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Sample records for ab-initio crystal structure

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

    Science.gov (United States)

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

    2014-09-16

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

  2. The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2: Ab Initio Calculations

    Science.gov (United States)

    Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.

    2016-12-01

    Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.

  3. Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data

    DEFF Research Database (Denmark)

    Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M

    2012-01-01

    Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...

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

    Science.gov (United States)

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

    2016-08-01

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

  5. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, Gianluca; Brocks, Geert; Brink, van den Jeroen

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome

  6. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

  7. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome

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

    Science.gov (United States)

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

    2015-11-19

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

  9. Ab-initio optimization of the crystal structure ksi and ksi* in Al- Mn-Pd

    Energy Technology Data Exchange (ETDEWEB)

    Sanatana Bonilla, Alejandro [Universitaet Stuttgart (Germany). Institut fuer Theoretische und Angewandte Physik; Grupo de Sistemas Complejos, Universidad Antonio, Bogota (Colombia); Engel, Michael [Univ. of Michigan, Ann Arbor (United States); Trebin, Hans-Rainer [Universitaet Stuttgart (Germany). Institut fuer Theoretische und Angewandte Physik; Mihalkovic, Marek [Inst. of Physics, Slovak Academy of Sciences Bratslava (Slovakia)

    2010-07-01

    A structural model is given for two approximants, {xi} and {xi}{sup *}, of the decagonal Al-Mn-Pd phase. Both structures were shown to be completely described by two sorts of interpenetrating clusters, namely ''Distorted Bergman Cluster'' (DBC) and by ''Pseudo Mackay Cluster'' (PMC). On the basis of these two atomic clusters the two phases can be characterized as some simple periodic tiling of assembly of the column clusters projected onto the plane perpendicular to the 1.6 nm stacking axis. From crystallographic studies the skeleton of heavy atoms was fully described, whereas the inner shell from PMC was poorly detailed. The structural models have been investigated using ab initio and molecular dynamics numerical methods. For this study, suitable improved pair potentials were used in order to determine the ideal cluster structure and the interactions between adjacent clusters. Plausibility of the suggested structures was tested using competing crystalline phases obtained through convex hull calculations and allowing us to suggest a reliable atomic model for the inner shell of the PMC. 3.

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

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row

    2001-10-01

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

  11. Ab-Initio Theory of Charge Transport in Organic Crystals

    Science.gov (United States)

    Hannewald, K.; Bobbert, P. A.

    2005-06-01

    A theory of charge transport in organic crystals is presented. Using a Holstein-Peierls model, an explicit expression for the charge-carrier mobilities as a function of temperature is obtained. Calculating all material parameters from ab initio calculations, the theory is applied to oligo-acene crystals and a brief comparison to experiment is given.

  12. Cu(II) bifunctional (N,O,O‧) coordination polymer: A case study for complex ab-initio crystal structure determination from PXRD data

    Science.gov (United States)

    Colombo, Valentina; Cimino, Alessandro; Maspero, Angelo; Tollari, Stefano; Palmisano, Giovanni; Sironi, Angelo

    2017-09-01

    The synthesis of a novel Cu(II) bifunctional (N,O,O‧) coordination polymer, the Cu(PzHP) compound, has been carried out by coupling Cu(II) salts and the newely synthesized H2(PzHP) organic linker (H2(PzHP) = 1-[4-(1H) -pyrazolyl]-2-methyl-3-hydroxy-4(1H)-pyridinone). Despite to the numerous attempts done for the growth of suitable single crystals and to the synthetic trials carried out to ameliorate the crystallinity of the Cu(PzHP) coordination polymer, its diffraction pattern was always characterized by a discouraging, less-than-ideal, crystallinity. Notwithstanding the extended disorder, leading to a higher than required space group symmetry, we succeeded in the description of its relevant structural features by following an unconventional route to ab-initio structure solution. In this process consideration on the coordination ability of the ligand and on the space group symmetry have been taken into account to 'manually' achieve the initial structural model, highlighting that, in some cases, it is still possible to ascertain by PXRD the crystal structure of a material that shows challenging, broad, PXRD pattern.

  13. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter

    2004-01-01

    The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...

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

    Science.gov (United States)

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

    2017-01-01

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

  15. Ab initio calculation of electronic structures and 4f-5d transitions of some rare earth ions doped in crystal YPO4

    Institute of Scientific and Technical Information of China (English)

    WANG Dajun; XIA Shangda; YIN Min

    2008-01-01

    The ab initio self-consistent DV-Xα (discrete variational Xα) method was used in its relativistic and spin-polarized model to investigate the ground-state electronic structures of the crystal YPO4 and YPO4:RE3+ (RE=Ce, Pr and Sm) and f-d transition energies of the lattice. The calculation was performed on the clusters Y5P10O32 and REY4P10O32 embedded in a microcrystal containing about 1500 ions, respectively. The ground-state calculation provided the locations of the 4f and 5d crystal-field one-electron levels of RE3+ relative to the valence and conduction bands of host, the curve of total and the partial density of states, and the corresponding occupation numbers, etc. Especially, the transition-state calculation was performed to obtain the 4f→5d transition energies of RE3+ in comparison to the experimental observations. The lattice relaxation caused by the dopant ion RE3+ was discussed based on the total energy calculation and the transition-state calculation of the f-d transition energies.

  16. Magnetic interactions and electronic structure of uvarovite and andradite garnets. An ab initio all-electron simulation with the CRYSTAL06 program

    Science.gov (United States)

    Meyer, A.; Pascale, F.; Zicovich-Wilson, C. M.; Dovesi, R.

    The ground-state electronic structure of a number of magnetic phases of the garnets andradite (Ca3Fe2Si3O12) and uvarovite (Ca3Cr2Si3O12) has been investigated at the density functional theory level of approximation using the periodic ab initio code CRYSTAL. An all-electron Gaussian-type basis has been used in conjunction with the B3LYP hybrid functional. The exchange coupling constants between the first (J1a and J1b differentiating the two nonidentical sites), second (J2), and third (J3) nearest neighbors have been evaluated and are found to be in good agreement with the experimental data that is available for andradite. As a consequence of both the different J1a to J1b ratio and the opposite sign of J2 in the two minerals, different antiferromagnetic (AF) ground states are found for uvarovite and andradite, which is in agreement with experimental observation. Strong support for the additivity and transferability of the J constants is provided by calculations in which Cr and Fe ions are embedded in the related grossular structure. The mechanism for the stabilization of the AF states is discussed within the Anderson theory of superexchange; the kinetic energy gain in the AF states is calculated, and the spin density maps and profiles are examined. Density of states, charge density maps, and Mulliken population data complete the analysis of the electronic structure.

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

    NARCIS (Netherlands)

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

    1990-01-01

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

  18. Ab initio lattice dynamics of complex structures

    DEFF Research Database (Denmark)

    Voss, Johannes

    2008-01-01

    systems in particular. A more detailed analysis of the phonon spectrum has been performed for the compound Mg(BH4)2, where several crystal symmetries have been proposed theoretically and experimentally. By means of an analysis of the instabilities of these structures, a new, stable phase has been......In this thesis, density functional theory is applied in a study of thermodynamic properties of so-called complex metal hydrides, which are promising materials for hydrogen storage applications. Since the unit cells of these crystals can be relatively large with many symmetrically inequivalent...... determined. Aiming at finding scaling relationships between alloy stabilities and computationally inexpensive properties, the stabilities of cation-alloyed metal aluminum hexahydrides have been studied. The analysis shows that charge density symmetries are correlated to the stability. In addition...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-28

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

  20. Ab-initio study of the electronic structure of sup 1 sup 9 F implanted in GaAs and GaN crystals

    CERN Document Server

    Park, J H; Cho, H S; Shin, Y N

    1998-01-01

    We have studied the nuclear quadrupole interaction of a fluorine atom implanted in gallium arsenide and gallium nitride cluster models using the ab-initio Hartree-Fock theory. For the three possible fluorine sites in GaAs and GaN, we have determined the location of the implanted fluorine atom by using a self-consistent calculation, the electric field gradient at the implanted atom, and the electronic structure. Good agreement is found with experimental data wherever they are available. Predictions are made for the implanted fluorine site associated with the total energy and the electric field gradient which are expected to be measurable by a variety of experimental techniques.

  1. Ab initio structure dertermination and property characterization of high-pressure Ca-O compounds and Li2(OH)Br crystals

    Science.gov (United States)

    Higgins, Christopher A.

    Theoretical modeling and computational simulations play an important role in materials research. In this thesis, we report on the study of two material systems using various computational methods. The first material system studied here are Cax-Oy compounds under high pressure. Calcium and oxygen are amongst the most abundant elements on Earth, and they form the compound calcium oxide (CaO) that is widely used and very stable at ambient pressures. Although the crystal structure and chemical composition of CaO seems to be simple and well understood, metastable or stable Ca-O compounds with unconventional stoichiometry may exist at high pressures. In this work, first-principles density functional theory calculations and ab initio evolutionary simulations have been used to predict high pressure Ca-O structures. We show that under increasing pressure, the stability of the Ca-O system changes and new materials emerge with different stable or metastable structures. In addition to CaO, we systematically examined structures for Ca, Ca2O, Ca2O3, Ca3O, Ca 3O2, Ca7O, CaO2, CaO3, CaO 7, and O at high pressures. The high-pressure phase diagram for these compounds is determined along with the electronic density of states and stoichiometry plots. Our energetic analysis identified three new stable Ca-O compounds, namely Ca2O3 and CaO2 that are thermodynamically stable above 40 GPa, and CaO3 becomes thermodynamically stable at 150 GPa. The second material system studied in this work is the compound Li 2(OH)Br. This compound has been shown by experiment to be a promising solid electrolyte for advanced solid state ionic battery applications. However, the crystal structure of this compound is highly complex and has not been determined accurately. This has impeded its further investigation and potential applications. We modeled the structure effectively using the density functional theory via VASP software. Having successfully determined the correct structure within our model and

  2. Ab Initio Calculation of 4f→5d Transition Energy and Electronic Structure of Ce3+ Doped in LiYF4 Crystal

    Institute of Scientific and Technical Information of China (English)

    Jiang Ying; Zeng Zhi; Xia Shangda; Yin Min

    2005-01-01

    The electronic structures of LiYF4:Ce3+ and LiYF4 crystals simulated by an embedded (in a microcrystal containing 1938 ions) cluster CeY4Li8F24, and Y5Li8F24 respectively, were computed by the ab initio self-consistent relativistic DV-Xa(discrete variational Xa) method. The ground-state calculation showed that only the lowest 5d level Ed of Ce3+ ion lies around the BCB (bottom of the conduction band) while the lowest 4f levels is 2.5 eV lower than BCB. The CB states consist of 4p of Y mixed with 5d of Ce, even for the wavefunctions (WFS) of Ed under BCB there are still 24% of Y-4p and 9% of F-2p as components. Furthermore, transition state (TS) calculation was performed in this work to obtain the 4f→5d transition energies Efd, to improve the calculation of Ref.[6] in which a small CeF8 cluster embedded in an array of point charge was used and the results of ground-state calculation were roughly used to compare directly with the observed 4f→5d transition energies. The ionic radius of Ce3+ is larger than that of Y3+, for modeling approximately the lattice relaxation, we simply let the eight fluorine ions of the nearest-neighbor and next-nearest-neighbor move out radially and simultaneously. As results, the CeY4Li8F24 cluster with 4.56% outward relaxation of the eight fluorines has the lowest total energy and gave satisfactory 4f→5d energies Efd, but the calculated ground-state Ed is 0.68 eV higher than BCB. For another cluster with 7.36% outward relaxation the Ed is 0.43 eV lower than BCB, which makes the observation of fine structure (including zero-phonon line) of the lowest 5d band understandable easier, but the splits between the transition energies Efd were not as good as the former. Therefore, we consider the relaxation is somehow around 4.56%~7.36% outward, not as large as 10%.

  3. Unified ab initio approaches to nuclear structure and reactions

    CERN Document Server

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

    2016-01-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in {\\em ab initio} nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches - built upon the No-Core Shell Model - that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the $^6$He halo nucleus, of five- and six...

  4. Finite Elements in Ab Initio Electronic-Structure Calulations

    Science.gov (United States)

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

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

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

    CERN Document Server

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

    2016-01-01

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

  7. Local structure analysis in ab initio liquid water

    Science.gov (United States)

    Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    2015-09-01

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.

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

    Science.gov (United States)

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

    2004-04-01

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

  9. Ab initio theory of charge-carrier conduction in ultrapure organic crystals

    Science.gov (United States)

    Hannewald, K.; Bobbert, P. A.

    2004-08-01

    We present an ab initio description of charge-carrier mobilities in organic molecular crystals of high purity. Our approach is based on Holstein's original concept of small-polaron bands but generalized with respect to the inclusion of nonlocal electron-phonon coupling. By means of an explicit expression for the mobilities as a function of temperature in combination with ab initio calculations of the material parameters, we demonstrate the predictive power of our theory by applying it to naphthalene. The results show a good qualitative agreement with experiment and provide insight into the difference between electron and hole mobilities as well as their peculiar algebraic and anisotropic temperature dependencies.

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

    CERN Document Server

    Awoonor-Williams, Ernest

    2016-01-01

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

  11. Ab initio modeling of radiation damage in MgF{sub 2} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Abuova, F.U. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Kotomin, E.A., E-mail: kotomin@latnet.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Lisitsyn, V.M. [Tomsk Polytechnical University, Tomsk 634003 (Russian Federation); Akilbekov, A.T. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Piskunov, S. [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia)

    2014-05-01

    MgF{sub 2} with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F−H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F{sub 2} interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.

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

    Science.gov (United States)

    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.

  13. Applications of the diffraction technique in solid state chemistry from "ab-initio" structure solution to final structure refinement: powder and single crystal

    OpenAIRE

    Napolitano, Emilio

    2011-01-01

    Establishing the crystal structure in solid state chemistry is often a pre-requisite for understanding and predicting the function and technological properties of the matter. The single crystal and powder diffraction approaches play a fundamental role to achieve this goal. These two methods are non-destructive analytical techniques which provide detailed information about the internal lattice of crystalline substances, unit cell dimensions, bond-lengths, bond-angles, and details of site-or...

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

    CERN Document Server

    Heuvel, Willem Van den; Soncini, Alessandro

    2015-01-01

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

  15. Crystal structure of [NBu{sub 4}]{sub 2}[Pd{sub 2}{l_brace}C{sub 4}(COOMe){sub 4}{r_brace}{sub 2}({mu}-OH){sub 2}] determined ab initio by charge flipping

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz, Angel L. [Departamento de Ingenieria Mecanica, Energetica y de los Materiales, Escuela de Ingenierias Industriales, Universidad de Extremadura, 06071 Badajoz (Spain)], E-mail: alortiz@unex.es; Cumbrera, Francisco L. [Departamento de Fisica, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain); Perez, Jose [Departamento de Ingenieria Minera, Geologica y Cartografica, Area de Quimica Inorganica, Universidad Politecnica de Cartagena, Cartagena (Murcia) (Spain); Melendez-Martinez, Juan J. [Departamento de Fisica, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz (Spain); Palatinus, Lukas [Ecole Polytechnique Federale de Lausanne, Laboratoire de Cristallographie, BSP, CH-1015 Lausanne (Switzerland)

    2009-01-07

    The crystal structure of bis(tetra-n-butylammonium)bis({mu}{sub 2}-hydroxo)-bis(1,2,3,4-tetrakis (methoxycarbonyl)-1,3-butadiene-1,4-diyl)-di-palladium, [NBu{sub 4}]{sub 2}[Pd{sub 2}{l_brace}C{sub 4}(COOMe){sub 4}{r_brace}{sub 2} ({mu}-OH){sub 2}], was determined ab initio by X-ray single-crystal diffractometry using the charge flipping method. The compound crystallizes in the monoclinic system with P2{sub 1}/c as space group and the following cell parameters: a = 12.8481(6) A, b = 63.744(3) A, c = 16.6102(8) A, {beta} = 111.943(10). The asymmetric unit is formed by two molecules, and the unit cell contains eight molecules (Z = 8) giving a density of 1.369 g cm{sup -3}. The coordination around the Pd(II) atoms is approximately planar, the methoxycarbonyl groups at the {alpha} and {beta} positions relative to Pd are perpendicular and parallel to the palladacycle ring, respectively, and the {l_brace}Pd({mu}-O){r_brace}{sub 2} core has a bent conformation. The structure closely resembles the features reported previously for other palladacyclopentadiene complexes.

  16. Ab initio structure determination of new compound Ba 3(BO 3)(PO 4)

    Science.gov (United States)

    Ma, H. W.; Liang, J. K.; Wu, L.; Liu, G. Y.; Rao, G. H.; Chen, X. L.

    2004-10-01

    The crystal structure of new compound Ba3BPO7 was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to Rp=5.92%, Rwp=8.87%, Rexp=5.00% with the following details: Hexagonal, space group P63mc, a=5.4898 (1) Å, c=14.7551(1) Å, Z=2. The basic unit of the structure is the [BaO10]-[BO3]-[PO4] polar polyhedra-chain composed of Ba1-B-P-O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.

  17. Ab initio study of Al(III) adsorption on stepped {100} surfaces of KDP crystals

    Energy Technology Data Exchange (ETDEWEB)

    Salter, E A; Wierzbicki, A; Land, T A

    2004-04-01

    Crystals of potassium dihydrogen phosphate (KH{sub 2}PO{sub 4}, KDP) are grown in large scale for use as nonlinear material in laser components. Traces of trivalent metal impurities are often added to the supernatant to achieve habit control during crystal growth, selectively inhibiting the growth of the {l_brace}100{r_brace} face. Model systems representing AlPO{sub 4}-doped KDP {l_brace}100{r_brace} stepped surfaces are prepared and studied using ab initio quantum methods. Results of Hartree-Fock partial optimizations are presented, including estimated energies of ion pair binding to the steps. We find that the PO{sub 4}{sup 3-} ion takes a position not unlike that of a standard phosphate in the crystal lattice, while the aluminum atom is displaced far from a K{sup +} ion position to establish coordinations with the PO{sub 4}{sup 3-} ion and to bind with another lattice-bound phosphate. Our optimized structures suggest that it is the formation of a fourth coordination of Al(III) to a third phosphate ion from solution, or perhaps from a nearby position in the lattice, that disrupts further deposition, pinning the steps.

  18. Ab initio electronic structure, magnetism, and magnetocrystalline anisotropy of UGa2

    Science.gov (United States)

    Diviš, Martin; Richter, Manuel; Eschrig, Helmut; Steinbeck, Lutz

    1996-04-01

    Ab initio electronic structure calculations for the intermetallic compound UGa2 were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5f states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5f states, which have been treated by self-interaction corrected local-density theory. This approach with 5f2 occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant.

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

    NARCIS (Netherlands)

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

    2010-01-01

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

  20. Ab initio electronic-structure calculations on the Nb/Zr multilayer system

    NARCIS (Netherlands)

    Leuken, H. v.; Czyżyk, M.T.; Springelkamp, F.; Groot, R.A. de

    1990-01-01

    Ab initio electronic-structure calculations are performed for the Nb/Zr metallic multilayer system in the coherent bcc structure and in the incoherent bcc/hcp structure, observed for small and larger modulation wavelengths, respectively. A new calculational scheme, the localized-spherical-wave

  1. Crystal Structure, Vibrational Spectroscopy and ab Initio Density Functional Theory Calculations on the Ionic Liquid forming 1,1,3,3-Tetramethylguanidinium bis{(trifluoromethyl)sulfonyl}amide

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Riisager, Anders; Nguyen van Buu, Olivier;

    2009-01-01

    The salt 1,1,3,3-tetramethylguanidinium bis{(trifluoromethyl)sulfonyl}amide, [((CH3)(2)N)(2)C=NH2](+)[N(SO2-CF3)(2)](-) or [tmgH][NTf2], easily forms an ionic liquid with high SO2 absorbing capacity. The crystal structure of the salt was determined at 120(2) K by X-ray diffraction. The structure...

  2. Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

    Science.gov (United States)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent

    2012-01-01

    From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.

  3. The structural phase transition and loss of magnetic moments in NpO2: ab initio approach to the crystal and mean field

    OpenAIRE

    Nikolaev, A. V.; Michel, K.H.

    2002-01-01

    We discuss the triple-$\\vec{q}^X$ structures for the ordered cubic phase of NpO$_2$, which are $Pn{\\bar 3}m$ and $Pa{\\bar 3}$. A special care should be taken to discriminate between these two cases. We analyze the relevant structure-factor amplitudes and the effect of domains on resonant X-ray scattering experiments. We formulate the technique of multipole expansion of the Coulomb interaction and use it to study the crystal electric field and mean field for a number of neptunium many electron...

  4. Sodium-gold binaries: novel structures for ionic compounds from an ab initio structural search

    Science.gov (United States)

    Sarmiento-Pérez, Rafael; Cerqueira, Tiago F. T.; Valencia-Jaime, Irais; Amsler, Maximilian; Goedecker, Stefan; Botti, Silvana; Marques, Miguel A. L.; Romero, Aldo H.

    2013-11-01

    Intermetallic compounds made of alkali metals and gold have intriguing electronic and structural properties that have not been extensively explored. We perform a systematic study of the phase diagram of one binary system belonging to this family, namely NaxAu1-x, using the ab initio minima hopping structural prediction method. We discover that the most stable composition is NaAu2, in agreement with available experimental data. We also confirm the crystal structures of NaAu2 and Na2Au, that were fully characterized in experiments, and identify a candidate ground-state structure for the experimental stoichiometry NaAu. Moreover, we obtain three other stoichiometries, namely Na3Au2, Na3Au and Na5Au, that could be thermodynamically stable. We do not find any evidence for the existence of the experimentally proposed composition NaAu5. Finally, we perform phonon calculations to check the dynamical stability of all reported phases and we simulate x-ray diffraction spectra for comparison with future experimental data.

  5. Structural properties of rutherfordium: An ab-initio study

    Science.gov (United States)

    Gyanchandani, Jyoti; Sikka, S. K.

    2012-01-01

    The structural and electronic properties of rutherfordium, the latest group IV B element, have been evaluated by first principles density functional theory in scalar relativistic formalism with and without spin-orbit coupling and compared with its 5d homologue Hf. It is found that Rf will crystallize in the hexagonal close packed structure as in Hf. However, under pressure, it will have different sequence of phase transitions than Hf: hcp→bcc instead of hcp→ω→bcc. An explanation is offered for this difference in terms of the competition between the band structure and the Ewald energy contributions.

  6. Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs.

    Science.gov (United States)

    Quarti, Claudio; Milani, Alberto; Civalleri, Bartolomeo; Orlando, Roberto; Castiglioni, Chiara

    2012-07-19

    State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.

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

    Science.gov (United States)

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

    2006-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-15

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

  9. Ab initio simulations and neutron scattering studies of structure and dynamics in PdH

    CERN Document Server

    Totolici, I E

    2001-01-01

    The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...

  10. X-ray Crystal Structure, Raman Spectroscopy and Ab Initio Density Functional Theory Calculations on 1,1,3,3-Tetramethylguanidinium Bromide

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Riisager, Anders; Nguyen van Buu, Olivier

    2010-01-01

    = 104.31(3)°, Z = 2, based on 11769 reflections, measured from θ = 2.71-28.00° on a small colorless needle crystal. Raman and IR spectra are presented and assigned. When heated, both the chloride and the bromide salts form vapor phases. The Raman spectra of the vapors are surprisingly alike, showing......, for example, a characteristic strong band at 2229 cm-1. This band was interpreted by some of us to show that the [tmgH]Cl gas phase should consist of monomeric ion pair “molecules” held together by a single N-H+ · · · Cl- hydrogen bond, the stretching vibration of which should be causing the band, based on ab...

  11. Structural properties of rutherfordium: An ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    Gyanchandani, Jyoti [Material Science Division, Bhabha Atomic Research Center, Mumbai 400085 (India); Sikka, S.K., E-mail: sksikka@barc.gov.in [Bhabha Atomic Research Center, Mumbai 400085 (India)

    2012-01-09

    The structural and electronic properties of rutherfordium, the latest group IV B element, have been evaluated by first principles density functional theory in scalar relativistic formalism with and without spin–orbit coupling and compared with its 5d homologue Hf. It is found that Rf will crystallize in the hexagonal close packed structure as in Hf. However, under pressure, it will have different sequence of phase transitions than Hf: hcp→bcc instead of hcp→ω→bcc. An explanation is offered for this difference in terms of the competition between the band structure and the Ewald energy contributions. -- Highlights: ► The solid properties of the new element Rf have been found for the first time. ► The density functional theory is used including spin–orbit interactions. ► The atomic volume of Rf is found to be expanded compared to its homologue Hf. ► It is shown that Rf will have different phase transformations than Hf under pressure. ► The absence of the omega phase in Rf and its presence in Hf is explained.

  12. SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

    Science.gov (United States)

    Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

    2017-10-01

    As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

  13. Ab initio calculation of structural stability, electronic and optical properties of Ag{sub 2}Se

    Energy Technology Data Exchange (ETDEWEB)

    Rameshkumar, S.; Jayalakshmi, V., E-mail: karthikajayam@yahoo.co.in [Department of Physics, SRM University, Ramapuram Campus, Chennai – 600089 (India); Jaiganesh, G. [Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam – 603102 (India); Palanivel, B. [Department of Physics, Pondicherry Engineering College, Puducherry – 605014 (India)

    2015-06-24

    The structural stability, electronic and optical properties of Ag{sub 2}Se compound is studied using ab initio packages. Ag{sub 2}Se is found to crystallize in orthorhombic structure with two different space groups i.e. P2{sub 1}2{sub 1}2{sub 1} (No. 19) and P222{sub 1} (No. 17). For this compound in these two space groups, the total energy has been computed as a function of volume. Our calculated results suggest that the P2{sub 1}2{sub 1}2{sub 1}–phase is more stable than that of the P222{sub 1}–phase. The band structure calculation show that Ag{sub 2}Se is semimetallic with an overlap of about 0.014 eV in P2{sub 1}2{sub 1}2{sub 1}–phase whereas is metallic in nature in P222{sub 1}–phase. Moreover, the optical properties including the dielectric function, energy loss spectrum are obtained and analysed.

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

    Energy Technology Data Exchange (ETDEWEB)

    Herbig, Alexander

    2016-02-12

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

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

    CERN Document Server

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

    2009-01-01

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

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

    Science.gov (United States)

    Correa, J. D.; Cisternas, E.

    2016-09-01

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

  17. Ca- and Sr-tetrafluoroisophthalates: mechanochemical synthesis, characterization, and ab initio structure determination.

    Science.gov (United States)

    Al-Terkawi, Abdal-Azim; Scholz, Gudrun; Buzanich, Ana Guilherme; Reinsch, Stefan; Emmerling, Franziska; Kemnitz, Erhard

    2017-05-09

    New fluorinated coordination polymers were prepared mechanochemically by milling the alkaline earth metal hydroxides M(II)(OH)2·xH2O (M(II): Ca, Sr) with tetrafluoroisophthalic acid (H2mBDC-F4). The structures of [{Ca(mBDC-F4)(H2O)2}·H2O] (1) and [{Sr(mBDC-F4)(H2O)2}·H2O] (2) were determined based on ab initio calculations and their powder X-ray diffraction (PXRD) data. The compounds are isomorphous and crystallize in the orthorhombic space group P212121. The determined structures were validated by using extended X-ray absorption (EXAFS) data. The new materials were thoroughly characterized using elemental analysis, thermal analysis, magic angle spinning NMR, and attenuated total reflection-infrared spectroscopy. Further characterization methods such as BET, dynamic vapor sorption, and scanning electron microscopy imaging were also used. Our investigations indicate that mechanochemistry is an efficient method for preparing such materials.

  18. Ab-initio DFT FP-LAPW GGA and LDA TB-mBJ and SO theoretical study of structural and elastic properties of Zinc-Blende crystal phase GaAs1-xBix alloys

    Science.gov (United States)

    Menezla, S.; Kadri, A.; Zitouni, K.; Djelal, A.; Djermouni, M.; Hallouche, A.; Zaoui, A.

    2015-12-01

    We present an ab-initio theoretical study of structural and elastic properties of GaAs1-xBix alloys in the Zinc-Blende (ZB) phase. We use a recent version of Wien2k package code based on Density Functional Theory (DFT) Full Potential and Linearized Augmented Plane Waves (FP-LAPW) method including recent Tran-Blaha modified Becke-Johnson correction of the exchange potential (TB-mBJ) and the spin-orbit interaction (SO). The calculations are performed within the Local Density Approximation (LDA) as well as the Generalized Gradient Approximation (GGA). We study first the structural properties of GaAs1-xBix alloys by solving Murnaghan equation of state. Our results show that the ZB phase is the lowest equilibrium crystal structure of GaAs1-xBix in the whole alloy composition range, in agreement with previous theoretical predictions. The variations versus Bi contents of the ZB GaAs1-xBix lattice constant a0, bulk modulus B0 and its pressure derivative B0‧ are also found very close to other theoretical and experimental data, but with much smaller bowing effects indicating a better resolution thanks to TB-mBJ correction. The variations of B0 versus the reverse equilibrium volume of the unit cell (1/V0) are found to be described by the simple linear empirical expression B0 = -0.21068 + 0.16695/V0 which is close to the theoretical prediction for III-V semiconductors with, however, somewhat lower linear coefficients values, suggesting a more metallic behavior. In a second part of this work, we use Birch-Murnaghan approach to study the elastic properties of GaAs1-xBix alloys. The elastic stiffness coefficients, C11, C12 and C44, and their variations versus alloy composition were determined for ZB GaAs1-xBix alloy. Their values in GaAs and GaBi binary compounds are found in very good agreement with available experimental and/or theoretical data. Their variations in GaAs1-xBix alloy show a monotonic decrease with increasing Bi contents, indicating a softening behavior as is

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-01

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

  20. Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An ab initio Molecular Dynamics Study

    Science.gov (United States)

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

    2014-03-01

    Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.

  1. Ab initio calculations of yttrium nitride: structural and electronic properties

    Energy Technology Data Exchange (ETDEWEB)

    Zerroug, S.; Ali Sahraoui, F. [Universite Ferhat Abbas, Laboratoire d' Optoelectronique et Composants, Departement de Physique, Setif (Algeria); Bouarissa, N. [King Khalid University, Department of Physics, Faculty of Science, P.O. Box 9004, Abha (Saudi Arabia)

    2009-11-15

    Using first principles total energy calculations within the full-potential linearized augmented plane wave method, we have studied the structural and electronic properties of yttrium nitride (YN) in the three phases, namely wurtzite, caesium chloride and rocksalt structures. The calculations are performed at zero and under hydrostatic pressure. In agreement with previous findings, it is found that the favored phase for YN is the rocksalt-like structure. We predict that at zero pressure YN in the rocksalt structure is a semiconductor with an indirect bandgap of 0.8 eV. A phase transition from a rocksalt to a caesium chloride structure is found to occur at {proportional_to}134 GPa. Besides, a transition from an indirect ({gamma}-X) bandgap semiconductor to a direct (X-X) one is predicted at pressure of {proportional_to}84 GPa. For the electron effective mass of rocksalt YN, these are the first results, to our knowledge. The information derived from the present study may be useful for the use of YN as an active layer in electronic devices such as diodes and transistors. (orig.)

  2. Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.

    Science.gov (United States)

    Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya

    2016-12-01

    An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.

  3. Ab initio nuclear structure from lattice effective field theory

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dean [Department of Physics, North Carolina State University, Raleigh NC 27695 (United States)

    2014-11-11

    This proceedings article reviews recent results by the Nuclear Lattice EFT Collaboration on an excited state of the {sup 12}C nucleus known as the Hoyle state. The Hoyle state plays a key role in the production of carbon via the triple-alpha reaction in red giant stars. We discuss the structure of low-lying states of {sup 12}C as well as the dependence of the triple-alpha reaction on the masses of the light quarks.

  4. Novel silicon allotropes for photovoltaic applications from ab initio structure prediction

    Science.gov (United States)

    Amsler, Maximilian; Goedecker, Stefan; Botti, Silvana; Marques, Miguel A. L.

    2015-03-01

    Sophisticated structure prediction methods have been developed and become essential tools when theoretically designing new materials with desired properties. Their successful applications to many systems at various conditions and increasing computational power have strongly contributed to their popularity. However, an accurate prediction from ab initio calculations still remains an extremely challenging task. The Minima Hopping Method is a powerful tool to find low energy structures given only the chemical composition of a system and allows the prediction of structures at any boundary condition. I will present the results of our studies on low density silicon phases with potential use in photovoltaic applications.

  5. Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations

    Science.gov (United States)

    Koudriachova, M. V.

    2008-06-01

    A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.

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

    CERN Document Server

    Schaefer III, Henry F

    2004-01-01

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

  7. Modeling the diffraction process of molecular crystals: computation of X-ray scattering intensities from ab initio electron densities

    NARCIS (Netherlands)

    Bruning, W.; Feil, D.

    1992-01-01

    An algorithm for calculating the scattering factors of atomic fragments in molecules as defined by the Stockholder recipe is presented. This method allows the calculation, from ab initio molecular wave functions, of structure factors including individual anisotropic atomic temperature factors. These

  8. Interplay between the structure and dynamics in liquid and undercooled boron: An ab initio molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Jakse, N.; Pasturel, A. [Sciences et Ingénierie des Matériaux et Procédés, UMR CNRS 5266, Grenoble INP, BP 75, 38402 Saint-Martin d’Hères Cedex (France)

    2014-12-21

    In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-09-24

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

  10. Ab initio calculation of the spectrum and structure of $^{16}$O

    CERN Document Server

    Epelbaum, Evgeny; Lähde, Timo A; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam

    2013-01-01

    We present ab initio lattice calculations of the low-energy even-parity states of $^{16}$O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.

  11. Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations

    Institute of Scientific and Technical Information of China (English)

    LIAO Long-Zhong; LIU Zheng-Hui; ZHANG Zhao-Hui

    2008-01-01

    Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms.

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

    Science.gov (United States)

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

    2017-01-01

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

  13. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

    Science.gov (United States)

    Kihara, D; Lu, H; Kolinski, A; Skolnick, J

    2001-08-28

    The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab initio folding. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Furthermore, to generate representative protein structures, a reduced lattice-based protein model is used with replica exchange Monte Carlo to explore conformational space. We report results on the application of this methodology, termed TOUCHSTONE, to 65 proteins whose lengths range from 39 to 146 residues. For 47 (40) proteins, a cluster centroid whose rms deviation from native is below 6.5 (5) A is found in one of the five lowest energy centroids. The number of correctly predicted proteins increases to 50 when atomic detail is added and a knowledge-based atomic potential is combined with clustered and nonclustered structures for candidate selection. The combination of the ratio of the relative number of contacts to the protein length and the number of clusters generated by the folding algorithm is a reliable indicator of the likelihood of successful fold prediction, thereby opening the way for genome-scale ab initio folding.

  14. Ab initio study of structural, electronic, and thermal properties of Ir1-xRhx alloys

    Directory of Open Access Journals (Sweden)

    Sh. Ahmed

    2015-06-01

    Full Text Available The structural, electronic, mechanical and thermal properties of Ir1-xRhx alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.

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

    Science.gov (United States)

    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.

  16. Ammonium azide: a commented example of an Ab initio structure (Re-) determination from X-ray powder diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Salim de Amorim, H.; Amaral, M.R. do [Instituto de Fisica, Universidade Federal do Rio de Janeiro, CP 68528, 21495-970 Rio de Janeiro (Brazil); Pattison, P. [Institute of Crystallography, BSP, University of Laussane, CH-1015, Laussane (Switzerland); Pereira L, I.; Mendes, J.C. [Departamento de Geologia, Universidade Federal do Rio de Janeiro, 21949-900, Rio de Janeiro (Brazil)

    2002-07-01

    The structure of ammonium azide (NH{sub 4})N{sub 3} was (re-)determined ab initio from x-ray powder diffraction experiment using synchrotron radiation. We tried to detail and comment the different steps involved in the structure determination. The compound crystallize in the orthorhombic Pmna space group (no.53) with a = 8.937(1) A, b= 3.8070(5) A, c = 8.664(1) A, V = 294.79(7) A{sup 3}; Z= 4. It was possible to locate and refine the hydrogen coordinates, in two different approaches, and to establish the H-bonds. The final structural parameters are in good agreement with previous results based on three-dimensional neutron diffraction. (Author)

  17. The Role of Anharmonicity and Nuclear Quantum Effects in the Pyridine Molecular Crystal: An ab initio Molecular Dynamics Study

    Science.gov (United States)

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

    Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

  18. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  19. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

    Science.gov (United States)

    Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

    2016-09-01

    We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  20. Ab initio study of pressure induced structural and electronic properties in TmPo

    Energy Technology Data Exchange (ETDEWEB)

    Makode, Chandrabhan, E-mail: cbmakode@gmail.com; Pataiya, Jagdish; Sanyal, Sankar P. [Department of Physics, Barkatullah University, Bhopal-462026 (India); Panwar, Y. S.; Aynyas, Mahendra [Department of Physics, C.S.A. Govt. P.G. College, Sehore-466001 (India)

    2015-06-24

    We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.

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

    Science.gov (United States)

    Alptekin, Sebahaddin

    2013-01-01

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

  2. Ab initio calculation of structure and thermodynamic properties of Zintl aluminide SrAl{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Zhi-Jian [Chongqing Key Laboratory of Micro/Nano Materials Engineering and Technology, Chongqing (China); Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics; Jia, Li-Jun [Chongqing Univ. of Arts and Sciences Library (China); Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong [Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; Sun, Xiao-Wei [Lanzhou Jiaotong Univ. (China). School of Mathematics and Physics; Chen, Qi-Feng [China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics

    2015-07-01

    The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl{sub 2} at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory method within the generalised gradient approximation (GGA). The calculated lattice parameters are in agreement with the available experimental data and other theoretical results. The phase transition predicted takes place at 0.5 GPa from the orthorhombic to the cubic structure at zero temperature. The thermodynamic properties of the zinc-blende structure SrAl{sub 2} are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations in the thermal expansion a are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.

  3. Ab-initio study of magnetism behavior in TiO2 semiconductor with structural defects

    Science.gov (United States)

    Zarhri, Z.; Houmad, M.; Ziat, Y.; El Rhazouani, O.; Slassi, A.; Benyoussef, A.; El Kenz, A.

    2016-05-01

    Magnetic, electronic and structural properties of titanium dioxide material with different structural defects are studied using the first-principles ab-initio calculations and the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA) method in connection with the local density approximation (LDA). We investigated all structural defects in rutile TiO2 such as Titanium interstitial (Tii), Titanium anti-sites (Tio), Titanium vacancies (VTi), Oxygen interstitial (Oi), Oxygen anti-sites (OTi) and oxygen vacancies (Vo). Mechanisms of hybridization and interaction between magnetic atoms are investigated. The transition temperature is computed using the Mean Field Approximation (MFA).Magnetic stability energy of ferromagnetic and disordered local moment states is calculated to determine the most stable state. Titanium anti-sites have a half-metallic aspect. We also studied the change type caused by structural defects in this material.

  4. Structure and dynamics of liquid Zn: an analysis of ab-initio simulations

    Directory of Open Access Journals (Sweden)

    del Rio B. G.

    2017-01-01

    Full Text Available The static and dynamic properties of liquid Zn have been studied using an ab initio molecular dynamics method. Results are reported for the thermodynamic states at 723K near which inelastic neutron and x-ray scattering data are available. The calculated static structure shows very good agreement with experimental measurements, including an asymmetric main peak. The dynamic structure reveals the existence of propagating density fluctuations, and the associated dispersion relation has also been calculated. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in several liquid metals under high pressures; the second region is around qp/2, as suggested by inelastic scattering experiments for liquid Zn and other metals.

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

    Science.gov (United States)

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

    2016-09-01

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

  6. Ab Initio Molecular Dynamics Simulations on Structural Properties of Liquid In20Sn80

    Institute of Scientific and Technical Information of China (English)

    ZHAO Gang; LIU Chang-Song; ZHU Zhen-Gang

    2005-01-01

    @@ Ab initio molecular dynamics simulations on liquid In20Sn80 alloy are carried out at six different temperatures from 798 K to 1193 K. The temperature dependences of binding energy, volume, pair-correlation function and structurefactor are studied. The first-peak position of our calculated pair correlation function is in agreement with the experimental data. A shoulder is reproduced in the high wave number side of the first peak in our calculated structure factor, implying the existence of the residual directional bonds of Sn atoms in liquid In20Sn80 alloy. The first-peak height of our calculated structure factor and the coordination number of Sn atom decrease more sharply in the low-temperature region from 798K to 986K than that in the high-temperature region from 986K to 1193K, suggesting that a discontinuous structural change may occur at around 986K in liquid In20Sn80 alloy.

  7. Electronic Structure and Physical-Chemistry Property Relationship for Oxazole Derivatives by Ab Initio and DFT Methods

    OpenAIRE

    2011-01-01

    The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.

  8. Electronic Structure and Physical-Chemistry Property Relationship for Oxazole Derivatives by Ab Initio and DFT Methods

    Directory of Open Access Journals (Sweden)

    Salah Belaidi

    2011-01-01

    Full Text Available The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.

  9. Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

    KAUST Repository

    Heryadi, Dodi

    2011-01-01

    Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.

  10. Comparison of ab initio molecular properties of EDO-TTF with the properties of the (EDO-TTF) 2PF 6 crystal

    Science.gov (United States)

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

    2010-03-01

    We performed ab initio quantum chemical calculations for the geometrical and electronic structure of the EDO-TTF (ethylenedioxy-tetrathiafulvalene) molecule using HF, CASSCF and DFT methods. We compare these in vacuo results with the properties of the (EDO-TTF) 2PF 6 crystal at near room temperature. We demonstrate that, by bending and charging the molecule in vacuum, the deformation that is thought to be the origin of charge ordering in this material is an inherent property of the EDO-TTF molecule. We further show that deformations can be readily made at ambient temperatures.

