Density, structure, and dynamics of water: The effect of van der Waals interactions

NASA Astrophysics Data System (ADS)

Wang, Jue; Román-Pérez, G.; Soler, Jose M.; Artacho, Emilio; Fernández-Serra, M.-V.

2011-01-01

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.

Deorbitalization strategies for meta-generalized-gradient-approximation exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Mejia-Rodriguez, Daniel; Trickey, S. B.

2017-11-01

We explore the simplification of widely used meta-generalized-gradient approximation (mGGA) exchange-correlation functionals to the Laplacian level of refinement by use of approximate kinetic-energy density functionals (KEDFs). Such deorbitalization is motivated by the prospect of reducing computational cost while recovering a strictly Kohn-Sham local potential framework (rather than the usual generalized Kohn-Sham treatment of mGGAs). A KEDF that has been rather successful in solid simulations proves to be inadequate for deorbitalization, but we produce other forms which, with parametrization to Kohn-Sham results (not experimental data) on a small training set, yield rather good results on standard molecular test sets when used to deorbitalize the meta-GGA made very simple, Tao-Perdew-Staroverov-Scuseria, and strongly constrained and appropriately normed functionals. We also study the difference between high-fidelity and best-performing deorbitalizations and discuss possible implications for use in ab initio molecular dynamics simulations of complicated condensed phase systems.

Electron correlation and the self-interaction error of density functional theory

NASA Astrophysics Data System (ADS)

Polo, Victor; Kraka, Elfi; Cremer, Dieter

The self-interaction error (SIE) of commonly used DFT functionals has been systematically investigated by comparing the electron density distribution ρ( r ) generated by self-interaction corrected DFT (SIC-DFT) with a series of reference densities obtained by DFT or wavefunction theory (WFT) methods that cover typical electron correlation effects. Although the SIE of GGA functionals is considerably smaller than that of LDA functionals, it has significant consequences for the coverage of electron correlation effects at the DFT level of theory. The exchange SIE mimics long range (non-dynamic) pair correlation effects, and is responsible for the fact that the electron density of DFT exchange-only calculations resembles often that of MP4, MP2 or even CCSD(T) calculations. Changes in the electron density caused by SICDFT exchange are comparable with those that are associated with HF exchange. Correlation functionals contract the density towards the bond and the valence region, thus taking negative charge out of the van der Waals region where these effects are exaggerated by the influence of the SIE of the correlation functional. Hence, SIC-DFT leads in total to a relatively strong redistribution of negative charge from van der Waals, non-bonding, and valence regions of heavy atoms to the bond regions. These changes, although much stronger, resemble those obtained when comparing the densities of hybrid functionals such as B3LYP with the corresponding GGA functional BLYP. Hence, the balanced mixing of local and non-local exchange and correlation effects as it is achieved by hybrid functionals mimics SIC-DFT and can be considered as an economic way to include some SIC into standard DFT. However, the investigation shows also that the SIC-DFT description of molecules is unreliable because the standard functionals used were optimized for DFT including the SIE.

First principle investigations of the physical properties of hydrogen-rich MgH2

NASA Astrophysics Data System (ADS)

Zarshenas, Mohammed; Ahmed, R.; Benali Kanoun, Mohammed; Haq, Bakhtiar ul; Radzi Mat Isa, Ahmad; Goumri-Said, Souraya

2013-12-01

Hydrogen being a cleaner energy carrier has increased the importance of hydrogen-containing light metal hydrides, in particular those with large gravimetric hydrogen density like magnesium hydride (MgH2). In this study, density functional and density functional perturbation theories are combined to investigate the structural, elastic, thermodynamic, electronic and optical properties of MgH2. Our structural parameters calculated with those proposed by Perdew, Burke and Ernzerof generalized gradient approximation (PBE-GGA) and Wu-Cohen GGA (WC-GGA) are in agreement with experimental measurements, however the underestimated band gap values calculated using PBE-GGA and WC-GGA were greatly improved with the GGA suggested by Engle and Vosko and the modified Becke-Johnson exchange correlation potential by Trans and Blaha. As for the thermodynamic properties the specific heat values at low temperatures were found to obey the T3 rule and at higher temperatures Dulong and Petit's law. Our analysis of the optical properties of MgH2 also points to its potential application in optoelectronics.

Engel-Vosko GGA calculations of the structural, electronic and optical properties of LiYO2

NASA Astrophysics Data System (ADS)

Muhammad, Nisar; Khan, Afzal; Haidar Khan, Shah; Sajjaj Siraj, Muhammad; Shah, Syed Sarmad Ali; Murtaza, Ghulam

2017-09-01

Structural, electronic and optical properties of lithium yttrium oxide (LiYO2) are investigated using density functional theory (DFT). These calculations are based on full potential linearized augmented plane wave (FP-LAPW) method implemented by WIEN2k. The generalized gradient approximation (GGA) is used as an exchange correlation potential with Perdew-Burk-Ernzerhof (PBE) and Engel-Vosko (EV) as exchange correlation functional. The structural properties are calculated with PBE-GGA as it gives the equilibrium lattice constants very close to the experimental values. While, the band structure and optical properties are calculated with EV-GGA obtain much closer results to their experimental values. Our calculations confirm LiYO2 as large indirect band gap semiconductor having band gap of 5.23 eV exhibiting the characteristics of ultrawide band gap materials showing the properties like higher critical breakdown field, higher temperature operation and higher radiation tolerance. In this article, we report the density of states (DOS) in terms of contribution from s, p, and d-states of the constituent atoms, the band structure, the electronic structure, and the frequency-dependent optical properties of LiYO2. The optical properties presented in this article reveal LiYO2 a suitable candidate for the field of optoelectronic and optical devices.

What correlation effects are covered by density functional theory?

NASA Astrophysics Data System (ADS)

He, Yuan; Grafenstein, Jurgen; Kraka, Elfi; Cremer, Dieter

The electron density distribution rho(r) generated by a DFT calculation was systematically studied by comparison with a series of reference densities obtained by wavefunction theory (WFT) methods that cover typical electron correlation effects. As a sensitive indicator for correlation effects the dipole moment of the CO molecule was used. The analysis reveals that typical LDA and GGA exchange functionals already simulate effects that are actually reminiscent of pair and three-electron correlation effects covered by MP2, MP4, and CCSD(T) in WFT. Correlation functionals contract the density towards the bond and the valence region thus taking negative charge out of the van der Waals region. It is shown that these improvements are relevant for the description of van der Waals interactions. Similar to certain correlated single-determinant WFT methods, BLYP and other GGA functionals underestimate ionic terms needed for a correct description of polar bonds. This is compensated for in hybrid functionals by mixing in HF exchange. The balanced mixing of local and non-local exchange and correlation effects leads to the correct description of polar bonds as in the B3LYP description of the CO molecule. The density obtained with B3LYP is closer to CCSD and CCSD(T) than to MP2 or MP4, which indicates that the B3LYP hybrid functional mimics those pair and three-electron correlation effects, which in WFT are only covered by coupled cluster methods.

Structural, electronic and optical properties of LiNbO3 using GGA-PBE and TB-mBJ functionals: A DFT study

NASA Astrophysics Data System (ADS)

Arshad Javid, M.; Khan, Zafar Ullah; Mehmood, Zahid; Nabi, Azeem; Hussain, Fayyaz; Imran, M.; Nadeem, Muhammad; Anjum, Naeem

2018-06-01

In the present work, first-principles calculations were performed to obtain the structural, electronic and optical properties of lithium niobate crystal using two exchange-correlation functionals (GGA-PBE and TB-mBJ). The calculated structural parameters were very close to the experimental values. TB-mBJ functional was found to be good when compared to LDA and GGA functionals in case of bandgap energy of 3.715 eV of lithium niobate. It was observed that the upper valence and lower conduction bands consist mainly the O-2p and Nb-4d states, respectively. Furthermore, calculations for real and imaginary parts of frequency-dependent dielectric function 𝜀(ω) of lithium niobate crystal were performed using TD-DFT method. The ordinary refractive index no(ω), extraordinary refractive index ne(ω), its birefringence and absorption peaks in imaginary dielectric function 𝜀2(ω) were also calculated.

Importance of nonlocal electron correlation in the BaNiS2 semimetal from quantum oscillations studies

NASA Astrophysics Data System (ADS)

Klein, Yannick; Casula, Michele; Santos-Cottin, David; Audouard, Alain; Vignolles, David; Fève, Gwendal; Freulon, Vincent; Plaçais, Bernard; Verseils, Marine; Yang, Hancheng; Paulatto, Lorenzo; Gauzzi, Andrea

2018-02-01

By means of Shubnikov-de Haas and de Haas-van Alphen oscillations, and ab initio calculations, we have studied the Fermi surface of high-quality BaNiS2 single crystals, with mean free path l ˜400 Å . The angle and temperature dependence of quantum oscillations indicates a quasi-two-dimensional Fermi surface, made of an electronlike tube centered at Γ , and of four holelike cones, generated by Dirac bands, weakly dispersive in the out-of-plane direction. Ab initio electronic structure calculations, in the density functional theory framework, show that the inclusion of screened exchange is necessary to account for the experimental Fermi pockets. Therefore, the choice of the functional becomes crucial. A modified HSE hybrid functional with 7% of exact exchange outperforms both GGA and GGA +U density functionals, signaling the importance of nonlocal screened-exchange interactions in BaNiS2, and, more generally, in 3 d compensated semimetals.

Spin-polarized structural, elastic, electronic and magnetic properties of half-metallic ferromagnetism in V-doped ZnSe

NASA Astrophysics Data System (ADS)

Monir, M. El Amine.; Baltache, H.; Murtaza, G.; Khenata, R.; Ahmed, Waleed K.; Bouhemadou, A.; Omran, S. Bin; Seddik, T.

2015-01-01

Based on first principles spin-polarized density functional theory, the structural, elastic electronic and magnetic properties of Zn1-xVxSe (for x=0.25, 0.50, 0.75) in zinc blende structure have been studied. The investigation was done using the full-potential augmented plane wave method as implemented in WIEN2k code. The exchange-correlation potential was treated with the generalized gradient approximation PBE-GGA for the structural and elastic properties. Moreover, the PBE-GGA+U approximation (where U is the Hubbard correlation terms) is employed to treat the "d" electrons properly. A comparative study between the band structures, electronic structures, total and partial densities of states and local moments calculated within both GGA and GGA+U schemes is presented. The analysis of spin-polarized band structure and density of states shows the half-metallic ferromagnetic character and are also used to determine s(p)-d exchange constants N0α (conduction band) and N0β (valence band) due to Se(4p)-V(3d) hybridization. It has been clearly evidence that the magnetic moment of V is reduced from its free space change value of 3 μB and the minor atomic magnetic moment on Zn and Se are generated.

Density functional theory calculations of III-N based semiconductors with mBJLDA

NASA Astrophysics Data System (ADS)

Gürel, Hikmet Hakan; Akıncı, Özden; Ünlü, Hilmi

2017-02-01

In this work, we present first principles calculations based on a full potential linear augmented plane-wave method (FP-LAPW) to calculate structural and electronic properties of III-V based nitrides such as GaN, AlN, InN in a zinc-blende cubic structure. First principles calculation using the local density approximation (LDA) and generalized gradient approximation (GGA) underestimate the band gap. We proposed a new potential called modified Becke-Johnson local density approximation (MBJLDA) that combines modified Becke-Johnson exchange potential and the LDA correlation potential to get better band gap results compared to experiment. We compared various exchange-correlation potentials (LSDA, GGA, HSE, and MBJLDA) to determine band gaps and structural properties of semiconductors. We show that using MBJLDA density potential gives a better agreement with experimental data for band gaps III-V nitrides based semiconductors.

The half-metallicity of Co2FeGe full Heusler alloy in (001) thin film: First principles study

NASA Astrophysics Data System (ADS)

Hyun, Jung-Min; Kim, Miyoung

2018-01-01

The electronic and magnetic properties of the Co2FeGe full Heusler alloy in (001) thin film are investigated using the first-principles electronic structure calculations within the density functional theory. We employ various exchange correlation functionals including the local density approximation (LDA), the generalized gradient approximation (GGA), and the additional + U corrections for strong on-site Coulomb interaction of transition metal 3d states, aiming to examine the correlation effect on the electronic structures which determine the spin gap and thus the half-metallicity. Our results reveal that the Co2FeGe thin film is metallic in both LDA and GGA, while the + U correction opens up the spin gap for spin minority channel in GGA+ U but not in LDA+U in contrast to its bulk alloy which is predicted to be half-metallic in both LDA+ U and GGA+ U approaches with total spin magnetic moment of 6 μ B . It is found that the surface states developed around the Fermi level and the enhanced 3d e g - t 2 g band splitting for the spin minority channel due to the correlation effect play critical roles to determine the emergence of the half-metallicity.

Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

PubMed

Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2015-11-10

Calculations of the principal components of magnetic-shielding tensors in crystalline solids require the inclusion of the effects of lattice structure on the local electronic environment to obtain significant agreement with experimental NMR measurements. We assess periodic (GIPAW) and GIAO/symmetry-adapted cluster (SAC) models for computing magnetic-shielding tensors by calculations on a test set containing 72 insulating molecular solids, with a total of 393 principal components of chemical-shift tensors from 13C, 15N, 19F, and 31P sites. When clusters are carefully designed to represent the local solid-state environment and when periodic calculations include sufficient variability, both methods predict magnetic-shielding tensors that agree well with experimental chemical-shift values, demonstrating the correspondence of the two computational techniques. At the basis-set limit, we find that the small differences in the computed values have no statistical significance for three of the four nuclides considered. Subsequently, we explore the effects of additional DFT methods available only with the GIAO/cluster approach, particularly the use of hybrid-GGA functionals, meta-GGA functionals, and hybrid meta-GGA functionals that demonstrate improved agreement in calculations on symmetry-adapted clusters. We demonstrate that meta-GGA functionals improve computed NMR parameters over those obtained by GGA functionals in all cases, and that hybrid functionals improve computed results over the respective pure DFT functional for all nuclides except 15N.

Semiclassical neutral atom as a reference system in density functional theory.

PubMed

Constantin, Lucian A; Fabiano, E; Laricchia, S; Della Sala, F

2011-05-06

We use the asymptotic expansions of the semiclassical neutral atom as a reference system in density functional theory to construct accurate generalized gradient approximations (GGAs) for the exchange-correlation and kinetic energies without any empiricism. These asymptotic functionals are among the most accurate GGAs for molecular systems, perform well for solid state, and overcome current GGA state of the art in frozen density embedding calculations. Our results also provide evidence for the conjointness conjecture between exchange and kinetic energies of atomic systems.

First-principles study of structural, electronic, linear and nonlinear optical properties of Ga{2}PSb ternary chalcopyrite

NASA Astrophysics Data System (ADS)

Ouahrani, T.; Reshak, A. H.; de La Roza, A. Otero; Mebrouki, M.; Luaña, V.; Khenata, R.; Amrani, B.

2009-12-01

We report results from first-principles density functional calculations using the full-potential linear augmented plane wave (FP-LAPW) method. The generalized gradient approximation (GGA) and the Engel-Vosko-generalized gradient approximation (EV-GGA) were used for the exchange-correlation energy of the structural, electronic, linear and nonlinear optical properties of the chalcopyrite Ga2PSb compound. The valence band maximum (VBM) is located at the Γv point, and the conduction band minimum (CBM) is located at the Γc point, resulting in a direct band gap of about 0.365 eV for GGA and 0.83 eV for EV-GGA. In comparison with the experimental one (1.2 eV) we found that EV-GGA calculation gives energy gap in reasonable agreement with the experiment. The spin orbit coupling has marginal influence on the optical properties. The ground state quantities such as lattice parameters (a, c and u), bulk modules B and its pressure derivative B^primeare evaluated.

Semi-Local DFT Functionals with Exact-Exchange-Like Features: Beyond the AK13

NASA Astrophysics Data System (ADS)

Armiento, Rickard

The Armiento-Kümmel functional from 2013 (AK13) is a non-empirical semi-local exchange functional on generalized gradient approximation form (GGA) in Kohn-Sham (KS) density functional theory (DFT). Recent works have established that AK13 gives improved electronic-structure exchange features over other semi-local methods, with a qualitatively improved orbital description and band structure. For example, the Kohn-Sham band gap is greatly extended, as it is for exact exchange. This talk outlines recent efforts towards new exchange-correlation functionals based on, and extending, the AK13 design ideas. The aim is to improve the quantitative accuracy, the description of energetics, and to address other issues found with the original formulation. Swedish e-Science Research Centre (SeRC).

Components of the Bond Energy in Polar Diatomic Molecules, Radicals, and Ions Formed by Group-1 and Group-2 Metal Atoms.

PubMed

Yu, Haoyu; Truhlar, Donald G

2015-07-14

Although many transition metal complexes are known to have high multireference character, the multireference character of main-group closed-shell singlet diatomic molecules like BeF, CaO, and MgO has been less studied. However, many group-1 and group-2 diatomic molecules do have multireference character, and they provide informative systems for studying multireference character because they are simpler than transition metal compounds. The goal of the present work is to understand these multireference systems better so that, ultimately, we can apply what we learn to more complicated multireference systems and to the design of new exchange-correlation functionals for treating multireference systems more adequately. Fourteen main-group diatomic molecules and one triatomic molecule (including radicals, cations, and anions, as well as neutral closed-shell species) have been studied for this article. Eight of these molecules contain a group-1 element, and six contain a group-2 element. Seven of these molecules are multireference systems, and eight of them are single-reference systems. Fifty-three exchange-correlation functionals of 11 types [local spin-density approximation (LSDA), generalized gradient approximation (GGA), nonseparable gradient approximation (NGA), global-hybrid GGA, meta-GGA, meta-NGA, global-hybrid meta GGA, range-separated hybrid GGA, range-separated hybrid meta-GGA, range-separated hybrid meta-NGA, and DFT augmented with molecular mechanics damped dispersion (DFT-D)] and the Hartree-Fock method have been applied to calculate the bond distance, bond dissociation energy (BDE), and dipole moment of these molecules. All of the calculations are converged to a stable solution by allowing the symmetry of the Slater determinant to be broken. A reliable functional should not only predict an accurate BDE but also predict accurate components of the BDE, so each bond dissociation energy has been decomposed into ionization potential (IP) of the electropositive element, electron affinity of the electronegative bonding partner (EA), atomic excitation energy (EE) to prepare the valence states of the interacting partners, and interaction energy (IE) of the valence-prepared states. Adding Hartree-Fock exchange helps to obtain better results for atomic excitation energy, and this leads to improvements in getting the right answer for the right reason. The following functionals are singled out for reasonably good performance on all three of bond distance, BDE, and dipole moment: B97-1, B97-3, MPW1B95, M05, M06, M06-2X, M08-SO, N12-SX, O3LYP, TPSS, τ-HCTHhyb, and GAM; all but two (TPSS and GAM) of these functionals are hybrid functionals.

A meta-GGA level screened range-separated hybrid functional by employing short range Hartree-Fock with a long range semilocal functional.

PubMed

Jana, Subrata; Samal, Prasanjit

2018-03-28

The range-separated hybrid density functionals are very successful in describing a wide range of molecular and solid-state properties accurately. In principle, such functionals are designed from spherically averaged or system averaged as well as reverse engineered exchange holes. In the present attempt, the screened range-separated hybrid functional scheme has been applied to the meta-GGA rung by using the density matrix expansion based semilocal exchange hole (or functional). The hybrid functional proposed here utilizes the spherically averaged density matrix expansion based exchange hole in the range separation scheme. For slowly varying density correction the range separation scheme is employed only through the local density approximation based exchange hole coupled with the corresponding fourth order gradient approximate Tao-Mo enhancement factor. The comprehensive testing and performance of the newly constructed functional indicates its applicability in describing several molecular properties. The most appealing feature of this present screened hybrid functional is that it will be practically very useful in describing solid-state properties at the meta-GGA level.

Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2014-03-25

The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored in this paper by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the trainingmore » and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. Finally, the range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.« less

DFT study on the crystal, electronic and magnetic structures of tantalum based double perovskite oxides Ba2MTaO6 (M = Cr, Mn, Fe) via GGA and GGA + U

NASA Astrophysics Data System (ADS)

Saad, H.-E.; Musa, M.; Elhag, Ahmed

2018-06-01

In this paper, we study the crystal, electronic and magnetic structures of three tantalum based double perovskite oxides Ba2MTaO6 (M = Cr, Mn, Fe). All calculations were performed using the full-potential linear augmented plane-wave (PF-LAPW) method based on the first-principles density functional theory (DFT). For the exchange correlation potential, the generalized gradient approximation (GGA) and GGA plus on-site Coulomb parameter (GGA + U) were employed. The structural optimization reveals that the three compounds are stable in cubic structure (space group Fm-3m; tilt system a0a0a0). The band structure, density of states (DOS), charge density and spin magnetic moments were calculated and analyzed in details. By analysis the band structure and DOS, Ba2MTaO6 exhibits an insulating behavior (M = Cr, Fe) and a half-metallic (HM) nature (M = Mn). GGA + U method yields quite accurate results for the band-gap (Eg) as compared with GGA. We found that all three compounds have stable ferromagnetic (FM) ground state within GGA and GGA + U calculations. The M3+ (3d) ions contribute the majority in the total spin magnetic-moments, while, the empty T5+ (5d) ions carry very small induced magnetic moment via the M (3d)-O (2p)-Ta (5d) hybridization.

First principles study on the elastic and electronic properties of CdX (X = S, Se and Te)

NASA Astrophysics Data System (ADS)

Sharma, Sheetal; Verma, Ajay Singh; Sarkar, Bimal Kumar; Bhandari, Rajiv; Jindal, Vijay Kumar

2011-12-01

Wide band gap semiconductors are emerging as a potential candidate for optically active materials in blue green spectral region and operating at high power level and high temperature. CdX, X = S, Se and Te are wide band gap semiconductors having applications in optoelectronics devices. In this paper we investigated the elastic and electronic properties of Cadmium chalcogenide (cubic zinc-blende (ZB) structure) using standard Kohn-Sham self consistent density functional theory method (DFT) that uses non conserving pseudopotentials in fully nonlocal form within the generalized gradient approximation (GGA) for the exchange-correlation potential. The independent elastic constants, C11, C12 and C44, are calculated from direct computation of stresses generated by small strains. The shear modulus and Young's modulus are estimated for CdX. Using the GGA for the exchange correlation potential, the calculated direct fundamental band gap value is in very good agreement with the measured one.

Improving Rydberg Excitations within Time-Dependent Density Functional Theory with Generalized Gradient Approximations: The Exchange-Enhancement-for-Large-Gradient Scheme.

PubMed

Li, Shaohong L; Truhlar, Donald G

2015-07-14

Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals such as the local and hybrid generalized gradient approximations (GGA) seriously underestimates the excitation energies of Rydberg states, which limits its usefulness for applications such as spectroscopy and photochemistry. We present here a scheme that modifies the exchange-enhancement factor to improve GGA functionals for Rydberg excitations within the TDDFT framework while retaining their accuracy for valence excitations and for the thermochemical energetics calculated by ground-state density functional theory. The scheme is applied to a popular hybrid GGA functional and tested on data sets of valence and Rydberg excitations and atomization energies, and the results are encouraging. The scheme is simple and flexible. It can be used to correct existing functionals, and it can also be used as a strategy for the development of new functionals.

Improving Rydberg Excitations within Time-Dependent Density Functional Theory with Generalized Gradient Approximations: The Exchange-Enhancement-for-Large-Gradient Scheme

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

Li, Shaohong L.; Truhlar, Donald G.

Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals such as the local and hybrid generalized gradient approximations (GGA) seriously underestimates the excitation energies of Rydberg states, which limits its usefulness for applications such as spectroscopy and photochemistry. We present here a scheme that modifies the exchange-enhancement factor to improve GGA functionals for Rydberg excitations within the TDDFT framework while retaining their accuracy for valence excitations and for the thermochemical energetics calculated by ground-state density functional theory. The scheme is applied to a popular hybrid GGA functional and tested on data sets of valence and Rydberg excitations andmore » atomization energies, and the results are encouraging. The scheme is simple and flexible. It can be used to correct existing functionals, and it can also be used as a strategy for the development of new functionals.« less

Improving Rydberg Excitations within Time-Dependent Density Functional Theory with Generalized Gradient Approximations: The Exchange-Enhancement-for-Large-Gradient Scheme

DOE PAGES

Li, Shaohong L.; Truhlar, Donald G.

2015-05-22

Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals such as the local and hybrid generalized gradient approximations (GGA) seriously underestimates the excitation energies of Rydberg states, which limits its usefulness for applications such as spectroscopy and photochemistry. We present here a scheme that modifies the exchange-enhancement factor to improve GGA functionals for Rydberg excitations within the TDDFT framework while retaining their accuracy for valence excitations and for the thermochemical energetics calculated by ground-state density functional theory. The scheme is applied to a popular hybrid GGA functional and tested on data sets of valence and Rydberg excitations andmore » atomization energies, and the results are encouraging. The scheme is simple and flexible. It can be used to correct existing functionals, and it can also be used as a strategy for the development of new functionals.« less

Jacob's Ladder as Sketched by Escher: Assessing the Performance of Broadly Used Density Functionals on Transition Metal Surface Properties.

PubMed

Vega, Lorena; Ruvireta, Judit; Viñes, Francesc; Illas, Francesc

2018-01-09

The present work surveys the performance of various widely used density functional theory exchange-correlation (xc) functionals in describing observable surface properties of a total of 27 transition metals with face-centered cubic (fcc), body-centered cubic (bcc), or hexagonal close-packed (hcp) crystallographic structures. A total of 81 low Miller index surfaces were considered employing slab models. Exemplary xc functionals within the three first rungs of Jacob's ladder were considered, including the Vosko-Wilk-Nusair xc functional within the local density approximation, the Perdew-Burke-Ernzerhof (PBE) functional within the generalized gradient approximation (GGA), and the Tao-Perdew-Staroverov-Scuseria functional as a meta-GGA functional. Hybrids were excluded in the survey because they are known to fail in properly describing metallic systems. In addition, two variants of PBE were considered, PBE adapted for solids (PBEsol) and revised PBE (RPBE), aimed at improving adsorption energies. Interlayer atomic distances, surface energies, and surface work functions were chosen as the scrutinized properties. A comparison with available experimental data, including single-crystal and polycrystalline values, shows that no xc functional is best at describing all of the surface properties. However, in statistical mean terms the PBEsol xc functional is advised, while PBE is recommended when considering both bulk and surface properties. On the basis of the present results, a discussion of adapting GGA functionals to the treatment of metallic surfaces in an alternative way to meta-GGA or hybrids is provided.

Better GGA and meta-GGA Functionals: VT84, meta-VMT, meta-VT84

NASA Astrophysics Data System (ADS)

Vela, Alberto; Martin Del Campo, J.; Gazquez, J. L.; Trickey, S. B.

2011-03-01

The goal of fast DFT calculations on large families of highly complicated systems (e.g. large clusters, biomolecules) implicitly conflicts with the heavy emphasis of recent years on inclusion of exact exchange. In response we have worked on improving non-empirical GGA X functionals. Here we report extension of our VMT GGA functional (J. Chem. Phys. 130 244103 (2009)) to satisfy a relevant asymptotic constraint, yielding the VT{84} X functional. With the PBE C functional, VT{84} gives about 10% improvement over VMT in energetics on the G3 223 molecule set. At the meta-GGA level of complexity, we have both meta-VMT and meta-{84}. The former is about 10% better on the G3 set than the TPSS meta-GGA, while meta-VT{84} gives roughly 10% further improvement over meta-VMT. Details of these assessments, including improvements in chemical shifts, will be presented. SBT acknowledges US DOE Grant DE-SC0002139.

Vibrational and thermodynamic properties of β-HMX: a first-principles investigation.

PubMed

Wu, Zhongqing; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya

2011-05-28

Thermodynamic properties of β-HMX crystal are investigated using the quasi-harmonic approximation and density functional theory within the local density approximation (LDA), generalized gradient approximation (GGA), and GGA + empirical van der Waals (vdW) correction. It is found that GGA well describes the thermal expansion coefficient and heat capacity but fails to produce correct bulk modulus and equilibrium volume. The vdW correction improves the bulk modulus and volume, but worsens the thermal expansion coefficient and heat capacity. In contrast, LDA describes all thermodynamic properties with reasonable accuracy, and overall is a good exchange-correlation functional for β-HMX molecular crystal. The results also demonstrate significant contributions of phonons to the equation of state. The static calculation of equilibrium volume for β-HMX differs from the room-temperature value incorporating lattice vibrations by over 5%. Therefore, for molecular crystals, it is essential to include phonon contributions when calculated equation of state is compared with experimental data at ambient condition. © 2011 American Institute of Physics

Molecular Excitation Energies from Time-Dependent Density Functional Theory Employing Random-Phase Approximation Hessians with Exact Exchange.

PubMed

Heßelmann, Andreas

2015-04-14

Molecular excitation energies have been calculated with time-dependent density-functional theory (TDDFT) using random-phase approximation Hessians augmented with exact exchange contributions in various orders. It has been observed that this approach yields fairly accurate local valence excitations if combined with accurate asymptotically corrected exchange-correlation potentials used in the ground-state Kohn-Sham calculations. The inclusion of long-range particle-particle with hole-hole interactions in the kernel leads to errors of 0.14 eV only for the lowest excitations of a selection of three alkene, three carbonyl, and five azabenzene molecules, thus surpassing the accuracy of a number of common TDDFT and even some wave function correlation methods. In the case of long-range charge-transfer excitations, the method typically underestimates accurate reference excitation energies by 8% on average, which is better than with standard hybrid-GGA functionals but worse compared to range-separated functional approximations.

Growth of carbon structured over Pd, Pt and Ni: A comparative DFT study

NASA Astrophysics Data System (ADS)

Quiroga, Matías Abel

2013-03-01

To elucidate the graphene-like structures mechanisms growth over the M(1 1 1) surface (M = Pd, Pt and Ni) we performed ab initio calculus in the frame of density functional theory with the exchange-correlation functional treated according to the Generalized Gradient Approximation (GGA). In order to avoid the problem that represent the complex interaction between the well formed graphene layer and the metallic surface, we recreate the carbon rings formation initial steps, by adding one by one carbon atoms over M(1 1 1) surface. With this strategy, the chemical bonding is always present until the graphene layer is well formed, in which case the GGA neglects van der Waals dispersive forces. We investigate the electronic properties by studying the band structure and the density of states.

Calculation of strained BaTiO3 with different exchange correlation functionals examined with criterion by Ginzburg-Landau theory, uncovering expressions by crystallographic parameters

NASA Astrophysics Data System (ADS)

Watanabe, Yukio

2018-05-01

In the calculations of tetragonal BaTiO3, some exchange-correlation (XC) energy functionals such as local density approximation (LDA) have shown good agreement with experiments at room temperature (RT), e.g., spontaneous polarization (PS), and superiority compared with other XC functionals. This is due to the error compensation of the RT effect and, hence, will be ineffective in the heavily strained case such as domain boundaries. Here, ferroelectrics under large strain at RT are approximated as those at 0 K because the strain effect surpasses the RT effects. To find effective XC energy functionals for strained BaTiO3, we propose a new comparison, i.e., a criterion. This criterion is the properties at 0 K given by the Ginzburg-Landau (GL) theory because GL theory is a thermodynamic description of experiments working under the same symmetry-constraints as ab initio calculations. With this criterion, we examine LDA, generalized gradient approximations (GGA), meta-GGA, meta-GGA + local correlation potential (U), and hybrid functionals, which reveals the high accuracy of some XC functionals superior to XC functionals that have been regarded as accurate. This result is examined directly by the calculations of homogenously strained tetragonal BaTiO3, confirming the validity of the new criterion. In addition, the data points of theoretical PS vs. certain crystallographic parameters calculated with different XC functionals are found to lie on a single curve, despite their wide variations. Regarding these theoretical data points as corresponding to the experimental results, analytical expressions of the local PS using crystallographic parameters are uncovered. These expressions show the primary origin of BaTiO3 ferroelectricity as oxygen displacements. Elastic compliance and electrostrictive coefficients are estimated. For the comparison of strained results, we show that the effective critical temperature TC under strain <-0.01 is >1000 K from an approximate method combining ab initio results with GL theory. In addition, in a definite manner, the present results show much more enhanced ferroelectricity at large strain than the previous reports.

Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.

PubMed

Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M

2015-09-08

We present the self-consistent implementation of current-dependent (hybrid) meta-generalized gradient approximation (mGGA) density functionals using London atomic orbitals. A previously proposed generalized kinetic energy density is utilized to implement mGGAs in the framework of Kohn-Sham current density functional theory (KS-CDFT). A unique feature of the nonperturbative implementation of these functionals is the ability to seamlessly explore a wide range of magnetic fields up to 1 au (∼235 kT) in strength. CDFT functionals based on the TPSS and B98 forms are investigated, and their performance is assessed by comparison with accurate coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) data. In the weak field regime, magnetic properties such as magnetizabilities and nuclear magnetic resonance shielding constants show modest but systematic improvements over generalized gradient approximations (GGA). However, in the strong field regime, the mGGA-based forms lead to a significantly improved description of the recently proposed perpendicular paramagnetic bonding mechanism, comparing well with CCSD(T) data. In contrast to functionals based on the vorticity, these forms are found to be numerically stable, and their accuracy at high field suggests that the extension of mGGAs to CDFT via the generalized kinetic energy density should provide a useful starting point for further development of CDFT approximations.

Ab-initio calculations of structural, electronic, and optical properties of Zn3(VO4)2

NASA Astrophysics Data System (ADS)

Ahmed, Nisar; Mukhtar, S.; Gao, Wei; Zafar Ilyas, Syed

2018-03-01

The structural, electronic, and optical properties of Zn3(VO4)2 are investigated using full potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory (DFT). Various approaches are adopted to treat the exchange and correlation potential energy such as generalized gradient approximation (GGA), GGA+U, and the Tran–Blaha modified Becke–Johnson (TB-mBJ) potential. The calculated band gap of 3.424 eV by TB-mBJ is found to be close to the experimental result (3.3 eV). The optical anisotropy is analyzed through optical constants, such as dielectric function and absorption coefficient along parallel and perpendicular crystal orientations. The absorption coefficient reveals high absorption (1.5× {10}6 {cm}}-1) of photons in the ultraviolet region.

Periodic density functional theory study of spin crossover in the cesium iron hexacyanochromate prussian blue analog

NASA Astrophysics Data System (ADS)

Wojdeł, Jacek C.; Moreira, Ibério de P. R.; Illas, Francesc

2009-01-01

This paper presents a detailed theoretical analysis of the electronic structure of the CsFe[Cr(CN)6] prussian blue analog with emphasis on the structural origin of the experimentally observed spin crossover transition in this material. Periodic density functional calculations using generalized gradient approximation (GGA)+U and nonlocal hybrid exchange-correlation potentials show that, for the experimental low temperature crystal structure, the t2g6eg0 low spin configuration of FeII is the most stable and CrIII (S =3/2, t2g3eg0) remains the same in all cases. This is also found to be the case for the low spin GGA+U fully relaxed structure with the optimized unit cell. A completely different situation emerges when calculations are carried out using the experimental high temperature structure. Here, GGA+U and hybrid density functional theory calculations consistently predict that the t2g4eg2 FeII high spin configuration is the ground state. However, the two spin configurations appear to be nearly degenerate when calculations are carried out for the geometries arising from a GGA+U full relaxation of the atomic structure carried out at experimental high temperature lattice constant. A detailed analysis of the energy difference between the two spin configurations as a function of the lattice constant strongly suggests that the observed spin crossover transition has a structural origin with non-negligible entropic contributions of the high spin state.

Modelling charge transfer reactions with the frozen density embedding formalism.

PubMed

Pavanello, Michele; Neugebauer, Johannes

2011-12-21

The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5'-GG-3' and 5'-GT-3'. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.

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

Verma, U. P.; Nayak, V.

Quantum mechanical first principle calculations have been performed to study the electronic and structural properties of TiN and TiAs in zinc blende (ZB) and rock salt (RS) structures. The full-potential linearized augmented plane wave (FP-LAPW) method has been used within the framework of density functional theory (DFT). The exchange correlation functional has been solved employing generalized gradient approximation (GGA). Our predicted results for lattice constants are in good agreement with the earlier findings. The electronic band structures of TiX are metallic in both the phases.

Structural and opto-electronic properties of 2D AlSb monolayer

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

Singh, Deobrat, E-mail: deobratsingh9@gmail.com; Sonvane, Yogesh; Gupta, Sanjeev K.

2016-05-23

We have investigated dielectric function related optical properties such as refractive index, absorption coefficient of two-dimensional hexagonal system of aluminum antimony (AlSb). We have also find structural and electronic properties of AlSb which show direct/indirect band gap with planar structure, employing the density functional theory using the generalized gradient approximation (GGA) given by Perdew-Burke-Ernzerhof (PBE) functional for exchange-correlation potential. The refractive index n(ω) increases with frequency in the near infrared region but in visible region n(ω) increasing after decrease.

Approximating the Shifted Hartree-Exchange-Correlation Potential in Direct Energy Kohn-Sham Theory.

PubMed

Sharpe, Daniel J; Levy, Mel; Tozer, David J

2018-02-13

Levy and Zahariev [Phys. Rev. Lett. 113 113002 (2014)] have proposed a new approach for performing density functional theory calculations, termed direct energy Kohn-Sham (DEKS) theory. In this approach, the electronic energy equals the sum of orbital energies, obtained from Kohn-Sham-like orbital equations involving a shifted Hartree-exchange-correlation potential, which must be approximated. In the present study, density scaling homogeneity considerations are used to facilitate DEKS calculations on a series of atoms and molecules, leading to three nonlocal approximations to the shifted potential. The first two rely on preliminary Kohn-Sham calculations using a standard generalized gradient approximation (GGA) exchange-correlation functional and the results illustrate the benefit of describing the dominant Hartree component of the shift exactly. A uniform electron gas analysis is used to eliminate the need for these preliminary Kohn-Sham calculations, leading to a potential with an unconventional form that yields encouraging results, providing strong motivation for further research in DEKS theory.

Experimental and first principle studies on electronic structure of BaTiO{sub 3}

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

Sagdeo, Archna, E-mail: archnaj@rrcat.gov.in; Ghosh, Haranath, E-mail: archnaj@rrcat.gov.in; Chakrabarti, Aparna, E-mail: archnaj@rrcat.gov.in

2014-04-24

We have carried out photoemission experiments to obtain valence band spectra of various crystallographic symmetries of BaTiO{sub 3} system which arise as a function of temperature. We also present results of a detailed first principle study of these symmetries of BaTiO{sub 3} using generalized gradient approximation for the exchange-correlation potential. Here we present theoretical results of density of states obtained from DFT based simulations to compare with the experimental valence band spectra. Further, we also perform calculations using post density functional approaches like GGA + U method as well as non-local hybrid exchange-correlation potentials like PBE0, B3LYP, HSE in ordermore » to understand the extent of effect of correlation on band gaps of different available crystallographic symmetries (5 in number) of BaTiO{sub 3}.« less

Electronic structure properties of UO2 as a Mott insulator

NASA Astrophysics Data System (ADS)

Sheykhi, Samira; Payami, Mahmoud

2018-06-01

In this work using the density functional theory (DFT), we have studied the structural, electronic and magnetic properties of uranium dioxide with antiferromagnetic 1k-, 2k-, and 3k-order structures. Ordinary approximations in DFT, such as the local density approximation (LDA) or generalized gradient approximation (GGA), usually predict incorrect metallic behaviors for this strongly correlated electron system. Using Hubbard term correction for f-electrons, LDA+U method, as well as using the screened Heyd-Scuseria-Ernzerhof (HSE) hybrid functional for the exchange-correlation (XC), we have obtained the correct ground-state behavior as an insulator, with band gaps in good agreement with experiment.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

A first-principles study of the influence of helium atoms on the optical response of small silver clusters.

PubMed

Pereiro, M; Baldomir, D; Arias, J E

2011-02-28

Optical excitation spectra of Ag(n) and Ag(n)@He(60) (n = 2, 8) clusters are investigated in the framework of the time-dependent density functional theory (TDDFT) within the linear response regime. We have performed the ab initio calculations for two different exact exchange functionals (GGA-exact and LDA-exact). The computed spectra of Ag(n)@He(60) clusters with the GGA-exact functional accounting for exchange-correlation effects are found to be generally in a relatively good agreement with the experiment. A strategy is proposed to obtain the ground-state structures of the Ag(n)@He(60) clusters and in the initial process of the geometry optimization, the He environment is simulated with buckyballs. A redshift of the silver clusters spectra is observed in the He environment with respect to the ones of bare silver clusters. This observation is discussed and explained in terms of a contraction of the Ag-He bonding length and a consequent confinement of the s valence electrons in silver clusters. Likewise, the Mie-Gans predictions combined with our TDDFT calculations also show that the dielectric effect produced by the He matrix is considerably less important in explaining the redshifting observed in the optical spectra of Ag(n)@He(60) clusters.

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

Half-metallic antiferromagnetism in double perovskite BiPbCrCuO{sub 6}

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

Weng, Ke-Chuan; Wang, Y. K., E-mail: kant@ntnu.edu.tw

2015-05-07

The electronic structure and magnetic properties of BiPbCrCuO{sub 6} double perovskite are investigated based on first-principles density functional calculations with generalized gradient approximation (GGA) and GGA incorporated with Coulomb correlation interaction U (GGA + U). The results suggest the half-metallic (HM) and antiferromagnetic (AFM) properties of BiPbCrCuO{sub 6} double perovskite. The HM-AFM property of the double perovskite is caused by the double-exchange mechanism between neighboring Cr{sup 5+}(t{sub 2g}{sup 1}↓) and Cu{sup 2+}(t{sub 2g}{sup 3}↑t{sub 2g}{sup 3}↓e{sub g}{sup 2}↑e{sub g}↓) via the intermediate O{sup 2−}(2s{sup 2}2p{sup 6}) ion.

Invited Paper - Density functional theory: coverage of dynamic and non-dynamic electron correlation effects

NASA Astrophysics Data System (ADS)

Cremer, Dieter

The electron correlation effects covered by density functional theory (DFT) can be assessed qualitatively by comparing DFT densities ρ(r) with suitable reference densities obtained with wavefunction theory (WFT) methods that cover typical electron correlation effects. The analysis of difference densities ρ(DFT)-ρ(WFT) reveals that LDA and GGA exchange (X) functionals mimic non-dynamic correlation effects in an unspecified way. It is shown that these long range correlation effects are caused by the self-interaction error (SIE) of standard X functionals. Self-interaction corrected (SIC) DFT exchange gives, similar to exact exchange, for the bonding region a delocalized exchange hole, and does not cover any correlation effects. Hence, the exchange SIE is responsible for the fact that DFT densities often resemble MP4 or MP2 densities. The correlation functional changes X-only DFT densities in a manner observed when higher order coupling effects between lower order N-electron correlation effects are included. Hybrid functionals lead to changes in the density similar to those caused by SICDFT, which simply reflects the fact that hybrid functionals have been developed to cover part of the SIE and its long range correlation effects in a balanced manner. In the case of spin-unrestricted DFT (UDFT), non-dynamic electron correlation effects enter the calculation both via the X functional and via the wavefunction, which may cause a double-counting of correlation effects. The use of UDFT in the form of permuted orbital and broken-symmetry DFT (PO-UDFT, BS-UDFT) can lead to reasonable descriptions of multireference systems provided certain conditions are fulfilled. More reliable, however, is a combination of DFT and WFT methods, which makes the routine description of multireference systems possible. The development of such methods implies a separation of dynamic and non-dynamic correlation effects. Strategies for accomplishing this goal are discussed in general and tested in practice for CAS (complete active space)-DFT.

Modelling charge transfer reactions with the frozen density embedding formalism

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

Pavanello, Michele; Neugebauer, Johannes

2011-12-21

The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two {pi}-stacked nucleobase dimers of B-DNA: 5{sup '}-GG-3{sup '} and 5{sup '}-GT-3{sup '}. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionalsmore » are used the electronic couplings are grossly overestimated.« less

First-Principles Study of Electronic Structure, Mechanical, and Thermoelectric Properties of Ternary Palladates CdPd3O4 and TlPd3O4

NASA Astrophysics Data System (ADS)

Khan, Amin; Ali, Zahid; Khan, Imad; Ahmad, Iftikhar

2018-03-01

Ternary palladates CdPd3O4 and TlPd3O4 have been studied theoretically using the generalized gradient approximation (GGA), modified Becke-Johnson, and spin-orbit coupling (GGA-SOC) exchange-correlation functionals in the density functional theory (DFT) framework. From the calculated ground-state properties, it is found that SOC effects are dominant in these palladates. Mechanical properties reveal that both compounds are ductile in nature. The electronic band structures show that CdPd3O4 is metallic, whereas TlPd3O4 is an indirect-bandgap semiconductor with energy gap of 1.1 eV. The optical properties show that TlPd3O4 is a good dielectric material. The dense electronic states, narrow-gap semiconductor nature, and Seebeck coefficient of TlPd3O4 suggest that it could be used as a good thermoelectric material. The magnetic susceptibility calculated by post-DFT treatment confirmed the paramagnetic behavior of these compounds.

Rationale for switching to nonlocal functionals in density functional theory

NASA Astrophysics Data System (ADS)

Lazić, P.; Atodiresei, N.; Caciuc, V.; Brako, R.; Gumhalter, B.; Blügel, S.

2012-10-01

Density functional theory (DFT) has been steadily improving over the past few decades, becoming the standard tool for electronic structure calculations. The early local functionals (LDA) were eventually replaced by more accurate semilocal functionals (GGA) which are in use today. A major persisting drawback is the lack of the nonlocal correlation which is at the core of dispersive (van der Waals) forces, so that a large and important class of systems remains outside the scope of DFT. The vdW-DF correlation functional of Langreth and Lundqvist, published in 2004, was the first nonlocal functional which could be easily implemented. Beyond expectations, the nonlocal functional has brought significant improvement to systems that were believed not to be sensitive to nonlocal correlations. In this paper, we use the example of graphene nanodomes growing on the Ir(111) surface, where with an increase of the size of the graphene islands the character of the bonding changes from strong chemisorption towards almost pure physisorption. We demonstrate how the seamless character of the vdW-DF functionals makes it possible to treat all regimes self-consistently, proving to be a systematic and consistent improvement of DFT regardless of the nature of bonding. We also discuss the typical surface science example of CO adsorption on (111) surfaces of metals, which shows that the nonlocal correlation may also be crucial for strongly chemisorbed systems. We briefly discuss open questions, in particular the choice of the most appropriate exchange part of the functional. As the vdW-DF begins to appear implemented self-consistently in a number of popular DFT codes, with numerical costs close to the GGA calculations, we draw the attention of the DFT community to the advantages and benefits of the adoption of this new class of functionals.

Rationale for switching to nonlocal functionals in density functional theory.

PubMed

Lazić, P; Atodiresei, N; Caciuc, V; Brako, R; Gumhalter, B; Blügel, S

2012-10-24

Density functional theory (DFT) has been steadily improving over the past few decades, becoming the standard tool for electronic structure calculations. The early local functionals (LDA) were eventually replaced by more accurate semilocal functionals (GGA) which are in use today. A major persisting drawback is the lack of the nonlocal correlation which is at the core of dispersive (van der Waals) forces, so that a large and important class of systems remains outside the scope of DFT. The vdW-DF correlation functional of Langreth and Lundqvist, published in 2004, was the first nonlocal functional which could be easily implemented. Beyond expectations, the nonlocal functional has brought significant improvement to systems that were believed not to be sensitive to nonlocal correlations. In this paper, we use the example of graphene nanodomes growing on the Ir(111) surface, where with an increase of the size of the graphene islands the character of the bonding changes from strong chemisorption towards almost pure physisorption. We demonstrate how the seamless character of the vdW-DF functionals makes it possible to treat all regimes self-consistently, proving to be a systematic and consistent improvement of DFT regardless of the nature of bonding. We also discuss the typical surface science example of CO adsorption on (111) surfaces of metals, which shows that the nonlocal correlation may also be crucial for strongly chemisorbed systems. We briefly discuss open questions, in particular the choice of the most appropriate exchange part of the functional. As the vdW-DF begins to appear implemented self-consistently in a number of popular DFT codes, with numerical costs close to the GGA calculations, we draw the attention of the DFT community to the advantages and benefits of the adoption of this new class of functionals.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Density of states, optical and thermoelectric properties of perovskite vanadium fluorides Na3VF6

NASA Astrophysics Data System (ADS)

Reshak, A. H.; Azam, Sikander

2014-05-01

The electronic structure, charge density and Fermi surface of Na3VF6 compound have been examined with the support of density functional theory (DFT). Using the full potential linear augmented plane wave method, we employed the local density approximation (LDA), generalized gradient approximation (GGA) and Engel-Vosko GGA (EVGGA) to treat the exchange correlation potential to solve Kohn-Sham equations. The calculation show that Na3VF6 compound has metallic nature and the Fermi energy (EF) is assessed by overlapping of V-d state. The calculated density of states at the EF are about 18.655, 51.932 and 13.235 states/eV, and the bare linear low-temperature electronic specific heat coefficient (γ) is found to be 3.236 mJ/mol-K2, 9.008 mJ/mol-K2 and 2.295 mJ/mol-K2 for LDA, GGA and EVGGA, respectively. The Fermi surface is composed of two sheets. The chemical bonding of Na3VF6 compound is analyzed through the electronic charge density in the (1 1 0) crystallographic plane. The optical constants and thermal properties were also calculated and discussed.

From clusters to bulk: A relativistic density functional investigation on a series of gold clusters Aun, n=6,…,147

NASA Astrophysics Data System (ADS)

Häberlen, Oliver D.; Chung, Sai-Cheong; Stener, Mauro; Rösch, Notker

1997-03-01

A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold-gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold-gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold-gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge, and face-centered sites; sites in the first subsurface layer show still small positive shifts.

Apparent violation of the sum rule for exchange-correlation charges by generalized gradient approximations.

PubMed

Kohut, Sviataslau V; Staroverov, Viktor N

2013-10-28

The exchange-correlation potential of Kohn-Sham density-functional theory, vXC(r), can be thought of as an electrostatic potential produced by the static charge distribution qXC(r) = -(1∕4π)∇(2)vXC(r). The total exchange-correlation charge, QXC = ∫qXC(r) dr, determines the rate of the asymptotic decay of vXC(r). If QXC ≠ 0, the potential falls off as QXC∕r; if QXC = 0, the decay is faster than coulombic. According to this rule, exchange-correlation potentials derived from standard generalized gradient approximations (GGAs) should have QXC = 0, but accurate numerical calculations give QXC ≠ 0. We resolve this paradox by showing that the charge density qXC(r) associated with every GGA consists of two types of contributions: a continuous distribution and point charges arising from the singularities of vXC(r) at each nucleus. Numerical integration of qXC(r) accounts for the continuous charge but misses the point charges. When the point-charge contributions are included, one obtains the correct QXC value. These findings provide an important caveat for attempts to devise asymptotically correct Kohn-Sham potentials by modeling the distribution qXC(r).

Hybrid functional studies of stability and diffusion of hydrogen in Mg-doped GaN

NASA Astrophysics Data System (ADS)

Park, Ji-Sang; Chang, K. J.

2012-02-01

Nitride semiconductors are known to suffer from low p-type doping efficiency due to the high activation energy of Mg acceptors and the compensation of hole carriers. To enhance hole carrier concentration, the hydrogen co-doping method is widely used, in which hydrogen is intentionally doped with Mg dopants and removed by subsequent thermal annealing. In this work, we perform first-principles density functional calculations to study the stability and diffusion of hydrogen in Mg-doped GaN. For the exchange-correlation potential, we employ both the generalized gradient approximation (GGA) proposed by Perdew, Burke, and Ernzerhof and the hybrid density functional of Heyd, Scuseria, and Ernzerhof. We examine the diffusion pathways and dissociation barriers of H from the Mg-H complex using the nudged elastic band and dimer methods. We compare the results of the GGA and hybrid density functional calculations for the stability of various H interstitial configurations and the migration barriers for H diffusion. Finally, using the calculated migration barriers as inputs, we perform kinetic Monte Carlo simulations for the dissociation of the Mg-H complex and find that the Mg acceptors are activated by thermal annealing up to 700-800 ^oC, in good agreement with experiments.

A density functional theory study of the influence of exchange-correlation functionals on the properties of FeAs.

PubMed

Griffin, Sinéad M; Spaldin, Nicola A

2017-06-01

We use density functional theory within the local density approximation (LDA), LDA  +  U, generalised gradient approximation (GGA), GGA  +  U, and hybrid-functional methods to calculate the properties of iron monoarsenide. FeAs, which forms in the MnP structure, is of current interest for potential spintronic applications as well as being the parent compound for the pnictide superconductors. We compare the calculated structural, magnetic and electronic properties obtained using the different functionals to each other and to experiment, and investigate the origin of a recently reported magnetic spiral. Our results indicate the appropriateness or otherwise of the various functionals for describing FeAs and the related Fe-pnictide superconductors.

Influence of Van der Waals interaction on the thermodynamics properties of NaCl

NASA Astrophysics Data System (ADS)

Marcondes, M. L.; Wentzcovitch, R. M.; Assali, L. V. C.

2016-12-01

Equations of state (EoS) are extremely important in several scientific domains. However, many applications require EoS parameters at high pressures and temperatures. Experimental determination of these parameters is limited in such conditions and ab initio calculations have become important in computing them. Density Functional Theory (DFT) with its various approximations for exchange and correlation energy is the method of choice, but lack of a good description of the exchange-correlation energy results in large errors in EoS parameters. It is well known that the alkali halides have been problematic from the onset and the quest for DFT functionals appropriate for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate the thermal equation of state and thermodynamic properties of the B1 NaCl phase. Our results show a remarkable improvement over the performance of standard the LDA and GGA functionals. This is hardly surprising given that ions in this system have nearly closed shell configurations.

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer.

PubMed

Chalabala, Jan; Uhlig, Frank; Slavíček, Petr

2018-03-29

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

Four-Component Relativistic Density-Functional Theory Calculations of Nuclear Spin-Rotation Constants: Relativistic Effects in p-Block Hydrides.

