, Kimihiko

    2015-10-14

    Since the advent of hybrid functional in 1993, it has become a main quantum chemical tool for the calculation of energies and properties of molecular systems. Following the introduction of long-range corrected hybrid scheme for density functional theory a decade later, the applicability of the hybrid functional has been further amplified due to the resulting increased performance on orbital energy, excitation energy, non-linear optical property, barrier height, and so on. Nevertheless, the high cost associated with the evaluation of Hartree-Fock (HF) exchange integrals remains a bottleneck for the broader and more active applications of hybrid functionals to large molecular and periodic systems. Here, we propose a very simple yet efficient method for the computation of long-range corrected hybrid scheme. It uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. As a result, the two-Gaussian HF operator, which mimics the shape of the error function operator, reduces computational time dramatically (e.g., about 14 times acceleration in C diamond calculation using periodic boundary condition) and enables lower scaling with system size, while maintaining the improved features of the long-range corrected density functional theory.

  11. The V + I defects in diamond: An ab initio investigation of the electronic structure, of the Raman and IR spectra, and of their possible recombination.

    PubMed

    Salustro, S; Nöel, Y; Zicovich-Wilson, C M; Olivero, P; Dovesi, R

    2016-11-14

    The double defect in diamond, vacancy (V) plus 〈100〉 self-split-interstitial (V+I), is investigated at the ab initio quantum mechanical level, by considering the vicinal case VI 1 (V is one of the first neighbors of one of the two C atoms constituting the I defect) and the two possible "second neighbors" cases, VI 2 D , VI 2 S , in which a carbon atom is a first neighbor of both V and I. The case in which the two defects are at a larger distance is simulated by considering the two isolated defects separately (VI ∞ ). A 6-21G local Gaussian-type basis set and the B3LYP hybrid functional are used for most of the calculations; richer basis sets and other functionals (a global hybrid as PBE0, a range-separated hybrid as HSE06, LDA, PBE, and Hartree-Fock) have also been used for comparison. With this computational approach we evaluate the energy difference between the various spin states, the location of the corresponding bands in the energy gap of pristine diamond, as well as the defect formation energy of the four defects. The path for the recombination of V and I is explored for the vicinal case, by using the distinguished reaction coordinate strategy. A barrier as high as 0.75 eV is found with B3LYP between VI 1 and the perfect diamond recombined structure; when other hybrids are used, as PBE0 or HSE06, the barrier increases up to 1.01 eV (pure density functional theory produces lower barriers: 0.62 and 0.67 for PBE and LDA, respectively). Such a barrier is lower than the one estimated in a very indirect way through experimental data, ranging from 1.3 to 1.7 eV. It confirms however the evidence of the extremely low recombination rate also at high temperature. The Raman (and IR) spectra of the various defects are generated, which permit one to unambiguously attribute to these defects (thanks also to the graphical animation of the modes) many of the peaks observed in damaged diamond above the dominant peak of perfect bulk. For the residual non-attributed peaks

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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.

  18. Description of plasmon-like band in silver clusters: the importance of the long-range Hartree-Fock exchange in time-dependent density-functional theory simulations.

    PubMed

    Rabilloud, Franck

    2014-10-14

    Absorption spectra of Ag20 and Ag55(q) (q = +1, -3) nanoclusters are investigated in the framework of the time-dependent density functional theory in order to analyse the role of the d electrons in plasmon-like band of silver clusters. The description of the plasmon-like band from calculations using density functionals containing an amount of Hartree-Fock exchange at long range, namely, hybrid and range-separated hybrid (RSH) density functionals, is in good agreement with the classical interpretation of the plasmon-like structure as a collective excitation of valence s-electrons. In contrast, using local or semi-local exchange functionals (generalized gradient approximations (GGAs) or meta-GGAs) leads to a strong overestimation of the role of d electrons in the plasmon-like band. The semi-local asymptotically corrected model potentials also describe the plasmon as mainly associated to d electrons, though calculated spectra are in fairly good agreement with those calculated using the RSH scheme. Our analysis shows that a portion of non-local exchange modifies the description of the plasmon-like band.

  19. 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.

  20. 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

  1. Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

    PubMed

    Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

    2013-02-28

    A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

  2. Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

    PubMed

    Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

    2015-09-28

    Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

  3. Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

    NASA Astrophysics Data System (ADS)

    Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

    1998-08-01

    A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

  4. Wavelets in electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Modisette, Jason Perry

    1997-09-01

    Ab initio calculations of the electronic structure of bulk materials and large clusters are not possible on today's computers using current techniques. The storage and diagonalization of the Hamiltonian matrix are the limiting factors in both memory and execution time. The scaling of both quantities with problem size can be reduced by using approximate diagonalization or direct minimization of the total energy with respect to the density matrix in conjunction with a localized basis. Wavelet basis members are much more localized than conventional bases such as Gaussians or numerical atomic orbitals. This localization leads to sparse matrices of the operators that arise in SCF multi-electron calculations. We have investigated the construction of the one-electron Hamiltonian, and also the effective one- electron Hamiltonians that appear in density-functional and Hartree-Fock theories. We develop efficient methods for the generation of the kinetic energy and potential matrices, the Hartree and exchange potentials, and the local exchange-correlation potential of the LDA. Test calculations are performed on one-electron problems with a variety of potentials in one and three dimensions.