  11. Synthesis, ab initio X-ray powder diffraction crystal structure, and magnetic properties of Mn3(OH)2(C6H2O4S)2 metal-organic framework.

    Science.gov (United States)

    Sibille, Romain; Mazet, Thomas; Elkaïm, Erik; Malaman, Bernard; François, Michel

    2013-01-18

    A new hydroxythiophenedicarboxylate metal-organic framework based on Mn(II) cations has been obtained by an aqueous two-step procedure including hydrothermal treatment. The structure of Mn(3)(OH)(2)(C(6)H(2)O(4)S)(2) has been determined ab initio from synchrotron X-ray powder diffraction data and consists of infinite inorganic ribbons which are interlinked by 2,5-thiophenedicarboxylate (tdc) molecules (monoclinic, space group P2(1)/c, a = 3.4473(1) Å, b = 19.1287(1) Å, c = 11.0069(1) Å, β = 97.48(1)°, V = 719.65(1) Å(3), and Z = 2). Each ribbon is built of three vertex-sharing chains of edge-sharing MnO(6) octahedrons. These ribbons are bridged together by the carboxylate functions of the tdc molecule to form a pseudo-2D inorganic subnetwork, while this molecule develops in the third dimension to pillar these pseudo-2D layers. An unprecedented hexadentate symmetric bridging mode is adopted by tdc which bridges two chains of a ribbon on one side and two ribbons of a pseudo-2D inorganic subnetwork on the other side. Magnetic measurements suggest that the titled compound is antiferromagnetic below T(N) = 17.7 K. Heat capacity measurements confirm the existence of a magnetic phase transition toward a 3D long-range ordered state. These C(P)(T) data have also been used for the calculation of the thermal variations of both the adiabatic temperature change ΔT(ad) and magnetic entropy change ΔS(m) of the material, namely its magnetocaloric effect.

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

    Energy Technology Data Exchange (ETDEWEB)

    Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Department of Nano Science, Computational Physical Science Research Laboratory, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

    2008-10-01

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

  13. Ab initio study of the electronic structure andelastic properties of Al5C3N

    Institute of Scientific and Technical Information of China (English)

    Xu Xue-Wen; Hu Long; Yu Xiao; Lu Zun-Ming; Fan Ying; Li Yang-xian; Tang Cheng-Chun

    2011-01-01

    We investigate the electronic structure,chemical bonding and elastic properties of the hexagonal aluminum carbonitride,Al5C3N,by ab initio calculations.Al5C3N is a semiconductor with a narrow indirect gap of 0.81 eV.The valence bands below the Fermi level (EF) originate from the hybridized Al p-C p and Al p-N p states.The calculated bulk and Young's moduli are 201 GPa and 292 GPa,which are slightly lower than those of Ti3SiC2.The values of the bulk-to-shear-modulus and bulk-modulus-to-c44 are 1.73 and 1.97,respectively,which axe higher than those of Ti2AlCand Ti2AlN,indicating that Al5C3N is a ductile ceramic.

  14. Minimal parameter implicit solvent model for ab initio electronic structure calculations

    CERN Document Server

    Dziedzic, Jacek; Skylaris, Chris-Kriton; Mostofi, Arash A; Payne, Mike C

    2011-01-01

    We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.

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

    Science.gov (United States)

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

    2005-10-01

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

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

    Science.gov (United States)

    Zhang, Yang

    2014-02-01

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

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

    OpenAIRE

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

    2007-01-01

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

  18. Ab-initio calculations of Judd–Ofelt intensity parameters for transitions between crystal-field levels

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Jun, E-mail: wenjunkd@mail.ustc.edu.cn [School of Physics and Electric Engineering, Anqing Normal University, Anqing 246011 (China); Department of Physics, University of Science and Technology of China, Hefei 230026 (China); Reid, Michael F. [Department of Physics and Astronomy and MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, PB4800 Christchurch (New Zealand); Ning, Lixin [Department of Physics, Anhui Normal University, Wuhu 241000 (China); Zhang, Jie [School of Physics and Electric Engineering, Anqing Normal University, Anqing 246011 (China); Zhang, Yongfan [Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350002 (China); Duan, Chang-Kui; Yin, Min [Department of Physics, University of Science and Technology of China, Hefei 230026 (China)

    2014-08-01

    Wavefunction-based ab-initio calculations of the electric-dipole moments of 4f{sup N}–4f{sup N} transitions of lanthanide ions are performed to extract the A{sub tp}{sup λ} intensity parameters. The extraction method is an extension of our earlier calculations of crystal-field (CF) parameters for lanthanide ions in crystals. The CASSCF/RASSI-SO (Complete-Active-Space Self-Consistent-Field/Restricted-Active-Space State-Interaction Spin-Orbit) calculations have been carried out on the chosen model system of CaF{sub 2}: Ce{sup 3+} with an interstitial fluoride ion (F{sub i}{sup −}) on z-axis (Ce{sup 3+} ion occupying the C{sub 4v} symmetry site). In consideration of the site symmetry and the coordination situation of Ce{sup 3+} ion at C{sub 4v} site in CaF{sub 2} as well as the superposition model (SM), the calculated intensity parameters for Ce{sup 3+} ion can be classified into three categories, and detailed discussions are then given. - Highlights: • Extraction of transition intensity parameters from ab-initio calculations. • CASSCF/RASSI-SO calculations are performed for Ce{sup 3+}-doped CaF{sub 2} crystal (C{sub 4v} case). • Extracted parameters are analyzed and compared with experiment and other calculation.

  19. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    Science.gov (United States)

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  20. Optimizing weights of protein energy function to improve ab initio protein structure prediction

    CERN Document Server

    Wang, Chao; Liu, Juntao; Zhang, Haicang; Ling, Bin; Li, Shuai Cheng; Zheng, Wei-Mou; Bu, Dongbo

    2013-01-01

    Predicting protein 3D structure from amino acid sequence remains as a challenge in the field of computational biology. If protein structure homologues are not found, one has to construct 3D structural conformations from the very beginning by the so-called ab initio approach, using some empirical energy functions. A successful algorithm in this category, Rosetta, creates an ensemble of decoy conformations by assembling selected best short fragments of known protein structures and then recognizes the native state as the highly populated one with a very low energy. Typically, an energy function is a combination of a variety of terms characterizing different structural features, say hydrophobic interactions, van der Waals force, hydrogen bonding, etc. It is critical for an energy function to be capable to distinguish native-like conformations from non-native ones and to drive most initial conformations assembled from fragments to a native-like one in a conformation search process. In this paper we propose a linea...

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

    Science.gov (United States)

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

    2013-03-27

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

  2. Structural Rearrangement of Au-Pd Nanoparticles under Reaction Conditions: An ab Initio Molecular Dynamics Study.

    Science.gov (United States)

    Xu, Cong-Qiao; Lee, Mal-Soon; Wang, Yang-Gang; Cantu, David C; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

    2017-02-28

    The structure, composition, and atomic distribution of nanoalloys under operating conditions are of significant importance for their catalytic activity. In the present work, we use ab initio molecular dynamics simulations to understand the structural behavior of Au-Pd nanoalloys supported on rutile TiO2 under different conditions. We find that the Au-Pd structure is strongly dependent on the redox properties of the support, originating from strong metal-support interactions. Under reducing conditions, Pd atoms are inclined to move toward the metal/oxide interface, as indicated by a significant increase of Pd-Ti bonds. This could be attributed to the charge localization at the interface that leads to Coulomb attractions to positively charged Pd atoms. In contrast, under oxidizing conditions, Pd atoms would rather stay inside or on the exterior of the nanoparticle. Moreover, Pd atoms on the alloy surface can be stabilized by hydrogen adsorption, forming Pd-H bonds, which are stronger than Au-H bonds. Our work offers critical insights into the structure and redox properties of Au-Pd nanoalloy catalysts under working conditions.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-29

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

  4. Ab initio calculations of the electronic structure and bonding characteristics of LaB6

    Science.gov (United States)

    Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.

    2005-12-01

    Lanthanum hexaboride ( LaB6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB6 system and partially explains its high efficiency as a thermionic emitter.

  5. Local Structure in Ab Initio Liquid Water: Signatures of Amorphous Phases

    Science.gov (United States)

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

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water This work was supported by the DOE: DE-SC0008626, DE-SC0005180.

  6. The Structure, Density, and Local Environment Distribution in Ab Initio Liquid Water

    Science.gov (United States)

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

    2014-03-01

    We have performed extensive ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions in the canonical (NVT) and isothermal-isobaric (NPT) ensembles to understand the individual and collective importance of exact exchange, van der Waals interactions, and nuclear quantum effects on the structural properties of liquid water. AIMD simulations which include these effects result in oxygen-oxygen radial distribution functions which are in excellent agreement with experiments and a liquid water structure having an equilibrium density within 1% of the experimental value of 1 g/cm3. A detailed analysis of the distribution of local structure in ambient liquid water has revealed that the inherent potential energy surface is bimodal with respect to high- and low-density molecular environments, consistent with the existence of polymorphism in the amorphous phases of water. With these findings in mind, the methodology presented herein overcomes the well-known limitations of semi-local density functional theory (GGA-DFT) providing a detailed and accurate microscopic description of ambient liquid water. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500.

  7. Structural insights and ab initio sequencing within the DING proteins family

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

  8. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

    Science.gov (United States)

    Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

    2015-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

  9. Electronic Structure of Hydrogenated and Surface-Modified GaAs Nanocrystals: Ab Initio Calculations

    Directory of Open Access Journals (Sweden)

    Hamsa Naji Nasir

    2012-01-01

    Full Text Available Two methods are used to simulate electronic structure of gallium arsenide nanocrystals. The cluster full geometrical optimization procedure which is suitable for small nanocrystals and large unit cell that simulates specific parts of larger nanocrystals preferably core part as in the present work. Because of symmetry consideration, large unit cells can reach sizes that are beyond the capabilities of first method. The two methods use ab initio Hartree-Fock and density functional theory, respectively. The results show that both energy gap and lattice constant decrease in their value as the nanocrystals grow in size. The inclusion of surface part in the first method makes valence band width wider than in large unit cell method that simulates the core part only. This is attributed to the broken symmetry and surface passivating atoms that split surface degenerate states and adds new levels inside and around the valence band. Bond length and tetrahedral angle result from full geometrical optimization indicate good convergence to the ideal zincblende structure at the centre of hydrogenated nanocrystal. This convergence supports large unit cell methodology. Existence of oxygen atoms at nanocrystal surface melts down density of states and reduces energy gap.

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

    Energy Technology Data Exchange (ETDEWEB)

    Monteseguro, V. [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Rodríguez-Hernández, P.; Muñoz, A., E-mail: amunoz@ull.es [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Instituto de Materiales y Nanotecnología. Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain)

    2015-12-28

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

  11. Ab initio study of structural, electronic, and thermal properties of Pt1-xPdx alloys

    Science.gov (United States)

    Ahmed, Shabbir; Zafar, Muhammad; Shakil, M.; Choudhary, M. A.; Hashmi, Muhammad Raza-Ur-Rehman

    2017-01-01

    We report a systematic theoretical study of Pt1-xPdx alloys using ab initio density functional theory (DFT) by pseudo potential method. We have used super cell approach to investigate structural, electronic and thermal properties of Platinum (Pt), Palladium (Pd) and their alloys Pt1-xPdx(x = 0.00, 0.25, 0.50, 0.75, 1.00). The calculated lattice constants and bulk moduli are in good agreement with available literature data. The results of electronic properties revealed that the alloys are metallic in nature. The thermal properties were investigated through density functional perturbation theory (DFPT) and quasi-harmonic approximation. The contribution to the free energy from the lattice vibration was calculated using the phonon densities of states (DOS) derived by means of the linear-response theory. The DFPT with quasi-harmonic approximation methods was applied to determine the phonon DOS and thermal quantities i.e., the Debye temperatures, vibration energy, entropy and constant-volume specific heat.

  12. Katoite under pressure: an ab initio investigation of its structural, elastic and vibrational properties sheds light on the phase transition.

    Science.gov (United States)

    Erba, Alessandro; Navarrete-López, Alejandra M; Lacivita, Valentina; D'Arco, Philippe; Zicovich-Wilson, Claudio M

    2015-01-28

    The evolution under pressures up to 65 GPa of structural, elastic and vibrational properties of the katoite hydrogarnet, Ca3Al2(OH)12, is investigated with an ab initio simulation performed at the B3LYP level of theory, by using all-electron basis sets with the Crystal periodic program. The high-symmetry Ia3d phase of katoite, stable under ambient conditions, is shown to be destabilized, as pressure increases, by interactions involving hydrogen atoms and their neighbors which weaken the hydrogen bonding network of the structure. The corresponding thermodynamical instability is revealed by anomalous deviations from regularity of its elastic constants and by numerous imaginary phonon frequencies, up to 50 GPa. Interestingly, as pressure is further increased above 50 GPa, the Ia3d structure is shown to become stable again (all positive phonon frequencies and regular elastic constants). However, present calculations suggest that, above about 15 GPa and up to at least 65 GPa, a phase of I4[combining macron]3d symmetry (a non-centrosymmetric subgroup of Ia3d) becomes more stable than the Ia3d one, being characterized by strengthened hydrogen bonds. At low-pressures (between about 5 GPa and 15 GPa), both phases show some instabilities (more so for I4[combining macron]3d than for Ia3d), thus suggesting either the existence of a third phase or a possible phase transition of second order.

  13. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure.

    Science.gov (United States)

    Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I

    2016-07-20

    We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  14. Structure and dynamics of La(III) in aqueous solution An ab initio QM/MM MD approach

    Science.gov (United States)

    Hofer, Thomas S.; Scharnagl, Harald; Randolf, Bernhard R.; Rode, Bernd M.

    2006-08-01

    Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion-ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.

  15. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  16. Ab initio determination of dark structures in radiationless transitions for aromatic carbonyl compounds.

    Science.gov (United States)

    Fang, Wei-Hai

    2008-03-01

    photoexcitation of aromatic carbonyl compounds. The importance of ab initio determination of transient structures in the photodissociation dynamics has been demonstrated for the case of the aromatic carbonyl compounds. In addition, the detailed knowledge of mechanistic photochemistry for aromatic carbonyl compounds forms the basis for further investigating photodissociation dynamics of a polyatomic molecule.

  17. Structure of protonated carbon dioxide clusters: infrared photodissociation spectroscopy and ab initio calculations.

    Science.gov (United States)

    Douberly, G E; Ricks, A M; Ticknor, B W; Duncan, M A

    2008-02-07

    The infrared photodissociation spectra (IRPD) in the 700 to 4000 cm(-1) region are reported for H+ (CO2)n clusters (n = 1-4) and their complexes with argon. Weakly bound Ar atoms are attached to each complex upon cluster formation in a pulsed electric discharge/supersonic expansion cluster source. An expanded IRPD spectrum of the H+ (CO2)Ar complex, previously reported in the 2600-3000 cm(-1) range [Dopfer, O.; Olkhov, R.V.; Roth, D.; Maier, J.P. Chem. Phys. Lett. 1998, 296, 585-591] reveals new vibrational resonances. For n = 2 to 4, the vibrational resonances involving the motion of the proton are observed in the 750 to 1500 cm(-1) region of the spectrum, and by comparison to the predictions of theory, the structure of the small clusters are revealed. The monomer species has a nonlinear structure, with the proton binding to the lone pair of an oxygen. In the dimer, this nonlinear configuration is preserved, with the two CO2 units in a trans configuration about the central proton. Upon formation of the trimer, the core CO2 dimer ion undergoes a rearrangement, producing a structure with near C2v symmetry, which is preserved upon successive CO2 solvation. While the higher frequency asymmetric CO2 stretch vibrations are unaffected by the presence of the weakly attached Ar atom, the dynamics of the shared proton motions are substantially altered, largely due to the reduction in symmetry of each complex. For n = 2 to 4, the perturbation due to Ar leads to blue shifts of proton stretching vibrations that involve motion of the proton mostly parallel to the O-H+-O axis of the core ion. Moreover, proton stretching motions perpendicular to this axis exhibit smaller shifts, largely to the red. Ab initio (MP2) calculations of the structures, complexation energies, and harmonic vibrational frequencies are also presented, which support the assignments of the experimental spectra.

  18. Ab initio molecular dynamics study of the interlayer and micropore structure of aqueous montmorillonite clays

    Science.gov (United States)

    Suter, James L.; Kabalan, Lara; Khader, Mahmoud; Coveney, Peter V.

    2015-11-01

    Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (1 1 0) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (1 1 0) clay edge, we find the adjacent exposed apical oxygen behaves as a Brönsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (1 1 0) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (0 1 0) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (tbnd Sisbnd Osbnd H → tbnd Sisbnd O- + H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (0 1 0) surface can act as a Brönsted acid, even at neutral pH.

  19. Input/Output of ab-initio nuclear structure calculations for improved performance and portability

    Energy Technology Data Exchange (ETDEWEB)

    Laghave, Nikhil [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    Many modern scientific applications rely on highly computation intensive calculations. However, most applications do not concentrate as much on the role that input/output operations can play for improved performance and portability. Parallelizing input/output operations of large files can significantly improve the performance of parallel applications where sequential I/O is a bottleneck. A proper choice of I/O library also offers a scope for making input/output operations portable across different architectures. Thus, use of parallel I/O libraries for organizing I/O of large data files offers great scope in improving performance and portability of applications. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab-initio nuclear structure calculations. We develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient I/O of large datasets along with their portability and ease of use in the down-stream processing. Even situations where the amount of data to be written is not huge, proper use of input/output operations can boost the performance of scientific applications. Application checkpointing offers enormous performance improvement and flexibility by doing a negligible amount of I/O to disk. Checkpointing saves and resumes application state in such a manner that in most cases the application is unaware that there has been an interruption to its execution. This helps in saving large amount of work that has been previously done and continue application execution. This small amount of I/O provides substantial time saving by offering restart/resume capability to applications. The need for checkpointing in optimization code NEWUOA has been identified and checkpoint/restart capability has been implemented in NEWUOA by using simple file I/O.

  20. Structural, elastic and thermodynamic properties of tetragonal and orthorhombic polymorphs of Sr2GeN2: an ab initio investigation

    Science.gov (United States)

    Bedjaoui, A.; Bouhemadou, A.; Bin-Omran, S.

    2016-04-01

    The structural, elastic and thermodynamic properties of the α (tetragonal) and β (orthorhombic) polymorphs of the Sr2GeN2 compound have been examined in detail using ab initio density functional theory pseudopotential plane-wave calculations. Apart the structural properties at the ambient conditions, all present reported results are predicted for the first time. The calculated equilibrium lattice parameters and inter-atomic bond-lengths of the considered polymorphs are in good agreement with the available experimental data. It is found that α-Sr2GeN2 is energetically more stable than β-Sr2GeN2. The two examined polymorphs are very similar in their crystal structures and have almost identical local environments. The single-crystal and polycrystalline elastic parameters and related properties - including elastic constants, bulk, shear and Young's moduli, Poisson's ratio, anisotropy indexes, Pugh's criterion, elastic wave velocities and Debye temperature - have been predicted. Temperature and pressure dependence of some macroscopic properties - including the unit-cell volume, bulk modulus, volume thermal expansion coefficient, heat capacity and Debye temperature - have been evaluated using ab initio calculations combined with the quasi-harmonic Debye model.

  1. TOUCHSTONE II: a new approach to ab initio protein structure prediction.

    Science.gov (United States)

    Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey

    2003-08-01

    We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These

  2. Ab initio electronic structure study of one-electron reduction of polychlorinated ethylenes.

    Science.gov (United States)

    Bylaska, Eric J; Dupuis, Michel; Tratnyek, Paul G

    2005-07-07

    Polychlorethylene radicals, anions, and radical anions are potential intermediates in the reduction of polychlorinated ethylenes (C(2)Cl(4), C(2)HCl(3), trans-C(2)H(2)Cl(2), cis-C(2)H(2)Cl(2), 1,1-C(2)H(2)Cl(2), C(2)H(3)Cl). Ab initio electronic structure methods were used to calculate the thermochemical properties, (298.15 K), S degrees (298.15 K,1 bar), and DeltaG(S)(298.15 K, 1 bar) of 37 different polychloroethylenyl radicals, anions, and radical anion complexes, C(2)H(y)Cl(3)(-)(y)(*), C(2)H(y)Cl(3)(-)(y)(-), and C(2)H(y))Cl(4)(-)(y)(*)(-) for y = 0-3, for the purpose of characterizing reduction mechanisms of polychlorinated ethylenes. In this study, 8 radicals, 7 anions, and 22 radical anions were found to have stable structures, i.e., minima on the potential energy surfaces. This multitude of isomers for C(2)H(y)Cl(4)(-)(y)(*)(-) radical anion complexes are pi*, sigma*, and -H...Cl(-) structures. Several stable pi* radical anionic structures were obtained for the first time through the use of restricted open-shell theories. On the basis of the calculated thermochemical estimates, the overall reaction energetics (in the gas phase and aqueous phase) for several mechanisms of the first electron reduction of the polychlorinated ethylenes were determined. In almost all of the gas-phase reactions, the thermodynamically most favorable pathways involve -H...Cl(-) complexes of the C(2)H(y)Cl(4)(-)(y)(*)(-) radical anion, in which a chloride ion is loosely bound to a hydrogen of a C(2)H(x)Cl(2)(-)(x))(*) radical. The exception is for C(2)Cl(4), in which the most favorable anionic structure is a loose sigma* radical anion complex, with a nearly iso-energetic pi* radical anion. Solvation significantly changes the product energetics with the thermodynamically most favorable pathway leading to C(2)H(y)Cl(3)(-)(y)(*) + Cl(-). The results suggest that a higher degree of chlorination favors reduction, and that reduction pathways involving the C(2)H(y)Cl(3)(-)(y)(-) anions

  3. Origin of the Hadži ABC structure: An ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Van Hoozen, Brian L.; Petersen, Poul B. [Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 (United States)

    2015-11-14

    Medium and strong hydrogen bonds are well known to give rise to broad features in the vibrational spectrum often spanning several hundred wavenumbers. In some cases, these features can span over 1000 cm{sup −1} and even contain multiple broad peaks. One class of strongly hydrogen-bonded dimers that includes many different phosphinic, phosphoric, sulfinic, and selenic acid homodimers exhibits a three-peaked structure over 1500 cm{sup −1} broad. This unusual feature is often referred to as the Hadži ABC structure. The origin of this feature has been debated since its discovery in the 1950s. Only a couple of theoretical studies have attempted to interpret the origin of this feature; however, no previous study has been able to reproduce this feature from first principles. Here, we present the first ab initio calculation of the Hadži ABC structure. Using a reduced dimensionality calculation that includes four vibrational modes, we are able to reproduce the three-peak structure and much of the broadness of the feature. Our results indicate that Fermi resonances of the in-plane bend, out-of-plane bend, and combination of these bends play significant roles in explaining this feature. Much of the broadness of the feature and the ability of the OH stretch mode to couple with many overtone bending modes are captured by including an adiabatically separated dimer stretch mode in the model. This mode modulates the distance between the monomer units and accordingly the strength of the hydrogen-bonds causing the OH stretch frequency to shift from 2000 to 3000 cm{sup −1}. Using this model, we were also able to reproduce the vibrational spectrum of the deuterated isotopologue which consists of a single 500 cm{sup −1} broad feature. Whereas previous empirical studies have asserted that Fermi resonances contribute very little to this feature, our study indicates that while not appearing as a separate peak, a Fermi resonance of the in-plane bend contributes substantially to

  4. Obtaining detailed structural information about supramolecular systems on surfaces by combining high-resolution force microscopy with ab initio calculations.

    Science.gov (United States)

    Kawai, Shigeki; Sadeghi, Ali; Xu, Feng; Feng, Xu; Peng, Lifen; Lifen, Peng; Pawlak, Rémy; Glatzel, Thilo; Willand, Alexander; Orita, Akihiro; Otera, Junzo; Goedecker, Stefan; Meyer, Ernst

    2013-10-22

    State-of-the art experimental techniques such as scanning tunneling microscopy have great difficulties in extracting detailed structural information about molecules adsorbed on surfaces. By combining atomic force microscopy and Kelvin probe force microscopy with ab initio calculations, we demonstrate that we can obtain a wealth of detailed structural information about the molecule itself and its environment. Studying an FFPB molecule on a gold surface, we are able to determine its exact location on the surface, the nature of its bonding properties with neighboring molecules that lead to the growth of one-dimensional strips, and the internal torsions and bendings of the molecule.

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

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-19

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

  6. Ab initio study of structural, electronic, and thermal properties of Ir_{1-x}Rh_{x} alloys

    Directory of Open Access Journals (Sweden)

    Sh. Ahmed

    2015-06-01

    Full Text Available The structural, electronic, mechanical and thermal properties of Ir_{1-x}Rh_{x} alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.

  7. Ab initio simulations of the structure, energetics and mobility of radiation-induced point defects in bcc Nb

    Science.gov (United States)

    Cerdeira, M. A.; Palacios, S. L.; González, C.; Fernández-Pello, D.; Iglesias, R.

    2016-09-01

    The formation, binding and migration energetics of helium clusters inside a niobium crystal have been analysed via ab initio simulations. The effect of placing several He atoms within an n-vacancy previously formed or as interstitials inside the initial perfect bulk matrix has been studied. DFT-based results show that He atoms prefer to aggregate forming small clusters at n-vacancy sites rather than at interstitial positions in the perfect crystal. The minimum formation energy is found when NHe is equal to the number of vacancies, n. It follows that vacancies act as almost perfect traps for He atoms, as is well known for other metals. The migration barriers of He atoms inside vacancies increase considerably when compared to what happens for vacancies alone. A secondary consequence is that the full set of energies obtained will be highly relevant as an input for new approaches to KMC simulations of defects in Nb.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hoy, Erik P.; Mazziotti, David A., E-mail: damazz@uchicago.edu [Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    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.

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

    Science.gov (United States)

    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.

  10. Structural transformation between long and short-chain form of liquid sulfur from \\textit{ab initio} molecular dynamics

    CERN Document Server

    Plašienka, Dušan; Martoňák, Roman

    2014-01-01

    We present results of \\textit{ab initio} molecular dynamics study of a structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the chain-breakage phenomenon recently observed experimentally by Liu \\textit{et al.} [1] and to the electronic transition reported by Brazhkin \\textit{et al.} [2,3]. We performed an extensive \\textit{ab initio} study and confirmed the existence of one transformation separating two distinct liquid polymeric phases: one composed of short chain-like fragments and another one with very long chains. We have not observed additional transformations reported in Refs. [2,3] and in the recent theoretical study by Zhao and Mu [4] and our findings are in agreement with the most recent experiment [1]. We offer a structural description of this liquid-liquid transformation in terms of chain lengths, cross-linking and geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in configurational energy...

  11. Drastic changes of electronic structure and crystal chemistry upon oxidation of SnII2TiO4E2 into SnIV2TiO6: An ab initio study

    Science.gov (United States)

    Matar, Samir F.; Maglione, Mario; Nakhl, Michel; Kfoury, Charbel N.; Etourneau, Jean

    2016-09-01

    From DFT based calculations establishing energy-volume equations of state and electron localization mapping, the electronic structure and crystal chemistry changes from Sn2TiO4 to Sn2TiO6 by oxidation are rationalized; the key effect being the destabilization of divalent tin SnII towards tetravalent state SnIV leading to rutile Sn2TiO6 as experimentally observed. The subsequent electronic structure change is highlighted in the relative change of the electronic band gap which increases from ∼1 eV up to 2.2 eV and the 1.5 times increase of the bulk modulus assigned to the change from covalently SnII based compound to the more ionic SnIV one. Such trends are also confronted with the relevant properties of black SnIIO.

  12. Ab initio calculations of optical constants of GaSe and InSe layered crystals

    Science.gov (United States)

    Sarkisov, S. Yu.; Kosobutsky, A. V.; Brudnyi, V. N.; Zhuravlev, Yu. N.

    2015-09-01

    The dielectric functions, refractive indices, and extinction coefficients of GaSe and InSe layered crystals have been calculated within the density functional theory. The calculations have been performed for the values of theoretical structural parameters optimized using the exchange-correlation functional, which allows one to take into account the dispersion interactions. It has been found that optical functions are characterized by the most pronounced polarization anisotropy in the range of photon energies of ˜4-7 eV. The frequency dependences for InSe compound in the range up to 4 eV demonstrate the more pronounced anisotropy as compared to GaSe. The results obtained for GaSe crystal agree better with the experimental data as compared to the previous calculations.

  13. Ab initio calculation of electron-phonon coupling in monoclinic β-Ga2O3 crystal

    Science.gov (United States)

    Ghosh, Krishnendu; Singisetti, Uttam

    2016-08-01

    The interaction between electrons and vibrational modes in monoclinic β-Ga2O3 is theoretically investigated using ab-initio calculations. The large primitive cell of β-Ga2O3 gives rise to 30 phonon modes all of which are taken into account in transport calculation. The electron-phonon interaction is calculated under density functional perturbation theory and then interpolated using Wannier-Fourier interpolation. The long-range interaction elements between electrons and polar optical phonon (POP) modes are calculated separately using the Born effective charge tensor. The direction dependence of the long-range POP coupling in a monoclinic crystal is explored and is included in the transport calculations. Scattering rate calculations are done using the Fermi golden rule followed by solving the Boltzmann transport equation using the Rode's method to estimate low field mobility. A room temperature mobility of 115 cm2/V s is observed. Comparison with recent experimentally reported mobility is done for a wide range of temperatures (30 K-650 K). It is also found that the POP interaction dominates the electron mobility under low electric field conditions. The relative contribution of the different POP modes is analyzed and the mode 21 meV POP is found to have the highest impact on low field electron mobility at room temperature.

  14. Coupling of temperature with pressure induced initial decomposition mechanisms of two molecular crystals: An ab initio molecular dynamics study

    Indian Academy of Sciences (India)

    QIONG WU; DONG XIANG; GUOLIN XIONG; WEIHUA ZHU; HEMING XIAO

    2016-05-01

    Ab initio molecular dynamics simulations were performed to study the initiation of decompositionand formation of first products of two molecular crystals pentaerythritol tetranitrate (PETN) and 5-nitro-2,4-dihydro-1,2,4-triazole-3-one (NTO) under thermal decomposition temperature (475 K for PETN and 531 Kfor NTO) coupled with different pressures (1-5 GPa). The pressure effects on the initial decomposition stepsand initially generated products on PETN and NTO were very different. PETN was triggered by C-H... O intermolecular hydrogen transfer. The initial decomposition mechanism was independent of the pressure. ForNTO, two different initial decomposition mechanisms were found. At 1, 2, and 3 GPa, it was triggered by NH....O intermolecular hydrogen transfer, while at 4 and 5 GPa, it was triggered by N-H.....N intermolecularhydrogen transfer. This indicates that the initial decomposition mechanism was dependent on the pressure.Our study may provide new insights into initial mechanisms and decomposition reactions of molecular crystalexplosives under thermal decomposition temperature coupled with different pressures with details at atomiclevel.

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  16. Precise Lifetime Measurements in Light Nuclei for Benchmarking Modern Ab-initio Nuclear Structure Models

    Energy Technology Data Exchange (ETDEWEB)

    Lister, C.J. [Department of Physics, University of Massachusetts, Lowell, Lowell MA 01854 (United States); McCutchan, E.A. [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)

    2014-06-15

    A new generation of ab-initio calculations, based on realistic two- and three-body forces, is having a profound impact on our view of how nuclei work. To improve the numerical methods, and the parameterization of 3-body forces, new precise data are needed. Electromagnetic transitions are very sensitive to the dynamics which drive mixing between configurations. We have made a series of precise (< 3%) measurements of electromagnetic transitions in the A=10 nuclei {sup 10}C and {sup 10}Be by using the Doppler Shift Attenuation method carefully. Many interesting features can be reproduced including the strong α clustering. New measurements on {sup 8}Be and {sup 12}Be highlight the interplay between the alpha clusters and their valence neutrons.

  17. Effect of pressure on the lattice structure and dynamics of elpasolites Cs2Na RF6 ( R = Y, Yb): ab initio calculation

    Science.gov (United States)

    Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.

    2015-06-01

    The effect of hydrostatic compression on the lattice structure and dynamics of elpasolites Cs2NaYbF6 and Cs2NaYF6 (sp. gr. 225) has been investigated ab initio. The frequencies and types of fundamental oscillations are determined, and elastic constants are calculated. The computation is performed within the molecular orbitals-linear combinations of atomic orbitals (MO LCAO) approach using the density functional theory (DFT) method with hybrid functionals B3LYP and PBE0 in the CRYSTAL09 program. The rare-earth ion was described by representing the inner (in particular, 4 f) orbitals in the form of a pseudopotential. The outer 5 s and 5 p orbitals, which determine chemical bonding, were described using valence basis sets.

  18. Bulk dislocation-U defect interaction, surface excitons and adsorptivity of atomic H on dislocated surfaces of LiH crystal: ab initio calculations

    Science.gov (United States)

    Shalabi, A. S.; Eid, Kh M.; El-Mahdy, A. M.; Kamel, M. A.; El-Barbary, A. A.

    2001-03-01

    An ab initio embedded cluster method was used to examine the bulk dislocation-U defect interaction, surface excitons and the adsorptivity of atomic H on dislocated surfaces of LiH using the Hartree-Fock approximation and the second-order Moller-Plesset perturbation correction. In the LiH crystal bulk, the results confirm: (1) U1 and U2 centres make dislocations more facile, (2) dislocation processes do not reduce the ionic conductivity of highly populated edge centred hydride interstitials and (3) the dislocation-U defect interaction increases monotonically in the series face→volume→edge centred interstitial structures. On LiH crystal surfaces the results confirm: (1) the exclusive dependence of band gaps and exciton bands on dislocation, (2) the strongest adsorption of atomic H on a surface is associated with X-dislocations, (3) dislocations are unable to change the nature of physical adsorption to chemical adsorption and (4) the mobility of atomic H over the Z-dislocated surface is more facile than that over the X-dislocated surface. As X-surface dislocation proceeds, the HOMO and LUMO levels of the substrate shift to higher energies and the band gap becomes narrower. This change in the electronic structure suggests that charge transfer from the X-dislocated surface is more facile in the course of adsorbate-substrate interaction.

  19. Electronic Band Structure of Transition Metal Dichalcogenides from Ab Initio and Slater–Koster Tight-Binding Model

    Directory of Open Access Journals (Sweden)

    Jose Ángel Silva-Guillén

    2016-10-01

    Full Text Available Semiconducting transition metal dichalcogenides present a complex electronic band structure with a rich orbital contribution to their valence and conduction bands. The possibility to consider the electronic states from a tight-binding model is highly useful for the calculation of many physical properties, for which first principle calculations are more demanding in computational terms when having a large number of atoms. Here, we present a set of Slater–Koster parameters for a tight-binding model that accurately reproduce the structure and the orbital character of the valence and conduction bands of single layer MX 2 , where M = Mo, W and X = S, Se. The fit of the analytical tight-binding Hamiltonian is done based on band structure from ab initio calculations. The model is used to calculate the optical conductivity of the different compounds from the Kubo formula.

  20. An ab initio study of the structure and atomic transport in bulk liquid Ag and its liquid-vapor interface

    Science.gov (United States)

    del Rio, Beatriz G.; González, David J.; González, Luis E.

    2016-10-01

    Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals propagating excitations whose dispersion at long wavelengths is compatible with the experimental sound velocity. Results are also reported for other transport coefficients. Additional simulations have also been performed so as to study the structure of the free liquid surface. The calculated longitudinal ionic density profile shows an oscillatory behaviour, whose properties are analyzed through macroscopic and microscopic methods. The intrinsic X-ray reflectivity of the surface is predicted to show a layering peak associated to the interlayer distance.

  1. Structural, magnetic and electronic properties of FexCoyIrz (x + y + z = 5, 6) clusters: an ab initio study

    KAUST Repository

    Devi, Assa Aravindh Sasikala

    2014-05-01

    Investigations on freestanding binary and ternary clusters of Fe (x) Co (y) Ir (z) (x + y + z = 5, 6) are carried out using ab initio density functional theory techniques. The geometry, chemical order, binding energy, magnetic moment and electronic structure of the clusters are analyzed for the entire range of composition. Composition dependent structural transition is observed in the five atom clusters, while octahedral geometry prevailed in clusters with six atoms. Both the clusters show increment in binding energy with the increase in number of heterogeneous bonds. Analysis based on the chemical order parameter indicates that clusters favor mixing rather than segregation. The clusters exhibit ferromagnetic ordering and the inter-dependence of optimal cluster geometry to the magnetic moments and electronic structure is observed.

  2. Metallic VS2 Monolayer Polytypes as Potential Sodium-Ion Battery Anode via ab Initio Random Structure Searching.

    Science.gov (United States)

    Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai

    2016-07-27

    We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications.

  3. Structural Dynamics of Fe along the New \\textit{Ab Initio} Determined Hugoniot Curve from Warm to Hot Dense Regime

    CERN Document Server

    Dai, Jiayu; Zhao, Zengxiu; Wu, Yanqun; Yuan, Jianmin

    2011-01-01

    A new determined principal Hugoniot curve of Fe in the temperature range of 0.1-100 eV from Ab initio is presented, and the structural dynamics along this curve is shown. All experiments are on top or above our Hugoniot data, which are along the lower envelop of the distribution of experiments. The present data are the converged limit for experiments to remove the external effects such as preheating. In particular, the experimental data on the bottom of the distribution below 10 Mbar can be considered nearly free of errors caused by the external effects compared with our data. The dynamics of ionic structures shows the stable existence of complex clusters with persisted time length of hundreds of femto-seconds from cold to hot dense matter.

  4. Electronic structure of AlCrN films investigated using various photoelectron spectroscopies and ab initio calculations

    Science.gov (United States)

    Tatemizo, N.; Imada, S.; Miura, Y.; Yamane, H.; Tanaka, K.

    2017-03-01

    The valence band (VB) structures of wurtzite AlCrN (Cr concentration: 0-17.1%), which show optical absorption in the ultraviolet-visible-infrared light region, were investigated via photoelectron yield spectroscopy (PYS), x-ray/ultraviolet photoelectron spectroscopy (XPS/UPS), and ab initio density of states (DOS) calculations. An obvious photoelectron emission threshold was observed ~5.3 eV from the vacuum level for AlCrN, whereas no emission was observed for AlN in the PYS spectra. Comparisons of XPS and UPS VB spectra and the calculated DOS imply that Cr 3d states are formed both at the top of the VB and in the AlN gap. These data suggest that Cr doping could be a viable option to produce new materials with relevant energy band structures for solar photoelectric conversion.

  5. Structural, Conformational and Vibrational Studies of Isocyanocyclopentane from Infrared, Raman Spectra and AB Initio Calculations

    Science.gov (United States)

    Sawant, Dattatray K.; Klaassen, Joshua J.; Durig, James R.

    2013-06-01

    The infrared and Raman spectra (3200 to 50 cm^{-1}) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, _{c}-C_{5}H_{9}NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-55 to -100°C) studies of the infrared spectra (3200 to 400 cm^{-1}) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102 ± 10 cm^{-1} (1.21 ± 0.03 kJ mol^{-1}) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38 ± 1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The heavy atom distances (Å): C≡N = 1.176 ; C_{α}-N≡C= 1.432; C_{α}-C_{β},C_{β}' = 1.534; C_{β}-C_{γ}, C_{γ}' = 1.542; C_{γ}-C_{γ}' = 1.554 and angles (°:angleC_{α}-N≡C = 177.8; angleC_{β}C_{α}-N≡C = 110.4; angleC_{β}C_{α}C_{β}'= 102.9; angleC_{α}C_{β}C_{γ} = 103.6; angleC_{β}C_{γ}C_{γ}' = 105.9. The results are discussed and compared to the corresponding properties of some related molecules.

  6. Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

    DEFF Research Database (Denmark)

    Møgelhøj, Andreas; Kelkkanen, Kari André; Wikfeldt, K Thor

    2011-01-01

    The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal...... shows some resemblance with experiment for high-density water ( Soper , A. K. and Ricci , M. A. Phys. Rev. Lett. 2000 , 84 , 2881 ), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation...... protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals...

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

    Science.gov (United States)

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

    1989-01-01

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

  8. Ab Initio Determination of the Torsion-Wagging and Wagging-Bending Infrared Band Structure Spectrum of Methylamine.

    Science.gov (United States)

    Smeyers; Villa; Senent

    1998-10-01

    The infrared band structure for the methyl torsion and amine hydrogen symmetric wagging in methylamine is calculated by ab initio procedures. The influence of the amine hydrogen symmetric bending on the wagging spectrum is considered explicitly. For this purpose, the potential energy surfaces and kinetic parameters were determined at the RHF/MP2 level with the 6-311G++(3df, 3dp) basis set. The numerical results were fitted to symmetry adapted functional forms. The Schrödinger equations for the nuclear motions were solved by expanding the solutions into products of trigonometric functions. The band frequencies and intensities were calculated from the energy levels, the vibrational functions, and the electric dipole moment variations. The calculated spectra were compared with the available experimental data. It was found that the torsional splittings and frequencies are relatively well reproduced, whereas the wagging and bending frequencies are slightly too high. Copyright 1998 Academic Press.