PubMed

Komorovsky, Stanislav; Repisky, Michal; Malkin, Elena; Demissie, Taye B; Ruud, Kenneth

2015-08-11

We present an implementation of the nuclear spin-rotation (SR) constants based on the relativistic four-component Dirac-Coulomb Hamiltonian. This formalism has been implemented in the framework of the Hartree-Fock and Kohn-Sham theory, allowing assessment of both pure and hybrid exchange-correlation functionals. In the density-functional theory (DFT) implementation of the response equations, a noncollinear generalized gradient approximation (GGA) has been used. The present approach enforces a restricted kinetic balance condition for the small-component basis at the integral level, leading to very efficient calculations of the property. We apply the methodology to study relativistic effects on the spin-rotation constants by performing calculations on XHn (n = 1-4) for all elements X in the p-block of the periodic table and comparing the effects of relativity on the nuclear SR tensors to that observed for the nuclear magnetic shielding tensors. Correlation effects as described by the density-functional theory are shown to be significant for the spin-rotation constants, whereas the differences between the use of GGA and hybrid density functionals are much smaller. Our calculated relativistic spin-rotation constants at the DFT level of theory are only in fair agreement with available experimental data. It is shown that the scaling of the relativistic effects for the spin-rotation constants (varying between Z(3.8) and Z(4.5)) is as strong as for the chemical shieldings but with a much smaller prefactor.

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

Communication: Correct charge transfer in CT complexes from the Becke'05 density functional

NASA Astrophysics Data System (ADS)

Becke, Axel D.; Dale, Stephen G.; Johnson, Erin R.

2018-06-01

It has been known for over twenty years that density functionals of the generalized-gradient approximation (GGA) type and exact-exchange-GGA hybrids with low exact-exchange mixing fraction yield enormous errors in the properties of charge-transfer (CT) complexes. Manifestations of this error have also plagued computations of CT excitation energies. GGAs transfer far too much charge in CT complexes. This error has therefore come to be called "delocalization" error. It remains, to this day, a vexing unsolved problem in density-functional theory (DFT). Here we report that a 100% exact-exchange-based density functional known as Becke'05 or "B05" [A. D. Becke, J. Chem. Phys. 119, 2972 (2003); 122, 064101 (2005)] predicts excellent charge transfers in classic CT complexes involving the electron donors NH3, C2H4, HCN, and C2H2 and electron acceptors F2 and Cl2. Our approach is variational, as in our recent "B05min" dipole moments paper [Dale et al., J. Chem. Phys. 147, 154103 (2017)]. Therefore B05 is not only an accurate DFT for thermochemistry but is promising as a solution to the delocalization problem as well.

Band structure calculations of CuAlO2, CuGaO2, CuInO2, and CuCrO2 by screened exchange

NASA Astrophysics Data System (ADS)

Gillen, Roland; Robertson, John

2011-07-01

We report density functional theory band structure calculations on the transparent conducting oxides CuAlO2, CuGaO2, CuInO2, and CuCrO2. The use of the hybrid functional screened-exchange local density approximation (sX-LDA) leads to considerably improved electronic properties compared to standard LDA and generalized gradient approximation (GGA) approaches. We show that the resulting electronic band gaps compare well with experimental values and previous quasiparticle calculations, and show the correct trends with respect to the atomic number of the cation (Al, Ga, In). The resulting energetic depths of Cu d and O p levels and the valence-band widths are considerable improvements compared to LDA and GGA and are in good agreement with available x-ray photoelectron spectroscopy data. Lastly, we show the calculated imaginary part of the dielectric function for all four systems.

Ab initio DFT+U study of He atom incorporation into UO(2) crystals.

PubMed

Gryaznov, Denis; Heifets, Eugene; Kotomin, Eugene

2009-09-07

We present and discuss results of the density functional theory (DFT) for perfect UO(2) crystals with He atoms in octahedral interstitial positions therein. We have calculated basic bulk crystal properties and He incorporation energies into the low temperature anti-ferromagnetic UO(2) phase using several exchange-correlation functionals within the spin-polarized local density (LDA) and generalized gradient (GGA) approximations. In all DFT calculations we included the on-site correlation corrections using the Hubbard model (DFT+U approach). We analysed a potential crystalline symmetry reduction from tetragonal down to orthorhombic structure and confirmed the presence of the Jahn-Teller effect in a perfect UO(2). We discuss also the problem of a conducting electronic state arising when He is placed into a tetragonal antiferromagnetic phase of UO(2) commonly used in defect modelling. Consequently, we found a specific monoclinic lattice distortion which allowed us to restore the semiconducting state and properly estimate He incorporation energies. Unlike the bulk properties, the He incorporation energy strongly depends on several factors, including the supercell size, the use of spin polarization, the exchange-correlation functionals and on-site correlation corrections. We compare our results for the He incorporation with the previous shell model and ab initio DFT calculations.

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

Castaño-González, E.-E.; Seña, N.; Mendoza-Estrada, V.

In this paper, we carried out first-principles calculations in order to investigate the structural and electronic properties of the binary compound gallium antimonide (GaSb). This theoretical study was carried out using the Density Functional Theory within the plane-wave pseudopotential method. The effects of exchange and correlation (XC) were treated using the functional Local Density Approximation (LDA), generalized gradient approximation (GGA): Perdew–Burke–Ernzerhof (PBE), Perdew-Burke-Ernzerhof revised for solids (PBEsol), Perdew-Wang91 (PW91), revised Perdew–Burke–Ernzerhof (rPBE), Armiento–Mattson 2005 (AM05) and meta-generalized gradient approximation (meta-GGA): Tao–Perdew–Staroverov–Scuseria (TPSS) and revised Tao–Perdew–Staroverov–Scuseria (RTPSS) and modified Becke-Johnson (MBJ). We calculated the densities of state (DOS) and band structuremore » with different XC potentials identified and compared them with the theoretical and experimental results reported in the literature. It was discovered that functional: LDA, PBEsol, AM05 and RTPSS provide the best results to calculate the lattice parameters (a) and bulk modulus (B{sub 0}); while for the cohesive energy (E{sub coh}), functional: AM05, RTPSS and PW91 are closer to the values obtained experimentally. The MBJ, Rtpss and AM05 values found for the band gap energy is slightly underestimated with those values reported experimentally.« less

Tuning of electronic band gaps and optoelectronic properties of binary strontium chalcogenides by means of doping of magnesium atom(s)- a first principles based theoretical initiative with mBJ, B3LYP and WC-GGA functionals

NASA Astrophysics Data System (ADS)

Debnath, Bimal; Sarkar, Utpal; Debbarma, Manish; Bhattacharjee, Rahul; Chattopadhyaya, Surya

2018-02-01

First principle based theoretical initiative is taken to tune the optoelectronic properties of binary strontium chalcogenide semiconductors by doping magnesium atom(s) into their rock-salt unit cells at specific concentrations x = 0.0, 0.25, 0.50, 0.75 and 1.0 and such tuning is established by studying structural, electronic and optical properties of designed binary compounds and ternary alloys employing WC-GGA, B3LYP and mBJ exchange-correlation functionals. Band structure of each compound is constructed and respective band gaps under all the potential schemes are measured. The band gap bowing and its microscopic origin are calculated using quadratic fit and Zunger's approach, respectively. The atomic and orbital origins of electronic states in the band structure of any compound are explored from its density of states. The nature of chemical bonds between the constituent atoms in each compound is explored from the valence electron density contour plots. Optical properties of any specimen are explored from the computed spectra of its dielectric function, refractive index, extinction coefficient, normal incidence reflectivity, optical conductivity optical absorption and energy loss function. Several calculated results are compared with available experimental and earlier theoretical data.

Magnetism by embedding 3d transition metal atoms into germanene

NASA Astrophysics Data System (ADS)

Sharma, Durgesh Kumar; Kumar, Sudhir; Auluck, Sushil

2018-06-01

We have performed a series of first-principles calculations within the framework of density functional theory for germanene including mono vacancy (MV) and double vacancy (DV). Perdew–Burke–Ernzerhof generalized gradient approximation (GGA) in the form of exchange-correlation potential was used. Ten transition metals (TMs) i.e. Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn, have been embedded at MV and DV site for the purpose to introduce magnetism into germanene. We find TM embedded germanene is stable and the value of magnetic moment can be tune with the TM impurities. Further, carbon (C) or nitrogen (N) in the vicinity of MV has been considered to find its influence on stability and total magnetic moment. Present predictions indicate Mn impurity shows largest magnetic moment among considered ten TMs. The Heyd–Scuseria–Ernzerhof (HSE06) hybrid functional based calculations have been also carried out for Mn system only for shake of comparison standpoint. The GGA/HSE06 calculations show better stability of TM embedded germanene after doping of C or N in vicinity of TM. Our calculations may provide a promising approach to design germanene based spintronic devices.

Study of the electronic structure and half-metallicity of CaMnO3/BaTiO3 superlattice

NASA Astrophysics Data System (ADS)

Wang, Kai; Jiang, Wei; Chen, Jun-Nan; Huang, Jian-Qi

2016-09-01

In this paper, the electronic structure, magnetic properties and half-metallicity of the CaMnO3/BaTiO3 superlattice are investigated by employing the first-principle calculation based on density functional theory within the GGA or GGA + U exchange-correlation functional. The CaMnO3/BaTiO3 superlattice is constructed by the cubic CaMnO3 and the tetragonal ferroelectric BaTiO3 growing alternately along (0 0 1) direction. The cubic CaMnO3 presents a robust half-metallicity and a metastable ferromagnetic phase. Its magnetic moment is an integral number of 3.000 μB per unit cell. However, the CaMnO3/BaTiO3 superlattice has a stable ferromagnetic phase, for which the magnetic moment is 12.000 μB per unit cell. It also retains the robust half-metallicity which mainly results from the strong hybridization between Mn and O atoms. The results show that the constructed CaMnO3/BaTiO3 superlattice exhibits superior magnetoelectric properties. It may provide a theoretical reference for the design and preparation of new multiferroic materials.

Orbital nodal surfaces: Topological challenges for density functionals

NASA Astrophysics Data System (ADS)

Aschebrock, Thilo; Armiento, Rickard; Kümmel, Stephan

2017-06-01

Nodal surfaces of orbitals, in particular of the highest occupied one, play a special role in Kohn-Sham density-functional theory. The exact Kohn-Sham exchange potential, for example, shows a protruding ridge along such nodal surfaces, leading to the counterintuitive feature of a potential that goes to different asymptotic limits in different directions. We show here that nodal surfaces can heavily affect the potential of semilocal density-functional approximations. For the functional derivatives of the Armiento-Kümmel (AK13) [Phys. Rev. Lett. 111, 036402 (2013), 10.1103/PhysRevLett.111.036402] and Becke88 [Phys. Rev. A 38, 3098 (1988), 10.1103/PhysRevA.38.3098] energy functionals, i.e., the corresponding semilocal exchange potentials, as well as the Becke-Johnson [J. Chem. Phys. 124, 221101 (2006), 10.1063/1.2213970] and van Leeuwen-Baerends (LB94) [Phys. Rev. A 49, 2421 (1994), 10.1103/PhysRevA.49.2421] model potentials, we explicitly demonstrate exponential divergences in the vicinity of nodal surfaces. We further point out that many other semilocal potentials have similar features. Such divergences pose a challenge for the convergence of numerical solutions of the Kohn-Sham equations. We prove that for exchange functionals of the generalized gradient approximation (GGA) form, enforcing correct asymptotic behavior of the potential or energy density necessarily leads to irregular behavior on or near orbital nodal surfaces. We formulate constraints on the GGA exchange enhancement factor for avoiding such divergences.

Thermodynamical study of boron doped CeX{sub 3} (X=Pd, Rh)

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

Sharma, Ramesh; Dwivedi, Shalini; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com

2016-05-06

The structural, electronic, thermal, and optical properties of cubic non magnetic CeX{sub 3}(X=Pd, Rh) compounds which crystallize in the Au{sub 3}Cu structure have been studied using the projected augmented wave (PAW) method within the density functional theory (DFT) with generalized gradient approximation (GGA) for exchange correlation potential. In this paper we have calculated the band structure which are interpreted using the density of states. The optical properties such as extinction coefficients clearly illustrate the changes in CeX{sub 3} due to intercalation of boron. Lattice instability is observed in CePd{sub 3}B from the calculated dynamical properties.

Electronic and Piezoelectric properties of half-Heusler compounds: A first principles study

NASA Astrophysics Data System (ADS)

Rai, D. P.; Sandeep; Shankar, A.; Aly, Abeer E.; Patra, P. K.; Thapa, R. K.

2016-10-01

We have investigated the semiconducting and piezoelectric properties of bulk MNiSn (M=Ti, Zr, Hf) type a half-Heusler compound with cubic F-43m symmetry by means of density functional theory (DFT). For electron exchange correlation a generalized gradient approximation (GGA) was used. Special attention was paid to establish a most favourble ground state configuration on magnetic as well as non-magnetic ordering. With fully optimized structure the electronic and ferroelectric calculation was performed. The formation of band gap was discussed on the basis of d-d orbital hybridization. Further we have calculated the spontaneous polarization by means of structural deformation.

Density-functional theory applied to d- and f-electron systems

NASA Astrophysics Data System (ADS)

Wu, Xueyuan

Density functional theory (DFT) has been applied to study the electronic and geometric structures of prototype d- and f-electron systems. For the d-electron system, all electron DFT with gradient corrections to the exchange and correlation functionals has been used to investigate the properties of small neutral and cationic vanadium clusters. Results are in good agreement with available experimental and other theoretical data. For the f-electron system, a hybrid DFT, namely, B3LYP (Becke's 3-parameter hybrid functional using the correlation functional of Lee, Yang and Parr) with relativistic effective core potentials and cluster models has been applied to investigate the nature of chemical bonding of both the bulk and the surfaces of plutonium monoxide and dioxide. Using periodic models, the electronic and geometric structures of PuO2 and its (110) surface, as well as water adsorption on this surface have also been investigated using DFT in both local density approximation (LDA) and generalized gradient approximation (GGA) formalisms.

First-principles study of the structural, electronic and thermal properties of CaLiF3

NASA Astrophysics Data System (ADS)

Chouit, N.; Amara Korba, S.; Slimani, M.; Meradji, H.; Ghemid, S.; Khenata, R.

2013-09-01

Density functional theory calculations have been performed to study the structural, electronic and optical properties of CaLiF3 cubic fluoroperovskite. Our calculations were carried out by means of the full-potential linearized augmented plane-wave method. The exchange-correlation potential is treated by the local density approximation and the generalized gradient approximation (GGA) (Perdew, Burke and Ernzerhof). Moreover, the alternative form of GGA proposed by Engel and Vosko is also used for band structure calculations. The calculated total energy versus volume allows us to obtain structural properties such as the lattice constant (a0), bulk modulus (B0) and pressure derivative of the bulk modulus (B'0 ). Band structure, density of states and band gap pressure coefficients are also given. Our calculations show that CaLiF3 has an indirect band gap (R-Γ). Following the quasi-harmonic Debye model, in which the phononic effects are considered, the temperature and pressure effects on the lattice constant, bulk modulus, thermal expansion coefficient, Debye temperature and heat capacities are calculated.

Orbital-occupancy versus charge ordering and the strength of electron correlations in electron-doped CaMnO3.

PubMed

Luo, Weidong; Franceschetti, Alberto; Varela, Maria; Tao, Jing; Pennycook, Stephen J; Pantelides, Sokrates T

2007-07-20

The structural, electronic, and magnetic properties of mixed-valence compounds are believed to be governed by strong electron correlations. Here we report benchmark density-functional calculations in the spin-polarized generalized-gradient approximation (GGA) for the ground-state properties of doped CaMnO(3). We find excellent agreement with all available data, while inclusion of strong correlations in the GGA+U scheme impairs this agreement. We demonstrate that formal oxidation states reflect only orbital occupancies, not charge transfer, and resolve outstanding controversies about charge ordering.

Orbital-Occupancy versus Charge Ordering and the Strength of Electron Correlations in Electron-Doped CaMnO3

NASA Astrophysics Data System (ADS)

Luo, Weidong; Franceschetti, Alberto; Varela, Maria; Tao, Jing; Pennycook, Stephen J.; Pantelides, Sokrates T.

2007-07-01

The structural, electronic, and magnetic properties of mixed-valence compounds are believed to be governed by strong electron correlations. Here we report benchmark density-functional calculations in the spin-polarized generalized-gradient approximation (GGA) for the ground-state properties of doped CaMnO3. We find excellent agreement with all available data, while inclusion of strong correlations in the GGA+U scheme impairs this agreement. We demonstrate that formal oxidation states reflect only orbital occupancies, not charge transfer, and resolve outstanding controversies about charge ordering.

ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-12-18

A 10-parameter, range-separated hybrid (RSH), generalized gradient approximation (GGA) density functional with nonlocal correlation (VV10) is presented in this paper. Instead of truncating the B97-type power series inhomogeneity correction factors (ICF) for the exchange, same-spin correlation, and opposite-spin correlation functionals uniformly, all 16 383 combinations of the linear parameters up to fourth order (m = 4) are considered. These functionals are individually fit to a training set and the resulting parameters are validated on a primary test set in order to identify the 3 optimal ICF expansions. Through this procedure, it is discovered that the functional that performs best onmore » the training and primary test sets has 7 linear parameters, with 3 additional nonlinear parameters from range-separation and nonlocal correlation. The resulting density functional, ωB97X-V, is further assessed on a secondary test set, the parallel-displaced coronene dimer, as well as several geometry datasets. Finally and furthermore, the basis set dependence and integration grid sensitivity of ωB97X-V are analyzed and documented in order to facilitate the use of the functional.« less

Theoretical investigation of structural, electronic and optical properties of MgxBa1-xS, MgxBa1-xSe and MgxBa1-xTe ternary alloys using DFT based FP-LAPW approach

NASA Astrophysics Data System (ADS)

Bhattacharjee, Rahul; Chattopadhyaya, Surya

2017-11-01

Density functional theory (DFT) based full-potential linearized augmented plane wave (FP-LAPW) methodology has been employed to investigate theoretically the structural, electronic and optical properties of MgxBa1-xS, MgxBa1-xSe and MgxBa1-xTe ternary alloys for 0 ≤ x ≤ 1 in their rock-salt (B1) crystallographic phase. The exchange-correlation potentials for the structural properties have been computed using the Wu-Cohen generalized-gradient approximation (WC-GGA) scheme, while those for the electronic and optical properties have been computed using both the WC-GGA and the recently developed Tran-Blaha modified Becke-Johnson (TB-mBJ) schemes. The thermodynamic stability of all the ternary alloys have been investigated by calculating their respective enthalpy of formation. The atomic and orbital origin of different electronic states in the band structure of the compounds have been identified from the respective density of states (DOS). Using the approach of Zunger and co-workers, the microscopic origin of band gap bowing has been discussed in term of volume deformation, charge exchange and structural relaxation. Bonding characteristics among the constituent atoms of each of the specimens have been discussed from their charge density contour plots. Optical properties of the binary compounds and ternary alloys have been investigated theoretically in terms of their respective dielectric function, refractive index, normal incidence reflectivity and optical conductivity. Several calculated results have been compared with available experimental and other theoretical data.

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

Gledhill, Jonathan D.; Tozer, David J., E-mail: d.j.tozer@durham.ac.uk

Density scaling considerations are used to derive an exchange–correlation explicit density functional that is appropriate for the electron deficient side of the integer and which recovers the exact r → ∞ asymptotic behaviour of the exchange–correlation potential. The functional has an unconventional mathematical form with parameters that are system-dependent; the parameters for an N-electron system are determined in advance from generalised gradient approximation (GGA) calculations on the N- and (N − 1)-electron systems. Compared to GGA results, the functional yields similar exchange–correlation energies, but HOMO energies that are an order of magnitude closer to the negative of the vertical ionisationmore » potential; for anions, the HOMO energies are negative, as required. Rydberg excitation energies are also notably improved and the exchange–correlation potential is visibly lowered towards the near-exact potential. Further development is required to improve valence excitations, static isotropic polarisabilities, and the shape of the potential in non-asymptotic regions. The functional is fundamentally different to conventional approximations.« less

Effect of tellurium concentration on the structural, electronic and mechanical properties of beryllium sulphide: A DFT approach

NASA Astrophysics Data System (ADS)

Iyorzor, B. E.; Babalola, M. I.; Adetunji, B. I.; Bakare, F. O.

2018-05-01

The structural, electronic and mechanical properties of Be{S}1-xT{e}x are studied within the concentration range of 0≤slant x≤slant 1 using first-principles plane–wave Pseudopotential density functional theory (DFT) approach. We have used generalized gradient approximation (GGA) to treat the exchange-correlation potentials. The elastic constants, bulk, shear and Young’s moduli, Poisson’s ratio, and Zener’s anisotropic factors are calculated. The results were found to be in agreement with other available theoretical and experimental values. It was also observed that the existence and increase of Tellurium concentration decreases the hardness of the alloy.

Insights in the electronic structure and redox reaction energy in LiFePO{sub 4} battery material from an accurate Tran-Blaha modified Becke Johnson potential

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

Araujo, Rafael B., E-mail: rafael.barros@physics.uu.se; Almeida, J. de S; Instituto de Física, Universidade Federal da Bahia, Salvador, Bahia

The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, thatmore » the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.« less

Ab initio study on rare-earth iron-pnictides RFeAsO (R = Pr, Nd, Sm, Gd) in low-temperature Cmma phase

NASA Astrophysics Data System (ADS)

Eryigit, Resul; Gurel, Tanju; Erturk, Esra; Lukoyanov, A. V.; Akcay, Guven; Anisimov, V. I.

2014-03-01

We present density functional theory calculations on iron-based pnictides RFeAsO (R = Pr, Nd, Sm, Gd). The calculations have been carried out using plane-waves and projector augmented wave (PAW) pseudopotential approach. Structural, magnetic and electronic properties are studied within generalized gradient approximation (GGA) and also within GGA+U in order to investigate the influence of electron correlation effects. Low-temperature Cmma structure is fully optimized by GGA considering both non-magnetic and magnetic cells. We have found that spin-polarized structure improves the agreement with experiments on equilibrium lattice parameters, particularly c lattice parameter and Fe-As bond-lengths. Electronic band structure, total density of states, and spin-dependent orbital-resolved density of states are also analyzed in the frameworks of GGA and GGA+U and discussed. For all materials, by including on-site Coulomb correction, rare earth 4f states move away from the Fermi level and the Fermi level features of the systems are found to be mostly defined by the 3d electron-electron correlations in Fe. This work was supported by the Scientific and Technological Research Council of Turkey (TUBITAK Project No. TBAG-111T796) and the Russian Foundation for Basic Research (Project No. 12-02-91371-CT_a).

The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.

PubMed

Bende, Attila; Muntean, Cristina M

2014-03-01

The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.

Design and investigation of potential Sn-Te-P and Zr-Te-P class of Dirac materials

NASA Astrophysics Data System (ADS)

Sarswat, Prashant; Sarkar, Sayan; Free, Michael

A motivation of new Dirac materials design and synthesis by perturbing the symmetry, was explored by substitution of a Sn vacancy by P that maintains the intrinsic band inversion at the L point but also the direct bandgap shrinkage upon the incorporation of spin-orbit coupling. In a similar line of investigation, Zr-Te-P was also systematically studied. The synthesis of both Sn-Te-P and Zr-Te-P system of compounds resulted in the formation of long needles type crystals and the bulk porous deposits. The exotic morphology of the P-doped SnTe needles possesses the pierced surface throughout its extension. First principle based calculations were also carried out for these sets of compounds using General Gradient Approximation (GGA) with Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. In order to ensure structural optimization, a limited memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm was employed and the total energy in PBE exchange-correlation functional was considered for the calculation of the formation energy per atom. The new modifications have a potential to establish the new class of Dirac materials ushering upon new frontiers of interest.

A DFT study on the enthalpies of thermite reactions and enthalpies of formation of metal composite oxide

NASA Astrophysics Data System (ADS)

Zhang, Yu-ying; Wang, Meng-jie; Chang, Chun-ran; Xu, Kang-zhen; Ma, Hai-xia; Zhao, Feng-qi

2018-05-01

The standard thermite reaction enthalpies (ΔrHmθ) for seven metal oxides were theoretically analyzed using density functional theory (DFT) under five different functional levels, and the results were compared with experimental values. Through the comparison of the linear fitting constants, mean error and root mean square error, the Perdew-Wang functional within the framework of local density approximation (LDA-PWC) and Perdew-Burke-Ernzerhof exchange-correlation functional within the framework of generalized gradient approximation (GGA-PBE) were selected to further calculate the thermite reaction enthalpies for metal composite oxides (MCOs). According to the Kirchhoff formula, the standard molar reaction enthalpies for these MCOs were obtained and their standard molar enthalpies of formation (ΔfHmθ) were finally calculated. The results indicated that GGA-PBE is the most suitable one out of the total five methods to calculate these oxides. Tungstate crystals present the maximum deviation of the enthalpies of thermite reactions for MCOs and these of their physical metal oxide mixtures, but ferrite crystals are the minimum. The correlation coefficients are all above 0.95, meaning linear fitting results are very precise. And the molar enthalpies of formation for NiMoO4, CuMoO4, PbZrO3 (Pm/3m), PbZrO3 (PBA2), PbZrO3 (PBam), MgZrO3, CdZrO3, MnZrO3, CuWO4 and Fe2WO6 were first obtained as -1078.75, -1058.45, -1343.87, -1266.54, -1342.29, -1333.03, -1210.43, -1388.05, -1131.07 and - 1860.11 kJ·mol-1, respectively.

DFT calculations of electronic and optical properties of SrS with LDA, GGA and mGGA functionals

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

Sharma, Shatendra, E-mail: shatendra@gmai.com; Sharma, Jyotsna; Sharma, Yogita

2016-05-06

The theoretical investigations of electronic and optical properties of SrS are made using the first principle DFT calculations. The calculations are performed for the local-density approximation (LDA), generalized gradient approximation (GGA) and for an alternative form of GGA i.e. metaGGA for both rock salt type (B1, Fm3m) and cesium chloride (B2, Pm3m) structures. The band structure, density of states and optical spectra are calculated under various available functional. The calculations with LDA and GGA functional underestimate the values of band gaps with all functional, however the values with mGGA show reasonably good agreement with experimental and those calculated by usingmore » other methods.« less

Understanding the HIV-1 protease reactivity with DFT: what do we gain from recent functionals?

PubMed

Garrec, J; Sautet, P; Fleurat-Lessard, P

2011-07-07

The modeling of HIV-1 plays a crucial role in the understanding of its reactivity and its interactions with specific drugs. In this work, we propose a medium sized model to test the ability of a variety of quantum chemistry approaches to provide reasonable geometric parameters and energetics for this system. Although our model is large enough to include the main polarizing groups of the active site, it is small enough to be used within full quantum studies up to the second order Møller-Plesset (MP2) level with extrapolations to coupled cluster CCSD(T) level. These high level calculations are used as reference to assess the ability of electronic structure methods (semiempirical and DFT) to provide accurate geometries and energies for the HIV-1 protease reaction. All semiempirical methods fail to describe the geometry of the protease active site. Within DFT, pure generalized gradient approximation (GGA) functionals have difficulty in reproducing the reaction energy and underestimate the barrier. Hybrid and/or meta GGA approaches do not yield a consistent improvement. The best results are obtained with hybrid GGA B3LYP or X3LYP and with hybrid meta GGA functionals with a fraction of exact exchange around 30-40%, such as M06, B1B95, or BMK functionals. On the basis of these results, we propose an accurate and computationally efficient strategy, employing quantum chemistry methods. This is applied here to study the protonation state of the reaction intermediate and could be easily used in further QM/MM studies.

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

NASA Astrophysics Data System (ADS)

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

2005-04-01

The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case.

Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics.

PubMed

Gani, Terry Z H; Kulik, Heather J

2017-11-14

Accurate predictions of spin-state ordering, reaction energetics, and barrier heights are critical for the computational discovery of open-shell transition-metal (TM) catalysts. Semilocal approximations in density functional theory, such as the generalized gradient approximation (GGA), suffer from delocalization error that causes them to overstabilize strongly bonded states. Descriptions of energetics and bonding are often improved by introducing a fraction of exact exchange (e.g., erroneous low-spin GGA ground states are instead correctly predicted as high-spin with a hybrid functional). The degree of spin-splitting sensitivity to exchange can be understood based on the chemical composition of the complex, but the effect of exchange on reaction energetics within a single spin state is less well-established. Across a number of model iron complexes, we observe strong exchange sensitivities of reaction barriers and energies that are of the same magnitude as those for spin splitting energies. We rationalize trends in both reaction and spin energetics by introducing a measure of delocalization, the bond valence of the metal-ligand bonds in each complex. The bond valence thus represents a simple-to-compute property that unifies understanding of exchange sensitivity for catalytic properties and spin-state ordering in TM complexes. Close agreement of the resulting per-metal-organic-bond sensitivity estimates, together with failure of alternative descriptors demonstrates the utility of the bond valence as a robust descriptor of how differences in metal-ligand delocalization produce differing relative energetics with exchange tuning. Our unified description explains the overall effect of exact exchange tuning on the paradigmatic two-state FeO + /CH 4 reaction that combines challenges of spin-state and reactivity predictions. This new descriptor-sensitivity relationship provides a path to quantifying how predictions in transition-metal complex screening are sensitive to the method used.

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.

PubMed

Giese, Timothy J; York, Darrin M

2010-12-28

We extend the Kohn-Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a "Jacob's ladder" comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn-Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.

Sizable band gap in organometallic topological insulator

NASA Astrophysics Data System (ADS)

Derakhshan, V.; Ketabi, S. A.

2017-01-01

Based on first principle calculation when Ceperley-Alder and Perdew-Burke-Ernzerh type exchange-correlation energy functional were adopted to LSDA and GGA calculation, electronic properties of organometallic honeycomb lattice as a two-dimensional topological insulator was calculated. In the presence of spin-orbit interaction bulk band gap of organometallic lattice with heavy metals such as Au, Hg, Pt and Tl atoms were investigated. Our results show that the organometallic topological insulator which is made of Mercury atom shows the wide bulk band gap of about ∼120 meV. Moreover, by fitting the conduction and valence bands to the band-structure which are produced by Density Functional Theory, spin-orbit interaction parameters were extracted. Based on calculated parameters, gapless edge states within bulk insulating gap are indeed found for finite width strip of two-dimensional organometallic topological insulators.

X-ray photoelectron spectrum and electronic properties of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4): LDA, GGA, and EV-GGA.

PubMed

Reshak, Ali Hussain; Khenata, R; Kityk, I V; Plucinski, K J; Auluck, S

2009-04-30

An all electron full potential linearized augmented plane wave method has been applied for a theoretical study of the band structure, density of states, and electron charge density of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4) using three different approximations for the exchange correlation potential. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma resulting in a direct energy gap of about 2.0, 2.2, and 2.8 eV for local density approximation (LDA), generalized gradient approximation (GGA), and Engel-Vosko (EVGGA) compared to the experimental value of 2.84 eV. We notice that EVGGA shows excellent agreement with the experimental data. This agreement is attributed to the fact that the Engel-Vosko GGA formalism optimizes the corresponding potential for band structure calculations. We make a detailed comparison of the density of states deduced from the X-ray photoelectron spectra with our calculations. We find that there is a strong covalent bond between the Hg and S atoms and Ga and S atoms. The Hg-Hg, Ga-Ga, and S-S bonds are found to be weaker than the Hg-S and Ga-S bonds showing that a covalent bond exists between Hg and S atoms and Ga and S atoms.

Structural, electronic, magnetic, elastic, and thermal properties of Co-based equiatomic quaternary Heusler alloys

NASA Astrophysics Data System (ADS)

Paudel, Ramesh; Zhu, Jingchuan

2018-05-01

In this research work, we have predicted the physical properties of CoFeZrGe and CoFeZrSb for the first time by utilizing first principle calculations based on density functional theory. The exchange-correlation potentials are treated within the generalized-gradient approximation of Perdew-Burke and Ernzerhof (GGA-PBE). The investigated equilibrium lattice parameters of CoFeCrSi are in agreement with available theoretical data and for CoFeZrZ(Z = Ge,Sb) are 6.0013 and 6.2546 Å respectively. The calculated magnetic moments are 1.01μB /fu , 2μB /fu and 1μB /fu for CoFeZrZ(Z = Ge, Sb and Si) respectively, and agree with the Slater-Pauling rule, Mt =Zt - 24 . The CoFeZrGe, CoFeZrSb and CoFeZrSi composites showed half-metallic behaviour with 100 % spin polarization at equilibrium lattice parameters with band gap of 0.43, 0.70 and 0.59 eV for GGA and an improved band gap of 0.86, 1.01 and 1.08 for GGA + U respectively. Elastic properties are also discussed in this paper and it is found that all the materials are mechanically stable and ductile in nature. The CoFeZrSi alloy is found to be stiffer than CoFeZrZ(Z = Ge and Sb) alloys. The Debye temperatures are predicted by using calculated elastic constants. Moreover, the volume heat capacities (Cv) are investigated by utilizing the quasi-harmonic Debye model.

The structural, electronic, magnetic, and mechanical properties of perovskite oxides PbM1/2Nb1/2O3 (M = Fe, Co and Ni)

NASA Astrophysics Data System (ADS)

Erkisi, A.; Surucu, G.; Deligoz, E.

2018-03-01

In this study, the structural, electronic, magnetic, and mechanical properties of perovskite oxides PbM1/2Nb1/2O3 (M = Fe, Co and Ni) are investigated. The systems are treated in ferromagnetic order. The calculations are carried out in the framework of density functional theory (DFT) within the plane-wave pseudopotential method. The exchange-correlation potential is approximated by generalized-gradient spin approach (GGA). The intra-atomic Coulomb repulsion is also taken into account in calculations (GGA + U). We have considered two generalized-gradient spin approximation functionals, which are Perdew-Burke-Ernzerhof (PBE) and PBE for solids (PBEsol) for structural parameter calculations when it included Hubbard potential. Although the spin-polarized electronic band structures of PbCo1/2Nb1/2O3 and PbNi1/2Nb1/2O3 systems exhibit metallic property in ferromagnetic phase, a bandgap is observed in spin-down states of PbFe1/2Nb1/2O3 resulting in half-metallic behavior. The main reason for this behavior is attributed to the hybridization between d-states of transition metal atoms and p-states of oxygen atoms. The stability mechanically and the calculated mechanical properties by using elastic constants show that these compounds are mechanically stable in tetragonal phase and have anisotropic character mechanically.

Prediction for electronic, vibrational and thermoelectric properties of chalcopyrite AgX(X=In,Ga)Te2: PBE + U approach

PubMed Central

Yang, Jianhui; Cheng, Xinlu

2017-01-01

The electronic, vibrational and thermoelectric transport characteristics of AgInTe2 and AgGaTe2 with chalcopyrite structure have been investigated. The electronic structures are calculated using the density-functional theory within the generalized gradient approximation (GGA) of Perdew–Burke–Ernzerhof functional considering the Hubbard-U exchange correlation. The band-gaps of AgInTe2 and AgGaTe2 are much larger than previous standard GGA functional results and agree well with the existing experimental data. The effective mass of the hole and the shape of density of states near the edge of the valence band indicate AgInTe2 and AgGaTe2 are considerable p-type thermoelectric materials. An analysis of lattice dynamics shows the low thermal conductivities of AgInTe2 and AgGaTe2. The thermoelectric transport properties' dependence on carrier concentration for p-type AgInTe2 and AgGaTe2 in a wide range of temperatures has been studied in detail. The results show that p-type AgInTe2 and AgGaTe2 at 800 K can achieve the merit values of 0.91 and 1.38 at about 2.12 × 1020 cm−3 and 1.97 × 1020 cm−3 carrier concentrations, respectively. This indicates p-type AgGaTe2 is a potential thermoelectric material at high temperature. PMID:29134079

Prediction for electronic, vibrational and thermoelectric properties of chalcopyrite AgX(X=In,Ga)Te2: PBE + U approach.

PubMed

Yang, Jianhui; Fan, Qiang; Cheng, Xinlu

2017-10-01

The electronic, vibrational and thermoelectric transport characteristics of AgInTe 2 and AgGaTe 2 with chalcopyrite structure have been investigated. The electronic structures are calculated using the density-functional theory within the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof functional considering the Hubbard-U exchange correlation. The band-gaps of AgInTe 2 and AgGaTe 2 are much larger than previous standard GGA functional results and agree well with the existing experimental data. The effective mass of the hole and the shape of density of states near the edge of the valence band indicate AgInTe 2 and AgGaTe 2 are considerable p-type thermoelectric materials. An analysis of lattice dynamics shows the low thermal conductivities of AgInTe 2 and AgGaTe 2 . The thermoelectric transport properties' dependence on carrier concentration for p-type AgInTe 2 and AgGaTe 2 in a wide range of temperatures has been studied in detail. The results show that p-type AgInTe 2 and AgGaTe 2 at 800 K can achieve the merit values of 0.91 and 1.38 at about 2.12 × 10 20  cm -3 and 1.97 × 10 20  cm -3 carrier concentrations, respectively. This indicates p-type AgGaTe 2 is a potential thermoelectric material at high temperature.

Electronic structure of LiCoO2 thin films: A combined photoemission spectroscopy and density functional theory study

NASA Astrophysics Data System (ADS)

Ensling, David; Thissen, Andreas; Laubach, Stefan; Schmidt, Peter C.; Jaegermann, Wolfram

2010-11-01

The electronic properties of LiCoO2 have been studied by theoretical band-structure calculations (using density functional theory) and experimental methods (photoemission). Synchrotron-induced photoelectron spectroscopy, resonant photoemission spectroscopy (ResPES), and soft x-ray absorption (XAS) have been applied to investigate the electronic structure of both occupied and unoccupied states. High-quality PES spectra were obtained from stoichiometric and highly crystalline LiCoO2 thin films deposited “in situ” by rf magnetron sputtering. An experimental approach of separating oxygen- and cobalt-derived (final) states by ResPES in the valence-band region is presented. The procedure takes advantage of an antiresonant behavior of cobalt-derived states at the 3p-3d excitation threshold. Information about the unoccupied density of states has been obtained by OK XAS. The structure of the CoL absorption edge is compared to semiempirical charge-transfer multiplet calculations. The experimental results are furthermore compared with band-structure calculations considering three different exchange potentials [generalized gradient approximation (GGA), using a nonlocal Hubbard U (GGA+U) and using a hybrid functional (Becke, three-parameter, Lee-Yang-Parr [B3LYP])]. For these different approaches total density of states and partial valence-band density of states have been investigated. The best qualitative agreement with experimental results has been obtained by using a GGA+U functional with U=2.9eV .

Development of Fast and Reliable Free-Energy Density Functional Methods for Simulations of Dense Plasmas from Cold- to Hot-Temperature Regimes

NASA Astrophysics Data System (ADS)

Karasiev, V. V.

2017-10-01

Free-energy density functional theory (DFT) is one of the standard tools in high-energy-density physics used to determine the fundamental properties of dense plasmas, especially in cold and warm regimes when quantum effects are essential. DFT is usually implemented via the orbital-dependent Kohn-Sham (KS) procedure. There are two challenges of conventional implementation: (1) KS computational cost becomes prohibitively expensive at high temperatures; and (2) ground-state exchange-correlation (XC) functionals do not take into account the XC thermal effects. This talk will address both challenges and report details of the formal development of new generalized gradient approximation (GGA) XC free-energy functional which bridges low-temperature (ground state) and high-temperature (plasma) limits. Recent progress on development of functionals for orbital-free DFT as a way to address the second challenge will also be discussed. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

Real-Space Multiple-Scattering Theory and Its Applications at Exascale

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

Eisenbach, Markus; Wang, Yang

In recent decades, the ab initio methods based on density functional theory (DFT) (Hohenberg and Kohn 1964, Kohn and Sham 1965) have become a widely used tool in computational materials science, which allows theoretical prediction of physical properties of materials from the first principles and theoretical interpretation of new physical phenomena found in experiments. In the framework of DFT, the original problem that requires solving a quantum mechanical equation for a many-electron system is reduced to a one-electron problem that involves an electron moving in an effective field, while the effective field potential is made up of an electrostatic potential,more » also known as Hartree potential, arising from the electronic and ion charge distribution in space and an exchange–correlation potential, which is a function of the electron density and encapsulates the exchange and correlation effects of the many-electron system. Even though the exact functional form of the exchange-correlation potential is formally unknown, a local density approximation (LDA) or a generalized gradient approximation (GGA) is usually applied so that the calculation of the exchange–correlation potential, as well as the exchange–correlation energy, becomes tractable while a required accuracy is retained. Based on DFT, ab initio electronic structure calculations for a material generally involve a self-consistent process that iterates between two computational tasks: (1) solving an one-electron Schrödinger equation, also known as Kohn–Sham equation, to obtain the electron density and, if needed, the magnetic moment density, and (2) solving the Poisson equation to obtain the electrostatic potential corresponding to the electron density and constructing the effective potential by adding the exchange–correlation potential to the electrostatic potential. This self-consistent process proceeds until a convergence criteria is reached.« less

A new DFT functional based on spin-states and SN2 barriers

NASA Astrophysics Data System (ADS)

Swart, M.; Solà, M.; Bickelhaupt, F. M.

2012-12-01

We recently reported a study into what causes the dramatic differences between OPBE and PBE for reaction barriers, spin-state energies, hydrogen-bonding and π-π stacking energies.1 It was achieved by smoothly switching from OPBE to PBE at a predefined point P of the reduced density gradient s. By letting the point P run as function of the reduced density gradient s, with values from s=0.1 to s=10, we could determine which part of the exchange functional determines its behavior for the different interactions. Based on the thus obtained results, we created a new exchange functional that showed the good results of OPBE for reaction barriers and spin-state energies, and combined it with the good (H-bonds) and reasonable (π-stacking) results of PBE for weak interactions. In other words, it combined the best of OPBE with the best of PBE. Encouraged by these good results, we have further improved the new exchange functional and fine-tuned its parameters.2 Similar to the switched functional from ref. 1, our new SSB functional2 works well for SN2 barriers (see e.g. ref. 3), spin states and H-bonding interactions. Moreover, by including Grimme's dispersion corrections4,5 (to give our final SSB-D functional) it also works well for π-π stacking interactions.2 In summary, we have constructed a new GGA exchange functional that when combined with the sPBE correlation functional6 gives the correct spin ground-state of iron complexes, and small deviations for SN2 barriers (2.7 kcalṡmol-1), geometries (0.005 Å), Hbond distances (0.012 Å), weak interactions (S22 set, 0.5 kcalṡmol-1), and transition-metal ligand distances (0.008 Å).

Mechanical, electronic and thermodynamic properties of full Heusler compounds Fe2VX(X = Al, Ga)

NASA Astrophysics Data System (ADS)

Khalfa, M.; Khachai, H.; Chiker, F.; Baki, N.; Bougherara, K.; Yakoubi, A.; Murtaza, G.; Harmel, M.; Abu-Jafar, M. S.; Omran, S. Bin; Khenata, R.

2015-11-01

The electronic structure, mechanical and thermodynamic properties of Fe2VX, (with X = Al and Ga), have been studied self consistently by employing state-of-the-art full-potential linearized approach of augmented plane wave plus local orbitals (FP-LAPW + lo) method. The exchange-correlation potential is treated with the local density and generalized gradient approximations (LDA and GGA). Our predicted ground state properties such as lattice constants, bulk modulus and elastic constants appear more accurate when we employed the GGA rather than the LDA, and these results are in very good agreement with the available experimental and theoretical data. Further, thermodynamic properties of Fe2VAl and Fe2VGa are predicted with pressure and temperature in the ranges of 0-40 GPa and 0-1500 K using the quasi-harmonic Debye model. We have obtained successfully the variations of the heat capacities, primitive cell volume and volume expansion coefficient.

DFT-BASED AB INITIO STUDY OF THE ELECTRONIC AND OPTICAL PROPERTIES OF CESIUM BASED FLUORO-PEROVSKITE CsMF3 (M = Ca AND Sr)

NASA Astrophysics Data System (ADS)

Harmel, M.; Khachai, H.; Ameri, M.; Khenata, R.; Baki, N.; Haddou, A.; Abbar, B.; UǦUR, Ş.; Omran, S. Bin; Soyalp, F.

2012-12-01

Density functional theory (DFT) is performed to study the structural, electronic and optical properties of cubic fluoroperovskite AMF3 (A = Cs; M = Ca and Sr) compounds. The calculations are based on the total-energy calculations within the full-potential linearized augmented plane wave (FP-LAPW) method. The exchange-correlation potential is treated by local density approximation (LDA) and generalized gradient approximation (GGA). The structural properties, including lattice constants, bulk modulus and their pressure derivatives are in very good agreement with the available experimental and theoretical data. The calculations of the electronic band structure, density of states and charge density reveal that compounds are both ionic insulators. The optical properties (namely: the real and the imaginary parts of the dielectric function ɛ(ω), the refractive index n(ω) and the extinction coefficient k(ω)) were calculated for radiation up to 40.0 eV.

Effects of doping of calcium atom(s) on structural, electronic and optical properties of binary strontium chalcogenides - A theoretical investigation using DFT based FP-LAPW methodology

NASA Astrophysics Data System (ADS)

Bhattacharjee, Rahul; Chattopadhyaya, Surya

2017-09-01

The effects of doping of Ca atom(s) on structural, electronic and optical properties of binary strontium chalcogenide semiconductor compounds have been investigated theoretically using DFT based FP-LAPW approach by modeling the rock-salt (B1) ternary alloys CaxSr1-xS, CaxSr1-xSe and CaxSr1-xTe at some specific concentrations 0 ≤ x ≤ 1 and studying their aforesaid properties. The exchange-correlation potentials for their structural properties have been computed using the Wu-Cohen generalized-gradient approximation (WC-GGA) scheme, while those for the electronic and optical properties have been computed using recently developed Tran-Blaha modified Becke-Johnson (TB-mBJ) scheme. In addition, we have computed the electronic and optical properties with the traditional BLYP and PBE-GGA schemes for comparison. The atomic and orbital origin of different electronic states in the band structure of each of the compounds have been identified from the respective density of states (DOS). Using the approach of Zunger and co-workers, the microscopic origin of band gap bowing has been discussed in term of volume deformation, charge exchange and structural relaxation. Bonding characteristics among the constituent atoms of each of the specimens have been discussed from their charge density contour plots. Optical properties of the binary compounds and ternary alloys have been investigated theoretically in terms of their respective dielectric function, refractive index, normal incidence reflectivity and optical conductivity. Several calculated results have been compared with available experimental and other theoretical data.

Analysis of the structural, electronic and optic properties of Ni doped MgSiP{sub 2} semiconductor chalcopyrite compound

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

Kocak, Belgin, E-mail: koakbelgin@gmail.com; Ciftci, Yasemin Oztekin, E-mail: yasemin@gazi.edu.tr

2016-03-25

The structural, electronic band structure and optic properties of the Ni doped MgSiP{sub 2} chalcopyrite compound have been performed by using first-principles method in the density functional theory (DFT) as implemented in Vienna Ab-initio Simulation Package (VASP). The generalized gradient approximation (GGA) in the scheme of Perdew, Burke and Ernzerhof (PBE) is used for the exchange and correlation functional. The present lattice constant (a) follows generally the Vegard’s law. The electronic band structure, total and partial density of states (DOS and PDOS) are calculated. We present data for the frequency dependence of imaginary and real parts of dielectric functions ofmore » Ni doped MgSiP{sub 2}. For further investigation of the optical properties the reflectivity, refractive index, extinction coefficient and electron energy loss function are also predicted. Our obtained results indicate that the lattice constants, electronic band structure and optical properties of this compound are dependent on the substitution concentration of Ni.« less

Charge localization and ordering in A 2 Mn 8 O 16 hollandite group oxides: Impact of density functional theory approaches

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

Kaltak, Merzuk; Fernandez-Serra, Marivi; Hybertsen, Mark S.

The phases of A 2Mn 8O 16 hollandite group oxides emerge from the competition between ionic interactions, Jahn-Teller effects, charge ordering, and magnetic interactions. Their balanced treatment with feasible computational approaches can be challenging for commonly used approximations in density functional theory. Three examples (A = Ag, Li, and K) are studied with a sequence of different approximate exchange-correlation functionals. Starting from a generalized gradient approximation (GGA), an extension to include van der Waals interactions and a recently proposed meta-GGA are considered. Then local Coulomb interactions for the Mn 3d electrons are more explicitly considered with the DFT + Umore » approach. Finally, selected results from a hybrid functional approach provide a reference. Results for the binding energy of the A species in the parent oxide highlight the role of van der Waals interactions. Relatively accurate results for insertion energies can be achieved with a low-U and a high-U approach. In the low-U case, the materials are described as band metals with a high-symmetry, tetragonal crystal structure. In the high-U case, the electrons donated by A result in formation of local Mn 3+ centers and corresponding Jahn-Teller distortions characterized by a local order parameter. The resulting degree of monoclinic distortion depends on charge ordering and magnetic interactions in the phase formed. The reference hybrid functional results show charge localization and ordering. Comparison to low-temperature experiments of related compounds suggests that charge localization is the physically correct result for the hollandite group oxides studied here. Lastly, while competing effects in the local magnetic coupling are subtle, the fully anisotropic implementation of DFT + U gives the best overall agreement with results from the hybrid functional.« less

Charge localization and ordering in A 2 Mn 8 O 16 hollandite group oxides: Impact of density functional theory approaches

DOE PAGES

Kaltak, Merzuk; Fernandez-Serra, Marivi; Hybertsen, Mark S.

2017-12-01

The phases of A 2Mn 8O 16 hollandite group oxides emerge from the competition between ionic interactions, Jahn-Teller effects, charge ordering, and magnetic interactions. Their balanced treatment with feasible computational approaches can be challenging for commonly used approximations in density functional theory. Three examples (A = Ag, Li, and K) are studied with a sequence of different approximate exchange-correlation functionals. Starting from a generalized gradient approximation (GGA), an extension to include van der Waals interactions and a recently proposed meta-GGA are considered. Then local Coulomb interactions for the Mn 3d electrons are more explicitly considered with the DFT + Umore » approach. Finally, selected results from a hybrid functional approach provide a reference. Results for the binding energy of the A species in the parent oxide highlight the role of van der Waals interactions. Relatively accurate results for insertion energies can be achieved with a low-U and a high-U approach. In the low-U case, the materials are described as band metals with a high-symmetry, tetragonal crystal structure. In the high-U case, the electrons donated by A result in formation of local Mn 3+ centers and corresponding Jahn-Teller distortions characterized by a local order parameter. The resulting degree of monoclinic distortion depends on charge ordering and magnetic interactions in the phase formed. The reference hybrid functional results show charge localization and ordering. Comparison to low-temperature experiments of related compounds suggests that charge localization is the physically correct result for the hollandite group oxides studied here. Lastly, while competing effects in the local magnetic coupling are subtle, the fully anisotropic implementation of DFT + U gives the best overall agreement with results from the hybrid functional.« less

Charge localization and ordering in A2Mn8O16 hollandite group oxides: Impact of density functional theory approaches

NASA Astrophysics Data System (ADS)

Kaltak, Merzuk; Fernández-Serra, Marivi; Hybertsen, Mark S.

2017-12-01

The phases of A2Mn8O16 hollandite group oxides emerge from the competition between ionic interactions, Jahn-Teller effects, charge ordering, and magnetic interactions. Their balanced treatment with feasible computational approaches can be challenging for commonly used approximations in density functional theory. Three examples (A = Ag, Li, and K) are studied with a sequence of different approximate exchange-correlation functionals. Starting from a generalized gradient approximation (GGA), an extension to include van der Waals interactions and a recently proposed meta-GGA are considered. Then local Coulomb interactions for the Mn 3 d electrons are more explicitly considered with the DFT + U approach. Finally, selected results from a hybrid functional approach provide a reference. Results for the binding energy of the A species in the parent oxide highlight the role of van der Waals interactions. Relatively accurate results for insertion energies can be achieved with a low-U and a high-U approach. In the low-U case, the materials are described as band metals with a high-symmetry, tetragonal crystal structure. In the high-U case, the electrons donated by A result in formation of local Mn3 + centers and corresponding Jahn-Teller distortions characterized by a local order parameter. The resulting degree of monoclinic distortion depends on charge ordering and magnetic interactions in the phase formed. The reference hybrid functional results show charge localization and ordering. Comparison to low-temperature experiments of related compounds suggests that charge localization is the physically correct result for the hollandite group oxides studied here. Finally, while competing effects in the local magnetic coupling are subtle, the fully anisotropic implementation of DFT + U gives the best overall agreement with results from the hybrid functional.

Electronic and magnetic properties of NiS2, NiSSe and NiSe2 by a combination of theoretical methods

NASA Astrophysics Data System (ADS)

Schuster, Cosima; Gatti, Matteo; Rubio, Angel

2012-09-01

We investigate the electronic and magnetic properties of NiS2, which, by varying the chemical composition substituting S by Se atoms or applying pressure, can be driven across various electronic and magnetic phase transitions. By combining several theoretical methods, we highlight the different role played by the chalcogen dimers and the volume compression in determining the phase transitions, through variations of the chalcogen p bonding-antibonding gap, the crystal-field splitting and the broadening of the bandwidths. While the generalized gradient approximation (GGA) of density-functional theory fails to reproduce the insulating nature of NiS2, it describes well the magnetic boundaries of the phase diagram. The large GGA delocalization error is corrected to a large extent by the use of GGA + U, hybrid functionals or the self-consistent COHSEX + GW approximation. We also discuss the advantages and the shortcomings of the different approximations in the various regions of the phase diagram of this prototypical correlated compound.