  5. Carbonate-Bridged Lanthanoid Triangles: Single-Molecule Magnet Behavior, Inelastic Neutron Scattering, and Ab Initio Studies.

    PubMed

    Giansiracusa, Marcus J; Vonci, Michele; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

    2016-06-06

    Optimization of literature synthetic procedures has afforded, in moderate yield, homogeneous and crystalline samples of the five analogues Na11[{RE(OH2)}3CO3(PW9O34)2] (1-RE; RE = Y, Tb, Dy, Ho, and Er). Phase-transfer methods have allowed isolation of the mixed salts (Et4N)9Na2[{RE(OH2)}3CO3(PW9O34)2] (2-RE; RE = Y and Er). The isostructural polyanions in these compounds are comprised of a triangular arrangement of trivalent rare-earth ions bridged by a μ3-carbonate ligand and sandwiched between two trilacunary Keggin {PW9O34} polyoxometalate ligands. Alternating-current (ac) magnetic susceptibility studies of 1-Dy, 1-Er, and 2-Er reveal the onset of frequency dependence for the out-of-phase susceptibility in the presence of an applied magnetic field at the lowest measured temperatures. Inelastic neutron scattering (INS) spectra of 1-Ho and 1-Er exhibit transitions between the lowest-lying crystal-field (CF) split states of the respective J = 8 and (15)/2 ground-state spin-orbit multiplets of the Ho(III) and Er(III) ions. Complementary ab initio calculations performed for these two analogues allow excellent reproduction of the experimental magnetic susceptibility and low-temperature magnetization data and are in reasonable agreement with the experimental INS data. The ab initio calculations reveal that the slight difference in coordination environments of the three Ln(III) ions in each complex gives rise to differences in the CF splitting that are not insignificant. This theoretical result is consistent with the observation of multiple relaxation processes by ac magnetic susceptibility and the broadness of the measured INS peaks. The ab initio calculations also indicate substantial mixing of the MJ contributions to the CF split energy levels of each Ln(III) ion. Calculations indicate that the CF ground states of the Ho(III) centers in 1-Ho are predominantly comprised of contributions from small MJ, while those of the Er(III) centers in 1-Er are predominantly

  6. 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

  7. A poly-epoxy surface explored by Hartree-Fock ΔSCF simulations of C1s XPS spectra

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gavrielides, A.; Duguet, T., E-mail: thomas.duguet@ensiacet.fr, E-mail: Paul.Bagus@unt.edu; Esvan, J.

    Whereas poly-epoxy polymers represent a class of materials with a wide range of applications, the structural disorder makes them difficult to model. In the present work, we use good experimental model samples in the sense that they are pure, fully polymerized, flat and smooth, defect-free, and suitable for ultrahigh vacuum x-ray photoelectron spectroscopy, XPS, experiments. In parallel, we perform Hartree-Fock, HF, calculations of the binding energies, BEs, of the C1s electrons in a model molecule composed of the two constituents of the poly-epoxy sample. These C1s BEs were determined using the HF ΔSCF method, which is known to yield accuratemore » values, especially for the shifts of the BEs, ΔBEs. We demonstrate the benefits of combining rigorous theory with careful XPS measurements in order to obtain correct assignments of the C1s XPS spectra of the polymer sample. Both the relative binding energies—by the ΔSCF method—and relative intensities—in the sudden approximation, SA, are calculated. It results in an excellent match with the experimental spectra. We are able to identify 9 different chemical environments under the C1s peak, where an exclusively experimental work would have found only 3 contributions. In addition, we observe that some contributions are localized at discrete binding energies, whereas others allow a much wider range because of the variation of their second neighbor bound polarization. Therefore, HF-ΔSCF simulations significantly increase the spectral resolution of XPS and thus offer a new avenue for the exploration of the surface of polymers.« less

  8. 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.

  9. 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

  10. 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

  11. Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

    NASA Astrophysics Data System (ADS)

    Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

    1992-08-01

    The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

  12. Roothaan's approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior.

    PubMed

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

  13. 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.

  14. 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.

  15. 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.