  9. Ab initio investigation of the structure and nonlinear optical properties of five-membered heterocycles containing sulfur

    Science.gov (United States)

    Spassova, Milena; Enchev, Venelin

    2004-03-01

    An ab initio HF and MP2 study of the static (hyper)polarizabilities of 2,4-substituted imidazoles and thiazoles is presented. The comparison of the two types of five-membered heterocycles suggests, that the exocyclic heteroatoms have much more influence upon the calculated hyperpolarizabilities, than the ring heteroatoms. It has been found, that adding diffuse functions to the 6-31G** basis set and inclusion of the electron correlation result in drastic changes in the second hyperpolarizability. The changes are more pronounced for the structures with larger number of sulfur atoms. A HF/6-31G** investigation of a push-pull system, in which thiorhodanine has been chosen as acceptor fragment shows an enhancement of the molecular polarizabilities with respect to the corresponding typical donor-acceptor NH 2/NO 2 polyene.

  10. Ab-initio calculation of elastic constants of crystalline systems with the CRYSTAL code

    Science.gov (United States)

    Perger, W. F.; Criswell, J.; Civalleri, B.; Dovesi, R.

    2009-10-01

    An automated procedure for calculating second-order elastic constants for crystalline systems of any symmetry using the CRYSTAL program is described. Second derivatives with respect to strain are evaluated numerically from analytical gradients. The internal co-ordinates are re-optimized with each applied strain. Point group symmetry is exploited to reduce the number of needed deformations according to Laue classes. A set of test cases covering many of the crystal classes is used to document the numerical accuracy of the scheme, and to define default values of the computational parameters so as to reduce the input file to a single keyword.

  11. Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

    Science.gov (United States)

    Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

    2015-12-01

    A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data.

  12. Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)

    Science.gov (United States)

    Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola

    Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  13. Ab initio study of the structural, elastic, thermodynamic, electronic and vibration properties of TbMg intermetallic compound

    Science.gov (United States)

    Mogulkoc, Y.; Ciftci, Y. O.; Kabak, M.; Colakoglu, K.

    2014-07-01

    The structural, elastic, thermodynamic, electronic and vibrational properties of CsCl-type TbMg have been studied by performing ab initio calculations based on density functional theory using the Vienna Ab initio Simulation Package (VASP). The exchange correlation potential within the generalized-gradient approximation (GGA) of projector augmented wave (PAW) method is used. The calculated structural parameters, such as the lattice constant, bulk modulus, its pressure derivative, formation energy and second-order elastic constants are presented in this paper. The obtained results are compared with related experimental and theoretical studies. The electronic band calculations, total density of states (DOS), partial DOS and charge density are also presented. Formation enthalpy and Cauchy pressure are determined. In order to obtain more information the elastic properties such as Zener anisotropy factor, Poisson’s ratio, Young modulus, isotropic shear modulus, Debye temperature and melting point have been carried out. The elastic constants are calculated in zero and different pressure ranges (0-50 GPa) with bulk modulus. We have performed the thermodynamic properties of TbMg by using quasi-harmonic Debye model. The temperature and pressure variation of the volume, bulk modulus, and thermal expansion coefficient have been predicted over a pressure range of 0-25 GPa for of TbMg. Pressure dependence of the anisotropy factors, Young’s modulus, Poisson’s ratios, bulk modulus and axis compressibility of TbMg are presented along different directions and planes. Finally, the phonon dispersion curves are presented for TbMg.

  14. Study of the Molecular Geometry, Electronic Structure, and Thermal Stability of Phosphazene and Heterophosphazene Rings with ab Initio Molecular Orbital Calculations

    NARCIS (Netherlands)

    Jaeger, C.R.; Debowski, M.A.; Manners, I.; Vancso, G.J.

    1999-01-01

    Ab initio molecular orbital calculations at the MP2/6-31G* level of theory have been used to study the molecular geometry, electronic structure, and the thermal stability of six-membered phosphazene and heterophosphazene rings. The studies included the phosphazene ring [NPCl2]3, the carbophosphazene

  15. A self-starting method for obtaining analytic potential-energy surfaces from ab initio electronic structure calculations.

    Science.gov (United States)

    Agrawal, P M; Malshe, M; Narulkar, R; Raff, L M; Hagan, M; Bukkapatnum, S; Komanduri, R

    2009-02-05

    Previous methods proposed for obtaining analytic potential-energy surfaces (PES) from ab initio electronic structure calculations are not self-starting. They generally require that the sampling of configuration space important in the reaction dynamics of the process being investigated be initiated by using chemical intuition or a previously developed semiempirical potential-energy surface. When the system under investigation contains four or more atoms undergoing three- and four-center reactions in addition to bond scission processes, obtaining a sufficiently converged initial sampling can be very difficult due to the extremely large volume of configuration space that is important in the reaction dynamics. It is shown that by combining direct dynamics (DD) with previously reported molecular dynamics (MD), novelty sampling (NS), and neural network (NN) methods, an analytical surface suitable for MD computations for large systems may be obtained. Application of the method to the investigation of N-O bond scission and cis-trans isomerization reactions of HONO followed by comparison of the resulting neural network potential-energy surface to one obtained by using a semiempirical potential to initiate the sampling shows that the two potential surfaces are the same within the fitting accuracy of the surfaces. It is concluded that the combination of direct dynamics, molecular dynamics, novelty sampling, and neural network fitting provides a self-starting, robust, and accurate DD/MD/NS/NN method for the execution of first-principles, ab initio, molecular dynamics studies in systems containing four or more atoms which are undergoing simultaneous two-, three-, and four-center reactions.

  16. Ab initio calculation of electronic structure, crystal field, and intrinsic magnetic properties of Sm2Fe17, Sm2Fe17N3, Sm2Fe17C3, and Sm2Co17

    Science.gov (United States)

    Steinbeck, Lutz; Richter, Manuel; Nitzsche, Ulrike; Eschrig, Helmut

    1996-03-01

    In a comparative study we calculated the spin and orbital moments, spin and charge densities, and 4f crystal field (CF) parameters of the rare-earth transition-metal intermetallics Sm2Fe17, Sm2Fe17Z3 (Z=C,N), and Sm2Co17 using a relativistic optimized linear combination of atomic orbitals method. The itinerant valence electron states were treated in the local-spin-density approximation (LSDA), whereas the localized 4f states were described as open core states within the self-interaction-corrected LSDA. The calculations yield magnetic moments in good agreement with experiment. While all local moments of Sm2Fe17 increase upon lattice expansion, the moments of atoms neighboring the interstitial sites decrease and those of more distant Fe atoms increase upon insertion of interstitial N or C. In N interstitial atoms all 2pα orbitals are polarized antiparallel to their respective Fe and Sm neighbor atoms in the bond direction, whereas in C all 2pα orbitals are polarized antiparallel to the Fe atoms neighboring the interstitial site. The second-order CF parameters A02 dominating the rare-earth magnetocrystalline anisotropy are found to have the same sign and order of magnitude as those derived from magnetization data. In accordance with experiment the calculated negative A02 is larger for the Co compound than for the Fe parent compound and is strongly increased upon insertion of interstitial N or C. The agreement between theory and experiment is improved by taking into account the CF contribution arising from the asphericity of the exchange-correlation potential of the non-4f states.

  17. The Structure, Dynamics and Electronic Structure of Liquid Ag-Se Alloys Investigated by ab initio Simulation

    CERN Document Server

    Kirchhoff, F; Gillan, M J

    1996-01-01

    Ab initio molecular-dynamics simulations have been used to investigate the structure, dynamics and electronic properties of the liquid alloy Ag(1-x)Se(x) at 1350 K and at the three compositions x=0.33, 0.42 and 0.65. The calculations are based on density-functional theory in the local density approximation and on the pseudopotential plane-wave method. The reliability of the simulations is confirmed by detailed comparisons with very recent neutron diffraction results for the partial structure factors and radial distribution functions (RDF) of the stoichiometric liquid Ag2Se. The simulations show a dramatic change of the Se-Se RDF with increasing Se content. This change is due to the formation of Se clusters bound by covalent bonds, the Se-Se bond length being almost the same as in pure c-Se and l-Se. The clusters are predominantly chain-like, but for higher x a large fraction of 3-fold coordinated Se atoms is also found. It is shown that the equilibrium fractions of Se present as isolated atoms and in clusters...

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

    Science.gov (United States)

    Petrenko, Y M

    2015-01-01

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

  19. AB-INITIO SOLUTION OF MISFIT LAYER STRUCTURES BY AUTOMATIC PATTERSON AND DIRECT-METHODS

    NARCIS (Netherlands)

    BEURSKENS, PT; BEURSKENS, G; LAM, EJW; VANSMAALEN, S; FAN, HF

    1994-01-01

    A procedure is presented for the automatic solution of composite (misfit) layer compounds, for the case when the composite crystal structure consists of two types of layer, each of which can be approximately described as a three-dimensional periodic structure with, however, mutually incommensurate l

  20. Surface structure of CdSe Nanorods revealed by combined X-rayabsorption fine structure measurements and ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois; Galli, Giulia; Alivisatos, A. Paul

    2006-01-27

    We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.

  1. Ab initio prediction of the polymorphic structures of pyrazinamide: A validation study

    Directory of Open Access Journals (Sweden)

    David Stephen Arputhara

    2016-01-01

    Full Text Available A validation study to predict the possible stable polymorphs of Pyrazinamide within a low energy conformational region of the flexible torsion angle was made through a potential energy surface (PES scan by gas phase optimisation using the MP2/6-31G(d,p method. Hypothetical crystal structures with favourable packing density for each of the stable conformers generated from the PES scan were generated using a global search with a repulsion only potential field. The densest crystal structures with stable energy were analyzed with more accurate lattice energy minimisation via distributed multipole analysis using a repulsion-dispersion potential. The stability of the predicted crystal structures with similar close packing to the known experimental polymorphs of Pyrazinamide molecule was analyzed by inspecting their intermolecular short contacts. Studies to analyze the second derivative mechanical properties from the hessian matrix were carried out to emphasise the thermodynamic stability of predicted polymorphs of Pyrazinamide.

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

    Science.gov (United States)

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

    2007-07-01

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

  3. Structure electronique de nanorubans de graphene avec des contacts metalliques: Une etude ab initio

    Science.gov (United States)

    Archambault, Chloe

    Graphene, a graphite monolayer presenting novel exciting properties, has attracted much attention recently in the scientific community as well as in the high-technology industry. In electronics, nanoribbons -- narrow strips of graphene which happen to be semiconducting-- could possibly allow further miniaturization of electronic devices such as transistors because of their atomic thickness. On the other hand, once making devices, the problem of metallic contacts, which can have critical impact at the nanoscopic scale, cannot be evaded. For example, metal induced gap states may short-circuit very short devices. With this in mind, the interaction of gold, palladium and titanium contacts with finite size graphene nanoribbons has been studied using ab initio density functional theory calculations. This theoretical approach made it possible to study separately and then conjugate four important aspects of the metal-ribbon interaction: bonding, charge transfer, electrostatics and metal induced gap states. Another goal of this project was to study size effects related to the ribbons' dimensions and to estimate the minimal channel length necessary for a device to operate as expected without the unwanted effect of induced gap states. Aside from the high precision achieved, these calculations stand out from earlier studies because they take into account finite size effects which often prevail in small ribbons. Using this model for the metal-nanoribbon junction, it was shown that, as for two-dimensional graphene, the bonding between a ribbon and a metal can be of two types depending on the electronic configuration of the metal. In the first case, physisorption, weak bonding resulting in a large separation distance between ribbon and electrode, is illustrated by the gold contact. On the other hand, titanium, because of its high density of states at the Fermi level, binds more strongly with graphene nanoribbons. This chemisorption is characterized by strong hybridization between

  4. Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

    2011-04-18

    An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.

  5. Competing structural ordering tendencies in new high-TC ferromagnetic Fe-Co-based Heusler alloys from ab initio investigations

    Energy Technology Data Exchange (ETDEWEB)

    Dannenberg, Antje; Gruner, Markus; Entel, Peter [Faculty of Physics, University of Duisburg-Essen, 47048 Duisburg (Germany); Wuttig, Manfred [Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742 (United States)

    2011-07-01

    Fe-Co-based Heuslers are candidates for new ferromagnetic shape memory alloys (FSMA) as they promise higher operation temperatures compared with prototype Ni2MnGa. Of interest are also the corresponding binary systems FeZn and Fe3Ga which show a huge magnetostriction. We present results of ab initio and Monte Carlo calculations regarding structural, magnetic, and electronic properties of Fe2CoGa1-xZnx alloys in conventional X2YZ and inverse (XY)XZ Heusler structures. All systems exhibit high Curie temperatures TC. The preference of the cubic inverse structures is believed to originate from the bcc-like environment of two inequivalent Fe atoms and their strong hybridization with the Co- states. Weakening the Co-Fe hybridization by substitution of Ga by Zn reduces this preference and leads to higher TC but simultaneously reduces the miscibility. Despite the strong spin-dependent Fe-Co hybridization we find a localized character of the spin moments. Extraordinary Z-elements like Cu, Ag, and Au or further enhancement of the Zn content induces a martensitic instability also in the inverse structures. Thus, we conclude that it is possible to find new FSMA with rather high Curie temperatures.

  6. An ab initio study of the structural, elastic, electronic and optical properties of the newly synthesized nitridoaluminate LiCaAlN2

    Science.gov (United States)

    Haddadi, K.; Bouhemadou, A.; Bin-Omran, S.; Maabed, S.; Khenata, R.

    2015-01-01

    The structural parameters, elastic constants, electronic structure and optical properties of the recently reported monoclinic quaternary nitridoaluminate LiCaAlN2 are investigated in detail using the ab initio plane-wave pseudopotential method within the generalized gradient approximation. The calculated equilibrium structural parameters are in excellent agreement with the experimental data, which validate the reliability of the applied theoretical method. The chemical and structural stabilities of LiCaAlN2 are confirmed by calculating the cohesion energy and enthalpy of formation. Chemical band stiffness is calculated to explain the pressure dependence of the lattice parameters. Through the band structure calculation, LiCaAlN2 is predicted to be an indirect band gap of 2.725 eV. The charge-carrier effective masses are estimated from the band structure dispersions. The frequency-dependent dielectric function, absorption coefficient, refractive index, extinction coefficient, reflectivity coefficient and electron energy loss function spectra are calculated for polarized incident light in a wide energy range. Optical spectra exhibit a noticeable anisotropy. Single-crystal and polycrystalline elastic constants and related properties, including isotropic sound velocities and Debye temperatures, are numerically estimated. The calculated elastic constants and elastic compliances are used to analyse and visualize the elastic anisotropy of LiCaAlN2. The calculated elastic constants demonstrate the mechanical stability and brittle behaviour of the considered material.

  7. A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in FIREBALL

    Science.gov (United States)

    Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.

    2009-03-01

    FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_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.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are

  8. Ab initio Study of the Structural, Tautomeric, Pairing and Electronic Properties of Seleno-Derivatives of Thymine

    Energy Technology Data Exchange (ETDEWEB)

    Vazquez-Mayagoitia, Alvaro [ORNL; Fuentes-Cabrera, Miguel A [ORNL; Sumpter, Bobby G [ORNL; Luque, Javier [Universitat de Barcelona; Huertas, Oscar [Universitat de Barcelona; Orozco, Modesto [Institut de Recerca Biomedica, Parc Cientific de Barcelona, Barcelona, Spain; Felice, Rosa [INFM-CNR National Research Center S3; Brancolini, Giorgia [ORNL; Migliore, Agostino [University of Pennsylvania

    2009-01-01

    The structural, tautomeric, hydrogen-bonding, stacking and electronic properties of a seleno-derivative of thymine (T), denoted here as 4SeT and created by replacing O4 in T with Se, are investigated by means of ab initio computational techniques. The structural properties of T and 4SeT are very similar and the geometrical differences are mainly limited to the adjacent environment of the C-Se bond. The canonical keto form is the most stable tautomer, in gas phase and in aqueous solution, for both T and 4SeT. It is argued that the competition between two opposite trends, i.e. a decrease in the base-pairing ability and an increase of the stacking interaction upon incorporation of 4SeT into a duplex, likely explains the similar experimental melting points of a seleno-derivative duplex (Se-DNA) and its native counterpart. Interestingly, the underlying electronic structure shows that replacement of O4 with Se promotes a reduction in the HOMO-LUMO gap and an increase in inter-plane coupling, which suggests that Se-DNA could be potentially useful for nanodevice applications. This finding is further supported by the fact that transfer integrals between 4SeT---A stacked base pairs are larger than those determined for similarly stacked natural T---A pairs.

  9. The evolution of the structural, vibrational and electronic properties of the cyclic ethers - on ring size. An ab initio study

    Science.gov (United States)

    Ford, Thomas A.

    2014-09-01

    The molecular structures, vibrational spectra and atomic charges of the alicyclic ethers containing from two to five carbon atoms have been determined by means of ab initio calculations, at the level of second order Møller-Plesset perturbation theory and using Dunning's augmented correlation-consistent polarized valence triple-zeta basis set. Two isomers of the oxetane, tetrahydrofuran and tetrahydropyran molecules have been identified and their relative energies determined. Structural properties, such as the COC bond angles and the CH bond lengths, are found to increase steadily with increasing ring size and with decreasing ionization energy. The mean CH2 stretching and bending wavenumbers exhibit the reverse behaviour, while the mean wavenumbers of the CH2 wagging and twisting modes follow the same trend as the structural features. The ring mode wavenumbers vary in a less regular way. The charges of the oxygen, α-carbon and axial and equatorial α- and β-hydrogen atoms also do not show systematic dependences on ring size or ionization energy. The trends in the values of these properties have been rationalized.

  10. Structural characterization of tellurite glasses doped with transition metal oxides using Raman spectra and ab initio calculations

    Science.gov (United States)

    Mohamed, Tarek A.; Shaltout, I.; Al Yahyaei, K. M.

    2006-05-01

    Systems of iron tellurite glasses were prepared by melt quenching with compositions of [85%TeO 2 + 5%Fe 2O 3 + 10%TMO], where transition metal oxides (TMO) are TiO 2, V 2O 5, MnO, CoO, NiO and CuO. Furthermore, the main structural units of these samples have been characterized by means of Raman spectra (150-1200 cm -1) as well as wavenumber predictions by means of Gaussian 98 ab initio calculations for the proposed site symmetries of TeO 44- triagonal bipyramid ( C2v) and Te 2O 76- bridged tetrahedra ( Cs and C1). Aided by normal coordinate analysis, calculated vibrational frequencies, Raman scattering activities, force constants in internal coordinates and potential energy distributions (PEDs), revised vibrational assignments for the fundamental modes have been proposed. The main structural features are correlated to the dominant units of triagonal bipyramid (tbp) or bridged tetrahedral (TeO 3+1 binds to TeO 3 through TeOTe bridge; corner sharing). Moreover, the Raman spectra of the investigated tellurites reflect a structural change from tbp (coordination number is four) to triagonal pyramidal (coordination number is three).

  11. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

    Science.gov (United States)

    Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

    2016-09-21

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

  12. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    Science.gov (United States)

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362

  13. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO-

    Science.gov (United States)

    Roy, Soumendra K.; Jian, Tian; Lopez, Gary V.; Li, Wei-Li; Su, Jing; Bross, David H.; Peterson, Kirk A.; Wang, Lai-Sheng; Li, Jun

    2016-02-01

    The observation of the gaseous UFO- anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO- is linear with an O-U-F structure and a 3H4 spectral term derived from a U 7sσ25fφ15fδ1 electron configuration, whereas the ground state of neutral UFO has a 4H7/2 spectral term with a U 7sσ15fφ15fδ1 electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.

  14. Structural and dynamical properties of hydrogen fluoride in aqueous solution: an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Hofer, Thomas S; Rode, Bernd M

    2008-09-25

    The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.

  15. Experimental and ab initio molecular dynamics study of the structure and physical properties of liquid GeTe

    Science.gov (United States)

    Weber, Hans; Schumacher, Mathias; Jóvári, Pál; Tsuchiya, Yoshimi; Skrotzki, Werner; Mazzarello, Riccardo; Kaban, Ivan

    2017-08-01

    GeTe is a prototypical phase-change material employed in data storage devices. In this work, the atomic structure of liquid GeTe is studied by x-ray and neutron diffraction in the temperature range from 1197 to 998 K. The dynamic viscosity is measured from 1273 to 953 K, which is 55 K below the solidification point, using an oscillating-cup viscometer. The density of liquid GeTe between 1293 and 973 K is determined by the high-energy γ -ray attenuation method. The experiments are complemented with ab initio molecular dynamics (AIMD) simulations based on density functional theory (DFT). Compatibility of the AIMD-DFT models with the diffraction data is proven by simultaneous fitting of all data sets in the frame of the reverse Monte Carlo simulation technique. It is shown that octahedral order dominates in liquid GeTe, although tetrahedral structures are also present. The viscosity of the equilibrium and weakly undercooled liquid GeTe obeys the Arrhenius law with a small activation energy of the order of 0.3 eV, which is indicative of a highly fragile liquid. The calculated density of states and electronic wave functions point to the existence of a pseudogap and localized electron states within the gap in the equilibrium liquid near the melting point as well as in the undercooled liquid.

  16. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott (Michigan); (Kansas); (HWMRI)

    2012-02-13

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

  17. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu60Ti20Zr20 alloy

    Science.gov (United States)

    Amokrane, S.; Ayadim, A.; Levrel, L.

    2015-11-01

    We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.

  18. AB initio calculations of the structure and stability of the non-rigid LiBF 4 molecule

    Science.gov (United States)

    Zakzhevzskii, V. G.; Boldyrev, A. I.; Charkin, O. P.

    1980-07-01

    Ab initio calculations of the potential energy surface, equilibrium geometry and energetic stability of the non-rigid LiBF4 molecule have been performed using the basis sets of Roos and Siegbahn, and Huzinaga and Dunning in a doublezeta contraction. The results are compared with similar ab initio data for LiBH 4, LiAlH 4, LiBeH -4, LiCH +4, Li 2 F 2, and LiBeF 3 ‡The geometry of the most disadvantageous configuration (m) was not optimized completely

  19. Structural phase transitions in Ruddlesden-Popper phases of strontium titanate: {\\em ab initio} and inhomogeneous Ginzburg-Landau approaches

    CERN Document Server

    Lee, Jeehye

    2010-01-01

    We present the first systematic {\\em ab initio} study of anti-ferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr$_{1+n}$Ti$_n$O$_{3n+1}$, as a function of both compressive epitaxial strain and phase number $n$. We find all RP phases to exhibit AFD order under a significant range of strains, recovering the bulk AFD order as $\\sim 1/n^2$. A Ginzburg-Landau Hamiltonian generalized to include inter-octahedral interactions reproduces our {\\em ab initio} results well, opening a pathway to understanding other nanostructured perovskite systems.

  20. On the structure of crystalline and molten cryolite: Insights from the ab initio molecular dynamics in NpT ensemble

    Science.gov (United States)

    Bučko, Tomáš; Šimko, František

    2016-02-01

    Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F- ions observed in X-ray diffraction experiments. The isolated AlF63-, AlF52-, AlF4-, as well as the bridged Al 2 Fm 6 - m ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5 2 - has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn 3 - n species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment.

  1. Multi-scale modelling of radiation damage in Fe-Cr based on ab initio electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, Paer

    2004-04-01

    The efficiency of fast neutron reactors, such as for fusion, breeding and transmutation, depend strongly on the neutron radiation resistance of the materials used in the reactors. The binary Fe-Cr alloy, which has many attractive properties in this regard, is the base for the best steels of today which are, however, still not up to the required standards. Therefore, substantial effort has been devoted to finding new materials that can cope with the demands better. Experimental studies must be complemented with extensive theoretical modelling in order to understand the effects that different alloying elements has on the resistance properties of materials. To this end, the first steps of multi-scale modelling has been taken, starting out with ab initio calculations of the electronic structure of the complete concentration range range of the disordered binary Fe-C alloy. The mixing enthalpy of Fe-Cr has been quantitatively predicted and has, together with data from literature, been used in order to fit two sets of interatomic potentials for the purpose of simulating defect evolution with molecular dynamics and kinetic Monte-Carlo codes. These dedicated Fe-Cr alloy potentials are new and represent important additions to the pure element potentials that can be found in literature.

  2. Electronic structure of TiO{sub 2} rutile with oxygen vacancies: Ab initio simulations and comparison with the experiment

    Energy Technology Data Exchange (ETDEWEB)

    Perevalov, T. V., E-mail: timson@isp.nsc.ru; Gritsenko, V. A., E-mail: grits@isp.nsc.ru [Russian Academy of Sciences, Institute of Semiconductor Physics, Siberian Branch (Russian Federation)

    2011-02-15

    The electronic structure of TiO{sub 2} rutile with oxygen vacancies, which is a promising insulator, has been analyzed. The ab initio density functional calculations, as well as the comparative analysis of the results obtained in the {sigma}-GGA spin-polarized generalized approximation and those obtained by the {sigma}-GGA + U method with allowance for Coulomb correlations of d electrons titanium atoms in the Hartree-Fock approximation for the Hubbard model, have been performed. It has been found that the effective electron mass in rutile is anisotropic and there are both light (m{sub e}{sup *} = (0.6-0.8)m{sub 0}, where m{sub 0} is the free-electron mass) and heavy (m{sub e}* > 1m{sub 0}) electrons, whereas holes in rutile are only heavy (m{sub e}* Greater-Than-Or-Slanted-Equal-To 2m{sub 0}). It has been shown that the {sigma}-GGA + U method gives a deep occupied level in the band gap and that an oxygen vacancy in rutile is an electron and hole trap.

  3. The infrared spectra and structure of acetylsalicylic acid (aspirin) and its oxyanion: an ab initio force field treatment

    Science.gov (United States)

    Binev, I. G.; Stamboliyska, B. A.; Binev, Y. I.

    1996-05-01

    The structures of acetylsalicylic acid (aspirin) (I) and its oxyanion (II) have been studied by means of infrared spectra and ab initio 3-21 G force field calculations. The 3100-1100 cm -1 region bands of both the aspirin molecule and its oxyanion have been assigned. The theoretical infrared data for the free aspirin anion are in good agreement with the experimental data for aspirin alkali-metal salts in dimethyl sulfoxide- d6. The theoretical geometrical parameters for the isolated aspirin molecule are close to the literature X-ray diffraction data for its dimer in the solid state, except for those of the carboxy group, which participates directly in hydrogen bond formation. The changes in both the spectral and geometrical parameters, caused by the conversion of the aspirin molecule into the anion, are essential, but they are localized mainly within the carboxy group and the adjacent C-Ph bond. This is also true for the changes in the corresponding bond indices and electronic charges.

  4. {ital Ab initio} electronic structure, magnetism, and magnetocrystalline anisotropy of UGa{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Divis, M. [Department of Metal Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic)]|[Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany); Richter, M.; Eschrig, H.; Steinbeck, L. [Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany)

    1996-04-01

    {ital Ab} {ital initio} electronic structure calculations for the intermetallic compound UGa{sub 2} were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5{ital f} states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5{ital f} states, which have been treated by self-interaction corrected local-density theory. This approach with 5{ital f}{sup 2} occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant. {copyright} {ital 1996 The American Physical Society.}

  5. Ab initio powder structure analysis and theoretical study of two thiazole derivatives

    Science.gov (United States)

    Hazra, Dipak K.; Mukherjee, Monika; Mukherjee, Alok K.

    2013-05-01

    Crystal structures of 2-amino-5-methylthiazole (1) and 4-(6-methyl-2-benzothiazolyl) aniline (2) have been determined from laboratory X-ray powder diffraction data along with an analysis of the Hirshfeld surfaces and 2D-fingerprint plots, facilitating a comparison of intermolecular interactions. The DFT optimized molecular geometries in (1) and (2) agree closely with those obtained from the crystallographic studies. An interplay of Nsbnd H⋯N/S hydrogen bonds and C/Nsbnd H⋯π interactions connects the molecules of (1) and (2) into two-dimensional framework. Hirshfeld surface analysis of (1) indicates that the H⋯H and H⋯π contacts can account for 56.9% of the Hirshfeld surface area, whereas the corresponding fraction in (2) is 80.5%.

  6. Ab-initio study of structural and electronic properties of AlAs

    Science.gov (United States)

    Munjal, N.; Sharma, G.; Vyas, V.; Joshi, K. B.; Sharma, B. K.

    2012-08-01

    The structural properties, i.e. equilibrium lattice constant, transition pressure, bulk modulus and its pressure derivatives, together with electronic properties, i.e. energy bands, Compton profile and autocorrelation function, of AlAs are presented in this work. The linear combination of atomic orbitals (LCAO) method of the CRYSTAL code was applied considering the Perdew-Burke-Ernzerhof correlation energy functional and Becke's ansatz for the exchange. The total energy of AlAs as a function of primitive cell volume has also been calculated for the zincblende (B3), nickel arsenide (B8), sodium chloride (B1) and cesium chloride (B2) phases. Structural parameters of the B3, B8, B1 and B2 phases are determined. The calculated structural parameters are found to be in good agreement with the results of previous investigations. The spherically averaged theoretical values of Compton profile are in good agreement with an earlier measurement. The LCAO calculation shows an indirect band gap of 1.85 eV, in reasonable agreement with earlier data. On the basis of the equal-valence-electron-density Compton profile, it is found that AlAs is more ionic compared to AlSb.

  7. Structure and lattice dynamics of GaN and AlN. Ab-initio investigations of strained polytypes and superlattices

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Jan-Martin

    2004-10-14

    In this dissertation, ab-initio investigations of the strain influence on vibrational properties of GaN and AlN as well as of short-period GaN/AlN superlattices are presented. Based on densityfunctional theory and density-functional perturbation theory, for differently strained structures complete phonon spectra and related properties are calculated using the local-density approximation and norm-conserving pseudopotentials. (orig.)

  8. Orbital-free ab initio molecular dynamics study of the static structure and dynamic properties of the free liquid surface of Sn

    Directory of Open Access Journals (Sweden)

    del Rio B. G.

    2017-01-01

    Full Text Available We report results of an orbital-free ab initio molecular dynamics (OF-AIMD study of the free liquid surface (FLS of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.

  9. Orbital-free ab initio molecular dynamics study of the static structure and dynamic properties of the free liquid surface of Sn

    Science.gov (United States)

    del Rio, B. G.; González, L. E.

    2017-08-01

    We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface (FLS) of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.

  10. Core structure of screw dislocations in Fe from first-principles; Simulation ab initio des coeurs de dislocation vis dans le fer

    Energy Technology Data Exchange (ETDEWEB)

    Ventelon, L

    2008-11-15

    The various methods appropriate for the simulation of dislocations within first-principles calculations have been set up, improved and compared between them. They have been applied to study screw dislocations in body-centered cubic iron using the SIESTA code. A non-degenerate core structure is obtained; its detailed analysis reveals a dilatation effect. Taking it into account in an anisotropic elasticity model, allows explaining the cell-size dependence of the energetics, obtained within the dipole approach. The Peierls potential obtained in ab initio suggests that the metastable core configuration at halfway position in the Peierls barrier, predicted by empirical potential, does not exist. We show how to construct tri-periodic cells optimized to study kinked dislocations. Using empirical potential, we demonstrate the feasibility of ab initio calculations of Peierls stress and kink formation. (author)

  11. Structural, electronic and energetic properties of giant icosahedral fullerenes up to C6000: insights from an ab initio hybrid DFT study.

    Science.gov (United States)

    Noël, Yves; De La Pierre, Marco; Zicovich-Wilson, Claudio M; Orlando, Roberto; Dovesi, Roberto

    2014-07-14

    The properties of the (n,n) icosahedral family of carbon fullerenes up to n = 10 (6000 atoms) have been investigated through ab initio quantum-mechanical simulation by using a Gaussian type basis set of double zeta quality with polarization functions (84,000 atomic orbitals for the largest case), the hybrid B3LYP functional and the CRYSTAL14 code featuring generalization of symmetry treatment. The geometry of giant fullerenes shows hybrid features, between a polyhedron and a sphere; as n increases, it approaches the former. Hexagon rings at face centres take a planar, graphene-like configuration; the 12 pentagon rings at vertices impose, however, a severe structural constraint to which hexagon rings at the edges must adapt smoothly, adopting a bent (rather than sharp) transversal profile and an inward longitudinal curvature. The HOMO and LUMO electronic levels, as well as the band gap, are well described using power laws. The gap is predicted to become zero for n ≥ 34 (69,360 atoms). The atomic excess energy with respect to the ideal graphene sheet goes to zero following the log(Nat)/Nat law, which is well described through the continuum elastic theory applied to graphene; the limits for the adopted model are briefly outlined. Compared to larger fullerenes of the series, C60 shows unique features with respect to all the considered properties; C240 presents minor structural and energetic peculiarities, too.

  12. Ab initio valence calculations in chemistry

    CERN Document Server

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  13. Ab initio MO calculations on the Structure and Raman and Infrared Spectra of the [Al4O2Cl10]2- oxide species in chloroaluminate melts

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2007-01-01

    The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures that may be formed in addition to [AlCl4]-: [Al2OCl6]2-, [Al3OCl8]-, [Al2O2Cl4]2-, [Al3O2Cl6]- and [Al4O2Cl10]2-. Ab initio Molecular Orbital (MO) calculat......The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures that may be formed in addition to [AlCl4]-: [Al2OCl6]2-, [Al3OCl8]-, [Al2O2Cl4]2-, [Al3O2Cl6]- and [Al4O2Cl10]2-. Ab initio Molecular Orbital (MO...... system of staggered (approximate D3d symmetry), in analogy with the linear Al-O-Al geometry of the analogous [Al2OF6]2- ion, found previously. The calculations included determination of the vibrational harmonic normal modes and the infrared and Raman spectra, (vibrational band wavenumbers and intensities......), without any empiric adjustments of the harmonic force constants, using constants directly predicted from the Gaussian 03W program. Previously obtained IR absorption and Raman scattering spectra of melts are assigned, by comparing to the ab initio quantum mechanical vibrational analysis results...

  14. The electronic structure of MgO nanotubes. An ab initio quantum mechanical investigation.

    Science.gov (United States)

    El-Kelany, Khaled E; Ferrabone, Matteo; Rérat, Michel; Carbonnière, Philippe; Zicovich-Wilson, Claudio M; Dovesi, Roberto

    2013-08-28

    The structural, vibrational and response properties of the (n,0) and (m,m) MgO nanotubes are computed by using a Gaussian type basis set, a hybrid functional (B3LYP) and the CRYSTAL09 code. Tubes in the range 6 ≤ n ≤ 140 and 3 ≤ m ≤ 70 were considered, being n = 2 × m the number of MgO units in the unit cell (so, the maximum number of atoms is 280). Tubes are built by rolling up the fully relaxed 2-D conventional cell (2 MgO units, with oxygen atoms protruding from the Mg plane alternately up and down by 0.38 Å). The relative stability of the (n,0) with respect to the (m,m) family, the relaxation energy and equilibrium geometry, the band gap, the IR vibrational frequencies and intensities, and the electronic and ionic contributions to the polarizability are reported. All these properties are shown to converge smoothly to the monolayer values. Absence of negative vibrational frequencies confirms that the tubes have a stable structure. The parallel component of the polarizability α(∥) converges very rapidly to the monolayer value, whereas α(⊥) is still changing at n = 140; however, when extrapolated to very large n values, it coincides with the monolayer value to within 1%. The electronic contribution to α is in all cases (α(∥) and α(⊥); 6 ≤ n ≤ 140) smaller than the vibrational contribution by about a factor of three, at variance with respect to more covalent tubes such as the BN ones, for which the ratio between the two contributions is reversed.

  15. Ab initio calculations on 2-imidazolyl-2-thiazolyl azo compounds - an investigation of potential near-infrared absorbing structures

    DEFF Research Database (Denmark)

    Åstrand, P.-O.; Bak, K.L.; Sauer, S.P.A.

    2001-01-01

    The two lowest singlet excitation energies of 26 2-imidazolyl-2-thiazolylazo compounds have been investigated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Various combinations of 4- and 5-substituents at both the imidazole and thiazole units have bee...

  16. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

    NARCIS (Netherlands)

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

    1997-01-01

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

  17. Ab Initio Study of the Structure and Stability of High-Pressure Iron-Bearing Dolomite

    Science.gov (United States)

    Solomatova, N. V.; Asimow, P. D.

    2016-12-01

    Carbon is subducted into the mantle primarily in the form of metasomatically calcium-enriched basaltic rock, calcified serpentinites and carbonaceous ooze, all of which often contain dolomite. End-member CaMg(CO3)2 dolomite typically breaks down upon compression into two carbonates at 5-6 GPa in the temperature range of 800-1200 K [1]. However, high-pressure X-ray diffraction experiments have recently shown that the presence of iron may be sufficient to stabilize high-pressure dolomite over single-cation carbonates above 35 GPa [2,3]. The structure and equation of state of high-pressure dolomite phases have been debated, creating a need for theoretical calculations. Using density functional theory interfaced with a genetic algorithm that predicts crystal structures (USPEX), we have found a monoclinic phase with space group C2/c. The C2/c structure has a lower energy than previously reported dolomite structures at relevant pressures. It is possible that this phase is not achieved experimentally due to a large energy barrier and a correspondingly large required volume drop, resulting in the transformation to metastable dolomite II. We calculate the equation of state of trigonal dolomite, dolomite III and monoclinic C2/c dolomite to 80 GPa with 0 and 50 mol% CaFe(CO3)2 and compare their enthalpies to single-carbonate assemblages. Although end-member C2/c CaMg(CO3)2 dolomite is not stable relative to single-cation carbonates, C2/c CaMg0.5Fe0.5(CO3)2 is preferred over single-cation carbonates at high pressures. Thus, iron-bearing C2/c dolomite may be an important host phase for carbon in slabs subducted into the lower mantle. [1] Shirasaka, M., et al. (2002) American Mineralogist, 87, 922-930. [2] Mao, Z. et al. (2011) Geophysical Research Letters, 38. [3] Merlini, M. et al. (2012) Proceedings of the National Academy of Sciences, 109, 13509-13514.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-10-01

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

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

    Science.gov (United States)

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

    2014-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    DiStasio, Robert A.; Santra, Biswajit [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Li, Zhaofeng [Department of Physics, Princeton University, Princeton, New Jersey 08544 (United States); Wu, Xifan [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States); Car, Roberto [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Department of Physics, Princeton University, Princeton, New Jersey 08544 (United States); Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544 (United States); Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-08-28

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

  1. Theoretical study of the VUV spectroscopy of Ce3+ and Tb3+ in BaBPO5 crystal using an empirical-ab initio hybrid method

    Institute of Scientific and Technical Information of China (English)

    HU

    2010-01-01

    The f-d transition of Ce3+and Tb3+in BaBPO5 was studied theoretically using the parametric Hamiltonian model.In order to overcome the difficulty in determining many of the parameter values,we adopted the model-space effective Hamiltonian method to determine the crystal-field parameters and spin-orbit parameters values.The method made use of the energies and eigenvectors,which were obtained from an ab initio calculation using the relativistic self-consistent discrete variational Slater software package(DV-Xα).Other parameters,which were less dependent on host crystals,were taken from published data.The calculated values of parameters were reasonable,and the energy-levels and f-d transition spectra agreed reasonably well with the measured excitation spectra of 5d-4f emission.

  2. Calculation of the paramagnetic susceptibility and specific heat in UGa{sub 2} and UPd{sub 2}Al{sub 3} from ab initio crystal field theory

    Energy Technology Data Exchange (ETDEWEB)

    Richter, M.; Forstreuter, J.; Koepernik, K.; Eschrig, H. [Univ. of Technol., Dresden (Germany). MPG Res. Group Electron Systems; Divis, M. [Univ. of Technol., Dresden (Germany). MPG Res. Group Electron Systems]|[Karlova Univ., Prague (Czechoslovakia). Dept. of Metal Physics; Steinbeck, L. [Univ. of Technol., Dresden (Germany). MPG Res. Group Electron Systems]|[York Univ. (United Kingdom). Dept. of Physics

    1997-02-01

    In the framework of the self-interaction corrected local density approximation, ab initio calculations have been carried out to obtain crystal field parameters for the paramagnetic state of UGa{sub 2} and UPd{sub 2}Al{sub 3}. In two sets of calculations localized 5f states with occupation two and three, respectively, have been assumed. Using these parameters and adjusted anisotropic molecular field constants, the paramagnetic susceptibility for both compounds and the Schottky contribution to the specific heat in UPd{sub 2}Al{sub 3} have been obtained by crystal field model calculations. Very good agreement between theoretical and experimental data is found for 5f{sup 2} occupation in UGa{sub 2}. For UPd{sub 2}Al{sub 3}, the 5f{sup 2} assumption yields qualitatively reasonable results as well, but it does not explain the T = 50 K maximum in the experimental data. (orig.).

  3. Calculation of the paramagnetic susceptibility and specific heat in UGa 2 and UPd 2Al 3 from ab initio crystal field theory

    Science.gov (United States)

    Richter, Manuel; Diviš, Martin; Forstreuter, Jörg; Koepernik, Klaus; Steinbeck, Lutz; Eschrig, Helmut

    1997-02-01

    In the framework of the self-interaction corrected local density approximation, ab initio calculations have been carried out to obtain crystal field parameters for the paramagnetic state of UGa 2 and UPd 2Al 3. In two sets of calculations localized 5f states with occupation two and three, respectively, have been assumed. Using these parameters and adjusted anisotropic molecular field constants, the paramagnetic susceptibility for both compounds and the Schottky contribution to the specific heat in UPd 2Al 3 have been obtained by crystal field model calculations. Very good agreement between theoretical and experimental data is found for 5f 2 occupation in UGa 2. For UPd 2Al 3, the 5f 2 assumption yields qualitatively reasonable results as well, but it does not explain the T = 50 K maximum in the experimental data.