Full potential study of the elastic, electronic, and optical properties of spinels MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4} under pressure effect

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

Semari, F.; Khenata, R.; Depatment of Physics and Astronomy, King Saud University, PO Box 2455, Riyadh 11451

2010-12-15

The structural, elastic, electronic, and optical properties of cubic spinel MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4} compounds have been calculated using a full relativistic version of the full-potential linearized-augmented plane wave with the mixed basis FP/APW+lo method. The exchange and correlation potential is treated by the generalized-gradient approximation (GGA). Moreover, the Engel-Vosko GGA formalism is also applied to optimize the corresponding potential for band structure calculations. The ground state properties, including the lattice constants, the internal parameter, the bulk modulus, and the pressure derivative of the bulk modulus are in reasonable agreement with the available data. Using the totalmore » energy-strain technique, we have determined the full set of first-order elastic constants C{sub ij} and their pressure dependence, which have not been calculated or measured yet. The shear modulus, Young's modulus, and Poisson's ratio are calculated for polycrystalline XIn{sub 2}S{sub 4} aggregates. The Debye temperature is estimated from the average sound velocity. Electronic band structures show a direct band gap ({Gamma}-{Gamma}) for MgIn{sub 2}S{sub 4} and an indirect band gap (K-{Gamma}) for CdIn{sub 2}S{sub 4}. The calculated band gaps with EVGGA show a significant improvement over the GGA. The optical constants, including the dielectric function {epsilon}({omega}), the refractive index n({omega}), the reflectivity R({omega}), and the energy loss function L({omega}) were calculated for radiation up to 30 eV. -- Graphical abstract: Calculated total and partial densities of states for MgIn{sub 2}S{sub 4} and CdIn{sub 2}S{sub 4}« less

Quantification of uncertainty in first-principles predicted mechanical properties of solids: Application to solid ion conductors

NASA Astrophysics Data System (ADS)

Ahmad, Zeeshan; Viswanathan, Venkatasubramanian

2016-08-01

Computationally-guided material discovery is being increasingly employed using a descriptor-based screening through the calculation of a few properties of interest. A precise understanding of the uncertainty associated with first-principles density functional theory calculated property values is important for the success of descriptor-based screening. The Bayesian error estimation approach has been built in to several recently developed exchange-correlation functionals, which allows an estimate of the uncertainty associated with properties related to the ground state energy, for example, adsorption energies. Here, we propose a robust and computationally efficient method for quantifying uncertainty in mechanical properties, which depend on the derivatives of the energy. The procedure involves calculating energies around the equilibrium cell volume with different strains and fitting the obtained energies to the corresponding energy-strain relationship. At each strain, we use instead of a single energy, an ensemble of energies, giving us an ensemble of fits and thereby, an ensemble of mechanical properties associated with each fit, whose spread can be used to quantify its uncertainty. The generation of ensemble of energies is only a post-processing step involving a perturbation of parameters of the exchange-correlation functional and solving for the energy non-self-consistently. The proposed method is computationally efficient and provides a more robust uncertainty estimate compared to the approach of self-consistent calculations employing several different exchange-correlation functionals. We demonstrate the method by calculating the uncertainty bounds for several materials belonging to different classes and having different structures using the developed method. We show that the calculated uncertainty bounds the property values obtained using three different GGA functionals: PBE, PBEsol, and RPBE. Finally, we apply the approach to calculate the uncertainty associated with the DFT-calculated elastic properties of solid state Li-ion and Na-ion conductors.

Accurate, precise, and efficient theoretical methods to calculate anion-π interaction energies in model structures.

PubMed

Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei

2015-01-13

A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta-GGA functionals for the present test set.

Microsatellite mapping of QTLs affecting resistance to coccidiosis (Eimeria tenella) in a Fayoumi x White Leghorn cross.

PubMed

Pinard-van der Laan, Marie-Hélène; Bed'hom, Bertrand; Coville, Jean-Luc; Pitel, Frédérique; Feve, Katia; Leroux, Sophie; Legros, Hélène; Thomas, Aurélie; Gourichon, David; Repérant, Jean-Michel; Rault, Paul

2009-01-20

Avian coccidiosis is a major parasitic disease of poultry, causing severe economical loss to poultry production by affecting growth and feed efficiency of infected birds. Current control strategies using mainly drugs and more recently vaccination are showing drawbacks and alternative strategies are needed. Using genetic resistance that would limit the negative and very costly effects of the disease would be highly relevant. The purpose of this work was to detect for the first time QTL for disease resistance traits to Eimeria tenella in chicken by performing a genome scan in an F2 cross issued from a resistant Fayoumi line and a susceptible Leghorn line. The QTL analysis detected 21 chromosome-wide significant QTL for the different traits related to disease resistance (body weight growth, plasma coloration, hematocrit, rectal temperature and lesion) on 6 chromosomes. Out of these, a genome-wide very significant QTL for body weight growth was found on GGA1, five genome-wide significant QTL for body weight growth, plasma coloration and hematocrit and one for plasma coloration were found on GGA1 and GGA6, respectively. Two genome-wide suggestive QTL for plasma coloration and rectal temperature were found on GGA1 and GGA2, respectively. Other chromosme-wide significant QTL were identified on GGA2, GGA3, GGA6, GGA15 and GGA23. Parent-of-origin effects were found for QTL for body weight growth and plasma coloration on GGA1 and GGA3. Several QTL for different resistance phenotypes were identified as co-localized on the same location. Using an F2 cross from resistant and susceptible chicken lines proved to be a successful strategy to identify QTL for different resistance traits to Eimeria tenella, opening the way for further gene identification and underlying mechanisms and hopefully possibilities for new breeding strategies for resistance to coccidiosis in the chicken. From the QTL regions identified, several candidate genes and relevant pathways linked to innate immune and inflammatory responses were suggested. These results will be combined with functional genomics approaches on the same lines to provide positional candidate genes for resistance loci for coccidiosis. Results suggested also for further analysis, models tackling the complexity of the genetic architecture of these correlated disease resistance traits including potential epistatic effects.

Electronic and magnetic properties of double perovskite Sr2CoUO6: Heisenberg model

NASA Astrophysics Data System (ADS)

Nid-bahami, A.; Ahmed, S. Sidi; Ait-Tamerd, M.; Zaari, H.; El Kenz, A.; Benyoussef, A.

2018-01-01

This work will be focused on the electronic and magnetic properties of Sr2CoUO6 (SCUO) using ab-initio calculations and Monte Carlo Simulation (MCS). Firstly, we calculate the exchange coupling and the crystal field, then, the electronic and magnetic properties will be studied, using the full-potential linearized augmented plane wave (FP-LAPW) method, as implemented in the Wien2k code. This method employing the generalized gradient approximation (GGA) for exchange-correlation term. The half-metallic ferromagnetic nature implies a potential application of this new compound in spintronics devices. Also, we have presented the results of the band structures and densities of states for the two up and down spin polarizations. The exchange coupling and the crystal field calculated are J = 0 . 567 meV and δ = 0 . 559meV, and total spin magnetic moments is 2.96 μB closed to experimental values 3 μB. Secondly, we have presented the results for the magnetization and the susceptibility as a function of temperature. Finally, we obtain the critical temperature T = 9 . 20 K by MCS in good agreement with the experimental value.

Electronic and optical properties of RESn{sub 3} (RE=Pr & Nd) intermetallics: A first principles study

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

Pagare, G., E-mail: gita-pagare@yahoo.co.in; Abraham, Jisha A.; Department of Physics, National Defence Academy, Pune-411023

2015-06-24

A theoretical study of structural, electronic and optical properties of RESn{sub 3} (RE = Pr & Nd) intermetallics have been investigated systematically using first principles density functional theory. The calculations are carried out within the PBE-GGA and LSDA for the exchange correlation potential. The ground state properties such as lattice parameter (a{sub 0}), bulk modulus (B) and its pressure derivative (B′) are calculated and the calculated lattice parameters show well agreement with the experimental results. We first time predict elastic constants for these compounds. From energy dispersion curves, it is found that these compounds are metallic in nature. The linearmore » optical response of these compounds are also studied and the higher value of static dielectric constant shows the possibility to use them as good dielectric materials.« less

Density functional theory investigation of the LiIn 1-xGa xSe 2 solid solution

DOE PAGES

Wiggins, Brenden; Batista, Enrique; Burger, Arnold; ...

2016-06-07

Here, the electronic structure and optical properties of the LiIn 1-xGa xSe 2 (x=0, 0.25, 0.5, 0.75, 1) solid solution were studied by density functional theory (DFT) with pure functionals. The exchange-correlation is treated within the local density approximation (LDA) and generalized-gradient approximation (GGA). The electronic structures for each respective compound are discussed in detail. Calculations reveal that gallium incorporation can be used to tune the optical-electrical properties of the solid solution and correlates with the lattice parameter. The band gap trend of the LiIn 1-xGa xSe 2 system follows a nonlinear behavior between the LiInSe 2 and LiGaSe 2more » ternary boundaries. The bowing parameter is estimated to be on the order of 0.1- 0.3 eV at the point. Low-temperature optical absorption revealed a 30% change in the temperature dependence of the band gap for the intermediate compound LiIn 0.6Ga 0.4Se 2 compared to ternary boundaries and suggests the heat capacity to be another control element through strain.« less

Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

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

Buda, I. G.; Lane, C.; Barbiellini, B.

We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

Characterization of Thin Film Materials using SCAN meta-GGA, an Accurate Nonempirical Density Functional

DOE PAGES

Buda, I. G.; Lane, C.; Barbiellini, B.; ...

2017-03-23

We discuss self-consistently obtained ground-state electronic properties of monolayers of graphene and a number of ’beyond graphene’ compounds, including films of transition-metal dichalcogenides (TMDs), using the recently proposed strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) to the density functional theory. The SCAN meta-GGA results are compared with those based on the local density approximation (LDA) as well as the generalized gradient approximation (GGA). As expected, the GGA yields expanded lattices and softened bonds in relation to the LDA, but the SCAN meta-GGA systematically improves the agreement with experiment. Our study suggests the efficacy of the SCAN functionalmore » for accurate modeling of electronic structures of layered materials in high-throughput calculations more generally.« less

Dependence of Excited State Potential Energy Surfaces on the Spatial Overlap of the Kohn-Sham Orbitals and the Amount of Nonlocal Hartree-Fock Exchange in Time-Dependent Density Functional Theory.

PubMed

Plötner, Jürgen; Tozer, David J; Dreuw, Andreas

2010-08-10

Time-dependent density functional theory (TDDFT) with standard GGA or hybrid exchange-correlation functionals is not capable of describing the potential energy surface of the S1 state of Pigment Yellow 101 correctly; an additional local minimum is observed at a twisted geometry with substantial charge transfer (CT) character. To investigate the influence of nonlocal exact orbital (Hartree-Fock) exchange on the shape of the potential energy surface of the S1 state in detail, it has been computed along the twisting coordinate employing the standard BP86, B3LYP, and BHLYP xc-functionals as well as the long-range separated (LRS) exchange-correlation (xc)-functionals LC-BOP, ωB97X, ωPBE, and CAM-B3LYP and compared to RI-CC2 benchmark results. Additionally, a recently suggested Λ-parameter has been employed that measures the amount of CT in an excited state by calculating the spatial overlap of the occupied and virtual molecular orbitals involved in the transition. Here, the error in the calculated S1 potential energy curves at BP86, B3LYP, and BHLYP can be clearly related to the Λ-parameter, i.e., to the extent of charge transfer. Additionally, it is demonstrated that the CT problem is largely alleviated when the BHLYP xc-functional is employed, although it still exhibits a weak tendency to underestimate the energy of CT states. The situation improves drastically when LRS-functionals are employed within TDDFT excited state calculations. All tested LRS-functionals give qualitatively the correct potential energy curves of the energetically lowest excited states of P. Y. 101 along the twisting coordinate. While LC-BOP and ωB97X overcorrect the CT problem and now tend to give too large excitation energies compared to other non-CT states, ωPBE and CAM-B3LYP are in excellent agreement with the RI-CC2 results, with respect to both the correct shape of the potential energy curve as well as the absolute values of the calculated excitation energies.

The unique GGA clathrin adaptor of Drosophila melanogaster is not essential.

PubMed

Luan, Shan; Ilvarsonn, Anne M; Eissenberg, Joel C

2012-01-01

The Golgi-localized, γ-ear-containing, ARF binding proteins (GGAs) are a highly conserved family of monomeric clathrin adaptor proteins implicated in clathrin-mediated protein sorting between the trans-Golgi network and endosomes. GGA RNAi knockdowns in Drosophila have resulted in conflicting data concerning whether the Drosophila GGA (dGGA) is essential. The goal of this study was to define the null phenotype for the unique Drosophila GGA. We describe two independently derived dGGA mutations. Neither allele expresses detectable dGGA protein. Homozygous and hemizygous flies with each allele are viable and fertile. In contrast to a previous report using RNAi knockdown, GGA mutant flies show no evidence of age-dependent retinal degeneration or cathepsin missorting. Our results demonstrate that several of the previous RNAi knockdown phenotypes were the result of off-target effects. However, GGA null flies are hypersensitive to dietary chloroquine and to starvation, implicating GGA in lysosomal function and autophagy.

Computational Investigation of the Geometrical and Electronic Structures of VGen-/0 (n = 1-4) Clusters by Density Functional Theory and Multiconfigurational CASSCF/CASPT2 Method.

PubMed

Tran, Van Tan; Nguyen, Minh Thao; Tran, Quoc Tri

2017-10-12

Density functional theory and the multiconfigurational CASSCF/CASPT2 method have been employed to study the low-lying states of VGe n -/0 (n = 1-4) clusters. For VGe -/0 and VGe 2 -/0 clusters, the relative energies and geometrical structures of the low-lying states are reported at the CASSCF/CASPT2 level. For the VGe 3 -/0 and VGe 4 -/0 clusters, the computational results show that due to the large contribution of the Hartree-Fock exact exchange, the hybrid B3LYP, B3PW91, and PBE0 functionals overestimate the energies of the high-spin states as compared to the pure GGA BP86 and PBE functionals and the CASPT2 method. On the basis of the pure GGA BP86 and PBE functionals and the CASSCF/CASPT2 results, the ground states of anionic and neutral clusters are defined, the relative energies of the excited states are computed, and the electron detachment energies of the anionic clusters are evaluated. The computational results are employed to give new assignments for all features in the photoelectron spectra of VGe 3 - and VGe 4 - clusters.

Geranylgeranylacetone blocks doxorubicin-induced cardiac toxicity and reduces cancer cell growth and invasion through RHO pathway inhibition.

PubMed

Sysa-Shah, Polina; Xu, Yi; Guo, Xin; Pin, Scott; Bedja, Djahida; Bartock, Rachel; Tsao, Allison; Hsieh, Angela; Wolin, Michael S; Moens, An; Raman, Venu; Orita, Hajime; Gabrielson, Kathleen L

2014-07-01

Doxorubicin is a widely used chemotherapy for solid tumors and hematologic malignancies, but its use is limited due to cardiotoxicity. Geranylgeranylacetone (GGA), an antiulcer agent used in Japan for 30 years, has no significant adverse effects, and unexpectedly reduces ovarian cancer progression in mice. Because GGA reduces oxidative stress in brain and heart, we hypothesized that GGA would prevent oxidative stress of doxorubicin cardiac toxicity and improve doxorubicin's chemotherapeutic effects. Nude mice implanted with MDA-MB-231 breast cancer cells were studied after chronic treatment with doxorubicin, doxorubicin/GGA, GGA, or saline. Transthoracic echocardiography was used to monitor systolic heart function and xenografts evaluated. Mice were euthanized and cardiac tissue evaluated for reactive oxygen species generation, TUNEL assay, and RHO/ROCK pathway analysis. Tumor metastases were evaluated in lung sections. In vitro studies using Boyden chambers were performed to evaluate GGA effects on RHO pathway activator lysophosphatidic acid (LPA)-induced motility and invasion. We found that GGA reduced doxorubicin cardiac toxicity, preserved cardiac function, prevented TUNEL-positive cardiac cell death, and reduced doxorubicin-induced oxidant production in a nitric oxide synthase-dependent and independent manner. GGA also reduced heart doxorubicin-induced ROCK1 cleavage. Remarkably, in xenograft-implanted mice, combined GGA/doxorubicin treatment decreased tumor growth more effectively than doxorubicin treatment alone. As evidence of antitumor effect, GGA inhibited LPA-induced motility and invasion by MDA-MB-231 cells. These anti-invasive effects of GGA were suppressed by geranylgeraniol suggesting GGA inhibits RHO pathway through blocking geranylation. Thus, GGA protects the heart from doxorubicin chemotherapy-induced injury and improves anticancer efficacy of doxorubicin in breast cancer. ©2014 American Association for Cancer Research.

ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation

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

Mardirossian, Narbe; Head-Gordon, Martin

2016-06-07

A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation is presented in this paper. The final 12-parameter functional form is selected from approximately 10 × 10 9 candidate fits that are trained on a training set of 870 data points and tested on a primary test set of 2964 data points. The resulting density functional, ωB97M-V, is further tested for transferability on a secondary test set of 1152 data points. For comparison, ωB97M-V is benchmarked against 11 leading density functionals including M06-2X, ωB97X-D, M08-HX, M11, ωM05-D, ωB97X-V, and MN15. Encouragingly, the overall performance of ωB97M-V on nearlymore » 5000 data points clearly surpasses that of all of the tested density functionals. Finally, in order to facilitate the use of ωB97M-V, its basis set dependence and integration grid sensitivity are thoroughly assessed, and recommendations that take into account both efficiency and accuracy are provided.« less

Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

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

Willow, Soohaeng Y.; Zeng, Xiao Cheng; Xantheas, Sotiris S.

To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trendsmore » derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.« less

Etude, par principes premiers, des effets de la correlation entre electrons sur les proprietes electroniques et magnetiques de polymeres pontes et de supraconducteurs a haute temperature critique

NASA Astrophysics Data System (ADS)

Pesant, Simon

Description of complex systems by Density functional theory is treated in this thesis. First, the Density functional theory and a few functionals used to simulate cristals are presented. Specifically, the LDA and GGA functionnals are described and their limits are exposed. Furthermore, the Hubbard model as well as the LDA+U functionnal are addressed in this chapter. These methods enable the study of highly correlated materials. Then, results obtained on polymers are summarized in two articles. The first one treats the band gap variation of ladder-type polymers compared to non ladder type ones. The second article considers small band gap polymers. In this case, it will be shown that an hybrid functional, which contains exact exchange, is required to describe the electronic properties of the polymers under study. Finally, the last chapter address the study of cuprates superconductors. The LDA+U can account for the localization of electrons in copper orbitals. Consequently, a study of the impact of this functionnal on electronic properties of cuprates is conducted. The chapter is ended by an article treating magnetic orders in doped La 2CuO4. Supplementary materials of the second article and a description of the theory of superconductivity of Bardeen, Cooper and Schrieffer are put in annex. Keywords : Electronic correlation, DFT, LDA+U, cuprates, polymers, magnetic orders

Topological Phase Transitions in Zinc-Blende Semimetals Driven Exclusively by Electronic Temperature

NASA Astrophysics Data System (ADS)

Trushin, Egor; Görling, Andreas

2018-04-01

We show that electronic phase transitions in zinc-blende semimetals with quadratic band touching (QBT) at the center of the Brillouin zone, like GaBi, InBi, or HgTe, can occur exclusively due to a change of the electronic temperature without the need to involve structural transformations or electron-phonon coupling. The commonly used Kohn-Sham density-functional methods based on local and semilocal density functionals employing the local density approximation (LDA) or generalized gradient approximations (GGAs), however, are not capable of describing such phenomena because they lack an intrinsic temperature dependence and account for temperature only via the occupation of bands, which essentially leads only to a shift of the Fermi level without changing the shape or topology of bands. Kohn-Sham methods using the exact temperature-dependent exchange potential, not to be confused with the Hartree-Fock exchange potential, on the other hand, describe such phase transitions. A simple modeling of correlation effects can be achieved by screening of the exchange. In the considered zinc-blende compounds the QBT is unstable at low temperatures and a transition to electronic states without QBT takes place. In the case of HgTe and GaBi Weyl points of type I and type II, respectively, emerge during the transitions. This demonstrates that Kohn-Sham methods can describe such topological phase transitions provided they are based on functionals more accurate than those within the LDA or GGA. Moreover, the electronic temperature is identified as a handle to tune topological materials.

Defect-induced magnetism in graphene nanoflakes

NASA Astrophysics Data System (ADS)

Martinez-Guerra, E.; Cifuentas-Quintal, M. E.; de Coss, R.

2009-03-01

The interaction between electron spin and the magnetic moments of vacancies in graphene could open new opportunities for spintronic and quantum computation. In that direction, we have studied the magnetic properties of graphene nanoflakes (C6n2H6n) with vacancies within the framework of density functional theory, using the pseudopotential LCAO method with a Generalized Gradient Approximation (GGA) for the exchange-correlation energy functional. In particular, we have calculated the magnetic moment of graphene nanoflakes of different diameters with a simple vacancy. We have found that the total spin-polarization of the graphene nanoflakes with a simple vacancy decreases as the diameter increases. In particular, we show that the vacancy induces the appereance of a midgap state at Fermi level. Thus, the spin degeneracy is broken, being only one of the spin channels of the midgap state occupied, the other being empty. This feature could be exploited for future spintronic applications. This research was supported by Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grant No. 83604.

Electronic and Magnetic Properties of Cd-Doped PuRhIn5

NASA Astrophysics Data System (ADS)

Zhu, Jian-Xin

Since their discovery nearly a decade ago, plutonium-based superconductors have attracted considerable interest, which is now heightened by the latest discovery of superconductivity in other Pu-115 compounds. Within the generalized gradient approximation (GGA) of density functional theory and its combination with the dynamical mean-field theory, we present a study of electronic structure in the paramagnetic state of Cd-doped PuRhIn5. A doping-induced delocalization-localization transition is identified. In addition, the spin-polarized GGA-based total energy calculations are performed to determine the magnetic exchange interactions in the pristine PuRhIn5. The implication to the nature of quantum criticality is discussed. This work was carried out under the auspices of the National Nuclear Security Administration of the U.S. Department of Energy at LANL under Contract No. DE-AC52-06NA25396, and was supported by the LANL ASC Program.

Accelerating large scale Kohn-Sham density functional theory calculations with semi-local functionals and hybrid functionals

NASA Astrophysics Data System (ADS)

Lin, Lin

The computational cost of standard Kohn-Sham density functional theory (KSDFT) calculations scale cubically with respect to the system size, which limits its use in large scale applications. In recent years, we have developed an alternative procedure called the pole expansion and selected inversion (PEXSI) method. The PEXSI method solves KSDFT without solving any eigenvalue and eigenvector, and directly evaluates physical quantities including electron density, energy, atomic force, density of states, and local density of states. The overall algorithm scales as at most quadratically for all materials including insulators, semiconductors and the difficult metallic systems. The PEXSI method can be efficiently parallelized over 10,000 - 100,000 processors on high performance machines. The PEXSI method has been integrated into a number of community electronic structure software packages such as ATK, BigDFT, CP2K, DGDFT, FHI-aims and SIESTA, and has been used in a number of applications with 2D materials beyond 10,000 atoms. The PEXSI method works for LDA, GGA and meta-GGA functionals. The mathematical structure for hybrid functional KSDFT calculations is significantly different. I will also discuss recent progress on using adaptive compressed exchange method for accelerating hybrid functional calculations. DOE SciDAC Program, DOE CAMERA Program, LBNL LDRD, Sloan Fellowship.

First-principles study of structural stability, electronic, optical and elastic properties of binary intermetallic: PtZr

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

Pagare, Gitanjali, E-mail: gita-pagare@yahoo.co.in; Jain, Ekta, E-mail: jainekta05@gmail.com; Sanyal, S. P., E-mail: sps.physicsbu@gmail.com

2016-05-06

Structural, electronic, optical and elastic properties of PtZr have been studied using the full-potential linearized augmented plane wave (FP-LAPW) method within density functional theory (DFT). The energy against volume and enthalpy vs. pressure variation in three different structures i.e. B{sub 1}, B{sub 2} and B{sub 3} for PtZr has been presented. The equilibrium lattice parameter, bulk modulus and its pressure derivative have been obtained using optimization method for all the three phases. Furthermore, electronic structure was discussed to reveal the metallic character of the present compound. The linear optical properties are also studied under zero pressure for the first time.more » Results on elastic properties are obtained using generalized gradient approximation (GGA) for exchange correlation potentials. Ductile nature of PtZr compound is predicted in accordance with Pugh’s criteria.« less

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Electronic structure and bonding properties of potassium (K) on graphite under external electric field.

NASA Astrophysics Data System (ADS)

Tapia, Alejandro; Canto, Gabriel

2005-03-01

The effect of an external electric field on the potassium (K) adsorption on the graphite surface, are studied by means of first-principles total-energy calculations. The results were obtained with the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. The structural parameters, bonding properties, and electronic structure of the K-graphite system are studied in the triangular (2x2) overlayer phase as a function of the external electric field magnitude. We find an important change in the K-graphite bonding as a consequence of the charge transfer from the adatom towards the substrate induced by the electric field. The results are discussed in the light of the experimental observed difussion of K into graphite induced by external electric fields. This work was supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grants No. 43830-F and No. 44831-F.

Optical Absorption in Molecular Crystals from Time-Dependent Density Functional Theory

DTIC Science & Technology

2017-04-18

fundamental gap but there is little effect on the optical spectra. We therefore believe that the method is robust and can be used for studies of... quantitative DFT- based prediction of excited-state properties in molecu- lar solids.[28, 29] In this approach, one first computes the underlying gas...gradient ap- proximation (GGA). In some cases , the fraction of SR Fock exchange, α, can be determined from first-principles based on satisfaction of

Half-metallic ferromagnetism in Fe, Co and Ni doped BaS: First principles calculations

NASA Astrophysics Data System (ADS)

Maurya, Savita; Sharma, Ramesh; Bhamu, K. C.

2018-04-01

The first principle investigation of structural, electronic, magnetic and optical properties of Ba1-xTMxS (x = 0.25) have been done using FPLAW method within the density functional theory (DFT) using generalized gradient approximation (GGA) for exchange correlation potential using two different functionals which are the PBE-sol and the modified Becke and Johnson local (spin) density approximation (mBJLDA). It was found that mBJLDA functional offer better account for the electronic structure of the Fe, Co and Ni-doped BaS. It was also observed that Fe/Co/Ni d, S p and Ba d states play a major role in determining the electronic properties of this alloy system. Investigation results shows that Ba0.75(Fe/Co/Ni)0.25S is ferromagnetic with magnetic moment of 3.72 µB, 2.73908 µB and 1.74324 µB at Fe, Co and Ni sites respectively. Complex dielectric constant ɛ(ω) and normal incidence reflectivity R(ω) are also been investigate for broad range of photon energies. These results are compared with the some reported existing experimental values.

Band gap characterization of ternary BBi1-xNx (0≤x≤1) alloys using modified Becke-Johnson (mBJ) potential

NASA Astrophysics Data System (ADS)

Yalcin, Battal G.

2015-04-01

The semi-local Becke-Johnson (BJ) exchange-correlation potential and its modified form proposed by Tran and Blaha have attracted a lot of interest recently because of the surprisingly accurate band gaps they can deliver for many semiconductors and insulators (e.g., sp semiconductors, noble-gas solids, and transition-metal oxides). The structural and electronic properties of ternary alloys BBi1-xNx (0≤x≤1) in zinc-blende phase have been reported in this study. The results of the studied binary compounds (BN and BBi) and ternary alloys BBi1-xNx structures are presented by means of density functional theory. The exchange and correlation effects are taken into account by using the generalized gradient approximation (GGA) functional of Wu and Cohen (WC) which is an improved form of the most popular Perdew-Burke-Ernzerhof (PBE). For electronic properties the modified Becke-Johnson (mBJ) potential, which is more accurate than standard semi-local LDA and PBE calculations, has been chosen. Geometric optimization has been implemented before the volume optimization calculations for all the studied alloys structure. The obtained equilibrium lattice constants of the studied binary compounds are in coincidence with experimental works. And, the variation of the lattice parameter of ternary alloys BBi1-xNx almost perfectly matches with Vegard's law. The spin-orbit interaction (SOI) has been also considered for structural and electronic calculations and the results are compared to those of non-SOI calculations.

Electronic properties of RDX and HMX: Compton scattering experiment and first-principles calculation.

PubMed

Ahuja, B L; Jain, Pradeep; Sahariya, Jagrati; Heda, N L; Soni, Pramod

2013-07-11

The first-ever electron momentum density (EMD) measurements of explosive materials, namely, RDX (1,3,5-trinitro-1,3,5-triazacyclohexane, (CH2-N-NO2)3) and HMX (1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane, (CH2-N-NO2)4), have been reported using a 740 GBq (137)Cs Compton spectrometer. Experimental Compton profiles (CPs) are compared with the EMDs derived from linear combination of atomic orbitals with density functional theory. It is found that the CPs deduced from generalized gradient approximation (GGA) with Wu-Cohen exchange energies give a better agreement with the corresponding experimental profiles than those from local density approximation and other schemes of GGA. Further, Mulliken population, energy bands, partial and total density of states, and band gap have also been reported using GGA calculations. Present ground state calculations unambiguously show large band gap semiconductor nature of both RDX and HMX. A similar type of bonding in these materials is uniquely established using Compton data and density of states. It is also outstandingly consistent with the Mulliken population, which predicts almost equal amount of charge transfer (0.84 and 0.83 e(-)) from H1 + H2 + N2 to C1 + N1 + O1 + O2 in both the explosives.

Accurate Energies and Orbital Description in Semi-Local Kohn-Sham DFT

NASA Astrophysics Data System (ADS)

Lindmaa, Alexander; Kuemmel, Stephan; Armiento, Rickard

2015-03-01

We present our progress on a scheme in semi-local Kohn-Sham density-functional theory (KS-DFT) for improving the orbital description while still retaining the level of accuracy of the usual semi-local exchange-correlation (xc) functionals. DFT is a widely used tool for first-principles calculations of properties of materials. A given task normally requires a balance of accuracy and computational cost, which is well achieved with semi-local DFT. However, commonly used semi-local xc functionals have important shortcomings which often can be attributed to features of the corresponding xc potential. One shortcoming is an overly delocalized representation of localized orbitals. Recently a semi-local GGA-type xc functional was constructed to address these issues, however, it has the trade-off of lower accuracy of the total energy. We discuss the source of this error in terms of a surplus energy contribution in the functional that needs to be accounted for, and offer a remedy for this issue which formally stays within KS-DFT, and, which does not harshly increase the computational effort. The end result is a scheme that combines accurate total energies (e.g., relaxed geometries) with an improved orbital description (e.g., improved band structure).

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

Matanovic, Ivana; Atanassov, Plamen; Kiefer, Boris

The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energymore » for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of 22.62 and 21.1% for the NAN stretching and RhAH stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the RhAH and NAN stretching modes from the bulk phonons and by solving one- and two-dimensional Schr€odinger equation associated with the RhAH, RhAN, and NAN potential energy we calculated the anharmonic correction for NAN and RhAH stretching modes as 231 cm21 and 277 cm21 at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments.« less

Genetic parameters and genome-wide association study of hyperpigmentation of the visceral peritoneum in chickens.

PubMed

Luo, Chenglong; Qu, Hao; Wang, Jie; Wang, Yan; Ma, Jie; Li, Chunyu; Yang, Chunfen; Hu, Xiaoxiang; Li, Ning; Shu, Dingming

2013-05-16

Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered much attention in the poultry industry because of the possible risk to the health of affected animals and the damage it causes to the appearance of commercial chicken carcasses. However, the heritable characters of HVP remain unclear. The objective of this study was to investigate the genetic parameters of HVP by genome-wide association study (GWAS) in chickens. HVP was found to be influenced by genetic factors, with a heritability score of 0.33. HVP had positive genetic correlations with growth and carcass traits, such as leg muscle weight (rg = 0.34), but had negative genetic correlations with immune traits, such as the antibody response to Newcastle disease virus (rg = -0.42). The GWAS for HVP using 39,833 single nucleotide polymorphisms indicated the genetic factors associated with HVP displayed an additive effect rather than a dominance effect. In addition, we determined that three genomic regions, involving the 50.5-54.0 Mb region of chicken (Gallus gallus) chromosome 1 (GGA1), the 58.5-60.5 Mb region of GGA1, and the 10.5-12.0 Mb region of GGA20, were strongly associated (P < 6.28 × 10-7) with HVP in chickens. Variants in these regions explained >50% of additive genetic variance for HVP. This study also confirmed that expression of BMP7, which codes for a bone morphogenetic protein and is located in one of the candidate regions, was significantly higher in the visceral peritoneum of Huiyang Beard chickens with HVP than in that of chickens without pigmentation (P < 0.05). HVP is a quantitative trait with moderate heritability. Genomic variants resulting in HVP were identified on GGA1 and GGA20, and expression of the BMP7 gene appears to be upregulated in HVP-affected chickens. Findings from this study should be used as a basis for further functional validation of candidate genes involved in HVP.

Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.

PubMed

Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

2013-01-15

Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (ωB97X, ωB97, LC-ωPBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ωB97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ωB97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ωB97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

Ab-initio study of structural and electronic properties of WS2/h-BN van der Waals heterostructure

NASA Astrophysics Data System (ADS)

Ghasemi majd, Zahra; Amiri, Peiman; Taghizadeh, Seyed Fardin

2018-06-01

First-principle calculations with different exchange-correlation functionals, including LDA, GGA, semi-empirical and ab-initio van der Waals in the forms of vdW-DF2B86R and vdW-DF2 were performed to evaluate the performance of different functionals in describing the bonding mechanism, adsorption energy and interlayer distance of WS2 monolayer on and between h-BN layers. The finding was that the vdW-DF2B86R seems to be the approach best lending itself to this purpose. In order to include the van der Waals (vdW) interactions in our calculations, we used the DFT-D2 and vdW methods, which gave rise to a physical adsorption with no net charge transfer between the WS2 layer and the corresponding substrates. In addition, we investigated the electronic and structural properties of WS2 and h-BN heterolayers, using vdW-DF2B86R functional. Based on density functional theory calculations, WS2 on and between h-BN layers showed a direct band gap at the K-point, which was experimentally observed.

Density-functional energy gaps of solids demystified

NASA Astrophysics Data System (ADS)

Perdew, John P.; Ruzsinszky, Adrienn

2018-06-01

The fundamental energy gap of a solid is a ground-state second energy difference. Can one find the fundamental gap from the gap in the band structure of Kohn-Sham density functional theory? An argument of Williams and von Barth (WB), 1983, suggests that one can. In fact, self-consistent band-structure calculations within the local density approximation or the generalized gradient approximation (GGA) yield the fundamental gap within the same approximation for the energy. Such a calculation with the exact density functional would yield a band gap that also underestimates the fundamental gap, because the exact Kohn-Sham potential in a solid jumps up by an additive constant when one electron is added, and the WB argument does not take this effect into account. The WB argument has been extended recently to generalized Kohn-Sham theory, the simplest way to implement meta-GGAs and hybrid functionals self-consistently, with an exchange-correlation potential that is a non-multiplication operator. Since this operator is continuous, the band gap is again the fundamental gap within the same approximation, but, because the approximations are more realistic, so is the band gap. What approximations might be even more realistic?

Identifying Molecular Regulators of Neuronal Functions Affected in the Movement Disorder Dystonia

DTIC Science & Technology

2015-08-01

GC-3’ (forward), 5’-CGT GTG GCT GTT GGG GTT GTT GCT GAG GTA-3’ (reverse) for the 498-bp amplicon, 5’-CAC CCT ATC AGG GGA GGA CAA CTT TCG-3’ (forward...3’ (reverse) for the 983- bp amplicon, and 5’-CAC CCT ATC AGG GGA GGA CAA CTT TCG-3’ (forward), 5’-ACA GTG TAG TAA GGC AAA GCA AGG AG-3’ (reverse) for

Electronic structure and metallization of cubic GdH{sub 3} under pressure: Ab initio many-body GW calculations

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

Kong, Bo, E-mail: kong79@yeah.net, E-mail: yachao.zhang@pku.edu.cn; Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang 550018; Zhang, Yachao, E-mail: kong79@yeah.net, E-mail: yachao.zhang@pku.edu.cn

The electronic structures of the cubic GdH{sub 3} 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 + G{sub 0}W{sub 0} calculations give a fundamental band gap of 1.72 eV, while GGA+ GW{sub 0} 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 localizationmore » 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) GdH{sub 3} can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G{sub 0}W{sub 0} calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW{sub 0} and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G{sub 0}W{sub 0} calculations in the 4f-core case is the closest to the real result. By G{sub 0}W{sub 0} 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 GdH{sub 3} occurs around 40 GPa, which might be a satisfied prediction.« less

Computational study of TiO2 Brookite (100), (010) and (210) surface doped with Ruthenium for application in Dye Sensitised Solar Cells

NASA Astrophysics Data System (ADS)

Dima, R. S.; Maluta, N. E.; Maphanga, R. R.; Sankaran, V.

2017-10-01

Titanium dioxide (TiO2) polymorphs are widely used in many energy-related applications due to their peculiar electronic and physicochemical properties. The electronic structures of brookite TiO2 surfaces doped with transition metal ruthenium have been investigated by ab initio band calculations based on the density functional theory with the planewave ultrasoft pseudopotential method. The generalized gradient approximation (GGA) was used in the scheme of Perdew-Burke-Ernzerhof (PBE) to describe the exchange-correlation functional. All calculations were carried out with CASTEP (Cambridge Sequential Total EnergyPackage) code in Materials Studio of Accelrys Inc. The surface structures of Ru doped TiO2 were constructed by cleaving the 1 × 1 × 1 optimized bulk structure of brookite TiO2. The results indicate that Ru doping can narrow the band gap of TiO2, leading to the improvement in the photoreactivity of TiO2, and simultaneously maintain strong redox potential. The theoretical calculations could provide meaningful guide to develop more active photocatalysts with visible light response.

Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

NASA Astrophysics Data System (ADS)

Ratcliff, Laura E.; Degomme, A.; Flores-Livas, José A.; Goedecker, Stefan; Genovese, Luigi

2018-03-01

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding or even out of reach if high quality basis sets are used. We present a highly optimized multiple graphics processing unit implementation of the exact exchange operator which allows one to perform fast hybrid functional density-functional theory (DFT) calculations with systematic basis sets without additional approximations for up to a thousand atoms. With this method hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution that is of the same order of magnitude as traditional semilocal-GGA functionals. The method is implemented in a portable open-source library.

Electronic structure of clathrates Bax@AlySi46-y ; thermoelectric devices

NASA Astrophysics Data System (ADS)

Eguchi, Haruki; Nagano, Takatoshi; Takenaka, Hiroyuki; Tsumuraya, Kazuo

2002-03-01

Clathrates have received much attention as a candidate of high performance thermoelectric devices. This is because they have a) low thermal conductivity due to rattle effect of the alkali or heavy alkali-earth metals such as Ba atoms in the cages of clusters of the clathrates, and b) adjustablity of the Fermi levels through replacement of frame Si atoms with acceptor Al atoms and addition of the cage atoms as donors. We present the dispersion curves with LDA and GGA approximations for the exchange correlation of electrons using the planewave based pseudopotential methods and predict the electronic properties of the clathrates.

Phonon renormalization and anharmonicity in Al-doped MgB2

NASA Astrophysics Data System (ADS)

Ortiz, Filiberto; Aguayo, Aarón

2005-03-01

We have studied the evolution of the E2g phonon mode dynamics in Mg1-xAlxB2 as a function of doping using the Frozen Phonon Approximation (FPA). The doping was modeled in the ab-initio Virtual Crystal Approximation (VCA). The results were obtained by means of first-principles total-energy calculations using the full potential Linearized Augmented Plane Wave (LAPW) method and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We present results for the evolution of the phonon frequency and anharmonicity of the E2g mode as a function of Al concentration (x). From a comparison of the experimental data with the calculated E2g phonon frequency we show that the VCA-FPA reproduces the observed phonon renormalization in the whole range of Al concentrations. More interestingly, we find that the anharmonicity gradually decreases with Al doping and vanishes for x(Al)>0.5, that behaviour correlates with the evolution of the measured Raman linewidth in Al-doped MgB2. The significance of these results are discussed in the light of the experimentally observed loss of superconductivity in Mg1- xAlxB2.This work was supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant. No. 43830-F.

Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules.

PubMed

Jacquemin, Denis; Wathelet, Valérie; Perpète, Eric A; Adamo, Carlo

2009-09-08

Extensive Time-Dependent Density Functional Theory (TD-DFT) calculations have been carried out in order to obtain a statistically meaningful analysis of the merits of a large number of functionals. To reach this goal, a very extended set of molecules (∼500 compounds, >700 excited states) covering a broad range of (bio)organic molecules and dyes have been investigated. Likewise, 29 functionals including LDA, GGA, meta-GGA, global hybrids, and long-range-corrected hybrids have been considered. Comparisons with both theoretical references and experimental measurements have been carried out. On average, the functionals providing the best match with reference data are, one the one hand, global hybrids containing between 22% and 25% of exact exchange (X3LYP, B98, PBE0, and mPW1PW91) and, on the other hand, a long-range-corrected hybrid with a less-rapidly increasing HF ratio, namely LC-ωPBE(20). Pure functionals tend to be less consistent, whereas functionals incorporating a larger fraction of exact exchange tend to underestimate significantly the transition energies. For most treated cases, the M05 and CAM-B3LYP schemes deliver fairly small deviations but do not outperform standard hybrids such as X3LYP or PBE0, at least within the vertical approximation. With the optimal functionals, one obtains mean absolute deviations smaller than 0.25 eV, though the errors significantly depend on the subset of molecules or states considered. As an illustration, PBE0 and LC-ωPBE(20) provide a mean absolute error of only 0.14 eV for the 228 states related to neutral organic dyes but are completely off target for cyanine-like derivatives. On the basis of comparisons with theoretical estimates, it also turned out that CC2 and TD-DFT errors are of the same order of magnitude, once the above-mentioned hybrids are selected.

Ab-Initio Investigations of Magnetic Properties and Induced Half-Metallicity in Ga1-xMnxP (x = 0.03, 0.25, 0.5, and 0.75) Alloys.

PubMed

Laref, Amel; AlMudlej, Abeer; Laref, Slimane; Yang, Jun Tao; Xiong, Yong-Chen; Luo, Shi Jun

2017-07-07

Ab-initio calculations are performed to examine the electronic structures and magnetic properties of spin-polarized Ga 1- x Mn x P ( x = 0.03, 0.25, 0.5, and 0.75) ternary alloys. In order to perceive viable half-metallic (HM) states and unprecedented diluted magnetic semiconductors (DMSs) such as spintronic materials, the full potential linearized augmented plane wave method is utilized within the generalized gradient approximation (GGA). In order to tackle the correlation effects on 3d states of Mn atoms, we also employ the Hubbard U (GGA + U) technique to compute the magnetic properties of an Mn-doped GaP compound. We discuss the emerged global magnetic moments and the robustness of half-metallicity by varying the Mn composition in the GaP compound. Using GGA + U, the results of the density of states demonstrate that the incorporation of Mn develops a half-metallic state in the GaP compound with an engendered band gap at the Fermi level ( E F ) in the spin-down state. Accordingly, the half-metallic feature is produced through the hybridization of Mn-d and P-p orbitals. However, the half-metallic character is present at a low x composition with the GGA procedure. The produced magnetic state occurs in these materials, which is a consequence of the exchange interactions between the Mn-element and the host GaP system. For the considered alloys, we estimated the X-ray absorption spectra at the K edge of Mn. A thorough clarification of the pre-edge peaks is provided via the results of the theoretical absorption spectra. It is inferred that the valence state of Mn in Ga 1- x Mn x P alloys is +3. The predicted theoretical determinations surmise that the Mn-incorporated GaP semiconductor could inevitably be employed in spintronic devices.

Effects of temperature and pressure on thermodynamic properties of Cd0.50 Zn0.50 Se alloy

NASA Astrophysics Data System (ADS)

Aarifeen, Najm ul; Afaq, A.

2017-09-01

Thermodynamic properties of \\text{C}{{\\text{d}}0.50} \\text{Z}{{\\text{n}}0.50} Se alloy are studied using quasi harmonic model for pressure range 0-10 GPa and temperature range 0-1000 K. The structural optimization is obtained by self consistent field calculations and full-potential linear muffin-tin orbital method with GGA+U as an exchange correlation functional where U=2.3427 eV is the hubbard potential. The effects of temperature and pressure on the bulk modulus, Helmholtz free energy, internal energy, entropy, Debye temperature, Grüneisen parameter, thermal expansion coefficient and heat capacities of the material are observed and discussed. The bulk modulus, Helmholtz free energy and Debye temperature are found to decrease with increasing temperature while there is an increasing behavior when the pressure rises. Whereas internal energy has increasing trend with rises in temperature and it almost remains insensitive to pressure. The entropy of the system increases (decreases) with a rise of pressure (temperature).

The Calculation Study of Electronic Properties of Doped RE (Eu, Er and Tm)-GaN using Density Functional Theory

NASA Astrophysics Data System (ADS)

Zaharo, Aflah; Purqon, Acep

2017-07-01

The calculation of the structure and electronic properties of Rare Earth (RE) at the wurtzite Gallium Nitride (GaN) based on DFT has completed. GGA approximation used for exchange correlation and Ultra soft pseudo potential too. The stability structure of GaN is seen that difference lattice parameter 11% lower than another calculation and experiment result. It is shown the stability structure GaN have direct band gap energy on Gamma point hexagonal lattice Brillouin zone. The width Eg is 2.6 eV. When one atom Ga is substituted with one atom RE, the bond length is change 12 % longest. An in good agreement with theoretical doping RE concentration increases, the edge of energy level shifted towards to make the band gap narrow which is allow the optical transitions and help to improve the optical performance of GaN. The RE doped GaN is potentially applicable for various color of LED with lower energy consumption and potentially energy saving application

The ab initio Calculation of Electric Field Gradient at the Site of P Impurity in α-Al3O2

NASA Astrophysics Data System (ADS)

Zhang, Qiao-Li; Yuan, Da-Qing; Zhang, Huan-Qiao; Fan, Ping; Zuo, Yi; Zheng, Yong-Nan; Masuta, K.; Fukuda, M.; Mihara, M.; Minamisono, T.; Kitagawa, A.; Zhu, Sheng-Yun

2012-09-01

An ab initio calculation of the electric-field gradient (EFG) at the site of a phosphorous impurity substituting an Al atom in α-Al2O3 is carried out using the WIEN2k code with the full-potential linearized augmented plane wave plus local orbital method (LAPW+lo) in the frame of density functional theory. The atomic lattice relaxations caused by the implanted impurities were calculated for two different charged states to well describe the electronic structure of the doped system. The EFG at the site of the phosphorous impurity in the charged supercell calculated with the exchange-correlation potential of the Wu-Cohen generalized gradient approximation (WC-GGA) is 0.573 × 1021 V/m2. Then, the nuclear quadrupole moment of the I = 3 state in 28P is deduced to be 137 mb from the quadrupole interaction frequency of 190 kHz measured recently by the β-NQR method.

Calculation of exchange integrals and Curie temperature for La-substituted barium hexaferrites.

PubMed

Wu, Chuanjian; Yu, Zhong; Sun, Ke; Nie, Jinlan; Guo, Rongdi; Liu, Hai; Jiang, Xiaona; Lan, Zhongwen

2016-10-31

As the macro behavior of the strength of exchange interaction, state of the art of Curie temperature T c , which is directly proportional to the exchange integrals, makes sense to the high-frequency and high-reliability microwave devices. Challenge remains as finding a quantitative way to reveal the relationship between the Curie temperature and the exchange integrals for doped barium hexaferrites. Here in this report, for La-substituted barium hexaferrites, the electronic structure has been determined by the density functional theory (DFT) and generalized gradient approximation (GGA). By means of the comparison between the ground and relative state, thirteen exchange integrals have been calculated as a function of the effective value U eff . Furthermore, based on the Heisenberg model, the molecular field approximation (MFA) and random phase approximation (RPA), which provide an upper and lower bound of the Curie temperature T c , have been adopted to deduce the Curie temperature T c . In addition, the Curie temperature T c derived from the MFA are coincided well with the experimental data. Finally, the strength of superexchange interaction mainly depends on 2b-4f 1 , 4f 2 -12k, 2a-4f 1 , and 4f 1 -12k interactions.

The investigation of topological phase of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys under hydrostatic pressure

NASA Astrophysics Data System (ADS)

Saeidi, Parviz; Nourbakhsh, Zahra

2018-04-01

Topological phase of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys have been studied utilizing density function theory by WIEN2k code. The generalized gradient approximation (GGA), generalized gradient approximation plus Hubbard parameter (GGA + U), Modified Becke and Johnson (MBJ) and GGA Engel-vosko in the presence of spin orbit coupling have been used to investigate the topological band structure of Gd1-xYxAuPb alloys at zero pressure. The topological phase and band order of these alloys within GGA and GGA + U approaches under hydrostatic pressure are also investigated. We find that under hydrostatic pressure in some percentages of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys in both GGA and GGA + U approaches, the trivial topological phase is converted into nontrivial topological phase. In addition, the band inversion strength versus lattice constant of these alloys is studied. Moreover, the schematic plan is represented in order to show the trivial and nontrivial topological phase of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys in both GGA and GGA + U approaches.

FeP(Im)–AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O2)

PubMed Central

Liao, Meng-Sheng; Huang, Ming-Ju; Watts, John D.

2011-01-01

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (Ebond) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O2). The results indicate that an accurate prediction of Ebond for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield Ebond values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O2, respectively, which are in reasonable agreement with experimental data (0.78 – 0.85 eV for CO, 0.99 eV for NO, and 0.44 – 0.53 eV for O2). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined. PMID:22228914

Structural, elastic and electronic properties of transition metal carbides ZnC, NbC and their ternary alloys ZnxNb1-xC

NASA Astrophysics Data System (ADS)

Zidi, Y.; Méçabih, S.; Abbar, B.; Amari, S.

2018-02-01

We have investigated the structural, electronic and elastic properties of transition-metal carbides ZnxNb1-xC alloys in the range of 0 ≤ x ≤ 1 using the density functional theory (DFT). The full potential linearized augmented plane wave (FP-LAPW) method within a framework of the generalized gradient approximation (GGA) and GGA + U (where U is the Hubbard correlation terms) approach is used to perform the calculations presented here. The lattice parameters, the bulk modulus, its pressure derivative and the elastic constants were determined. We have obtained Young's modulus, shear modulus, Poisson's ratio, anisotropy factor by the aid of the calculated elastic constants. We discuss the total and partial densities of states and charge densities.

Depletion of GGA3 stabilizes BACE and enhances β-secretase activity

PubMed Central

Tesco, Giuseppina; Koh, Young Ho; Kang, Eugene; Cameron, Andrew; Das, Shinjita; Sena-Esteves, Miguel; Hiltunen, Mikko; Yang, Shao-Hua; Zhong, Zhenyu; Shen, Yong; Simpkins, James; Tanzi, Rudolph E.

2007-01-01

Summary Beta-site APP-cleaving enzyme (BACE) is required for production of the Alzheimer's disease (AD)-associated Aβ protein. BACE levels are elevated in AD brain, and increasing evidence reveals BACE as a stress-related protease that is upregulated following cerebral ischemia. However, the molecular mechanism responsible is unknown. We show that increases in BACE and β-secretase activity are due to post-translational stabilization following caspase activation. We also found that during cerebral ischemia, levels of GGA3, an adaptor protein involved in BACE trafficking, are reduced, while BACE levels are increased. RNAi silencing of GGA3 also elevated levels of BACE and Aβ. Finally, in AD brain samples, GGA3 protein levels were significantly decreased and inversely correlated with increased levels of BACE. In summary, we have elucidated a novel GGA3-dependent mechanism regulating BACE levels and β-secretase activity. This mechanism may explain increased cerebral levels of BACE and Aβ following cerebral ischemia and in AD. PMID:17553422

Blunted activation of NF-{kappa}B and NF-{kappa}B-dependent gene expression by geranylgeranylacetone: Involvement of unfolded protein response

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

Hayakawa, Kunihiro; Hiramatsu, Nobuhiko; Okamura, Maro

2008-01-04

Geranylgeranylacetone (GGA), an anti-ulcer agent, has anti-inflammatory potential against experimental colitis and ischemia-induced renal inflammation. However, molecular mechanisms involved in its anti-inflammatory effects are largely unknown. We found that, in glomerular mesangial cells, GGA blocked activation of nuclear factor-{kappa}B and consequent induction of monocyte chemoattractant protein 1 (MCP-1) by inflammatory cytokines. It was inversely correlated with induction of unfolded protein response (UPR) evidenced by expression of 78 kDa glucose-regulated protein (GRP78) and suppression of endoplasmic reticulum stress-responsive alkaline phosphatase. Various inducers of UPR including tunicamycin, thapsigargin, A23187, 2-deoxyglucose, dithiothreitol, and AB{sub 5} subtilase cytotoxin reproduced the suppressive effects of GGA.more » Furthermore, attenuation of UPR by stable transfection with GRP78 diminished the anti-inflammatory effects of GGA. These results disclosed a novel, UPR-dependent mechanism underlying the anti-inflammatory potential of GGA.« less

Genetic parameters and genome-wide association study of hyperpigmentation of the visceral peritoneum in chickens

PubMed Central

2013-01-01

Background Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered much attention in the poultry industry because of the possible risk to the health of affected animals and the damage it causes to the appearance of commercial chicken carcasses. However, the heritable characters of HVP remain unclear. The objective of this study was to investigate the genetic parameters of HVP by genome-wide association study (GWAS) in chickens. Results HVP was found to be influenced by genetic factors, with a heritability score of 0.33. HVP had positive genetic correlations with growth and carcass traits, such as leg muscle weight (rg = 0.34), but had negative genetic correlations with immune traits, such as the antibody response to Newcastle disease virus (rg = −0.42). The GWAS for HVP using 39,833 single nucleotide polymorphisms indicated the genetic factors associated with HVP displayed an additive effect rather than a dominance effect. In addition, we determined that three genomic regions, involving the 50.5–54.0 Mb region of chicken (Gallus gallus) chromosome 1 (GGA1), the 58.5–60.5 Mb region of GGA1, and the 10.5–12.0 Mb region of GGA20, were strongly associated (P < 6.28 × 10-7) with HVP in chickens. Variants in these regions explained >50% of additive genetic variance for HVP. This study also confirmed that expression of BMP7, which codes for a bone morphogenetic protein and is located in one of the candidate regions, was significantly higher in the visceral peritoneum of Huiyang Beard chickens with HVP than in that of chickens without pigmentation (P < 0.05). Conclusions HVP is a quantitative trait with moderate heritability. Genomic variants resulting in HVP were identified on GGA1 and GGA20, and expression of the BMP7 gene appears to be upregulated in HVP-affected chickens. Findings from this study should be used as a basis for further functional validation of candidate genes involved in HVP. PMID:23679099

Dispersion interactions in room-temperature ionic liquids: Results from a non-empirical density functional

NASA Astrophysics Data System (ADS)

Kohanoff, Jorge; Pinilla, Carlos; Youngs, Tristan G. A.; Artacho, Emilio; Soler, José M.