  16. Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

    NASA Astrophysics Data System (ADS)

    Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi

    2007-04-01

    The intermolecular potentials for the NO(XΠ2)-Kr and NO(AΣ+2)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1A'2 state [NO(XΠ2)-Kr ] and the multireference singles and doubles configuration interaction method for the excited 2A'2 state [NO(AΣ+2)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic

  17. Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

    2017-02-14

    Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16 O 3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV 3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν 3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm -1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

  18. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  20. 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)

  1. The generator coordinate Dirac-Fock method for open-shell atomic systems

    NASA Astrophysics Data System (ADS)

    Malli, Gulzari L.; Ishikawa, Yasuyuki

    1998-11-01

    Recently we developed generator coordinate Dirac-Fock and Dirac-Fock-Breit methods for closed-shell systems assuming finite nucleus and have reported Dirac-Fock and Dirac-Fock-Breit energies for the atoms He through Nobelium (Z=102) [see Refs. Reference 10Reference 11Reference 12Reference 13]. In this paper, we generalize our earlier work on closed-shell systems and develop a generator coordinate Dirac-Fock method for open-shell systems. We present results for a number of representative open-shell heavy atoms (with nuclear charge Z>80) including the actinide and superheavy transactinide (with Z>103) atomic systems: Fr (Z=87), Ac (Z=89), and Lr (Z=103) to E113 (eka-thallium, Z=113). The high accuracy obtained in our open-shell Dirac-Fock calculations is similar to that of our closed-shell calculations, and we attribute it to the fact that the representation of the relativistic dynamics of an electron in a spherical ball finite nucleus near the origin in terms of our universal Gaussian basis set is as accurate as that provided by the numerical finite difference method. The DF SCF energies calculated by Desclaux [At. Data. Nucl. Data Tables 12, 311 (1973)] (apart from a typographic error for Fr pointed out here) are higher than those reported here for atoms of some of the superheavy transactinide elements by as much as 5 hartrees (136 eV). We believe that this is due to the use by Desclaux of much larger atomic masses than the currently accepted values for these elements.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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

  3. 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.

  4. 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.

  5. 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

  6. 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].

  7. IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

    PubMed

    Qu, Chen; Bowman, Joel M

    2018-05-17

    We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

  8. 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.

  9. Ab-Initio Description and Prediction of Properties of Carbon-Based and Other Non-Metallic Materials

    NASA Technical Reports Server (NTRS)

    Bagayoko, D.; Zhao, G. L.; Hasan, S.

    2001-01-01

    We have resolved the long-standing problem consisting of 30%-50% theoretical underestimates of the band gaps of non-metallic materials. We describe the Bagayoko, Zhao, and Williams (BZW) method that rigorously circumvents the basis-set and variational effect presumed to be a cause of these underestimates. We present ab-initio, computational results that are in agreement with experiment for diamond (C), silicon (Si), silicon carbides (3C-SiC and 4H-SiC), and other semiconductors (GaN, BaTiO3, AlN, ZnSe, ZnO). We illustrate the predictive capability of the BZW method in the case of the newly discovered cubic phase of silicon nitride (c-Si3N4) and of selected carbon nanotabes [(10,0), and (8,4)]. Our conclusion underscores the inescapable need for the BZW method in ab-initio calculations that employ a basis set in a variational approach. Current nanoscale trends amplify this need. We estimate that the potential impact of applications of the BZW method in advancing our understanding of nonmetallic materials, in informing experiment, and particularly in guiding device design and fabrication is simply priceless.

  10. Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

    NASA Astrophysics Data System (ADS)

    Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

    2006-05-01

    Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to

  11. 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.

  12. Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

    PubMed

    Hagiwara, Yohsuke; Tateno, Masaru

    2010-10-20

    We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

  13. 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

  14. 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.

  15. 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.

  16. The multi-layer multi-configuration time-dependent Hartree method for bosons: theory, implementation, and applications.

    PubMed

    Cao, Lushuai; Krönke, Sven; Vendrell, Oriol; Schmelcher, Peter

    2013-10-07

    We develop the multi-layer multi-configuration time-dependent Hartree method for bosons (ML-MCTDHB), a variational numerically exact ab initio method for studying the quantum dynamics and stationary properties of general bosonic systems. ML-MCTDHB takes advantage of the permutation symmetry of identical bosons, which allows for investigations of the quantum dynamics from few to many-body systems. Moreover, the multi-layer feature enables ML-MCTDHB to describe mixed bosonic systems consisting of arbitrary many species. Multi-dimensional as well as mixed-dimensional systems can be accurately and efficiently simulated via the multi-layer expansion scheme. We provide a detailed account of the underlying theory and the corresponding implementation. We also demonstrate the superior performance by applying the method to the tunneling dynamics of bosonic ensembles in a one-dimensional double well potential, where a single-species bosonic ensemble of various correlation strengths and a weakly interacting two-species bosonic ensemble are considered.

  17. 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.

  18. Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

    2015-02-01

    The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized

  19. Roothaan’s approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energiesmore » always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.« less

  20. 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.