  4. Ab initio localized basis set study of structural parameters and elastic properties of HfO{sub 2} polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Caravaca, M A [Facultad de Ingenieria, Universidad Nacional del Nordeste, Avenida Las Heras 727, 3500-Resistencia (Argentina); Casali, R A [Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad, 5600-Corrientes (Argentina)

    2005-09-21

    The SIESTA approach based on pseudopotentials and a localized basis set is used to calculate the electronic, elastic and equilibrium properties of P 2{sub 1}/c, Pbca, Pnma, Fm3m, P4{sub 2}nmc and Pa3 phases of HfO{sub 2}. Using separable Troullier-Martins norm-conserving pseudopotentials which include partial core corrections for Hf, we tested important physical properties as a function of the basis set size, grid size and cut-off ratio of the pseudo-atomic orbitals (PAOs). We found that calculations in this oxide with the LDA approach and using a minimal basis set (simple zeta, SZ) improve calculated phase transition pressures with respect to the double-zeta basis set and LDA (DZ-LDA), and show similar accuracy to that determined with the PPPW and GGA approach. Still, the equilibrium volumes and structural properties calculated with SZ-LDA compare better with experiments than the GGA approach. The bandgaps and elastic and structural properties calculated with DZ-LDA are accurate in agreement with previous state of the art ab initio calculations and experimental evidence and cannot be improved with a polarized basis set. These calculated properties show low sensitivity to the PAO localization parameter range between 40 and 100 meV. However, this is not true for the relative energy, which improves upon decrease of the mentioned parameter. We found a non-linear behaviour in the lattice parameters with pressure in the P 2{sub 1}/c phase, showing a discontinuity of the derivative of the a lattice parameter with respect to external pressure, as found in experiments. The common enthalpy values calculated with the minimal basis set give pressure transitions of 3.3 and 10.8?GPa for P2{sub 1}/c {yields} Pbca and Pbca {yields} Pnma, respectively, in accordance with different high pressure experimental values.

  5. A combined photoelectron spectroscopy and relativistic ab initio studies of the electronic structures of UFO and UFO(-).

    Science.gov (United States)

    Roy, Soumendra K; Jian, Tian; Lopez, Gary V; Li, Wei-Li; Su, Jing; Bross, David H; Peterson, Kirk A; Wang, Lai-Sheng; Li, Jun

    2016-02-28

    The observation of the gaseous UFO(-) anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO(-) is linear with an O-U-F structure and a (3)H4 spectral term derived from a U 7sσ(2)5fφ(1)5fδ(1) electron configuration, whereas the ground state of neutral UFO has a (4)H(7/2) spectral term with a U 7sσ(1)5fφ(1)5fδ(1) electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.

  6. Free Energies for Degradation Reactions of 1,2,3-Trichloropropane from ab initio Electronic Structure Theory

    Energy Technology Data Exchange (ETDEWEB)

    Bylaska, Eric J.; Glaesemann, Kurt R.; Felmy, Andrew R.; Vasiliu, Monica; Dixon, David A.; Tratnyek, P. G.

    2010-11-25

    Electronic structure methods were used to calculate the gas-phase and aqueous phase reaction energies for reductive dechlorination (i.e. hydrogenolysis), reductive Beta-elimination, dehydrochlorination, and nucleophilic substitution by OH- of 1,2,3-trichloropropane. The thermochemical properties Delta Hof(298.15K), So(298.15K,1 bar), and Delta GS(298.15K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely metabolites. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive Beta-elimination (Delta Gorxn ≈ -32 kcal/mol), followed closely by reductive dechlorination (Delta Gorxn ≈ -27 kcal/mol), dehydrochlorination (Delta Gorxn ≈ -27kcal/mol), and nucleophilic substitution by OH- (Delta Gorxn ≈ -25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate CH2-CHCl-CH2Cl , and CH2Cl-CH-CH2Cl species, was not favorable in the standard state (Delta Gorxn ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely.

  7. Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study.

    Science.gov (United States)

    Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M

    2015-02-14

    The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter

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

    Science.gov (United States)

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

    2012-08-01

    Zinc(II) and copper(II) complexes of a tridentate Mannich base L1 derived from 2-hydroxy-1,4-naphthoquinone, pyridinecarboxyaldehyde and 2-aminomethylpyridine, [ZnL1Cl(2)]·H(2)O 1 and [CuL1Cl(2)]·2H(2)O 2, have been synthesized and fully characterized. The structure of complex 1 has been elucidated by a single crystal X-ray diffraction study: the zinc atom is pentacoordinate and the coordination geometry is a distorted square base pyramid, with a geometric structural parameter τ equal to 0.149. Vibrational spectroscopy and ab initio DFT calculations of both compounds have confirmed that the two complexes exhibit similar structures. Full assignment of the vibrational spectra was also supported by careful analysis of the distorted geometries generated by the normal modes. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Pressure induced structural phase transition in SnS—An ab initio study

    Indian Academy of Sciences (India)

    M Rajagopalan; G Kalpana; V Priyamvadha

    2006-02-01

    The structural behaviour of SnS under pressure has been investigated by first principle density functional calculations of the total energy by the TB–LMTO approach. We find that SnS undergoes a structural phase transition from orthorhombic type to monoclinic type structure around 17 GPa which is in good agreement with the recent experimental study. In addition, the ground state properties are computed and compared with the available results.

  10. Raman spectra and ab initio calculation of a structure of aqueous solutions of methanol

    Science.gov (United States)

    Hushvaktov, H. A.; Tukhvatullin, F. H.; Jumabaev, A.; Tashkenbaev, U. N.; Absanov, A. A.; Hudoyberdiev, B. G.; Kuyliev, B.

    2017-03-01

    Small amount of low molecular weight alcohols leads to appearance of some special properties of alcohol-water solutions. In the literature it is associated with structural changes in solution with changing concentration. However, the problem special properties and structure of solutions at low concentration of alcohol is not very clear. Accordingly, we carried out quantum-chemical calculations and experimental studies of aqueous solutions of methyl alcohol. The calculations performed for ten molecular alcohol-water mixtures showed that with a low concentration of methyl alcohol in water the solubility of alcohol is poor: the alcohol molecules are displaced from the water structure and should form a particular structure. Thus, with low concentration of alcohol in the aqueous solution there are two types of structures: the structure of water and the structure of alcohol that should lead to the presence of specific properties. At high concentration of alcohol the structure of water is destroyed and there is just the structure made of alcohol-water aggregates. This interpretation is consistent with the experimental data of Raman spectroscopy. The band of Csbnd O vibrations of alcohol is detected to be of complex character just in the region of the presence of specific properties. Formation of intermolecular H-bonds also complicates the Raman spectra of Osbnd H or O-D vibrations of pure alcohol: a non-coincidence of peak frequencies, a shift of the band towards low-frequency region, a strong broadening of the band.

  11. Ab initio self-consistent x-ray absorption fine structure analysis for metalloproteins.

    Science.gov (United States)

    Dimakis, Nicholas; Bunker, Grant

    2006-12-01

    X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.

  12. The atomistic structure of yttria stabilised zirconia at 6.7 mol%: an ab initio study.

    Science.gov (United States)

    Parkes, Michael A; Tompsett, David A; d'Avezac, Mayeul; Offer, Gregory J; Brandon, Nigel P; Harrison, Nicholas M

    2016-11-16

    Yttria stabilized zirconia (YSZ) is an important oxide ion conductor used in solid oxide fuel cells, oxygen sensing devices, and for oxygen separation. Doping pure zirconia (ZrO2) with yttria (Y2O3) stabilizes the cubic structure against phonon induced distortions and this facilitates high oxide ion conductivity. The local atomic structure of the dopant is, however, not fully understood. X-ray and neutron diffraction experiments have established that, for dopant concentrations below 40 mol% Y2O3, no long range order is established. A variety of local structures have been suggested on the basis of theoretical and computational models of dopant energetics. These studies have been restricted by the difficulty of establishing force field models with predictive accuracy or exploring the large space of dopant configurations with first principles theory. In the current study a comprehensive search for all symmetry independent configurations (2857 candidates) is performed for 6.7 mol% YSZ modelled in a 2 × 2 × 2 periodic supercell using gradient corrected density functional theory. The lowest energy dopant structures are found to have oxygen vacancy pairs preferentially aligned along the 〈210〉 crystallographic direction in contrast to previous results which have suggested that orientation along the 〈111〉 orientation is favourable. Analysis of the defect structures suggests that the Y(3+)-Ovac interatomic separation is an important parameter for determining the relative configurational energies. Current force field models are found to be poor predictors of the lowest energy structures. It is suggested that the energies from a simple point charge model evaluated at unrelaxed geometries is actually a better descriptor of the energy ordering of dopant structures. Using these observations a pragmatic procedure for identifying low energy structures in more complicated material models is suggested. Calculation of the oxygen vacancy migration activation energies within

  13. Electronic structure calculations of rare-earth intermetallic compound YAg using ab initio methods

    Institute of Scientific and Technical Information of China (English)

    (S).U(g)ur; G.U(g)ur; F.Soyalp; R.Ellialtio(g)lu

    2009-01-01

    The structural,elastic and electronic properties of YAg-B2(CsC1) were investigated using the first-principles calculations.The energy band structure and the density of states were studied in detail,including partial density of states (PDOS),in order to identify the character of each band.The structural parameters (lattice constant,bulk modulus,pressure derivative of bulk modulus) and elastic constants were also obtained.The results were consistent with the experimental data available in the literature,as well as other theoretical results.

  14. Electronic structure and mechanical properties of ternary ZrTaN alloys studied by ab initio calculations and thin-film growth experiments

    Science.gov (United States)

    Abadias, G.; Kanoun, M. B.; Goumri-Said, S.; Koutsokeras, L.; Dub, S. N.; Djemia, Ph.

    2014-10-01

    The structure, phase stability, and mechanical properties of ternary alloys of the Zr-Ta-N system are investigated by combining thin-film growth and ab initio calculations. Zr1-xTaxN films with 0≤x≤1 were deposited by reactive magnetron cosputtering in Ar +N2 plasma discharge and their structural properties characterized by x-ray diffraction. We considered both ordered and disordered alloys, using supercells and special quasirandom structure approaches, to account for different possible metal atom distributions on the cation sublattice. Density functional theory within the generalized gradient approximation was employed to calculate the electronic structure as well as predict the evolution of the lattice parameter and key mechanical properties, including single-crystal elastic constants and polycrystalline elastic moduli, of ternary Zr1-xTaxN compounds with cubic rocksalt structure. These calculated values are compared with experimental data from thin-film measurements using Brillouin light scattering and nanoindentation tests. We also study the validity of Vegard's empirical rule and the effect of growth-dependent stresses on the lattice parameter. The thermal stability of these Zr1-xTaxN films is also studied, based on their structural and mechanical response upon vacuum annealing at 850 °C for 3 h. Our findings demonstrate that Zr1-xTaxN alloys with Ta fraction 0.51⩽x⩽0.78 exhibit enhanced toughness, while retaining high hardness ˜30 GPa, as a result of increased valence electron concentration and phase stability tuning. Calculations performed for disordered or ordered structures both lead to the same conclusion regarding the mechanical behavior of these nitride alloys, in agreement with recent literature findings [H. Kindlund, D. G. Sangiovanni, L. Martinez-de-Olcoz, J. Lu, J. Jensen, J. Birch, I. Petrov, J. E. Greene, V. Chirita, and L. Hultman, APL Materials 1, 042104 (2013), 10.1063/1.4822440].

  15. Ab initio calculations of electronic structure of anatase TiO2

    Institute of Scientific and Technical Information of China (English)

    Chen Qiang; Cao Hong-Hong

    2004-01-01

    This paper presents the results of the self-consistent calculations on the electronic structure of anatase phase of TiO2. The calculations were performed using the full potential-linearized augmented plane wave method (FP-LAPW)in the framework of the density functional theory (DFT) with the generalized gradient approximation (GGA). The fully optimized structure, obtained by minimizing the total energy and atomic forces, is in good agreement with experiment.We also calculated the band structure and the density of states. In particular, the calculated band structure prefers an indirect transition between wlence and conduction bands of anatase TiO2, which may be helpful for clarifying the ambiguity in other theoretical works.

  16. Structural stability and masnetism of metastable Ni-Pt intermetallic compounds studied by ab initio calculation

    Institute of Scientific and Technical Information of China (English)

    CHE XingLai; LI diaHao; DAI Ye; LIU BaiXin

    2009-01-01

    The self-consistent electronic structure calculations were carried out with the accurate frozen-core full-potential projector augmented-wave method on 13 Ni-Pt intermetallic compounds of simple crys-talline structures, i.e. A15, D019, D03 and L12 Ni3Pt and NiPt3, and α-NiAs, B1, B2, L28, and L10 NiPt. The calculations reveal that the L12 Ni3Pt, L10 NiPt and L12 NiPt3 are energetically more stable than their respective competitive structures, indicating that the three structures may be formed in some appro-priate conditions. The obtained results match well with the experimental observation or other theory predictions. It is found that there is hybridization between Ni 3d and Pt 5d states, which may signifi-cantly affect the structural stability and magnetism of metastable Ni-Pt intermetallic compounds.

  17. Structural stability and magnetism of metastable Ni-Pt intermetallic compounds studied by ab initio calculation

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The self-consistent electronic structure calculations were carried out with the accurate frozen-core full-potential projector augmented-wave method on 13 Ni-Pt intermetallic compounds of simple crystalline structures,i.e. A15,D019,D03 and L12 Ni3Pt and NiPt3,and α-NiAs,B1,B2,L2a,and L10 NiPt. The calculations reveal that the L12 Ni3Pt,L10 NiPt and L12 NiPt3 are energetically more stable than their respective competitive structures,indicating that the three structures may be formed in some appropriate conditions. The obtained results match well with the experimental observation or other theory predictions. It is found that there is hybridization between Ni 3d and Pt 5d states,which may significantly affect the structural stability and magnetism of metastable Ni-Pt intermetallic compounds.

  18. An ab initio study of the electronic structure of indium and gallium chalcogenide bilayers

    Science.gov (United States)

    Ayadi, T.; Debbichi, L.; Said, M.; Lebègue, S.

    2017-09-01

    Using first principle calculations, we have studied the structural and electronic properties of two dimensional bilayers of indium and gallium chalcogenides. With density functional theory corrected for van der Waals interactions, the different modes of stacking were investigated in a systematic way, and several of them were found to compete in energy. Then, their band structures were obtained with the GW approximation and found to correspond to indirect bandgap semiconductors with a small dependency on the mode of stacking. Finally, by analysing the electron density, it appeared that GaSe-InS is a promising system for electron-hole separation.

  19. Ab-initio study of electronic structure and elastic properties of ZrC

    Science.gov (United States)

    Mund, H. S.; Ahuja, B. L.

    2016-05-01

    The electronic and elastic properties of ZrC have been investigated using the linear combination of atomic orbitals method within the framework of density functional theory. Different exchange-correlation functionals are taken into account within generalized gradient approximation. We have computed energy bands, density of states, elastic constants, bulk modulus, shear modulus, Young's modulus, Poisson's ratio, lattice parameters and pressure derivative of the bulk modulus by calculating ground state energy of the rock salt structure type ZrC.

  20. Ab-initio calculations of electronic structure and optical properties of TiAl alloy

    Science.gov (United States)

    Hussain, Altaf; Sikandar Hayat, Sardar; Choudhry, M. A.

    2011-05-01

    The electronic structures and optical properties of TiAl intermetallic alloy system are studied by the first-principle orthogonalized linear combination of atomic orbitals method. Results on the band structure, total and partial density of states, localization index, effective atomic charges, and optical conductivity are presented and discussed in detail. Total density of states spectra reveal that (near the Fermi level) the majority of the contribution is from Ti-3d states. The effective charge calculations show an average charge transfer of 0.52 electrons from Ti to Al in primitive cell calculations of TiAl alloy. On the other hand, calculations using supercell approach reveal an average charge transfer of 0.48 electrons from Ti to Al. The localization index calculations, of primitive cell as well as of supercell, show the presence of relatively localized states even above the Fermi level for this alloy. The calculated optical conductivity spectra of TiAl alloy are rich in structures, showing the highest peak at 5.73 eV for supercell calculations. Calculations of the imaginary part of the linear dielectric function show a prominent peak at 5.71 eV and a plateau in the range 1.1-3.5 eV.

  1. A comparative study of the reported performance of ab initio protein structure prediction algorithms.

    Science.gov (United States)

    Helles, Glennie

    2008-04-01

    Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades, many different algorithmic approaches have been attempted, and although progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power are simply insufficient to solve a problem of such high complexity. Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review, the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared. The average normalized r.m.s.d. scores reported range from 11.17 to 3.48. With a performance measure including both r.m.s.d. scores and CPU time, the currently best-performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings--protein representation and fragment assembly--were found to have definite positive influence on the running time and the predicted structures, respectively. There thus appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.

  2. Structure and energy of point defects in TiC: An ab initio study

    Science.gov (United States)

    Sun, Weiwei; Ehteshami, Hossein; Korzhavyi, Pavel A.

    2015-04-01

    We employ first-principles calculations to study the atomic and electronic structure of various point defects such as vacancies, interstitials, and antisites in the stoichiometric as well as slightly off-stoichiometric Ti1 -cCc (including both C-poor and C-rich compositions, 0.49 ≤c ≤0.51 ). The atomic structure analysis has revealed that both interstitial and antisite defects can exist in split conformations involving dumbbells. To characterize the electronic structure changes caused by a defect, we introduce differential density of states (dDOS) defined as a local perturbation of the density of states (DOS) on the defect site and its surrounding relative to the perfect TiC. This definition allows us to identify the DOS peaks characteristic of the studied defects in several conformations. So far, characteristic defect states have been discussed only in connection with carbon vacancies. Here, in particular, we have identified dDOS peaks of carbon interstitials and dumbbells, which can be used for experimental detection of such defects in TiC. The formation energies of point defects in TiC are derived in the framework of a grand-canonical formalism. Among the considered defects, carbon vacancies and interstitials are shown to have, respectively, the lowest and the second-lowest formation energies. Their formation energetics are consistent with the thermodynamic data on the phase stability of nonstoichiometric TiC. A cluster type of point defect is found to be next in energy, a titanium [100] dumbbell terminated by two carbon vacancies.

  3. Ab initio electronic structure studies in molecular spectroscopy and chemical thermodynamics

    Science.gov (United States)

    Partridge, Harry; Bauschlicher, Charles W.; Langhoff, Stephen R.

    1994-01-01

    This article provides an overview of the principal computational approaches to the electronic structure of molecules and their applications in the areas of spectroscopy and thermodynamics. The emphasis is on techniques that include electron correlation to a high level with extended basis sets. Applications in spectroscopy include radiative lifetimes, electronic state separations, and identification of new band systems. Applications in thermodynamics are focused on C-H, O-H, metal-oxygen, and metal ion-rare-gas binding energies. Future developments of computational methods and methods of exploiting new computer hardware are expected to significantly extend the range of systems that can be treated reliably.

  4. Ab initio investigations of the electronic structure of HeCH + and HeCH 2+

    Science.gov (United States)

    Hughes, Jason M.; von Nagy-Felsobuki, Ellak I.

    1997-07-01

    The 1A' and 3A″ electronic states of HeCH + and the 2A' ground electronic state of HeCH 2+ have been investigated using an all electron coupled cluster single, double and triple excitation [CCSD(T)] method coupled with an augmented correlation-consistent polarised core valence triple zeta basis set (aug-cc-pCVTZ). For the 1A' and 3A″ electronic states of HeCH +, the CCSD(T)a aug-cc-pCVTZ model yielded an optimised geometry of C s symmetry eith a { rCHe, rCH, θHCHe} structural parameters of {2.172 Å, 1.129 Å, 81.4°} and {1.675 Å, 1.121 Å, 101.4°} respectively. Moreover, this electronic model yielded the singlet state to be 26.3 kcal mol -1 lower in energy in energy when compared with the triplet state. For the 2A' ground electronic state of HeCH 2+ the optimised structural parameters were {1.388 Å, 1.253 Å, 110.5°}, respectively. The calculated harmonic frequencies for all these electronic states were found to be real.

  5. Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Abdulsattar, Mudar Ahmed, E-mail: mudarahmed3@yahoo.com [Ministry of Science and Technology, Baghdad (Iraq); Hussein, Mohammed T.; Hameed, Hadeel Ali [Department of Physics, College of Science, University of Baghdad, Baghdad (Iraq)

    2014-12-15

    Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm{sup -1}) compared to experimental 0.035 eV (285.2 cm{sup -1}). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.

  6. Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals

    Directory of Open Access Journals (Sweden)

    Mudar Ahmed Abdulsattar

    2014-12-01

    Full Text Available Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm-1 compared to experimental 0.035 eV (285.2 cm-1. Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å. Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.

  7. Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals

    Science.gov (United States)

    Abdulsattar, Mudar Ahmed; Hussein, Mohammed T.; Hameed, Hadeel Ali

    2014-12-01

    Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm-1) compared to experimental 0.035 eV (285.2 cm-1). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.

  8. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch [Nanoscale Simulations, Department of Materials, ETH Zürich, Wolfgang-Pauli-Str. 27, CH-8093 Zürich (Switzerland)

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  9. Ab Initio Investigation of the Structural and Electronic Properties of HgTe/CdTe Superlattices

    Science.gov (United States)

    Laref, A.; Alsagri, M.; Laref, S.; Luo, S. J.

    2017-08-01

    We carried out first-principle calculations to examine the impact of layer periodicity and strain on the structural and electronic features of HgTe/CdTe superlattices (SLs). The full-potential linearized augmented plane wave methodology is used to determine the electronic characteristics of these CdTe-HgTe heterojunctions. The CdTe and HgTe layers have a strong effect on the emerged fundamental energy gap of the SLs owing to the peculiar quantum confinement effect. The impact of layer thickness changes and strain are indispensable for engineering the energy band gap of HgTe/CdTe SLs. This could lead to an enormous development in the optoelectronic characteristics of these SLs, which may result in their broad applications in electronic devices.

  10. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine.

    Science.gov (United States)

    Srivastava, Santosh K; Singh, Vipin B

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  12. Ab initio electronic band structure study of III-VI layered semiconductors

    Science.gov (United States)

    Olguín, Daniel; Rubio-Ponce, Alberto; Cantarero, Andrés

    2013-08-01

    We present a total energy study of the electronic properties of the rhombohedral γ-InSe, hexagonal ɛ-GaSe, and monoclinic GaTe layered compounds. The calculations have been done using the full potential linear augmented plane wave method, including spin-orbit interaction. The calculated valence bands of the three compounds compare well with angle resolved photoemission measurements and a discussion of the small discrepancies found has been given. The present calculations are also compared with recent and previous band structure calculations available in the literature for the three compounds. Finally, in order to improve the calculated band gap value we have used the recently proposed modified Becke-Johnson correction for the exchange-correlation potential.

  13. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    Science.gov (United States)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  14. Ab initio calculations of structural, electronic, and mechanical stability properties of magnesium sulfide

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hai-Ying; Zhou, Ping; Han, Xiang-Yu [Jiaotong Univ., Chongqing (China). School of Science; Chen, Ya-Hong [North Univ. of China, Taiyuan (China). Scholl of Chemical Engineering and Environment; Liu, Zi-Jiang [Lanzhou City Univ. (China). Dept. of Physics

    2014-08-15

    The structural, electronic, and mechanical stability properties of magnesium sulfide in different phases are presented using the plane wave pseudopotential method within the generalized gradient approximation. Eight different phases such as rocksalt (B1), zincblende (B3), wurtzite (B4), nickel arsenide (B8), cesium chloride (B2), PH{sub 4}I-type (B11), FeSi-type (B28), and MnP-type (B31) are considered in great detail. The calculated ground-state properties of these phases are consistent with available experimental and theoretical data. It is found that MgS in the B1 and B8 phases are indirect band gap materials, the B3, B4, B11, B28, and B31 phases are all direct gap materials, while the B2 phase displays the metallic character. The B1, B3, B4, B8, B28, and B31 phases are mechanically stable at ambient conditions, but the B2 and B11 phases are mechanically unstable under zero pressure and zero temperature.

  15. Ab initio structure determination of new compound Li 4CaB 2O 6

    Science.gov (United States)

    Wu, L.; Wang, C.; Chen, X. L.; Li, X. Z.; Xu, Y. P.; Cao, Y. G.

    2004-06-01

    A new compound, Li 4CaB 2O 6, has been synthesized by solid-state reaction and its structure has been determined from powder X-ray diffraction data by direct methods. The refinement was carried out using the Rietveld methods and the final refinement converged with Rp=10.4%, Rwp=14.2%, Rexp=4.97%. This compound belongs to the orthorhombic space group Pnnm, with lattice parameters a=9.24036(9) Å, b=8.09482(7) Å, and c=3.48162(4) Å. Fundamental building units are isolated [BO 3] 3- anionic groups, which are all parallel to the a- b plane stacked along the c-axis. The Ca atoms are six-coordinated by the O atoms to form octahedral coordination polyhedra, which are joined together through edges along the c-axis, forming infinitely long three-dimensional chains. The Li atoms have a four-fold and a five-fold coordination with O atoms that lead to complex Li-O-Li chains that also extend along the c-axis. The infrared spectrum of Li 4CaB 2O 6 was also studied, which is consistent with the crystallographic study.

  16. An ab-initio study of adsorption of gaseous molecules on doped graphene structures

    Science.gov (United States)

    Balangi, H. R.; Shokri, A. A.

    2015-11-01

    In this work, electronic properties of bare and doped graphene layers in the presence of N, B and a type of defective impurities are investigated under adsorption of CO, NO, NH3 and NO2 molecules on it's external surface. We use a fully self-consistent density function theory (DFT) based calculations as implemented in SIESTA package. The local-density approximation (LDA) is considered for the exchange-correlation function. Total density of state (TDOS), partial density of state (PDOS) and charge density calculations are also considered to elucidate the difference in the CO, NO, NH3 and NO2 gases detection mechanism of pristine and doped graphene structures. With regard to that the charge transfer is occurring between the graphene sheet and gaseous molecules, the NO2 and NH3 molecules are considered as the recipient and donor of electrons, respectively. We show that the states contributed by the adsorbed CO and NO molecules are quite localized near the center of original band gap and they suggest that the charge transport in such systems cannot be enhanced considerably, while NO2 and NH3 molecules adsorption acts as the acceptor and donor, respectively. Our results can serve as a base for developments in designing nano-electronic devices.

  17. Ab initio structural study on Nb-doped Pb(Zr{sub 0.97}Ti{sub 0.03})O{sub 3} ceramic material by synchrotron X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Hongchao Liu; Toraya, Hideo [Ceramics Research Lab., Nagoya Inst. of Tech., Tajimi, Aichi (Japan)

    1999-06-01

    X-ray powder diffraction pattern of Nb-doped Pb(Zr{sub 0.97}Ti{sub 0.03})O{sub 3} ceramic material was collected with synchrotron radiation source. Its crystal structure was investigated by ab initio crystal structure analysis based on the powder diffraction data. The result showed that this material is in orthorhombic symmetry and unit-cell parameters are a=5.86295(4)A, b=11.74014(7)A and c=8.20686(4)A. Both the full profile fitting and structural analysis supported that the most appropriate space group is Pnnm, rather than the widely accepted Pbam or Pba2. The structural data revealed Zr displacement along z-axis and local disorder in the oxygen substructure. (author)

  18. Electronic Properties of the Zirconium Crystal with Vacancies and Dynamics of Vacancies: ab-initio Calculations and Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    V.O. Kharchenko

    2015-06-01

    Full Text Available Within this paper we have the studied structural and electronic properties of zirconium crystal with vacancies from the first principles. We have defined the optimal values for the lattice constants. The corresponding densities of states and energetic spectrum were calculated. These results gave a possibility to define the Fermi structure of the zirconium crystal with vacancies. In the framework of the molecular dynamics simulations we have studied the dynamics of the ensemble of periodically located vacancies in the zirconium crystal with an increase in temperature. We have analyzed the reconstruction of atomic structure and change in the total volume of the crystal with the temperature growth. The dependencies of the volume expansion coefficient for the pure zirconium without vacancies end zirconium crystal with different vacancies concentration on the temperature were studied.

  19. Electronic structure and metallization of cubic GdH3 under pressure: Ab initio many-body GW calculations

    Science.gov (United States)

    Kong, Bo; Zhang, Yachao

    2016-07-01

    The electronic structures of the cubic GdH3 are extensively investigated using the ab initio many-body GW calculations treating the Gd 4f electrons either in the core (4f-core) or in the valence states (4f-val). Different degrees of quasiparticle (QP) self-consistent calculations with the different starting points are used to correct the failures of the GGA/GGA + U/HSE03 calculations. In the 4f-core case, GGA + G0W0 calculations give a fundamental band gap of 1.72 eV, while GGA+ GW0 or GGA + GW calculations present a larger band gap. In the 4f-val case, the nonlocal exchange-correlation (xc) functional HSE03 can account much better for the strong localization of the 4f states than the semilocal or Hubbard U corrected xc functional in the Kohn-Sham equation. We show that the fundamental gap of the antiferromagnetic (AFM) or ferromagnetic (FM) GdH3 can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G0W0 calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW0 and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G0W0 calculations in the 4f-core case is the closest to the real result. By G0W0 calculations in the 4f-core case, we find that H or Gd defects can strongly affect the band structure, especially the H defects. We explain the mechanism in terms of the possible electron correlation on the hydrogen site. Under compression, the insulator-to-metal transition in the cubic GdH3 occurs around 40 GPa, which might be a satisfied prediction.

  20. Vacancy or not: An insight on the intrinsic vacancies in rocksalt-structured GeSbTe alloys from ab initio calculations

    Science.gov (United States)

    Zhou, J.; Sun, Z.; Pan, Y.; Song, Z.; Ahuja, R.

    2011-07-01

    Rocksalt-structured GeSbTe (GST) phase-change materials contain significant amounts of intrinsic vacancies at one sublattice. On the basis of ab initio total energy calculations, we have shown that the so-called intrinsic vacancies result from geometrical voids that originate from packing spaces for lone pairs of electrons tightly bound to specific Te layers where a weak bonding exists. The existence of such geometrical voids is concomitant with a narrow band gap. The present results will shed new insights on the intrinsic vacancies in rocksalt-structured GST.

  1. Microwave, infrared and Raman spectra, r0 structural parameters, ab initio calculations and vibrational assignment of 1-fluoro-1-silacyclopentane.

    Science.gov (United States)

    Durig, James R; Panikar, Savitha S; Obenchain, Daniel A; Bills, Brandon J; Lohan, Patrick M; Peebles, Rebecca A; Peebles, Sean A; Groner, Peter; Guirgis, Gamil A; Johnston, Michael D

    2012-01-28

    The microwave spectrum (6500-18 ,500 MHz) of 1-fluoro-1-silacyclopentane, c-C(4)H(8)SiHF has been recorded and 87 transitions for the (28)Si, (29)Si, (30)Si, and (13)C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm(-1)) of the gas and solid and Raman spectrum (3100-40 cm(-1)) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much lower energy than the planar conformer. By utilizing the microwave rotational constants for seven isotopomers ((28)Si, (29)Si, (30)Si, and four (13)C) combined with the structural parameters predicted from the MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the twist conformer. The heavy atom distances in Å are: r(0)(SiC(2)) = 1.875(3); r(0)(SiC(3)) = 1.872(3); r(0)(C(2)C(4)) = 1.549(3); r(0)(C(3)C(5)) = 1.547(3); r(0)(C(4)C(5)) = 1.542(3); r(0)(SiF) = 1.598(3) and the angles in degrees are: [angle]CSiC = 96.7(5); [angle]SiC(2)C(4) = 103.6(5); [angle]SiC(3)C(5) = 102.9(5); [angle]C(2)C(4)C(5) = 108.4(5); [angle]C(3)C(5)C(4) = 108.1(5); [angle]F(6)Si(1)C(2) = 110.7(5); [angle]F(6)Si(1)C(3) = 111.6(5). The heavy atom ring parameters are compared to the corresponding r(s) parameters. Normal coordinate calculations with scaled force constants from MP2(full)/6-31G(d) calculations were carried out to predict the fundamental vibrational frequencies, infrared intensities, Raman activities, depolarization values, and infrared band contours. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.

  2. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2016-01-01

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).

  3. Free energies for degradation reactions of 1,2,3-trichloropropane from ab initio electronic structure theory.

    Science.gov (United States)

    Bylaska, Eric J; Glaesemann, Kurt R; Felmy, Andrew R; Vasiliu, Monica; Dixon, David A; Tratnyek, Paul G

    2010-11-25

    Electronic structure methods were used to calculate the gas and aqueous phase reaction energies for reductive dechlorination (i.e., hydrogenolysis), reductive β-elimination, dehydrochlorination, and nucleophilic substitution by OH− of 1,2,3-trichloropropane. The thermochemical properties ΔH(f)°(298.15 K), S°(298.15 K, 1 bar), and ΔG(S)(298.15 K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely degradation products: CH3−CHCl−CH2Cl, CH2Cl−CH2−CH2Cl, C•H2−CHCl−CH2Cl, CH2Cl−C•H−CH2Cl, CH2═CCl−CH2Cl, cis-CHCl═CH−CH2Cl, trans-CHCl═CH−CH2Cl, CH2═CH−CH2Cl, CH2Cl−CHCl−CH2OH, CH2Cl−CHOH−CH2Cl, CH2═CCl−CH2OH, CH2═COH−CH2Cl, cis-CHOH═CH−CH2Cl, trans-CHOH═CH−CH2Cl, CH(═O)−CH2−CH2Cl, and CH3−C(═O)−CH2Cl. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive β-elimination (ΔG(rxn)° ≈ −32 kcal/mol), followed closely by reductive dechlorination (ΔG(rxn)° ≈ −27 kcal/mol), dehydrochlorination (ΔG(rxn)° ≈ −27 kcal/mol), and nucleophilic substitution by OH− (ΔG(rxn)° ≈ −25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate C•H2−CHCl−CH2Cl and the CH2Cl−C•H−CH2Cl species, was not favorable in the standard state (ΔG(rxn)° ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely.

  4. Investigations of the structure of silicate glasses and carbohydrates by silicon-29 and carbon-13 nuclear magnetic resonance and by ab initio calculations

    Science.gov (United States)

    Zhang, Ping

    Measurements of the relative abundance of anionic species, commonly described as Qn species in silicate glasses are essential for any structure-based model of thermodynamic or transport properties of silicate liquids and magmas. Solid-state 29Si NMR has provided the most convincing evidence that the Qn species distribution in alkali glasses is not random but closer to binary. Unfortunately, for most silicate glasses 29Si MAS NMR spectra are incompletely resolved. A 2D NMR technique is reported that cannot only determine the distribution of Qn species without any a priori assumptions about the lineshapes, but also provide over an order of magnitude improvement in the precision of Qn species quantification. Results of this approach on a few carefully chosen composition should lead to a major improvement of structure-based thermodynamic models of silicate liquids. Another important aspect of structure of silicate glasses is the environment of nonbridging oxygen atoms. In other words, how the cations are distributed around non-bridging oxygen atoms. 17O solid-state NMR has been shown to be a powerful probe for studying the local structure of non-bridging oxygen. One challenge in exploiting techniques such as DOR, DAS, or MQ-MAS is the development of appropriate models to describe the relationships between NMR parameters and local structure. Ab initio calculations on the model cluster [(OH)3Si-OMn] OH 3Si-OMn n-1 + (M = Na, K; n = 3,4,5) have been performed. A point charge model is also used to derive approximate expressions to describe the dependence of the 17O quadrupole coupling parameters on the cation-non-bridging oxygen distance and its orientation. Solid-state NMR and ab initio quantum mechanical methods are used to characterize the possible molecular conformations of trehalose. Combining ab initio derived maps and using the 13 C lineshape as constraints, the torsion angle distribution map for alpha-alpha ' trehalose was constructed. Measurements of 13C isotropic

  5. Structural, electronic and optical properties of cubic SrTiO{sub 3} and KTaO{sub 3}: Ab initio and GW calculations

    Energy Technology Data Exchange (ETDEWEB)

    Benrekia, A.R., E-mail: benrekia.ahmed@yahoo.com [Faculty of Science and Technology, University of Medea (Algeria); Benkhettou, N. [Laboratoire des Materiaux Magnetiques, Faculte des Sciences, Universite Djillali Liabes de Sidi Bel Abbes (Algeria); Nassour, A. [Laboratoire de Cristallographie, Resonance Magnetique et Modelisations (CRM2, UMR CNRS 7036) Institut Jean Barriol, Nancy Universite BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-les-Nancy (France); Driz, M. [Applied Material Laboratory (AML), Electronics Department, University of Sidi bel Abbes (DZ 22000) (Algeria); Sahnoun, M. [Laboratoire de Physique Quantique de la Matiere et Modelisations Mathematique (LPQ3M), Faculty of Science and Technology,University of Mascara (Algeria); Lebegue, S. [Laboratoire de Cristallographie, Resonance Magnetique et Modelisations (CRM2, UMR CNRS 7036) Institut Jean Barriol, Nancy Universite BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-les-Nancy (France)

    2012-07-01

    We present first-principles VASP calculations of the structural, electronic, vibrational, and optical properties of paraelectric SrTiO{sub 3} and KTaO{sub 3}. The ab initio calculations are performed in the framework of density functional theory with different exchange-correlation potentials. Our calculated lattice parameters, elastic constants, and vibrational frequencies are found to be in good agreement with the available experimental values. Then, the bandstructures are calculated with the GW approximation, and the corresponding band gap is used to obtain the optical properties of SrTiO{sub 3} and KTaO{sub 3}.

  6. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

    CERN Document Server

    Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-01-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

  7. Conformational and structural studies of 1-chloropropane and 1-bromopropane from temperature-dependant FT-IR spectra of rare gas solutions and ab initio calculations

    Science.gov (United States)

    Durig, J. R.; Zhu, X.; Shen, S.

    2001-08-01

    Variable temperature (-55 to -150°C) studies of the infrared spectra (3500-400 cm -1) of 1-chloropropane (CH 3CH 2CH 2Cl) and 1-bromopropane (CH 3CH 2CH 2Br) dissolved in liquid krypton and xenon, respectively, have been recorded. Utilizing two conformer pairs in krypton solution for chloride and three conformer pairs in xenon solution for bromide, enthalpy differences of 52±3 cm -1 (0.62±0.06 kJ/mol) and 72±7 cm -1 (0.86±0.08 kJ/mol) were obtained for the chloride and bromide, respectively, with the gauche form being the more stable conformer for both molecules. From these data, it is estimated that 28 and 26% of trans form are present at ambient temperature for the chloride and bromide, respectively. The conformation stabilities, harmonic force constants, fundamental frequencies, infrared intensities and Raman activities have been obtained from RHF/6-31G(d) and/or MP2/6-31G(d) ab initio calculations for both halopropanes and these quantities have been compared to the experimental values when appropriate. The optimized geometries have also been obtained with several different ab initio basis sets with full electron correlation by the perturbation method up to MP2/6-311+G(2d,2p). The r0 structural parameters of both halopropanes have been obtained by combining the ab initio data with the previously reported microwave rotational constants for both conformers. The quantities are compared to the corresponding results for some similar molecules.

  8. Determinação da estrutura molecular do ciclooctano por métodos ab initio e difração de elétrons na fase gasosa Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    Directory of Open Access Journals (Sweden)

    Wagner B. De Almeida

    2000-10-01

    Full Text Available The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase and ab initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions.

  9. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    Science.gov (United States)

    Campetella, M.; Bovi, D.; Caminiti, R.; Guidoni, L.; Bencivenni, L.; Gontrani, L.

    2016-07-01

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm-1), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm-1 where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  10. Ab initio phase diagram of iridium

    Science.gov (United States)

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

    2016-09-01

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

  11. Ab initio study of magnesium and magnesium hydride nanoclusters and nanocrystals: examining optimal structures and compositions for efficient hydrogen storage.

    Science.gov (United States)

    Koukaras, Emmanuel N; Zdetsis, Aristides D; Sigalas, Michael M

    2012-09-26

    On the basis of the attractive possibility of efficient hydrogen storage in light metal hydrides, we have examined a large variety of Mg(n)H(m) nanoclusters and (MgH(2))(n) nanocrystals (n = 2-216, m = 2-436) using high level coupled cluster, CCSD(T), ab initio methods, and judicially chosen density functional calculations of comparable quality and (near chemical) accuracy. Our calculated desorption energies as a function of size and percentage of hydrogen have pinpointed optimal regions of sizes and concentrations of hydrogen which are in full agreement with recent experimental findings. Furthermore, our results reproduce the experimental desorption energy of 75.5 kJ/mol for the infinite system with remarkable accuracy (76.5 ± 1.5 kJ/mol).