2011-10-01

The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004), 10.1103/PhysRevLett.92.246401], as efficiently implemented in the SIESTA code [G. Román-Pérez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009), 10.1103/PhysRevLett.103.096102]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by ≈7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Pópolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007), 10.1063/1.2715571]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010), 10.1088/0953-8984/22/7/074203]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields.

Insight into the optoelectronic and thermoelectric properties of Ca-based Zintl phase CaCd2X2 (X = P, As) from first principles calculation

NASA Astrophysics Data System (ADS)

Belfarh, T.; Batouche, M.; Seddik, T.; Uğur, G.; Omran, S. Bin; Bouhemadou, A.; Sandeep; Wang, Xiaotian; Sun, Xiao-Wei; Khenata, R.

2018-06-01

We have studied the structural, optical, electronic and thermoelectric properties of the CaCd2X2 (X = P, As) compounds by using the full-potential augmented plane wave plus local orbitals method (FP-APW + lo). The exchange-correlation potential was treated using both the gradient generalized approximation (WC-GGA) and local density approximation (LDA). The estimated structural parameters, including the lattice parameters and internal coordinates agree well with the available experimental data. Our computed band structure shows that both studied compounds are semiconductors, with direct band gaps (Γ-Γ) of approximately 1.78 eV and 1.2 eV for CaCd2P2 and CaCd2As2, respectively, using GGA-TB-mBJ approach. The calculated optical spectra reveal a strong response of these materials in the energy range between the visible light and extreme UV regions, making them a good candidate for optoelectronic devices. Thermoelectric parameters, such as thermal conductivity, electrical conductivity, Seebeck coefficient, power factor and figure of merit were calculated. We note that both the CaCd2P2 and CaCd2As2 compounds show promising thermoelectric properties.

Electronic properties of functionalized (5,5) beryllium oxide nanotubes.

PubMed

Chigo Anota, Ernesto; Cocoletzi, Gregorio Hernández

2013-05-01

Using the density functional theory (DFT) we study the structural and electronic properties of functionalized (5,5) chirality single wall beryllium oxide nanotubes (SW-BeONTs), i.e. armchair nanotubes. The nanotube surface and ends are functionalized by the hydroxyl (OH) functional group. Our calculations consider the Hamprecht-Cohen-Tozer-Handy functional in the generalized gradient approximation (HCTH-GGA) to deal with the exchange-correlation energies, and the base function with double polarization (DNP). The geometry optimization of both defects free and with point defects nanotubes is done applying the criterion of minimum energy. Six configurations are considered: The OH oriented toward the Be (on the surface and at the end), toward the O (on the surface and at the end) and placed at the nanotube ends. Simulation results show that the nanotube functionalization takes place at the nanotube ends with the BeO bond displaying hydrogen-like bridge bonds. Moreover the nanotube semiconductor behavior remains unchanged. The polarity is high (it shows a transition from covalent to ionic) favoring solvatation. On the other hand, the work function low value suggests this to be a good candidate for the device fabrication. When the nanotube contains surface point defects the work function is reduced which provides excellent possibilities for the use of this material in the electronic industry. Copyright © 2013 Elsevier Inc. All rights reserved.

Density functional theory and chromium: Insights from the dimers

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

Würdemann, Rolf; Kristoffersen, Henrik H.; Moseler, Michael

2015-03-28

The binding in small Cr clusters is re-investigated, where the correct description of the dimer in three charge states is used as criterion to assign the most suitable density functional theory approximation. The difficulty in chromium arises from the subtle interplay between energy gain from hybridization and energetic cost due to exchange between s and d based molecular orbitals. Variations in published bond lengths and binding energies are shown to arise from insufficient numerical representation of electron density and Kohn-Sham wave-functions. The best functional performance is found for gradient corrected (GGA) functionals and meta-GGAs, where we find severe differences betweenmore » functionals from the same family due to the importance of exchange. Only the “best fit” from Bayesian error estimation is able to predict the correct energetics for all three charge states unambiguously. With this knowledge, we predict small bond-lengths to be exclusively present in Cr{sub 2} and Cr{sub 2}{sup −}. Already for the dimer cation, solely long bond-lengths appear, similar to what is found in the trimer and in chromium bulk.« less

Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals

DOE PAGES

Ruiz Pestana, Luis; Mardirossian, Narbe; Head-Gordon, Martin; ...

2017-02-27

We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm –3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreementmore » with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.« less

Assessing Many-Body Effects of Water Self-Ions. I: OH-(H2O) n Clusters.

PubMed

Egan, Colin K; Paesani, Francesco

2018-04-10

The importance of many-body effects in the hydration of the hydroxide ion (OH - ) is investigated through a systematic analysis of the many-body expansion of the interaction energy carried out at the CCSD(T) level of theory, extrapolated to the complete basis set limit, for the low-lying isomers of OH - (H 2 O) n clusters, with n = 1-5. This is accomplished by partitioning individual fragments extracted from the whole clusters into "groups" that are classified by both the number of OH - and water molecules and the hydrogen bonding connectivity within each fragment. With the aid of the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method, this structure-based partitioning is found to largely correlate with the character of different many-body interactions, such as cooperative and anticooperative hydrogen bonding, within each fragment. This analysis emphasizes the importance of a many-body representation of inductive electrostatics and charge transfer in modeling OH - hydration. Furthermore, the rapid convergence of the many-body expansion of the interaction energy also suggests a rigorous path for the development of analytical potential energy functions capable of describing individual OH - -water many-body terms, with chemical accuracy. Finally, a comparison between the reference CCSD(T) many-body interaction terms with the corresponding values obtained with various exchange-correlation functionals demonstrates that range-separated, dispersion-corrected, hybrid functionals exhibit the highest accuracy, while GGA functionals, with or without dispersion corrections, are inadequate to describe OH - -water interactions.

First principles LDA + U and GGA + U study of protactinium and protactinium oxides: dependence on the effective U parameter

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Chetty, N.

2013-04-01

The electronic structure and properties of protactinium and its oxides (PaO and PaO2) have been studied within the framework of the local density approximation (LDA), the Perdew-Burke-Ernzerhof generalized gradient approximation [GGA(PBE)], LDA + U and GGA(PBE) + U implementations of density functional theory. The dependence of selected observables of these materials on the effective U parameter has been investigated in detail. The examined properties include lattice constants, bulk moduli, the effect of charge density distributions, the hybridization of the 5f orbital and the energy of formation for PaO and PaO2. The LDA gives better agreement with experiment for the bulk modulus than the GGA for Pa but the GGA gives better structural properties. We found that PaO is metallic and PaO2 is a Mott-Hubbard insulator. This is consistent with observations for the other actinide oxides. We discover that GGA and LDA incorrectly give metallic behavior for PaO2. The GGA(PBE) + U calculated indirect band gap of 3.48 eV reported for PaO2 is a prediction and should stimulate further studies of this material.

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

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.

Modification of band gaps and optoelectronic properties of binary calcium chalcogenides by means of doping of magnesium atom(s) in rock-salt phase- a first principle based theoretical initiative

NASA Astrophysics Data System (ADS)

Debnath, Bimal; Sarkar, Utpal; Debbarma, Manish; Bhattacharjee, Rahul; Chattopadhyaya, Surya

2018-02-01

The band gaps and optoelectronic properties of binary calcium chalcogenide semiconductors have been modified theoretically by doping magnesium atom(s) into their respective rock-salt unit cells at some specific concentrations x = 0.0, 0.25, 0.50, 0.75 and 1.0 and confirmed such modifications by studying their structural, electronic and optical properties using DFT based FP-LAPW approach. The WC-GGA functional is used to calculate structural properties, while mBJ, B3LYP and WC-GGA are used for calculating electronic and optical properties. The concentration dependences of lattice parameter, bulk modulus and fundamental band gap for each alloy system exhibit nonlinearity. The atomic and orbital origin of different electronic states in the band structure of each compound are explored from its density of states (DOS). The microscopic origin of band gap bowing for each of the alloy systems is explored in terms of volume deformation, charge exchange and structural relaxation. The chemical bonds between the constituent atoms in each compound are found as ionic in nature. Optical properties of each specimen are calculated from its computed spectra of dielectric function, refractive index, extinction coefficient, normal incidence reflectivity, optical conductivity, optical absorption and energy loss function. Several calculated results have been compared with available experimental and other theoretical data.

High-temperature high-pressure properties of silica from Quantum Monte Carlo and Density Functional Perturbation Theory

NASA Astrophysics Data System (ADS)

Cohen, R. E.; Driver, K.; Wu, Z.; Militzer, B.; Rios, P. L.; Towler, M.; Needs, R.

2009-03-01

We have used diffusion quantum Monte Carlo (DMC) with the CASINO code with thermal free energies from phonons computed using density functional perturbation theory (DFPT) with the ABINIT code to obtain phase transition curves and thermal equations of state of silica phases under pressure. We obtain excellent agreement with experiments for the metastable phase transition from quartz to stishovite. The local density approximation (LDA) incorrectly gives stishovite as the ground state. The generalized gradient approximation (GGA) correctly gives quartz as the ground state, but does worse than LDA for the equations of state. DMC, variational quantum Monte Carlo (VMC), and DFT all give good results for the ferroelastic transition of stishovite to the CaCl2 structure, and LDA or the WC exchange correlation potentials give good results within a given silica phase. The δV and δH from the CaCl2 structure to α-PbO2 is small, giving uncertainly in the theoretical transition pressure. It is interesting that DFT has trouble with silica transitions, although the electronic structures of silica are insulating, simple closed-shell with ionic/covalent bonding. It seems like the errors in DFT are from not precisely giving the ion sizes.

Modified Fourth-Order Kinetic Energy Gradient Expansion with Hartree Potential-Dependent Coefficients.

PubMed

Constantin, Lucian A; Fabiano, Eduardo; Della Sala, Fabio

2017-09-12

Using the semiclassical neutral atom theory, we developed a modified fourth-order kinetic energy (KE) gradient expansion (GE4m) that keeps unchanged all the linear-response terms of the uniform electron gas and gives a significant improvement with respect to the known semilocal functionals for both large atoms and jellium surfaces. On the other hand, GE4m is not accurate for light atoms; thus, we modified the GE4m coefficients making them dependent on a novel ingredient, the reduced Hartree potential, recently introduced in the Journal of Chemical Physics 2016, 145, 084110, in the context of exchange functionals. The resulting KE gradient expansion functional, named uGE4m, belongs to the novel class of u-meta-generalized-gradient-approximations (uMGGA) whose members depend on the conventional ingredients (i.e., the reduced gradient and Laplacian of the density) as well as on the reduced Hartree potential. To test uGE4m, we defined an appropriate benchmark (including total KE and KE differences for atoms, molecules and jellium clusters) for gradient expansion functionals, that is, including only those systems which are mainly described by a slowly varying density regime. While most of the GGA and meta-GGA KE functionals (we tested 18 of them) are accurate for some properties and inaccurate for others, uGE4m shows a consistently good performance for all the properties considered. This represents a qualitative boost in the KE functional development and highlights the importance of the reduced Hartree potential for the construction of next-generation KE functionals.

Pressure induced elastic softening in framework aluminosilicate- albite (NaAlSi 3O 8)

DOE PAGES

Mookherjee, Mainak; Mainprice, David; Maheshwari, Ketan; ...

2016-10-13

Albite (NaAlSi 3O 8) is an aluminosilicate mineral. Its crystal structure consists of 3-D framework of Al and Si tetrahedral units. We have used Density Functional Theory to investigate the high-pressure behavior of the crystal structure and how it affects the elasticity of albite. Our results indicate elastic softening between 6–8 GPa. This is observed in all the individual elastic stiffness components. Our analysis indicates that the softening is due to the response of the three-dimensional tetrahedral framework, in particular by the pressure dependent changes in the tetrahedral tilts. At pressure <6 GPa, the PAW-GGA can be described by amore » Birch-Murnaghan equation of state with V GGA 0 = 687.4Å 3, K GGA 0 = 51.7 GPa, and G GGA 0 = 4.7. The shear modulus and its pressure derivative are K ⊕GGA 0 = 33.7 GPa, and G ⊕GGA 0 = 2.9. At 1 bar, the azimuthal compressional and shear wave anisotropy AV GGA P = 42.8%, and AV GGA S = 50.1%. We also investigate the densification of albite to a mixture of jadeite and quartz. The transformation is likely to cause a discontinuity in density, compressional, and shear wave velocity across the crust and mantle. Furthermore, this could partially account for the Mohorovicic discontinuity in thickened continental crustal regions.« less

First principles study of structural, electronic and optical properties of perovskites CaZrO3 and CaHfO3 in cubic phase

NASA Astrophysics Data System (ADS)

Hoat, D. M.; Silva, J. F. Rivas; Blas, A. Méndez

2018-07-01

In this work, we present the first principles calculations for structural, electronic and optical properties of perovskites CaZrO3 and CaHfO3 using the full-potential linearized augmented plane wave method (FP-LAPW) within the framework of density functional theory (DFT) as implemented in WIEN2k package. The exchange-correlation potential is treated with local density approximation (LDA) and generalized gradient approximation (GGA-PBE and PBESol). Additionally, the Tran Blaha modified Becke-Johnson exchange potential (mBJ) also is employed for electronic and optical calculations due to that it gives very accurate band gap of solids. Our obtained structural parameters are in good agreement with experimental datas and other theoretical results. The energy band gap obtained with mBJ is 4.56 eV for CaZrO3 and 5.27 eV for CaHfO3. The hybridization of states of O atom with those of Zr and Hf atoms in CaZrO3 and CaHfO3, respectively, is observed. The spin-orbit coupling effect on electronic properties of considered compounds also is investigated. Finally, the linear optical properties of CaZrO3 and CaHfO3 are derived from their complex dielectric function calculated with mBJ potential for wide energy range up to 45 eV, and all of them analyzed in details.

From the Kohn-Sham band gap to the fundamental gap in solids. An integer electron approach.

PubMed

Baerends, E J

2017-06-21

It is often stated that the Kohn-Sham occupied-unoccupied gap in both molecules and solids is "wrong". We argue that this is not a correct statement. The KS theory does not allow to interpret the exact KS HOMO-LUMO gap as the fundamental gap (difference (I - A) of electron affinity (A) and ionization energy (I), twice the chemical hardness), from which it indeed differs, strongly in molecules and moderately in solids. The exact Kohn-Sham HOMO-LUMO gap in molecules is much below the fundamental gap and very close to the much smaller optical gap (first excitation energy), and LDA/GGA yield very similar gaps. In solids the situation is different: the excitation energy to delocalized excited states and the fundamental gap (I - A) are very similar, not so disparate as in molecules. Again the Kohn-Sham and LDA/GGA band gaps do not represent (I - A) but are significantly smaller. However, the special properties of an extended system like a solid make it very easy to calculate the fundamental gap from the ground state (neutral system) band structure calculations entirely within a density functional framework. The correction Δ from the KS gap to the fundamental gap originates from the response part v resp of the exchange-correlation potential and can be calculated very simply using an approximation to v resp . This affords a calculation of the fundamental gap at the same level of accuracy as other properties of crystals at little extra cost beyond the ground state bandstructure calculation. The method is based on integer electron systems, fractional electron systems (an ensemble of N- and (N + 1)-electron systems) and the derivative discontinuity are not invoked.

Exploration of near the origin and the asymptotic behaviors of the Kohn-Sham kinetic energy density for two-dimensional quantum dot systems with parabolic confinement

NASA Astrophysics Data System (ADS)

Jana, Subrata; Samal, Prasanjit

2018-01-01

The behaviors of the positive definite Kohn-Sham kinetic energy density near the origin and at the asymptotic region play a major role in designing meta-generalized gradient approximations (meta-GGAs) for exchange in low-dimensional quantum systems. It is shown that near the origin of the parabolic quantum dot, the Kohn-Sham kinetic energy differs from its von Weizsäcker counterpart due to the p orbital contributions, whereas in the asymptotic region, the difference between the above two kinetic energy densities goes as ˜ρ/(r ) r2 . All these behaviors have been explored using the two-dimensional isotropic quantum harmonic oscillator as a test case. Several meta-GGA ingredients are then studied by making use of the above findings. Also, the asymptotic conditions for the exchange energy density and the potential at the meta-GGA level are proposed using the corresponding behaviors of the two kinetic energy densities.

Exploration of near the origin and the asymptotic behaviors of the Kohn-Sham kinetic energy density for two-dimensional quantum dot systems with parabolic confinement.

PubMed

Jana, Subrata; Samal, Prasanjit

2018-01-14

The behaviors of the positive definite Kohn-Sham kinetic energy density near the origin and at the asymptotic region play a major role in designing meta-generalized gradient approximations (meta-GGAs) for exchange in low-dimensional quantum systems. It is shown that near the origin of the parabolic quantum dot, the Kohn-Sham kinetic energy differs from its von Weizsäcker counterpart due to the p orbital contributions, whereas in the asymptotic region, the difference between the above two kinetic energy densities goes as ∼ρ(r)r 2 . All these behaviors have been explored using the two-dimensional isotropic quantum harmonic oscillator as a test case. Several meta-GGA ingredients are then studied by making use of the above findings. Also, the asymptotic conditions for the exchange energy density and the potential at the meta-GGA level are proposed using the corresponding behaviors of the two kinetic energy densities.

GGA3 Functions as a Switch to Promote Met Receptor Recycling, Essential for Sustained ERK and Cell Migration

PubMed Central

Parachoniak, Christine Anna; Luo, Yi; Abella, Jasmine Vanessa; Keen, James H.; Park, Morag

2011-01-01

Summary Cells are dependent on correct sorting of activated receptor tyrosine kinases (RTKs) for the outcome of growth factor signaling. Upon activation, RTKs are coupled through the endocytic machinery for degradation, or recycled to the cell surface. However, the molecular mechanisms governing RTK recycling are poorly understood. Here, we show that Golgi-localized gamma-ear containing Arf-binding protein 3 (GGA3) interacts selectively with the Met/Hepatocyte Growth Factor RTK when stimulated, to sort it for recycling in association with “gyrating”-clathrin. GGA3 loss abrogates Met recycling from a Rab4 endosomal subdomain, resulting in pronounced trafficking of Met towards degradation. Decreased Met recycling attenuates ERK activation and cell migration. Met recycling, sustained ERK activation and migration require interaction of GGA3 with Arf6 and an unexpected association with the Crk adaptor. The data show that GGA3 defines an active recycling pathway and support a broader role for GGA3-mediated cargo selection in targeting receptors destined for recycling. PMID:21664574

Theoretical and experimental investigations of optical, structural and electronic properties of the lower-dimensional hybrid [NH3-(CH2)10-NH3]ZnCl4

NASA Astrophysics Data System (ADS)

El Mrabet, R.; Kassou, S.; Tahiri, O.; Belaaraj, A.; Guionneau, P.

2016-10-01

In the current study, a combination between theoretical and experimental studies has been made for the hybrid perovskite [NH3-(CH2)10-NH3]ZnCl4. The density functional theory (DFT) was performed to investigate structural and electronic properties of the tilted compound. A local approximation (LDA) and semi-local approach (GGA) were employed. The results are obtained using, respectively, the local exchange correlation functional of Perdew-Wang 92 (PW92) and semi local functional of Perdew-Burke-Ernzerhof (PBE). The optimized cell parameters are in good agreement with the experimental results. Electronic properties have been studied through the calculation of band structures and density of state (DOS), while structural properties are investigated by geometry optimization of the cell. Fritz-Haber-Institute (FHI) pseudopotentials were employed to perform all calculations. The optical diffuse reflectance spectra was mesured and applied to deduce the refractive index ( n), the extinction coefficient ( k), the absorption coefficient (α), the real and imaginary dielectric permittivity parts (ɛr,ɛi)) and the optical band gap energy Eg. The optical band gap energy value shows good consistent with that obtained from DFT calculations and reveals the insulating behavior of the material.

Insight into the structural, electronic, elastic and optical properties of the alkali hydride compounds, XH (X = Rb and Cs)

NASA Astrophysics Data System (ADS)

Jaradat, Raed; Abu-Jafar, Mohammed; Abdelraziq, Issam; Mousa, Ahmad; Ouahrani, Tarik; Khenata, Rabah

2018-04-01

The equilibrium structural parameters, electronic and optical properties of the alkali hydrides RbH and CsH compounds in rock-salt (RS) and cesium chloride (CsCl) structures have been studied using the full-potential linearized augmented plane-wave (FP-LAPW) method. Wu and Cohen generalized gradient approximation (WC-GGA) was used for the exchange-correlation potential to compute the equilibrium structural parameters, such as the lattice constant (a0), the bulk modulus (B) and bulk modulus first order pressure derivative (B'). In addition to the WC-GGA, the modified Becke Johnson (mBJ) scheme has been also used to overcome the underestimation of the band gap energies. RbH and CsH compounds are found to be semiconductors (wide energy-band gap) using the WC-GGA method, while they are insulators using the mBJ-GGA method. Elastic constants, mechanical and thermodynamic properties were obtained by using the IRelast package. RbH and CsH compounds at ambient pressure are mechanically stable in RS and CsCl structures; they satisfy the Born mechanical stability criteria. Elastic constants (Cij), bulk modulus (B), shear modulus (S) and Debye temperatures (θD) of RbH and CsH compounds decrease as the alkali radius increases. The RS structure of these compounds at ambient conditions is mechanically stronger than CsCl structure. RbH and CsH in RS and CsCl structures are suitable as dielectric compounds. The wide direct energy band gap for these compounds make them promising compounds for optoelectronic UV device applications. Both RbH and CsH have a wide absorption region, on the other hand RbH absorption is very huge compared to the CsH absorption, RbH is an excellent absorbent material, maximum absorption regions are located in the middle ultraviolet (MUV) region and far ultraviolet (FUV) region. The absorption coefficient α (w), imaginary part of the dielectric constant ɛ2(w) and the extinction coefficient k(w) vary in the same way. The present calculated results are in good agreement with the experimental data, indicating the high accuracy of the performed calculations and reliability of the obtained results.

Electron-phonon coupling and superconductivity in MgB2 under hydrostatic pressure.

NASA Astrophysics Data System (ADS)

Quijano, Ramiro; Aguayo, Aaron

2005-03-01

We have studied the dynamics and coupling of the E2g phonon mode with the σ-band in MgB2 under pressure using the Frozen Phonon Approximation. The results were obtained by means of first-principles total-energy calculations using the full potential Linearized Augmented Plane Wave (LAPW) method and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We present results for the evolution of the anharmonicity and phonon frequency of the E2g mode, the electron-phonon coupling constant, and Tc as a function of hydrostatic pressure in the range 0-40 GPa. We find that the phonon frequency increases monotonically with pressure, but the the anharmonicity, the electron-phonon coupling and Tc decreases with pressure. We have obtained a very good agreement between the calculated Tc(P) and the experimental data available in the literature, in particular with the experimental data corresponding to monocystalline samples. This work was supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant No. 43830-F.

First principles study of NH3 adsorption on carbon nanowires

NASA Astrophysics Data System (ADS)

Tapia, Jorge-Alejandro; Sanchez, Alvaro-Daniel; Acosta, Cesar; Canto, Gabriel

2009-03-01

Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. Theoretical and experimental studies of the NH3 adsorption in the carbon nanotubes report changes in the electronic properties of the carbon nanotubes. In the present work we have studied the electronic and structure properties of carbon nanowires (chain@SWCNT) when NH3 atoms are adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure and density of states (DOS). We found that the electronic character of the carbon chain of the chain@SWCNT system, can be modulate by NH3 adsorption. This research was supported by SEP under Grant No. PROMEP/103.5/07/2595 and the Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 82497 and 60534.

Influence of xc functional on thermal-elastic properties of Ceria: A DFT-based Debye-Grüneisen model approach

NASA Astrophysics Data System (ADS)

Lee, Ji-Hwan; Tak, Youngjoo; Lee, Taehun; Soon, Aloysius

Ceria (CeO2-x) is widely studied as a choice electrolyte material for intermediate-temperature (~ 800 K) solid oxide fuel cells. At this temperature, maintaining its chemical stability and thermal-mechanical integrity of this oxide are of utmost importance. To understand their thermal-elastic properties, we firstly test the influence of various approximations to the density-functional theory (DFT) xc functionals on specific thermal-elastic properties of both CeO2 and Ce2O3. Namely, we consider the local-density approximation (LDA), the generalized gradient approximation (GGA-PBE) with and without additional Hubbard U as applied to the 4 f electron of Ce, as well as the recently popularized hybrid functional due to Heyd-Scuseria-Ernzehof (HSE06). Next, we then couple this to a volume-dependent Debye-Grüneisen model to determine the thermodynamic quantities of ceria at arbitrary temperatures. We find an explicit description of the strong correlation (e.g. via the DFT + U and hybrid functional approach) is necessary to have a good agreement with experimental values, in contrast to the mean-field treatment in standard xc approximations (such as LDA or GGA-PBE). We acknowledge support from Samsung Research Funding Center of Samsung Electronics (SRFC-MA1501-03).

Visualisation and orbital-free parametrisation of the large-Z scaling of the kinetic energy density of atoms

NASA Astrophysics Data System (ADS)

Cancio, Antonio C.; Redd, Jeremy J.

2017-03-01

The scaling of neutral atoms to large Z, combining periodicity with a gradual trend to homogeneity, is a fundamental probe of density functional theory, one that has driven recent advances in understanding both the kinetic and exchange-correlation energies. Although research focus is normally upon the scaling of integrated energies, insights can also be gained from energy densities. We visualise the scaling of the positive-definite kinetic energy density (KED) in closed-shell atoms, in comparison to invariant quantities based upon the gradient and Laplacian of the density. We notice a striking fit of the KED within the core of any atom to a gradient expansion using both the gradient and the Laplacian, appearing as an asymptotic limit around which the KED oscillates. The gradient expansion is qualitatively different from that derived from first principles for a slowly varying electron gas and is correlated with a nonzero Pauli contribution to the KED near the nucleus. We propose and explore orbital-free meta-GGA models for the kinetic energy to describe these features, with some success, but the effects of quantum oscillations in the inner shells of atoms make a complete parametrisation difficult. We discuss implications for improved orbital-free description of molecular properties.

GGA3 mediates TrkA endocytic recycling to promote sustained Akt phosphorylation and cell survival

PubMed Central

Li, Xuezhi; Lavigne, Pierre; Lavoie, Christine

2015-01-01

Although TrkA postendocytic sorting significantly influences neuronal cell survival and differentiation, the molecular mechanism underlying TrkA receptor sorting in the recycling or degradation pathways remains poorly understood. Here we demonstrate that Golgi-localized, γ adaptin-ear–containing ADP ribosylation factor-binding protein 3 (GGA3) interacts directly with the TrkA cytoplasmic tail through an internal DXXLL motif and mediates the functional recycling of TrkA to the plasma membrane. We find that GGA3 depletion by siRNA delays TrkA recycling, accelerates TrkA degradation, attenuates sustained NGF-induced Akt activation, and reduces cell survival. We also show that GGA3’s effect on TrkA recycling is dependent on the activation of Arf6. This work identifies GGA3 as a key player in a novel DXXLL-mediated endosomal sorting machinery that targets TrkA to the plasma membrane, where it prolongs the activation of Akt signaling and survival responses. PMID:26446845

Electronic and optical properties of graphene-like InAs: An ab initio study

NASA Astrophysics Data System (ADS)

Sohrabi, Leila; Boochani, Arash; Ali Sebt, S.; Mohammad Elahi, S.

2018-03-01

The present work initially investigates structural, optical, and electronic properties of graphene-like InAs by using the full potential linear augmented plane wave method in the framework of density functional theory and is then compared with the bulk Indium Arsenide in the wurtzite phase. The lattice parameters are optimized with GGA-PBE and LDA approximations for both 2D- and 3D-InAs. In order to study the electronic properties of graphene-like InAs and bulk InAs in the wurtzite phase, the band gap is calculated by GGA-PBG and GGA-EV approximations. Moreover, optical parameters of graphene-like InAs and bulk InAs such as the real and imaginary parts of dielectric function, electron energy loss function, refractivity, extinction and absorption coefficients, and optical conductivity are investigated. Plasmonic frequencies of 2D- and 3D-InAs are also calculated by using maximum electron energy loss function and the roots of the real part of the dielectric function.

Theoretical and experimental studies on wide-band-gap p-type conductive BaCuSeF and related compounds

NASA Astrophysics Data System (ADS)

Sakakima, Hiroshi; Nishitani, Mikihiko; Yamamoto, Koichi; Wada, Takahiro

2015-08-01

BaCuSeF and related compounds, MCuQF (M = Ba, Sr; Q = Se, S), are known to show p-type conduction. The formation energies of the Cu vacancy ΔH[VCu] in a MCuQF system were computed by first-principles calculation with a generalized gradient approximation (GGA) of the Perdew-Burke-Ernzerhof (PBE) functional as an electron exchange and correlation functional. The density of states (DOS) of BaCuSeF was calculated with the hybrid functional of Heyd-Scuseria-Ernzerhof (HSE) 06. ΔH[VCu] was found to be very small under both the Cu- and Q-rich conditions, which probably contributes to p-type conduction. The electronic structure of BaCuSeF was studied by X-ray photoelectron spectroscopy (XPS) with UV photoelectron yield spectroscopy (UVPYS) and photoemission yield spectroscopy (PYS). The determined depth of the top of the valence band relative to the vacuum level was about 4.9 eV. This value is desirable for applications in compound semiconductor thin-film tandem solar cells since the absorbers of polycrystalline thin-film solar cells, such as CdTe and Cu(In,Ga)Se2, are p-type semiconductors. The DOS of BaCuSeF calculated with the HSE06 functional was almost consistent with the XPS spectrum.

First-principles investigations on structural, elastic and mechanical properties of BNxAs1‑x ternary alloys

NASA Astrophysics Data System (ADS)

Zhang, Junqin; Ma, Huihui; Zhao, Bin; Wei, Qun; Yang, Yintang

2018-05-01

A systematic investigation of the structural optimization, elastic and mechanical properties of the BNxAs1‑x ternary alloys are reported in the present work using the density-functional theory with the generalized gradient approximation (GGA) of the exchange-correlation functional. Some of the constants which are used to analyze the properties including elastic constants and modulus, and some parameters describing the elastic anisotropy and Debye temperature are also calculated. Our calculations were performed to evaluate the equilibrium lattice constant and band structure compared with the available theoretical works. On the one hand, our results might be expected to provide a theoretical basis for future study of BNxAs1‑x alloys towards elastic or mechanical properties. On the other hand, we draw a conclusion that BNxAs1‑x alloys show direct bandgap when x equals 0.25, 0.5 or 0.75. We obtained the elastic modulus, Poisson’s ratio and universal anisotropic index which are used to demonstrate the elastic anisotropy of these alloys which is proved according to our calculations. Also, we calculated the Debye temperature to illustrate covalent interactions and obtained the lower limit of the thermal conductivity for further research.

Electron Transfer Mechanism in Gold Surface Modified with Self-Assembly Monolayers from First Principles

NASA Astrophysics Data System (ADS)

Lima, Filipe C. D. A.; Iost, Rodrigo M.; Crespilho, Frank N.; Caldas, Marília J.; Calzolari, Arrigo; Petrilli, Helena M.

2013-03-01

We report the investigation of electron tunneling mechanism of peptide ferrocenyl-glycylcystamine self-assembled monolayers (SAMs) onto Au (111) electrode surfaces. Recent experimental investigations showed that electron transfer in peptides can occur across long distances by separating the donor from the acceptor. This mechanism can be further fostered by the presence of electron donor terminations of Fc terminal units on SAMs but the charge transfer mechanism is still not clear. We study the interaction of the peptide ferrocenyl-glycylcystamine on the Au (111) from first principles calculations to evaluate the electron transfer mechanism. For this purpose, we used the Kohn Sham (KS) scheme for the Density Functional Theory (DFT) as implemented in the Quantum-ESPRESSO suit of codes, using Vandebilt ultrasoft pseudopotentials and GGA-PBE exchange correlation functional to evaluate the ground-state atomic and electronic structure of the system. The analysis of KS orbital at the Fermi Energy showed high electronic density localized in Fc molecules and the observation of a minor contribution from the solvent and counter ion. Based on the results, we infer evidences of electron tunneling mechanism from the molecule to the Au(111). We acknowledge FAPESP for grant support. Also, LCCA/USP, RICE and CENAPAD for computational resources.

Investigating the Energetic Ordering of Stable and Metastable TiO 2 Polymorphs Using DFT+ U and Hybrid Functionals

DOE PAGES

Curnan, Matthew T.; Kitchin, John R.

2015-08-12

Prediction of transition metal oxide BO 2 (B = Ti, V, etc.) polymorph energetic properties is critical to tunable material design and identifying thermodynamically accessible structures. Determining procedures capable of synthesizing particular polymorphs minimally requires prior knowledge of their relative energetic favorability. Information concerning TiO 2 polymorph relative energetic favorability has been ascertained from experimental research. In this study, the consistency of first-principles predictions and experimental results involving the relative energetic ordering of stable (rutile), metastable (anatase and brookite), and unstable (columbite) TiO 2 polymorphs is assessed via density functional theory (DFT). Considering the issues involving electron–electron interaction and chargemore » delocalization in TiO 2 calculations, relative energetic ordering predictions are evaluated over trends varying Ti Hubbard U 3d or exact exchange fraction parameter values. Energetic trends formed from varying U 3d predict experimentally consistent energetic ordering over U 3d intervals when using GGA-based functionals, regardless of pseudopotential selection. Given pertinent linear response calculated Hubbard U values, these results enable TiO 2 polymorph energetic ordering prediction. Here, the hybrid functional calculations involving rutile–anatase relative energetics, though demonstrating experimentally consistent energetic ordering over exact exchange fraction ranges, are not accompanied by predicted fractions, for a first-principles methodology capable of calculating exact exchange fractions precisely predicting TiO 2 polymorph energetic ordering is not available.« less

Exchange coupling transformations in Cu (II) heterospin complexes of “breathing crystals” under structural phase transitions

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

Morozov, Vitaly A.; Petrova, Marina V.; Lukzen, Nikita N., E-mail: luk@tomo.nsc.ru

2015-08-15

Family of “breathing crystals” is the polymer-chain complexes of Cu(hfac){sub 2} with nitroxides. The polymer chains consist of one-, two- or three-spin clusters. The “breathing crystals” experience simultaneous magnetic and Jahn-Teller type structural phase transitions with change of total cluster spin and drastic change of bond lengths (ca. 10-12%). For the first time the intra-cluster magnetic couplings in ”breathing crystals” have been calculated both by band structure methods GGA + U and hybrid DFT (B3LYP and PBE0) for the isolated exchange clusters. The temperature dependence of the magnetic coupling constant was calculated for two polymer-chain compounds of the “breathing crystal”more » family - C{sub 21}H{sub 19}CuF{sub 12}N{sub 4}O{sub 6} with the chains containing two-spin clusters and C{sub 22}H{sub 21}CuF{sub 12}N{sub 4}O{sub 6} with the chains of alternating three-spin clusters and one-spin sites. It was found that adding a Hubbard-like parameter not only to the copper 3d electrons but also to the oxygen 2p electrons (GGA + U{sub d} + U{sub p} approach) results in an improved description of exchange coupling in the “breathing crystal” compounds. At the same time treatment of the isolated clusters by a large basis hybrid DFT with high computational cost provides a similar quality fit of the experimental magneto-chemical data as that for the GGA + U{sub d} + U{sub p} band structure calculation scheme. Our calculations also showed that in spite of the abrupt transformation of the magnetic coupling constant under the phase transition, the band gap in the “breathing crystals” remains about the same value with temperature decrease.« less

Robust diamond-like Fe-Si network in the zero-strain Na xFeSiO 4 cathode

DOE PAGES

Ye, Zhuo; Zhao, Xin; Li, Shouding; ...

2016-07-14

Sodium orthosilicates Na 2 MSiO 4 ( M denotes transition metals) have attracted much attention due to the possibility of exchanging two electrons per formula unit. In this work, we report a group of sodium iron orthosilicates Na 2FeSiO 4. Their crystal structures are characterized by a diamond-like Fe-Si network. The Fe-Si network is quite robust against the charge/discharge process, which explains the high structural stability observed in experiment. Furthermore, using the density functional theory within the GGA + U framework and X-ray diffraction studies, the crystal structures and structural stabilities during the sodium extraction/re-insertion process are systematically investigated.

Which Density Functional Should Be Used to Describe Protonated Water Clusters?

PubMed

Shi, Ruili; Huang, Xiaoming; Su, Yan; Lu, Hai-Gang; Li, Si-Dian; Tang, Lingli; Zhao, Jijun

2017-04-27

Protonated water cluster is one of the most important hydrogen-bond network systems. Finding an appropriate DFT method to study the properties of protonated water clusters can substantially improve the economy in computational resources without sacrificing the accuracy compared to high-level methods. Using high-level MP2 and CCSD(T) methods as well as experimental results as benchmark, we systematically examined the effect of seven exchange-correlation GGA functionals (with BLYP, B3LYP, X3LYP, PBE0, PBE1W, M05-2X, and B97-D parametrizations) in describing the geometric parameters, interaction energies, dipole moments, and vibrational properties of protonated water clusters H + (H 2 O) 2-9,12 . The overall performance of all these functionals is acceptable, and each of them has its advantage in certain aspects. X3LYP is the best to describe the interaction energies, and PBE0 and M05-2X are also recommended to investigate interaction energies. PBE0 gives the best anharmonic frequencies, followed by PBE1W, B97-D and BLYP methods. PBE1W, B3LYP, B97-D, and X3LYP can yield better geometries. The capability of B97-D to distinguish the relative energies between isomers is the best among all the seven methods, followed by M05-2X and PBE0.

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

Ruiz Pestana, Luis; Mardirossian, Narbe; Head-Gordon, Martin

We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm –3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreementmore » with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.« less

BACE1 elevation engendered by GGA3 deletion increases β-amyloid pathology in association with APP elevation and decreased CHL1 processing in 5XFAD mice.

PubMed

Kim, WonHee; Ma, Liang; Lomoio, Selene; Willen, Rachel; Lombardo, Sylvia; Dong, Jinghui; Haydon, Philip G; Tesco, Giuseppina

2018-02-02

β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is the rate-limiting enzyme in the production of amyloid beta (Aβ), the toxic peptide that accumulates in the brains of Alzheimer's disease (AD) patients. Our previous studies have shown that the clathrin adaptor Golgi-localized γ-ear-containing ARF binding protein 3 (GGA3) plays a key role in the trafficking of BACE1 to lysosomes, where it is normally degraded. GGA3 depletion results in BACE1 stabilization both in vitro and in vivo. Moreover, levels of GGA3 are reduced and inversely related to BACE1 levels in post-mortem brains of AD patients. In order to assess the effect of GGA3 deletion on AD-like phenotypes, we crossed GGA3 -/- mice with 5XFAD mice. BACE1-mediated processing of APP and the cell adhesion molecule L1 like protein (CHL1) was measured as well as levels of Aβ42 and amyloid burden. In 5XFAD mice, we found that hippocampal and cortical levels of GGA3 decreased while BACE1 levels increased with age, similar to what is observed in human AD brains. GGA3 deletion prevented age-dependent elevation of BACE1 in GGA3KO;5XFAD mice. We also found that GGA3 deletion resulted in increased hippocampal levels of Aβ42 and amyloid burden in 5XFAD mice at 12 months of age. While levels of BACE1 did not change with age and gender in GGAKO;5XFAD mice, amyloid precursor protein (APP) levels increased with age and were higher in female mice. Moreover, elevation of APP was associated with a decreased BACE1-mediated processing of CHL1 not only in 12 months old 5XFAD mice but also in human brains from subjects affected by Down syndrome, most likely due to substrate competition. This study demonstrates that GGA3 depletion is a leading candidate mechanism underlying elevation of BACE1 in AD. Furthermore, our findings suggest that BACE1 inhibition could exacerbate mechanism-based side effects in conditions associated with APP elevation (e.g. Down syndrome) owing to impairment of BACE1-mediated processing of CHL1. Therefore, therapeutic approaches aimed to restore GGA3 function and to prevent the down stream effects of its depletion (e.g. BACE1 elevation) represent an attractive alternative to BACE inhibition for the prevention/treatment of AD.

First-principles study of the electronic properties and discharge profile of AgNa(VO2F2)2

NASA Astrophysics Data System (ADS)

Onoue, Masatoshi; Trimarchi, Giancarlo; Freeman, Arthur J.

2014-03-01

Implantable cardiac defibrillators (ICDs) require batteries with high capacities and high discharge rates to ensure the optimal operation of the device over several years. Ag2V4O11 has been a cathode material of choice for the ICDs owing to its high capacity and fast rate of electronic discharge. To reduce ICD size and improve ICD performance, a new cathode material would need to display a higher volumetric capacity and redox potential. Recently, the new cathode compound AgNa(VO2F2)2 (SSVOF) was synthesized and displayed favorable voltage for sodium-ion batteries. However, the discharge reaction has been unclear. In this presentation, we study the discharge reaction of SSVOF through DFT calculations. All calculations are performed within the PAW method using the GGA and GGA + U functionals. Among several possible reactions, we focus on the reaction Ag X + A --> AX + Ag, where X is Na(VO2F2)2 and A is Li or Na. In this reaction, the discharge occurs by replacing Ag with A. The calculated discharge potential for Li is 3.3 V in GGA and 2.9 V in GGA + U and that for Na is 3.1 V in GGA and 2.8 V in GGA + U . These values are consistent with the experimental ones. Supported by the DOE ER46536 Program.

Improved half-metallic gap of zincblende half-metal superlattices with the Tran-Blaha modified Becke-Johnson density functional

NASA Astrophysics Data System (ADS)

Guo, San-Dong

2016-08-01

Binary transition-metal pnictides and chalcogenides half-metallic ferromagnetic materials with zincblende structure, being compatible with current semiconductor technology, can be used to make high-performance spintronic devices. Here, we investigate electronic structures and magnetic properties of composite structure ((CrX)2 /(YX)2 (X=As, Sb; Se, Te and Y=Ga; Zn) superlattices) of zincblende half-metallic ferromagnetism and semiconductor by using Tran and Blaha's modified Becke and Johnson (mBJ) exchange potential. Calculated results show that they all are half-metallic ferromagnets with both generalized gradient approximation (GGA) and mBJ, and the total magnetic moment per formula unit follows a Slater-Pauling-like "rule of 8". The key half-metallic gaps by using mBJ are enhanced with respect to GGA results, which is because mBJ makes the occupied minority-spin p-bands move toward lower energy, but toward higher energy for empty minority-spin Cr-d bands. When the spin-orbit coupling (SOC) is included, the spin polarization deviates from 100%, and a most reduced polarization of 98.3% for (CrSb)2 /(GaSb)2, which indicates that SOC has small effects, of the order of 1%, in the considered four kinds of superlattice.

Effect of the electric field on buckled and puckered arsenene

NASA Astrophysics Data System (ADS)

Chavez, Victor Hugo; Fernandez-Escamilla, Hector Noe; Martínez-Guerra, Edgar

With the emergence of new 2D materials, more recently phosphorene, arsenene appears as a new candidate to be explored for electronic devices. We have studied the stability of arsenene pristine and the effect of a transversal electric field on its electronic properties. The calculations were performed using the SIESTA code, with the GGA exchange-correlation functional in the PBE form. We have used numerical atomic orbitals as the basis set for the valence wavefunctions employing a double ζ-polarized basis. We use the Perdew-Becke pseudopotential for an As atom that includes the scalar-relativistic effect and Troullier-Martins parametrization. We adopt the Monkhorst-Pack scheme for k-point sampling of Brillouin zone integrations with 25 ×25 ×1 and 25 ×25 ×1 for the buckled/planar and puckered systems, respectively. We found that buckled and puckered arsenenes are stable and posses indirect gap. The effect of the electric field on the electronic structure of the buckled arsenene is the modulation of indirect to direct gap, while in puckered arsenene the gap linearly decreases as electric field is increased. This research was supported by Consejo Nacional de Ciencia y Tecnología (Conacyt) under Grant No. 43830-F.

Ab initio study of boron nitride lines on graphene

NASA Astrophysics Data System (ADS)

Mata-Carrizal, Berenice; Sanginés-Mendoza, Raúl; Martinez, Edgar

2013-03-01

Graphene has unusual electronic properties which make it a promising material for electronic devices. Neverthless, the absence of a band gap sets limitations on its practical applications. Thus, it is crucial to find methods to create and tune the band gap of systems based on graphene. In this way, we explore the modulation of the electronic properties of graphene through doping with boron nitride lines. In particular, we studied the electronic structure of graphene sheets doped with boron nitride lines armchair and zigzag type. The calculations were performed using the pseudopotential LCAO method with a Generalized Gradient Approximation (GGA) for the exchange-correlation energy functional. We found that both doping lines type induce a bandgap and that the energy gap increases as the length of doping lines increases. Accordingly to our DFT calculations, we found that the energy gap on graphene doped with armchair and zigzag lines is due to a two different mechanisms to drain charge from pi- to sigma- orbitals. Thus, we found that doping graphene with boron nitride lines is a useful way to induce and modulate the bandgap on graphene. This research was supported by Consejo Nacional de Ciencia y Tecnología (Conacyt) under Grant No. 133022.

First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

PubMed

Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

2015-02-01

Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.

First principles study of hydrogen adsorption on carbon nanowires.

NASA Astrophysics Data System (ADS)

Tapia, Alejandro; Aguilera, Luis; Murrieta, Gabriel; de Coss, Romeo

2007-03-01

Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. In the present work we have studied the changes in the electronic structure of a carbon nanowires and (5,5) single-walled carbon nanotubes (SWCN) when a hydrogen atom is adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure, density of states (LDOS), and the local orbital population. We found charge transfer from the nanotube to the linear chain and the hydrogen atom, the electronic character of the chain and nanotube sub-systems in chain@SWCN is the same that in the corresponding isolated systems, chain or SWCN. But the hydrogen adsorption produced changes in the atomic estructure and the electronic properties. This research was supported by PRIORI-UADY under Grant No. FING-05-004 and Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 43830-F and 49985-J.

Role of dispersion corrected hybrid GGA class in accurately calculating the bond dissociation energy of carbon halogen bond: A benchmark study

NASA Astrophysics Data System (ADS)

Kosar, Naveen; Mahmood, Tariq; Ayub, Khurshid

2017-12-01

Benchmark study has been carried out to find a cost effective and accurate method for bond dissociation energy (BDE) of carbon halogen (Csbnd X) bond. BDE of C-X bond plays a vital role in chemical reactions, particularly for kinetic barrier and thermochemistry etc. The compounds (1-16, Fig. 1) with Csbnd X bond used for current benchmark study are important reactants in organic, inorganic and bioorganic chemistry. Experimental data of Csbnd X bond dissociation energy is compared with theoretical results. The statistical analysis tools such as root mean square deviation (RMSD), standard deviation (SD), Pearson's correlation (R) and mean absolute error (MAE) are used for comparison. Overall, thirty-one density functionals from eight different classes of density functional theory (DFT) along with Pople and Dunning basis sets are evaluated. Among different classes of DFT, the dispersion corrected range separated hybrid GGA class along with 6-31G(d), 6-311G(d), aug-cc-pVDZ and aug-cc-pVTZ basis sets performed best for bond dissociation energy calculation of C-X bond. ωB97XD show the best performance with less deviations (RMSD, SD), mean absolute error (MAE) and a significant Pearson's correlation (R) when compared to experimental data. ωB97XD along with Pople basis set 6-311g(d) has RMSD, SD, R and MAE of 3.14 kcal mol-1, 3.05 kcal mol-1, 0.97 and -1.07 kcal mol-1, respectively.

Magnetic properties and stability of Cu3V2O8 compound in the different phases

NASA Astrophysics Data System (ADS)

Jezierski, Andrzej

2016-11-01

The magnetic and thermodynamic properties of Cu3V2O8 compound in four structures (P-1, P21/c, P21/m and Cmca) are reported. The calculations are performed by using the Full-Potential Local Orbital Minimum Basis (FPLO) and Vienna ab initio Simulation Package (VASP) methods. We have applied the local density approximation (LDA) with the generalized gradient corrections (GGA). The effect of electron correlations was also included in GGA+U approximation. The thermodynamic properties were obtained in the quasi-harmonic Debye-Grüneisen model using the equation of states (EOS) in the form of Poirier-Tarantola. Our ab-intio results indicate that α (P-1) phase is stable below 1.87 GPa, β (P21/c) exists in the region 1.87

Electronic and optical properties of GaN under pressure: DFT calculations

NASA Astrophysics Data System (ADS)

Javaheri, Sahar; Boochani, Arash; Babaeipour, Manuchehr; Naderi, Sirvan

2017-12-01

Optical and electronic properties of ZB, RS and WZ structures of gallium nitride (GaN) are studied in equilibrium and under pressure using the first-principles calculation in the density functional theory (DFT) framework to obtain quantities like dielectric function, loss function, reflectance and absorption spectra, refractive index and their relation parameters. The electronic properties are studied using EV-GGA and GGA approximations and the results calculated by EV-GGA approximation were found to be much closer to the experimental results. The interband electron transitions are studied using the band structure and electron transition peaks in the imaginary part of the dielectric function; these transitions occur in three structures from N-2p orbital to Ga-4s and Ga-4p orbitals in the conduction band. Different optical properties of WZ structure were calculated in two polarization directions of (100) and (001) and the results were close to each other. Plasmon energy corresponding to the main peak of the energy-loss function in RS with the value of 26 eV was the highest one, which increased under pressure. In general, RS shows more different properties than WZ and ZB.

E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

PubMed

Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias

2008-06-01

We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

Electronic structure of ferromagnetic semiconductor material on the monoclinic and rhombohedral ordered double perovskites La{sub 2}FeCoO{sub 6}

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

Fuh, Huei-Ru; Chang, Ching-Ray; Graduate Institute of Applied Physics, National Taiwan University, Taipei 106, Taiwan

2015-05-07

Double perovskite La{sub 2}FeCoO{sub 6} with monoclinic structure and rhombohedra structure show as ferromagnetic semiconductor based on density functional theory calculation. The ferromagnetic semiconductor state can be well explained by the superexchange interaction. Moreover, the ferromagnetic semiconductor state remains under the generalized gradient approximation (GGA) and GGA plus onsite Coulomb interaction calculation.

Vibrational mode frequencies of H2S and H2O adsorbed on Ge(0 0 1)-(2 × 1) surfaces

NASA Astrophysics Data System (ADS)

Hartnett, M.; Fahy, S.

2015-02-01

The equilibrium geometry and vibrational modes of H2S and H2O-terminated Ge(0 0 1)-(2 × 1) surfaces are calculated in a supercell approach using first-principles density functional theory in the local density (LDA), generalized gradient (GGA) approximations and van der Waals (vdW) interactions. Mode frequencies are found using the frozen phonon method. For the H2S-passivated surface, the calculated frequencies in LDA (GGA) are 2429 cm-1 (2490) for the Hsbnd S stretch mode, 712 cm-1 (706) for the Hsbnd S bond bending mode, 377 cm-1 (36) for the Gesbnd S stretch mode and 328 cm-1 (337) for Hsbnd S wag mode. Frequencies for the H2O passivated surface are 3590 cm-1 (3600) for the Hsbnd O stretch mode, 921 cm-1 (947) for the bending mode, 609 cm-1 (559) for the Gesbnd O stretch, 1995 cm-1 (1991) for the Gesbnd H stretch mode, 498 cm-1 (478) for the Gesbnd H bending mode and 342 cm-1 (336) for the Hsbnd O wag mode. The differences between the functionals including vdW terms and the LDA or GGA are less than the differences between LDA and GGA for the vibrational mode frequencies.

Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

2016-04-01

Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

First principles study on structural, electronic and optical properties of Ga1-xBxP ternary alloys (x = 0, 0.25, 0.5, 0.75 and 1)

NASA Astrophysics Data System (ADS)

Hoat, D. M.; Rivas Silva, J. F.; Méndez Blas, A.

2018-07-01

The structural, electronic and optical properties of GaP, BP binary compounds and their ternary alloys Ga1-xBxP (x = 0.25, 0.5 and 0.75) have been studied by full-potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory (DFT) as implemented in WIEN2k package. Local density approximation (LDA) and generalized gradient approximation (GGA) as proposed by Perdew-Burke-Ernzerhof (PBE), Wu-Cohen (WC) and PBE for solid (PBESol) were used for treatment of exchange-correlation effect in calculations. Additionally, the Tran-Blaha modified Becke-Johnson (mBJ) potential was also employed for electronic and optical calculations due to that it gives very accurate band gap of solids. As B concentration increases, the lattice constant reduces and the energy band gap firstly decreases for small composition x and then it shows increasing trend until pure BP. Our results show that the indirect-direct band gap transition can be reached from x = 0.33. The linear optical properties, such as reflectivity, absorption coefficient, refractive index and optical conductivity of binary compounds and ternary alloys were derived from their calculated complex dielectric function in wide energy range up to 30 eV, and the alloying effect on these properties was also analyzed in detail.

Sensitivity of the Properties of Ruthenium “Blue Dimer” to Method, Basis Set, and Continuum Model

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

Ozkanlar, Abdullah; Clark, Aurora E.

2012-05-23

The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structuremore » of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.« less

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: IV. Growth performance.