  12. Huge susceptibility increase within the (1−x) TeO{sub 2} + x TeO{sub 3} crystal system: Ab initio calculation study

    Energy Technology Data Exchange (ETDEWEB)

    Plat, A.; Cornette, J.; Colas, M.; Mirgorodsky, A.P. [Laboratoire de Science des Procédés Céramiques et de Traitements de Surface UMR 7315 CNRS, Centre Européen de la Céramique, Université de Limoges, 12 rue Atlantis, 87068 Limoges Cedex (France); Smirnov, M.B. [Physical Department, Saint Petersburg State University, 198504 Petrodvorets, Saint Petersburg (Russian Federation); Noguera, O.; Masson, O. [Laboratoire de Science des Procédés Céramiques et de Traitements de Surface UMR 7315 CNRS, Centre Européen de la Céramique, Université de Limoges, 12 rue Atlantis, 87068 Limoges Cedex (France); Thomas, P., E-mail: philippe.thomas@unilim.fr [Laboratoire de Science des Procédés Céramiques et de Traitements de Surface UMR 7315 CNRS, Centre Européen de la Céramique, Université de Limoges, 12 rue Atlantis, 87068 Limoges Cedex (France)

    2014-02-25

    Highlights: • Minor role of the electron lone pairs of Te atom on non-linear optic properties. • Te{sup IV}O{sub 4} → Te{sup VI}O{sub 6} evolution induces an augmentation of the χ{sup 3} susceptibility. • The Te-O-Te chain -length influences on the lattice χ{sup 3} susceptibility. -- Abstract: The ab initio calculations performed for the TeO{sub 2} → Te{sub 4}O{sub 9} → Te{sub 2}O{sub 5} → TeO{sub 3} series of crystal lattices have revealed that, in this series, the average χ{sup 3} non-linear susceptibility increases for about 10 times. Such a huge effect is attributed to the strong augmentation of the Te atom d-function contributions in valence molecular orbitals, which accompanies the Te{sup 4+} → Te{sup 6+} transformation. The results obtained allow concluding that the TeO{sub 3}-related materials can be of interest in non-linear optic device engineering.

  13. Ab initio study of the structural, thermodynamic and electronic properties of the Cu{sub 10}In{sub 7} intermetallic phase

    Energy Technology Data Exchange (ETDEWEB)

    Ramos de Debiaggi, S., E-mail: sbramos@yahoo.com [Facultad de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, (8300) Neuquen (Argentina); CONICET (Argentina); Cabeza, G.F. [CONICET (Argentina); Dpto. de Fisica, Universidad Nacional del Sur, Bahia Blanca (Argentina); Toro, C. Deluque [Facultad de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, (8300) Neuquen (Argentina); Monti, A.M. [CNEA e Instituto Sabato (Univ. Nac. de San Martin/CNEA), Centro Atomico Constituyentes, Avda. General Paz 1499, B1650KNA, San Martin, Buenos Aires (Argentina); Sommadossi, S. [Facultad de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, (8300) Neuquen (Argentina); CONICET (Argentina); Guillermet, A. Fernandez [CONICET (Argentina); Centro Atomico Bariloche e Instituto Balseiro, Avda. Bustillo 9500, (8400) Bariloche (Argentina)

    2011-02-17

    Research highlights: > Cu{sub 10}In{sub 7} and Cu{sub 11}In{sub 9} are thermodynamically stable with respect to elements at 0 K. > Cu{sub 10}In{sub 7} phase is more stable than the modelled Cu{sub 11}In{sub 9} compound by only 0.92 kJ/mol. > The present ab initio results reproduce very well the available structural data. > Similar DOS for both phases, the most prominent bonding band comes from Cu-d states. > Enhanced relative thermodynamic stability is predicted for phases with 40-45 at.% In. - Abstract: The physico-chemical properties of the intermetallic phases in the Cu-In system have been a matter of considerable theoretical and experimental interest in connection with, i.a., the application of In-Sn alloys as lead-free micro-soldering alloys. Recently, a new binary compound with the chemical formula Cu{sub 10}In{sub 7} has been detected in a study of the {eta}-phase field. The structure of the Cu{sub 10}In{sub 7} phase has been determined as closely related to that of the Cu{sub 11}In{sub 9} compound occurring in the phase diagram, but no experimental or theoretical information on its electronic structure, thermodynamic and equation-of-state properties has yet been reported. In the present work we report the lattice parameters, bulk modulus, energy of formation from the constituent elements and the electronic structure of the new phase, calculated by applying an ab initio density-functional-theory method. Our calculation technique uses the projector augmented wave potentials and the exchange-correlation functions of Perdew and Wang in the generalized gradient approximation. The present results for the Cu{sub 10}In{sub 7} phase are compared with the experimental data available, and with the trends in structural and thermodynamic properties emerging from ab initio calculations also performed in the present study for various structurally related and neighboring compounds in the Cu-In phase diagram, viz., the ideal B8{sub 2}-Cu{sub 2}In, B8{sub 1}-CuIn, B8{sub 2

  14. Structural, elastic, and electronic properties of recently discovered ternary silicide superconductor Li2IrSi3:An ab-initio study

    Institute of Scientific and Technical Information of China (English)

    M. A. Hadi; M. A. Alam; M. Roknuzzaman; M. T. Nasir; A. K. M. A. Islam; S. H. Naqib

    2015-01-01

    The structural, elastic, and electronic properties of the very recently discovered ternary silicide superconductor, Li2IrSi3, are calculated using an ab-initio technique. We adopt the plane-wave pseudopotential approach within the frame-work of the first-principles density functional theory (DFT) implemented by the CASTEP code. The calculated structural parameters show reasonable agreement with the experimental results. The elastic moduli of this interesting material are calculated for the first time. The electronic band structure and electronic energy density of states indicate the strong cova-lent Ir–Si and Si–Si bonding, which leads to the formation of the rigid structure of Li2IrSi3. Strong covalency gives rise to a high Debye temperature in this system. We discuss the theoretical results in detail in this paper.

  15. Ab-initio study of the magnetism, structure and spin dependent electronic states of Ti substituted MO (M = Mg, Ca, Sr)

    Energy Technology Data Exchange (ETDEWEB)

    Jaiganesh, G., E-mail: jaiganesh@igcar.gov.in; Jaya, S. Mathi [Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam - 603102 (India)

    2015-06-24

    The magnetism, structure and spin polarized electronic structure of Ti substituted MO (M = Mg, Ca, Sr) are studied using the ab-initio techniques within the framework of the density functional theory. Appropriately constructed supercell along with the full structural optimization of these cells is used for studying the influence of Ti substitution on the magnetism and electronic structure of these compounds. We find from our calculations that the Ti substituted MO compounds energetically favor magnetically ordered state. The Ti concentration is found to be important in deciding the magnetic order and we have observed antiferromagnetic order for the Ti concentration of 0.25. The Ti substituted MO compounds are thus an interesting class of materials that deserve further studies.

  16. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.

    Science.gov (United States)

    Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

    2011-01-01

    I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment-guided molecular dynamics (FG-MD), were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles, and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of β-proteins are still needed to further improve the I-TASSER pipeline. Copyright © 2011 Wiley-Liss, Inc.

  17. Experimental and ab initio investigations of the x-ray absorption near edge structure of orthorhombic LuMnO3

    Science.gov (United States)

    Hu, Y.; Borca, C. N.; Kleymenov, E.; Nachtegaal, M.; Delley, B.; Janousch, M.; Dönni, A.; Tachibana, M.; Kitazawa, H.; Takayama-Muromachi, E.; Kenzelmann, M.; Niedermayer, C.; Lippert, T.; Wokaun, A.; Schneider, C. W.

    2012-06-01

    X-ray near edge absorption spectroscopy was used to probe the electronic structure of multiferroic orthorhombic LuMnO3 polycrystalline samples and strained, twin-free orthorhombic (1-10) LuMnO3 films grown by pulsed laser deposition on (1-10) YAlO3 substrates. For all o-LuMnO3 samples x-ray near edge absorption spectroscopy spectra reveal that the pre-edge structure is influenced by the increase in MnO6 distortion as a result of the smaller Re-ion or film strain. Furthermore there is clear evidence of anisotropic Mn-O bonding and Mn orbital ordering along the c- and [110] direction. The experimental film and bulk data are in agreement with ab initio simulations.

  18. Quantitative structure-property relationship study of the solubility of thiazolidine-4-carboxylic acid derivatives using ab initio and genetic algorithm-partial least squares

    Institute of Scientific and Technical Information of China (English)

    Ali Niazi; Saeed Jameh-Bozorghi; Davood Nori-Shargh

    2007-01-01

    A quantitative structure-activity relationships (QSAR) study is suggested for the prediction of solubility of some thiazolidine-4-carboxylic acid derivatives in aqueous solution. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. Modeling of the solubility of thiazolidine4-carboxylic acid derivatives as a function of molecular structures was established by means of the partial least squares (PLS). The subset of descriptors, which resulted in the low prediction error, was selected by genetic algorithm. This model was applied for the prediction of the solubility of some thiazolidine-4-carboxylic acid derivatives, which were not in the modeling procedure. The relative errors of prediction lower that -4% was obtained by using GA-PLS method. The resulted model showed high prediction ability with RMSEP of 3.8836 and 2.9500 for PLS and GA-PLS models, respectively.

  19. Structural Properties of Liquid Water and Ice Ih from Ab-Initio Molecular Dynamics with a Non-Local Correlation Functional

    Directory of Open Access Journals (Sweden)

    Niall J. English

    2015-08-01

    Full Text Available Equilibrium Born-Oppenheimer molecular dynamics simulations have been performed in the canonical ensemble to investigate the structural properties of liquid water and ice Ih (hexagonal ice at 298 and 273 K, respectively, using a state-of-the-art non-local correlation functional, whilst size effects have been examined explicitly in the case of liquid water. This has led to improved agreement with experiments for pair distribution functions, in addition to molecular dipole moments, vis-à-vis previous flavours of ab-initio molecular dynamics simulation of water, highlighting the importance of appropriate dispersion. Intramolecular geometry has also been examined, in addition to hydrogen-bonding interactions; it was found that an improved description of dispersion via non-local correlation helps to reduce over-structuring associated with the Perdew-Becke-Ernzerhof (PBE and other commonly-used functionals.

  20. Nano-crystallization and magnetic mechanisms of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy by ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro [Institute for Material Research, Tohoku University, Sendai 980-8577 (Japan); Liang, Yunye [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kawazoe, Yoshiyuki [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kutateladze Institute of Thermophysics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk (Russian Federation)

    2014-05-07

    Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-07-01

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

  2. Molecular structures and vibrational frequencies of xanthine and its methyl derivatives (caffeine and theobromine) by ab initio Hartree-Fock and density functional theory calculations

    Science.gov (United States)

    Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile

    2007-06-01

    The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.

  3. Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2011-11-01

    Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.

  4. Ab initio investigation of the effect of pressure on the structure and electronic properties of alkali metal oxides and peroxides

    Science.gov (United States)

    Aleinikova, M. V.; Zhuravlev, Yu. N.; Korabelnikov, D. V.

    2012-10-01

    Within the framework of a gradient approximation of the all-electron density functional theory (DFT), using a linear combination of atomic orbitals of the CRYSTAL09 software package, the structural and electronic properties of lithium, sodium, and potassium oxides and peroxides are investigated under hydrostatic conditions in the range of pressures from -3 to 15 GPa. The crystal structure parameters are determined, the band structure, densities of state (DOSs), atomic charges, and overlap populations are calculated, and their dependence on pressure is established. The energy band gap is shown to increase with pressure.

  5. Ab initio investigation of the mechanical properties of copper

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

  6. Effects of isotopic disorder on the Raman spectra of crystals: Theory and ab initio calculations for diamond and germanium

    Science.gov (United States)

    Vast, Nathalie; Baroni, Stefano

    2000-04-01

    We present a method to study the effects of isotopic composition on the Raman spectra of crystals, in which disorder is treated exactly without resorting to any kind of mean-field approximation. The Raman cross section is expressed in terms of a suitable diagonal element of the vibrational Green's function, which is accurately and efficiently calculated using the recursion technique. This method can be used in conjunction with both semiempirical lattice-dynamical models and with first-principles interatomic force constants. We have applied our technique to diamond and germanium using the most accurate interatomic force constants presently available, obtained from density-functional perturbation theory. Our method correctly reproduces the light scattering in diamond-where isotopic effects dominates over the anharmonic ones-as well as in germanium, where anharmonic effects are larger.

  7. Ab initio RNA folding.

    Science.gov (United States)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

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

  8. Lattice dynamics of rare-earth titanates with the structure of pyrochlore R 2Ti2O7 ( R = Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu): Ab initio calculation

    Science.gov (United States)

    Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.

    2015-05-01

    The ab initio calculation has been performed for the crystal structure and the phonon spectrum of titanates with the structure of pyrochlore R 2Ti2O7 ( R = Gd-Lu). The frequencies and types of fundamental vibrations have been found. For R = Tb, Tm, and Yb, this calculation has been carried out for the first time; furthermore, there is no available information on experimental studies of the phonon spectrum for Tm and Yb. The influence of hydrostatic pressure to 35 GPa on the structure, dynamics, and elastic properties of the Gd2Ti2O7 lattice has been investigated. The dependence of the phonon frequencies on the pressure has been obtained. The calculations have predicted that the relative change in the pyrochlore structure volume during compression at pressures to 35 GPa is well described by the third-order Birch-Murnaghan equation of states. The results of the calculations agree with the available experimental data. It has been shown that the structural, dynamic, and elastic properties of the R 2Ti2O7 crystal lattice can be adequately described in the case where the inner shells of the RE ion up to 4 f are replaced by the pseudopotential.

  9. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    Science.gov (United States)

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

    1995-01-01

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

  10. The gas-phase molecular structure of 1,1-diethynylsilacyclobutane as determined by means of electron diffraction and ab initio calculations

    Science.gov (United States)

    Dakkouri, Marwan; Grosser, Martin

    2002-06-01

    As a continuation of our systematic investigation of the effect of substituents on the ring geometry and dynamics in silacyclobutanes and in order to explore the role of the silicon atom as a mediator for electronic interactions between the attached fragments, we studied the molecular structure of 1,1-diethynylsilacyclobutane (DESCB) by means of gas-phase electron diffraction and ab initio calculations. The structural refinement of the electron diffraction data yielded the following bond lengths (ra) and bond angles (uncertainties are 3σ): r(Si-C)=1.874(2) Å,r(Si-Ctbnd)=1.817(1) Å,r(-Ctbnd C-)=1.209(1)Å,r(C-C)=1.563(2)Å, ∠(C-Si-C)=79.2(6)°, ∠(tbnd C-Si-Ctbnd)=106.5(6)°. The geminal Si-Ctbnd C moieties were found to be bent outwards by 3.1(15)° and the puckering angle was determined to be 30.0(15)°. The evidently short Si-Ctbnd bond length, which was also reproduced by the ab initio calculations, could be rationalized as being the consequence of the electronic interaction between the outer π charges of the triple bond and the 3pπ orbitals at the silicon atom. It is also likely that the conjugation of the geminal ethynyl groups leads to an enhancement of this bond contraction. Electrostatic interactions and the subsequent reduction of the covalent radius of the silicon atom may also contribute to this bond shortening. It has been found that the endocyclic Si-C bond length fits nicely within a scheme describing a monotonous decrease of the Si-C bond length with the increase of the electronegativity of the substituent in various geminally substituted silacyclobutanes. A series of related silacyclobutanes and acyclic diethynylsilanes have been studied by applying various ab initio methods and their optimized structures were compared to the structure of DESCB. Among these compounds are 1,1-dicyanosilacyclobutane (DCYSCB), which is isoelectronic to DESCB, 1,1-diethynylcyclobutane (DECB) which is isovalent to DESCB, monoethynylsilacyclobutane (MESCB) and

  11. Ab initio study of the cohesive properties, electronic structure and thermodynamic stability of the Ni–In and Ni–Sn intermetallics

    Energy Technology Data Exchange (ETDEWEB)

    Ramos de Debiaggi, S., E-mail: sbramos@yahoo.com [Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén (Argentina); CONICET (Argentina); Deluque Toro, C. [Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén (Argentina); Cabeza, G.F. [CONICET (Argentina); Dpto. de Física, Universidad Nacional del Sur, Alem 1253, 8000 Bahía Blanca (Argentina); Fernández Guillermet, A. [CONICET (Argentina); Centro Atómico Bariloche e Instituto Balseiro, Avda. Bustillo 9500, 8400 Bariloche (Argentina)

    2013-11-05

    Graphical abstract: -- Highlights: •A DFT study of Ni–In and Ni–Sn compounds in Ni–In–Sn soldering alloys is reported. •Cohesive, electronic structure, and thermodynamic stability trends are established. •Phase-stabilities at low T are well reproduced by the 0 K thermodynamic values. •Available structural and equation-of-state data are satisfactorily accounted for. •Ab initio and CALPHAD data of hypothetical phases involved in sublattice models are compared. -- Abstract: A comprehensive study of the structural, cohesive and electronic properties of several stable, metastable and non-stable intermetallic phases (IPs) of the Ni–In and Ni–Sn systems have been performed by ab initio density-funcional-theory (DFT) methods. Using the projector augmented wave method we have performed systematic spin polarized calculations with the exchange and correlation functions of Perdew and Wang in the generalized gradient approximation (GGA), as well as those by Ceperley and Alder in the local-density-approximation (LDA). Structural properties, the energy-of-formation (EOF) from the elements and the cohesive properties of the various phases have been established by minimizing the internal structural parameters. We present trends at 0 K in the composition dependence of the molar volumen, bulk modulus and its pressure derivative, electronic density of states, magnetic moments and the EOF of several stable and metastable IPs reported in the Ni–In and Ni–Sn systems as well as various non-stable (hypothetical) compounds which are relevant in connection with the thermodynamic analysis of the Ni–In and Ni–Sn systems using Gibbs energy models and the so-called CALPHAD techniques. The results are compared with the available experimental data and with previously reported theoretical results. The present study of the thermodynamic and cohesive properties of Ni–In/Sn intermetallic phases should contribute to the understanding of the phase-stability systematics in

  12. Effects of K doping on electronic structure of Ba{sub 1−x}K{sub x}Fe{sub 2}As{sub 2} superconductor by ab-initio density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Sandoghchi, M. [Advanced Materials Laboratory (AML), Department of Physics, Sharif University of Technology, P.O. Box 11365-9161, Tehran (Iran, Islamic Republic of); Khosroabadi, H., E-mail: khosroabadi@sharif.edu [Advanced Materials Laboratory (AML), Department of Physics, Sharif University of Technology, P.O. Box 11365-9161, Tehran (Iran, Islamic Republic of); Magnet Research Laboratory (MRL), Department of Physics, Sharif University of Technology, P.O. Box 11365-916, Tehran (Iran, Islamic Republic of); Akhavan, M. [Magnet Research Laboratory (MRL), Department of Physics, Sharif University of Technology, P.O. Box 11365-916, Tehran (Iran, Islamic Republic of)

    2014-12-15

    Highlights: • The lattice parameters changes by K doping is explained by ionic charge and the metal–metal bonding scenario. • Creation of a larger peak near the Fermi level and increase the DOS at the Fermi level by K doping. • The effects of K on DOS has been related to the magnetic transition, change of the lattice parameters and FeAs{sub 4} tetrahedron. • Investigation of the number of Fermi level crossed bands by K doping and the band changes near the Fermi level. - Abstract: The crystal and electronic structures of normal phase of Ba{sub 1−x}K{sub x}Fe{sub 2}As{sub 2} for x = 0.0, 0.5 and 1.0 have been studied by using pseudopotential Quantum Espresso code based on ab-initio density functional theory. Effects of K doping on the crystal structure and lattice parameters have been calculated and compared with the experimental and computational reported data for similar compounds. The metal–metal bonding scenario was used to explain the changes of lattice parameters by K doping. The electronic structure of this system including of density of states and band structure have been calculated and investigated by K doping. One of the interesting results is that a larger peak is appeared near the Fermi level by increasing of the K doping. These changes could produce a potential for creation of the superconducting state in this system.

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

    NARCIS (Netherlands)

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

    1996-01-01

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

  14. Structure, energetics, and electronic properties of the surface of a promoted MoS{sub 2} catalyst: An ab initio local density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Raybaud, P.; Hafner, J.; Kresse, G.; Kasztelan, S.; Toulhoat, H.

    2000-02-15

    The determination of the local structure of cobalt- or nickel-promoted MoS{sub 2}-based hydrodesulfurization catalysts is of interest for understanding the mechanism leading to an increased activity brought by cobalt or nickel, the so-called synergetic effect. For that reason, the authors carried out ab initio calculations using density functional theory under the generalized gradient approximation for periodic systems. The edge substitution model emerges as the most stable structure and provides an excellent agreement with local structures experimentally determined on real catalysts by in situ extended X-ray absorption fine structure. The authors studied the absorption of sulfur on the active edge surface of the promoted MoS{sub 2} catalyst and determined the equilibrium coverage under sulfiding conditions. It is demonstrated that the incorporation of promoter atoms has a strong influence on the sulfur-metal bond energy at the surface and in particular leads to a reduction of the equilibrium S coverage of the active metal sites. A comparative study on the effects of Co, Ni, and Cu atoms as promoters was performed. Detailed results on the surface electronic structure of promoted MoS{sub 2} are presented.

  15. Ab Initio Prediction of the Structural, Electronic, Elastic, and Thermoelectric Properties of Half-Heusler Ternary Compounds TiIrX (X = As and Sb)

    Science.gov (United States)

    Chibani, S.; Arbouche, O.; Zemouli, M.; Amara, K.; Benallou, Y.; Azzaz, Y.; Belgoumène, B.; Bentayeb, A.; Ameri, M.

    2017-08-01

    The structural, electronic, elastic, and thermoelectric properties of TiIrX (X = As and Sb) half-Heusler compounds with 18 valence electrons were studied using density functional theory. The generalized gradient approximation of Perdew-Burke and Ernzerhof used for calculation of the structural parameters and elastic properties of TiIrAs and TiIrSb denotes that the computed lattice constants were in excellent agreement with the available experimental data and previous theoretical works. Furthermore, the calculated elastic constants for both compounds satisfy the Born criteria indicating their mechanical stabilities. The modified Becke-Johnson potential (TB-mBJ) was used to provide a better description of the electronic structures, which indicate that both compounds are narrow-gap semiconductors. Additionally, the investigations of thermoelectric performance were carried out using the results of ab initio band-structure calculations and the semi-classical Boltzmann theory within the constant relaxation time approximations. The predicted values of the figure of merit ZT e are close to unity at room temperature. This reveals that TiIrAs and TiIrSb compounds are excellent candidates for practical applications in the thermoelectric devices.

  16. Friction of water on graphene and hexagonal boron nitride from ab initio methods: very different slippage despite very similar interface structures.

    Science.gov (United States)

    Tocci, Gabriele; Joly, Laurent; Michaelides, Angelos

    2014-12-10

    Friction is one of the main sources of dissipation at liquid water/solid interfaces. Despite recent progress, a detailed understanding of water/solid friction in connection with the structure and energetics of the solid surface is lacking. Here, we show for the first time that ab initio molecular dynamics can be used to unravel the connection between the structure of nanoscale water and friction for liquid water in contact with graphene and with hexagonal boron nitride. We find that although the interface presents a very similar structure between the two sheets, the friction coefficient on boron nitride is ≈ 3 times larger than that on graphene. This comes about because of the greater corrugation of the energy landscape on boron nitride arising from specific electronic structure effects. We discuss how a subtle dependence of the friction on the atomistic details of a surface, which is not related to its wetting properties, may have a significant impact on the transport of water at the nanoscale, with implications for the development of membranes for desalination and for osmotic power harvesting.

  17. Pressure-induced phase transitions and structural properties of CoF2: An ab-initio molecular dynamics study

    Science.gov (United States)

    Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya

    2016-04-01

    The crystal structure of CoF2 was studied theoretically using first-principles density functional theory (DFT) methods within the generalized gradient approximation (GGA) and local density approximation (LDA) under rapid hydrostatic pressure up to 144 GPa. CoF2 undergoes a structural phase transformation from the rutile-type tetragonal parent phase with space group P42/mnm to the CaCl2-type orthorhombic parent phase with space group Pnnm at 64 GPa with GGA and at 96 GPa with LDA methods. Another phase transformation occurs from the CaCl2-type structure to monoclinic parent phase with space group P21/c at 96 GPa with a GGA method. These phase transitions are also studied by enthalpy and total energy calculations. According to these calculations, we obtained the first phase transformation at about 6.5 GPa both GGA and LDA methods and the later phase transformation at about 45 GPa with the GGA method.

  18. Adsorption of atomic oxygen, electron structure and elastic moduli of TiC(0 0 1) surface during its laser reconstruction: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Ilyasov, V.V., E-mail: viily@mail.ru; Pham, Khang D., E-mail: dinhkhang307@gmail.com; Holodova, O.M.; Ershov, I.V., E-mail: thijd@mail.ru

    2015-10-01

    We have performed ab initio simulation of oxygen atom adsorption on TiC(0 0 1) laser-reconstructed surface. Relaxed atomic structures of the O/Ti{sub x}C{sub y}(0 0 1) surface observed upon thermal impact have been studied. DFT calculations of their thermodynamic, electronic, and elastic properties have been carried out. For the first time we have established the bond length and adsorption energy for various reconstructions of the O/Ti{sub x}C{sub y}(0 0 1) surface atomic structure. We have examined the effects of the oxygen adatom upon the band and electron spectra of the O/TiC(0 0 1) surface in its various reconstructions. For the first time we have established a correlation between the energy level of flat bands (−5.4 eV and −5.8 eV) responsible for the doublet of singular peaks of partial densities of oxygen 2p electrons, and the adsorption energy of oxygen atom in non-stoichiometric O/TiC{sub y}(0 0 1) systems. Effective charges of titanium and carbon atoms surrounding the oxygen adatom in various reconstructions have been identified. We have established charge transfer from titanium atom to oxygen and carbon atoms determined by the reconstruction of local atomic and electron structures which correlate with atomic electronegativity values and chemisorption processes. Potential mechanisms for laser nanostructuring of titanium carbide surface have been suggested.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-05

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

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

    Science.gov (United States)

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

    2010-03-01

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

  1. Ab initio calculations on the structural, mechanical, electronic, dynamic, and optical properties of semiconductor half-Heusler compound ZrPdSn

    Energy Technology Data Exchange (ETDEWEB)

    Ciftci, Yasemin Oe. [Gazi Univ., Ankara (Turkey). Dept. of Physics; Coban, Cansu [Balikesir Univ. (Turkey). Dept. of Physics

    2016-05-01

    The structural, mechanical, electronic, dynamic, and optical properties of the ZrPdSn compound crystallising into the MgAgAs structure are investigated by the ab initio calculations based on the density functional theory. The lattice constant, bulk modulus, and first derivative of bulk modulus were obtained by fitting the calculated total energy-atomic volume results to the Murnaghan equation of state. These results were compared to the previous data. The band structure and corresponding density of states (DOS) were also calculated and discussed. The elastic properties were calculated by using the stress-strain method, which shows that the MgAgAs phase of this compound is mechanically stable. The presented phonon dispersion curves and one-phonon DOS confirms that this compound is dynamically stable. In addition, the heat capacity, entropy, and free energy of ZrPdSn were calculated by using the phonon frequencies. Finally, the optical properties, such as dielectric function, reflectivity function, extinction coefficient, refractive index, and energy loss spectrum, were obtained under different pressures.

  2. Magnetism and metal insulator transition in FeSi and FeGe. Ab Initio investigations of the electronic structure; Magnetismus und Metall-Isolator-Uebergang in FeSi und FeGe. Ab-initio-Untersuchungen der elektronischen Struktur

    Energy Technology Data Exchange (ETDEWEB)

    Neef, Matthias

    2007-03-19

    Aim of this thesis was to reach by a systematic study of different ab initio procedures an improved description of the electronic properties of FeSi and FeGe. Central result is the itinerant description of FeSi as a semiconductor in the neighbourhood of a ferromagnetic instability. The regardment of the nonlocal exchange in the effective one-particle approximation leads to a metastable magnetic state scarcely above the magnetic ground state. The application of the hybrid functional leads to a 1st order metal-isolator transition for large lattice parameters: FeSi transforms at increasement of the lattice parameter from an unmagnetic isolator to a magnetic metal. A similar behavior is found in the isostructural compound FeGe. The two systems FeSi and FeGe were systematically and detailedly analyzed by means of ab initio procedures. Thereby the structural, electronic, and magnetic properties were studied with DFT and HF calculations. Both calculations with spin polarization and without spin polarization were performed.

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

    Directory of Open Access Journals (Sweden)

    G. Misra

    2011-01-01

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

  4. Structural, vibrational, electronic, NMR and reactivity analyses of 2-amino-4H-chromene-3-carbonitrile (ACC) by ab initio HF and DFT calculations.

    Science.gov (United States)

    Sridevi, C; Shanthi, G; Velraj, G

    2012-04-01

    This study represents an integrated approach towards understanding the vibrational, electronic, NMR, reactivity and structural aspects of 2-amino-4H-chromene-3-carbonitrile (ACC). A detailed interpretation of the FT IR, UV and NMR spectra were reported. Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. The electronic properties was also studied and the most prominent transition corresponds to π→π*. The lower frontier orbital energy gap and high dipole moment illustrates the high reactivity of the title molecule. The NMR results indicated that the observed chemical shifts depend not only on the structure of the molecule being studied, but also on the solvent used. ACC exhibited good nonlinear optical activity and was much greater than that of urea. Molecular electrostatic potential (MEP) results predicted that the enaminonitrile fragment of ACC to be the most reactive site for both electrophilic and nucleophilic attack. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Characterization of structure and dynamics of an aqueous scandium(III) ion by an extended ab initio QM/MM molecular dynamics simulation.

    Science.gov (United States)

    Vchirawongkwin, Viwat; Kritayakornupong, Chinapong; Tongraar, Anan; Rode, Bernd M

    2012-10-14

    Hydration structure and dynamics of an aqueous Sc(III) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(III) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(III)-O bond length of 2.14 Å was identified for six prism water molecules with one capping water located at around 2.26 Å, reproducing well the X-ray diffraction data. The Sc(III)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(III) ion predict a mean ligand residence time of 7.3 ps.

  6. Benzyl alcohol-ammonia (1:1) cluster structure investigated by combined IR-UV double resonance spectroscopy in jet and ab initio calculation

    Indian Academy of Sciences (India)

    Nikhil Guchhait

    2001-06-01

    Laser-induced fluorescence excitation and IR-UV double resonance spectroscopy have been used to determine the hydrogen-bonded structure of benzyl alcohol-ammonia (1:1) cluster in a jet-cooled molecular beam. In addition, ab initio quantum chemical calculations have been performed at HF/6-31G and HF/6-31G(d, p) levels for different ground state equilibrium structures of the cluster to correlate the calculated OH and NH frequencies and their intensities with experimental results. The broad red-shifted OH-stretching mode in the IR-UV double resonance spectrum suggests strong hydrogen bonding between the hydroxyl hydrogen and the lone pair of the ammonia nitrogen. The position and intensity distribution of the calculated NH and OH modes for the minimum-energy gauche form at HF/6-31 level have better correlation with the experimental results compared to other calculated ground state equilibrium conformers. These results lead to the conclusion that the minimum energy gauche form of the cluster is populated in the jet-cooled condition.

  7. Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Yaghlane, Saida Ben [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications – LSAMA, Université de Tunis, Tunis (Tunisia); Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 49707 (United States); Linguerri, Roberto; Hochlaf, Majdi, E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée (France)

    2013-11-07

    Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

  8. Ab initio study of the structural and electronic properties of the complex structures of RuO 2

    Science.gov (United States)

    Benyahia, K.; Nabi, Z.; Tadjer, A.; Khalfi, A.

    2003-11-01

    We have studied structural and electronic properties of RuO 2 in the two complex structures (rutile and orthorhombic) by means of accurate first principle total energy calculations using the full potential linearized augmented plane wave (FP-LAPW). The calculations are presented within the local-density approximation and the generalized gradient approximation. The orthorhombic (CaCl 2-type Pnnm) structure is just a deformation of the rutile (P4 2/mnm). Until now, considerable work has been performed on the rutile structure; however, no work has been performed on the orthorhombic structure. The structural properties are in good agreement with experiment. Our calculations of the electronic properties have been compared with experiment and previous calculations and a good agreement is found.

  9. Ab initio study of the structural and electronic properties of the complex structures of RuO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Benyahia, K.; Nabi, Z.; Tadjer, A.; Khalfi, A

    2003-11-01

    We have studied structural and electronic properties of RuO{sub 2} in the two complex structures (rutile and orthorhombic) by means of accurate first principle total energy calculations using the full potential linearized augmented plane wave (FP-LAPW). The calculations are presented within the local-density approximation and the generalized gradient approximation. The orthorhombic (CaCl{sub 2}-type Pnnm) structure is just a deformation of the rutile (P4{sub 2}/mnm). Until now, considerable work has been performed on the rutile structure; however, no work has been performed on the orthorhombic structure. The structural properties are in good agreement with experiment. Our calculations of the electronic properties have been compared with experiment and previous calculations and a good agreement is found.

  10. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu{sub 60}Ti{sub 20}Zr{sub 20} alloy

    Energy Technology Data Exchange (ETDEWEB)

    Amokrane, S.; Ayadim, A.; Levrel, L. [Groupe “Physique des Liquides et Milieux Complexes,” Faculté des Sciences et Technologie, Université Paris-Est (Créteil), 61 av. du Général de Gaulle, 94010 Créteil Cedex (France)

    2015-11-21

    We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.

  11. Structural, electronic, and mechanical properties of CoN and NiN. An ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Amudhavalli, A.; Manikandan, M.; Cinthia, A. Jemmy; Rajeswarapalanichamy, R. [NMSSVN College, Tamil Nadu (India). Dept. of Physics; Iyakutti, K. [SRM Univ., Tamil Nadu (India). Dept. of Physics and Nanotechnology

    2017-07-01

    The structural stabilities of cobalt mononitride (CoN) and nickel mono-nitride (NiN) were investigated among the crystal structures, namely, NaCl (B1), CsCl (B2), and zinc blende (B3). It was found that the zinc blende (B3) phase was the most stable phase for both nitrides. A pressure-induced structural phase transition from B3 to B1 phase was predicted in these nitrides. The computed lattice parameter values were in agreement with the experimental values and other theoretical values. The electronic structures reveal that these nitrides are metallic at zero pressure. The computed elastic constants indicate that CoN and NiN are mechanically stable in the B1 and B3 phases. The variations of the elastic constants, bulk modulus, shear modulus, Poisson's ratio, and elastic anisotropy factor with pressure were investigated. The Debye temperature θ{sub D} values are reported for both the nitrides in their B1 and B3 phases. The high-pressure NaCl phase of both CoN and NiN were found to be ferromagnetic.

  12. HfO_2and ZrO2 : Comparison of Structures and Thermodynamic and Electronic Properties Based on Ab Initio Calculations and Experiment

    Science.gov (United States)

    Demkov, Alexander A.; Navrotsky, Alexandra

    2001-03-01

    The International Technology Roadmap for Semiconductors (ITRS) predicts that the strategy of scaling complementary metal-oxide-semiconductor (CMOS) devices will come to an abrupt end around the year 2012. The main reason for this will be the unacceptably high leakage current through the silicon dioxide gate with a thickness below 20 ÅFinding a gate insulator alternative to SiO2 has proven to be far from trivial. Hafnium and zirconium dioxides and silicates have been recently considered as gate dielectrics with intermediate dielectric constants. Hafnia and ziconia are important ceramic materials as well, and their phase relations are rather well studied. There is also interest in hafnia as a constituent of ceramic waste forms for plutonium, based on its refractory nature and high neutron absorption cross section. We use a combination of the ab-initio calculations and calorimetry to investigate thermodynamic and electronic properties of hafnia and zirconia. We describe the cubic to tetragonal phase transition in the fluorite structure by computing the total energy surface for zone-edge distortions correct to fourth order in the soft-mode displacement with the strain coupling renormalization included. We compare the two materials using some simple chemical concepts.

  13. Ab initio study of the structural, elastic, and thermodynamic properties of tungsten monocarbide at high pressure and high temperature

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lei, E-mail: leoleu.hp@gmail.com [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan 621900 (China); Bi, Yan, E-mail: biyan_cn@yahoo.com.cn [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan 621900 (China); Xu, Jian [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan 621900 (China); Chen, Xiangrong [School of Physical Science and Technology, Sichuan University, Chengdu 610064 (China)

    2013-03-15

    Tungsten monocarbide (WC) exhibits unique physical and chemical properties. It is an indispensable industrial material used as cutting tools and has many potential applications in catalyst, energy storage, and so on. We performed calculations of the electronic structure in the framework of the density functional theory (DFT) with generalized gradient approximation (GGA) to investigate structural and elastic properties of WC. Bulk WC is very incompressible, but its bulk modulus is still smaller than diamond though Lin et al. reported that nano-crystalline WC was as incompressible as diamond. WC undergoes different compressibilities along a and c directions: the a-axis is more compressible than the c-axis. The ratio of shear modulus to bulk modulus (G/B) was studied and it was found that WC translated from the brittle to ductile state at ∼63 GPa. In order to compare with the EOS determined at finite temperature, the vibration effects of the crystal lattice are taken into account based on quasi-harmonic Debye model. The temperature effect on bulk modulus is discussed and the thermodynamic properties of WC, such as heat capacity C{sub V}, Debye temperature θ{sub D}, and thermal expansion α, are calculated simultaneously.

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

    Science.gov (United States)

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

    2014-06-10

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-07

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

  16. Insights into the structure and dynamics of a room-temperature ionic liquid: ab initio molecular dynamics simulation studies of 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and the [bmim][PF6]-CO2 mixture.

    Science.gov (United States)

    Bhargava, B L; Balasubramanian, S

    2007-05-03

    Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.

  17. Ab Initio Investigation on Structural, Elastic and Electronic Properties of η-Phase Cu4.5Ni1Au0.5Sn5 and Cu5Ni1Sn4.5In0.5 Intermetallic Compounds

    Science.gov (United States)

    Li, Xuezheng; Ma, Yong; Zhou, Wei; Wu, Ping

    2017-10-01

    The structural, elastic and electronic properties of quaternary intermetallic compounds η-Cu4.5Ni1Au0.5Sn5 and η-Cu5Ni1Sn4.5In0.5 are investigated by an ab initio method. The calculated heat of formation determines preferential occupancy sites for Ni, Au and In atoms which lead to thermodynamically stable compounds. Variation of lattice constants reveals that the change of atomic bonding has a directional discrepancy in η-Cu4.5Ni1Au0.5Sn5; the polycrystalline moduli obtained from single-crystal elastic stiffness show an increase after both Ni/Au and Ni/In additions. Also, the anisotropy of Young's modulus and shear modulus is significantly weakened in η-Cu4.5Ni1Au0.5Sn5. The density of states and maps of charge density distribution suggest that the atomic bonding in the quaternary intermetallic compounds is strengthened by the addition of Ni and Au but weakened by the addition of In.

  18. Structural and electronic properties of Sin, Sin+, and AlSin-1 (n=2-13) clusters: Theoretical investigation based on ab initio molecular orbital theory

    Science.gov (United States)

    Nigam, Sandeep; Majumder, Chiranjib; Kulshreshtha, S. K.

    2004-10-01

    The geometric and electronic structures of Sin, Sin+, and AlSin-1 clusters (2⩽n⩽13) have been investigated using the ab initio molecular orbital theory under the density functional theory formalism. The hybrid exchange-correlation energy function (B3LYP) and a standard split-valence basis set with polarization functions [6-31G(d)] were employed for this purpose. Relative stabilities of these clusters have been analyzed based on their binding energies, second difference in energy (Δ 2E) and fragmentation behavior. The equilibrium geometry of the neutral and charged Sin clusters show similar structural growth. However, significant differences have been observed in the electronic structure leading to their different stability pattern. While for neutral clusters, the Si10 is magic, the extra stability of the Si11+ cluster over the Si10+ and Si12+ bears evidence for the magic behavior of the Si11+ cluster, which is in excellent agreement with the recent experimental observations. Similarly for AlSin-1 clusters, which is isoelectronic with Sin+ clusters show extra stability of the AlSi10 cluster suggesting the influence of the electronic structures for different stabilities between neutral and charged clusters. The ground state geometries of the AlSin-1 clusters show that the impurity Al atom prefers to substitute for the Si atom, that has the highest coordination number in the host Sin cluster. The fragmentation behavior of all these clusters show that while small clusters prefers to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size.

  19. An ab initio study of hydroxylated graphane

    Science.gov (United States)

    Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola

    2017-09-01

    Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.

  20. Giant magnetoresistance An ab-initio description

    CERN Document Server

    Binder, J

    2000-01-01

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

  1. Ab initio study of structural, elastic, electronic and optical properties of spinel SnMg{sub 2}O{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Reffas, M. [Laboratory for Developing New Materials and their Characterization, Department of Physics, Faculty of Science, University of Setif, 19000 Setif (Algeria); Bouhemadou, A., E-mail: a_bouhemadou@yahoo.f [Laboratory for Developing New Materials and their Characterization, Department of Physics, Faculty of Science, University of Setif, 19000 Setif (Algeria); Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Khenata, R. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Laboratoire de Physique Theorique, B.P. 230, Universite de Tlemcen, Tlemcen 13000 (Algeria); Ouahrani, T. [Laboratoire de Physique Quantique et de Modelisation Mathematique, Universite de Mascara, 29000 Mascara (Algeria); Bin-Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia)

    2010-09-15

    Ab initio study of structural, elastic, electronic and optical properties of the cubic spinel oxide SnMg{sub 2}O{sub 4} has been reported using the pseudo-potential plane-wave method within the local density approximation and the gradient generalized approximation for the exchange and correlation potential. Computed lattice constant and internal free parameters are in good agreement with the available experimental results. The elastic constants and their pressure dependence are predicted using the static finite strain technique. A linear pressure dependence of the elastic stiffnesses is found. A set of isotropic elastic parameters and related properties, namely bulk and shear moduli, Young's modulus, Poisson's ratio, Lame's coefficients, average sound velocity and Debye temperature are numerically estimated in the frame-work of the Voigt-Reuss-Hill approximation for SnMg{sub 2}O{sub 4} polycrystalline. Band structure shows that SnMg{sub 2}O{sub 4} has a direct band gap ({Gamma}-{Gamma}), which increases with increase in pressure. Density of states and Mulliken population analysis show that the Mg-O bond is typically covalent due to the O-2p and Mg-2p states hybridizations. In order to understand the optical properties of SnMg{sub 2}O{sub 4}, the dielectric function, optical reflectivity, refractive index, extinction coefficient and electron energy loss function are calculated for radiation up to 40 eV. The pressure dependence of the zero-frequency limit of the real part of the dielectric function {epsilon}{sub 1}(0) and of the refractive index n(0) has been investigated. This is the first quantitative theoretical prediction of the elastic, electronic and optical properties of the SnMg{sub 2}O{sub 4} compound, and it still awaits experimental confirmation.

  2. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  4. Iron -chromium alloys and free surfaces: from ab initio calculations to thermodynamic modeling; Demixtion et segregation superficielle dans les alliages fer-chrome: de la structure electronique aux modeles thermodynamiques

    Energy Technology Data Exchange (ETDEWEB)

    Levesque, M.

    2010-11-15

    Ferritic steels possibly strengthened by oxide dispersion are candidates as structural materials for generation IV and fusion nuclear reactors. Their use is limited by incomplete knowledge of the iron-chromium phase diagram at low temperatures and of the phenomena inducing preferential segregation of one element at grain boundaries or at surfaces. In this context, this work contributes to the multi-scale study of the model iron-chromium alloy and their free surfaces by numerical simulations. This study begins with ab initio calculations of properties related to the mixture of atoms of iron and chromium. We highlight complex dependency of the magnetic moments of the chromium atoms on their local chemical environment. Surface properties are also proving sensitive to magnetism. This is the case of impurity segregation of chromium in iron and of their interactions near the surface. In a second step, we construct a simple energy model for high numerical efficiency. It is based on pair interactions on a rigid lattice to which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that we compare to Monte Carlo simulations. The last step of our work is to introduce free surfaces in our model. We then study the effect of ab initio calculated bulk and surface properties on surface segregation.Finally, we calculate segregation isotherms. We therefore propose an evolution model of surface composition of iron-chromium alloys as a function of bulk composition. which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that

  5. Ab initio analysis of a vacancy and a self-interstitial near single crystal silicon surfaces: Implications for intrinsic point defect incorporation during crystal growth from a melt

    Energy Technology Data Exchange (ETDEWEB)

    Kamiyama, Eiji; Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan); Vanhellemont, Jan [Department of Solid State Sciences, Ghent University, Krijgslaan 281-S1, Gent 9000 (Belgium)

    2012-10-15

    The microscopic model of the Si (001) crystal surface was investigated by first principles calculations to clarify the behavior of intrinsic point defects near crystal surfaces. A c(4 x 2) structure model was used to describe the crystal surface in contact with vacuum. The calculations show lower formation energy near the surface and the existence of formation energy differences between the surface and the bulk for both types of intrinsic point defects. The tetrahedral (T)-site and the dumbbell (DB)-site, in which a Si atom is captured from the surface and forms a self-interstitial, are found as stable sites near the third atomic layer. The T-site has a barrier of 0.48 eV, whereas the DB-site has no barrier for the interstitial to penetrate into the crystal from the vacuum. Si atoms in a melt can migrate and reach at the third layer during crystal growth when bulk diffusion coefficient is used. Therefore, the melt/solid interface is always a source of intrinsic point defects. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Si doped T6 carbon structure as an anode material for Li-ion batteries: An ab initio study

    Science.gov (United States)

    Rajkamal, A.; Kumar, E. Mathan; Kathirvel, V.; Park, Noejung; Thapa, Ranjit

    2016-11-01

    First-principles calculations are performed to identify the pristine and Si doped 3D metallic T6 carbon structure (having both sp2 and sp3 type hybridization) as a new carbon based anode material. The π electron of C2 atoms (sp2 bonded) forms an out of plane network that helps to capture the Li atom. The highest Li storage capacity of Si doped T6 structure with conformation Li1.7Si1C5 produces theoretical specific capacity of 632 mAh/g which substantially exceeding than graphite. Also, open-circuit voltage (OCV) with respect to Li metal shows large negative when compared to the pristine T6 structure. This indicates modifications in terms of chemical properties are required in anode materials for practical application. Among various doped (Si, Ge, Sn, B, N) configuration, Si doped T6 structure provides a stable positive OCV for high Li concentrations. Likewise, volume expansion study also shows Si doped T6 structure is more stable with less pulverization and substantial capacity losses in comparison with graphite and silicon as an anode materials. Overall, mixed hybridized (sp2 + sp3) Si doped T6 structure can become a superior anode material than present sp2 hybridized graphite and sp3 hybridized Si structure for modern Lithium ion batteries.

  7. Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

    Science.gov (United States)

    Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.

    2017-01-01

    The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc.

  8. Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

    Science.gov (United States)

    Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.

    2017-01-01

    The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc. PMID:28054595

  9. Ab initio study of the effects of dilute defects on the local structure of unalloyed δ-plutonium

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, Sarah Christine [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kisiel, Elliot Steven [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Freibert, Franz Joseph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-11-22

    We used density functional theory to examine the effects impurities and vacancies in the dilute limit in order to explore the effects on the local structure of the unalloyed face centered cubic δ-Pu lattice. The impurities considered are the radioactive daughter U or stabilizers in δ-phase stabilizer Ga. These impurities were placed at various interstitial sites, including octahedral, tetrahedral, and split interstitial along the (100) direction, as well as substitutional lattice sites. Self-interstitials, mono and di-vacancies were also considered. In addition we examined impurity-vacancy complexes at first and second nearest neighboring distances from each other. Radial distribution functions were plotted to gauge the local structural variations around the defect within the lattice and volume change with structural variation quantifies influence on thermodynamics. These local distortions will be discussed in this report.

  10. FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data.

    Science.gov (United States)

    Heinonen, Markus; Rantanen, Ari; Mielikäinen, Taneli; Kokkonen, Juha; Kiuru, Jari; Ketola, Raimo A; Rousu, Juho

    2008-10-01

    We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MS(n) product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS(n) product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS(n) product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid.

  11. Electronic structure and magnetic properties of PbMO3 (M = Fe, Co, Ni) magnetic perovskites: An ab initio study

    Science.gov (United States)

    Erkişi, Aytaç; Yıldırım, Erdem Kamil; Gökoğlu, Gökhan

    2014-08-01

    We present the electronic, magnetic and structural properties of the magnetic transition metal oxides PbMO3 (M = Fe, Co, Ni) in cubic perovskite structure. The calculations are based on the density functional theory (DFT) within plane-wave pseudopotential method and local spin density approximation (LSDA) of the exchange-correlation functional. On-site Coulomb interaction is also included in calculations (LSDA+U). The systems are considered in ferromagnetic (FM) and G-type antiferromagnetic (G-AFM) order. FM structures are energetically more favored than G-AFM and than non-magnetic states for all the systems studied. The spin-polarized electronic band structures show that all the structures have metallic property in FM order without Hubbard-U interaction (Ueff = 0). However, the inclusion of on-site Coulomb interaction (Ueff = 7 eV) opens a semiconducting gap for majority spin channel of PbFeO3 and of PbNiO3 resulting in a half-metallic character. PbCoO3 system remains as metallic with LSDA+U scheme. Bonding features of all structures are largely determined by the hybridizations between O-p and d-states of transition metal atoms. The partial magnetic moment of Fe atom in PbFeO3 is enhanced by inclusion of Hubbard-U interaction (2.55 μB ⇒ 3.78 μB). Total magnetic moments of half-metallic PbFeO3 and of PbNiO3 compounds are very close to integer values.

  12. Finding the Stable Structures of WxN1-x with an ab-initio High-Throughput Approach

    Science.gov (United States)

    2014-03-13

    of NaCl) we looked at all 255 combinations. We found 34 unique structures, including NbO itself, CsCl, S3U4, ReO3,[59] cubic perovskite (with formula...simulation of the liquid-metal/amorphous- semiconductor transition in germanium, Phys. Rev. B 49, 14251–14269 (1994). [36] G. Kresse, , Ph.D. thesis

  13. Structural stability and decomposition of Mg(BH4)2 isomorphs - an ab initio free energy study

    DEFF Research Database (Denmark)

    Voss, Johannes; Hummelshøj, Jens Strabo; Lodziana, Z.

    2009-01-01

    We present the first comprehensive comparison between free energies, based on a phonon dispersion calculation within density functional theory, of theoretically predicted structures and the experimentally proposed a (P6(1)) and beta (Fddd) phases of the promising hydrogen storage material Mg(BH4)...... temperature stability and decomposition temperatures of novel borohydride systems....

  14. Ab initio calculations for structural, electronic and magnetic behaviors of nitrogenized monolayer graphene decorated with 5d transition metal atoms

    Science.gov (United States)

    Rafique, Muhammad; Shuai, Yong; Xu, Meng; Zhang, Guohua; Guo, Yanming

    2017-09-01

    Graphene-based magnetic materials have revealed great potential for developing high-performance electronic units at sub-nanometer such as spintronic data storage devices. However, a significant ferromagnetism behavior and ample band gap in the electronic structure of graphene is required before it can be used for actual engineering applications. Based on first-principles calculations, here we demonstrate the structural, electronic and magnetic behaviors of 5d transition metal (TM) atom-substituted nitrogenized monolayer graphene. We find that, during TMN(3)4 cluster-substitution, tight bonding occurs between impurity atoms and graphene with significant binding energies. Charge transfer occurs from graphene layer to the TMN(3)4 clusters. Interestingly, PtN3, TaN4 and ReN4 cluster-doped graphene structures exhibit dilute magnetic semiconductor behavior with 1.00 μB, 1.04 μB and 1.05 μB magnetic moments, respectively. While, OsN4 and PtN4 cluster-doped structures display nonmagnetic direct band gap semiconductor behavior. Remaining, TMN(3)4 cluster-doped graphene complexes exhibit half metal properties. Detailed analysis of density of states (DOS) plots indicate that d orbitals of TM atoms should be responsible for arising magnetic moments in graphene. Given results pave a new route for potential applications of dilute magnetic semiconductors and half-metals in spintronic devices by employing TMN(3)4 cluster-doped graphene complexes.

  15. Ab initio investigation of structure, stability, thermal behavior, bonding, and infrared spectra of ionized water cluster (H2O)6+

    Science.gov (United States)

    Liu, Lei; Hu, Cui-E.; Tang, Mei; Chen, Xiang-Rong; Cai, Ling-Cang

    2016-10-01

    The low-lying isomers of cationic water cluster (H2O)6+ have been globally explored by using particle swarm optimization algorithm in conjunction with quantum chemical calculations. Compared with previous results, our searching method covers a wide range of structural isomers of (H2O)6+ and therefore turns out to be more effective. With these local minima, geometry optimization and vibrational analysis are performed for the most interesting clusters at second-order Møller-Plesset (MP2)/aug-cc-pVDZ level, and their energies are further refined at MP2/aug-cc-pVTZ and coupled-cluster theory with single, double, and perturbative triple excitations/aug-cc-pVDZ level. The interaction energies using the complete basis set limits at MP2 level are also reported. The relationships between their structure arrangement and their energies are discussed. Based on the results of thermal simulation, structural change from a four-numbered ring to a tree-like structure occurs at T ≈ 45 K, and the relative population of six lowest-free-energy isomers is found to exceed 4% at some point within the studied temperature range. Studies reveal that, among these six isomers, two new-found isomers constitute 10% of isomer population at 180 K, and the experimental spectra can be better explained with inclusions of the two isomers. The molecular orbitals for six representative cationic water clusters are also studied. Through topological and reduced density gradient analysis, we investigated the structural characteristics and the bonding strengths of these water cluster radical cations.

  16. Ab Initio Quantum Mechanical Study of the Structure and Stability of the Alkaline Earth Metal Oxides and Peroxides

    Science.gov (United States)

    Königstein, Markus; Catlow, C. Richard A.

    1998-10-01

    We report a detailed computationally study of the stability of the alkaline earth metal peroxidesMO2(M=Ba, Sr, Ca, Mg, Be) with respect to decomposition into the corresponding oxidesMOand molecular oxygen using Hartree-Fock and density functional theory (DFT) techniques. A comparison between calculated and experimental binding energies indicates that the DFT method is most suitable for a correct description of the peroxide bond. The DFT reaction energies for the peroxide decompositionMO2→MO+{1}/{2}O2show that only BaO2and SrO2are thermodynamically stable compounds, while CaO2(in the calcium carbide structure), MgO2, and BeO2(in the pyrite structure) are energetically unstable with reaction energies of -24.7, -26.8, and -128.7kJ/mol, respectively, and are therefore unlikely to exist as pure compounds. The published calcium carbide structure for CaO2is probably incorrect, at least for pure calcium peroxide, since apart from the thermodynamical instability the compound is more stable in the pyrite structure by 25.5 kJ/mol. Our analysis suggests that the water and/or hydrogen peroxide content of experimentally prepared MgO2samples is necessary for the stabilization of the structure, while BeO2is clearly unstable under ambient conditions. We studied also the effect of the zero point energies and the entropies on the decomposition free energies and, for this purpose, performed atomistic lattice simulations based on interatomic potentials, which we derived from ourab initiodata; the results indicate a negligible effect of the zero point energies, while the entropy terms favor the decomposition reaction by ca. 20 kJ/mol at 298.15 K.

  17. Structure, stability and bonding of (BC 2N) n, n=2,3: an ab initio study

    Science.gov (United States)

    Kar, T.; Cuma, M.; Scheiner, S.

    2000-12-01

    The dimer and trimer of BC 2N are studied at the HF and MPn levels using 3-21G, 6-31G ∗ and 6-31+G ∗ basis sets. It is found that stability is enhanced by maintaining -BN- units together in the cyclic form. Both molecules have cyclic ground state structures with cumulenic-type equal bond lengths in the -BNBN- and polyacetylenic -CCCC- fragments. The linear-cyclic energy difference increases with the size of the cluster. Electron correlation substantially favors the cyclic structures over the linear forms. No general trend of atomic combination has been found in the linear isomers. Diffuse functions have negligible effects on the relative energies and geometries of the dimers.

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

    Science.gov (United States)

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

    2013-04-26

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

  19. Ab-initio investigation of structural, electronic and optical properties BSb compound in bulk and surface (110 states

    Directory of Open Access Journals (Sweden)

    H A Badehian

    2015-07-01

    Full Text Available In recent work the structural, electronic and optical properties of BSb compound in bulk and surface (110 states have been studied. Calculations have been performed using Full-Potential Augmented Plane Wave (FP-LAPW method by WIEN2k code in Density Functional Theory (DFT framework. The structural properties of the bulk such as lattice constant, bulk module and elastic constants have been investigated using four different approximations. The band gap energy of the bulk and the (110 surface of BSb were obtained about 1.082 and 0.38 eV respectively. Moreover the surface energy, the work function, the surface relaxation, surface state and the band structure of BSb (110 were investigated using symmetric and stoichiometric 15 layers slabs with the vacuum of 20 Bohr. In addition, the real and imaginary parts of the dielectric function of the bulk and the BSb (110 slab were calculated and compared to each other. Our obtained results have a good agreement with the available results.

  20. Metallic behavior of NiS thin film under the structural, optical, electrical and ab initio investigation frameworks

    Energy Technology Data Exchange (ETDEWEB)

    Boughalmi, R. [Unité de physique des dispositifs à semi-conducteurs, Faculté des sciences de Tunis, Tunis El Manar University, 2092 Tunis (Tunisia); Rahmani, R. [Laboratoire de Physique des Couches Minces et Matériaux pour l' Electronique (LPC2ME). Département de physique, Faculté des Sciences, Université d' Oran Es-Sénia, Oran (Algeria); Département de physique, Université des Sciences et de la Technologie d' Oran- Mohamed-Boudiaf, Oran (Algeria); Boukhachem, A., E-mail: abdelwaheb.boukhachem@laposte.net [Unité de physique des dispositifs à semi-conducteurs, Faculté des sciences de Tunis, Tunis El Manar University, 2092 Tunis (Tunisia); Amrani, B.; Driss-Khodja, K. [Laboratoire de Physique des Couches Minces et Matériaux pour l' Electronique (LPC2ME). Département de physique, Faculté des Sciences, Université d' Oran Es-Sénia, Oran (Algeria); Amlouk, M. [Unité de physique des dispositifs à semi-conducteurs, Faculté des sciences de Tunis, Tunis El Manar University, 2092 Tunis (Tunisia)

    2015-08-01

    Nickel sulfide (NiS) thin films were deposited on the glass substrates by spray pyrolysis at 250 °C using an aqueous solution which contains nickel chloride hexahydrate and thiourea as precursors. X-ray diffraction analysis confirms that the hexagonal structure is being part of P6{sub 3}/mmc space group of the deposited films with (100) preferred orientation and lattice parameters a = 3.441 Å and c = 5.320 Å. The optical properties, investigated through transmittance and reflectance measurements reveal that the direct band gap energy (Eg) is around 0.55 eV. The electrical study shows a metallic behavior of the current II-VI binary compound. This behavior regarding NiS II-VI binary sulfide was confirmed by numerical studies based on the density functional theory (DFT) were adopted. The ground state quantities, such as lattice parameter, bulk modulus and its pressure derivative as well as the elastic constants were obtained. The values are consistent with the stability of hexagonal structure. The band structure and the states densities of such material were studied. The results show that there is an agreement between experimental and simulation. - Highlights: • NiS thin films are synthesized by Spray pyrolysis. • NiS is a low band gap compound. • These films have interesting electrical properties showing a metallic behavior. • Computational study confirms the electrical measurements.

  1. Structural, electronic, magnetic and thermodynamic properties of full-Heusler compound Co{sub 2}VSi: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Bentouaf, Ali, E-mail: lilo.btf@gmail.com [Département de Physique, Faculté des Sciences, Université de Hassiba Ben Bouali, Chlef 02000 (Algeria); Hassan, Fouad El Haj [Université Libanaise, Faculté des Sciences (I), Laboratoire de Physique et d' Electronique (LPE), Elhadath, Beirut (Lebanon); Condensed Matter Section, The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34014 Trieste (Italy)

    2015-05-01

    Density functional theory based on full-potential linearized augmented plane wave (FP LAPW) method is used to investigate the structural, electronic and magnetic properties of Co{sub 2}VSi Heusler alloys, with L2{sub 1} structure. It is shown that calculated lattice constants and spin magnetic moments using the general gradient approximation method are in good agreement with experimental values. We also presented the thermal effects using the quasi-harmonic Debye model, in which the lattice vibrations are taken into account. Temperature and pressure effects on the structural parameters, heat capacities, thermal expansion coefficient, and Debye temperatures are determined from the non-equilibrium Gibbs functions. - Highlights: • Our calculated total magnetic moment is 2.96 μB. • The quasi-harmonic Debye model has been used to predict the thermal properties. • The GGA method is a good tool to calculate the magnetic moment. • The total DOS is calculated for the majority and minority spin densities. • The d–d hybridization is essential for the formation of the gap at E{sub F}.

  2. Structures and electronic properties of B3Sin(-) (n = 4-10) clusters: A combined ab initio and experimental study.

    Science.gov (United States)

    Wu, Xue; Lu, Sheng-Jie; Liang, Xiaoqing; Huang, Xiaoming; Qin, Ying; Chen, Maodu; Zhao, Jijun; Xu, Hong-Guang; King, R Bruce; Zheng, Weijun

    2017-01-28

    The anionic silicon clusters doped with three boron atoms, B3Sin(-) (n = 4-10), have been generated by laser vaporization and investigated by anion photoelectron spectroscopy. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) of these anionic clusters are determined. The lowest energy structures of B3Sin(-) (n = 4-10) clusters are globally searched using genetic algorithm incorporated with density functional theory (DFT) calculations. The photoelectron spectra, VDEs, ADEs of these B3Sin(-) clusters (n = 4-10) are simulated using B3LYP/6-311+G(d) calculations. Satisfactory agreement is found between theory and experiment. Most of the lowest-energy structures of B3Sin(-) (n = 4-10) clusters can be derived by using the squashed pentagonal bipyramid structure of B3Si4(-) as the major building unit. Analyses of natural charge populations show that the boron atoms always possess negative charges, and that the electrons transfer from the 3s orbital of silicon and the 2s orbital of boron to the 2p orbital of boron. The calculated average binding energies, second-order differences of energies, and the HOMO-LUMO gaps show that B3Si6(-) and B3Si9(-) clusters have relatively high stability and enhanced chemical inertness. In particular, the B3Si9(-) cluster with high symmetry (C3v) stands out as an interesting superatom cluster with a magic number of 40 skeletal electrons and a closed-shell electronic configuration of 1S(2)1P(6)1D(10)2S(2)2P(6)1F(14) for superatom orbitals.

  3. Structures and electronic properties of B3Sin- (n = 4-10) clusters: A combined ab initio and experimental study

    Science.gov (United States)

    Wu, Xue; Lu, Sheng-Jie; Liang, Xiaoqing; Huang, Xiaoming; Qin, Ying; Chen, Maodu; Zhao, Jijun; Xu, Hong-Guang; King, R. Bruce; Zheng, Weijun

    2017-01-01

    The anionic silicon clusters doped with three boron atoms, B3Sin- (n = 4-10), have been generated by laser vaporization and investigated by anion photoelectron spectroscopy. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) of these anionic clusters are determined. The lowest energy structures of B3Sin- (n = 4-10) clusters are globally searched using genetic algorithm incorporated with density functional theory (DFT) calculations. The photoelectron spectra, VDEs, ADEs of these B3Sin- clusters (n = 4-10) are simulated using B3LYP/6-311+G(d) calculations. Satisfactory agreement is found between theory and experiment. Most of the lowest-energy structures of B3Sin- (n = 4-10) clusters can be derived by using the squashed pentagonal bipyramid structure of B3Si4- as the major building unit. Analyses of natural charge populations show that the boron atoms always possess negative charges, and that the electrons transfer from the 3s orbital of silicon and the 2s orbital of boron to the 2p orbital of boron. The calculated average binding energies, second-order differences of energies, and the HOMO-LUMO gaps show that B3Si6- and B3Si9- clusters have relatively high stability and enhanced chemical inertness. In particular, the B3Si9- cluster with high symmetry (C3v) stands out as an interesting superatom cluster with a magic number of 40 skeletal electrons and a closed-shell electronic configuration of 1S21P61D102S22P61F14 for superatom orbitals.

  4. Ab initio study of structural, mechanical, thermal and electronic properties of perovskites Sr(Li,Pd)H3

    Science.gov (United States)

    Benlamari, S.; Amara Korba, S.; Lakel, S.; Meradji, H.; Ghemid, S.; El Haj Hassan, F.

    2016-01-01

    The structural, elastic, thermal and electronic properties of perovskite hydrides SrLiH3 and SrPdH3 have been investigated using the all-electron full-potential linear augmented plane wave (FP-LAPW) method based on the density functional theory (DFT). For the exchange-correlation potential, local-density approximation (LDA) and generalized gradient approximation (GGA) have been used to calculate theoretical lattice parameters, bulk modulus, and its pressure derivative. The present results are in good agreement with available theoretical and experimental data. The three independent elastic constants (C11, C12 and C44) are also reported. From electronic band structure and density of states (DOSs), it is found that SrLiH3 is an insulator characterized by an indirect gap of 3.48 eV, while SrPdH3 is metallic with a calculated DOSs at Fermi energy of 0.745 states/eV-unit cell. Poisson’s ratio (σ), Young’s modulus (E), shear modulus (G), anisotropy factor (A), average sound velocities (vm) and density (ρ) of these compounds are also estimated for the first time. The Debye temperature is deduced from the average sound velocity. Variation of elastic constants and bulk modulus of these compounds as a function of pressure is also reported. Pressure and thermal effects on some macroscopic properties are predicted using the quasi-harmonic Debye model.

  5. Computation and interpretation of vibrational spectra on the structure of Losartan using ab initio and Density Functional methods

    Science.gov (United States)

    Latha, B.; Gunasekaran, S.; Srinivasan, S.; Ramkumaar, G. R.

    2014-11-01

    The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm-1. The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. (1)H and (13)C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.

  6. Ab initio study of structural and electronic properties of (GaN)n/(AlN)n superlattices

    Science.gov (United States)

    Djoudi, L.; Merabet, M.; Dahmane, F.; Boucharef, M.; Benalia, S.; Rached, D.

    2016-10-01

    Structural and electronic properties of binary GaN and AlN compounds and their superlattices (SLs) (GaN)n/(AlN)n are investigated using the first-principles full potential linear muffin-tin orbitals method (FP-LMTO). The exchange-correlation potential is treated with the local density approximation of Perdew and Wang (LDA-PW). The ground-state properties are determined for the bulk materials GaN, AlN, and their superlattices (GaN)n/(AlN)n) in cubic phase. The calculated structural properties of GaN and AlN compounds are in good agreement with available experimental and theoretical data. It is found that AlN exhibit an indirect fundamental band gap while that GaN and the superlattices (SLs) exhibit a direct fundamental band gap, which might make the superlattices (GaN)n/(AlN)n materials promising and useful for optoelectronic applications. The fundamental band gap decreases with increasing the number of monolayer.

  7. Coupling of Magnetization and Structural Distortions in Multiferroic BiFeO3:an Ab Initio Density Functional Theory Study

    Institute of Scientific and Technical Information of China (English)

    FENG Hong-Jian; LIU Fa-Min

    2008-01-01

    The coupling between magnetism and structural distortions in BiFeO3 (BFO) is investigated using density functional theory by considering the spin-orbit effect.Computational results show that the resulting magnetization M is rotated by reversal of sense of rotation of the oxygen octahedra in the double cell.The resulting magnetization is determined by the antiferrodistortive (AFD) distortions and ferroelectric (FE) displacements.This work clarifies the previous view that magnetism is only coupled with,and determined by,FE displacements.The excellent ferroelectricity is attributed significantly to the anomaly of Born effective charge of Bi,which is caused by the stereochemically active long pair of Bi 6s.

  8. Structural, electronic, optical and thermodynamic properties of cubic REGa{sub 3} (RE = Sc or Lu) compounds: Ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Murtaza, G., E-mail: murtaza@icp.edu.pk [Materials Modeling Laboratory, Department of Physics, Islamia College Peshawar (Pakistan); Gupta, S.K. [Department of Physics, Michigan Technological University, Houghton, MI 49931 (United States); Seddik, T. [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 Mascara (Algeria); Khenata, R., E-mail: khenata_rabah@yahoo.fr [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 Mascara (Algeria); Alahmed, Z.A. [Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451 (Saudi Arabia); Ahmed, R. [Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor (Malaysia); Khachai, H. [Physics Department, Djillali Liabes University of Sidi Bel-Abbes (Algeria); Jha, P.K. [Department of Physics, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar 364001 (India); Bin Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451 (Saudi Arabia)

    2014-06-01

    Highlights: • REGa{sub 3} (RE = Sc or Lu) compounds are mechanical stabile. • Both ScGa{sub 3} and LuGa{sub 3} exhibit metallic behavior just like other REGa{sub 3} compounds. • Melting temperature T{sub m} (K) for ScGa{sub 3} and LuGa{sub 3} are 1244.2 and 1143.8. • High absorption observed in the visible energy region. • The present study would be helpful for future experimental/theoretical explorations. - Abstract: Structural, elastic, optoelectronic and thermodynamic properties of REGa{sub 3} (RE = Sc and Lu) compounds have been studied self consistently by employing state of the art full potential (FP) linearized (L) approach of augmented plane wave (APW) plus local orbitals method. Calculations were executed at the level of Perdew–Burke and Ernzerhof (PBE) parameterized generalized gradient approximation (GGA) for exchange correlation functional in addition to modified Becke–Johnson (mBJ) potential. Our obtained results of lattice parameters show reasonable agreement to the previously reported experimental and other theoretical studies. Analysis of the calculated band structure of ScGa{sub 3} and LuGa{sub 3} compounds demonstrates their metallic character. Moreover, a positive value of calculated Cauchy pressure, in addition to reflecting their ductile nature, endorses their metallic character as well. To understand optical behavior calculations related to the important optical parameters; real and imaginary parts of the dielectric function, reflectivity R(ω), refractive index n(ω) and electron energy-loss function L(ω) have also been performed. In the present work, thermodynamically properties are also investigated by employing lattice vibrations integrated in quasi harmonic Debye model. Obtained results of volume, heat capacity and Debye temperature as a function of temperature for both compounds, at different values of pressure, are found to be consistent. The calculated value of melting temperature for both compounds (ScGa{sub 3} and Lu

  9. Ab initio studies of the structure and energies of the NO sup minus He and NO sup minus Ar complexes

    Energy Technology Data Exchange (ETDEWEB)

    Chalasinski, G.; Kukawska-Tarnawska, B. (Univ. of Warsaw (Poland))

    1990-05-03

    The structure and energy of the NO{sup {minus}}({sup 3}{Sigma}{sup {minus}}){hor ellipsis}He({sup 1}S) system have been studied by means of the Moeller-Plesset perturbation theory. The potential energy surface was found to be very flat and fairly isotropic, with three shallow minima. The global minimum was found for the collinear configuration N-O{hor ellipsis}He, R{sub NO} = 1.28 {angstrom}, R{sub OHe} = 3.25 {angstrom}, and D{sub e} = 69 cm{sup {minus}1}. For the same configuration the authors also studied the NO{sup {minus}}({sup 3}{Sigma}{sup {minus}}){hor ellipsis}Ar({sup 1}S) complex and found the well parameters R{sub OAr} = 3.25 {angstrom} and D{sub e} = 509 cm{sup {minus}1}, to be compared with the experimental estimate of D{sub e} = 460 cm{sup {minus}1}. In both systems the electron correlation contribution is very important and constitutes about half of the total interaction energy.

  10. Environmental effects on the structure of metal ion-DOTA complexes: An ab initio study of radiopharmaceutical metals.

    Energy Technology Data Exchange (ETDEWEB)

    Lau, E Y; Lightstone, F C; Colvin, M E

    2006-02-10

    Quantum mechanical calculations were performed to study the differences between the important radiopharmaceutical metals yttrium (Y) and indium (In) bound by DOTA and modified DOTA molecules. Energies were calculated at the MP2/6-31+G(d)//HF/6-31G(d) levels, using effective core potentials on the Y and In ions. Although the minimum energy structures obtained are similar for both metal ion-DOTA complexes, changes in coordination and local environment significantly affect the geometries and energies of these complexes. Coordination by a single water molecule causes a change in the coordination number and a change in the position of the metal ion in In-DOTA; but, Y-DOTA is hardly affected by water coordination. When one of the DOTA carboxylates is replaced by an amide, the coordination energy for the amide arm shows a large variation between the Y and In ions. Optimizations including water and guandinium moieties to approximate the effects of antibody binding indicate a large energy cost for the DOTA-chelated In to adopt the ideal conformation for antibody binding.

  11. Structural, vibrational and bonding properties of hydro-nitrogen solids under high pressure: An ab-initio study

    Indian Academy of Sciences (India)

    G VAITHEESWARAN; N YEDUKONDALU; B MOSES ABRAHAM

    2016-10-01

    Hydro-nitrogen solids are potential high energy density materials (HEDMs) due to high mass ratio of nitrogen which find wide range of applications as propellants and explosives. In the present work, we report the structural and vibrational properties of Tetramethyl Ammonium Azide (TMAA) and HydroZonium Azide(HZA) using density functional theory calculations by treating weak intermolecular interactions. The obtained ground state parameters using vdW-TS method are in good agreement with the experimental data. The pressure dependent lattice constants, compressibility and equation of state are discussed. The obtained equilibrium bulk moduli show the soft nature of these materials. The compressibility curves reveal that these compounds are highly compressible along crystallographic a-axis.We have also calculated the zone-center phonon frequencies and made a complete analysis of vibrational spectra at ambient as well as at high pressure. Contraction and elongation of C-H and N-H (NH₃ stretching) bonds under pressure lead to blue- and red-shift of the frequencies in the mid-IR region for TMAA and HZA compounds, respectively

  12. An ab initio study of niobium(n=2-11)clusters:structure,stability and magnetism

    Institute of Scientific and Technical Information of China (English)

    Ren Feng-Zhu; Wang Yuan-Xu; Zhang Guang-Biao; Wei Shu-Ke; Luo You-Hua

    2009-01-01

    The ground-state configurations of the Nbn(n2-11)clusters are studied through the first-principles calculations.It is found that niobium clusters(n=2-11)tend to form compact structures with low symmetry.The clusters with 4,8 and 10 atoms axe found to be magic and have relatively large highest occupied-lowest unoccupied molecular orbital(HOMO-LUMO)gaps.The Nbn clusters possess low magnetic moments,which exhibit an odd-even oscillational character.The analyses of calculated electronic density and population of the lowest-energy niobium clusters for n=2,3,5,7,9,11 show that the total magnetic moments of Nbn originate mainly from a few Nb atoms with longer spacings between them in most cases,while thcy are located on two Nb atoms for n=2,3,5.The total magnetic moments come mainly from the 4d local moments but with the exception of the Nb5 cluster.

  13. Hydrogen insertion effects on the electronic structure of equiatomic MgNi traced by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Matar, Samir F. [CNRS, ICMCB, UPR 9048, Pessac (France); Bordeaux Univ., Pessac (France). ICMCB, UPR 9048; Al Alam, Adel F.; Ouaini, Naim [Univ. Saint Esprit de Kaslik (USEK), Jounieh (Lebanon). URA GREVE, CSR-USEK

    2013-01-15

    For equiatomic MgNi which can be hydrogenated up to the composition MgNiH{sub 1.6} at an absorption/desorption temperature of 200 C, the effects of hydrogen absorption are approached with the model structures MgNiH, MgNiH{sub 2} and MgNiH{sub 3}. From full geometry optimization and calculated cohesive energies obtained within DFT, the MgNiH{sub 2} composition close to the experimental limit is identified as most stable. Charge density analysis shows an increasingly covalent character of hydrogen: MgNiH(H{sup -0.67}) {yields} MgNiH{sub 2}(H{sup -0.63}) {yields} MgNiH{sub 3}(H{sup -0.55}). While Mg-Ni bonding prevails in MgNi and hydrogenated model phases, extra itinerant low-energy Ni states appear when hydrogen is introduced signaling Ni-H bonding which prevails over Mg-H as evidenced from total energy calculations and chemical bonding analyses. (orig.)

  14. Water structure as a function of temperature from X-ray scatteringexperiments and ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hura, Greg; Russo, Daniela; Glaeser, Robert M.; Head-Gordon,Teresa; Krack, Matthias; Parrinello, Michele

    2003-03-01

    We present high-quality X-ray scattering experiments on pure water taken over a temperature range of 2 to 77 C using a synchrotron beam line at the advanced light source (ALS) at Lawrence Berkeley National Laboratory. The ALS X-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older X-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead, we consider the direct calculation of X-ray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here.

  15. First attempts at an elucidation of the interface structure resulting from the interaction between methacrylonitrile and a platinum anode: an experimental and theoretical (ab initio) study

    Science.gov (United States)

    Bureau, Christophe; Deniau, Guy; Valin, Françoise; Guittet, Marie-Joseph; Lécayon, Gérard; Delhalle, Joseph

    1996-06-01

    The aim of the present paper is to contribute to the elucidation of the molecular structures obtained on a platinum surface as this surface is submitted to an anodic potential (with respect to a silver reference electrode) when dipped into pure 2-methyl 2-propenenitrile (methacrylonitrile). Modified surfaces are examined using X- and UV-photoelectron spectroscopies (UPS and XPS). The results evidence the formation of an ultra-thin (20-40 Å) grafted oligomer film, which is not classical polymethacrylonitrile (PMAN), as obtained through a radical or anionic mechanism: spectral characteristics argue in the sense of a cationic polymerization of methacrylonitrile through its nitrile groups, as evidenced by a lowering of the gap as well as by the UPS and XPS (N 1s region) spectra. Molecular models of the reactants and reaction intermediates are proposed for the cationic polymerization of methacrylonitrile, and show that this polymerization is about as feasible as that of acetonitrile, at least on kinetic control grounds. Two different mechanisms are nonetheless possible, leading either to a quasi conjugated poly-imine type -(N  C) n-, or to a poly-cumulene type -(N  C  C) n- network. Theoretical consierations on reactants properties lead us to select the poly-imine way as the most plausible. Along with literature data concerning chemisorbed nitriles on platinum surfaces, a molecular model of the final state of the poly-imine reaction is then designed, comprising a three atom cluster to render the grafting site, and a dimer to render the grafted structure. A full geometry optimization is performed on the organic moiety at the Hartree-Fock (ab initio) level of theory, and a rough evaluation of the spectral footprint of the interface bond in the N 1s region is performed on the basis of Koopmans theorem with calibration on the bulk polymer peak. A preliminary 2.7 eV downward shift is predicted for N 1s interface nitrogens with respect to the polymer peak, which can

  16. Assessing the Thermoelectric Properties of Sintered Compounds via High-Throughput Ab-Initio Calculations

    Science.gov (United States)

    Wang, Shidong; Wang, Zhao; Setyawan, Wahyu; Mingo, Natalio; Curtarolo, Stefano

    2011-10-01

    Several thousand compounds from the Inorganic Crystal Structure Database have been considered as nanograined, sintered-powder thermoelectrics with the high-throughput ab-initio AFLOW framework. Regression analysis unveils that the power factor is positively correlated with both the electronic band gap and the carrier effective mass, and that the probability of having large thermoelectric power factors increases with the increasing number of atoms per primitive cell. Avenues for further investigation are revealed by this work. These avenues include the role of experimental and theoretical databases in the development of novel materials.

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

    Science.gov (United States)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

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

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

    Science.gov (United States)

    Shiga, Motoyuki; Nakayama, Akira

    2008-01-01

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

  19. Hydrogen adsorption on boron doped graphene: an {\\it ab initio} study

    OpenAIRE

    Miwa, R. H.; Martins, T B; Fazzio, A.

    2007-01-01

    The electronic and structural properties of (i) boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by {\\it ab initio} total energy calculations.

  20. Study of Nuclear Clustering from an Ab Initio Perspective

    Science.gov (United States)

    Kravvaris, Konstantinos; Volya, Alexander

    2017-08-01

    We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.

  1. Uniaxial Phase Transition in Si : Ab initio Calculations

    OpenAIRE

    Cheng, C.

    2002-01-01

    Based on a previously proposed thermodynamic analysis, we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, beta-tin, sh, sc, and hcp structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different conributions to the relative pahse stability, we identified the most important factors in reducing t...

  2. Thermochemical data for CVD modeling from ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-31

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

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

    Science.gov (United States)

    Klippenstein, Stephen

    2015-05-01

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

  4. Ab initio compressive phase retrieval

    CERN Document Server

    Marchesini, S

    2008-01-01

    Any object on earth has two fundamental properties: it is finite, and it is made of atoms. Structural information about an object can be obtained from diffraction amplitude measurements that account for either one of these traits. Nyquist-sampling of the Fourier amplitudes is sufficient to image single particles of finite size at any resolution. Atomic resolution data is routinely used to image molecules replicated in a crystal structure. Here we report an algorithm that requires neither information, but uses the fact that an image of a natural object is compressible. Intended applications include tomographic diffractive imaging, crystallography, powder diffraction, small angle x-ray scattering and random Fourier amplitude measurements.

  5. Ab initio and Monte Carlo investigations of structural, electronic and magnetic properties of new ferromagnetic Heusler alloys with high Curie temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Dannenberg, Antje

    2011-08-30

    The mechanism which causes many of the unusual thermomechanical properties of martensitic alloys, as for example, superelasticity and the shape-memory effect, is the martensitic transformation. The prototype ferromagnetic shape memory alloy (FSMA) is Ni{sub 2}MnGa. But a technological breakthrough is missing due to its poor ductility and low operation temperatures. The goal of this thesis is the proposal of new FSMA appropriate for future technological applications. I focus on X{sub 2}YZ Heusler alloys which are mainly based on Mn, Fe, Co, and Ni for the X and Y sites and Z=Ga or Zn. The big challenge of this work is to find material classes which combine the unique magnetomechanical properties of FSMA which are large recoverable magnetostrictive strains, high magnetocrystalline anisotropy energy, and highly mobile twin boundaries with transformation temperatures clearly above room temperature and a reduced brittleness. Such a study, providing material classes which from a theoretical point of view are promising candidates for future FSMA, will help the experimental physicists to select interesting subgroups in the vast number of possible chemical compositions of X{sub 2}YZ Heusler alloys. I have systematically varied the composition in the new Heusler alloys in order to find trends indicating generic tendencies of the material properties, for instance, as a function of the valence electron concentration e/a. A main feature of this thesis is the attempt to find the origin of the competing structural ordering tendencies between conventional X{sub 2}YZ and inverse (XY)XZ Heusler structures which are observed for all systems investigated. In the first part of this work the accuracy and predictive power of ab initio and Monte Carlo simulations is demonstrated by reproducing the experimental phase diagram of Ni-Mn-(Ga,In,Sn,Sb). The linear increasing and decreasing slopes of T{sub M} and T{sub C} can be reproduced by total and free energy calculations and the analysis

  6. Ab initio calculation of the Hoyle state

    CERN Document Server

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

    2011-01-01

    The Hoyle state plays a crucial role in the hydrogen burning of stars heavier than our sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle^{1} as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago^{2,3}, nuclear theorists have not yet uncovered the nature of this state from first principles. In this letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...