PubMed

Nassar, M K; Goraga, Z S; Brockmann, G A

2015-08-01

Reciprocal crosses between the inbred lines New Hampshire (NHI) and White Leghorn (WL77) comprising 579 F2 individuals were used to map QTL for body weight and composition. Here, we examine the growth performance until 20 weeks of age. Linkage analysis provided evidence for highly significant QTL on GGA1, 2, 4, 10 and 27 which had specific effects on early or late growth. The highest QTL effects, accounting for 4.6-25.6% of the phenotypic F2 variance, were found on the distal region of GGA4 between 142 and 170 cM (F ≥ 13.68). The NHI QTL allele increased body mass by 141.86 g at 20 weeks. Using body weight as a covariate in the analysis of body composition traits provided evidence for genes in the GGA4 QTL region affecting fat mass independently of body mass. The QTL effect size differed between sexes and depended on the direction of cross. TBC1D1, CCKAR and PPARGC1A are functional candidate genes in the QTL peak region. Our study confirmed the importance of the distal GGA4 region for chicken growth performance. The strong effect of the GGA4 QTL makes fine mapping and gene discovery feasible. © 2015 Stichting International Foundation for Animal Genetics.

Density functional theory study of the reaction mechanism for competitive carbon-hydrogen and carbon-halogen bond activations catalyzed by transition metal complexes.

PubMed

Yang, Xinzheng; Hall, Michael B

2009-03-12

Carbon-hydrogen and carbon-halogen bond activations between halobenzenes and metal centers were studied by density functional theory with the nonempirical meta-GGA Tao-Perdew-Staroverov-Scuseria functional and an all-electron correlation-consistent polarized valence double-zeta basis set. Our calculations demonstrate that the hydrogen on the metal center and halogen in halobenzene could exchange directly through a kite-shaped transition state. Transition states with this structure were previously predicted to have high energy barriers (J. Am. Chem. Soc. 2005, 127, 279), and this prediction misled others in proposing a mechanism for their recent experimental study (J. Am. Chem. Soc. 2006, 128, 3303). Furthermore, other halo-carbon activation pathways were found in the detailed mechanism for the competitive reactions between cationic titanium hydride complex [Cp*((t)Bu(3)P=N)TiH](+) and chlorobenzene under different pressure of H(2). These pathways include the ortho-C-H and Ti-H bond activations for the formation and release of H(2) and the indirect C-Cl bond activation via beta-halogen elimination for the movement of the C(6)H(4) ring and the formation of a C-N bond in the observed final product. A new stable isomer of the observed product with a similar total energy and an unexpected bridging between the Cp* ring and the metal center by a phenyl ring is also predicted.

Construction of exchange-correlation functionals through interpolation between the non-interacting and the strong-correlation limit

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

Zhou, Yongxi; Ernzerhof, Matthias, E-mail: Matthias.Ernzerhof@UMontreal.ca; Bahmann, Hilke

Drawing on the adiabatic connection of density functional theory, exchange-correlation functionals of Kohn-Sham density functional theory are constructed which interpolate between the extreme limits of the electron-electron interaction strength. The first limit is the non-interacting one, where there is only exchange. The second limit is the strong correlated one, characterized as the minimum of the electron-electron repulsion energy. The exchange-correlation energy in the strong-correlation limit is approximated through a model for the exchange-correlation hole that is referred to as nonlocal-radius model [L. O. Wagner and P. Gori-Giorgi, Phys. Rev. A 90, 052512 (2014)]. Using the non-interacting and strong-correlated extremes, variousmore » interpolation schemes are presented that yield new approximations to the adiabatic connection and thus to the exchange-correlation energy. Some of them rely on empiricism while others do not. Several of the proposed approximations yield the exact exchange-correlation energy for one-electron systems where local and semi-local approximations often fail badly. Other proposed approximations generalize existing global hybrids by using a fraction of the exchange-correlation energy in the strong-correlation limit to replace an equal fraction of the semi-local approximation to the exchange-correlation energy in the strong-correlation limit. The performance of the proposed approximations is evaluated for molecular atomization energies, total atomic energies, and ionization potentials.« less

Comparison of bottom-track to global positioning system referenced discharges measured using an acoustic Doppler current profiler

USGS Publications Warehouse

Wagner, Chad R.; Mueller, David S.

2011-01-01

A negative bias in discharge measurements made with an acoustic Doppler current profiler (ADCP) can be caused by the movement of sediment on or near the streambed. The integration of a global positioning system (GPS) to track the movement of the ADCP can be used to avoid the systematic negative bias associated with a moving streambed. More than 500 discharge transects from 63 discharge measurements with GPS data were collected at sites throughout the US, Canada, and New Zealand with no moving bed to compare GPS and bottom-track-referenced discharges. Although the data indicated some statistical bias depending on site conditions and type of GPS data used, these biases were typically about 0.5% or less. An assessment of differential correction sources was limited by a lack of data collected in a range of different correction sources and different GPS receivers at the same sites. Despite this limitation, the data indicate that the use of Wide Area Augmentation System (WAAS) corrected positional data is acceptable for discharge measurements using GGA as the boat-velocity reference. The discharge data based on GPS-referenced boat velocities from the VTG data string, which does not require differential correction, were comparable to the discharges based on GPS-referenced boat velocities from the differentially-corrected GGA data string. Spatial variability of measure discharges referenced to GGA, VTG and bottom-tracking is higher near the channel banks. The spatial variability of VTG-referenced discharges is correlated with the spatial distribution of maximum Horizontal Dilution of Precision (HDOP) values and the spatial variability of GGA-referenced discharges is correlated with proximity to channel banks.

Antiferromagnetic vs. non-magnetic ε phase of solid oxygen. Periodic density functional theory studies using a localized atomic basis set and the role of exact exchange.

PubMed

Ramírez-Solís, A; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ochoa-Calle, A J

2017-01-25

The question of the non-magnetic (NM) vs. antiferromagnetic (AF) nature of the ε phase of solid oxygen is a matter of great interest and continuing debate. In particular, it has been proposed that the ε phase is actually composed of two phases, a low-pressure AF ε 1 phase and a higher pressure NM ε 0 phase [Crespo et al., Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 10427]. We address this problem through periodic spin-restricted and spin-polarized Kohn-Sham density functional theory calculations at pressures from 10 to 50 GPa using calibrated GGA and hybrid exchange-correlation functionals with Gaussian atomic basis sets. The two possible configurations for the antiferromagnetic (AF1 and AF2) coupling of the 0 ≤ S ≤ 1 O 2 molecules in the (O 2 ) 4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O 2 ) 4 unit cells were done to study the pressure evolution of the enthalpy difference between the non-magnetic and both antiferromagnetic structures. We also address the evolution of structural parameters and the spin-per-molecule vs. pressure. We find that the spin-less solution becomes more stable than both AF structures above 50 GPa and, crucially, the spin-less solution yields lattice parameters in much better agreement with experimental data at all pressures than the AF structures. The optimized AF2 broken-symmetry structures lead to large errors of the a and b lattice parameters when compared with experiments. The results for the NM model are in much better agreement with the experimental data than those found for both AF models and are consistent with a completely non-magnetic (O 2 ) 4 unit cell for the low-pressure regime of the ε phase.

Design of exchange-correlation functionals through the correlation factor approach

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

Pavlíková Přecechtělová, Jana, E-mail: j.precechtelova@gmail.com, E-mail: Matthias.Ernzerhof@UMontreal.ca; Institut für Chemie, Theoretische Chemie / Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin; Bahmann, Hilke

The correlation factor model is developed in which the spherically averaged exchange-correlation hole of Kohn-Sham theory is factorized into an exchange hole model and a correlation factor. The exchange hole model reproduces the exact exchange energy per particle. The correlation factor is constructed in such a manner that the exchange-correlation energy correctly reduces to exact exchange in the high density and rapidly varying limits. Four different correlation factor models are presented which satisfy varying sets of physical constraints. Three models are free from empirical adjustments to experimental data, while one correlation factor model draws on one empirical parameter. The correlationmore » factor models are derived in detail and the resulting exchange-correlation holes are analyzed. Furthermore, the exchange-correlation energies obtained from the correlation factor models are employed to calculate total energies, atomization energies, and barrier heights. It is shown that accurate, non-empirical functionals can be constructed building on exact exchange. Avenues for further improvements are outlined as well.« less

Density functional with full exact exchange, balanced nonlocality of correlations, and constraint satisfaction

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

Tao, Jianmin; Perdew, John P; Staroverov, Viktor N

2008-01-01

We construct a nonlocal density functional approximation with full exact exchange, while preserving the constraint-satisfaction approach and justified error cancellations of simpler semilocal functionals. This is achieved by interpolating between different approximations suitable for two extreme regions of the electron density. In a 'normal' region, the exact exchange-correlation hole density around an electron is semilocal because its spatial range is reduced by correlation and because it integrates over a narrow range to -1. These regions are well described by popular semilocal approximations (many of which have been constructed nonempirically), because of proper accuracy for a slowly-varying density or because ofmore » error cancellation between exchange and correlation. 'Abnormal' regions, where non locality is unveiled, include those in which exchange can dominate correlation (one-electron, nonuniform high-density, and rapidly-varying limits), and those open subsystems of fluctuating electron number over which the exact exchange-correlation hole integrates to a value greater than -1. Regions between these extremes are described by a hybrid functional mixing exact and semi local exchange energy densities locally (i.e., with a mixing fraction that is a function of position r and a functional of the density). Because our mixing fraction tends to 1 in the high-density limit, we employ full exact exchange according to the rigorous definition of the exchange component of any exchange-correlation energy functional. Use of full exact exchange permits the satisfaction of many exact constraints, but the nonlocality of exchange also requires balanced nonlocality of correlation. We find that this nonlocality can demand at least five empirical parameters (corresponding roughly to the four kinds of abnormal regions). Our local hybrid functional is perhaps the first accurate size-consistent density functional with full exact exchange. It satisfies other known exact constraints, including exactness for all one-electron densities, and provides an excellent, fit 1.0 the 223 molecular enthalpies of formation of the G3/99 set and the 42 reaction barrier heights of the BH42/03 set, improving both (but especially the latter) over most semilocal functionals and global hybrids. Exact constraints, physical insights, and paradigm examples hopefully suppress 'overfitting'.« less

AB INITIO STUDY OF THE ELECTRONIC AND MAGNETIC PROPERTIES OF GRAPHENE WITH AND WITHOUT ADSORPTION OF M ATOM (M = C, N, O, F, Cl)

NASA Astrophysics Data System (ADS)

Ismail, Ali I.; Mubarak, A. A.

We present here an ab initio study for the energetic, electronic, magnetic and optical structures of the graphene sheet with and without the adsorption of M atom (M = C, N, O, F, Cl). The calculations are preformed using the full-potential linearized augmented plane wave (FP-LAPW) within the generalized gradient approximation (GGA) to describe the exchange-correlation potential. The calculations show that N prefers the bridge site, while C, O, F and Cl prefer the top site above the graphene sheet. The calculated M-graphene bond length is found to be inversely proportional to the adsorption energy. The hybridization between sp-states of the graphene sheet and M adatom is determined by the analysis of the partial and local density of states (PDOS and TDOS). In case of O and F as adsorbed atoms, graphene sheets show a wide energy band-gap and some significant magnetic moments. The optical properties of the studied sheets are performed in different radiation regions using the real and imaginary parts of the dielectric function. We think that the energetic, electronic, optical and magnetic properties of the M-graphene sheets are governed by two main factors; the number of unpaired valence electrons and the electronegativity of the M atom.

FP-LAPW based investigation of structural, electronic and mechanical properties of CePb{sub 3} intermetallic compound

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

Pagare, Gitanjali, E-mail: gita-pagare@yahoo.co.in; Jain, Ekta, E-mail: jainekta05@gmail.com; Abraham, Jisha Annie, E-mail: disisjisha@yahoo.com

A theoretical study of structural, electronic, elastic and mechanical properties of CePb{sub 3} intermetallic compound has been investigated systematically using first principles density functional theory. The calculations are carried out within the three different forms of generalized gradient approximation (GGA) and LSDA for the exchange correlation potential. The ground state properties such as lattice parameter (a{sub 0}), bulk modulus (B) and its pressure derivative (B′) are calculated and obtained lattice parameter of this compound shows well agreement with the experimental results. We have calculated three independent second order elastic constants (C{sub 11}, C{sub 12} and C{sub 44}), which has notmore » been calculated and measured yet. From energy dispersion curves, it is found that the studied compound is metallic in nature. Ductility of this compound is analyzed using Pugh’s criteria and Cauchy's pressure (C{sub 11}-C{sub 12}). The mechanical properties such as Young's modulus, shear modulus, anisotropic ratio, Poison's ratio have been calculated for the first time using the Voigt–Reuss–Hill (VRH) averaging scheme. The average sound velocities (v{sub m}), density (ρ) and Debye temperature (θ{sub D}) of this compound are also estimated from the elastic constants.« less

Li-adsorption on doped Mo2C monolayer: A novel electrode material for Li-ion batteries

NASA Astrophysics Data System (ADS)

Mehta, Veenu; Tankeshwar, K.; Saini, Hardev S.

2018-04-01

A first principle calculation has been used to study the electronic and magnetic properties of pristine and N/Mn-doped Mo2C with and without Li-adsorption. The pseudopotential method implemented in SIESTA code based on density functional theory with generalized gradient approximation (GGA) as exchange-correlation (XC) potential has been employed. Our calculated results revealed that the Li gets favorably adsorbed on the hexagonal centre in pristine Mo2C and at the top of C-atom in case of N/Mn-doped Mo2C. The doping of Mn and N atom increases the adsorption of Li in Mo2C monolayer which may results in enhancement of storage capacity in Li-ion batteries. The metallic nature of Li-adsorbed pristine and N/Mn-doped Mo2C monolayer implies a good electronic conduction which is crucial for anode materials for its applications in rechargeable batteries. Also, the open circuit voltage for single Li-adsorption in doped Mo2C monolayer comes in the range of 0.4-1.0 eV which is the optimal range for any material to be used as an anode material. Our result emphasized the enhanced performance of doped Mo2C as an anode material in Li-ion batteries.

Geranylgeranylacetone prevents stress-induced decline of leptin secretion in mice.

PubMed

Itai, Miki; Kuwano, Yuki; Nishikawa, Tatsuya; Rokutan, Kazuhito; Kensei, Nishida

2018-01-01

Geranylgeranylacetone (GGA) is a chaperon inducer that protects various types of cell and tissue against stress. We examined whether GGA modulated energy intake and expenditure under stressful conditions. After mice were untreated or treated orally with GGA (0.16 g per kg body weight per day) for 10 days, they were subjected to 2-h restraint stress once or once a day for 5 consecutive days. GGA administration did not affect corticosterone response to the stress. Restraint stress rapidly decreased plasma leptin levels in control mice. GGA significantly increased circulating leptin levels without changing food intake and prevented the stress-induced decline of circulating leptin. However GGA-treated mice significantly reduced food intake during the repeated stress, compared with control mice. GGA prevented the stress-induced decline of leptin mRNA and its protein levels in epidydimal adipose tissues. We also found that GGA decreased ghrelin mRNA expression in gastric mucosa before the stress, whereas GGA-treated mice recovered the ghrelin mRNA expression to the baseline level after the repeated stress. Leptin and ghrelin are now recognized as regulators of anxiety and depressive mood. Our results suggest that GGA may regulate food intake and relief stress-induced mood disturbance through regulating leptin and ghrelin secretions. J. Med. Invest. 65:103-109, February, 2018.

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

Density Functional Theory and Beyond for Band-Gap Screening: Performance for Transition-Metal Oxides and Dichalcogenides.

PubMed

Li, Wenqing; Walther, Christian F J; Kuc, Agnieszka; Heine, Thomas

2013-07-09

The performance of a wide variety of commonly used density functionals, as well as two screened hybrid functionals (HSE06 and TB-mBJ), on predicting electronic structures of a large class of en vogue materials, such as metal oxides, chalcogenides, and nitrides, is discussed in terms of band gaps, band structures, and projected electronic densities of states. Contrary to GGA, hybrid functionals and GGA+U, both HSE06 and TB-mBJ are able to predict band gaps with an appreciable accuracy of 25% and thus allow the screening of various classes of transition-metal-based compounds, i.e., mixed or doped materials, at modest computational cost. The calculated electronic structures are largely unaffected by the choice of basis functions and software implementation, however, might be subject to the treatment of the core electrons.

Inhomogeneity induced and appropriately parameterized semilocal exchange and correlation energy functionals in two-dimensions.

PubMed

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-07

The construction of meta generalized gradient approximations based on the density matrix expansion (DME) is considered as one of the most accurate techniques to design semilocal exchange energy functionals in two-dimensional density functional formalism. The exchange holes modeled using DME possess unique features that make it a superior entity. Parameterized semilocal exchange energy functionals based on the DME are proposed. The use of different forms of the momentum and flexible parameters is to subsume the non-uniform effects of the density in the newly constructed semilocal functionals. In addition to the exchange functionals, a suitable correlation functional is also constructed by working upon the local correlation functional developed for 2D homogeneous electron gas. The non-local effects are induced into the correlation functional by a parametric form of one of the newly constructed exchange energy functionals. The proposed functionals are applied to the parabolic quantum dots with a varying number of confined electrons and the confinement strength. The results obtained with the aforementioned functionals are quite satisfactory, which indicates why these are suitable for two-dimensional quantum systems.

Inhomogeneity induced and appropriately parameterized semilocal exchange and correlation energy functionals in two-dimensions

NASA Astrophysics Data System (ADS)

Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

2018-04-01

The construction of meta generalized gradient approximations based on the density matrix expansion (DME) is considered as one of the most accurate techniques to design semilocal exchange energy functionals in two-dimensional density functional formalism. The exchange holes modeled using DME possess unique features that make it a superior entity. Parameterized semilocal exchange energy functionals based on the DME are proposed. The use of different forms of the momentum and flexible parameters is to subsume the non-uniform effects of the density in the newly constructed semilocal functionals. In addition to the exchange functionals, a suitable correlation functional is also constructed by working upon the local correlation functional developed for 2D homogeneous electron gas. The non-local effects are induced into the correlation functional by a parametric form of one of the newly constructed exchange energy functionals. The proposed functionals are applied to the parabolic quantum dots with a varying number of confined electrons and the confinement strength. The results obtained with the aforementioned functionals are quite satisfactory, which indicates why these are suitable for two-dimensional quantum systems.

Novel Therapeutic Strategy for the Prevention of Bone Fractures

DTIC Science & Technology

2013-06-01

AGA GAG GGA GAT GCT CAG TGT TGG M32599 18S AGT GCG GGT CAT AAG CTT GC GGG CCT CAC TAA AC CAT CCA V00851 β-actin GTT TGA GAC CTT CAA CAC CCC GTG ...GCC ATC TCC TGC TCG AAG TC Meredith et al 2011* Mstn ACT GGA CCT CTC GAT AGA ACA CTC ACT TAG TGC TGT GTG TGT GGA GAT NM_010834.2 IGF-1 CAG...ACA GGA GCC CAG GAA AG AAG TGC CGT ATC CCA GAG GA NM_184052 MHC ACA GTC AGA GGT GTG ACTC AGC CG CCG ACT TGC GGA GGA AAG GTG C NM_001099635 Murf1

Novel Therapeutic Strategy for the Prevention of Bone Fractures

DTIC Science & Technology

2014-08-01

GAC CTT CAA CAC CCC GTG GCC ATC TCC TGC TCG AAG TC Meredith et al 2011* Mstn ACT GGA CCT CTC GAT AGA ACA CTC ACT TAG TGC TGT GTG TGT GGA GAT...NM_010834.2 IGF-1 CAG ACA GGA GCC CAG GAA AG AAG TGC CGT ATC CCA GAG GA NM_184052 MHC ACA GTC AGA GGT GTG ACTC AGC CG CCG ACT TGC GGA GGA AAG GTG C...AGC AGA GA TGA GTG CCT GCG GTA CAG AT NM_007553.2 RUNX-2 GGA AAG GCA CTG ACT GAC CTA ACA AAT TCT AAG CTT GGG AGG A NM_009820 Osx ACT ACC CAC CCT TCC

Electronic and optical response of zirconium sulphoselenides: Compton spectroscopy and first-principles calculations

NASA Astrophysics Data System (ADS)

Kumar, Kishor; Bhatt, Samir; Jani, A. R.; Ahuja, B. L.

2015-12-01

We present the first-ever experimental Compton profiles (CPs) of ZrSSe2 and ZrS1.5Se1.5 using 100 mCi 241Am Compton spectrometer. To analyze the experimental momentum densities, we have computed for the first-time the CPs, energy bands and density of states using linear combination of atomic orbitals (LCAO) method. To model the exchange and correlation effects within LCAO approach, we have considered Hartree-Fock (HF), density functional theory (DFT) with revised functional of Perdew-Becke-Ernzerhof (PBEsol) and hybridization of HF and DFT. Going beyond computation of electronic properties using LCAO method, we have also derived electronic and optical properties using the modified Becke-Johnson (mBJ) potential within full potential linearized augmented plane wave (FP-LAPW) method. There is notable decrease in the energy band gap on replacing S by Se atoms in ZrSSe2 to obtain ZrS1.5Se1.5 composition, which is mainly attributed to readjustment of Zr-4d, S-3p and Se-4p states. It is seen that the CPs based on hybridization of HF and DFT show a better agreement with the experimental profiles than those based on individual HF and DFT-GGA-PBEsol schemes. The optical properties computed using FP-LAPW-mBJ method unambiguously depict feasibility of using both the sulphoselenides in photovoltaics and also utility of ZrS1.5Se1.5 in the field of non-linear optics.

Interconfigurational energies in transition-metal atoms using gradient-corrected density-functional theory

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

Kutzler, F.W.; Painter, G.S.

1991-03-15

The rapid variation of charge and spin densities in atoms and molecules provides a severe test for local-density-functional theory and for the use of gradient corrections. In the study reported in this paper, we use the Langreth, Mehl, and Hu (LMH) functional and the generalized gradient approximation (GGA) of Perdew and Yue to calculate {ital s}-{ital d} transition energies, 4{ital s} ionization energies, and 3{ital d} ionization energies for the 3{ital d} transition-metal atoms. These calculations are compared with results from the local-density functional of Vosko, Wilk, and Nusair. By comparison with experimental energies, we find that the gradient functionalsmore » are only marginally more successful than the local-density approximation in calculating energy differences between states in transition-metal atoms. The GGA approximation is somewhat better than the LMH functional for most of the atoms studied, although there are several exceptions.« less

Exchange and correlation in positronium-molecule scattering

NASA Astrophysics Data System (ADS)

Fabrikant, I. I.; Wilde, R. S.

2018-05-01

Exchange and correlations play a particularly important role in positronium (Ps) collisions with atoms and molecules, since the static potential for Ps interaction with a neutral system is zero. Theoretical description of both effects is a very challenging task. In the present work we use the free-electron-gas model to describe exchange and correlations in Ps collisions with molecules similar to the approach widely used in the theory of electron-molecule collisions. The results for exchange and correlation energies are presented as functions of the Fermi momentum of the electron gas and the Ps incident energy. Using the Thomas-Fermi model, these functions can be converted into exchange and correlation potentials for Ps interaction with molecules as functions of the distance between the projectile and the target.

Theoretical analysis of the electronic, optical and thermal properties of lead strontium telluride alloys Pb1-xSrxTe (x = 0.0-1.0)

NASA Astrophysics Data System (ADS)

Chouit, F.; Sifi, C.; Slimani, M.; Meradji, H.; Ghemid, S.; Khenata, R.; Rai, D. P.; Bin Omran, S.

2018-02-01

We have simulated different physical properties of Pb1-xSrxTe semiconductors, using the Ab-initio full potential augmented plane wave (FP-LAPW) method. The two commonly used exchange potentials viz., PBE-GGA and WC-GGA are used along with the most recently developed modified Becke and Johnson (mBJ) potential to study the electronic and optical properties. In this study, we have observed an increase in band gap values as well as the lattice parameter with increasing the concentration of Sr atoms in Pb1-xSrxTe alloys while the bulk modulus and the refractive index have reverse effect. The microscopic origin of the band gap bowing is explained using the approach of Zunger and co-workers. At ambient conditions (p = 0, T = 0), the calculations indicate that Pb1-xSrxTe is a direct band gap semiconductor R-R with x = 0.125, 0.25, 0.375, 0.5, 0.625, 0.75 and 0.875. The refractive indices are also calculated using the FP-LAPW method and the models of Moss, Ravindra and the Herve-Vandame. The obtained results are in consistent with the previous available data. To study the thermal effects, the temperature effect on the lattice parameters, thermal expansions, heat capacities the quasi-harmonic Debye model is applied. The Debye temperature is determined from the non-equilibrium Gibbs function.

Clathrin Terminal Domain-Ligand Interactions Regulate Sorting of Mannose 6-Phosphate Receptors Mediated by AP-1 and GGA Adaptors*

PubMed Central

Stahlschmidt, Wiebke; Robertson, Mark J.; Robinson, Phillip J.; McCluskey, Adam; Haucke, Volker

2014-01-01

Clathrin plays important roles in intracellular membrane traffic including endocytosis of plasma membrane proteins and receptors and protein sorting between the trans-Golgi network (TGN) and endosomes. Whether clathrin serves additional roles in receptor recycling, degradative sorting, or constitutive secretion has remained somewhat controversial. Here we have used acute pharmacological perturbation of clathrin terminal domain (TD) function to dissect the role of clathrin in intracellular membrane traffic. We report that internalization of major histocompatibility complex I (MHCI) is inhibited in cells depleted of clathrin or its major clathrin adaptor complex 2 (AP-2), a phenotype mimicked by application of Pitstop® inhibitors of clathrin TD function. Hence, MHCI endocytosis occurs via a clathrin/AP-2-dependent pathway. Acute perturbation of clathrin also impairs the dynamics of intracellular clathrin/adaptor complex 1 (AP-1)- or GGA (Golgi-localized, γ-ear-containing, Arf-binding protein)-coated structures at the TGN/endosomal interface, resulting in the peripheral dispersion of mannose 6-phosphate receptors. By contrast, secretory traffic of vesicular stomatitis virus G protein, recycling of internalized transferrin from endosomes, or degradation of EGF receptor proceeds unperturbed in cells with impaired clathrin TD function. These data indicate that clathrin is required for the function of AP-1- and GGA-coated carriers at the TGN but may be dispensable for outward traffic en route to the plasma membrane. PMID:24407285

Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers.

PubMed

Hamzić, Edin; Buitenhuis, Bart; Hérault, Frédéric; Hawken, Rachel; Abrahamsen, Mitchel S; Servin, Bertrand; Elsen, Jean-Michel; Pinard-van der Laan, Marie-Hélène; Bed'Hom, Bertrand

2015-11-25

Coccidiosis is the most common and costly disease in the poultry industry and is caused by protozoans of the Eimeria genus. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for the development of efficient vaccines, respectively. Therefore, the current control programs must be expanded with complementary approaches such as the use of genetics to improve the host response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima for which we investigated variability among animals in response to the challenge. As a follow-up to this challenge study, we performed a genome-wide association study (GWAS) to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis to increase our biological understanding of the underlying response to Eimeria maxima challenge. In total, we identified 22 single nucleotide polymorphisms (SNPs) with q value <0.1 distributed across five chromosomes. The highly significant SNPs were associated with body weight gain (three SNPs on GGA5, one SNP on GGA1 and one SNP on GGA3), plasma coloration measured as optical density at wavelengths in the range 465-510 nm (10 SNPs and all on GGA10) and the percentage of β2-globulin in blood plasma (15 SNPs on GGA1 and one SNP on GGA2). Biological pathways related to metabolic processes, cell proliferation, and primary innate immune processes were among the most frequent significantly enriched biological pathways. Furthermore, the network-based analysis produced two networks of high confidence, with one centered on large tumor suppressor kinase 1 (LATS1) and 2 (LATS2) and the second involving the myosin heavy chain 6 (MYH6). We identified several strong candidate genes and genomic regions associated with traits measured in response to Eimeria maxima in broilers. Furthermore, the post-GWAS functional analysis indicates that biological pathways and networks involved in tissue proliferation and repair along with the primary innate immune response may play the most important role during the early stage of Eimeria maxima infection in broilers.

Reversible upregulation of tropomyosin-related kinase receptor B by geranylgeranoic acid in human neuroblastoma SH-SY5Y cells.

PubMed

Sakane, Chiharu; Shidoji, Yoshihiro

2011-09-01

All-trans retinoic acid (ATRA) plays crucial roles in cell survival and differentiation of neuroblastoma cells. In the present study, we investigated the effects of geranylgeranoic acid (GGA), an acyclic retinoid, on differentiation and tropomyosin-related kinase receptor B (TrkB) gene expression in SH-SY5Y human neuroblastoma cells in comparison with ATRA. GGA induced growth suppression and neural differentiation to the same extent as ATRA. Two variants (145 and 95 kD) of the TrkB protein were dramatically increased by GGA treatment, comparable to the effect of ATRA. Following 6- to 8-day GGA treatment, the effect of GGA on TrkB was reversed after 2-4 days of its removal, whereas the effect of ATRA was irreversible under the same conditions. Both GGA and ATRA upregulated the cellular levels of three major TrkB messenger RNA splice variants in a time-dependent manner. Time-dependent induction of cell cycle-related genes, such as cyclin D1 and retinoblastoma protein, and amplification of the neural progenitor cell marker, brain lipid binding protein, were suppressed by GGA treatment and were completely abolished by ATRA. ATRA and GGA induced retinoic acid receptor β (RARβ) expression, whereas the time-dependent expression of both RARα and RARγ was abolished by ATRA, but not by GGA. Our results suggest that GGA may be able to restore neuronal properties of SH-SY5Y human neuroblastoma cells in a similar but not identical way to ATRA.

Mechanical and magneto-electronic properties of half-metallic ferromagnetism in Ti-doped ZnSe and CdSe alloys: Ab initio study

NASA Astrophysics Data System (ADS)

El Amine Monir, Mohammed; Ullah, Hayat; Baltach, Hadj; Gulbahar Ashiq, M.; Khenata, R.

2017-11-01

In this article we have studied the structural, elastic, electronic and magnetic properties of Zn1-xTixSe and Cd1-xTixSe alloys at (x = 0.25, 0.50, 0.75) using first principles density functional theory calculations with local spin density approximation (LSDA) and generalized gradient approximation plus Hubbard parameter (GGA+U) as exchange-correlation potential. The physical properties of both alloys were investigated in the zinc-blend phase. The structural parameters at equilibrium are consistent with experimental and earlier theoretical predictions. The elastic constants are also computed and compared with the literature. The DOS curves of Zn1-xTixSe and Cd1-xTixSe alloys for all the concentrations show the existence of hybridization among Ti (3d) and Se (4p) states. The calculated exchange constants N0α(s-d) and N0β (p-d) are useful to determine the contribution in the valence band and conduction band and are also shows the magnetic character of these alloys. In addition, the p-d hybridization in the PDOS reduces local magnetic moment of Ti from its free space charge of 2 μB and results small magnetic moments on the nonmagnetic Zn, Cd and Se sites. The calculated negative values of formation energy (Ef) reveal that all the Zn1-xTixSe and Cd1-xTixSe alloys are thermodynamically stables. A larger/Smaller value of Curie temperature (TC) for all the Zn1-xTixSe and Cd1-xTixSe alloys shows the strong/low interaction among the magnetic atoms respectively.

Importance of the correlation contribution for local hybrid functionals: range separation and self-interaction corrections.

PubMed

Arbuznikov, Alexei V; Kaupp, Martin

2012-01-07

Local hybrid functionals with their position-dependent exact-exchange admixture are a conceptually simple and promising extension of the concept of a hybrid functional. Local hybrids based on a simple mixing of the local spin density approximation (LSDA) with exact exchange have been shown to be successful for thermochemistry, reaction barriers, and a range of other properties. So far, the combination of this generation of local hybrids with an LSDA correlation functional has been found to give the most favorable results for atomization energies, for a range of local mixing functions (LMFs) governing the exact-exchange admixture. Here, we show that the choice of correlation functional to be used with local hybrid exchange crucially influences the parameterization also of the exchange part as well as the overall performance. A novel ansatz for the correlation part of local hybrids is suggested based on (i) range-separation of LSDA correlation into short-range (SR) and long-range (LR) parts, and (ii) partial or full elimination of the one-electron self-correlation from the SR part. It is shown that such modified correlation functionals allow overall larger exact exchange admixture in thermochemically competitive local hybrids than before. This results in improvements for reaction barriers and for other properties crucially influenced by self-interaction errors, as demonstrated by a number of examples. Based on the range-separation approach, a fresh view on the breakdown of the correlation energy into dynamical and non-dynamical parts is suggested.

Changes in the reflectivity of a lithium niobate crystal decorated with a graphene layer

NASA Astrophysics Data System (ADS)

Salas, O.; Garcés, E.; Castillo, F. L.; Magaña, L. F.

2017-01-01

Density functional theory and molecular dynamics were used to study the interaction of a graphene layer with the surface of lithium niobate. The simulations were performed at atmospheric pressure and 300K. We found that the graphene layer is physisorbed with an adsorption energy of -0.8205 eV/C-atom. Subsequently, the optical absorption of the graphene-(lithium niobate) system was calculated and compared with that of graphene solo and lithium niobate alone, respectively. The calculations were performed using the Quantum Espresso code with the GGA approximation and Vdw-DF2 (which includes long-range correlation effects as Van der Waals interactions).

Energetics and magnetic properties of V-doped MgO bulk and (001) surface: A GGA, GGA+U , and hybrid density functional study

NASA Astrophysics Data System (ADS)

Århammar, C.; Moyses Araujo, C.; Rao, K. V.; Norgren, Susanne; Johansson, Börje; Ahuja, Rajeev

2010-10-01

In this work, a first-principles study of the energetic and magnetic properties of V-doped MgO is presented, where both the bulk and (001) surface were investigated. It is found that V assumes a high-spin state with a local moment of about 3μB . In the bulk, the interaction between these local moments is very short ranged and the antiferromagnetic (AFM) ordering is energetically more favorable. The formation of V-VMg-V defect clusters is found to weaken the antiferromagnetic coupling in bulk MgO, degenerating the AFM and ferromagnetic state. However, these clusters are high in energy and will not form at equilibrium conditions. By employing the GGA+U approach, with U=5eV , the V3d states on the (001) surface are shifted below the Fermi level, and a reasonable surface geometry was achieved. A calculation with the hybrid HSE03 functional, contradicts the GGA+U results, indicating that the V-MgO surface should be metallic at this concentration. From the energetics it is concluded that, at the modeled concentration, VxOy phases will limit the solubility of V in MgO at equilibrium conditions, which is in agreement with previous experimental findings. In order to achieve higher concentrations of V, an off-equilibrium synthesis method is needed. Finally, we find that the formation energy of V at the surface is considerably higher than in the bulk and V is thus expected to diffuse from the surface into the bulk of MgO.

Electronic properties of carbon in the fcc phase.

NASA Astrophysics Data System (ADS)

Cab, Cesar; Canto, Gabriel

2005-03-01

The observation of a new carbon phase in nanoparticles obtained from Mexican crude oil having the face-centered-cubic structure (fcc) has been reported. However, more recently has been suggested that hydrogen is present in the samples forming CH with the zincblende structure. The structural and electronic properties of C(fcc) and CH(zincblende) are unknown. In the present work we have studied the electronic structure of C(fcc) and CH(zincblende) by means of first-principles total-energy calculations. The results were obtained with the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the band structure, the local density of states (LDOS), and orbital population. We find that in contrast to graphite and diamond, both fcc carbon and CH with the zincblende structure exhibit metallic behavior. This research was supported by Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt-M'exico) under Grants No. 43830-F, No. 44831-F, and No. 43828-Y.

Electronic-structure calculations of praseodymium metal by means of modified density-functional theory

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

Svane, A.; Trygg, J.; Johansson, B.

1997-09-01

Electronic-structure calculations of elemental praseodymium are presented. Several approximations are used to describe the Pr f electrons. It is found that the low-pressure, trivalent phase is well described using either the self-interaction corrected (SIC) local-spin-density (LSD) approximation or the generalized-gradient approximation (GGA) with spin and orbital polarization (OP). In the SIC-LSD approach the Pr f electrons are treated explicitly as localized with a localization energy given by the self-interaction of the f orbital. In the GGA+OP scheme the f-electron localization is described by the onset of spin and orbital polarization, the energetics of which is described by spin-moment formation energymore » and a term proportional to the total orbital moment, L{sub z}{sup 2}. The high-pressure phase is well described with the f electrons treated as band electrons, in either the LSD or the GGA approximations, of which the latter describes more accurately the experimental equation of state. The calculated pressure of the transition from localized to delocalized behavior is 280 kbar in the SIC-LSD approximation and 156 kbar in the GGA+OP approach, both comparing favorably with the experimentally observed transition pressure of 210 kbar. {copyright} {ital 1997} {ital The American Physical Society}« less

Rocksalt or cesium chloride: Investigating the relative stability of the cesium halide structures with random phase approximation based methods

NASA Astrophysics Data System (ADS)

Nepal, Niraj K.; Ruzsinszky, Adrienn; Bates, Jefferson E.

2018-03-01

The ground state structural and energetic properties for rocksalt and cesium chloride phases of the cesium halides were explored using the random phase approximation (RPA) and beyond-RPA methods to benchmark the nonempirical SCAN meta-GGA and its empirical dispersion corrections. The importance of nonadditivity and higher-order multipole moments of dispersion in these systems is discussed. RPA generally predicts the equilibrium volume for these halides within 2.4% of the experimental value, while beyond-RPA methods utilizing the renormalized adiabatic LDA (rALDA) exchange-correlation kernel are typically within 1.8%. The zero-point vibrational energy is small and shows that the stability of these halides is purely due to electronic correlation effects. The rAPBE kernel as a correction to RPA overestimates the equilibrium volume and could not predict the correct phase ordering in the case of cesium chloride, while the rALDA kernel consistently predicted results in agreement with the experiment for all of the halides. However, due to its reasonable accuracy with lower computational cost, SCAN+rVV10 proved to be a good alternative to the RPA-like methods for describing the properties of these ionic solids.

First-Principles Study of the Jahn-Teller Distortion in the Ti1-XVXH2 and Zr1-XNbxH2 Alloys

NASA Astrophysics Data System (ADS)

Quijano, Ramiro; de Coss, Romeo; Singh, David

2008-03-01

The transition metal dihydrides TiH2 and ZrH2 present the fluorite structure (CaF2) at high temperature but undergoes a tetragonal distortion with c/a<1 at low temperature. Electronic band structure calculations have shown that TiH2 and ZrH2 in the cubic phase display a very flat band at the Fermi level. Thus the low temperature tetragonal distortion has been associated to a Jahn-Teller effect. In order to understand the role of band filling in controlling the structural instability of the transition metal dihydrides, we have performed a first-principles total energy study of the Ti1-XVxH2 and Zr1-xNbxH2 alloys. The calculations were performed using FP-LAPW method within the (DFT) and we use the GGA for exchange correlation functional energy. The critical concentration for which the Jahn-Teller effect is suppressed, was determined from the evolution of the tetragonal-cubic energy barrier. We discuss the electronic mechanism of the structural-instability, in terms of the band filling. From the obtained results we conclude that the tetragonal distortion in TiH2 and ZrH2 is not produced only by a Jahn-Teller Effect. This research was supported by Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grant No. 43830-F.

Effect of biaxial strain on the magnetism of Fe16N2: Density-functional investigations

NASA Astrophysics Data System (ADS)

Zhou, Wei; Liu, Lijuan; Wu, Ping

2014-02-01

The effect of biaxial strain on the magnetism of α″-Fe16N2 was investigated by the first principles calculations. The GGA, GGA + U and HSE06 calculations give the same result that the magnetic moments increase with the biaxial strain in the ab plane. All non-equivalent Fe atoms contribute to the increase of magnetic moments, although the variations of inter-atomic distances between non-equivalent Fe and N are different. Additionally, the magnetic anisotropy of Fe16N2 could be controlled by the biaxial strain.

gga-miR-155 Enhances Type I Interferon Expression and Suppresses Infectious Burse Disease Virus Replication via Targeting SOCS1 and TANK

PubMed Central

Wang, Bin; Fu, Mengjiao; Liu, Yanan; Wang, Yongqiang; Li, Xiaoqi; Cao, Hong; Zheng, Shijun J.

2018-01-01

Infectious bursal disease (IBD) is an acute, highly contagious, and immunosuppressive avian disease caused by IBD virus (IBDV). MicroRNAs (miRNAs) are involved in host-pathogen interactions and innate immune response to viral infection. However, the role of miRNAs in host response to IBDV infection is not clear. We report here that gga-miR-155 acts as an anti-virus host factor inhibiting IBDV replication. We found that transfection of DF-1 cells with gga-miR-155 suppressed IBDV replication, while blockage of the endogenous gga-miR-155 by inhibitors enhanced IBDV replication. Furthermore, our data showed that gga-miR-155 enhanced the expression of type I interferon in DF-1 cells post IBDV infection. Importantly, we found that gga-miR-155 enhanced type I interferon expression via targeting SOCS1 and TANK, two negative regulators of type I IFN signaling. These results indicate that gga-miR-155 plays a critical role in cell response to IBDV infection. PMID:29564226

Effects of van der Waals density functional corrections on trends in furfural adsorption and hydrogenation on close-packed transition metal surfaces

NASA Astrophysics Data System (ADS)

Liu, Bin; Cheng, Lei; Curtiss, Larry; Greeley, Jeffrey

2014-04-01

The hydrogenation of furfural to furfuryl alcohol on Pd(111), Cu(111) and Pt(111) is studied with both standard Density Functional Theory (DFT)-GGA functionals and with van der Waals-corrected density functionals. VdW-DF functionals, including optPBE, optB88, optB86b, and Grimme's method, are used to optimize the adsorption configurations of furfural, furfuryl alcohol, and related intermediates resulting from hydrogenation of furfural, and the results are compared to corresponding values determined with GGA functionals, including PW91 and PBE. On Pd(111) and Pt(111), the adsorption geometries of the intermediates are not noticeably different between the two classes of functionals, while on Cu(111), modest changes are seen in both the perpendicular distance and the orientation of the aromatic ring with respect to the planar surface. In general, the binding energies increase substantially in magnitude as a result of van der Waals contributions on all metals. In contrast, however, dispersion effects on the kinetics of hydrogenation are relatively small. It is found that activation barriers are not significantly affected by the inclusion of dispersion effects, and a Brønsted-Evans-Polanyi relationship developed solely from PW91 calculations on Pd(111) is capable of describing corresponding results on Cu(111) and Pt(111), even when the dispersion effects are included. Finally, the reaction energies and barriers derived from the dispersion-corrected and pure GGA calculations are used to plot simple potential energy profiles for furfural hydrogenation to furfuryl alcohol on the three considered metals, and an approximately constant downshift of the energetics due to the dispersion corrections is observed.

First-principles calculations of electronic, magnetic and optical properties of HoN doped with TM (Ti, V, Cr, Mn, Co and Ni)

NASA Astrophysics Data System (ADS)

Rouchdi, M.; Salmani, E.; Dehmani, M.; Ez-Zahraouy, H.; Hassanain, N.; Benyoussef, A.; Mzerd, A.

2018-02-01

Using the first-principles calculations within the Korringa-Kohn-Rostoker (KKR) method combined with the coherent potential approximation (CPA), the structural, optical and magnetic properties of rare-earth nitride Ho0.95TM0.05N doped with transition metal (TM) atoms (Ti, V, Cr, Mn, Co and Ni) are investigated as a function the generalized gradient approximation and self-interaction correction (GGA-SIC) approximation. The optical properties are studied in detail by using ab-initio calculations. Using GGA-SIC we have showed that the bandgap value is in good agreement with the experimental value. Using GGA-SIC approximation for HoN, we have obtained a bandgap of 0.9 eV. Some of the dilute magnetic semiconductors (DMS) like Ho0.95TM0.05N under study exhibit a half-metallic behavior, which makes them suitable for spintronic applications. Moreover, the optical absorption spectra confirm the ferromagnetic stability based on the charge state of magnetic impurities.

Two-Component Noncollinear Time-Dependent Spin Density Functional Theory for Excited State Calculations.

PubMed

Egidi, Franco; Sun, Shichao; Goings, Joshua J; Scalmani, Giovanni; Frisch, Michael J; Li, Xiaosong

2017-06-13

We present a linear response formalism for the description of the electronic excitations of a noncollinear reference defined via Kohn-Sham spin density functional methods. A set of auxiliary variables, defined using the density and noncollinear magnetization density vector, allows the generalization of spin density functional kernels commonly used in collinear DFT to noncollinear cases, including local density, GGA, meta-GGA and hybrid functionals. Working equations and derivations of functional second derivatives with respect to the noncollinear density, required in the linear response noncollinear TDDFT formalism, are presented in this work. This formalism takes all components of the spin magnetization into account independent of the type of reference state (open or closed shell). As a result, the method introduced here is able to afford a nonzero local xc torque on the spin magnetization while still satisfying the zero-torque theorem globally. The formalism is applied to a few test cases using the variational exact-two-component reference including spin-orbit coupling to illustrate the capabilities of the method.

Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

PubMed Central

Kasai, Fumio; O'Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.

2012-01-01

The genome size in turtles and crocodiles is thought to be much larger than the 1.2 Gb of the chicken (Gallus gallus domesticus, GGA), according to the animal genome size database. However, GGA macrochromosomes show extensive homology in the karyotypes of the red eared slider (Trachemys scripta elegans, TSC) and the Nile crocodile (Crocodylus niloticus, CNI), and bird and reptile genomes have been highly conserved during evolution. In this study, size and GC content of all chromosomes are measured from the flow karyotypes of GGA, TSC and CNI. Genome sizes estimated from the total chromosome size demonstrate that TSC and CNI are 1.21 Gb and 1.29 Gb, respectively. This refines previous overestimations and reveals similar genome sizes in chicken, turtle and crocodile. Analysis of chromosome GC content in each of these three species shows a higher GC content in smaller chromosomes than in larger chromosomes. This contrasts with mammals and squamates in which GC content does not correlate with chromosome size. These data suggest that a common ancestor of birds, turtles and crocodiles had a small genome size and a chromosomal size-dependent GC bias, distinct from the squamate lineage. PMID:22491763

Charge versus orbital-occupancy ordering in manganites

NASA Astrophysics Data System (ADS)

Luo, Weidong; Varela, Maria; Tao, Jing; Pennycook, Stephen J.; Pantelides, Sokrates T.

2006-03-01

It is generally assumed that density-functional theory (DFT) in the local-spin-density approximation (LSDA) or the generalized- gradient approximation (GGA) is not adequate to describe mixed- valence manganites. Here we report benchmark DFT/GGA calculations for the ground-state structural, electronic and magnetic properties for both undoped and doped CaMnO3 and find the results to be in excellent agreement with available data, including new atomic-resolution Z-contrast imaging and electron-energy loss spectra. More specifically, we found that the DFT results predict two inequivalent Mn atoms in both 0.33 and 0.5 electron-doped CaMnO3, in agreement with experimental evidence of Mn^+3/Mn^+4 oxidation state ordering. The inequivalent Mn atoms are marked by their distinctive orbital occupancies, dissimilar local Jahn-Teller distortion and different magnetic moments from DFT calculations. We also show that the spherically integrated charges associated with the two inequivalent Mn atoms are the same, and they are actually the same as in the Mn metal. This charge neutrality with different orbital occupancies is the result of self-consistency and atomic relaxations in the crystal. We conclude that DFT without additional correlations can account for the observed properties of oxidation-state ordering in this system. The impact of the results on other mixed-valence systems will be discussed.

Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations.

PubMed

van Meer, R; Gritsenko, O V; Baerends, E J

2014-10-14

In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent density functional theory (TDDFT) calculations of excitation energies have been performed. The tested functionals do not approximate exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of molecular excitations. Benchmark calculations are performed for the statistical average of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential does not only perform satisfactorily for calculated vertical excitation energies of both valence and Rydberg transitions but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calculated with local density, generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in molecules: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).

Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

PubMed

Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

2016-07-12

In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

BH-DFTB/DFT calculations for iron clusters

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

Aktürk, Abdurrahman; Sebetci, Ali, E-mail: asebetci@mevlana.edu.tr

2016-05-15

We present a study on the structural, electronic, and magnetic properties of Fe{sub n}(n  =  2  −  20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima havemore » been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe{sub 9−13}), centered hexagonal antiprism (Fe{sub 14−17}, Fe{sub 20}), and truncated decahedral (Fe{sub 17(2)}, Fe{sub 18−19}). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fe{sub n}(n = 2 − 20) clusters is between 2.4 and 3.6 μ{sub B} for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe{sub 13} icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.« less

Structural, electronic, and elastic properties of CuFeS2: first-principles study

NASA Astrophysics Data System (ADS)

Zhou, Meng; Gao, Xiang; Cheng, Yan; Chen, Xiangrong; Cai, Lingcang

2015-03-01

The structural, electronic, and elastic properties of CuFeS2 have been investigated by using the generalized gradient approximation (GGA), GGA + U (on-site Coulomb repulsion energy), the local density approximation (LDA), and the LDA + U approach in the frame of density functional theory. It is shown that when the GGA + U formalism is selected with a U value of 3 eV for the 3d state of Fe, the calculated lattice constants agree well with the available experimental and other theoretical data. Our GGA + U calculations indicate that CuFeS2 is a semiconductor with a band gap of 0.552 eV and with a magnetic moment of 3.64 µB per Fe atom, which are well consistent with the experimental results. Combined with the density of states, the band structure characteristics of CuFeS2 have been analyzed and their origins have been specified, which reveals a hybridization existing between Fe-3d, Cu-3s, and S-3p, respectively. The charge and Mulliken population analyses indicate that CuFeS2 is a covalent crystal. Moreover, the calculated elastic constants prove that CuFeS2 is mechanically stable but anisotropic. The bulk modulus obtained from elastic constants is 87.1 GPa, which agrees well with the experimental value of 91 ± 15 GPa and better than the theoretical bulk modulus 74 GPa obtained from GGA method by Lazewski et al. The obtained shear modulus and Debye temperature are 21.0 GPa and 287 K, respectively, and the latter accords well with the available experimental value. It is expected that our work can provide useful information to further investigate CuFeS2 from both the experimental and theoretical sides.

Bands dispersion and charge transfer in β-BeH2

NASA Astrophysics Data System (ADS)

Trivedi, D. K.; Galav, K. L.; Joshi, K. B.

2018-04-01

Predictive capabilities of ab-initio method are utilised to explore bands dispersion and charge transfer in β-BeH2. Investigations are carried out using the linear combination of atomic orbitals method at the level of density functional theory. The crystal structure and related parameters are settled by coupling total energy calculations with the Murnaghan equation of state. Electronic bands dispersion from PBE-GGA is reported. The PBE-GGA, and PBE0 hybrid functional, show that β-BeH2 is a direct gap semiconductor with 1.18 and 2.40 eV band gap. The band gap slowly decreases with pressure and beyond l00 GPa overlap of conduction and valence bands at the r point is observed. Charge transfer is studied by means of Mullikan population analysis.

An ab initio density functional study of the optical functions of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystals.

PubMed

Reshak, Ali H; Kityk, I V; Khenata, R; Al-Douri, Y; Auluck, S

2012-09-01

An ab initio investigation of the optical constants of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystal is performed within a framework of local density approximation (LDA), and the Engel-Vosko generalized gradient approximation (EV-GGA) exchange correlation potentials. It is established that there are two independent molecules (A and B) exhibiting different intra-molecular interactions: C-H⋯O (A) and C-H⋯N (B). These intra-molecular interactions favor stabilization of the crystal structure for molecules A and B. It should be emphasized that there exist remarkable π-π interactions between the pyrimidine rings of the two neighbors B molecules giving extra strengths and stabilizations to the superamolecular structure. These different intra-molecular interactions C-H⋯O (A) and C-H⋯N (B) and the π-π interaction between the pyrimidine rings of the two neighbors B molecules give principal contribution to dispersion of optical properties. With a view to seek deeper insight into the electronic structure, the optical properties were investigated. Our calculations show that the optical constants are very anisotropic. The EVGGA calculation shows a blue spectral shift of around 0.024 eV with significant changes in the spectra compared to the LDA calculation. The observed spectral shifts are in agreement with the calculated band structure and corresponding electron density of states. Copyright © 2012 Elsevier B.V. All rights reserved.

Structural, optical and electronic properties of indium sulfide compositions under influence of copper impurity produced by chemical method

NASA Astrophysics Data System (ADS)

Esmaili, Parisa; Kangarlou, Haleh; Savaloni, Hadi; Ghorannevis, Mahmood

Aqueous solutions with 70 °C and pH = 2.5 constant values were prepared from convenient chemical compounds to produce In2S3: Cu crystals and thin films. Crystal compositions were grown in this solution under special conditions. Micrographs showed amorphous In2S3 orange powder and transparent vitreous pieces of CuInS2 crystals. Indium sulfide films were produced using the same solution in CBD method, on the glass substrates at different [Cu/In] molar ratio concentrations. Cu+ ions by different concentration doped from copper chloride source into In2S3 films. The produced films were post-annealed at 400 °C for about 1 h. Their crystallography, phase transitions, element analysis and nanostructures were investigated by X-ray diffraction, SEM, EDAX and AFM analyses. β-In2S3 phase was dominant and by doping copper impurity, XRD results suggested the formation of CuInS2 compositions. Morphology of the films, nano-structures, grain shapes and hardness was changed. Optical reflectance was measured in the UV-VIS wavelength range by a spectrophotometer. Other optical properties and optical band gaps were calculated using Kramers-Kronig relations on reflectivity curves. Electronic properties were calculated by full potential linearized augmented plane wave (FP-LAPW) method within density functional theory (DFT). In this approach, generalized gradient approximation (GGA) was used for the exchange-correlation potential calculation. Band gap structures, density of states and imaginary parts of dielectric function were calculated for In2S3: Cu compositions.