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

    Science.gov (United States)

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

    2014-08-07

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-07

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

  9. Ab initio calculation and spectral properties of nano- and bulk materials

    Energy Technology Data Exchange (ETDEWEB)

    Kulagin, N. A., E-mail: nkulagin@bestnet.kharkov.ua [Kharkov National University for Radioelectronics (Ukraine)

    2013-01-15

    This paper presents the development of ab initio calculation of the electronic structure of either clusters, nano-crystals, doped and unperfected bulk crystals. In addition, analysis of selected experimental data for {gamma}- or plasma irradiated pure and doped wide-band gap oxides such as sapphire, {alpha}-Al{sub 2}O{sub 3}, garnet, Y{sub 3}Al{sub 5}O{sub 12}, Gd{sub 3}Sc{sub 2}Al{sub 3}O{sub 12} and perovskites YAlO{sub 3}, SrTiO{sub 3} is presented. Change in the crystals surface morphology and spectroscopic properties of sapphire, perovskites, garnets as well as ion oxidation state in pure and doped {gamma}- and plasma irradiated crystals are discussed in detail using the optical and X ray spectroscopy experimental results.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-15

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

  11. Ab initio calculations of the optical properties of crystalline and liquid InSb

    Energy Technology Data Exchange (ETDEWEB)

    Sano, Haruyuki, E-mail: h-sano@ishikawa-nct.ac.jp [National Institute of Technology, Ishikawa College, Kitacyujo, Tsubata, Ishikawa 929-0392 (Japan); Mizutani, Goro [School of Materials Science, Japan Advanced Institute of Science and Technology, Tatsunokuchi, Ishikawa 923-1292 (Japan)

    2015-11-15

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  12. Electronic structure and magnetic properties of doped Al1- x Ti x N ( x = 0.03, 0.25) compositions based on cubic aluminum nitride from ab initio simulation data

    Science.gov (United States)

    Bannikov, V. V.; Beketov, A. R.; Baranov, M. V.; Elagin, A. A.; Kudyakova, V. S.; Shishkin, R. A.

    2016-05-01

    The phase stability, electronic structure, and magnetic properties of Al1- x Ti x N compositions based on the metastable aluminum nitride modification with the rock-salt structure at low ( x = 0.03) and high ( x = 0.25) concentrations of titanium in the system have been investigated using the results of ab initio band calculations. It has been shown that, at low values of x, the partial substitution is characterized by a positive enthalpy, which, however, changes sign with an increase in the titanium concentration. According to the results of the band structure calculations, the doped compositions have electronic conductivity. For x = 0.03, titanium impurity atoms have local magnetic moments (˜0.6 μB), and the electronic spectrum is characterized by a 100% spin polarization of near-Fermi states. Some of the specific features of the chemical bonding in Al1- x Ti x N cubic phases have been considered.

  13. Perceiving molecular themes in the structures and bonding of intermetallic phases: the role of Hückel theory in an ab initio era.

    Science.gov (United States)

    Stacey, Timothy E; Fredrickson, Daniel C

    2012-07-14

    Qualitative molecular orbital theory is central to our understanding of the bonding and reactivity of molecules and materials across chemistry. Advances in computational technology and methodology, however, have made ab initio or density functional theory calculations a simpler alternative, offering reliable results on increasingly large systems in a reasonable time-scale without the need for concerns about the approximations and parameterization of semi-empirical one-electron based methods. In this perspective, we illustrate how the availability of higher-level computational results can augment, rather than supplant, the insights provided by approaches such as the simple and extended Hückel methods. We begin by describing a way to parameterize Hückel-type Hamiltonians against DFT results for intermetallic systems. The potential for chemical understanding embodied by such orbital-based models is then demonstrated with two schemes of bonding analysis that originated in them (but can be extended to DFT results): the μ(3)-acid/base model and the μ(2)-Hückel chemical pressure analysis, which translate the molecular concepts of acidity and electronic/steric competition, respectively, into the context of intermetallic chemistry.

  14. Ab initio quantum mechanical investigation of structural and chemical-physical properties of selected minerals for minero-petrological, structural ceramic and biomaterial applications

    OpenAIRE

    Ulian, Gianfranco

    2014-01-01

    The purpose of this thesis is the atomic-scale simulation of the crystal-chemical and physical (phonon, energetic) properties of some strategically important minerals for structural ceramics, biomedical and petrological applications. These properties affect the thermodynamic stability and rule the mineral-environment interface phenomena, with important economical, (bio)technological, petrological and environmental implications. The minerals of interest belong to the family of phyllosilicates ...

  15. Reciprocity Theorems for Ab Initio Force Calculations

    CERN Document Server

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

    1996-01-01

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

  16. Discovering chemistry with an ab initio nanoreactor

    OpenAIRE

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

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerat...

  17. Ab initio study of phase equilibria in TiCx

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  18. Accelerating Ab Initio Nuclear Physics Calculations with GPUs

    CERN Document Server

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Simone Giusepponi

    2012-07-01

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

  20. Ab-initio study of transition metal hydrides

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-04-24

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

  1. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

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

  2. Ab initio Bogoliubov coupled cluster theory

    Science.gov (United States)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

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

  3. Experimental cross-sections energy dependence and an ab initio electronic structure survey of the ground singlet potential surface for reactive Li(+) + n-C(3)H(7)Cl collisions at low energies.

    Science.gov (United States)

    Lucas, José María; de Andrés, Jaime; Albertí, Margarita; Bofill, Josep Maria; Bassi, Davide; Aguilar, Antonio

    2010-11-07

    Reactive collisions between n-C(3)H(7)Cl molecules and lithium ions both in their ground electronic state have been studied in the 0.05-7.00 eV center of mass energy range using an octopole radio frequency guided-ion beam apparatus developed in our laboratory and recently modified. At low collision energies, dehydrohalogenation reactions leading to Li(C(3)H(6))(+) and Li(HCl)(+) are the main reaction channels, while on increasing energies C(3)H(7)(+) and C(2)H(3)(+) formation become dominant. Cross section energy dependences in arbitrary units for all these reactions have been measured. Also, ab initio electronic structure calculations at the MP2 level have been performed to obtain information about the potential energy surface on which the reactive processes take place. The reactants' entrance channel leads to the formation of a stable [Li-n-C(3)H(7)Cl](+) ion-molecule adduct that, following an intrinsic-reaction-coordinate pathway and surmounting a transition state, isomerizes to [Li-i-C(3)H(7)Cl](+). From this second minimum, dehydrohalogenation reactions for both n-C(3)H(7)Cl and i-C(3)H(7)Cl share a common reaction pathway leading to the same products. All potential barriers explored by reactions always lie below the reactants' energy. The entrance reaction channel [Li-n-C(3)H(7)Cl](+) adduct also leads adiabatically to C(3)H(7)(+) formation which, on increasing collision energy generates C(2)H(3)(+)via a unimolecular decomposition. A qualitative interpretation of the experimental results based on our ab initio calculations is also given.

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

    Directory of Open Access Journals (Sweden)

    Zhang Yang

    2007-05-01

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

  5. Study on the effects of fluorine and oxygen deficiency on YBa2Cu3O7 by ab initio method

    Institute of Scientific and Technical Information of China (English)

    刘洪霖; 曹晓卫; 瞿丽曼; 陈念贻

    1997-01-01

    The calculations of clusters modeling the fluorine-doping and oxygen deficiency of YBa2Cu3O2,have been performed by the method of all-electron ab initio Hartree-Fock with self-consistent crystal field Results show that in CuO planes electric charge significantly increases,the chemical valence of Cu decreases and the covalent bonding of Cu-O greatly weakens owing to oxygen deficiency,while the effect of F restores the local electronic structure of YBa2Cu3O7 The reported opinion that F occupied the oxygen vacancy in Cu-O chains seems disputable according to the calculated bonding characteristics.

  6. Ab initio calculations on nuclear quadrupole interactions of {sup 69,71}Ga and {sup 14}N nuclei in GaN of ionic crystal

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Junho [School of Electrical Engineering, University of Ulsan, Ulsan 680-749 (Korea, Republic of)], E-mail: jhjeong@mail.ulsan.ac.kr; Choh, S.H. [Department of Physics, School of Science, Korea University, Seoul 136-713 (Korea, Republic of); Sahoo, N. [Department of Radiation Physics, University of Texas MD Anderson Caner Center, Houston, TX 77030 (United States); Das, T.P. [Department of Physics, The University at Albany, Albany, NY 12222 (United States)

    2008-07-01

    This paper presents the results of our calculation of nuclear quadrupole coupling constant (NQCC) of {sup 69,71}Ga and {sup 14}N on wurtzite GaN crystal using the Hartree-Fock Roothaan Molecular Cluster procedure. We employed Ga{sub 4}N{sub 4}H{sub 18} cluster as well as the (GaN{sub 4}){sup 9-} and the (NGa{sub 4}){sup 9+} clusters surrounded by 1160 external Ga{sup 3+} and N{sup 3-} ions in 15 A radius lattice to simulate the covalent bonding and ionic bonding among the constituent atoms in the solid-state system and to calculate the electronic structure and the associated nuclear quadrupole interaction properties of {sup 14}N and {sup 69,71}Ga. The nuclear quadrupole coupling constant (NQCC) e{sup 2}qQ/h for {sup 69}Ga with a value of its Q as 0.168 barns was found to be 2.98 MHz in the (GaN{sub 4}){sup 9-} cluster and 34.43 MHz in the Ga{sub 4}N{sub 4}H{sub 18} cluster. The e{sup 2}qQ/h for the {sup 14}N in the (NGa{sub 4}){sup 9+} cluster representing the ionic bonding was found to be 0.0303 MHz using the nuclear quadrupole moment of {sup 14}N nucleus as 0.0193 barns. The calculated NQI parameters from the (GaN{sub 4}){sup 9-} and the (NGa{sub 4}){sup 9+} clusters agree well with the experimental values indicating the existence of the significant ionic bonding between the constituent atoms in the solid-state system.

  7. Ab initio calculations of the atomic and electronic structure of layered Ba{sub 0.5}Sr{sub 0.5}TiO{sub 3} structures

    Energy Technology Data Exchange (ETDEWEB)

    Piskunov, S. [Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga (Latvia); Kotomin, E.A. [Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga (Latvia) and Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstrasse 1, 70569 Stuttgart (Germany)]. E-mail: kotomin@latnet.lv; Fuks, D. [Materials Engineering Department, Ben-Gurion University of the Negev, POB 653, Beer-Sheva (Israel); Dorfman, S. [Department of Physics, Technion- Israel Institute of Technology, Haifa 32000 (Israel)

    2005-04-25

    Understanding of the atomic and electronic structure of Ba{sub c}Sr{sub 1-c}TiO{sub 3} (BST) solid solutions is important for several applications including the non-volatile ferroelectric memories (dynamic random access memory, DRAM). We present results of ab initio calculations of several spatial arrangements of Ba{sub 0.5}Sr{sub 0.5}TiO{sub 3} solid solutions based on DFT-HF B3PW hybrid method. We calculate the atomic and electronic structure, the effective charges, interatomic bond populations, the electronic density distribution, and densities of states for three layered structures with the same composition. The suggested method reproduces experimental lattice parameters of both pure BaTiO{sub 3} and SrTiO{sub 3}. The calculated optical band gaps for the pure SrTiO{sub 3} and BaTiO{sub 3} are in a good agreement with experimental data, much better than those from the standard LDA or HF calculations. In the studied BST structures with the equiatomic composition (c = 0.5) the gap is reduced by ca. 0.2 eV. The electron density maps demonstrate the covalency effects in the Ti-O bonding. The electron density near the Sr atoms is stronger localized, as compared with the Ba ions.

  8. Accurate ab initio spin densities

    CERN Document Server

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-01

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

  10. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

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

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

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

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

  12. On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu [Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    2016-01-14

    In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenol from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.

  13. Femtosecond Laser Processing of Germanium: An Ab Initio Molecular Dynamics Study

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtosecond laser processing is simulated by imposing the Nose Hoover thermostat to the electronic subsystem lasting for ~100 fs and continuing with microcanonical ensemble simulation of ~200 fs. The simulation results show solid, liquid and gas phases of germanium under adjusted intensities of the femtosecond laser irradiation. We find the irradiated germanium distinguishes from the usual germanium crystal by analyzing their melting and dynamic properties.

  14. Ab Initio Simulation of Electrical Currents Induced by Ultrafast Laser Excitation of Dielectric Materials

    Science.gov (United States)

    Wachter, Georg; Lemell, Christoph; Burgdörfer, Joachim; Sato, Shunsuke A.; Tong, Xiao-Min; Yabana, Kazuhiro

    2014-08-01

    We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab initio simulations based on time-dependent density functional theory give insight into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunnelinglike excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis, suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [A. Schiffrin et al., Nature (London) 493, 70 (2013)].

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

    Science.gov (United States)

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

    2015-02-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

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

    Indian Academy of Sciences (India)

    Anil Thakur; N S Negi; P K Ahluwalla

    2005-08-01

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

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

    Science.gov (United States)

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

    2007-04-01

    The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-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

  19. Ab initio calculations of reactions of light nuclei

    Science.gov (United States)

    Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr

    2017-09-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.

  20. Ab initio study of the compound-energy modeling of multisublattice structures: The (hP6) Ni{sub 2}In-type intermetallics of the Ni–In–Sn system

    Energy Technology Data Exchange (ETDEWEB)

    Ramos de Debiaggi, S., E-mail: susana.ramos@fain.uncoma.edu.ar [Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén (Argentina); Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas – CONICET-UNCo (Argentina); González Lemus, N.V. [Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén (Argentina); Deluque Toro, C. [Grupo de Nuevos Materiales, Universidad de la Guajira, Riohacha (Colombia); Fernández Guillermet, A. [CONICET - Instituto Balseiro, Centro Atómico Bariloche, Avda. Bustillo 9500, 8400 Bariloche (Argentina)

    2015-01-15

    Highlights: • A DFT study of the compounds involved in CALPHAD modeling of the Ni–In–Sn (hP6) phase. • Several three-sublattice compounds of Ni, In, Sn and vacancies are studied ab initio. • Structural, cohesive and thermodynamic properties and the electronic DOS are reported. • Trends in calculated properties are correlated with changes in electronic structure. • A picture of the chemical bonding trends for these s-p/d type compounds is discussed. - Abstract: The thermodynamic modeling of non-stoichiometric, multisublattice intermetallic phases using the Compound-Energy Formalism (CEF) involves the determination of parameters representing the Gibbs energy (G{sub m}) of binary compounds, the so-called “end-member compounds” (EMCs), which are often metastable or hypothetical. In current CALPHAD (i.e., “Calculation of Phase Diagrams”) work, these quantities are treated as free parameters to be determined by searching for the best fit to the available information in the optimization procedure. The general purpose of this paper is to propose a theoretical approach to the study of the EMCs which makes use of density-functional-theory (DFT) ab initio calculations. The present method is applied to the EMCs involved in the CEF modeling of the non-stoichiometric (hP6) Ni{sub 2}In-structure type phase of the Ni–In and Ni–In–Sn systems using the three-sublattice models (Ni){sub 1}(Ni,Va){sub 1}(In,Ni){sub 1} and (Ni,Va){sub 1}(Ni,Va){sub 1}(In,Ni,Sn){sub 1}, respectively. By means of systematic ab initio projected augmented waves (PAW) calculations using the VASP code we study the EMCs involved in the CEF formulations of the G{sub m} for this phase in the binary and the ternary systems. Specifically, we study the twelve EMCs corresponding to the following sublattice occupations: (Ni){sub 1}(Ni){sub 1}(In){sub 1}, which is usually described as Ni:Ni:In (i.e., a compound with formula “Ni{sub 2}In”), Ni:Ni:Ni (i.e., “Ni{sub 3}”), Ni:Ni:Sn (

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

    Institute of Scientific and Technical Information of China (English)

    崔崇威; 黄君礼

    2004-01-01

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

  2. Coherent view of crystal chemistry and ab initio analyses of Pb(II) and Bi(III) Lone Pair in square planar coordination

    OpenAIRE

    Matar, Samir F.; Galy, Jean

    2014-01-01

    The stereochemistry of 6s2 (E) lone pair of divalent Pb and trivalent Bi (PbII and BiIII designated by M*) in structurally related PbO, PbFX (X= Cl, Br, I), BiOX (X= F, Cl, Br, I) and Bi2NbO5F is rationalized. The lone pair LP presence determined by its sphere of influence E, equal to those of oxygen or fluorine anions, was settled by its center then giving M*-E directions and distances. Detailed description of structural features of both elements in the title compounds characterized by [PbEO...

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

    CERN Document Server

    Marsalek, Ondrej

    2015-01-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) 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 pro...

  4. Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

    DEFF Research Database (Denmark)

    Zhang, Hao; Lund, Ole; Nielsen, Morten

    2010-01-01

    potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...

  5. Atomic arrangement and electron band structure of Si(1 1 1)-ß-\\sqrt{3}\\times \\sqrt{3} -Bi reconstruction modified by alkali-metal adsorption: ab initio study

    Science.gov (United States)

    Eremeev, S. V.; Chukurov, E. N.; Gruznev, D. V.; Zotov, A. V.; Saranin, A. A.

    2015-08-01

    Using ab initio calculations, atomic structure and electronic properties of Si(1 1 1)\\sqrt{3}× \\sqrt{3} -Bi surface modified by adsorption of 1/3 monolayer of alkali metals, Li, Na, K, Rb and Cs, have been explored. Upon adsorption of all metals, a similar atomic structure develops at the surface where twisted chained Bi trimers are arranged into a honeycomb network and alkali metal atoms occupy the {{T}4} sites in the center of each honeycomb unit. Among other structural characteristics, the greatest variation concerns the relative heights at which alkali metals reside with respect to Bi-trimer layer. Except for Li, the other metals reside higher than Bi layer and their heights increase with atomic number. All adsorbed surface structures display similar electron band structures of which the most essential feature is metallic surface-state band with a giant spin splitting. This electronic property allows one to consider the Si(1 1 1)\\sqrt{3}× \\sqrt{3} -Bi surfaces modified by alkali metal adsorption as a set of material systems showing promise for spintronic applications.

  6. Atomic arrangement and electron band structure of Si(1 1 1)-ß-√3 x √3-Bi reconstruction modified by alkali-metal adsorption: ab initio study.

    Science.gov (United States)

    Eremeev, S V; Chukurov, E N; Gruznev, D V; Zotov, A V; Saranin, A A

    2015-08-05

    Using ab initio calculations, atomic structure and electronic properties of Si(1 1 1)[Formula: see text]-Bi surface modified by adsorption of 1/3 monolayer of alkali metals, Li, Na, K, Rb and Cs, have been explored. Upon adsorption of all metals, a similar atomic structure develops at the surface where twisted chained Bi trimers are arranged into a honeycomb network and alkali metal atoms occupy the [Formula: see text] sites in the center of each honeycomb unit. Among other structural characteristics, the greatest variation concerns the relative heights at which alkali metals reside with respect to Bi-trimer layer. Except for Li, the other metals reside higher than Bi layer and their heights increase with atomic number. All adsorbed surface structures display similar electron band structures of which the most essential feature is metallic surface-state band with a giant spin splitting. This electronic property allows one to consider the Si(1 1 1)[Formula: see text]-Bi surfaces modified by alkali metal adsorption as a set of material systems showing promise for spintronic applications.

  7. Electronic structure, magnetic and thermal properties of Rh{sub 2}MnZ (Z=Ge, Sn, Pb) compounds under pressure from ab-initio quasi-harmonic method

    Energy Technology Data Exchange (ETDEWEB)

    Benkhelifa, F.Z.; Lekhal, A.; Méçabih, S., E-mail: mecabihsa@yahoo.com; Abbar, B.; Bouhafs, B.

    2014-12-15

    We have investigated the electronic structure, magnetic and thermal properties of the ternary full-Heusler alloys Rh{sub 2}MnZ (Z=Ge, Sn, Pb) under pressure employing the full potential linearized augmented plane wave (FP-LAPW) plus local orbitals method based on the density functional theory (DFT), For the exchange–correlation effects we have adopted the generalized gradient approximation (GGA).Through the quasi-harmonic Debye model, we also study the thermodynamic properties of Rh{sub 2}MnZ (Z=Ge, Sn and Pb). The thermal expansion versus temperature and pressure, the thermodynamic parameters (Debye temperature and specific heat) with pressure P, and the heat capacity at various pressures and temperatures in the ranges of 0 GPa to 0.6 GPa and 0 K to 400 K have been obtained. - Highlights: • Ab-initio study of the electronic properties of Rh{sub 2}MnZ (Z=Ge, Sn, Pb). • Thermodynamic properties of Rh{sub 2}MnZ (Z=Ge, Sn and Pb) are predicted. • Pressure effect on the structural and electronic properties. • The effect of temperature and pressure on the Debye temperature.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-10-12

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

  9. Dispersion and Solvation Effects on the Structure and Dynamics of N719 Adsorbed to Anatase Titania (101) Surfaces in Room-Temperature Ionic Liquids: An ab Initio Molecular Simulation Study

    KAUST Repository

    Byrne, Aaron

    2015-12-24

    Ab initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect of explicit solvation on the dynamical and structural properties of a [bmim][NTf2] room-temperature ionic liquid (RTIL), solvating a N719 sensitizing dye adsorbed onto an anatase titania (101) surface. The effect of explicit dispersion on the properties of this dye-sensitized solar cell (DSC) interface has also been studied. Upon inclusion of dispersion interactions in simulations of the solvated system, the average separation between the cations and anions decreases by 0.6 Å; the mean distance between the cations and the surface decreases by about 0.5 Å; and the layering of the RTIL is significantly altered in the first layer surrounding the dye, with the cation being on average 1.5 Å further from the center of the dye. Inclusion of dispersion effects when a solvent is not explicitly included (to dampen longer-range interactions) can result in unphysical "kinking" of the adsorbed dye\\'s configuration. The inclusion of solvent shifts the HOMO and LUMO levels of the titania surface by +3 eV. At this interface, the interplay between the effects of dispersion and solvation combines in ways that are often subtle, such as enhancement or inhibition of specific vibrational modes. © 2015 American Chemical Society.

  10. Ab initio study on the band structure of P-doped anatase TiO2%磷掺杂锐钛矿二氧化钛能带结构的从头计算研究

    Institute of Scientific and Technical Information of China (English)

    王丽丽; 李阳; 刘颖; 刘跃

    2012-01-01

    The microstructures of pure and P-doped anatase TiO2 were optimized by ab initio method. Evidences for the possibility of studying band structures and density states using the density functional theory (DFT) with super cell model of P-doped anatase TiO2 were investigated. The results obtained by the calculations on the P-doped anatase TiO2 are significant for analyzing the mechanism of photo-catalysis of TiO2 and for improving catalytic activity of anatase TiO2.%用密度泛函方法优化了锐钛矿二氧化钛及其磷掺杂锐钛矿二氧化钛的晶体结构.研究揭示了用超胞模型研究未掺杂和P掺杂锐钛矿TiO2能带结构和态密度的可行性.计算结果对于提高TiO2光催化活性有意义.

  11. Operator evolution for ab initio nuclear theory

    CERN Document Server

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

    2014-01-01

    The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally-invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square-radius and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range and find at short ranges an increased contribution from such ind...

  12. Discovering chemistry with an ab initio nanoreactor

    Science.gov (United States)

    Martinez, Todd

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

  13. Ab initio alpha-alpha scattering

    CERN Document Server

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

    2015-01-01

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

  14. Discovering chemistry with an ab initio nanoreactor

    Science.gov (United States)

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

    2014-12-01

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

  15. Ab initio study of Mg(AlH4)2

    NARCIS (Netherlands)

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

    2005-01-01

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

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

    Science.gov (United States)

    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…

  17. Ab initio study of Mg(AlH4)2

    NARCIS (Netherlands)

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

    2005-01-01

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

  18. Effect of Fe doping in the structural, electronic and magnetic properties of CoCr2O4: insights from ab initio calculations

    Science.gov (United States)

    Das, Debashish; Ganguly, Shreemoyee; Sanyal, Biplab; Ghosh, Subhradip

    2016-10-01

    CoCr2O4 has attracted significant attention recently due to several interesting properties such as magnetostriction, magnetoelectricity etc. More recent experiments on Fe substituted CoCr2O4 observed a variety of novel phenomena such as the magnetic compensation accompanied by the occurrence of exchange bias, which reverses its sign. Understanding of such phenomena may lead to control the properties of these material in an efficient way to enhance its potential for multifunctional applications. In this paper, we study the fundamental understanding of Fe doping in modifying the structural and magnetic properties of CoCr2O4 with varying composition and substitution of Fe at different sublattices by first-principles density functional calculations. We have analysed in detail the effect of Fe substitution on crystal field and exchange splittings, magnetic moments and interatomic exchange parameters. It is also observed that with increasing concentration of Fe impurity, the system has a tendency towards forming an ‘inverse spinel’ structure as observed in experiments. Such tendencies are crucial to understand this system as it would lead to modifications in the magnetic exchange interactions associated with sites with different symmetry finally affecting the magnetic structure and the multiferrocity in turn.

  19. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...

  20. Ab initio Molecular Dynamics Study on Small Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    叶林晖; 刘邦贵; 王鼎盛

    2001-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    李吉海; 冯大诚; 冯圣玉

    1999-01-01

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

  2. Ab-initio determination of the incommensurate modulated structure of Bi-2212 from x-ray powder diffraction data-a simulation

    Institute of Scientific and Technical Information of China (English)

    陈建荣; 古元新; 郑朝德; 范海福

    2003-01-01

    A set of x-ray powder diffraction data of the high-Tc superconductor Bi2Sr2Ca1Cu2Oy (Bi-2212) was simulated based on the experimental single-crystal diffraction data by merging together reflections with diffraction angles (2θ) closer to each other than 0.04 degrees. There are three types of overlapping in the powder diffraction data, i.e. (i) overlapping of main reflections; (ii) overlapping of satellite reflections and (iii) overlapping of main and satellite reflections. The third type of overlapping was first separated into main and satellite components according to the ratio between the average intensity of that of types (i) and (ii). Then the overlapped reflections of main reflections and those of the satellites were uniformly partitioned. Heavy-atom sites in the basic/average structure were found using the uniformly decomposed main reflections by the conventional direct method. Phases of the satellites were derived by the multidimensional direct method. The resultant four-dimensional Fourier maps revealed correctly the essential feature of the modulation. No assumption on either the basic structure or the modulation is needed.

  3. Ab-initio study of structural, elastic, thermal, electronic and magnetic properties of quaternary Heusler alloys CoMnCrZ (Z = Al, As, Si, Ge)

    Science.gov (United States)

    Mohamedi, Mohamed Walid; Chahed, Abbes; Amar, Amina; Rozale, Habib; Lakdja, Abdelaziz; Benhelal, Omar; Sayede, Adlane

    2016-12-01

    First-principles approach is used to study the structural, electronic and magnetic properties of CoMnCrZ (Z = Al, Si, Ge and As) quaternary Heusler compounds, using full-potential linearized augmented plane wave (FP-LAPW) scheme within the generalized gradient approximation (GGA). The computed equilibrium lattice parameters agree well with the available theoretical data. The obtained negative formation energy shows that CoMnCrZ (Z = Al, Si, Ge, As) compounds have strong structural stability. The elastic constants Cij are calculated using the total energy variation with strain technique. The polycrystalline elastic moduli (namely: the shear modulus, Young's modulus, Poisson's ratio, sound velocities, Debye temperature and melting temperature were derived from the obtained single-crystal elastic constants. The ductility mechanism for the studied compounds is discussed via the elastic constants Cij. Our calculations with the GGA approximation predict that CoMnCrGe, CoMnCrAl, CoMnCrSi and CoMnCrAs are half-metallic ferrimagnets (HMFs) with a half-metallic gap EHM of 0.03 eV, 0.19 eV, 0.34 eV and 0.50 eV for, respectively. We also find that the half-metallicity is maintained on a wide range of lattice constants.

  4. Ab initio quantum dynamics using coupled-cluster.

    Science.gov (United States)

    Kvaal, Simen

    2012-05-21

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

  5. Ab initio quantum dynamics using coupled-cluster

    CERN Document Server

    Kvaal, Simen

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Varas Alejandro

    2016-08-01

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

  7. Ab-Initio Calculation of Electronic Structure of Lead Halide Perovskites with Formamidinium Cation as an Active Material for Perovskite Solar Cells

    Science.gov (United States)

    Indari, E. D.; Wungu, T. D. K.; Hidayat, R.

    2017-07-01

    Organic lead halide perovskite material based solar cells show impressive power conversion efficiencies, which can reach above 19 percent for perovskite solar cell with methyl-ammonium cations. These efficiencies are originated from efficient photoexcitation and charge carrier transport and not observed in conventional perovskite crystals. In this preliminary research work, we therefore performed Density Functional Theory (DFT) calculation of formamidinium lead iodide (FAPI), an alternative to methyl-ammonium lead iodide (MAPI), to predict their electronic structure and density of state (DOS). The calculation result at the most stable lattice parameters show a good agreement with the experiment results. The obtained band gap energy is 1.307 eV. The valence band is dominantly formed by the 5p orbitals of I- anions, while the conduction band is dominantly formed by the 6p orbitals of Pb2+ cations. The DOS of valence band of this perovskite seems smaller compared to the case of methyl-ammonium lead iodide perovskite, which then may explain the observation of smaller power conversion efficiencies in perovskite solar cells with this formamidinium cations.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-15

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

  9. On the hierarchical parallelization of ab initio simulations

    CERN Document Server

    Ruiz-Barragan, Sergi; Shiga, Motoyuki

    2016-01-01

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

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

    Science.gov (United States)

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

    2011-06-16

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

  11. Electronic properties of cubic TaC{sub x}N{sub 1-x}: A comparative study using self-consistent cluster and ab initio band-structure calculations and X-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lavrentyev, A.A.; Gabrelian, B.V.; Vorzhev, V.B.; Nikiforov, I.Ya. [Department of Physics, Don State Technical University, Gagarin Sq. 1, Rostov-on-Don (Russian Federation); Khyzhun, O.Yu. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky Street, UA-03142 Kyiv (Ukraine)], E-mail: khyzhun@ipms.kiev.ua

    2009-03-20

    To investigate the influence of substitution of carbon atoms for nitrogen atoms in the cubic TaC{sub x}N{sub 1-x} carbonitrides, total and partial densities of states were calculated for TaC, TaC{sub 0.5}N{sub 0.5} and TaN compounds (NaCl structure) using the self-consistent cluster (with the FEFF8 code) and ab initio band-structure augmented plane wave + local orbitals (APW + LO) methods. In the present work a rather good agreement of the theoretical FEFF8 and APW + LO data for electronic properties of the TaC{sub x}N{sub 1-x} system under consideration was obtained. The results indicate that a strong hybridization of the Ta 5d- and C(N) 2p-like states is characteristic for the valence band of the TaC{sub x}N{sub 1-x} carbonitrides. When going from TaC to TaN through the TaC{sub 0.5}N{sub 0.5} carbonitride, the main maxima of curves representing total and partial Ta 5d densities of states shift in the direction opposite to the position of the Fermi level. In the above sequence of compounds, an increase of occupation of the near-Fermi sub-band formed by contributions of Ta 5d(t{sub 2g}) states has been detected. The theoretical FEFF8 and APW + LO results for the electronic structure of the TaC{sub x}N{sub 1-x} carbonitrides were found to be in excellent agreement with the experimental data derived in the present work employing X-ray photoelectron, emission and absorption spectroscopy methods for cubic TaC{sub 0.98}, TaC{sub 0.52}N{sub 0.49} and TaN{sub 0.97} compounds.

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

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

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

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

    Science.gov (United States)

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

    1997-08-01

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

  14. Phonocatalysis. An ab initio simulation experiment

    Directory of Open Access Journals (Sweden)

    Kwangnam Kim

    2016-06-01

    Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  15. Ab initio phonon scattering by dislocations

    Science.gov (United States)

    Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.

    2017-06-01

    Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.

  16. Feasibility of novel (H3C)nX(SiH3)3-n compounds (X = B, Al, Ga, In): structure, stability, reactivity, and Raman characterization from ab initio calculations.

    Science.gov (United States)

    Dos Santos, Renato B; Rivelino, R; Mota, F de Brito; Kakanakova-Georgieva, A; Gueorguiev, G K

    2015-02-21

    We employ ab initio calculations to predict the equilibrium structure, stability, reactivity, and Raman scattering properties of sixteen different (H3C)nX(SiH3)3-n compounds (X = B, Al, Ga, In) with n = 0-3. Among this methylsilylmetal family, only the (H3C)3X members, i.e., trimethylboron (TMB), trimethylaluminum (TMA), trimethylgallium (TMG), and trimethylindium (TMI), are currently well-studied. The remaining twelve compounds proposed here open up a two-dimensional array of new possibilities for precursors in various deposition processes, and evoke potential applications in the chemical synthesis of other compounds. We infer that within the (H3C)nX(SiH3)3-n family, the compounds with fewer silyl groups (and consequently with more methyl groups) are less reactive and more stable. This trend is verified from the calculated cohesive energy, Gibbs free energy of formation, bond strength, and global chemical indices. Furthermore, we propose sequential reaction routes for the synthesis of (H3C)nX(SiH3)3-n by substitution of methyl by silyl groups, where the silicon source is the silane gas. The corresponding reaction barriers for these chemical transformations lie in the usual energy range typical for MOCVD processes. We also report the Raman spectra and light scattering properties of the newly proposed (H3C)nX(SiH3)3-n compounds, in comparison with available data of known members of this family. Thus, our computational experiment provides useful information for a systematic understanding of the stability/reactivity and for the identification of these compounds.

  17. Predictions of pressure-induced structural transition,mechanical and thermodynamic properties of α- and β-Si3N4 ceramics: ab initio and quasi-harmonic Debye modeling

    Institute of Scientific and Technical Information of China (English)

    Yu Ben-Hai; Chen Dong

    2012-01-01

    The plane-wave pseudo-potential method within the framework of ab initio technique is used to investigate the structural and elastic properties of α- and β-Si3N4.The ground-state parameters accord quite well with the experimental data.Our calculation reveals that α-Si3N4 can retain its stability to at least 40 GPa when compressed at 300 K.The α → β phase transformation would not occur in a pressure range of 0-40 GPa and a temperature range of 0-300 K.Actually,the α → β transition occurs at 1600 K and 7.98 GPa.For α- and β-Si3N4,the c axes are slightly more incompressible than the a axes.We conclude that β-Si3N4 is a hard material and ductile in nature.On the other hand,β-Si3N4 is also found to be an ionic material and can retain its mechanical stability in a pressure range of 0-10 GPa.Besides,the thermodynamic properties such as entropy,heat capacity,and Debye temperature of α- and β-Si3N4 are determined at various temperatures and pressures.Significant features in these properties are observed at high temperature.The calculated results are in good agreement with available experimental data and previous theoretical values.Many fundamental solid-state properties are reported at high pressure and high temperature.Therefore,our results may provide useful information for theoretical and experimental investigations of the Si3N4 polymorphs.

  18. Ab initio materials physics and microscopic electrodynamics of media

    OpenAIRE

    2016-01-01

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

  19. Phonon spectra of elpasolites Cs2NaRF6 (R=Y,Yb): Ab initio calculations

    Science.gov (United States)

    Chernyshev, Vladimir; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy

    2015-12-01

    The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs2NaYbF6 and Cs2NaYF6 (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.

  20. Phonon spectra of elpasolites Cs{sub 2}NaRF{sub 6} (R=Y,Yb): Ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Chernyshev, Vladimir, E-mail: Vladimir.Chernyshev@urfu.ru; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy [Ural Federal University, Ekaterinburg (Russian Federation)

    2015-12-07

    The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs{sub 2}NaYbF{sub 6} and Cs{sub 2}NaYF{sub 6} (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ganster, P

    2004-10-15

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

  2. Supplementary Material for Finding the Stable Structures of N1-xWX with an Ab-initio High-Throughput Approach

    Science.gov (United States)

    2015-05-08

    0 W (2d) 1/3 2/3 0.06202 1/3 2/3 0.06213 1/3 2/3 0.06200 Structure 14: N2W in an idealized high-temperature (β) cristobalite SiO2 structure. 25 Space...Molybdenum Trioxide, Acta Chem. Scan. 4, 793–797 (1950). 21 R. Rühl and W. Jeitschko, Preparation and structure of technetium triphosphide and rhenium

  3. Preparation and properties of gallaborane, GaBH(6): structure of the gaseous molecule H(2)Ga(mu-H)(2)BH(2) as determined by vibrational, electron diffraction, and ab initio studies, and structure of the crystalline solid at 110 K as determined by X-ray diffraction.

    Science.gov (United States)

    Downs, A J; Greene, T M; Johnsen, E; Brain, P T; Morrison, C A; Parsons, S; Pulham, C R; Rankin, D W; Aarset, K; Mills, I M; Page, E M; Rice, D A

    2001-07-02

    Gallaborane (GaBH(6), 1), synthesized by the metathesis of LiBH(4) with [H(2)GaCl](n) at ca. 250 K, has been characterized by chemical analysis and by its IR and (1)H and (11)B NMR spectra. The IR spectrum of the vapor at low pressure implies the presence of only one species, viz. H(2)Ga(mu-H)(2)BH(2), with a diborane-like structure conforming to C(2v) symmetry. The structure of this molecule has been determined by gas-phase electron diffraction (GED) measurements afforced by the results of ab initio molecular orbital calculations. Hence the principal distances (r(alpha) in A) and angles ( angle(alpha) in deg) are as follows: r(Ga.B), 2.197(3); r(Ga-H(t)), 1.555(6); r(Ga-H(b)), 1.800(6); r(B-H(t)), 1.189(7); r(B-H(b)), 1.286(7); angleH(b)-Ga-H(b), 71.6(4); and angleH(b)-B-H(b), 110.0(5) (t = terminal, b = bridging). Aggregation of the molecules occurs in the condensed phases. X-ray crystallographic studies of a single crystal at 110 K reveal a polymeric network with helical chains made up of alternating pseudotetrahedral GaH(4) and BH(4) units linked through single hydrogen bridges; the average Ga.B distance is now 2.473(7) A. The compound decomposes in the condensed phases at temperatures exceeding ca. 240 K with the formation of elemental Ga and H(2) and B(2)H(6). The reactions with NH(3), Me(3)N, and Me(3)P are also described.

  4. The electronic structure of sulfonamidyl radicals. An ESR spectroscopic and ab-initio MO study of sulfonamidyl and some carboxamidyl radicals

    NARCIS (Netherlands)

    Teeninga, Hermannus

    1983-01-01

    This thesis describes an investigation of the electronic structure of sulfonamidyl radicals (R1SO2NR2) and some structurally related carboxamidyl radicals (R1C(0)NR2). Both types of radicals have been invoked as intermediates in several chemical reactions. The present work originates from our intere

  5. Ab initio study of the structural, magnetic, and electronic properties of copper and silver clusters and their alloys with one palladium atom

    Directory of Open Access Journals (Sweden)

    S. J Hashemifar

    2015-01-01

    Full Text Available In this paper, the structural, magnetic, and electronic properties of two- to nine-atom copper and silver clusters and their alloys with one palladium atom are investigated by using full-potential all-electron density functional computations. After calculating minimized energy of several structural isomers of every nanocluster, it is argued that the small size nanoclusters (up to size of 6, ‎ prefer planar structures, while by increasing size a 2D-3D structural transformation is observed. The structural transformation of pure and copper-palladium clusters occurs in the size of seven and that of silver-palladium cluster in happens at the size of six. The calculated second difference and dissociation energies confirm that the two- and eight- atom pure clusters and three- and seven- atom alloyed clusters are magic clusters. The electronic and magnetic properties of stable isomers are calculated and considered after applying many body based GW correction.

  6. Ab initio search for global minimum structures of neutral and anionic B 4H 5 clusters. Optical isomerism in B 4H 5 and B4H5-

    Science.gov (United States)

    Olson, Jared K.; Boldyrev, Alexander I.

    2011-11-01

    Potential energy surfaces of neutral and anionic B 4H 5 clusters were sampled using the Coalescence Kick method. We found that the neutral B 4H 5 cluster has two optical isomers as either a global minimum structure, or as almost degenerate isomers with the global minimum structure. For the B4H5- anion only the third lowest isomer forms a pair of optical isomers. The chemical bonding patterns revealed by the Adaptive Natural Density Partitioning (AdNDP) analysis can easily explain the geometric structure of even very exotic isomers and global minima. Theoretical vertical electron detachment energies (VDEs) were calculated for comparison with future experimental work.

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

    Science.gov (United States)

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

    2013-11-01

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

  8. Ab initio study of the structural phase transitions of the double perovskites Sr2MWO6 (M=Zn, Ca, Mg)

    Science.gov (United States)

    Petralanda, U.; Etxebarria, I.

    2014-02-01

    We study the interplay of structural distortions in double perovskites Sr2MWO6 (M = Zn, Ca, Mg) by means of first-principles calculations and group theoretical analysis. Structure relaxations of the cubic, tetragonal, and monoclinic phases show that the ground states of the three compounds are monoclinic, although the energy difference between the monoclinic and tetragonal structures is very small in the case of Sr2MgWO6. The symmetry analysis of the distortions involved in the experimental and calculated low-temperature structures shows that the amplitude of two primary distortions associated to rigid rotations of the MX6 and WO6 octahedra are dominant, although the amplitude of a third mode related to deformations of the MX6 groups can not be neglected. The energy maps of the space spanned by the three relevant modes are calculated, and the couplings among the modes are evaluated, showing that the role of a hard secondary mode (in the Landau sense) coupled trilinearly to the two primary instabilities is crucial to stabilize the monoclinic ground state. Results suggest that the key role of the trilinear coupling among three modes could be rather common. A phenomenological theory including the effects of the chemical pressure is also developed. We find that the evolution of the stiffness constants in terms of the atomic substitution follows an accurate linear dependence and that the influence of quantum saturation of the order parameters could stabilize the tetragonal phase of Sr2MgWO6.