Computational study of dye adsorption onto Brookite TiO2 surfaces for the applications in dye sensitized solar cells

NASA Astrophysics Data System (ADS)

Maluta, N. E.; Dima, R. S.; Nemudzivhadi, H.; Maphanga, R. R.; Sankaran

2017-10-01

The theoretical and computational studies of dye sensitized solar cells (DSSCs) can contribute to a deeper understanding of these type of solar cells. In the current study the density functional theory (DFT) is used to understand the electronic properties of low index brookite (1 0 0) surface doped with ruthenium. The structural optimizations, band structure, and electronic density of states of doped and undoped titanium dioxide (TiO2) brookite surface was performed using the first-principles calculations based on DFT emplotying a plane-wave pseudopotential method. The generalized gradient approximation (GGA) was used in the scheme of Perdew-Burke-Ernzerhof (PBE) to describe the exchange-correlation functional. All calculations were carried out with CASTEP (Cambridge Sequential Total Energy Package) code in Materials Studio of Accelrys Inc. The two different doping methods employed in the current work are, doping by replacement and adsorption. The overlap among the Ruthenium (Ru) 3d, Titanium (Ti) 3d, and Oxygen (O) 2p states enhance photocatalytic activity in the visible light region. The adsorption method shows that an equilibrium position is reached for ruthenium element after optimization. All the methods show that the TiO2 brookite (1 0 0) surface reduces its band gap after been doped with the ruthenium element. From the two techniques used, the total energy of the doped structures show that they are energetically favorable, with the band gap being reduced to 0.263 eV compared to 2.376 eV of the pure system.

Distribution and differential expression of microRNAs in the intestinal mucosal layer of necrotic enteritis induced Fayoumi chickens

PubMed Central

Rengaraj, Deivendran; Truong, Anh Duc; Ban, Jihye; Lillehoj, Hyun S.; Hong, Yeong Ho

2017-01-01

Objective Despite an increasing number of investigations into the pathophysiology of necrotic enteritis (NE) disease, etiology of NE-associated diseases, and gene expression profiling of NE-affected tissues, the microRNA (miRNA) profiles of NE-affected poultry have been poorly studied. The aim of this study was to induce NE disease in the genetically disparate Fayoumi chicken lines, and to perform non-coding RNA sequencing in the intestinal mucosal layer. Methods NE disease was induced in the Fayoumi chicken lines (M5.1 and M15.2), and non-coding RNA sequencing was performed in the intestinal mucosal layer of both NE-affected and uninfected chickens to examine the differential expression of miRNAs. Next, quantitative real-time polymerase chain reaction (real-time qPCR) was performed to further examine four miRNAs that showed the highest fold differences. Finally, bioinformatics analyses were performed to examine the four miRNAs target genes involvement in the signaling pathways, and to examine their interaction. Results According to non-coding RNA sequencing, total 50 upregulated miRNAs and 26 downregulated miRNAs were detected in the NE-induced M5.1 chickens. While 32 upregulated miRNAs and 11 downregulated miRNAs were detected in the NE-induced M15.2 chickens. Results of real-time qPCR analysis on the four miRNAs (gga-miR-9-5p, gga-miR-20b-5p, gga-miR-196-5p, and gga-let-7d) were mostly correlated with the results of RNAseq. Overall, gga-miR-20b-5p was significantly downregulated in the NE-induced M5.1 chickens and this was associated with the upregulation of its top-ranking target gene, mitogen-activated protein kinase, kinase 2. Further bioinformatics analyses revealed that 45 of the gene targets of gga-miR-20b-5p were involved in signal transduction and immune system-related pathways, and 35 of these targets were predicted to interact with each other. Conclusion Our study is a novel report of miRNA expression in Fayoumi chickens, and could be very useful in understanding the role of differentially expressed miRNAs in a NE disease model. PMID:28111433

MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids.

PubMed

Yu, Haoyu S; He, Xiao; Truhlar, Donald G

2016-03-08

Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology.

Optimization of a hybrid exchange-correlation functional for silicon carbides

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

Oda, Takuji; Zhang, Yanwen; Weber, William J

2013-01-01

A hybrid exchange-correlation functional is optimized in order to accurately describe the nature of silicon carbides (SiC) in the framework of ab-initio calculations based on density functional theory (DFT), especially with an aim toward future applications in defect studies. It is shown that the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional with the screening parameter of 0.15 -1 outperforms conventional exchange-correlation functionals and other popular hybrid functionals regarding description of band structures in SiC. High transferability is proven through assessment over various SiC polytypes, silicon and diamond. Excellent performance is also confirmed for other fundamental material properties including elastic constants and phonon frequency.

Robust half-metallicity of hexagonal SrNiO{sub 3}

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

Chen, Gao-Yuan; Ma, Chun-Lan, E-mail: machunlan@126.com; Chen, Da

In the rich panorama of the electronic and magnetic properties of 3d transition metal oxides SrMO{sub 3} (M=Ti, V, Cr, Mn, Fe, Co, Ni, Cu), one member (SrNiO{sub 3}) is missing. In this paper we use GGA+U method based on density functional theory to examine its properties. It is found that SrNiO{sub 3} is a ferromagnetic half-metal. The charge density map shows a high degree of ionic bonding between Sr and other atoms. Meanwhile, a covalent-bonding Ni–O–Ni–O–Ni chain is observed. The spin density contour of SrNiO{sub 3} further indicates that the magnetic interaction between Ni atoms mediated by O ismore » semicovalent exchange. The density of states are examined to explore the unusual indirect magnetic-exchange mechanism. Corresponding to the total energies results, a robust half-metallic character is observed, suggesting a promising giant magneto-optical Kerr property of the material. The partial density of states are further examined to explore the origin of ferromagnetic half-metallicity. The O atoms are observed to have larger contribution at fermi level than Ni atoms to the spin-polarized states, demonstrating that O atoms play a critical role in ferromagnetic half-metallicity of SrNiO{sub 3}. Hydrostatic pressure effect is examined to evaluate how robust the half-metallic ferromagnetism is. - Graphical abstract: (a) The total energy as a function of the lattice constant a for hexagonal SrNiO3 with various magnetic phases. (b) The total electronic density of states for hexagonal SrNiO{sub 3} with FM configuration from GGA+U calculations. (c) Total electron-density distribution in the (110) plane. The colors gradually change from cyan (through pink) to yellow corresponding to charge density value from 0 to 4.0. (d) The magnetization density map in the (110) plane. The colors range from blue (through green) to red corresponding to magnetization density value from −0.15 to 0.45. Black and white contours stand for positive and negative values, respectively. - Highlights: • Hexagonal SrNiO{sub 3} is studied using first-principles method for the first time. • It is predicted that SrNiO{sub 3} is a ferromagnetic half metal. • The half-metallic ferromagnetism survives upon a pressure up to 20 GPa.« less

Correlation energy, correlated electron density, and exchange-correlation potential in some spherically confined atoms.

PubMed

Vyboishchikov, Sergei F

2016-12-05

We report correlation energies, electron densities, and exchange-correlation potentials obtained from configuration interaction and density functional calculations on spherically confined He, Be, Be 2+ , and Ne atoms. The variation of the correlation energy with the confinement radius R c is relatively small for the He, Be 2+ , and Ne systems. Curiously, the Lee-Yang-Parr (LYP) functional works well for weak confinements but fails completely for small R c . However, in the neutral beryllium atom the CI correlation energy increases markedly with decreasing R c . This effect is less pronounced at the density-functional theory level. The LYP functional performs very well for the unconfined Be atom, but fails badly for small R c . The standard exchange-correlation potentials exhibit significant deviation from the "exact" potential obtained by inversion of Kohn-Sham equation. The LYP correlation potential behaves erratically at strong confinements. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

NASA Astrophysics Data System (ADS)

Zheng, Lixin; Chen, Mohan; Sun, Zhaoru; Ko, Hsin-Yu; Santra, Biswajit; Dhuvad, Pratikkumar; Wu, Xifan

2018-04-01

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.

Electronic and Magnetic Structures, Magnetic Hyperfine Fields and Electric Field Gradients in UX3 (X = In, Tl, Pb) Intermetallic Compounds

NASA Astrophysics Data System (ADS)

Khan, Sajid; Yazdani-Kachoei, Majid; Jalali-Asadabadi, Saeid; Farooq, Muhammad Bilal; Ahmad, Iftikhar

2018-02-01

Cubic uranium compounds such as UX3 (X is a non-transition element of groups IIIA or IVA) exhibit highly diverse magnetic properties, including Pauli paramagnetism, spin fluctuation and anti-ferromagnetism. In the present paper, we explore the structural, electronic and magnetic properties as well as the hyperfine fields (HFFs) and electric field gradients (EFGs) with quadrupole coupling constant of UX3 (X = In, Tl, Pb) compounds using local density approximation, Perdew-Burke-Ernzerhof parametrization of generalized gradient approximation (PBE-GGA) including the Hubbard U parameter (GGA + U), a revised version of PBE-GGA that improves equilibrium properties of densely packed solids and their surfaces (PBEsol-GGA), and a hybrid functional (HF-PBEsol). The spin orbit-coupling calculations have been added to investigate the relativistic effect of electrons in these materials. The comparison between the experimental parameters and our calculated structural parameters we confirm the consistency and effectiveness of our theoretical tools. The computed magnetic moments show that magnetic moment increases from indium to lead in the UX3 family, and all these compounds are antiferromagnetic in nature. The EFGs and HFFs, as well as the quadrupole coupling constant of UX3 (X = In, Tl, Pb), are discussed in detail. These properties primarily originate from f and p states of uranium and post-transition sites.

Quantum Monte Carlo Simulations of the Quartz to Stishovite Transition in SiO2

NASA Astrophysics Data System (ADS)

Cohen, R. E.; Towler, Mike; Lopez Rios, Pablo; Drummond, Neil; Needs, Richard

2007-03-01

The quartz-stishovite transition has been a long standing problem for density functional theory (DFT). Although conventional DFT computations within the local density approximation (LDA) give reasonably good properties of silica phases individually, they do not give the energy difference between quartz and stishovite accurately. The LDA gives stishovite as a lower energy structure than quartz at zero pressure, which is incorrect. The generalized gradient approximation (GGA) has been shown to give the correct energy difference between quartz and stishovite (about 0.5 eV/formula unit) (Hamann, PRL 76, 660, 1996; Zupan et al., PRB 58, 11266, 1998), and it was generally thought that the GGA was simply a better approximation than the LDA. However, closer inspection shows that other properties are not better for the GGA than the LDA, so there is room for improvement. A new density functional that is an improvement for most materials unfortunately does not improve the quartz-stishovite transition (Wu and Cohen, PRB 73, 235116, 2006). We are performing QMC computations using the CASINO code to obtain the accurate energy difference between quartz and stishovite to obtain more accurate high pressure properties, and to better understand the errors on DFT and how DFT can be improved.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

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

Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

2016-06-13

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

PubMed

Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

2016-09-01

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

Constraint on the second functional derivative of the exchange-correlation energy

NASA Astrophysics Data System (ADS)

Joubert, D. P.

2012-09-01

Using the density functional adiabatic connection approach for an N-electron system it is shown that ? γ is the coupling constant that scales the electron-electron interaction strength. For the non-interacting Kohn-Sham Hamiltonian γ = 0 and for the fully interacting system γ = 1. ? is the Hartree plus exchange-correlation energy while f 0(r) and fγ(r) are the Fukui functions of the non-interacting and interacting systems, respectively. This identity can serve to test the internal self-consistency or quality of approximate functionals. The quality of some popular approximate exchange and correlation functionals are tested for a simple model system.

Nanostructured diamine-fullerene derivatives: computational density functional theory study and experimental evidence for their formation via gas-phase functionalization.

PubMed

Contreras-Torres, Flavio F; Basiuk, Elena V; Basiuk, Vladimir A; Meza-Laguna, Víctor; Gromovoy, Taras Yu

2012-02-16

Nanostructure derivatives of fullerene C(60) are used in emerging applications of composite matrices, including protective and decorative coating, superadsorbent material, thin films, and lightweight high-strength fiber-reinforced materials, etc. In this study, quantum chemical calculations and experimental studies were performed to analyze the derivatives of diamine-fullerene prepared by the gas-phase solvent-free functionalization technique. In particular, the aliphatic 1,8-diamino-octane and the aromatic 1,5-diaminonaphthalene, which are diamines volatile in vacuum, were studied. We addressed two alternative mechanisms of the amination reaction via polyaddition and cross-linking of C(60) with diamines, using the pure GGA BLYP, PW91, and PBE functionals; further validation calculations were performed using the semiempirical dispersion GGA B97-D functional which contains parameters that have been specially adjusted by a more realistic view on dispersion contributions. In addition, we looked for experimental evidence for the covalent functionalization by using laser desorption/ionization time-of-flight mass spectrometry, thermogravimetric analysis, and atomic force microscopy.

Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

PubMed

Tao, Jianmin; Mo, Yuxiang

2016-08-12

Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

The Role of Cargo Proteins in GGA Recruitment

PubMed Central

Hirst, Jennifer; Seaman, Matthew N J; Buschow, Sonja I; Robinson, Margaret S

2007-01-01

Coat proteins are recruited onto membranes to form vesicles that transport cargo from one compartment to another, but the extent to which the cargo helps to recruit the coat proteins is still unclear. Here we have examined the role of cargo in the recruitment of Golgi-localized, γ-ear-containing, ADP ribosylation factor (ARF)-binding proteins (GGAs) onto membranes in HeLa cells. Moderate overexpression of CD8 chimeras with cytoplasmic tails containing DXXLL-sorting signals, which bind to GGAs, increased the localization of all three GGAs to perinuclear membranes, as observed by immunofluorescence. GGA2 was also expressed at approximately twofold higher levels in these cells because it was degraded more slowly. However, this difference only partially accounted for the increase in membrane localization because there was a approximately fivefold increase in GGA2 associated with crude membranes and a ∼12-fold increase in GGA2 associated with clathrin-coated vesicles (CCVs) in cells expressing CD8-DXXLL chimeras. The effect of cargo proteins on GGA recruitment was reconstituted in vitro using permeabilized control and CD8-DXXLL-expressing cells incubated with cytosol containing recombinant GGA2 constructs. Together, these results demonstrate that cargo proteins contribute to the recruitment of GGAs onto membranes and to the formation of GGA-positive CCVs. PMID:17451558

Predicting critical temperatures of iron(II) spin crossover materials: Density functional theory plus U approach

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

Zhang, Yachao, E-mail: yczhang@nano.gznc.edu.cn

2014-12-07

A first-principles study of critical temperatures (T{sub c}) of spin crossover (SCO) materials requires accurate description of the strongly correlated 3d electrons as well as much computational effort. This task is still a challenge for the widely used local density or generalized gradient approximations (LDA/GGA) and hybrid functionals. One remedy, termed density functional theory plus U (DFT+U) approach, introduces a Hubbard U term to deal with the localized electrons at marginal computational cost, while treats the delocalized electrons with LDA/GGA. Here, we employ the DFT+U approach to investigate the T{sub c} of a pair of iron(II) SCO molecular crystals (αmore » and β phase), where identical constituent molecules are packed in different ways. We first calculate the adiabatic high spin-low spin energy splitting ΔE{sub HL} and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (ΔH and ΔS), and finally extract T{sub c} by exploiting the ΔH/T − T and ΔS − T relationships. The results are in agreement with experiment. Analysis of geometries and electronic structures shows that the local ligand field in the α phase is slightly weakened by the H-bondings involving the ligand atoms and the specific crystal packing style. We find that this effect is largely responsible for the difference in T{sub c} of the two phases. This study shows the applicability of the DFT+U approach for predicting T{sub c} of SCO materials, and provides a clear insight into the subtle influence of the crystal packing effects on SCO behavior.« less

Density functional theory meta-GGA + U study of water incorporation in the metal-organic framework material Cu-BTC.

PubMed

Cockayne, Eric; Nelson, Eric B

2015-07-14

Water absorption in the metal-organic framework (MOF) material Cu-BTC, up to a concentration of 3.5 H2O per Cu ion, is studied via density functional theory at the meta-GGA + U level. The stable arrangements of water molecules show chains of hydrogen-bonded water molecules and a tendency to form closed cages at high concentration. Water clusters are stabilized primarily by a combination of water-water hydrogen bonding and Cu-water oxygen interactions. Stability is further enhanced by van der Waals interactions, electric field enhancement of water-water bonding, and hydrogen bonding of water to framework oxygens. We hypothesize that the tendency to form such stable clusters explains the particularly strong affinity of water to Cu-BTC and related MOFs with exposed metal sites.

Magnetic Exchange Couplings from Semilocal Functionals Evaluated Nonself-Consistently on Hybrid Densities: Insights on Relative Importance of Exchange, Correlation, and Delocalization.

PubMed

Phillips, Jordan J; Peralta, Juan E

2012-09-11

Semilocal functionals generally yield poor magnetic exchange couplings for transition-metal complexes, typically overpredicting in magnitude the experimental values. Here we show that semilocal functionals evaluated nonself-consistently on densities from hybrid functionals can yield magnetic exchange couplings that are greatly improved with respect to their self-consistent semilocal values. Furthermore, when semilocal functionals are evaluated nonself-consistently on densities from a "half-and-half" hybrid, their errors with respect to experimental values can actually be lower than those from self-consistent calculations with standard hybrid functionals such as PBEh or TPSSh. This illustrates that despite their notoriously poor performance for exchange couplings, for many systems semilocal functionals are capable of delivering accurate relative energies for magnetic states provided that their electron delocalization error is corrected. However, while self-consistent calculations with hybrids uniformly improve results for all complexes, evaluating nonself-consistently with semilocal functionals does not give a balanced improvement for both ferro- and antiferromagnetically coupled complexes, indicating that there is more at play with the overestimation problem than simply the delocalization error. Additionally, we show that for some systems the conventional wisdom of choice of exchange functional mattering more than correlation does not hold. This combined with results from the nonself-consistent calculations provide insight on clarifying the relative roles of exchange, correlation, and delocalization in calculating magnetic exchange coupling parameters in Kohn-Sham Density Functional Theory.

First-principles study of the covalently functionalized graphene

NASA Astrophysics Data System (ADS)

Jha, Sanjiv Kumar

Theoretical investigations of nanoscale systems, such as functionalized graphene, present major challenges to conventional computational methods employed in quantum chemistry and solid state physics. The properties of graphene can be affected by chemical functionalization. The surface functionalization of graphene offers a promising way to increase the solubility and reactivity of graphene for use in nanocomposites and chemical sensors. Covalent functionalization is an efficient way to open band-gap in graphene for applications in nanoelectronics. We apply ab initio computational methods based on density functional theory to study the covalent functionalization of graphene with benzyne (C6H4), tetracyanoethylene oxide (TCNEO), and carboxyl (COOH) groups. Our calculations are carried out using the SIESTA and Quantum-ESPRESSO electronic structure codes combined with the generalized gradient (GGA) and local density approximations (LDA) for the exchange correlation functionals and norm-conserving Troullier-Martins pseudopotentials. Calculated binding energies, densities of states (DOS), band structures, and vibrational spectra of functionalized graphene are analyzed in comparison with the available experimental data. Our calculations show that the reactions of [2 + 2] and [2 + 4] cycloaddition of C6H4 to the surface of pristine graphene are exothermic, with binding energies of --0.73 eV and --0.58 eV, respectively. Calculated band structures indicate that the [2 + 2] and [2 + 4] attachments of benzyne results in opening small band gap in graphene. The study of graphene--TCNEO interactions suggests that the reaction of cycloaddition of TCNEO to the surface of pristine graphene is endothermic. On the other hand, the reaction of cycloaddition of TCNEO is found to be exothermic for the edge of an H-terminated graphene sheet. Simulated Raman and infrared spectra of graphene functionalized with TCNEO are consistent with experimental results. The Raman (non-resonant) and infrared (IR) spectra of graphene functionalized with carboxyl (COON) groups are studied in graphene with no surface defects, di-vacancies (DV), and Stone-Wales (SW) defects. Simulated Raman and IR spectra of carboxylated graphene are consistent with available experimental results. Computed vibrational spectra of carboxylated graphene show that the presence of point defects near the functionalization site affect the Raman and IR spectroscopic signatures of the functionalized graphene.

Crafting ferromagnetism in Mn-doped MgO surfaces with p-type defects

PubMed Central

Panigrahi, Puspamitra; Araujo, C Moyses; Hussen, Tanveer; Ahuja, Rajeev

2014-01-01

We have employed first-principles calculations based on density functional theory (DFT) to investigate the underlying physics of unusual magnetism in Mn-doped MgO surface. We have studied two distinct scenarios. In the first one, two Mn atoms are substitutionally added to the surface, occupying the Mg sites. Both are stabilized in the Mn valence state carrying a local moment of 4.3 having a high-spin configuration. The magnetic interaction between the local moments display a very short-ranged characteristic, decaying very quickly with distance, and having antiferromagnetic ordering lower in energy. The energetics analysis also indicates that the Mn ions prefer to stay close to each other with an oxygen atom bridging the local interaction. In the second scenario, we started exploring the effect of native defects on the magnetism by crafting both Mg and O vacancies, which are p- and n-type defects, respectively. It is found that the electrons and holes affect the magnetic interaction between Mn ions in a totally different manner. The n-type defect leads to very similar magnetism, with the AFM configuration being energetically preferred. However, in the presence of Mg vacancy, the situation is quite different. The Mn atoms are further oxidized, giving rise to mixed Mn(d) ionic states. As a consequence, the Mn atoms couple ferromagnetically, when placed in the close configuration, and the obtained electronic structure is coherent with the double-exchange type of magnetic interaction. To guarantee the robustness of our results, we have benchmarked our calculations with three distinct theory levels, namely DFT-GGA, DFT-GGA+U and DFT-hybrid functionals. On the surface, the Mg vacancy displays lower formation energy occurring at higher concentrations. Therefore, our model systems can be the basis to explain a number of controversial results regarding transition metal doped oxides. PMID:27877684

Guanidinylated 3-gluconamidopropyl methacrylamide-s-3-aminopropyl methacrylamide copolymer as siRNA carriers for inhibiting human telomerase reverse transcriptase expression.

PubMed

Wu, Yang; Ji, Jinkai; Yang, Ran; Zhang, Xiaoqiang; Li, Yuanhui; Pu, Yuepu; Li, Xinsong

2013-01-01

In this report, a series of well-defined glucose- and guanidine-based cationic copolymers as gene carriers were developed to inhibit human telomerase reverse transcriptase (hTERT) gene expression. First of all, guandinylated 3-gluconamidopropyl methacrylamide-s-3-aminopropyl methacrylamide copolymers (guanidinylated GAPMA-s-APMA, abbreviated as GGA) were prepared via aqueous reversible addition--fragmentation chain transfer polymerization (RAFT). Then, three target hTERT siRNA TERT-1, TERT-2 and TERT-3 were designed and combined with GGA copolymers to form siRNA/GGA polyplexes. The polyplexes were examined by dynamic light scattering and agarose gel electrophoresis. The results indicated that GGA copolymers can condense siRNA effectively to form particles with the diameter from 157 nm to 411 nm and zeta potential values in the range from +3.7 to +15.8 mV at various charge ratios (N/P). The MTT assay data of siRNA/GGA polyplexes on human hepatocellular liver carcinoma cells (HepG2) indicated that GGA copolymer had better cell viabilities than polyethylenimine (PEI). Furthermore, the transfection of siRNA/GGA polyplexes was detected by real-time quantitative PCR (RT-qPCR) in HepG2. It was found that siRNA/GGA polyplexes could effectively silence hTERT mRNA expression in serum-free media (p<0.01). In the presence of serum, the hTERT mRNA expression in HepG2 cells have significant difference (p<0.01) between siRNA/GGA3 polyplexes and blank. The results showed that the GAPMA component can reduce the aggregation of protein in serum media. Therefore, the enhancement of transfection may be attributed to the combination of guadino groups and glucose component. And, the guandinylated 3-gluconamidopropyl methacrylamide-s-3-aminopropyl methacrylamide copolymers might be promise in gene delivery.

Multicomponent density functional theory embedding formulation.

PubMed

Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Multicomponent density functional theory embedding formulation

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

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density ismore » separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF{sup −} molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.« less

Preinduction of HSP70 promotes hypoxic tolerance and facilitates acclimatization to acute hypobaric hypoxia in mouse brain

PubMed Central

Zhang, Kuan; Zhao, Tong; Huang, Xin; Liu, Zhao-hui; Xiong, Lei; Li, Ming-ming; Wu, Li-ying; Zhao, Yong-qi

2008-01-01

It has been shown that induction of HSP70 by administration of geranylgeranylacetone (GGA) leads to protection against ischemia/reperfusion injury. The present study was performed to determine the effect of GGA on the survival of mice and on brain damage under acute hypobaric hypoxia. The data showed that the mice injected with GGA survived significantly longer than control animals (survival time of 9.55 ± 3.12 min, n = 16 vs. controls at 4.28 ± 4.29 min, n = 15, P < 0.005). Accordingly, the cellular necrosis or degeneration of the hippocampus and the cortex induced by sublethal hypoxia for 6 h could be attenuated by preinjection with GGA, especially in the CA2 and CA3 regions of the hippocampus. In addition, the activity of nitric oxide synthase (NOS) of the hippocampus and the cortex was increased after exposure to sublethal hypoxia for 6 h but could be inhibited by the preinjection of GGA. Furthermore, the expression of HSP70 was significantly increased at 1 h after GGA injection. These results suggest that administration of GGA improved survival rate and prevented acute hypoxic damage to the brain and that the underlying mechanism involved induction of HSP70 and inhibition of NOS activity. PMID:19105051

Long-range corrected density functional through the density matrix expansion based semilocal exchange hole.

PubMed

Patra, Bikash; Jana, Subrata; Samal, Prasanjit

2018-03-28

The exchange hole, which is one of the principal constituents of the density functional formalism, can be used to design accurate range-separated hybrid functionals in association with appropriate correlation. In this regard, the exchange hole derived from the density matrix expansion has gained attention due to its fulfillment of some of the desired exact constraints. Thus, the new long-range corrected density functional proposed here combines the meta generalized gradient approximation level exchange functional designed from the density matrix expansion based exchange hole coupled with the ab initio Hartree-Fock exchange through the range separation of the Coulomb interaction operator using the standard error function technique. Then, in association with the Lee-Yang-Parr correlation functional, the assessment and benchmarking of the above newly constructed range-separated functional with various well-known test sets shows its reasonable performance for a broad range of molecular properties, such as thermochemistry, non-covalent interaction and barrier heights of the chemical reactions.

Investigating the Psychometric Properties of the ACEI Global Guidelines Assessment (GGA) in Four Countries

ERIC Educational Resources Information Center

Hardin, Belinda J.; Bergen, Doris; Hung, Hsuan-Fang

2013-01-01

The ACEI Global Guidelines Assessment (GGA) was developed to provide an international assessment tool that can be used by early childhood educators to develop, assess, and improve program quality worldwide. This pilot study was conducted in four countries to investigate the psychometric properties of the GGA within and across different countries.…

Electronic structure and optical properties of CsI, CsI(Ag), and CsI(Tl)

NASA Astrophysics Data System (ADS)

Zhang, Zheng; Zhao, Qiang; Li, Yang; Ouyang, Xiao-Ping

2016-05-01

The band structure, electronic density of states and optical properties of CsI and of CsI doped with silver or thallium are studied by using a first-principles calculation based on density functional theory (DFT). The exchange and the correlation potentials among the electrons are described by using the generalized gradient approximation (GGA). The results of our study show that the electronic structure changes somewhat when CsI is doped with silver or thallium. The band gaps of CsI(Ag) and CsI(Tl) are smaller than that of CsI, and the width of the conduction band of CsI is increased when CsI is doped with thallium or silver. Two peaks located in the conduction band of CsI(Ag) and CsI(Tl) are observed from their electronic densities of states. The absorption coefficients of CsI, CsI(Ag), and CsI(Tl) are zero when their photon energies are below 3.5 eV, 1.5 eV, and 3.1 eV, respectively. The results show that doping can improve the detection performance of CsI scintillators. Our study can explain why doping can improve the detection performance from a theoretical point of view. The results of our research provide both theoretical support for the luminescent mechanisms at play in scintillator materials when they are exposed to radiation and a reference for CsI doping from the point of view of the electronic structure.

The optical spectrum of ternary alloy BBi1-xAsx

NASA Astrophysics Data System (ADS)

Yalcin, Battal G.; Aslan, M.; Ozcan, M. H.; Rahnamaye Aliabad, H. A.

2016-06-01

Among the III-V semiconductors, boron BBi and BAs as well as their alloys have attracted both scientific and technological interest in recent years. We present a calculation of the structural, electronic and optical properties of ternary alloy BBi1-xAsx by means of the WIEN2k software package. The exchange-correlation potential is treated by the generalized gradient approximation (GGA) within the schema of Wu and Cohen. Also, we have used the modified Becke-Johnson (mBJ) formalism to improve the band gap results. All the calculations have been performed after geometry optimization. In this study, we have investigated structural properties such as the lattice constant (a0), bulk modulus (B0) and its pressure derivative (B‧), and calculated the electronic band structures of the studied materials. Accurate calculation of linear optical properties, such as real (ɛ 1) and imaginary (ɛ 2) dielectric functions, reflectivity (R), electron energy loss spectrum, absorption coefficient (α), refractive index (n) and sum rule (Neff) are investigated. Our obtained results for studied binary compounds, BBi and BAs, fairly coincide with other theoretical calculations and experimental measurements. According to the best of our knowledge, no experimental or theoretical data are presently available for the studied ternary alloy BBi1-xAsx (0 < x < 1). The role of electronic band structure calculation with regards to the linear optical properties of BBi1-xAsx is discussed. The effect of the spin-orbit interaction (SOI) is also investigated and found to be quite small.

Effect of alloying on screw dislocation structure in Mo: atomistic modelling approach with ab-initio parametrization

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.

2005-03-01

The plastic deformation in bcc metals is realized by the motion of screw dislocations with a complex star-like non-planar core. In this case, the direct investigation of the solute effect by first principles electronic structure calculations is a challenging problem for which we follow a combined approach that includes atomistic dislocation modelling with ab-initio parametrization of interatomic interactions. The screw dislocation core structure in Mo alloys is described within the model of atomic row displacements along a dislocation line with the interatomic row potential estimated from total energy full-potential linear muffin-tin orbital (FLMTO) calculations with the generalized gradient approximation (GGA) for the exchange-correlation potential. We demonstrate (1) that the solute effect on the dislocation structure is different for ``hard'' and ``easy'' cores and (2) that the softener addition in a ``hard'' core gives rise to a structural transformation into a configuration with a lower energy through an intermediate state. The softener solute is shown to disturb locally the three-fold symmetry of the dislocation core and the dislocation structure tends to the split planar core.

Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

PubMed

Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura

2015-08-11

The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.

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

PubMed

Vikramaditya, Talapunur; Lin, Shiang-Tai

2017-06-05

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

Exchange-Correlation Hole in Polarized Insulators: Implications for the Microscopic Functional Theory of Dielectrics

NASA Astrophysics Data System (ADS)

Ortiz, Gerardo; Souza, Ivo; Martin, Richard M.

1998-01-01

We present a simple and direct proof that the exchange-correlation hole, and therefore the exchange-correlation energy, in a polarized insulator is not determined by the bulk density alone. It is uniquely characterized by the density and the macroscopic electric polarization of the dielectric medium.

Impact of anion replacement on the optoelectronic and thermoelectric properties of CaMg2X2, X= (N, P, As, Sb, Bi) compounds

NASA Astrophysics Data System (ADS)

Khan, Abdul Ahad; Yaseen, M.; Laref, A.; Murtaza, G.

2018-07-01

The structural, electronic, optical and thermoelectric properties of ternary CaMg2X2 (X = N, P, As, Sb and Bi) compounds are investigated using all electrons full potential linearized augment plane wave method. By using generalized gradient approximation (GGA), unit cell volumes of the compounds are optimized. For calculations of optical and electronic properties the modified Becke Johnson exchange potential is used along with the GGA. The direct energy band gap decreases by replacing the pnictogen elements, while indirect bandgap also decreases except for CaMg2As2. The optical properties show a prominent variation over the change of anion from N to Bi. There is inverse variation between refractive index and the band gap. The refractive indices of these compounds are high in the visible region and sharply decreased in the ultraviolet region. The thermoelectric properties are also studied using Boltzmann statistics through BoltzTrap code. A positive non-zero value of Seebeck coefficient shows a P-type semiconducting behavior of these compounds. High figure of merits (ZT) and optical conductivity peaks for all compounds reveal that they are good candidates for the thermo-electric and optoelectronics devices.

Development and Characterization of Novel Bioluminecent Systems

DTIC Science & Technology

2013-07-01

Ppy I108R. The following primers and their respective reverse compliments were used: Y447E, 5´- CT TTA ATT AAA TAC AAA GGA GAG CAG GTG GCC CCC GCT G...3´ [EcoRV] and I108R, 5´- GGA GTT GCA GTG GCG CCC GCG AAC GAC CGT TAT AAT GAA CGT-3´ [KasI] (bold represents the mutated codons, underlined...primers and their respective reverse compliments: Y447C, 5´- G AAG TCT TTA ATA AAA TAC AAA GGA TGT CAG GTG GCC CCC GCT G -3´ [PacI] and I108C, 5´- GGA

Ab initio studies of structural, electronic, optical, elastic and thermal properties of silver gallium dichalcogenides (AgGaX{sub 2}: X = S, Se, Te)

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

Sharma, Sheetal; Department of Physics, Panjab University, Chandigarh 160014; Verma, A.S., E-mail: ajay_phy@rediffmail.com

2014-05-01

Graphical abstract: - Highlights: • FP-LAPW method has been used to compute the solid state properties of AgGaX{sub 2} (X = S, Se, Te). • Electronic and optical properties reported with recently developed mBJ potential. • Thermal expansion, heat capacity, Debye temperature, entropy and Grüneisen parameter were evaluated. • Hardness was calculated for the first time at different temperature and pressure. - Abstract: We have performed ab initio calculations for the structural, electronic, optical, elastic and thermal properties of the silver gallium dichalcogenides (AgGaX{sub 2}: X = S, Se, Te). In this study, we have used the accurate full potentialmore » linearized augmented plane wave (FP-LAPW) method to find the equilibrium structural parameters and to compute the six elastic constants (C{sub 11}, C{sub 12}, C{sub 13}, C{sub 33}, C{sub 44} and C{sub 66}). We have reported electronic and optical properties with the recently developed density functional theory of Tran and Blaha, and this theory is used along with the Wu-Cohen generalized gradient approximation (WC-GGA) for the exchange-correlation potential. Furthermore, optical features such as dielectric functions, refractive indices, extinction coefficient, optical reflectivity, absorption coefficients and optical conductivities were calculated for photon energies up to 40 eV. The thermodynamical properties such as thermal expansion, heat capacity, debye temperature, entropy, Grüneisen parameter and bulk modulus were calculated employing the quasi-harmonic Debye model at different temperatures (0–900 K) and pressures (0–8 GPa) and the silent results were interpreted. Hardness of the materials was calculated for the first time at different temperatures and pressures.« less

Expressed microRNA associated with high rate of egg production in chicken ovarian follicles.

PubMed

Wu, N; Gaur, U; Zhu, Q; Chen, B; Xu, Z; Zhao, X; Yang, M; Li, D

2017-04-01

MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P < 0.05), including 11 known and six novel miRNAs. We found that all 11 known miRNAs were involved mainly in pathways of reproduction regulation, such as steroid hormone biosynthesis and dopaminergic synapse. Additionally, expression profiling of six randomly selected differentially regulated miRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Some miRNAs, such as gga-miR-34b, gga-miR-34c and gga-miR-216b, were reported to regulate processes such as proliferation, cell cycle, apoptosis and metastasis and were expressed differentially in ovaries of chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation. © 2016 Stichting International Foundation for Animal Genetics.

Source-Free Exchange-Correlation Magnetic Fields in Density Functional Theory.

PubMed

Sharma, S; Gross, E K U; Sanna, A; Dewhurst, J K

2018-03-13

Spin-dependent exchange-correlation energy functionals in use today depend on the charge density and the magnetization density: E xc [ρ, m]. However, it is also correct to define the functional in terms of the curl of m for physical external fields: E xc [ρ,∇ × m]. The exchange-correlation magnetic field, B xc , then becomes source-free. We study this variation of the theory by uniquely removing the source term from local and generalized gradient approximations to the functional. By doing so, the total Kohn-Sham moments are improved for a wide range of materials for both functionals. Significantly, the moments for the pnictides are now in good agreement with experiment. This source-free method is simple to implement in all existing density functional theory codes.

Accuracy of electron densities obtained via Koopmans-compliant hybrid functionals

NASA Astrophysics Data System (ADS)

Elmaslmane, A. R.; Wetherell, J.; Hodgson, M. J. P.; McKenna, K. P.; Godby, R. W.

2018-04-01

We evaluate the accuracy of electron densities and quasiparticle energy gaps given by hybrid functionals by directly comparing these to the exact quantities obtained from solving the many-electron Schrödinger equation. We determine the admixture of Hartree-Fock exchange to approximate exchange-correlation in our hybrid functional via one of several physically justified constraints, including the generalized Koopmans' theorem. We find that hybrid functionals yield strikingly accurate electron densities and gaps in both exchange-dominated and correlated systems. We also discuss the role of the screened Fock operator in the success of hybrid functionals.

Adiabatic corrections to density functional theory energies and wave functions.

PubMed

Mohallem, José R; Coura, Thiago de O; Diniz, Leonardo G; de Castro, Gustavo; Assafrão, Denise; Heine, Thomas

2008-09-25

The adiabatic finite-nuclear-mass-correction (FNMC) to the electronic energies and wave functions of atoms and molecules is formulated for density-functional theory and implemented in the deMon code. The approach is tested for a series of local and gradient corrected density functionals, using MP2 results and diagonal-Born-Oppenheimer corrections from the literature for comparison. In the evaluation of absolute energy corrections of nonorganic molecules the LDA PZ81 functional works surprisingly better than the others. For organic molecules the GGA BLYP functional has the best performance. FNMC with GGA functionals, mainly BLYP, show a good performance in the evaluation of relative corrections, except for nonorganic molecules containing H atoms. The PW86 functional stands out with the best evaluation of the barrier of linearity of H2O and the isotopic dipole moment of HDO. In general, DFT functionals display an accuracy superior than the common belief and because the corrections are based on a change of the electronic kinetic energy they are here ranked in a new appropriate way. The approach is applied to obtain the adiabatic correction for full atomization of alcanes C(n)H(2n+2), n = 4-10. The barrier of 1 mHartree is approached for adiabatic corrections, justifying its insertion into DFT.

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 1. Accurate thermochemistry and barrier heights.

PubMed

Alecu, I M; Truhlar, Donald G

2011-04-07

The reactions of CH(3)OH with the HO(2) and CH(3) radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)(Q)), core-valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol(-1) agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.

The double-soft limit in cosmological correlation functions and graviton exchange effects

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

Alinea, Allan L.; Kubota, Takahiro; Misumi, Nobuhiko, E-mail: alinea@het.phys.sci.osaka-u.ac.jp, E-mail: kubota@celas.osaka-u.ac.jp, E-mail: misumi.nobu@gmail.com

The graviton exchange effect on cosmological correlation functions is examined by employing the double-soft limit technique. A new relation among correlation functions that contain the effects due to graviton exchange diagrams in addition to those due to scalar-exchange and scalar-contact-interaction, is derived by using the background field method and independently by the method of Ward identities associated with dilatation symmetry. We compare these three terms, putting small values for the slow-roll parameters and (1− n {sub s} ) ≈ 0.042, where n {sub s} is the scalar spectral index. It is argued that the graviton exchange effects are more dominantmore » than the other two and could be observed in the trispectrum in the double-soft limit. Our observation strengthens the previous work by Seery, Sloth and Vernizzi, in which it has been argued that the graviton exchange dominates in the counter-collinear limit for single field slow-roll inflation.« less

Nuclear 82-kDa choline acetyltransferase decreases amyloidogenic APP metabolism in neurons from APP/PS1 transgenic mice.

PubMed

Albers, Shawn; Inthathirath, Fatima; Gill, Sandeep K; Winick-Ng, Warren; Jaworski, Ewa; Wong, Daisy Y L; Gros, Robert; Rylett, R Jane

2014-09-01

Alzheimer disease (AD) is associated with increased amyloidogenic processing of amyloid precursor protein (APP) to β-amyloid peptides (Aβ), cholinergic neuron loss with decreased choline acetyltransferase (ChAT) activity, and cognitive dysfunction. Both 69-kDa ChAT and 82-kDa ChAT are expressed in cholinergic neurons in human brain and spinal cord with 82-kDa ChAT localized predominantly to neuronal nuclei, suggesting potential alternative functional roles for the enzyme. By gene microarray analysis, we found that 82-kDa ChAT-expressing IMR32 neural cells have altered expression of genes involved in diverse cellular functions. Importantly, genes for several proteins that regulate APP processing along amyloidogenic and non-amyloidogenic pathways are differentially expressed in 82-kDa ChAT-containing cells. The predicted net effect based on observed changes in expression patterns of these genes would be decreased amyloidogenic APP processing with decreased Aβ production. This functional outcome was verified experimentally as a significant decrease in BACE1 protein levels and activity and a concomitant reduction in the release of endogenous Aβ1-42 from neurons cultured from brains of AD-model APP/PS1 transgenic mice. The expression of 82-kDa ChAT in neurons increased levels of GGA3, which is involved in trafficking BACE1 to lysosomes for degradation. shRNA-induced decreases in GGA3 protein levels attenuated the 82-kDa ChAT-mediated decreases in BACE1 protein and activity and Aβ1-42 release. Evidence that 82-kDa ChAT can enhance GGA3 gene expression is shown by enhanced GGA3 gene promoter activity in SN56 neural cells expressing this ChAT protein. These studies indicate a novel relationship between cholinergic neurons and APP processing, with 82-kDa ChAT acting as a negative regulator of Aβ production. This decreased formation of Aβ could result in protection for cholinergic neurons, as well as protection of other cells in the vicinity that are sensitive to increased levels of Aβ. Decreasing levels of 82-kDa ChAT due to increasing age or neurodegeneration could alter the balance towards increasing Aβ production, with this potentiating the decline in function of cholinergic neurons. Copyright © 2014 Elsevier Inc. All rights reserved.

Insight into proton transfer in phosphotungstic acid functionalized mesoporous silica-based proton exchange membrane fuel cells.

PubMed

Zhou, Yuhua; Yang, Jing; Su, Haibin; Zeng, Jie; Jiang, San Ping; Goddard, William A

2014-04-02

We have developed for fuel cells a novel proton exchange membrane (PEM) using inorganic phosphotungstic acid (HPW) as proton carrier and mesoporous silica as matrix (HPW-meso-silica) . The proton conductivity measured by electrochemical impedance spectroscopy is 0.11 S cm(-1) at 90 °C and 100% relative humidity (RH) with a low activation energy of ∼14 kJ mol(-1). In order to determine the energetics associated with proton migration within the HPW-meso-silica PEM and to determine the mechanism of proton hopping, we report density functional theory (DFT) calculations using the generalized gradient approximation (GGA). These DFT calculations revealed that the proton transfer process involves both intramolecular and intermolecular proton transfer pathways. When the adjacent HPWs are close (less than 17.0 Å apart), the calculated activation energy for intramolecular proton transfer within a HPW molecule is higher (29.1-18.8 kJ/mol) than the barrier for intermolecular proton transfer along the hydrogen bond. We find that the overall barrier for proton movement within the HPW-meso-silica membranes is determined by the intramolecular proton transfer pathway, which explains why the proton conductivity remains unchanged when the weight percentage of HPW on meso-silica is above 67 wt %. In contrast, the activation energy of proton transfer on a clean SiO2 (111) surface is computed to be as high as ∼40 kJ mol(-1), confirming the very low proton conductivity on clean silica surfaces observed experimentally.

Monte Carlo and Ab-initio calculation of TM (Ti, V, Cr, Mn, Fe, Co, Ni) doped MgH2 hydride: GGA and SIC approximation

NASA Astrophysics Data System (ADS)

Salmani, E.; Laghrissi, A.; Laamouri, R.; Benchafia, E.; Ez-Zahraouy, H.; Benyoussef, A.

2017-02-01

MgH2: TM (TM: V, Cr, Mn, Fe, Co, Ni) based dilute magnetic semiconductors (DMS) are investigated using first principle calculations. Our results show that the ferromagnetic state is stable when TM introduces magnetic moments as well as intrinsic carriers in TM: Co, V, Cr, Ti; Mg0.95TM0.05H2. Some of the DMS Ferro magnets under study exhibit a half-metallic behavior, which make them suitable for spintronic applications. The double exchange is shown to be the underlying mechanism responsible for the magnetism of such materials. The exchange interactions obtained from first principle calculations and used in a classical Ising model by a Monte Carlo approach resulted in ferromagnetic states with Curie temperatures within the ambient conditions.

Spin crossover in liquid Fe2SiO4 at high pressures: an ab initio Molecular Dynamics study

NASA Astrophysics Data System (ADS)

Munoz Ramo, D.; Stixrude, L. P.

2010-12-01

Liquid iron silicate (Fe2SiO4) is an important component of natural silicate liquids appearing in Earth’s interior. The effect of iron in the properties of these melts is a crucial issue, as it displays a high-spin to low-spin transition at high pressures which is accompanied by volume reduction and changes in the optical absorption spectrum. This phenomenon has a major influence on properties like the buoyancy or the thermal conductivity of the melt, and ultimately on the chemical and thermal evolution of our planet. Computer simulations using ab initio methods have proven to be a powerful approach to the study of liquid silicate systems[1,2], although not yet including Fe. In this paper, we report ab initio molecular dynamics studies of liquid iron silicate at high pressure (up to 300 GPa) and high temperatures (from 3000K to 6000K) that allow us to predict different properties of the system. We use mainly the GGA density functional for the calculation of the electronic structure. We also perform simulations with the GGA+U formalism to estimate the impact of strong electron correlation effects in the properties of the system at high pressures. The spin-polarized formalism is also used in order to keep track of the evolution of the iron magnetic moments in the system. By means of these simulations we predict the short and medium-range structure and thermodynamic properties of the liquid. We compute the theoretical Hugoniot for the system and find very good agreement between the GGA results and the equation of state values obtained from shock experiments [3], while the GGA+U results overestimate the Hugoniot curve at high pressures. Density crossover with the solid is obtained at about 110 GPa at 3000 K. Our calculations show that the spin crossover in this system takes place at a wide pressure interval, dependent on temperature. At 3000K, the spin transition starts at around 10 GPa and finishes at pressures around 250 Gpa. Increase of the temperature to 6000K reduces the interval of the transition to 180 GPa. [1] N. P. de Koker, L. Stixrude, B. B. Karki, Geochim Cosmochim Acta 2008, 72, 1427. [2] B. B. Karki, D. Bhattarai, L. Stixrude, Phys. Rev. B 2007, 76, 104205. [3] G. Q. Chen, T. J. Ahrens, E. M. Stolper, Phys. Earth Planet. Inter. 2002, 134, 35.

Liquid Aluminum: Atomic diffusion and viscosity from ab initio molecular dynamics

PubMed Central

Jakse, Noel; Pasturel, Alain

2013-01-01

We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid. PMID:24190311

Beyond the random-phase approximation for the electron correlation energy: the importance of single excitations.

PubMed

Ren, Xinguo; Tkatchenko, Alexandre; Rinke, Patrick; Scheffler, Matthias

2011-04-15

The random-phase approximation (RPA) for the electron correlation energy, combined with the exact-exchange (EX) energy, represents the state-of-the-art exchange-correlation functional within density-functional theory. However, the standard RPA practice--evaluating both the EX and the RPA correlation energies using Kohn-Sham (KS) orbitals from local or semilocal exchange-correlation functionals--leads to a systematic underbinding of molecules and solids. Here we demonstrate that this behavior can be corrected by adding a "single excitation" contribution, so far not included in the standard RPA scheme. A similar improvement can also be achieved by replacing the non-self-consistent EX total energy by the corresponding self-consistent Hartree-Fock total energy, while retaining the RPA correlation energy evaluated using KS orbitals. Both schemes achieve chemical accuracy for a standard benchmark set of noncovalent intermolecular interactions.

Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems.

PubMed

Walsh, T R

2005-02-07

The Wilson-Levy (WL) correlation functional is used together with Hartree-Fock (HF) theory to evaluate interaction energies at intermediate separations (i.e. around equilibrium separation) for several weakly-bonded systems. The HF+WL approach reproduces binding trends for all complexes studied: selected rare-gas dimers, isomers of the methane dimer, benzene dimer and naphthalene dimer, and base-pair stacking structures for pyrimidine, cytosine, uracil and guanine dimers. These HF+WL data are contrasted against results obtained from some popular functionals (including B3LYP and PBE), as well as two newly-developed functionals, X3LYP and xPBE. The utility of HF+WL, with reference to exact-exchange (EXX) density-functional theory, is discussed in terms of a suggested EXXWL exchange-correlation functional.

Exact thermal density functional theory for a model system: Correlation components and accuracy of the zero-temperature exchange-correlation approximation

DOE PAGES

Smith, J. C.; Pribram-Jones, A.; Burke, K.

2016-06-14

Thermal density functional theory calculations often use the Mermin-Kohn-Sham scheme, but employ ground-state approximations to the exchange-correlation (XC) free energy. In the simplest solvable nontrivial model, an asymmetric Hubbard dimer, we calculate the exact many-body energies and the exact Mermin-Kohn-Sham functionals for this system and extract the exact XC free energy. For moderate temperatures and weak correlation, we find this approximation to be excellent. Here we extract various exact free-energy correlation components and the exact adiabatic connection formula.

Exact thermal density functional theory for a model system: Correlation components and accuracy of the zero-temperature exchange-correlation approximation

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

Smith, J. C.; Pribram-Jones, A.; Burke, K.

Thermal density functional theory calculations often use the Mermin-Kohn-Sham scheme, but employ ground-state approximations to the exchange-correlation (XC) free energy. In the simplest solvable nontrivial model, an asymmetric Hubbard dimer, we calculate the exact many-body energies and the exact Mermin-Kohn-Sham functionals for this system and extract the exact XC free energy. For moderate temperatures and weak correlation, we find this approximation to be excellent. Here we extract various exact free-energy correlation components and the exact adiabatic connection formula.

AB INITIO STUDY OF OPTOELECTRONIC PROPERTIES OF SPINEL ZnAl2O4 BEYOND GGA AND LDA

NASA Astrophysics Data System (ADS)

Yousaf, Masood; Saeed, M. A.; Isa, Ahmad Radzi Mat; Rahnamaye Aliabad, H. A.; Noor, N. A.

2012-12-01

Electronic band structure and optical parameters of ZnAl2O4 are investigated by first-principles technique based on a new potential approximation, known as modified Becke-Johnson (mBJ). This method describes the excited states of insulators and semiconductors more accurately The recent direct band gap result by EV-GGA is underestimated by about 15% compared to our band gap value using mBJ-GGA. The value of the band gap of ZnAl2O4 decreases as follows: Eg(mBJ-GGA/LDA) > Eg(GGA) > Eg(LDA). The band structure base optical parametric quantities (dielectric constant, index of refraction, reflectivity and optical conductivity) are also calculated, and their variations with energy range are discussed. The first critical point (optical absorption's edge) in ZnAl2O4 occurs at about 5.26 eV in case of mBJ. This study about the optoelectronic properties indicates that ZnAl2O4 can be used in optical devices.

Protective effect of geranylgeranylacetone against loxoprofen sodium-induced small intestinal lesions in rats.

PubMed

Iwai, Tomohisa; Ichikawa, Takafumi; Kida, Mitsuhiro; Goso, Yukinobu; Kurihara, Makoto; Koizumi, Wasaburo; Ishihara, Kazuhiko

2011-02-10

Nonsteroidal anti-inflammatory drugs induce small intestinal ulcers but the preventive measures against it remain unknown. So we evaluated the effect of geranylgeranylacetone (GGA), a mucosal protectant, on both the mucus content and loxoprofen sodium-induced lesions in the rat small intestine. Normal male Wistar rats were given GGA (200 or 400mg/kg p.o.) and euthanized 3h later for measurement of mucin content and immunoreactivity. Other Wistar rats were given loxoprofen sodium (30mg/kg s.c.) and euthanized 24h later. GGA (30-400mg/kg p.o.) was administered twice: 30min before and 6h after loxoprofen sodium. The total mucin content of the small intestinal mucosa increased, especially the ratio of sialomucin, which increased approximately 20% more than the control level after a single dose of GGA. Loxoprofen sodium provoked linear ulcers along the mesenteric margin of the distal jejunum, accompanied by an increase in enterobacterial translocation. Treatment of the animals with GGA dose-dependently prevented the development of intestinal lesions, and bacterial translocation following loxoprofen sodium was also significantly decreased. GGA protects the small intestine against loxoprofen sodium-induced lesions, probably by inhibiting enterobacterial invasion of the mucosa as a result of the increase in the mucosal barrier. 2010 Elsevier B.V. All rights reserved.

Insights into the phosphoregulation of beta-secretase sorting signal by the VHS domain of GGA1.

PubMed

Shiba, Tomoo; Kametaka, Satoshi; Kawasaki, Masato; Shibata, Masahiro; Waguri, Satoshi; Uchiyama, Yasuo; Wakatsuki, Soichi

2004-06-01

BACE (beta-site amyloid precursor protein cleaving enzyme, beta-secretase) is a type-I membrane protein which functions as an aspartic protease in the production of beta-amyloid peptide, a causative agent of Alzheimer's disease. Its cytoplasmic tail has a characteristic acidic-cluster dileucine motif recognized by the VHS domain of adaptor proteins, GGAs (Golgi-localizing, gamma-adaptin ear homology domain, ARF-interacting). Here we show that BACE is colocalized with GGAs in the trans-Golgi network and peripheral structures, and phosphorylation of a serine residue in the cytoplasmic tail enhances interaction with the VHS domain of GGA1 by about threefold. The X-ray crystal structure of the complex between the GGA1-VHS domain and the BACE C-terminal peptide illustrates a similar recognition mechanism as mannose 6-phosphate receptors except that a glutamine residue closes in to fill the gap created by the shorter BACE peptide. The serine and lysine of the BACE peptide point their side chains towards the solvent. However, phosphorylation of the serine affects the lysine side chain and the peptide backbone, resulting in one additional hydrogen bond and a stronger electrostatic interaction with the VHS domain, hence the reversible increase in affinity.