  9. The energetic, electronic and magnetic structures of Fe{sub 2−x}Co{sub x}VSn alloys: Ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Mahmoud, Nada T.; Khalifeh, Jamil M. [Physics Department, The University of Jordan, Amman 11942 (Jordan); Mousa, Ahmad A., E-mail: amousa@meu.edu.jo [Middle East University, P.O. Box 383, Amman 11831 (Jordan); Juwhari, Hassan K.; Hamad, Bothina A. [Physics Department, The University of Jordan, Amman 11942 (Jordan)

    2013-12-01

    Density Functional Theory (DFT) calculations of a series of the nonstoichiometric Fe{sub 2−x}Co{sub x}VSn full Heusler alloy were carried out utilizing the full potential linearized augmented plane wave (FP-LAPW) method to investigate the electronic, energetic, and magnetic structures of the above systems. Unlike many concentration curves, increasing the cobalt concentration had a crucial effect on the spin polarization as it flattened at 100% at x=1.50, 1.75, and 2.00 where the half- metallic behavior was located with negative formation energy. Moreover, the total magnetic moment of the host material is found to increase with increasing Co concentration. Finally, the half metallic compounds found in some structures of this series might be useful in spintronic devices.

  10. Ab initio study of the structural, electronic, elastic and thermal properties of RMn{sub 2}Ge{sub 2} (R = Ca, Nd and Y) intermetallic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Miloud Abid, O.; Yakoubi, A. [Laboratoire d’Etudes des Matériaux et Instrumentations Expérimentales, Université Djilali Liabes de Sidi Bel-Abbes, 22000 (Algeria); Tadjer, A. [Modeling and Simulation in Materials Science Laboratory, Physics Department, University of Sidi Bel-Abbes, Sidi Bel-Abbes (Algeria); Khenata, R., E-mail: khenata_rabah@yahoo.fr [Laboratoire de Physique Quantique de la Modélisation Mathématique (LPQ3M), Université de Mascara, 29000 (Algeria); Ahmed, R. [Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor (Malaysia); Murtaza, G. [Materials Modeling Laboratory, Department of Physics, Islamia College University, Peshawar (Pakistan); Bin Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Azam, Sikander [New Technologies – Research Center, University of West Bohemia, Univerzitni 8, 306 14 Pilsen (Czech Republic)

    2014-12-15

    Highlights: • The calculated structural parameters of RMn{sub 2}Ge{sub 2} (R = Ca, Nd and Y) compounds are found in good agreement with the experimental data. • The structural and band structure calculation reveals that these compounds are ferromagnetic brittle metals. • The elastic and thermodynamic properties for the herein studied compounds are investigated for the first time. - Abstract: Intermetallic RMn{sub 2}Ge{sub 2} ternary compounds have attracted considerable attention from researchers in recent years because they show strong indications for novel magnetic characteristics and they have the potential to reveal the mechanism of superlattices. The study of the paramagnetic, ferromagnetic and antiferromagnetic phases affirms the strong dependence to the distance between atomic species in these compounds. In this study, we investigated the structural, elastic, electronic and thermodynamic properties of the intermetallic RMn{sub 2}Ge{sub 2} (R = Ca, Nd and Y) compounds. To carry out this study, we used the full potential (FP) linearized (L) augmented plane wave plus local orbitals (APW + lo), a scheme of calculations developed within the frame work of density functional theory (DFT). To incorporate the exchange correlation (XC) energy and corresponding potential into the total energy calculations, local density approximation (LDA) parameterized by Perdew and Wang is taken into account. Analysis of the density of states (DOS) profile illustrates the conducting nature of these intermetallic compounds; with a predominantly contribution from the R and Mn-d states. At ambient conditions, calculations for elastic constants (C{sub 11}, C{sub 12}, C{sub 13}, C{sub 44}, C{sub 33} and C{sub 66}) are also performed, which point to their brittle character. In addition, the quasi harmonic Debye model was used to predict the thermal properties, together with relative expansion coefficients and heat capacity.

  11. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases

    Energy Technology Data Exchange (ETDEWEB)

    Arghavani Nia, Borhan, E-mail: b.arghavani@gmail.com [Department of Physics, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Sedighi, Matin [Department of Physics, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Shahrokhi, Masoud [Young Researchers and Elite Club, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Moradian, Rostam [Nano-Science and Nano-Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Computational Physics Science Research Laboratory, Department of Nano-Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-1795, Tehran (Iran, Islamic Republic of)

    2013-11-15

    A density functional theory study of structural, electronical and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. In the exchange–correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca{sub 3}Sb{sub 2} has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated. - Graphical abstract: A density functional theory study of structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. Display Omitted - Highlights: • Physical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases are investigated. • It is found that the hexagonal phase is an indirect gap semiconductor. • Ca{sub 3}Sb{sub 2} is a direct-gap semiconductor at the Γ point in the cubic phase. • By increasing pressure the semiconducting band gap and anti-symmetry gap are decreased.

  12. Effects of the structural order of canthaxanthin on the Raman scattering cross section in various solvents:A study by Raman spectroscopy and ab initio calculation

    Institute of Scientific and Technical Information of China (English)

    Wu Nan-Nan; Li Zuo-Wei; Liu Jing-Yao; OuYang Shun-Li

    2012-01-01

    In this work,we measure the Raman scattering cross sections (RSCSs) of the carbon-carbon (CC) stretching vibrational modes of canthaxanthin in benzene,acetone,n-heptane,cyclohexane,and m-xylene.It is found that the absolute RSCS of CC stretching mode of canthaxanthin reaches a value of 10-24 cm2·molecule-1·sr-1 at 8×10-5 M,which is 6 orders of magnitude larger than general RSCS (10-30 cm2·molecule- 1 ·sr-1 ),and the RSCSs of canthaxanthin in various solvents are very different due to the hydrogen bond.A theoretical interpretation of the magnetic experimental results is given,which is introduced in a qualitative nonlinear model of coherent weakly damped electron-lattice vibration in the structural order of polyene chains.In addition,the optimal structure and the bond length alternation (BLA) parameter of canthaxanthin are calculated using quantum chemistry calculation (at the b31yp/6-31g (d,p) level of theory).The theoretical calculations are in good agreement with the experimental results.Furthermore,the combination of Raman spectroscopy and the quantum chemistry calculation study would be a quite suitable method of studying the structures and the properties of the π-conjugated systems.

  13. Ab initio study of the structural, electronic and optical properties of BAs and BN compounds and BN{sub x}As{sub 1−x} alloys

    Energy Technology Data Exchange (ETDEWEB)

    Guemou, M., E-mail: guemoumhamed7@gmail.com [Engineering Physics Laboratory, Ibn Khaldoun University of Tiaret, Postbox 78-Zaaroura, 14000 Tiaret (Algeria); Abdiche, A.; Riane, R. [Applied Materials Laboratory, Research Center, University of Sidi Bel Abbes, 22000 Sidi Bel Abbes (Algeria); Khenata, R. [Laboratoire de Physique Quantique et de Modélisation Mathématique (LPQ3M), Département de Technologie, Université de Mascara, 29000 Mascara (Algeria)

    2014-03-01

    In this work, we present a density-functional theory study of structural, electronic and optical properties of BAs, BN binary compounds and their ternary BN{sub x}As{sub 1−x} solid solutions. The calculations are done by using the all-electron full potential linear augmented plane-wave method (FP-LAPW) as employed in WIEN2k code. For the exchange-correlation potential, local-density approximation (LDA) and generalized gradient approximation (GGA) have been used to calculate theoretical lattice parameters, bulk modulus, and its pressure derivative. The electronic band structure of these compounds have been calculated by using the above two approximations. We have also investigated in this article the density of state and the optical properties such as the dielectric function and the refractive index of BAs, BN and BN{sub 0.25}As{sub 0.75} compounds by using the above method. The results obtained for structural and electronic properties are compared with experimental data and other computational work. It has been found that the energy bands with all these approximations are similar except the band gap values. It has also been found that our results with LDA and GGA are in good agreement with other computational work wherever these are available.

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

    Science.gov (United States)

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

    2017-03-01

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

  15. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chung-De [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); National Tsing Hua University, Hsinchu, Taiwan (China); Huang, Yen-Chieh [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Chiang, Hsin-Lin [National Tsing Hua University, Hsinchu, Taiwan (China); Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Chen, Chun-Jung, E-mail: cjchen@nsrrc.org.tw [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); National Tsing Hua University, Hsinchu, Taiwan (China); National Cheng Kung University, Tainan City 701, Taiwan (China); National Cheng Kung University, Tainan City 701, Taiwan (China)

    2014-09-01

    A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

  16. Quantization and topological states in the spin Hall conductivity of low-dimensional systems: An ab initio study

    Science.gov (United States)

    Matthes, L.; Küfner, S.; Furthmüller, J.; Bechstedt, F.

    2016-03-01

    Ab initio relativistic band structure calculations are performed for the frequency-dependent spin Hall conductivity of two-dimensional atomically thin crystals and one-dimensional nanoribbons. We study the influence of topology, quantization, and topological edge states. As model systems fully halogenated germanene, GeI, and its zigzag nanoribbons are investigated. GeI represents a topological insulator (TI). For comparison, also the TI germanene and the trivial insulator hydrogenated germanene are studied. For the TIs we demonstrate the quantization of the static spin Hall conductivity. It is hardly influenced by temperature and Fermi level shift. Its frequency dependence is governed by the band-structure details. Topological edge states influence the conductivity mainly for vanishing frequencies.

  17. Electronic structure and magnetism in Ni{sub 0.0625}Zn{sub 0.9375}O: An ab initio study

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, Rafael Gonzalez [GFMC, Departamento de Fisica, Universidad del Norte, A. A. 1569, Barranquilla (Colombia) and GEMA, Departamento de Fisica, Universidad Nacional de Colombia, A. A. 5997, Bogota (Colombia)], E-mail: rgonzalezh@unal.edu.co; Perez, William Lopez [GFMC, Departamento de Fisica, Universidad del Norte, A. A. 1569, Barranquilla (Colombia); Jairo Arbey Rodriguez, M. [GEMA, Departamento de Fisica, Universidad Nacional de Colombia, A. A. 5997, Bogota (Colombia)], E-mail: jarodriguezm@unal.edu.co

    2009-09-15

    We carry out first principles spin polarized calculations in order to study the electronic structure and magnetism of Ni{sub 0.0625}Zn{sub 0.9375}O compound using density functional theory (DFT) within a plane-wave ultrasoft pseudopotential scheme. The electronic properties of Ni{sub x}Zn{sub 1-x}O at a concentration of 6.25% are analyzed using a 2x2x2 wurtzite ZnO supercell. We optimize the lattice constants of ZnO pure and Ni{sub 0.0625}Zn{sub 0.9375}O. We observe that if one Zn atom is substituted by one Ni atom in the wurtzite ZnO supercell, the lattice parameters decrease slightly some thousandths of angstrom. We also find a stable ferromagnetic state in Ni doped ZnO with a total magnetization of 2.04{mu}{sub B} per supercell. Using the optimized lattice parameters, we have calculated the band structure and density of states of Ni{sub 0.0625}Zn{sub 0.9375}O.

  18. Ab initio study of the structural, elastic, vibrational and thermodynamic properties of the hexagonal boron nitride: Performance of LDA and GGA

    Energy Technology Data Exchange (ETDEWEB)

    Hamdi, Ilyes, E-mail: ilyeshamdi@yahoo.f [Department of Electronics, Electro-technics and Automatics, Institute of Applied Sciences and Technology, 2100 Gafsa (Tunisia); UPMI units of research, Faculty of Sciences at Gafsa, 2100 Gafsa (Tunisia); Meskini, Noureddine [Physics Department, Faculty of Sciences at Tunis, 2092 Tunis (Tunisia)

    2010-07-01

    A first principles quantum mechanical approach is used to investigate the structural, elastic, vibrational and thermodynamic properties of the hexagonal boron nitride (h-BN) in the framework of the pseudopotential plane wave density-functional perturbation theory for the two popular exchange-correlation functionals: local density approximation and the revised Perdew-Burke-Ernzerhof generalized gradient approximation [Y. Zhang, W. Yang, Phys. Rev. Lett, 80 (1998), 890]. The LDA calculations of the structural parameters are in good agreement with experimental results, whereas GGA largely overestimated them. The computed elastic constants are improved by performing the calculations at room temperature and using the experimental lattice parameters. A good agreement with the experimental data is obtained for the phonon frequencies using both functionals. The thermodynamic properties such as the thermal equation of state, the in-plane and out-of-plane thermal expansion coefficients (LTEC), the bulk modulus and the heat capacity are calculated at the experimental lattice parameters using the quasiharmonic approximation (+ an empirical anharmonic term) for the Helmholtz free energy. Anharmonic corrections are important at high temperature. A good agreement with the experimental data for the LTEC has been obtained with the GGA functional, especially for the out-of-plane LTEC. In contrast with recent experimental findings, our calculated bulk modulus decreases with temperature for both functionals. This (decreasing) behavior is in a good agreement with other experimental data. The constant pressure heat capacity calculated with LDA and GGA is in very good agreement with experimental results.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-07-01

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

  20. Ab-initio study of structural, elastic, electronic and thermodynamic properties of BaxSr1−xS ternary alloys

    Directory of Open Access Journals (Sweden)

    Chelli S.

    2015-12-01

    Full Text Available The structural, elastic, electronic and thermodynamic properties of BaxSr1−xS ternary alloys have been investigated using the full-potential (linearized augmented plane wave method. The ground state properties, such as lattice constant, bulk modulus and elastic constants, are in good agreement with numerous experimental and theoretical data. The dependence of the lattice parameters, bulk modulus and band gap on the composition x was analyzed. Deviation of the lattice constant from Vegard’s law and the bulk modulus from linear concentration dependence (LCD was observed. The microscopic origins of the gap bowing were explained by using the approach of Zunger et al. The thermodynamic stability of BaxSr1−xS alloy was investigated by calculating the excess enthalpy of mixing, ΔHm and the calculated phase diagram showed a broad miscibility gap with a critical temperature.

  1. An ab initio study of the electronic structure and optical properties of CdS{sub 1-x}Te{sub x} alloys

    Energy Technology Data Exchange (ETDEWEB)

    Al-Douri, Y.; Ahmad, S.; Hashim, U. [Institute of Nano Electronic Engineering, University Malaysia Perlis, Kangar, Perlis (Malaysia); Reshak, Ali Hussain [Institute of Nano Electronic Engineering, University Malaysia Perlis, Kangar, Perlis (Malaysia); Institute of Physical Biology, South Bohemia University, Nove Hrady (Czech Republic); Baaziz, H.; Charifi, Z. [Physics Department, Faculty of Science and Engineering, University of M' sila (Algeria); Khenata, R. [Laboratoire de Physique Quantique et de Modelisation Mathematique (LPQ3M), Universite de Mascara (Algeria); Department of Physics and Astronomy, Faculty of Science, King Saud University, Riyadh (Saudi Arabia)

    2010-12-15

    The structural, electronic and optical properties of cubic CdS{sub 1-x}Te{sub x} alloys, with Te-concentrations varying from 0% up to 100% are investigated. The calculations are based on the total-energy calculations using the full potential-linearized augmented plane wave (FP-LAPW) method. The exchange and correlation potential is treated by the generalized-gradient approximation (GGA) for the total-energy calculations, while for electronic properties in addition to that the Engel-Vosko (EV-GGA) formalism was also applied. The ground state properties for all Te-concentrations are presented. The optical dielectric constant is also determined for both the binary and their related ternary alloys. (author)

  2. Electronic structure of an oxygen vacancy in Al{sub 2}O{sub 3} from the results of Ab Initio quantum-chemical calculations and photoluminescence experiments

    Energy Technology Data Exchange (ETDEWEB)

    Pustovarov, V. A. [Ural State Technical University (Russian Federation); Aliev, V. Sh.; Perevalov, T. V., E-mail: timson@isp.nsc.ru; Gritsenko, V. A., E-mail: grits@isp.nsc.ru [Russian Academy of Sciences, Institute of Semiconductor Physics, Siberian Branch (Russian Federation); Eliseev, A. P. [Russian Academy of Sciences, Institute of Geology and Mineralogy, Siberian Branch (Russian Federation)

    2010-01-15

    The electronic structure of an oxygen vacancy in {alpha}-Al{sub 2}O{sub 3} and {gamma}-Al{sub 2}O{sub 3} is calculated. The calculation predicts an absorption peak at an energy of 6.4 and 6.3 eV in {alpha}-Al{sub 2}O{sub 3} and {gamma}-Al{sub 2}O{sub 3}, respectively. The luminescence and luminescence excitation spectra of amorphous Al{sub 2}O{sub 3} are measured using synchrotron radiation. The presence of a luminescence band at 2.9 eV and a peak at 6.2 eV in the luminescence excitation spectrum indicates the presence of oxygen vacancies in amorphous Al{sub 2}O{sub 3}.

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

    Science.gov (United States)

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

    2010-02-01

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

  4. 第一性原理计算水对缬氨酸电子结构的等效势%Ab Initio Calculation of Equivalent Potential of Water for Electronic Structure of Valine

    Institute of Scientific and Technical Information of China (English)

    郑浩平; 吴丽华; 李根

    2013-01-01

    用第一性原理、全电子、从头计算方法构造了水溶液对缬氨酸(Val)电子结构的等效势.首先用自由团簇计算法得到能量最低时水分子与缬氨酸的相对空间位形,然后用团簇埋入自洽计算(SCCE)方法计算缬氨酸在水分子势下的电子结构,最后用偶极子势代替水分子势.结果表明:由于水溶液的存在,缬氨酸费米面下八个能级每个能级平均上升了约0.775 5 eV;水溶液对缬氨酸电子结构的影响可以很好地被偶极子势模拟.因此,所得的偶极子势可以直接运用到水溶液中蛋白质电子结构的计算中.%The equivalent potential of water for the electronic structure of valine (Val) was constructed on the basis of the first-principles, all-electron, ab initio calculations. The process involved three steps. First, a search for the minimum-energy configuration of the system Val + 7H2O was carried out by free cluster calculation. Then, the electronic structure of valine with the potential of water molecules was calculated with the self-consistent cluster-embedding (SCCE) method. Finally, the effect of water was simulated on valine by dipoles. Results show that the major effect of water on the electronic structure of valine is to raise the eigenvalues of eight orbitals under Fermi surface by about 0. 775 5 eV on average. The effect of water on the electronic structure of valine can be well simulated by dipoles. The equivalent potential obtained can be applied directly to the calculation of the electronic structures of proteins in solution.

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

    Science.gov (United States)

    Le Page, Yvon; Saxe, Paul

    2002-03-01

    generality of the approach described here enabled the creation of a robust user interface going seamlessly from the database search to the printout of the elastic coefficients. With it, even nonspecialist users can reliably produce technologically relevant results like those discussed here in a simple point-and-click fashion from corresponding entries in the CRYSTMET® and ICSD® structure databases, i.e., for all pure-phase nonorganic materials with known crystal structure. The case of Ti4As3 exposes, on a first cluster of properties, stiffness, compliance, and the isotropic properties that can be derived from them, the current reality of mining crystal structure databases with ab initio software for technological properties that were never measured before. Further developments in that direction are currently underway.

  6. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde.

    Science.gov (United States)

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M; Ben Altabef, Aída

    2015-02-05

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Studies on the Quantitative Structure-activity Relationship of Toxicity of Chlorophenol Serial Compounds in the ab initio Methods and Substitutive Position of Chlorine Atom (NPCS)

    Institute of Scientific and Technical Information of China (English)

    ZHENG Qing; WANG Lian-Sheng

    2007-01-01

    20 Quantum chemical parameters of chlorophenol compounds were fully optimized by using B3LYP method on both 6-31G* and 6-311G* basis sets. These structural parameters are taken as theoretical descriptors, and the experimental data of 20 compounds' aquatic photogen toxicity(-1gEC50) are used to perform stepwise regression in order to obtain two predicted -lgEC50 correlation models whose correlation coefficients R2 are respectively 0.9186 and 0.9567. In addition, parameters of chlorine atom's substitutive positions and their correlations (NPCs) are taken as descriptors to obtain another predicted -1gEC50 model with the correlation coefficient R2 of 0.9444. Correlation degree of each independent variable in the three models is verified by using variance inflation factors (VIF) and t value. In the cross-validation method, cross-validation coefficients q2 of 3 models are respectively 0.8748, 0.9119 and 0.8993, which indicates that the relativity and prediction ability of this model are superior to those of the model obtained by topological and BLYP methods.

  8. Electronic structure of {delta}-Ta{sub 2}O{sub 5} with oxygen vacancy: ab initio calculations and comparison with experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, Maxim V.; Perevalov, Timofey V.; Aliev, Vladimir S.; Gritsenko, Vladimir A. [A. V. Rzhanov Institute of Semiconductor Physics SB RAS, Novosibirsk, 630090 (Russian Federation); Kaichev, Vasily V. [Boreskov Institute of Catalysis SB RAS, Novosibirsk, 630090 (Russian Federation)

    2011-07-15

    Electronic structure of oxygen vacancies in Ta{sub 2}O{sub 5} have been studied theoretically by first-principles calculations and experimentally by x-ray photoelectron spectroscopy. Calculations of {delta}-Ta{sub 2}O{sub 5} were performed using density functional theory within gradient-corrected approximation with the +U approach. Results indicate that the oxygen vacancy causes a defect level in the energy gap at 1.2 eV above the top of the valence band. To produce oxygen vacancies, amorphous films of Ta{sub 2}O{sub 5} were bombarded with Ar{sup +} ions. XPS results indicate that the Ar-ion bombardment leads to the generation of the oxygen vacancies in Ta{sub 2}O{sub 5} that characterize the peak at 2 eV above the valence band. The calculated spectrum of crystalline {delta}-Ta{sub 2}O{sub 5} demonstrates qualitative correspondence with the XPS spectrum of the amorphous Ta{sub 2}O{sub 5} film after Ar-ion bombardment.

  9. Ab initio calculations of the structural, electronic, thermodynamic and thermal properties of BaSe1‑x Te x alloys

    Science.gov (United States)

    Drablia, S.; Boukhris, N.; Boulechfar, R.; Meradji, H.; Ghemid, S.; Ahmed, R.; Omran, S. Bin; El Haj Hassan, F.; Khenata, R.

    2017-10-01

    The alkaline earth metal chalcogenides are being intensively investigated because of their advanced technological applications, for example in photoluminescent devices. In this study, the structural, electronic, thermodynamic and thermal properties of the BaSe1‑x Te x alloys at alloying composition x = 0, 0.25, 0.50, 0.75 and 1 are investigated. The full potential linearized augmented plane wave plus local orbital method designed within the density functional theory was used to perform the total energy calculations. In this research work the effect of the composition on the results of the parameters and bulk modulus as well as on the band gap energy is analyzed. From our results, we found a deviation of the obtained results for the lattice constants from Vegard’s law as well as a deviation of the value of the bulk modulus from the linear concentration dependence. We also carried out a microscopic analysis of the origin of the band gap energy bowing parameter. Furthermore, the thermodynamic stability of the considered alloys was explored through the measurement of the miscibility critical temperature. The quasi-harmonic Debye model, as implemented in the Gibbs code, was used to predict the thermal properties of the BaSe1‑x Te x alloys, and these investigations comprise our first theoretical predictions concerning the BaSe1‑x Te x alloys.

  10. Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde

    Science.gov (United States)

    Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M.; Altabef, Aída Ben

    2015-02-01

    The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34 °C and decomposes at temperatures higher than 193 °C.

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

    Science.gov (United States)

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

    2008-12-11

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

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

    DEFF Research Database (Denmark)

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

    2003-01-01

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

  13. Speciation of magnesium in monohydrocalcite: XANES, ab initio and geochemical modeling

    Science.gov (United States)

    Fukushi, Keisuke; Suzuki, Yuma; Kawano, Jun; Ohno, Takeshi; Ogawa, Masahiro; Yaji, Toyonari; Takahashi, Yoshio

    2017-09-01

    Monohydrocalcite (MHC: CaCO3·H2O), a rare carbonate mineral formed under surface conditions, is usually observed in nature as containing a variable amount of Mg, with a 0.007-0.45 Mg/Ca mole ratio. The variable Mg composition in MHC is anticipated as a promising proxy to assess paleo-hydrochemistry especially in saline lakes. Although the roles of Mg on the formation and stability of MHC have been studied intensively, the Mg speciation in MHC has remained unclear and controversial. This study examined Mg speciation in MHC using X-ray absorption near edge structure (XANES), ab initio molecular simulation, and geochemical modeling. Mg-XANES spectra of MHC with different Mg/Ca ratios prepared from mixing solutions of Na2CO3, CaCl2 and MgCl2 revealed that the Mg in MHC is a mixture of amorphous Mg carbonate (AMC) and other Mg containing phase. The contribution of AMC to total Mg is negatively correlated to the crystallinity of MHC. Results show that AMC might play a protective role in the crystallization and the transformation to stable calcium carbonates. Ab initio calculation of Mg2+ substitution into MHC showed that a limited amount of Mg2+ can be incorporated into the MHC structure. Six-fold coordination of Mg2+ is substituted for eight-fold coordination of Ca2+ in the MHC structure. The other type of Mg in MHC revealed from the XANES analyses most likely corresponds to the structural Mg in MHC. The contribution of the structural Mg is almost constant at 0.06 in Mg/Ca, representing the limit of solid solubility of Mg in MHC. The solubility products of the MHC with the limit of solid solubility of Mg and the AMC associated with MHC were estimated from the reacted solution compositions. Prediction of the Mg/Ca ratio as a function of the initial solution conditions using solubility reasonably reproduces the observed apparent Mg/Ca ratios in MHC from the present study and earlier studies. The apparent Mg/Ca ratio of MHC is useful to elucidate water chemistry

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

    CERN Document Server

    Geng, Hua Y

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-15

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

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

    Science.gov (United States)

    Geng, Hua Y.

    2015-02-01

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

  17. Ab initio study of the interplay between superconductivity and magnetic fields in MgB{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Aperis, Alexandros; Maldonado, Pablo; Oppeneer, Peter M. [Uppsala University, Uppsala (Sweden)

    2015-07-01

    Among the bulk superconductors broadly accepted to be mediated by phonons, MgB{sub 2} exhibits a record high critical temperature of T{sub c}=39 K. The relatively simple crystal structure of this material makes it an ideal platform to investigate fundamental phenomena, such as the interplay between superconductivity and the Zeeman effect, at the ab initio level. Here we combine DFT calculations providing electronic band and phonon dispersions with numerical solutions of the fully anisotropic Eliashberg equations, to provide a complete picture of the modification of the two-band superconductivity in this compound at finite external magnetic fields and temperature. We predict interesting signatures in the H - T phase diagram which could be experimentally probed.

  18. New high-pressure phase of MgH2: An ab initio constant-pressure study

    Science.gov (United States)

    Durandurdu, Murat

    2014-02-01

    The stability of magnesium hydride (MgH2) at high pressure is studied using a constant-pressure ab initio technique. Two phase transformations are successfully observed through the simulations. The rutile structure undergoes a phase transformation into a CaCl2-type phase. Further increase in pressure results into a first-order phase transition into an orthorhombic state within Pbcm symmetry. This phase can be considered as a distorted CaF2-type crystal and does not correspond to the previously proposed MgH2 phases. The transformation mechanism of the CaCl2-Pbcm phase change at the atomistic level is successfully characterized and it is found that the CaCl2-to-Pbcm phase change proceeds via an ideal CaF2-type intermediate phase. These phase transformations are also analyzed using total energy-volume calculations.

  19. Embedded atom approach for gold–silicon system from ab initio molecular dynamics simulations using the force matching method

    Indian Academy of Sciences (India)

    A NASSOUR

    2016-09-01

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-17

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

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

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2009-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti...... systems in the future. A few examples will be discussed. Contents 12.1 Introduction...........307 12.2 Brief introduction to Raman spectroscopy ..............309 12.2.1 Basics .....................309 12.2.2 Experimental, fluorescence and fouriertransform- Raman spectroscopy instrumentation ...... 311 12.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...

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

    Science.gov (United States)

    Aravena, Daniel; Atanasov, Mihail; Neese, Frank

    2016-05-01

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

  4. Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

    We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's funct......'s function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations....

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-11-30

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

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

    Science.gov (United States)

    Senent, M. L.

    1995-06-01

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

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

    CERN Document Server

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

    2016-01-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO$_{\\rm sat}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to $^{56}$Ni. We derive an efficient scheme for including continuum effects in coupled-clust...

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

    Institute of Scientific and Technical Information of China (English)

    Anil Thakur; P. K. Ahluwalia

    2005-01-01

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

  9. Ab initio calculations for dissociative hydrogen adsorption on lithium oxide surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Sutjianto, A. [Argonne National Lab., IL (United States). Chemical Technology Div.]|[Michigan Technological Univ., Houghton, MI (United States). Physics Dept.; Tam, S.W.; Curtiss, L.A.; Johnson, C.E. [Argonne National Lab., IL (United States). Chemical Technology Div.; Pandey, R. [Michigan Technological Univ., Houghton, MI (United States). Physics Dept.

    1994-12-01

    Lithium ceramics are one class of materials being considered as tritium breeders for fusion technology,and hydrogen is known to enhance the release of tritium from lithium ceramic materials. Dissociative hydrogen chemisorption on the Li{sub 2}O surfaces of the (100), (110), and (111) planes has been investigated with ab initio Hartree-Fock calculations. Calculations for unrelaxed crystal Li{sub 2}O structures indicated that except for the (100) surface, the (110) and (111) surfaces are stable. Results on the heterolytic sites of n-layer (110) (where n {ge} 2) slabs and three-layer (111) slabs suggest that dissociative hydrogen chemisorption is endothermic. For a one-layer (110) slab at 100% surface coverage, the dissociative hydrogen chemisorption is exothermic, forming OH{sup {minus}} and Li{sup +}H{sup {minus}}Li{sup +}. The results also indicate that the low coordination environment in surface step structures, such as kinks and ledges, may plan an important role in the hydrogen chemisorption process. On the homolytic sites of the (110) and (111) surfaces, there is no hydrogen chemisorption.

  10. Ab-initio calculations for dilute magnetic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Belhadji, Brahim

    2008-03-03

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    CERN Document Server

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

    2016-01-01

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

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

    Science.gov (United States)

    Sammarruca, Francesca

    2017-01-01

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

  14. Ab initio modeling of decomposition in iron based alloys

    Science.gov (United States)

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

    2016-12-01

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

  15. Exocyclic push-pull conjugated compounds. Part 3. An experimental NMR and theoretical MO ab initio study of the structure, the electronic properties and barriers to rotation about the exocyclic partial double bond in 2- exo-methylene- and 2-cyanoimino-quinazolines and -benzodiazepines

    Science.gov (United States)

    Benassi, R.; Bertarini, C.; Hilfert, L.; Kempter, G.; Kleinpeter, E.; Spindler, J.; Taddei, F.; Thomas, S.

    2000-03-01

    The structure of a number of 2- exo-methylene substituted quinazolines and benzodiazepines, respectively, 1, 3a, b, 4( X=-CN, -COOEt ) and their 2-cyanoimino substituted analogues 2, 3c, d( X=-CN, -SO 2C 6H 4-Me (p) was completely assigned by the whole arsenal of 1D and 2D NMR spectroscopic methods. The E/ Z isomerism at the exo-cyclic double bond was determined by both NMR spectroscopy and confirmed by ab initio quantum chemical calculations; the Z isomer is the preferred one, its amount proved dependent on steric hindrance. Due to the push-pull effect in this part of the molecules the restricted rotation about the partial C 2,C 11 and C 2,N 11 double bonds, could also be studied and the barrier to rotation measured by dynamic NMR spectroscopy. The free energies of activation of this dynamic process proved very similar along the compounds studied but being dependent on the polarity of the solvent. Quantum chemical calculations at the ab initio level were employed to prove the stereochemistry at the exo-cyclic partial double bonds of 1- 4, to calculate the barriers to rotation but also to discuss in detail both the ground and the transition state of the latter dynamic process in order to better understand electronic, inter- and intramolecular effects on the barrier to rotation which could be determined experimentally. In the cyanoimino substituted compounds 2, 3c, d, the MO ab initio calculations evidence the isomer interconversion to be better described by the internal rotation process than by the lateral shift mechanism.

  16. Recent achievements in ab initio modelling of liquid water

    CERN Document Server

    Khaliullin, Rustam Z

    2013-01-01

    The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-06-01

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

  18. Rational design of electrolyte components by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-02-28

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-11-15

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

  20. Local Environment Distribution in Ab Initio Liquid Water

    Science.gov (United States)

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

    2013-03-01

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

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

    Science.gov (United States)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2016-09-01

    Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.

  2. Re-examination of the SiGe Raman spectra: Percolation/one-dimensional-cluster scheme and ab initio calculations

    Science.gov (United States)

    Pagès, O.; Souhabi, J.; Torres, V. J. B.; Postnikov, A. V.; Rustagi, K. C.

    2012-07-01

    We report on the detailed assignment of various features observed in the Raman spectra of SiGe alloys along the linear chain approximation (LCA), as achieved based on remarkable intensity interplays with composition between such neighboring features known from the literature but which so far have not been fully exploited. Such an assignment is independently supported by ab initio calculation of the frequencies of bond-stretching modes taking place in different local environments, which we define at one dimension (1D) for consistency with the LCA. Fair contour modeling of the SiGe Raman spectra is eventually obtained via a so-called 1D-cluster version of the phenomenological (LCA-based) percolation scheme, as originally developed for zincblende alloys, after ab initio calibration of the intrinsic Si-Si, Si-Ge, and Ge-Ge Raman efficiencies. The 1D-cluster scheme introduces a seven-oscillator [1 × (Ge-Ge), 4 × (Si-Ge), 2 × (Si-Si)] Raman behavior for SiGe, which considerably deviates from the currently accepted six-oscillator [1 × (Ge-Ge), 1 × (Si-Ge), 4 × (Si-Si)] behavior. Different numbers of Raman modes per bond are interpreted as different sensitivities to the local environment of Ge-Ge (insensitive), Si-Si (sensitive to first neighbors), and Si-Ge (sensitive to second neighbors) bond stretching. The as-obtained SiGe 1D-cluster/percolation scheme is also compared with the current version for zincblende alloys, using GaAsP as a natural reference. A marked deviation is concerned with an inversion of the like phonon branches in each multiplet. This is attributed either to the considerable Si and Ge phonon dispersions (Si-Si doublet) or to a basic difference in the lattice relaxations of diamond and zincblende alloys (Si-Ge multiplet). The SiGe vs GaAsP comparison is supported by ab initio calculation of the local lattice relaxation/dynamics related to prototype impurity motifs that are directly transposable to the two crystal structures.

  3. Mechanism of GeSbTe phase change materials: an ab initio molecular dynamics study

    Science.gov (United States)

    Raty, Jean-Yves; Otjacques, Céline; Gaspard, Jean-Pierre; Bichara, Christophe

    2008-03-01

    Among phase change materials, Ge2Sb2Te5 (225) is one of the most successfully used in applications. Accepted models are based on EXAFS spectra and suppose a complete reorganization of bonds during amorphization, with Ge changing from sixfold to tetrahedral coordination. We perform ab initio MD simulations of the (225), (124) and (415) liquid alloys. We show that the crystalline, liquid and amorphous structure of these systems are similar, with very little sp3 hybridization around Ge atoms and a majority of p-sigma bonds. Using a set of quenched liquid configurations we reproduce the EXAFS measurements on the (225) composition and explain how the static Debye Waller factor due to the vacancies in the crystal phase leads to a cancellation of individual neighbors contribution to the EXAFS signal while in the amorphous, a larger coherence occurs, enhancing the EXAFS signal. The computed electrical conductivities of the three phases (cubic solid, liquid and amorphous) prove to be very different, accordingly with the experiment.

  4. Crystal structure prediction and electronic properties of Li-based ternary compounds

    Energy Technology Data Exchange (ETDEWEB)

    Vergniory, Maia G.; Sanna, Antonio; Ernst, Arthur; Romero, Aldo H.; Gross, Eberhard K.U. [Max Planck Institute of Microstructure Physics, 06120 Halle (Germany); Marques, Miguel A.L.; Botti, Silvana; Valencia, Irais [Universite de Lyon, F-69000 Lyon, France and LPMCN, CNRS, UMR 5586, Universite Lyon 1, F-69622 Villeurbanne (France); Amsler, Max; Goedecker, Stefan [Department of Physics, Universitaet Basel, Klingelbergstr. 82, 4056 Basel (Switzerland); Chulkov, Evgueni V. [Donostia International Physics Center, 20018 Donostia-San Sebastian (Spain)

    2013-07-01

    On the basis of ab initio first principles and using the Minimal Hopping Algorithm we predict the crystal structure of non synthesized LiYZ (Y=Au,Ag, Z=Te,Se) based ternary compounds. We find that, as distinct from expectation, the crystal structure depends strongly on the composition, thus every compound belongs to a different symmetry group and has complexly different electronic properties. We analyze the fundamental physics below these features considering the calculated ground state structure.

  5. Gas phase ion chemistry of coumarins: ab initio calculations used to ...

    African Journals Online (AJOL)

    Gas phase ion chemistry of coumarins: ab initio calculations used to justify ... and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is ... Ab Initio calculations, Electron ionization, Positive chemical ionization, Negative ...

  6. Lattice dynamics of Cs2NaYbF6 and Cs2NaYF6 elpasolites: Ab initio calculation

    Science.gov (United States)

    Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.

    2015-06-01

    The ab initio calculations of the crystal structure and the phonon spectrum of Cs2NaYbF6 and Cs2NaYF6 crystals with the elpasolite structure have been performed. The frequencies and types of fundamental vibrations have been determined. The calculations have been performed in the framework of the density functional theory using the molecular orbital method with hybrid functionals in the CRYSTAL09 program developed for the simulation of periodic structures. The outer 5 s and 5 p shells of the rare-earth ion have been described in Gaussian-type basis sets. The influence of inner shells, including 4 f electron shells, on the outer shells has been described using the pseudopotential. It has been shown that this approach allows the description of the phonon spectrum with the inclusion of the splitting of the longitudinal and transverse optical modes.

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

    Science.gov (United States)

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

    2012-05-17

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  9. Ab initio study of alanine polypeptide chain twisting

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

    2006-01-01

    chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...

  10. Relaxation of Small Molecules: an ab initio Study

    Institute of Scientific and Technical Information of China (English)

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

    2002-01-01

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

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

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

    2015-08-01

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

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

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

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

  16. Ab initio calculations of ^12C and neutron drops

    Science.gov (United States)

    Pieper, Steven C.

    2009-10-01

    Ab initio calculations of nuclei, which treat a nucleus as a system of A nucleons interacting by realistic two- and three-nucleon forces, have made tremendous progress in the last 15 years. This is a result of better Hamiltonians, rapidly increasing computer power, and new or improved many-body methods. Three methods are principally being used: Green's function Monte Carlo (GFMC), no-core shell model, and coupled cluster. In the limit of large computer resources, all three methods produce exact eigenvalues of a given nuclear Hamiltonian. With DOE SciDAC and INCITE support, all three methods are using the largest computers available today. Under the UNEDF SciDAC grant, the Argonne GFMC program was modified to efficiently use more than 2000 processors. E. Lusk (Argonne), R.M. Butler (Middle Tennessee State U.) and I have developed an Asynchronous Dynamic Load-Balancing (ADLB) library. In addition all the cores in a node are used via OpenMP as one ADLB/MPI client. In this way we obtain very good scalability up to 30,000 processors on Argonne's IBM Blue Gene/P. Two systems of particular interest that require this computer power are ^12C and neutron drops. V.R. Pandharipande (UIUC, deceased), J. Carlson (LANL), R.B. Wiringa (Argonne), and I have developed new trial wave functions that explicitly contain the three-alpha particle structure of ^12C. These are being used with the Argonne V18 and Illinois-7 potentials which reproduce the energies of 51 states in 3energy-density functionals.

  17. Ab Initio Studies of Metal Hexaboride Materials

    Science.gov (United States)

    Schmidt, Kevin M.

    -terminations produce the lowest energies for di-cations of CaB6, SrB6 and BaB6, while tri-valent LaB6 minimizes its surface energy by arranging the metal ions in parallel rows on the surface. Studies involving hydrogen suggest that a single molecule per surface unit-cell is possible, and evidence is given for a dissociative adsorption pathway. Ternary mixtures of metal hexaborides containing two alkaline-earth cations in each crystal are also investigated with electronic structure methods. Multiple geometries are used to understand how spatial arrangements of cations within the mixture can affect properties related to stability. Bond-lengths within the boron framework are found to be heavily dependent upon the local cation environment, and energies taken at absolute zero suggest certain stoichiometries naturally lead to phase splitting.

  18. Ab initio phonon properties of half-Heusler NiTiSn, NiZrSn and NiHfSn.

    Science.gov (United States)

    Andrea, Luc; Hug, Gilles; Chaput, Laurent

    2015-10-28

    A theoretical investigation of phonon properties from first-principles calculations is carried out for the half-Heusler compounds NiXSn, [Formula: see text], Zr and Hf. The crystal structures are optimised via ab initio calculations within the framework of density functional theory. The phonon properties are retrieved from harmonic and anharmonic interatomic force constants calculations using the finite size displacements method and many-body perturbation theory. A solution to the linearized phonon Boltzmann transport equation is then used to compute the ab initio thermal conductivities. For X   =   Ti, Zr and Hf, we found 15.4, 13.3 and 15.8 W m(-1) K(-1) at 300 K, respectively. Thanks to a spectral analysis of the velocities and lifetimes we were able appreciate the differences in the thermal conductivities between the three compounds under study. Our results provide insights to understand the behaviour of the thermal conductivity and therefore to improve the thermoelectric figure of merit for such materials.

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2015-01-01

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