GGA + U studies of the early actinide mononitrides and dinitrides

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Chetty, N.

2013-11-01

We present a detailed comparative study of the electronic and mechanical properties of the early actinide mononitrides and dinitrides within the framework of the Perdew-Burke-Ernzerhof generalized gradient approximation (GGA [PBE]) and GGA + U implementations of density functional theory with the inclusion of spin-orbit coupling. The dependence of selected observables of these materials on the effective U-parameter is investigated in detail. The properties include the lattice constant, bulk modulus, charge density distribution, hybridization of the atomic orbitals, energy of formation and the lattice dynamics. The inclusion of the Hubbard U parameter results in a proper description of the 5f electrons, and is subsequently used in the determination of the structural and electronic properties of these compounds. The mononitrides and dinitrides of the early actinides are metallic except for UN2, which is a semiconductor. These actinide nitrides are non-magnetic with the exception of UN, NpN, PuN, NpN2 and PuN2 that are magnetic systems with orbital-dependent magnetic moments oriented in the z-axis. We observed that ThN2 is elastically unstable to isotropic pressure. We discovered that UN2 is thermodynamically unstable, but may be stabilized by N vacancy formation.

Effect of pressure on the Raman-active modes of zircon (ZrSiO4): a first-principles study

NASA Astrophysics Data System (ADS)

Sheremetyeva, Natalya; Cherniak, Daniele J.; Watson, E. Bruce; Meunier, Vincent

2018-02-01

Density-functional theory (DFT) was employed in a first-principles study of the effects of pressure on the Raman-active modes of zircon (ZrSiO4), using both the generalized gradient and local density approximations (GGA and LDA, respectively). Beginning with the equilibrium structure at zero pressure, we conducted a calibration of the effect of pressure in a manner procedurally similar to an experimental calibration. For pressures between 0 and 7 GPa, we find excellent qualitative agreement of frequency-pressure slopes partial ω /partial P calculated from GGA DFT with results of previous experimental studies. In addition, we were able to rationalize the ω vs. P behavior based on details of the vibrational modes and their atomic displacements. Most of the partial ω /partial P slopes are positive as expected, but the symmetry of the zircon lattice also results in two negative slopes for modes that involve slight shearing and rigid rotation of SiO4 tetrahedra. Overall, LDA yields absolute values of the frequencies of the Raman-active modes in good agreement with experimental values, while GGA reproduces the shift in frequency with pressure especially well.

Investigation of half-metallic ferromagnetism in Heusler compounds Co2VZ (Z = Ga, Ge, As, Se)

NASA Astrophysics Data System (ADS)

Han, Jiajia; Wang, Zhengwei; Xu, Weiwei; Wang, Cuiping; Liu, Xingjun

2017-11-01

The electronic structures and magnetic properties of 3d transition metal-based full Heusler compounds Co2VZ (Z = Ga, Ge, As, Se) are investigated using the projector augmented wave (PAW) pseudopotential method. By considering the strong localization of Co 3d-states and V 3d-states at the Fermi level, these Co2VZ (Z = Ga, Ge, As, Se) compounds were treated in the framework of the generalized gradient approximation (GGA)+U method, and the results from the conventional GGA method are presented for comparison. The results that were obtained from the density of states with the GGA+U and GGA methods show that the Co2VGa compound is a half-metallic ferromagnet. For the Co2VGe and Co2VAs compounds, the GGA+U method predicts that these two compounds are half-metallic ferromagnetic by shifting the Fermi level to a lower value with respect to the gap in the minority states, when compared to the conventional GGA method. The energy gaps are determined to be 0.283 eV and 0.425 eV, respectively. However, these results show that the density of states of the Co2VSe compound has a metallic character, although the 3d states were corrected when using the GGA+U method. We found that the characteristic of half-metallic ferromagnetism is attributed to the interaction between the V 3d-states other than Co 3d-states. The calculated total magnetic moments are 2.046 μB, 3.054 μB and 4.012 μB respectively for the Co2VZ (Z = Ga, Ge, As) compounds with the GGA+U method. The relationship between total spin magnetic moment per formula unit and total number of valence electrons of these Heusler compounds is in agreement with the Slater-Pauling rule.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

PubMed

Hartman, Joshua D; Day, Graeme M; Beran, Gregory J O

2016-11-02

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13 C and 15 N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions

PubMed Central

2016-01-01

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study. PMID:27829821

Study of pressure variation effect on structural, opto-electronic, elastic, mechanical, and thermodynamic properties of SrLiF3

NASA Astrophysics Data System (ADS)

Erum, Nazia; Iqbal, Muhammad Azhar

2017-11-01

The structural, electronic, elastic, optical and thermodynamic properties of cubic fluoroperovskite SrLiF3 at ambient and high-pressure are investigated by using first-principles total energy calculations within the framework of Generalized Gradient Approximation (GGA), combined with Quasi-harmonic Debye model in which the phonon effects are considered. The pressure effects are determined in the range of 0-50 GPa, in which cubic stability of SrLiF3 fluoroperovskite remains valid. The computed lattice parameters agree well with experimental and previous theoretical results. Decrease in lattice constant and bonds length is observed with the increase in pressure from 0 to 50 GPa. The effect of increase in pressure on electronic band structure calculations with GGA and GGA plus Tran-Blaha modified Becke-Johnson (TB-mBJ) potential reveals a predominant characteristic associated with widening of bandgap. The influence of pressure on elastic constants and their related mechanical parameters have been discussed in detail. All the calculated optical properties such as the complex dielectric function Ԑ(ω), optical conductivity σ(ω), energy loss function L(ω), absorption coefficient α(w), refractive index n (ω), reflectivity R (ω), and effective number of electrons neff, via sum rules shift towards the higher energies under the application of pressure. Moreover, important thermodynamic properties heat capacities (Cp and Cv), volume expansion coefficient (α), and Debye temperature (θD) are predicted successfully in the wide temperature and pressure ranges.

Thermal Density Functional Theory: Time-Dependent Linear Response and Approximate Functionals from the Fluctuation-Dissipation Theorem

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

Pribram-Jones, Aurora; Grabowski, Paul E.; Burke, Kieron

We present that the van Leeuwen proof of linear-response time-dependent density functional theory (TDDFT) is generalized to thermal ensembles. This allows generalization to finite temperatures of the Gross-Kohn relation, the exchange-correlation kernel of TDDFT, and fluctuation dissipation theorem for DFT. Finally, this produces a natural method for generating new thermal exchange-correlation approximations.

Thermal Density Functional Theory: Time-Dependent Linear Response and Approximate Functionals from the Fluctuation-Dissipation Theorem

DOE PAGES

Pribram-Jones, Aurora; Grabowski, Paul E.; Burke, Kieron

2016-06-08

We present that the van Leeuwen proof of linear-response time-dependent density functional theory (TDDFT) is generalized to thermal ensembles. This allows generalization to finite temperatures of the Gross-Kohn relation, the exchange-correlation kernel of TDDFT, and fluctuation dissipation theorem for DFT. Finally, this produces a natural method for generating new thermal exchange-correlation approximations.

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods.

PubMed

Antony, Jens; Grimme, Stefan; Liakos, Dimitrios G; Neese, Frank

2011-10-20

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.

Nonseparable exchange–correlation functional for molecules, including homogeneous catalysis involving transition metals

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

Yu, Haoyu S.; Zhang, Wenjing; Verma, Pragya

2015-01-01

The goal of this work is to develop a gradient approximation to the exchange–correlation functional of Kohn–Sham density functional theory for treating molecular problems with a special emphasis on the prediction of quantities important for homogeneous catalysis and other molecular energetics. Our training and validation of exchange–correlation functionals is organized in terms of databases and subdatabases. The key properties required for homogeneous catalysis are main group bond energies (database MGBE137), transition metal bond energies (database TMBE32), reaction barrier heights (database BH76), and molecular structures (database MS10). We also consider 26 other databases, most of which are subdatabases of a newlymore » extended broad database called Database 2015, which is presented in the present article and in its ESI. Based on the mathematical form of a nonseparable gradient approximation (NGA), as first employed in the N12 functional, we design a new functional by using Database 2015 and by adding smoothness constraints to the optimization of the functional. The resulting functional is called the gradient approximation for molecules, or GAM. The GAM functional gives better results for MGBE137, TMBE32, and BH76 than any available generalized gradient approximation (GGA) or than N12. The GAM functional also gives reasonable results for MS10 with an MUE of 0.018 Å. The GAM functional provides good results both within the training sets and outside the training sets. The convergence tests and the smooth curves of exchange–correlation enhancement factor as a function of the reduced density gradient show that the GAM functional is a smooth functional that should not lead to extra expense or instability in optimizations. NGAs, like GGAs, have the advantage over meta-GGAs and hybrid GGAs of respectively smaller grid-size requirements for integrations and lower costs for extended systems. These computational advantages combined with the relatively high accuracy for all the key properties needed for molecular catalysis make the GAM functional very promising for future applications.« less

Inclusion of electron correlation for the target wave function in low-energy e sup minus +N sub 2 scattering

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

Meyer, H.; Pal, S.; Riss, U.V.

1992-07-01

The interaction of a scattering electron with a correlated but frozen'' target may be called the correlated static-exchange interaction. There are two prior investigations (J.R. Rumble, W.J. Stevens, and D. Truhlar, J. Phys. B 17, 3151 (1984); C Weatherford, F.B. Brown, and A. Temkin, Phys. Rev. A 35, 4561 (1987)) on scattering off the correlated static-exchange potential. Both of these investigations concentrated on {ital e}{sup {minus}}+N{sub 2} scattering, and both have found that the correlated static-exchange potential is less attractive than the static-exchange potential. We will show, however, that the correlated static-exchange potential is more attractive than the static-exchange one---atmore » least for {ital e}{sup {minus}}+N{sub 2} scattering in {sup 2}{Pi}{sub {ital g}} symmetry. The two prior investigations were misled by an improper degree of correlation and by an improper treatment of the exchange.« less

The effect of basis set and exchange-correlation functional on time-dependent density functional theory calculations within the Tamm-Dancoff approximation of the x-ray emission spectroscopy of transition metal complexes.

PubMed

Roper, Ian P E; Besley, Nicholas A

2016-03-21

The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals.

Formation of a parallel-stranded DNA homoduplex by d(GGA) repeat oligonucleotides.

PubMed Central

Suda, T; Mishima, Y; Asakura, H; Kominami, R

1995-01-01

The GGA9-H molecules consisting of a double helical stretch followed by a single-stranded 3'-terminal overhang of nine GGA sequence repeats exhibited a gel mobility-shifted band in a concentration-dependent manner, suggestive of the intermolecular complex formation. The position of the shifted band in a gel was almost identical to that of the Y-shaped dimer marker of the same molecular weight that had the two double-helices at one side. This suggests that GGA9-H dimerizes in a parallel orientation without the formation of four-stranded hairpin structure. Since the GGA9-H homoduplex was stably formed at pH 4, 7 and 9, the formation does not require protonation or deprotonation of the N1 position of adenines. Neither does it require the N7 group of guanines responsible for Hoogsteen base pairing from the methylation interference and modification studies. Modification of the N7 group of guanines with dimethyl sulfate (DMS) did not inhibit the association and also the N7 group in the homoduplex was not protected from DMS. On the other hand, the GAA9-H having the G to A base substitution did not show such an association with either GGA9-H or GAA9-H. These results suggest that the homoduplex formation may be due to G.G base pairing through non-Hoogsteen hydrogen bonds. Images PMID:7479009

Molecular Cytogenetic Characterization of Multiple Intrachromosomal Rearrangements in Two Representatives of the Genus Turdus (Turdidae, Passeriformes)

PubMed Central

Kretschmer, Rafael; Gunski, Ricardo José; Garnero, Analía Del Valle; Furo, Ivanete de Oliveira; O'Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.; de Oliveira, Edivaldo Herculano Corrêa

2014-01-01

Turdus rufiventris and Turdus albicollis, two songbirds belonging to the family Turdidae (Aves, Passeriformes) were studied by C-banding, 18S rDNA, as well as the use of whole chromosome probes derived from Gallus gallus (GGA) and Leucopternis albicollis (LAL). They showed very similar karyotypes, with 2n = 78 and the same pattern of distribution of heterochromatic blocks and hybridization patterns. However, the analysis of 18/28S rDNA has shown differences in the number of NOR-bearing chromosomes and ribosomal clusters. The hybridization pattern of GGA macrochromosomes was similar to the one found in songbirds studied by Fluorescent in situ hybridization, with fission of GGA 1 and GGA 4 chromosomes. In contrast, LAL chromosome paintings revealed a complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) on chromosome 2, which corresponds to GGA1q. The first inversion changed the chromosomal morphology and the second and third inversions changed the order of chromosome segments. Karyotype analysis in Turdus revealed that this genus has derived characteristics in relation to the putative avian ancestral karyotype, highlighting the importance of using new tools for analysis of chromosomal evolution in birds, such as the probes derived from L. albicollis, which make it possible to identify intrachromosomal rearrangements not visible with the use of GGA chromosome painting solely. PMID:25058578

Effective homogeneity of the exchange-correlation and non-interacting kinetic energy functionals under density scaling.

PubMed

Borgoo, Alex; Teale, Andrew M; Tozer, David J

2012-01-21

Correlated electron densities, experimental ionisation potentials, and experimental electron affinities are used to investigate the homogeneity of the exchange-correlation and non-interacting kinetic energy functionals of Kohn-Sham density functional theory under density scaling. Results are presented for atoms and small molecules, paying attention to the influence of the integer discontinuity and the choice of the electron affinity. For the exchange-correlation functional, effective homogeneities are highly system-dependent on either side of the integer discontinuity. By contrast, the average homogeneity-associated with the potential that averages over the discontinuity-is generally close to 4/3 when the discontinuity is computed using positive affinities for systems that do bind an excess electron and negative affinities for those that do not. The proximity to 4/3 becomes increasingly pronounced with increasing atomic number. Evaluating the discontinuity using a zero affinity in systems that do not bind an excess electron instead leads to effective homogeneities on the electron abundant side that are close to 4/3. For the non-interacting kinetic energy functional, the effective homogeneities are less system-dependent and the effect of the integer discontinuity is less pronounced. Average values are uniformly below 5/3. The study provides information that may aid the development of improved exchange-correlation and non-interacting kinetic energy functionals. © 2012 American Institute of Physics

Extensive homology of chicken macrochromosomes in the karyotypes of Trachemys scripta elegans and Crocodylus niloticus revealed by chromosome painting despite long divergence times.

PubMed

Kasai, F; O'Brien, P C M; Martin, S; Ferguson-Smith, M A

2012-01-01

We report extensive chromosome homology revealed by chromosome painting between chicken (Gallus gallus domesticus, GGA, 2n = 78) macrochromosomes (representing 70% of the chicken genome) and the chromosomes of a turtle, the red-eared slider (Trachemys scripta elegans, TSC, 2n = 50), and the Nile crocodile (Crocodylus niloticus, CNI, 2n = 32). Our data show that GGA1-8 arms seem to be conserved in the arms of TSC chromosomes, GGA1-2 arms are separated and homologous to CNI1p, 3q, 4q and 5q. In addition to GGAZ homologues in our previous study, large-scale GGA autosome syntenies have been conserved in turtle and crocodile despite hundreds of millions of years divergence time. Based on phylogenetic hypotheses that crocodiles diverged after the divergence of birds and turtles, our results in CNI suggest that GGA1-2 and TSC1-2 represent the ancestral state and that chromosome fissions followed by fusions have been the mechanisms responsible for the reduction of chromosome number in crocodiles. Copyright © 2012 S. Karger AG, Basel.

Application of graphene from exfoliation in kitchen mixer allows mechanical reinforcement of PVA/graphene film

NASA Astrophysics Data System (ADS)

Ismail, Zulhelmi; Abdullah, Abu Hannifa; Zainal Abidin, Anis Sakinah; Yusoh, Kamal

2017-08-01

Mechanical properties of polyvinyl alcohol (PVA) can be reinforced from the addition of graphene into its matrix. However, pristine graphene lacks solubility in water and thus makes dispersion a challenging task. Notably, functionalisation of graphene is required to accommodate graphene presence in the water. In this work, we have used a kitchen mixer to produce gum Arabic-graphene (GGA) for the first time as filler for mechanical reinforcement of PVA. For the characterisation of exfoliated graphene, mean lateral size of GGA was measured from the imaging by transmission electron microscopy while the mean thickness of graphene was predicted from the obtained spectra by Raman spectroscopy. During the preparation of PVA/graphene film by solution casting, GGA was varied between 0, 0.05, 0.075, 0.10 and 0.15 wt% in concentration. We found that the presence of GGA in PVA improves the tensile stress and elastic modulus about 72-200 and 19-187% from the original values. The data from Halpin-Tsai meanwhile suggested that the mechanical reinforcement of PVA/graphene film is due to the random distribution network of GGA in PVA.

The gga-let-7 family post-transcriptionally regulates TGFBR1 and LIN28B during the differentiation process in early chick development.

PubMed

Lee, Sang In; Jeon, Mi-Hyang; Kim, Jeom Sun; Jeon, Ik-Soo; Byun, Sung June

2015-12-01

Early chick embryogenesis is governed by a complex mechanism involving transcriptional and post-transcriptional regulation, although how post-transcriptional processes influence the balance between pluripotency and differentiation during early chick development have not been previously investigated. Here, we characterized the microRNA (miRNA) signature associated with differentiation in the chick embryo, and found that as expression of the gga-let-7 family increases through early development, expression of their direct targets, TGFBR1 and LIN28B, decreases; indeed, gga-let-7a-5p and gga-let-7b miRNAs directly bind to TGFBR1 and LIN28B transcripts. Our data further indicate that TGFBR1 and LIN28B maintain pluripotency by regulating POUV, NANOG, and CRIPTO. Therefore, gga-let-7 miRNAs act as post-transcriptional regulators of differentiation in blastodermal cells by repressing the expression of the TGFBR1 and LIN28B, which intrinsically controls blastodermal cell differentiation in early chick development. © 2015 Wiley Periodicals, Inc.

Ab-initio calculation of EuO doped with 5% of (Ti, V, Cr and Fe): GGA and SIC approximation

NASA Astrophysics Data System (ADS)

Rouchdi, M.; Salmani, E.; Bekkioui, N.; Ez-Zahraouy, H.; Hassanain, N.; Benyoussef, A.; Mzerd, A.

2017-12-01

In this research, a simple theoretical method is proposed to investigate the electronic, magnetic and optical properties of Europium oxide (EuO) doped with 5% of (Ti, V, Cr and Fe). For a basic understanding of these properties, we employed Density-Functional Theory (DFT) based calculations with the Korringa-Kohn-Rostoker code (KKR) combined with the Coherent Potential Approximation (CPA). Also we investigated the half-metallic ferromagnetic behavior of EuO doped with 5% of (Ti, V, Cr and Fe) within the self-interaction-corrected Generalized Gradient Approximation (GGA-SIC). Our calculated results revealed that the Eu0.95TM0.05O is ferromagnetic with a high transition temperature. Moreover, the optical absorption spectra revealed that the half metallicity has been also predicted.

Electronic properties of Fe3O4: LCAO calculations and Compton spectroscopy

NASA Astrophysics Data System (ADS)

Panwar, Kalpana; Tiwari, Shailja; Heda, N. L.

2018-04-01

We report the Compton profile (CP) measurements of Fe3O4 using 100 mCi241Am Compton spectrometer at momentum resolution of 0.55 a.u. The experimental CP has been compared with the linear combination of atomic orbitals (LCAO) data within density functional theory (DFT). The local density and generalized gradient approximation (LDA and GGA, respectively) have been used under the framework of DFT scheme. It is found that the DFT-GGA scheme gives the better agreement than to DFT-LDA. In addition, we have also computed the M ulliken's population (M P) and density of states (DOS) using the DFT scheme. M P data predicts the charge transfer from Fe to O atoms while DOS have confirmed the half metallic character of the compound.

Soft Functionals for Hard Matter

NASA Astrophysics Data System (ADS)

Cooper, Valentino R.; Yuk, Simuck F.; Krogel, Jaron T.

Theory and computation are critical to the materials discovery process. While density functional theory (DFT) has become the standard for predicting materials properties, it is often plagued by inaccuracies in the underlying exchange-correlation functionals. Using high-throughput DFT calculations we explore the accuracy of various exchange-correlation functionals for modeling the structural and thermodynamic properties of a wide range of complex oxides. In particular, we examine the feasibility of using the nonlocal van der Waals density correlation functional with C09 exchange (C09x), which was designed for sparsely packed soft matter, for investigating the properties of hard matter like bulk oxides. Preliminary results show unprecedented performance for some prototypical bulk ferroelectrics, which can be correlated with similarities between C09x and PBEsol. This effort lays the groundwork for understanding how these soft functionals can be employed as general purpose functionals for studying a wide range of materials where strong internal bonds and nonlocal interactions coexist. Research was sponsored by the US DOE, Office of Science, BES, MSED and Early Career Research Programs and used resources at NERSC.

The one-electron oxidation of a dithiolate molecule: the importance of chemical intuition.

PubMed

Bushnell, Eric A C; Burns, Thomas D; Boyd, Russell J

2014-05-14

A series of nine commonly used density functional methods were assessed to accurately predict the oxidation potential of the (C2H2S2(-2)/C2H2S2(•-)) redox couple. It was found that due to their greater tendency for charge delocalization the GGA functionals predict a structure where the radical electron is delocalized within the alkene backbone of C2H2S2(•-), whereas the hybrid functionals and the reference QCISD/cc-pVTZ predict that the radical electron remains localized on the sulfurs. However, chemical intuition suggests that the results obtained with the GGA functionals should be correct. Indeed, with the use of the geometries obtained at the HCTH/6-311++G(3df,3pd) level of theory both the QCISD and hybrid DFT methods yield a molecule with a delocalized electron. Notably, this new molecule lies at least 53 kJ mol(-1) lower in energy than the previously optimized one that had a localized radical. Using these new structures the calculated oxidation potential was found to be 2.71-2.97 V for the nine DFT functionals tested. The M06-L functional provided the best agreement with the QCISD/cc-pVTZ reference oxidation potential of 3.28 V.

Ground-state properties of trapped Bose-Fermi mixtures: Role of exchange correlation

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

Albus, Alexander P.; Wilkens, Martin; Illuminati, Fabrizio

2003-06-01

We introduce density-functional theory for inhomogeneous Bose-Fermi mixtures, derive the associated Kohn-Sham equations, and determine the exchange-correlation energy in local-density approximation. We solve numerically the Kohn-Sham system, and determine the boson and fermion density distributions and the ground-state energy of a trapped, dilute mixture beyond mean-field approximation. The importance of the corrections due to exchange correlation is discussed by a comparison with current experiments; in particular, we investigate the effect of the repulsive potential-energy contribution due to exchange correlation on the stability of the mixture against collapse.

Recent developments in LIBXC - A comprehensive library of functionals for density functional theory

NASA Astrophysics Data System (ADS)

Lehtola, Susi; Steigemann, Conrad; Oliveira, Micael J. T.; Marques, Miguel A. L.

2018-01-01

LIBXC is a library of exchange-correlation functionals for density-functional theory. We are concerned with semi-local functionals (or the semi-local part of hybrid functionals), namely local-density approximations, generalized-gradient approximations, and meta-generalized-gradient approximations. Currently we include around 400 functionals for the exchange, correlation, and the kinetic energy, spanning more than 50 years of research. Moreover, LIBXC is by now used by more than 20 codes, not only from the atomic, molecular, and solid-state physics, but also from the quantum chemistry communities.

Structural, electronic and optical properties of monoclinic Na{sub 2}Ti{sub 3}O{sub 7} from density functional theory calculations: A comparison with XRD and optical absorption measurements

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

Araújo-Filho, Adailton A.; Silva, Fábio L.R.; Righi, Ariete

Powder samples of bulk monoclinic sodium trititanate Na{sub 2}Ti{sub 3}O{sub 7} were prepared carefully by solid state reaction, and its monoclinic P2{sub 1}/m crystal structure and morphology were characterized by X-ray powder diffraction (XRD) and scanning electron microscopy (SEM), respectively. Moreover, the sodium trititanate main energy band gap was estimated as E{sub g}=3.51±0.01 eV employing UV–Vis spectroscopy, which is smaller than the measured 3.70 eV energy gap published previously by other authors. Aiming to achieve a better understanding of the experimental data, density functional theory (DFT) computations were performed within the local density and generalized gradient approximations (LDA and GGA,more » respectively) taking into account dispersion effects through the scheme of Tkatchenko and Scheffler (GGA+TS). Optimal lattice parameters, with deviations relative to measurements Δa=−0.06 Å, Δb=0.02 Å, and Δc=−0.09 Å, were obtained at the GGA level, which was then used to simulate the sodium trititanate electronic and optical properties. Indirect band transitions have led to a theoretical gap energy value of about 3.25 eV. Our results, however, differ from pioneer DFT results with respect to the specific Brillouin zone vectors for which the indirect transition with smallest energy value occurs. Effective masses for electrons and holes were also estimated along a set of directions in reciprocal space. Lastly, our calculations revealed a relatively large degree of optical isotropy for the Na{sub 2}Ti{sub 3}O{sub 7} optical absorption and complex dielectric function. - Graphical abstract: Monoclinic sodium trititanate Na2Ti3O7 was characterized by experiment and dispersion-corrected DFT calculations. An indirect gap of 3.5 eV is predicted, with heavy electrons and anisotropic holes ruling its conductivity. - Highlights: • Monoclinic Na2Ti3O7 was characterized by experiment (XRD, SEM, UV–Vis spectroscopy). • DFT GGA+TS optimized geometry and optoelectronic properties were obtained. • An experimental (theoretical) indirect gap of 3.5 (3.25) eV is predicted. • Heavy electrons and anisotropic holes rule the conductivity. • Ti-O bond lengths and charge states probably cause oxygen reactivity variations.« less

Effect of the nonlocal exchange on the performance of the orbital-dependent correlation functionals from second-order perturbation theory.

PubMed

Schweigert, Igor V; Bartlett, Rodney J

2008-09-28

Adding a fraction of the nonlocal exchange operator to the local orbital-dependent exchange potential improves the many-body perturbation expansion based on the Kohn-Sham determinant. The effect of such a hybrid scheme on the performance of the orbital-dependent correlation functional from the second-order perturbation theory (PT2H) is investigated numerically. A small fraction of the nonlocal exchange is often sufficient to ensure the existence of the self-consistent solution for the PT2H potential. In the He and Be atoms, including 37% of the nonlocal exchange leads to the correlation energies and electronic densities that are very close to the exact ones. In molecules, varying the fraction of the nonlocal exchange may result in the PT2H energy closely reproducing the CCSD(T) value; however such a fraction depends on the system and does not always result in an accurate electronic density. We also numerically verify that the "semicanonical" perturbation series includes most of the beneficial effects of the nonlocal exchange without sacrificing the locality of the exchange potential.

Investigation of the structural, electronic, elastic and thermodynamic properties of Curium Monopnictides: An ab initio study

NASA Astrophysics Data System (ADS)

Baaziz, H.; Guendouz, Dj.; Charifi, Z.; Akbudak, S.; Uğur, G.; Uğur, Ş.; Boudiaf, K.

2017-12-01

The structural, electronic, elastic and thermodynamic properties of Curium Monopnictides CmX (X = N, P, As, Sb and Bi) are investigated using first-principles calculations based on the density functional theory (DFT) and full potential linearized augmented plane wave (FP-LAPW) method under ambient condition and high pressure. The exchange-correlation term is treated using two approximations spin-polarized local density approximation (LSDA) and spin-polarized generalized gradient approximation generalized (GGA). The structural parameters such as the equilibrium lattice parameters, bulk modulus and the total energies are calculated in two phases: namely NaCl (B1) and CsCl (B2). The obtained results are compared with the previous theoretical and experimental results. A structural phase transition from B1 phase to B2 phase for Curium pnictides has been obtained. The highest transition pressure is 122 GPa for CmN and the lowest one is 10.0 GPa for CmBi compound. The electronic properties show that these materials exhibit half-metallic behavior in both phases. The magnetic moment is found to be around 7.0 μB. The mechanical properties of CmX (X = N, P, As, Sb and Bi) are predicted from the calculated elastic constants. Our calculated results are in good agreement with the theoretical results in literature. The effect of pressure and temperature on the thermodynamic properties like the cell volume, bulk modulus and the specific heats C𝜗 and CP, the entropy 𝒮 and the Grüneisen parameter γ have been foreseen at expanded pressure and temperature ranges.

Evolution of the orbitals Dy-4f in the DyB2 compound using the LDA, PBE approximations, and the PBE0 hybrid functional

NASA Astrophysics Data System (ADS)

Rasero Causil, Diego; Ortega López, César; Espitia Rico, Miguel

2018-04-01

Computational calculations of total energy based on density functional theory were used to investigate the structural, electronic, and magnetic properties of the DyB2 compounds in the hexagonal structure. The calculations were carried out by means of the full-potential linearized augmented plane wave (FP-LAPW) method, employing the computational Wien2k package. The local density approximation (LDA) and the generalized gradient approximation (GGA) were used for the electron-electron interactions. Additionally, we used the functional hybrid PBE0 for a better description the electronic and magnetic properties, because the DyB2 compound is a strongly-correlated system. We found that the calculated lattice constant agrees well with the values reported theoretically and experimentally. The density of states (DOS) calculation shows that the compound exhibits a metallic behavior and has magnetic properties, with a total magnetic moment of 5.47 μ0/cell determined mainly by the 4f states of the rare earth elements. The functional PBE0 shows a strong localization of the Dy-4f orbitals.

Extension of the KLI approximation toward the exact optimized effective potential.

PubMed

Iafrate, G J; Krieger, J B

2013-03-07

The integral equation for the optimized effective potential (OEP) is utilized in a compact form from which an accurate OEP solution for the spin-unrestricted exchange-correlation potential, Vxcσ, is obtained for any assumed orbital-dependent exchange-correlation energy functional. The method extends beyond the Krieger-Li-Iafrate (KLI) approximation toward the exact OEP result. The compact nature of the OEP equation arises by replacing the integrals involving the Green's function terms in the traditional OEP equation by an equivalent first-order perturbation theory wavefunction often referred to as the "orbital shift" function. Significant progress is then obtained by solving the equation for the first order perturbation theory wavefunction by use of Dalgarno functions which are determined from well known methods of partial differential equations. The use of Dalgarno functions circumvents the need to explicitly address the Green's functions and the associated problems with "sum over states" numerics; as well, the Dalgarno functions provide ease in dealing with inherent singularities arising from the origin and the zeros of the occupied orbital wavefunctions. The Dalgarno approach for finding a solution to the OEP equation is described herein, and a detailed illustrative example is presented for the special case of a spherically symmetric exchange-correlation potential. For the case of spherical symmetry, the relevant Dalgarno function is derived by direct integration of the appropriate radial equation while utilizing a user friendly method which explicitly treats the singular behavior at the origin and at the nodal singularities arising from the zeros of the occupied states. The derived Dalgarno function is shown to be an explicit integral functional of the exact OEP Vxcσ, thus allowing for the reduction of the OEP equation to a self-consistent integral equation for the exact exchange-correlation potential; the exact solution to this integral equation can be determined by iteration with the natural zeroth order correction given by the KLI exchange-correlation potential. Explicit analytic results are provided to illustrate the first order iterative correction beyond the KLI approximation. The derived correction term to the KLI potential explicitly involves spatially weighted products of occupied orbital densities in any assumed orbital-dependent exchange-correlation energy functional; as well, the correction term is obtained with no adjustable parameters. Moreover, if the equation for the exact optimized effective potential is further iterated, one can obtain the OEP as accurately as desired.

Extension of the KLI approximation toward the exact optimized effective potential

NASA Astrophysics Data System (ADS)

Iafrate, G. J.; Krieger, J. B.

2013-03-01

The integral equation for the optimized effective potential (OEP) is utilized in a compact form from which an accurate OEP solution for the spin-unrestricted exchange-correlation potential, Vxcσ, is obtained for any assumed orbital-dependent exchange-correlation energy functional. The method extends beyond the Krieger-Li-Iafrate (KLI) approximation toward the exact OEP result. The compact nature of the OEP equation arises by replacing the integrals involving the Green's function terms in the traditional OEP equation by an equivalent first-order perturbation theory wavefunction often referred to as the "orbital shift" function. Significant progress is then obtained by solving the equation for the first order perturbation theory wavefunction by use of Dalgarno functions which are determined from well known methods of partial differential equations. The use of Dalgarno functions circumvents the need to explicitly address the Green's functions and the associated problems with "sum over states" numerics; as well, the Dalgarno functions provide ease in dealing with inherent singularities arising from the origin and the zeros of the occupied orbital wavefunctions. The Dalgarno approach for finding a solution to the OEP equation is described herein, and a detailed illustrative example is presented for the special case of a spherically symmetric exchange-correlation potential. For the case of spherical symmetry, the relevant Dalgarno function is derived by direct integration of the appropriate radial equation while utilizing a user friendly method which explicitly treats the singular behavior at the origin and at the nodal singularities arising from the zeros of the occupied states. The derived Dalgarno function is shown to be an explicit integral functional of the exact OEP Vxcσ, thus allowing for the reduction of the OEP equation to a self-consistent integral equation for the exact exchange-correlation potential; the exact solution to this integral equation can be determined by iteration with the natural zeroth order correction given by the KLI exchange-correlation potential. Explicit analytic results are provided to illustrate the first order iterative correction beyond the KLI approximation. The derived correction term to the KLI potential explicitly involves spatially weighted products of occupied orbital densities in any assumed orbital-dependent exchange-correlation energy functional; as well, the correction term is obtained with no adjustable parameters. Moreover, if the equation for the exact optimized effective potential is further iterated, one can obtain the OEP as accurately as desired.

Exchange-correlation approximations for reduced-density-matrix-functional theory at finite temperature: Capturing magnetic phase transitions in the homogeneous electron gas

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

Baldsiefen, Tim; Cangi, Attila; Eich, F. G.

Here, we derive an intrinsically temperature-dependent approximation to the correlation grand potential for many-electron systems in thermodynamical equilibrium in the context of finite-temperature reduced-density-matrix-functional theory (FT-RDMFT). We demonstrate its accuracy by calculating the magnetic phase diagram of the homogeneous electron gas. We compare it to known limits from highly accurate quantum Monte Carlo calculations as well as to phase diagrams obtained within existing exchange-correlation approximations from density functional theory and zero-temperature RDMFT.

Exchange-correlation approximations for reduced-density-matrix-functional theory at finite temperature: Capturing magnetic phase transitions in the homogeneous electron gas

DOE PAGES

Baldsiefen, Tim; Cangi, Attila; Eich, F. G.; ...

2017-12-18

Here, we derive an intrinsically temperature-dependent approximation to the correlation grand potential for many-electron systems in thermodynamical equilibrium in the context of finite-temperature reduced-density-matrix-functional theory (FT-RDMFT). We demonstrate its accuracy by calculating the magnetic phase diagram of the homogeneous electron gas. We compare it to known limits from highly accurate quantum Monte Carlo calculations as well as to phase diagrams obtained within existing exchange-correlation approximations from density functional theory and zero-temperature RDMFT.

Extent of Fock-exchange mixing for a hybrid van der Waals density functional?

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-05-01

The vdW-DF-cx0 exchange-correlation hybrid design [K. Berland et al., J. Chem. Phys. 146, 234106 (2017)] has a truly nonlocal correlation component and aims to facilitate concurrent descriptions of both covalent and non-covalent molecular interactions. The vdW-DF-cx0 design mixes a fixed ratio, a, of the Fock exchange into the consistent-exchange van der Waals density functional, vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)]. The mixing value a is sometimes taken as a semi-empirical parameter in hybrid formulations. Here, instead, we assert a plausible optimum average a value for the vdW-DF-cx0 design from a formal analysis; A new, independent determination of the mixing a is necessary since the Becke fit [A. D. Becke, J. Chem. Phys. 98, 5648 (1993)], yielding a' = 0.2, is restricted to semilocal correlation and does not reflect non-covalent interactions. To proceed, we adapt the so-called two-legged hybrid construction [K. Burke et al., Chem. Phys. Lett. 265, 115 (1997)] to a starting point in the vdW-DF-cx functional. For our approach, termed vdW-DF-tlh, we estimate the properties of the adiabatic-connection specification of the exact exchange-correlation functional, by combining calculations of the Fock exchange and of the coupling-constant variation in vdW-DF-cx. We find that such vdW-DF-tlh hybrid constructions yield accurate characterizations of molecular interactions (even if they lack self-consistency). The accuracy motivates trust in the vdW-DF-tlh determination of system-specific values of the Fock-exchange mixing. We find that an average value a' = 0.2 best characterizes the vdW-DF-tlh description of covalent and non-covalent interactions, although there exists some scatter. This finding suggests that the original Becke value, a' = 0.2, also represents an optimal average Fock-exchange mixing for the new, truly nonlocal-correlation hybrids. To enable self-consistent calculations, we furthermore define and test a zero-parameter hybrid functional vdW-DF-cx0p (having fixed mixing a' = 0.2) and document that this truly nonlocal correlation hybrid works for general molecular interactions (at reference and at relaxed geometries). It is encouraging that the vdW-DF-cx0p functional remains useful also for descriptions of some extended systems.

Water on BN doped benzene: A hard test for exchange-correlation functionals and the impact of exact exchange on weak binding

DOE PAGES

Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; ...

2014-10-22

Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we showmore » that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B₃N₃H₆) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.« less

Non-empirical exchange-correlation parameterizations based on exact conditions from correlated orbital theory.

PubMed

Haiduke, Roberto Luiz A; Bartlett, Rodney J

2018-05-14

Some of the exact conditions provided by the correlated orbital theory are employed to propose new non-empirical parameterizations for exchange-correlation functionals from Density Functional Theory (DFT). This reparameterization process is based on range-separated functionals with 100% exact exchange for long-range interelectronic interactions. The functionals developed here, CAM-QTP-02 and LC-QTP, show mitigated self-interaction error, correctly predict vertical ionization potentials as the negative of eigenvalues for occupied orbitals, and provide nice excitation energies, even for challenging charge-transfer excited states. Moreover, some improvements are observed for reaction barrier heights with respect to the other functionals belonging to the quantum theory project (QTP) family. Finally, the most important achievement of these new functionals is an excellent description of vertical electron affinities (EAs) of atoms and molecules as the negative of appropriate virtual orbital eigenvalues. In this case, the mean absolute deviations for EAs in molecules are smaller than 0.10 eV, showing that physical interpretation can indeed be ascribed to some unoccupied orbitals from DFT.

Non-empirical exchange-correlation parameterizations based on exact conditions from correlated orbital theory

NASA Astrophysics Data System (ADS)

Haiduke, Roberto Luiz A.; Bartlett, Rodney J.

2018-05-01

Some of the exact conditions provided by the correlated orbital theory are employed to propose new non-empirical parameterizations for exchange-correlation functionals from Density Functional Theory (DFT). This reparameterization process is based on range-separated functionals with 100% exact exchange for long-range interelectronic interactions. The functionals developed here, CAM-QTP-02 and LC-QTP, show mitigated self-interaction error, correctly predict vertical ionization potentials as the negative of eigenvalues for occupied orbitals, and provide nice excitation energies, even for challenging charge-transfer excited states. Moreover, some improvements are observed for reaction barrier heights with respect to the other functionals belonging to the quantum theory project (QTP) family. Finally, the most important achievement of these new functionals is an excellent description of vertical electron affinities (EAs) of atoms and molecules as the negative of appropriate virtual orbital eigenvalues. In this case, the mean absolute deviations for EAs in molecules are smaller than 0.10 eV, showing that physical interpretation can indeed be ascribed to some unoccupied orbitals from DFT.

Correlation functional in screened-exchange density functional theory procedures.

PubMed

Chan, Bun; Kawashima, Yukio; Hirao, Kimihiko

2017-10-15

In the present study, we have explored several prospects for the further development of screened-exchange density functional theory (SX-DFT) procedures. Using the performance of HSE06 as our measure, we find that the use of alternative correlation functionals (as oppose to PBEc in HSE06) also yields adequate results for a diverse set of thermochemical properties. We have further examined the performance of new SX-DFT procedures (termed HSEB-type methods) that comprise the HSEx exchange and a (near-optimal) reparametrized B97c (c OS,0  = c SS,0  = 1, c OS,1  = -1.5, c OS,2  = -0.644, c SS,1  = -0.5, and c SS,2  = 1.10) correlation functionals. The different variants of HSEB all perform comparably to or slightly better than the original HSE-type procedures. These results, together with our fundamental analysis of correlation functionals, point toward various directions for advancing SX-DFT methods. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Absence of B1-B2 structural transition in lithium halides under hydrostatic pressure

NASA Astrophysics Data System (ADS)

de Coss, Romeo; Murrieta, Gabriel

2005-03-01

We have investigated the B1-B2 structural transition in LiF, LiCl, LiBr, and LiI under hydrostatic pressure by means of first-principles total-energy calculations using the Full- Potential LAPW method. In order to analyze the gradient effects, we have performed calculations using the local density approximation (LDA) and the generalized gradient approximation (GGA), for the exchange and correlation potential. In agreement with the experimental observations, we find that even for pressures higher than 100 GPa, the Li halides do not present the B1-B2 structural transition. In order to understand this behavior, we have calculated the distribution of the electron densities. From the analysis of the distribution of electron densities for the Li halides in the B1 and B2 phases, we find that for this group of ionic compounds the B1 phase have a distribution of electron densities more homogeneous than in the B2 phase, preventing the B1-B2 structural transition. This work was partially supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant No. 43830-F.

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: III. Fat deposition and intramuscular fat content.

PubMed

Nassar, M K; Goraga, Z S; Brockmann, G A

2013-02-01

In this study, a genome scan was performed to detect genomic loci that affect fat deposition in white adipose tissues and muscles in 278 F (2) males of reciprocal crosses between the genetically and phenotypically extreme inbred chicken lines New Hampshire (NHI) and White Leghorn (WL77). Genome-wide highly significant quantitative trait loci (QTL) influencing fat deposition in white adipose tissues were found on GGA2 and 4. The peak QTL positions for different visceral and subcutaneous white adipose tissues were located between 41.4 and 112.4 Mb on GGA2 and between 76.2 and 78.7 Mb on GGA4, which explained 4.2-10.4% and 4.3-11.6% respectively of the phenotypic F (2) variances. Contrary to our expectations, the QTL allele descending from the lean line WL77 on GGA4 led to increased fat deposition. We suggest a transgressive action of the obesity allele only if it is not in the genetic background of the line WL77. Additional highly significant loci for subcutaneous adipose tissue mass were identified on GGA12 and 15. For intramuscular fat content, a suggestive QTL was located on GGA14. The analysed crosses provide a valuable resource for further fine mapping of fatness genes and subsequent gene discovery. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

The direct exchange mechanism of induced spin polarization of low-dimensional π-conjugated carbon- and h-BN fragments at LSMO(001) MnO-terminated interfaces

NASA Astrophysics Data System (ADS)

Kuklin, Artem V.; Kuzubov, Alexander A.; Kovaleva, Evgenia A.; Lee, Hyosun; Sorokin, Pavel B.; Sakai, Seiji; Entani, Shiro; Naramoto, Hiroshi; Avramov, Paul

2017-10-01

Induced spin polarization of π-conjugated carbon and h-BN low dimensional fragments at the interfaces formed by deposition of pentacene molecule and narrow zigzag graphene and h-BN nanoribbons on MnO2-terminated LSMO(001) thin film was studied using GGA PBE+U PAW D3-corrected approach. Induced spin polarization of π-conjugated low-dimensional fragments is caused by direct exchange with Mn ions of LSMO(001) MnO-derived surface. Due to direct exchange, the pentacene molecule changes its diamagnetic narrow-band gap semiconducting nature to the ferromagnetic semiconducting state with 0.15 eV energy shift between spin-up and spin-down valence bands and total magnetic moment of 0.11 μB. Direct exchange converts graphene nanoribbon to 100% spin-polarized half-metal with large amplitude of spin-up electronic density at the Fermi level. The direct exchange narrows the h-BN nanoribbon band gap from 4.04 to 1.72 eV in spin-up channel and converts the h-BN ribbon semiconducting diamagnetic nature to a semiconducting magnetic one. The electronic structure calculations demonstrate a possibility to control the spin properties of low-dimensional π-conjugated carbon and h-BN fragments by direct exchange with MnO-derived LSMO(001) surface for spin-related applications.

Generalization of the optimized-effective-potential model to include electron correlation: A variational derivation of the Sham-Schlueter equation for the exact exchange-correlation potential

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

Casida, M.E.

1995-03-01

The now classic optimized-effective-potential (OEP) approach of Sharp and Horton [Phys Rev. 90, 317 (1953)] and Talman and Shadwick [Phys. Rev. A 14, 36 (1976)] seeks the local potential that is variationally optimized to best approximate the Hartree-Fock exchange operator. The resulting OEP can be identified as the exchange potential of Kohn-Sham density-functional theory. The present work generalizes this OEP approach to treat the correlated case, and shows that the Kohn-Sham exchange-correlation potential is the variationally best local approximation to the exchange-correlation self-energy. This provides a variational derivation of the equation for the exact exchange-correlation potential that was derived bymore » Sham and Schlueter using a density condition. Implications for an approximate physical interpretation of the Kohn-Sham orbitals are discussesd. A correlated generalization of the Sharp-Horton--Krieger-Li-Iafrate [Phys Lett. A 146, 256 (1990)] approximation of the exchange potential is introduced in the quasiparticle limit.« less

Point defects in ZnO: an approach from first principles

PubMed Central

Oba, Fumiyasu; Choi, Minseok; Togo, Atsushi; Tanaka, Isao

2011-01-01

Recent first-principles studies of point defects in ZnO are reviewed with a focus on native defects. Key properties of defects, such as formation energies, donor and acceptor levels, optical transition energies, migration energies and atomic and electronic structure, have been evaluated using various approaches including the local density approximation (LDA) and generalized gradient approximation (GGA) to DFT, LDA+U/GGA+U, hybrid Hartree–Fock density functionals, sX and GW approximation. Results significantly depend on the approximation to exchange correlation, the simulation models for defects and the post-processes to correct shortcomings of the approximation and models. The choice of a proper approach is, therefore, crucial for reliable theoretical predictions. First-principles studies have provided an insight into the energetics and atomic and electronic structures of native point defects and impurities and defect-induced properties of ZnO. Native defects that are relevant to the n-type conductivity and the non-stoichiometry toward the O-deficient side in reduced ZnO have been debated. It is suggested that the O vacancy is responsible for the non-stoichiometry because of its low formation energy under O-poor chemical potential conditions. However, the O vacancy is a very deep donor and cannot be a major source of carrier electrons. The Zn interstitial and anti-site are shallow donors, but these defects are unlikely to form at a high concentration in n-type ZnO under thermal equilibrium. Therefore, the n-type conductivity is attributed to other sources such as residual impurities including H impurities with several atomic configurations, a metastable shallow donor state of the O vacancy, and defect complexes involving the Zn interstitial. Among the native acceptor-type defects, the Zn vacancy is dominant. It is a deep acceptor and cannot produce a high concentration of holes. The O interstitial and anti-site are high in formation energy and/or are electrically inactive and, hence, are unlikely to play essential roles in electrical properties. Overall defect energetics suggests a preference for the native donor-type defects over acceptor-type defects in ZnO. The O vacancy, Zn interstitial and Zn anti-site have very low formation energies when the Fermi level is low. Therefore, these defects are expected to be sources of a strong hole compensation in p-type ZnO. For the n-type doping, the compensation of carrier electrons by the native acceptor-type defects can be mostly suppressed when O-poor chemical potential conditions, i.e. low O partial pressure conditions, are chosen during crystal growth and/or doping. PMID:27877390

Influence of the exchange and correlation functional on the structure of amorphous InSb and In3SbTe2 compounds

NASA Astrophysics Data System (ADS)

Gabardi, Silvia; Caravati, Sebastiano; Los, Jan H.; Kühne, Thomas D.; Bernasconi, Marco

2016-05-01

We have investigated the structural, vibrational, and electronic properties of the amorphous phase of InSb and In3SbTe2 compounds of interest for applications in phase change non-volatile memories. Models of the amorphous phase have been generated by quenching from the melt by molecular dynamics simulations based on density functional theory. In particular, we have studied the dependence of the structural properties on the choice of the exchange-correlation functional. It turns out that the use of the Becke-Lee-Yang-Parr functional provides models with a much larger fraction of In atoms in a tetrahedral bonding geometry with respect to previous results obtained with the most commonly used Perdew-Becke-Ernzerhof functional. This outcome is at odd with the properties of Ge2Sb2Te5 phase change compound for which the two exchange-correlation functionals yield very similar results on the structure of the amorphous phase.

Influence of the exchange and correlation functional on the structure of amorphous InSb and In3SbTe2 compounds.

PubMed

Gabardi, Silvia; Caravati, Sebastiano; Los, Jan H; Kühne, Thomas D; Bernasconi, Marco

2016-05-28

We have investigated the structural, vibrational, and electronic properties of the amorphous phase of InSb and In3SbTe2 compounds of interest for applications in phase change non-volatile memories. Models of the amorphous phase have been generated by quenching from the melt by molecular dynamics simulations based on density functional theory. In particular, we have studied the dependence of the structural properties on the choice of the exchange-correlation functional. It turns out that the use of the Becke-Lee-Yang-Parr functional provides models with a much larger fraction of In atoms in a tetrahedral bonding geometry with respect to previous results obtained with the most commonly used Perdew-Becke-Ernzerhof functional. This outcome is at odd with the properties of Ge2Sb2Te5 phase change compound for which the two exchange-correlation functionals yield very similar results on the structure of the amorphous phase.

Ultra-sensitive pressure dependence of bandgap of rutile-GeO2 revealed by many body perturbation theory.

PubMed

Samanta, Atanu; Jain, Manish; Singh, Abhishek K

2015-08-14

The reported values of bandgap of rutile GeO2 calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (∼2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO2 using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Γ-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O-p and Ge-(s and p) orbitals. Furthermore, the parabolic nature of first conduction band along X-Γ-M direction changes towards a linear dispersion with volume expansion.

Electronic structure calculation of Sr2CoWO6 double perovskite using DFT+U

NASA Astrophysics Data System (ADS)

Mandal, Golak; Jha, Dhiraj; Himanshu, A. K.; Ray, Rajyavardhan; Mukherjee, P.; Das, Nisith; Singh, B. K.; Sreenivas, K.; Singh, M. N.; Sinha, A. K.

2018-04-01

Using the synchrotron and Raman spectroscopy we measured the lattice parameter and Raman modes of the half-metallic (HM) Sr2CoWO6 (SCoW) synthesied by the solid state reaction technique.. The physical properties of SCoW are studies within the framework of density function theory (DFT) under the generalised gradient approximation (GGA) of Perdew, Bruke, and Ernzerhof both by itself and including a coulomb repulsion via the Hubbard approach or GGA+U. Our results states that Sr2CoWO6 material behaves as insulators for the spin-up orientation and spindown orientation as found for the half metallic systems and at U = 0.06eV the ground state of spin up channel being insulating with spin gap of 2.27eV comparable to the experimental Band gap (BG).

The structural, electronic and optical properties of Nd doped ZnO using first-principles calculations

NASA Astrophysics Data System (ADS)

Wen, Jun-Qing; Zhang, Jian-Min; Chen, Guo-Xiang; Wu, Hua; Yang, Xu

2018-04-01

The density functional theory calculations using general gradient approximation (GGA) applying Perdew-Burke-Ernzerhof (PBE) as correlation functional have been systematically performed to research the formation energy, the electronic structures, band structures, total and partial DOS, and optical properties of Nd doping ZnO with the content from 6.25% to 12.5%. The formation energies are negative for both models, which show that two structures are energetically stable. Nd doping ZnO crystal is found to be a direct band gap semiconductor and Fermi level shifts upward into conduction band, which show the properties of n-type semiconductor. Band structures are more compact after Nd doping ZnO, implying that Nd doping induces the strong interaction between different atoms. Nd doping ZnO crystal presents occupied states at near Fermi level, which mainly comes from the Nd 4f orbital. The calculated optical properties imply that Nd doping causes a red-shift of absorption peaks, and enhances the absorption of the visible light.

Variations of Human DNA Polymerase Genes as Biomarkers of Prostate Cancer Progression

DTIC Science & Technology

2011-07-01

Forward sequence Reverse sequence Sequence contextb 1 g.39835C4Tc P169S 15 25 gTG GGG TC CTT g.39897C4T Intronic 22 15 AGA T GGt TA AAT g.39985T4C...Intronic 34 25 AGA TT tAA AAG g.40051C4Tc P184S 19 34 TGt CT GGA ATT 4 g.39835C4Tc P169S 19 29 gTG GGG TC CTT g.40051C4Tc P184S 23 34 TGt CT GGA ATT 6 g...39835C4Tc P169S 14 24 gTG GGG TC CTT g.40051C4Tc P184S 21 32 TGt CT GGA ATT 11 g.40055A4G D185G 28 35 TTC C AGA C AAG g.40073A4G Y191C 28 20 gGA T AtG CC

Global hybrids from the semiclassical atom theory satisfying the local density linear response.

PubMed

Fabiano, Eduardo; Constantin, Lucian A; Cortona, Pietro; Della Sala, Fabio

2015-01-13

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 2011, 106, 186406] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetic and structural testing, including thermochemistry and geometry, transition metal complexes, noncovalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semiempirical dispersion corrections are also provided.

Reconsideration of data and correlations for plate finned-tube heat exchangers

NASA Astrophysics Data System (ADS)

Otović, Milena; Mihailović, Miloš; Genić, Srbislav; Jaćimović, Branislav; Milovančević, Uroš; Marković, Saša

2018-04-01

This paper deals with heat exchangers having plain finned tubes in staggered (triangular) pattern. The objective of this paper is to provide the heat transfer and friction factor correlation which can be used in engineering practice. For this purpose, the experimental data of several (most cited) authors who deal with this type of heat exchangers are used. The new correlations are established to predict the air-side heat transfer coefficient and friction factor as a function of the Reynolds number and geometric variables of the heat exchanger - tube diameter, tube pitch, fin spacing, tube rows, etc. In those correlations the characteristic dimension in Reynolds number is calculated by using the new parameter - volumetric porosity. Also, there are given the errors of those correlations.

Bonding nature and electron delocalization of An(COT)2, An = Th, Pa, U.

PubMed

Páez-Hernández, Dayán; Murillo-López, Juliana A; Arratia-Pérez, Ramiro

2011-08-18

A systematic study of a series of An(COT)(2) compounds, where An = Th, Pa, U, and COT represents cyclooctatetraene, has been performed using relativistic density functional theory. The ZORA Hamiltonian was applied for the inclusion of relativistic effects, taking into account all of the electrons for the optimization and explicitly including spin-orbit coupling effects. Time-dependent density functional theory (TDDFT) was used to calculate the excitation energies with the GGA SAOP functional, and the electronic transitions were analyzed using double group irreducible representations. The calculated excitation energies are in perfect correlation with the increment of the ring delocalization as it increases along the actinide series. These results are sufficient to ensure that, for these complexes, the increment in delocalization, as indicated by ELF bifurcation and NICS analysis, leads to a shift in the maximum wavelength of absorption in the visible region. Also, delocalization in the COT ring increases along the actinide series, so the systems become more aromatic because of a modulation induced by the actinides. © 2011 American Chemical Society

Structural and vibrational properties of transition-metal oxides from first-principles calculations

NASA Astrophysics Data System (ADS)

Cococcioni, M.; Floris, A.; Himmetoglu, B.

2010-12-01

The calculation of the vibrational spectrum of minerals is of fundamental importance to assess their behavior (e.g. their elastic properties, or possible structural phase transitions) under the high-temperature, high-pressure conditions of the Earth’s interior. The ubiquitous presence of transition metals and the consequent importance of electronic correlations make the study of these materials quite difficult to approach with approximate DFT functionals (as LDA or GGA). The DFT+U, consisting in a Hubbard-modeled correction to the DFT energy functionals, has been successfully used to study the electronic, structural, and magnetic properties of several Fe-bearing minerals. However, the vibrational spectrum of these systems has never been determined entirely (frozen- phonon techniques are overly expensive except for zone-center phonons). In this work we introduce the extension of Density-Functional-Perturbation-Theory to DFT+U, that allows to efficiently compute the phonon spectrum of transition-metal compounds from their correlated ground states. A comparative analysis between the vibrational properties of MnO, FeO, CoO, and NiO (in the undistorted cubic cell) highlights a marked dependence of several features of their phonon spectrum on the occupancy of localized d orbitals and thus, on elec- tronic correlation. The new computational tool is also employed to evaluate the rhombohedral distortion of FeO (particularly abundant in the Earth’s lower mantle) and to assess the stability of its B1 phase in different conditions of pressure and temperature.

Efficient construction of exchange and correlation potentials by inverting the Kohn-Sham equations.

PubMed

Kananenka, Alexei A; Kohut, Sviataslau V; Gaiduk, Alex P; Ryabinkin, Ilya G; Staroverov, Viktor N

2013-08-21

Given a set of canonical Kohn-Sham orbitals, orbital energies, and an external potential for a many-electron system, one can invert the Kohn-Sham equations in a single step to obtain the corresponding exchange-correlation potential, vXC(r). For orbitals and orbital energies that are solutions of the Kohn-Sham equations with a multiplicative vXC(r) this procedure recovers vXC(r) (in the basis set limit), but for eigenfunctions of a non-multiplicative one-electron operator it produces an orbital-averaged potential. In particular, substitution of Hartree-Fock orbitals and eigenvalues into the Kohn-Sham inversion formula is a fast way to compute the Slater potential. In the same way, we efficiently construct orbital-averaged exchange and correlation potentials for hybrid and kinetic-energy-density-dependent functionals. We also show how the Kohn-Sham inversion approach can be used to compute functional derivatives of explicit density functionals and to approximate functional derivatives of orbital-dependent functionals.

A density difference based analysis of orbital-dependent exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Grabowski, Ireneusz; Teale, Andrew M.; Fabiano, Eduardo; Śmiga, Szymon; Buksztel, Adam; Della Sala, Fabio

2014-03-01

We present a density difference based analysis for a range of orbital-dependent Kohn-Sham functionals. Results for atoms, some members of the neon isoelectronic series and small molecules are reported and compared with ab initio wave function calculations. Particular attention is paid to the quality of approximations to the exchange-only optimised effective potential (OEP) approach: we consider both the localised Hartree-Fock as well as the Krieger-Li-Iafrate methods. Analysis of density differences at the exchange-only level reveals the impact of the approximations on the resulting electronic densities. These differences are further quantified in terms of the ground state energies, frontier orbital energy differences and highest occupied orbital energies obtained. At the correlated level, an OEP approach based on a perturbative second-order correlation energy expression is shown to deliver results comparable with those from traditional wave function approaches, making it suitable for use as a benchmark against which to compare standard density functional approximations.

Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.

PubMed

Soniat, Marielle; Rogers, David M; Rempe, Susan B

2015-07-14

A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.

Accurate critical pressures for structural phase transitions of group IV, III-V, and II-VI compounds from the SCAN density functional

NASA Astrophysics Data System (ADS)

Shahi, Chandra; Sun, Jianwei; Perdew, John P.

2018-03-01

Most of the group IV, III-V, and II-VI compounds crystallize in semiconductor structures under ambient conditions. Upon application of pressure, they undergo structural phase transitions to more closely packed structures, sometimes metallic phases. We have performed density functional calculations using projector augmented wave (PAW) pseudopotentials to determine the transition pressures for these transitions within the local density approximation (LDA), the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and the strongly constrained and appropriately normed (SCAN) meta-GGA. LDA underestimates the transition pressure for most of the studied materials. PBE under- or overestimates in many cases. SCAN typically corrects the errors of LDA and PBE for the transition pressure. The accuracy of SCAN is comparable to that of computationally expensive methods like the hybrid functional HSE06, the random phase approximation (RPA), and quantum Monte Carlo (QMC), in cases where calculations with these methods have been reported, but at a more modest computational cost. The improvement from LDA to PBE to SCAN is especially clearcut and dramatic for covalent semiconductor-metal transitions, as for Si and Ge, where it reflects the increasing relative stabilization of the covalent semiconducting phases under increasing functional sophistication.

Phase correlation of foreign exchange time series

NASA Astrophysics Data System (ADS)

Wu, Ming-Chya

2007-03-01

Correlation of foreign exchange rates in currency markets is investigated based on the empirical data of USD/DEM and USD/JPY exchange rates for a period from February 1 1986 to December 31 1996. The return of exchange time series is first decomposed into a number of intrinsic mode functions (IMFs) by the empirical mode decomposition method. The instantaneous phases of the resultant IMFs calculated by the Hilbert transform are then used to characterize the behaviors of pricing transmissions, and the correlation is probed by measuring the phase differences between two IMFs in the same order. From the distribution of phase differences, our results show explicitly that the correlations are stronger in daily time scale than in longer time scales. The demonstration for the correlations in periods of 1986-1989 and 1990-1993 indicates two exchange rates in the former period were more correlated than in the latter period. The result is consistent with the observations from the cross-correlation calculation.

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition.

PubMed

Nassar, M K; Goraga, Z S; Brockmann, G A

2012-12-01

In order to identify genetic factors influencing muscle weight and carcass composition in chicken, a linkage analysis was performed with 278 F(2) males of reciprocal crosses between the extremely different inbred lines New Hampshire (NHI) and White Leghorn (WL77). The NHI line had been selected for high meat yield and the WL77 for low egg weight before inbreeding. Highly significant quantitative trait loci (QTL) controlling body weight and the weights of carcass, breast muscle, drumsticks-thighs and wings were identified on GGA4 between 151.5 and 160.5 cM and on GGA27 between 4 and 52 cM. These genomic regions explained 13.7-40.2% and 5.3-13.8% of the phenotypic F(2) variances of the corresponding traits respectively. Additional genome-wide highly significant QTL for the weight of drumsticks-thighs were mapped on GGA1, 5 and 7. Moreover, significant QTL controlling body weight were found on GGA2 and 11. The data obtained in this study can be used for increasing the mapping resolution and subsequent gene targeting on GGA4 and 27 by combining data with other crosses where the same QTL were found. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Multidirectional chromosome painting in Synallaxis frontalis (Passeriformes, Furnariidae) reveals high chromosomal reorganization, involving fissions and inversions.

PubMed

Kretschmer, Rafael; de Lima, Vanusa Lilian Camargo; de Souza, Marcelo Santos; Costa, Alice Lemos; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A; de Oliveira, Edivaldo Herculano Corrêa; Gunski, Ricardo José; Garnero, Analía Del Valle

2018-01-01

In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes.

Multidirectional chromosome painting in Synallaxis frontalis (Passeriformes, Furnariidae) reveals high chromosomal reorganization, involving fissions and inversions

PubMed Central

Kretschmer, Rafael; de Lima, Vanusa Lilian Camargo; de Souza, Marcelo Santos; Costa, Alice Lemos; O’Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.; de Oliveira, Edivaldo Herculano Corrêa; Gunski, Ricardo José; Garnero, Analía Del Valle

2018-01-01

Abstract In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes. PMID:29675139

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium.

PubMed

Han, Jeong-Hwan; Oda, Takuji

2018-04-14

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium

NASA Astrophysics Data System (ADS)

Han, Jeong-Hwan; Oda, Takuji

2018-04-01

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Self-Interaction Error in Density Functional Theory: An Appraisal.

PubMed

Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

2018-05-03

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

The Kinetics and Thermodynamics of CO2 Capture by Aqueous Ammonia Derived Using Meta-GGA Density Functional Theory and Wavefunction-Based Model Chemistry Methods

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

Beste, Ariana; Attalla, Moetaz; Jackson, Phil

2012-01-01

A meta GGA-DFT study of CO{sub 2} activation in aqueous ammonia solutions, with an emphasis on the reaction barrier and molecularity, has been undertaken using the M06-2X functional with an augmented triple-zeta split-valence basis set (6-311++G(d,p)). Up to five base molecules were treated explicitly in order to establish the effects of solvent catalysis in the chemical capture process. Aqueous free energies of solvation were determined for optimized reactant and transition structures using SM8/M06-2X/6-311++G(d,p). The concept of the solvent pre-complex as presented by Dixon and coworkers (Nguyen, M. T.; Matus, M. H.; Jackson, V. E.; Ngan, V. T.; Rustad, J. R.;more » Dixon, D. A. J. Phys. Chem. A 2008, 112, 10386-10398) was exploited to account for the energetics of disruption of the hydrogen-bonding solvent nano-network prior to the CO{sub 2} activation step. Selected gas- and aqueous-phase thermodynamic quantities have also been derived.« less

Semilocal Exchange Energy Functional for Two-Dimensional Quantum Systems: A Step Beyond Generalized Gradient Approximations.

PubMed

Jana, Subrata; Samal, Prasanjit

2017-06-29

Semilocal density functionals for the exchange-correlation energy of electrons are extensively used as they produce realistic and accurate results for finite and extended systems. The choice of techniques plays a crucial role in constructing such functionals of improved accuracy and efficiency. An accurate and efficient semilocal exchange energy functional in two dimensions is constructed by making use of the corresponding hole which is derived based on the density matrix expansion. The exchange hole involved is localized under the generalized coordinate transformation and satisfies all the relevant constraints. Comprehensive testing and excellent performance of the functional is demonstrated versus exact exchange results. The accuracy of results obtained by using the newly constructed functional is quite remarkable as it substantially reduces the errors present in the local and nonempirical exchange functionals proposed so far for two-dimensional quantum systems. The underlying principles involved in the functional construction are physically appealing and hold promise for developing range separated and nonlocal exchange functionals in two dimensions.

Influence of molecular geometry, exchange-correlation functional, and solvent effects in the modeling of vertical excitation energies in phthalocyanines using time-dependent density functional theory (TDDFT) and polarized continuum model TDDFT methods: can modern computational chemistry methods explain experimental controversies?

PubMed

Nemykin, Victor N; Hadt, Ryan G; Belosludov, Rodion V; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2007-12-20

A time-dependent density functional theory (TDDFT) approach coupled with 14 different exchange-correlation functionals was used for the prediction of vertical excitation energies in zinc phthalocyanine (PcZn). In general, the TDDFT approach provides a more accurate description of both visible and ultraviolet regions of the UV-vis and magnetic circular dichroism (MCD) spectra of PcZn in comparison to the more popular semiempirical ZINDO/S and PM3 methods. It was found that the calculated vertical excitation energies of PcZn correlate with the amount of Hartree-Fock exchange involved in the exchange-correlation functional. The correlation was explained on the basis of the calculated difference in energy between occupied and unoccupied molecular orbitals. The influence of PcZn geometry, optimized using different exchange-correlation functionals, on the calculated vertical excitation energies in PcZn was found to be relatively small. The influence of solvents on the calculated vertical excitation energies in PcZn was considered for the first time using a polarized continuum model TDDFT (PCM-TDDFT) method and was found to be relatively small in excellent agreement with the experimental data. For all tested TDDFT and PCM-TDDFT cases, an assignment of the Q-band as an almost pure a1u (HOMO)-->eg (LUMO) transition, initially suggested by Gouterman, was confirmed. Pure exchange-correlation functionals indicate the presence of six 1Eu states in the B-band region of the UV-vis spectrum of PcZn, while hybrid exchange-correlation functionals predict only five 1Eu states for the same energy envelope. The first two symmetry-forbidden n-->pi* transitions were predicted in the Q0-2 region and in the low-energy tail of the B-band, while the first two symmetry-allowed n-->pi* transitions were found within the B-band energy envelope when pure exchange-correlation functionals were used for TDDFT calculations. The presence of a symmetry-forbidden but vibronically allowed n-->pi* transition in the Q0-2 spectral envelope explains the long-time controversy between the experimentally observed low-intensity transition in the Q0-2 region and previous semiempirical and TDDFT calculations, which were unable to predict any electronic transitions in this area. To prove the conceptual possibility of the presence of several degenerate 1Eu states in the B-band region of PcZn, room-temperature UV-vis and MCD spectra of zinc tetra-tert-butylphthalocyanine (PctZn) in non-coordinating solvents were recorded and analyzed using band deconvolution analysis. It was found that the B-band region of the UV-vis and MCD spectra of PctZn can be easily deconvoluted using six MCD Faraday A-terms and two MCD Faraday B-terms with energies close to those predicted by TDDFT calculations for 1Eu and 1A2u excited states, respectively. Such a good agreement between theory and experiment clearly indicates the possibility of employing a TDDFT approach for the accurate prediction of vertical excitation energies in phthalocyanines within a large energy range.

Elasticity of Pargasite Amphibole: A Hydrous Phase at Mid Lithospheric Discontinuity

NASA Astrophysics Data System (ADS)

Peng, Y.; Mookherjee, M.

2017-12-01

Mid Lithospheric Discontinuity (MLD) is characterized by a low shear wave velocity ( 3 to 10 %). In cratons, the depth of MLD varies between 80 and 100 km. The reduction of the shear wave velocity at MLD is similar to what is observed in the lithosphere-asthenosphere boundary (LAB). Such low velocity at MLD could be caused by partial melting, temperature induced grain boundary sliding, changes in the elastic anisotropy, and/or metasomatism which may lead to the formation of hydrous phases including mica and amphibole. Thus, it is clear that in order to assess the role of metasomatism at MLD, we need better constraints on the elasticity of hydrous phases. However, such elasticity data are scarce. In this study, we explore elasticity of pargasite amphibole [NaCa2(Mg4Al)(Si6Al2)O22(OH)2] using density functional theory (DFT) with local density approximation (LDA) and generalized gradient approximation (GGA). We find that the pressure-volume results can be adequately described by a finite strain equation with the bulk modulus, K0 being 102 and 85 GPa for LDA and GGA respectively. We also determined the full elastic constant tensor (Cij) using the finite difference method. The bulk modulus, K0 determined from the full elastic constant tensor is 104 GPa for LDA and 87 GPa for GGA. The shear modulus, G0 determined from the full elastic constant tensor is 64 GPa for LDA and 58 GPa for GGA. The bulk and shear moduli predicted with LDA are 5 and 1 % stiffer than the recent results [1]. In contrast, the bulk and shear moduli predicted with GGA are 12 and 10 % softer compared to the recent results [1]. The full elastic constant tensor for pargasite shows significant anisotropy. For instance, LDA predicts compressional (AVP) and shear (AVS) wave anisotropy of 22 and 20 % respectively. At higher pressure, elastic moduli stiffen. However, temperature is likely to have an opposite effect on the elasticity and this remains largely unknown for pargasite. Compared to the major mantle minerals, pargasite has softer elastic constants and significant anisotropy and may explain the reduction in shear wave velocity at MLD. Reference: [1] Brown, J. M., Abramson, E. H.,2016, Phys. Earth Planet. Int., 261, 161-171. Acknowledgement: This work is supported by US NSF award EAR 1639552.

Effect of pressure variation on structural, elastic, mechanical, optoelectronic and thermodynamic properties of SrNaF3 fluoroperovskite

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2017-12-01

The effect of pressure variation on structural, electronic, elastic, mechanical, optical and thermodynamic characteristics of cubic SrNaF3 fluoroperovskite have been investigated by employing first-principles method within the framework of gradient approximation (GGA). For the total energy calculations, we have used the full-potential linearized augmented plane wave (FP-LAPW) method. Thermodynamic properties are computed in terms of quasi-harmonic Debye model. The pressure effects are determined in the range of 0-25 GPa, in which mechanical stability of SrNaF3 fluoroperovskite remains valid. A prominent decrease in lattice constant and bonds length is observed with the increase in pressure from 0 to 25 GPa. The effect of increase in pressure on band structure calculations with GGA and GGA plus Tran-Blaha modified Becke-Johnson (TB-mBJ) potential reveals a predominant characteristic associated with widening of bandgap. The influence of pressure on set of isotropic elastic parameters and their related properties are numerically estimated for SrNaF3 polycrystalline aggregate. Apart of linear dependence of elastic coefficients, transition from brittle to ductile behavior is observed as pressure is increased from 0 to 25 GPa. We have successfully obtained variation of lattice constant, volume expansion, bulk modulus, Debye temperature and specific heat capacities with pressure and temperature in the range of 0-25 GPa and 0-600 K. All the calculated optical properties such as the complex dielectric function ɛ(ω), optical conductivity σ(ω), energy loss function L(ω), absorption coefficient α(w), refractive index n(ω), reflectivity R(ω), and effective number of electrons n eff, via sum rules shift towards the higher energies under the application of pressure.

Communication: Near-locality of exchange and correlation density functionals for 1- and 2-electron systems

NASA Astrophysics Data System (ADS)

Sun, Jianwei; Perdew, John P.; Yang, Zenghui; Peng, Haowei

2016-05-01

The uniform electron gas and the hydrogen atom play fundamental roles in condensed matter physics and quantum chemistry. The former has an infinite number of electrons uniformly distributed over the neutralizing positively charged background, and the latter only one electron bound to the proton. The uniform electron gas was used to derive the local spin density approximation to the exchange-correlation functional that undergirds the development of the Kohn-Sham density functional theory. We show here that the ground-state exchange-correlation energies of the hydrogen atom and many other 1- and 2-electron systems are modeled surprisingly well by a different local spin density approximation (LSDA0). LSDA0 is constructed to satisfy exact constraints but agrees surprisingly well with the exact results for a uniform two-electron density in a finite, curved three-dimensional space. We also apply LSDA0 to excited or noded 1-electron densities, where it works less well. Furthermore, we show that the localization of the exact exchange hole for a 1- or 2-electron ground state can be measured by the ratio of the exact exchange energy to its optimal lower bound.

Spin–orbit DFT with Analytic Gradients and Applications to Heavy Element Compounds

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

Zhang, Zhiyong

We have implemented the unrestricted DFT approach with one-electron spin–orbit operators in the massively parallel NWChem program. Also implemented is the analytic gradient in the DFT approach with spin–orbit interactions. The current capabilities include single-point calculations and geometry optimization. Vibrational frequencies can be calculated numerically from the analytically calculated gradients. The implementation is based on the spin–orbit interaction operator derived from the effective core potential approach. The exchange functionals used in the implementation are functionals derived for non-spin–orbit calculations, including GGA as well as hybrid functionals. Spin–orbit Hartree–Fock calculations can also be carried out. We have applied the spin–orbit DFTmore » methods to the Uranyl aqua complexes. We have optimized the structures and calculated the vibrational frequencies of both (UO2 2+)aq and (UO2 +)aq with and without spin–orbit effects. The effects of the spin–orbit interaction on the structures and frequencies of these two complexes are discussed. We also carried out calculations for Th2, and several low-lying electronic states are calculated. Our results indicate that, for open-shell systems, there are significant effects due to the spin–orbit effects and the electronic configurations with and without spin–orbit interactions could change due to the occupation of orbitals of larger spin–orbit interactions.« less

Thermodynamic properties of OsB under high temperature and high pressure

NASA Astrophysics Data System (ADS)

Chen, Hai-Hua; Li, Zuo; Cheng, Yan; Bi, Yan; Cai, Ling-Cang

2011-09-01

The energy-volume curves of OsB have been obtained using the first-principles plane-wave ultrasoft-pseudopotential density functional theory (DFT) within the generalized gradient approximation (GGA) and local density approximation (LDA). Using the quasi-harmonic Debye model we first analyze the specific heat, the coefficients of thermal expansion as well as the thermodynamic Grüneisen parameter of OsB in a wide temperature range at high pressure. At temperature 300 K, the coefficients of thermal expansion αV by LDA and GGA calculations are 1.67×10 -5 1/K and 2.01×10 -5 1/K, respectively. The specific heat of OsB at constant pressure (volume) is also calculated. Meanwhile, we find that the Debye temperature of OsB increases monotonically with increasing pressure. The present study leads to a better understanding of how the OsB materials respond to pressure and temperature.

Ferro and antiferro orbital ordering in Fe{sub 0.5}Mn{sub 0.5}V{sub 2}O{sub 4}

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

Dey, Dibyendu, E-mail: dibyendu@phy.iitkgp.ernet.in; Taraphder, A.; Maitra, T.

2016-05-23

Using density functional theory calculations, we have investigated the orbital ordering in Fe{sub 0.5}Mn{sub 0.5}V{sub 2}O{sub 4} where Fe and V sites are orbitally active. Our first principles study within GGA+U and GGA+U+SO shows ferro-orbital ordering of d{sub x2−y2} orbital at all Fe sites, whereas A-type antiferro-orbital ordering at V sites where one 3d electron occupies d{sub xy} orbital at every V site and another electron occupies either 1/√2 (d{sub xz} + d{sub yz}) or 1/√2 (d{sub xz} - d{sub yz}) orbital alternatively along c axis. Insulating nature and the orbital ordering of this compound are found to be correlationmore » driven while the effect of spin-orbit interaction on orbital ordering is not significant.« less

Ultra-sensitive pressure dependence of bandgap of rutile-GeO{sub 2} revealed by many body perturbation theory

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

Samanta, Atanu; Singh, Abhishek K.; Jain, Manish

2015-08-14

The reported values of bandgap of rutile GeO{sub 2} calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (∼2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO{sub 2} using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Γ-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O-p and Ge-(s and p)more » orbitals. Furthermore, the parabolic nature of first conduction band along X-Γ-M direction changes towards a linear dispersion with volume expansion.« less

Structural and electronic properties of Li-ion battery cathode material MoF{sub 3} from first-principles

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

Li, A.Y.; Wu, S.Q.; Yang, Y.

2015-07-15

The transition metal fluorides have been extensively investigated recently as the electrode materials with high working voltage and large capacity. The structural, electronic and magnetic properties of MoF{sub 3} are studied by the first-principles calculations within both the generalized gradient approximation (GGA) and GGA+U frameworks. Our results show that the antiferromagnetic configuration of MoF{sub 3} is more stable than the ferromagnetic one, which is consistent with experimental results. The analysis of the electronic density of states shows that MoF{sub 3} is a Mott–Hubbard insulator with a d–d type band gap, which is similar to the case of FeF{sub 3}. Moreover,more » small spin polarizations were found on the sites of fluorine ions, which accords with a fluorine-mediated superexchange mechanism for the Mo–Mo magnetic interaction. - Graphical abstract: Deformation charge density and spin-density for MoF{sub 3} in the AF configuration. - Highlights: • The ground state of MoF{sub 3} is shown to be antiferromagnetic, in consistent with experiments. • The electronic states show that MoF{sub 3} is a Mott–Hubbard insulator with a d–d type band gap. • A fluorine-mediated super-exchange mechanism for the Mo–Mo magnetic interaction is shown.« less

First principles study of structural, optoelectronic and thermoelectric properties of Cu{sub 2}CdSnX{sub 4} (X = S, Se, Te) chalcogenides

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

Hussain, Sajjad; Murtaza, G., E-mail: murtaza@icp.edu.pk; Haidar Khan, Shah

2016-07-15

Highlights: • Copper based quaternary chalcogenides are important for optoelectronic devices. • The WC-GGA shows that the materials are metallic in nature. • The EV-GGA predicts better band gaps compared to WC-GGA. • Absorption peaks are high in the visible and ultraviolet energy regions. • All the semiconductors have figure of merit above 0.70. - Abstract: In this work, structural, electronic, optical and thermoelectric properties of Cu{sub 2}CdSnX{sub 4} (X = S, Se, Te) have been studied through the full potential linearized augmented plane wave method. Calculated ground state lattice parameters are in good agreement with the experimental results. Latticemore » constant and bulk moduli vary inversely by replacing the anion X from S to Te in Cu{sub 2}CdSnX{sub 4}. The WC-GGA shows that the materials are metallic in nature. The EV-GGA predicts better band gaps compared to WC-GGA. The calculated bandgap values are 1.8, 1.06 and 0.8042 for Cu{sub 2}CdSnX{sub 4}, Cu{sub 2}CdSnX{sub 4}, Cu{sub 2}CdSnX{sub 4} respectively. Cd-d, Sn-s and X-p states contribute significantly in the density of states of the compounds. Absorption peaks and optical conductivity is high in the visible and ultraviolet energy regions. All the semiconductors have figure of merit above 0.70. The optical and thermoelectric properties clearly show that Cu{sub 2}CdSnX{sub 4} are potential candidates in the fields of solar cell and thermoelectric technology.« less

Influence of the exchange and correlation functional on the structure of amorphous InSb and In{sub 3}SbTe{sub 2} compounds

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

Gabardi, Silvia; Caravati, Sebastiano; Bernasconi, Marco, E-mail: marco.bernasconi@mater.unimib.it

2016-05-28

We have investigated the structural, vibrational, and electronic properties of the amorphous phase of InSb and In{sub 3}SbTe{sub 2} compounds of interest for applications in phase change non-volatile memories. Models of the amorphous phase have been generated by quenching from the melt by molecular dynamics simulations based on density functional theory. In particular, we have studied the dependence of the structural properties on the choice of the exchange-correlation functional. It turns out that the use of the Becke-Lee-Yang-Parr functional provides models with a much larger fraction of In atoms in a tetrahedral bonding geometry with respect to previous results obtainedmore » with the most commonly used Perdew-Becke-Ernzerhof functional. This outcome is at odd with the properties of Ge{sub 2}Sb{sub 2}Te{sub 5} phase change compound for which the two exchange-correlation functionals yield very similar results on the structure of the amorphous phase.« less

Finite-T correlations and free exchange-correlation energy of quasi-one-dimensional electron gas

NASA Astrophysics Data System (ADS)

Garg, Vinayak; Sharma, Akariti; Moudgil, R. K.

2018-02-01

We have studied the effect of temperature on static density-density correlations and plasmon excitation spectrum of quasi-one-dimensional electron gas (Q1DEG) using the random phase approximation (RPA). Numerical results for static structure factor, pair-correlation function, static density susceptibility, free exchange-correlation energy and plasmon dispersion are presented over a wide range of temperature and electron density. As an interesting result, we find that the short-range correlations exhibit a non-monotonic dependence on temperature T, initially growing stronger (i.e. the pair-correlation function at small inter-electron spacing assuming relatively smaller values) with increasing T and then weakening above a critical T. The cross-over temperature is found to increase with increasing coupling among electrons. Also, the q = 2kF peak in the static density susceptibility χ(q,ω = 0,T) at T = 0 K smears out with rising T. The free exchange-correlation energy and plasmon dispersion show a significant variation with T, and the trend is qualitatively the same as in higher dimensions.

Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird.

PubMed

Dawson, Deborah A; Akesson, Mikael; Burke, Terry; Pemberton, Josephine M; Slate, Jon; Hansson, Bengt

2007-07-01

Genome structure has been found to be highly conserved between distantly related birds and recent data for a limited part of the genome suggest that this is true also for the gene order (synteny) within chromosomes. Here, we confirm that synteny is maintained for large chromosomal regions in chicken and a passerine bird, the great reed warbler Acrocephalus arundinaceus, with few rearrangements, but in contrast show that the recombination-based linkage map distances differ substantially between these species. We assigned a chromosomal location based on sequence similarity to the chicken genome sequence to a set of microsatellite loci mapped in a pedigree of great reed warblers. We detected homologous loci on 14 different chromosomes corresponding to chicken chromosomes Gga1-5, 7-9, 13, 19, 20, 24, 25, and Z. It is known that 2 passerine macrochromosomes correspond to the chicken chromosome Gga1. Homology of 2 different great reed warbler linkage groups (LG13 and LG5) to Gga1 allowed us to locate the split to a position between 20.8 and 84.8 Mb on Gga1. Data from the 5 chromosomal regions (on Gga1, 2, 3, 5, and Z) with 3 or more homologous loci showed that synteny was conserved with the exception of 2 large previously unreported inversions on Gga1/LG5 and Gga2/LG3, respectively. Recombination data from the 9 chromosomal regions in which we identified 2 or more homologous loci (accounting for the inversions) showed that the linkage map distances in great reed warblers were only 6.3% and 13.3% of those in chickens for males and females, respectively. This is likely to reflect the true interspecific difference in recombination rate because our markers were not located in potentially low-recombining regions: several linkage groups covered a substantial part of their corresponding chicken chromosomes and were not restricted to centromeres. We conclude that recombination rates may differ strongly between bird species with highly conserved genome structure and synteny and that the chicken linkage map may not be suitable, in terms of genetic distances, as a model for all bird species.

Structural and electronic properties of Sr{sub x}Ba{sub 1-x}SnO{sub 3} from first principles calculations

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

Moreira, E.; Henriques, J.M.; Azevedo, D.L.

2012-03-15

Neutron diffraction data for Sr{sub x}Ba{sub 1-x}SnO{sub 3} (x=0.0, 0.2, 0.4, 0.6, 0.8 and 1.0) solid solutions were used as inputs to obtain optimized geometries and electronic properties using the density functional theory (DFT) formalism considering both the local density and generalized gradient approximations, LDA and GGA, respectively. The crystal structures and SnO{sub 6} octahedra tilting angles found after total energy minimization agree well with experiment, specially for the GGA data. Elastic constants were also obtained and compared with theoretical and experimental results for cubic BaSnO{sub 3}. While the alloys with cubic unit cell have an indirect band gap, tetragonalmore » and orthorhombic alloys exhibit direct band gaps (exception made to x=1.0). The Kohn-Sham minimum electronic band gap oscillates from 1.52 eV (cubic x=0.0, LDA) to 2.61 eV (orthorhombic x=1.0, LDA), and from 0.74 eV (cubic BaSnO{sub 3}, GGA) to 1.97 eV (orthorhombic SrSnO{sub 3}, GGA). Parabolic interpolation of bands has allowed us to estimate the effective masses for charge carriers, which are shown to be anisotropic and larger for holes. - Graphical Abstract: Highlights: Black-Right-Pointing-Pointer DFT calculations were performed on Sr{sub x}Ba{sub 1-x}SnO{sub 3} solid solutions. Black-Right-Pointing-Pointer Calculated crystal structures agree well with experiment. Black-Right-Pointing-Pointer Alloys have direct or indirect gaps depending on the Sr molar fraction. Black-Right-Pointing-Pointer The Kohn-Sham gap variation from x=0.0 to x=1.0 is close to the experimental value. Black-Right-Pointing-Pointer Carrier effective masses are very anisotropic, specially for holes.« less

First-principles energy band calculation of Ruddlesden–Popper compound Sr{sub 3}Sn{sub 2}O{sub 7} using modified Becke–Johnson exchange potential

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

Kamimura, Sunao, E-mail: kamimura-sunao@che.kyutech.ac.jp; National Institute of Advanced Industrial Science and Technology; Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Science, Kyushu University, 6-1 Kasuga Kouen, Kasuga, Fukuoka 816-8580 Japan

The electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is evaluated by the scalar-relativistic full potential linearized augmented plane wave (FLAPW+lo) method using the modified Becke–Johnson potential (Tran–Blaha potential) combined with the local density approximation correlation (MBJ–LDA). The fundamental gap between the valence band (VB) and conduction band (CB) is estimated to be 3.96 eV, which is close to the experimental value. Sn 5s states and Sr 4d states are predominant in the lower and upper CB, respectively. On the other hand, the lower VB is mainly composed of Sn 5s, 5p, and O 2p states, while the upper VB mainlymore » consists of O 2p states. These features of the DOS are well reflected by the optical transition between the upper VB and lower CB, as seen in the energy dependence of the dielectric function. Furthermore, the absorption coefficient estimated from the MBJ–LDA is similar to the experimental result. - Graphical abstract: Calculated energy band structure along the symmetry lines of the first BZ of Sr{sub 3}Sn{sub 2}O{sub 7} crystal obtained using the MBJ potential. - Highlights: • Electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is calculated on the basis of MBJ–LDA method for the first time. • Band gap of Sr{sub 3}Sn{sub 2}O{sub 7} is determined accurately on the basis of MBJ–LDA method. • The experimental absorption spectrum of Sr{sub 3}Sn{sub 2}O{sub 7} produced by MBJ–LDA is more accurate than that obtained by GGA method.« less

Ab initio 27Al NMR chemical shifts and quadrupolar parameters for Al2O3 phases and their precursors

NASA Astrophysics Data System (ADS)

Ferreira, Ary R.; Küçükbenli, Emine; Leitão, Alexandre A.; de Gironcoli, Stefano

2011-12-01

The gauge-including projector augmented wave (GIPAW) method, within the density functional theory (DFT) generalized gradient approximation (GGA) framework, is applied to compute solid state NMR parameters for 27Al in the α, θ, and κ aluminium oxide phases and their gibbsite and boehmite precursors. The results for well established crystalline phases compare very well with available experimental data and provide confidence in the accuracy of the method. For γ-alumina, four structural models proposed in the literature are discussed in terms of their ability to reproduce the experimental spectra also reported in the literature. Among the considered models, the Fd3¯m structure proposed by Paglia [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.71.224115 71, 224115 (2005)] shows the best agreement. We attempt to link the theoretical NMR parameters to the local geometry. Chemical shifts depend on coordination number but no further correlation is found with geometrical parameters. Instead, our calculations reveal that, within a given coordination number, a linear correlation exists between chemical shifts and Born effective charges.

Extended screened exchange functional derived from transcorrelated density functional theory.

PubMed

Umezawa, Naoto

2017-09-14

We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, H TC , is introduced by a similarity transformation of a many-body Hamiltonian, H, with respect to a complex function F: H TC =1FHF. It is proved that an expectation value of H TC for a normalized single Slater determinant, D n , corresponds to the total energy: E[n] = ⟨Ψ n |H|Ψ n ⟩/⟨Ψ n |Ψ n ⟩ = ⟨D n |H TC |D n ⟩ under the two assumptions: (1) The electron density nr associated with a trial wave function Ψ n = D n F is v-representable and (2) Ψ n and D n give rise to the same electron density nr. This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H - ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.

Gradient corrections to the exchange-correlation free energy

DOE PAGES

Sjostrom, Travis; Daligault, Jerome

2014-10-07

We develop the first-order gradient correction to the exchange-correlation free energy of the homogeneous electron gas for use in finite-temperature density functional calculations. Based on this, we propose and implement a simple temperature-dependent extension for functionals beyond the local density approximation. These finite-temperature functionals show improvement over zero-temperature functionals, as compared to path-integral Monte Carlo calculations for deuterium equations of state, and perform without computational cost increase compared to zero-temperature functionals and so should be used for finite-temperature calculations. Furthermore, while the present functionals are valid at all temperatures including zero, non-negligible difference with zero-temperature functionals begins at temperatures abovemore » 10 000 K.« less

Electron paramagnetic resonance study of neutral Mg acceptors in β-Ga2O3 crystals

NASA Astrophysics Data System (ADS)

Kananen, B. E.; Halliburton, L. E.; Scherrer, E. M.; Stevens, K. T.; Foundos, G. K.; Chang, K. B.; Giles, N. C.

2017-08-01

Electron paramagnetic resonance (EPR) is used to directly observe and characterize neutral Mg acceptors ( M gGa0 ) in a β-Ga2O3 crystal. These acceptors, best considered as small polarons, are produced when the Mg-doped crystal is irradiated at or near 77 K with x rays. During the irradiation, neutral acceptors are formed when holes are trapped at singly ionized Mg acceptors ( M gGa- ). Unintentionally present Fe3+ (3d5) and Cr3+ (3d3) transition-metal ions serve as the corresponding electron traps. The hole is localized in a nonbonding p orbital on a threefold-coordinated oxygen ion adjacent to an Mg ion at a sixfold-coordinated Ga site. These M gGa0 acceptors (S = 1/2) have a slightly anisotropic g matrix (principal values are 2.0038, 2.0153, and 2.0371). There is also partially resolved 69Ga and 71Ga hyperfine structure resulting from unequal interactions with the two Ga ions adjacent to the hole. With the magnetic field along the a direction, hyperfine parameters are 2.61 and 1.18 mT for the 69Ga nuclei at the two inequivalent neighboring Ga sites. The M gGa0 acceptors thermally convert back to their nonparamagnetic M gGa- charge state when the temperature of the crystal is raised above approximately 250 K.

A novel activity of HMG domains: promotion of the triple-stranded complex formation between DNA containing (GGA/TCC)11 and d(GGA)11 oligonucleotides.

PubMed Central

Suda, T; Mishima, Y; Takayanagi, K; Asakura, H; Odani, S; Kominami, R

1996-01-01

The high mobility group protein (HMG)-box is a DNA-binding domain found in many proteins that bind preferentially to DNA of irregular structures in a sequence-independent manner and can bend the DNA. We show here that GST-fusion proteins of HMG domains from HMG1 and HMG2 promote a triple-stranded complex formation between DNA containing the (GGA/TCC)11 repeat and oligonucleotides of d(GGA)11 probably due to G:G base pairing. The activity is to reduce association time and requirements of Mg2+ and oligonucleotide concentrations. The HMG box of SRY, the protein determining male-sex differentiation, also has the activity, suggesting that it is not restricted to the HMG-box domains derived from HMG1/2 but is common to those from other members of the HMG-box family of proteins. Interestingly, the box-AB and box-B of HMG1 bend DNA containing the repeat, but SRY fails to bend in a circularization assay. The difference suggests that the two activities of association-promotion and DNA bending are distinct. These results suggest that the HMG-box domain has a novel activity of promoting the association between GGA repeats which might be involved in higher-order architecture of chromatin. PMID:8972860

Exact exchange-correlation potentials of singlet two-electron systems

NASA Astrophysics Data System (ADS)

Ryabinkin, Ilya G.; Ospadov, Egor; Staroverov, Viktor N.

2017-10-01

We suggest a non-iterative analytic method for constructing the exchange-correlation potential, v XC ( r ) , of any singlet ground-state two-electron system. The method is based on a convenient formula for v XC ( r ) in terms of quantities determined only by the system's electronic wave function, exact or approximate, and is essentially different from the Kohn-Sham inversion technique. When applied to Gaussian-basis-set wave functions, the method yields finite-basis-set approximations to the corresponding basis-set-limit v XC ( r ) , whereas the Kohn-Sham inversion produces physically inappropriate (oscillatory and divergent) potentials. The effectiveness of the procedure is demonstrated by computing accurate exchange-correlation potentials of several two-electron systems (helium isoelectronic series, H2, H3 + ) using common ab initio methods and Gaussian basis sets.

Violation of the continuity equation in the Krieger-Li-Iafrate approximation for current-density functional theory

NASA Astrophysics Data System (ADS)

Siegmund, Marc; Pankratov, Oleg

2011-01-01

We show that the exchange-correlation scalar and vector potentials obtained from the optimized effective potential (OEP) equations and from the Krieger-Li-Iafrate (KLI) approximation for the current-density functional theory (CDFT) change under a gauge transformation such that the energy functional remains invariant. This alone does not assure, however, the theory’s compliance with the continuity equation. Using the model of a quantum ring with a broken angular symmetry which is penetrated by a magnetic flux we demonstrate that the physical current density calculated with the exact-exchange CDFT in the KLI approximation violates the continuity condition. In contrast, the current found from a solution of the full OEP equations satisfies this condition. We argue that the continuity violation stems from the fact that the KLI potentials are not (in general) the exact functional derivatives of a gauge-invariant exchange-correlation functional.

Benchmarking the Performance of Exchange-Correlation Functionals for Predicting Two-Photon Absorption Strengths.

PubMed

Beerepoot, Maarten T P; Alam, Md Mehboob; Bednarska, Joanna; Bartkowiak, Wojciech; Ruud, Kenneth; Zaleśny, Robert

2018-06-15

The present work investigates the performance of exchange-correlation functionals in the prediction of two-photon absorption (2PA) strengths. For this purpose, we considered six common functionals used for studying 2PA processes and tested these on six organoboron chelates. The set consisted of two semilocal (PBE and BLYP), two hybrid (B3LYP and PBE0), and two range-separated (LC-BLYP and CAM-B3LYP) functionals. The RI-CC2 method was chosen as a reference level and was found to give results consistent with the experimental data that are available for three of the molecules considered. Of the six exchange-correlation functionals studied, only the range-separated functionals predict an ordering of the 2PA strengths that is consistent with experimental and RI-CC2 results. Even though the range-separated functionals predict correct relative trends, the absolute values for the 2PA strengths are underestimated by a factor of 2-6 for the molecules considered. An in-depth analysis, on the basis of the derived generalized few-state model expression for the 2PA strength for a coupled-cluster wave function, reveals that the problem with these functionals can be linked to underestimated excited-state dipole moments and, to a lesser extent, overestimated excitation energies. The semilocal and hybrid functionals exhibit less predictable errors and a variation in the 2PA strengths in disagreement with the reference results. The semilocal and hybrid functionals show smaller average errors than the range-separated functionals, but our analysis reveals that this is due to fortuitous error cancellation between excitation energies and the transition dipole moments. Our results constitute a warning against using currently available exchange-correlation functionals in the prediction of 2PA strengths and highlight the need for functionals that correctly describe the electron density of excited electronic states.

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

NASA Astrophysics Data System (ADS)

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.

2017-11-01

Diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3 d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et al. [Science 355, 371 (2017), 10.1126/science.aag0410] in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VO2, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development. With our reference data, the accuracy of both the energy and the electron density can be monitored simultaneously, which is useful for functional development. So far, this kind of detailed high accuracy reference data for correlated materials has been absent from the literature.

Electronic Zero-Point Oscillations in the Strong-Interaction Limit of Density Functional Theory.

PubMed

Gori-Giorgi, Paola; Vignale, Giovanni; Seidl, Michael

2009-04-14

The exchange-correlation energy in Kohn-Sham density functional theory can be expressed exactly in terms of the change in the expectation of the electron-electron repulsion operator when, in the many-electron Hamiltonian, this same operator is multiplied by a real parameter λ varying between 0 (Kohn-Sham system) and 1 (physical system). In this process, usually called adiabatic connection, the one-electron density is kept fixed by a suitable local one-body potential. The strong-interaction limit of density functional theory, defined as the limit λ→∞, turns out to be like the opposite noninteracting Kohn-Sham limit (λ→0) mathematically simpler than the physical (λ = 1) case and can be used to build an approximate interpolation formula between λ→0 and λ→∞ for the exchange-correlation energy. Here we extend the systematic treatment of the λ→∞ limit [Phys. Rev. A 2007, 75, 042511] to the next leading term, describing zero-point oscillations of strictly correlated electrons, with numerical examples for small spherical atoms. We also propose an improved approximate functional for the zero-point term and a revised interpolation formula for the exchange-correlation energy satisfying more exact constraints.

Quantum Monte Carlo analysis of a charge ordered insulating antiferromagnet: The Ti 4O 7 Magneli phase

DOE PAGES

Benali, Anouar; Shulenburger, Luke; Krogel, Jaron T.; ...

2016-06-07

The Magneli phase Ti 4O 7 is an important transition metal oxide with a wide range of applications because of its interplay between charge, spin, and lattice degrees of freedom. At low temperatures, it has non-trivial magnetic states very close in energy, driven by electronic exchange and correlation interactions. We have examined three low- lying states, one ferromagnetic and two antiferromagnetic, and calculated their energies as well as Ti spin moment distributions using highly accurate Quantum Monte Carlo methods. We compare our results to those obtained from density functional theory- based methods that include approximate corrections for exchange and correlation.more » Our results confirm the nature of the states and their ordering in energy, as compared with density-functional theory methods. However, the energy differences and spin distributions differ. Here, a detailed analysis suggests that non-local exchange-correlation functionals, in addition to other approximations such as LDA+U to account for correlations, are needed to simultaneously obtain better estimates for spin moments, distributions, energy differences and energy gaps.« less

Ionization energies and electron affinities from a random-phase-approximation many-body Green's-function method including exchange interactions

NASA Astrophysics Data System (ADS)

Heßelmann, Andreas

2017-06-01

A many-body Green's-function method employing an infinite order summation of ring and exchange-ring contributions to the self-energy is presented. The individual correlation and relaxation contributions to the quasiparticle energies are calculated using an iterative scheme which utilizes density fitting of the particle-hole, particle-particle and hole-hole densities. It is shown that the ionization energies and electron affinities of this approach agree better with highly accurate coupled-cluster singles and doubles with perturbative triples energy difference results than those obtained with second-order Green's-function approaches. An analysis of the correlation and relaxation terms of the self-energy for the direct- and exchange-random-phase-approximation (RPA) Green's-function methods shows that the inclusion of exchange interactions leads to a reduction of the two contributions in magnitude. These differences, however, strongly cancel each other when summing the individual terms to the quasiparticle energies. Due to this, the direct- and exchange-RPA methods perform similarly for the description of ionization energies (IPs) and electron affinities (EAs). The coupled-cluster reference IPs and EAs, if corrected to the adiabatic energy differences between the neutral and charged molecules, were shown to be in very good agreement with experimental measurements.

Transcription arrest by a G quadruplex forming-trinucleotide repeat sequence from the human c-myb gene.

PubMed

Broxson, Christopher; Beckett, Joshua; Tornaletti, Silvia

2011-05-17

Non canonical DNA structures correspond to genomic regions particularly susceptible to genetic instability. The transcription process facilitates formation of these structures and plays a major role in generating the instability associated with these genomic sites. However, little is known about how non canonical structures are processed when encountered by an elongating RNA polymerase. Here we have studied the behavior of T7 RNA polymerase (T7RNAP) when encountering a G quadruplex forming-(GGA)(4) repeat located in the human c-myb proto-oncogene. To make direct correlations between formation of the structure and effects on transcription, we have taken advantage of the ability of the T7 polymerase to transcribe single-stranded substrates and of G4 DNA to form in single-stranded G-rich sequences in the presence of potassium ions. Under physiological KCl concentrations, we found that T7 RNAP transcription was arrested at two sites that mapped to the c-myb (GGA)(4) repeat sequence. The extent of arrest did not change with time, indicating that the c-myb repeat represented an absolute block and not a transient pause to T7 RNAP. Consistent with G4 DNA formation, arrest was not observed in the absence of KCl or in the presence of LiCl. Furthermore, mutations in the c-myb (GGA)(4) repeat, expected to prevent transition to G4, also eliminated the transcription block. We show T7 RNAP arrest at the c-myb repeat in double-stranded DNA under conditions mimicking the cellular concentration of biomolecules and potassium ions, suggesting that the G4 structure formed in the c-myb repeat may represent a transcription roadblock in vivo. Our results support a mechanism of transcription-coupled DNA repair initiated by arrest of transcription at G4 structures.

Pressure effects on band structures in dense lithium

NASA Astrophysics Data System (ADS)

Goto, Naoyuki; Nagara, Hitose

2012-07-01

We studied the change of the band structures in some structures of Li predicted at high pressures, using GGA and GW calculations. The width of the 1s band coming from the 1s electron of Li shows broadening by the pressurization, which is the normal behavior of bands at high pressure. The width of the band just below the Fermi level decreases by the pressurization, which is an opposite behavior to the normal bands. The character of this narrowing band is mostly p-like with a little s-like portion. The band gaps in some structures are really observed even by the GGA calculations. The gaps by the GW calculations increase to about 1.5 times the GGA values. Generally the one-shot GW calculation (diagonal only calculations) gives more reliable values than the GGA, but it may fail to predict band gaps for the case where band dispersion shows complex crossing near the Fermi level. There remains some structures for which GW calculations with off-diagonal elements taken into account are needed to identify the phase to be metallic or semiconducting.

Theoretical prediction of the band offsets at the ZnO/anatase TiO2 and GaN/ZnO heterojunctions using the self-consistent ab initio DFT/GGA-1/2 method.

PubMed

Fang, D Q; Zhang, S L

2016-01-07

The band offsets of the ZnO/anatase TiO2 and GaN/ZnO heterojunctions are calculated using the density functional theory/generalized gradient approximation (DFT/GGA)-1/2 method, which takes into account the self-energy corrections and can give an approximate description to the quasiparticle characteristics of the electronic structure of semiconductors. We present the results of the ionization potential (IP)-based and interfacial offset-based band alignments. In the interfacial offset-based band alignment, to get the natural band offset, we use the surface calculations to estimate the change of reference level due to the interfacial strain. Based on the interface models and GGA-1/2 calculations, we find that the valence band maximum and conduction band minimum of ZnO, respectively, lie 0.64 eV and 0.57 eV above those of anatase TiO2, while lie 0.84 eV and 1.09 eV below those of GaN, which agree well with the experimental data. However, a large discrepancy exists between the IP-based band offset and the calculated natural band offset, the mechanism of which is discussed. Our results clarify band alignment of the ZnO/anatase TiO2 heterojunction and show good agreement with the GW calculations for the GaN/ZnO heterojunction.

Time-dependent density functional theory beyond Kohn-Sham Slater determinants.

PubMed

Fuks, Johanna I; Nielsen, Søren E B; Ruggenthaler, Michael; Maitra, Neepa T

2016-08-03

When running time-dependent density functional theory (TDDFT) calculations for real-time simulations of non-equilibrium dynamics, the user has a choice of initial Kohn-Sham state, and typically a Slater determinant is used. We explore the impact of this choice on the exchange-correlation potential when the physical system begins in a 50 : 50 superposition of the ground and first-excited state of the system. We investigate the possibility of judiciously choosing a Kohn-Sham initial state that minimizes errors when adiabatic functionals are used. We find that if the Kohn-Sham state is chosen to have a configuration matching the one that dominates the interacting state, this can be achieved for a finite time duration for some but not all such choices. When the Kohn-Sham system does not begin in a Slater determinant, we further argue that the conventional splitting of the exchange-correlation potential into exchange and correlation parts has limited value, and instead propose a decomposition into a "single-particle" contribution that we denote v, and a remainder. The single-particle contribution can be readily computed as an explicit orbital-functional, reduces to exchange in the Slater determinant case, and offers an alternative to the adiabatic approximation as a starting point for TDDFT approximations.

Density functional theory for d- and f-electron materials and compounds

DOE PAGES

Mattson, Ann E.; Wills, John M.

2016-02-12

Here, the fundamental requirements for a computationally tractable Density Functional Theory-based method for relativistic f- and (nonrelativistic) d-electron materials and compounds are presented. The need for basing the Kohn–Sham equations on the Dirac equation is discussed. The full Dirac scheme needs exchange-correlation functionals in terms of four-currents, but ordinary functionals, using charge density and spin-magnetization, can be used in an approximate Dirac treatment. The construction of a functional that includes the additional confinement physics needed for these materials is illustrated using the subsystem-functional scheme. If future studies show that a full Dirac, four-current based, exchange-correlation functional is needed, the subsystemmore » functional scheme is one of the few schemes that can still be used for constructing functional approximations.« less

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

DOE PAGES

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan; ...

2017-11-27

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

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

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

DFT study on stability and H2 adsorption activity of bimetallic Au79-nPdn (n = 1-55) clusters

NASA Astrophysics Data System (ADS)

Liu, Xuejing; Tian, Dongxu; Meng, Changgong

2013-03-01

The stability and H2 adsorption activity of bimetallic Au79-nPdn (n = 1-55) clusters were studied by density functional theory with GGA-PW91 functional. The stability order for four Pd substitution types is face > mid-edge > corner > edge, and the stability is improved with increasing Pd content. In contrast with the stability order, H2 adsorption activity is corner ≈ edge > mid-edge > face. The Au36Pd43 (3) with Au:Pd ≈ 1:1 ratio and twenty-four Pd substitutions at (1 1 1) facets and nineteen Pd substitutions at subshell sites shows high stability and H2 non-activated dissociation activity. The partial density of d-states and d band center revealed that the electronic properties are closely associated with the geometric characteristic and adsorption activity. Correlating the d band center ɛd and the adsorption energies, the ɛd order agrees with the adsorption activity that the Pd substitution at edge and corner sites are more active than at face and mid-edge sites.

A general range-separated double-hybrid density-functional theory

NASA Astrophysics Data System (ADS)

Kalai, Cairedine; Toulouse, Julien

2018-04-01

A range-separated double-hybrid (RSDH) scheme which generalizes the usual range-separated hybrids and double hybrids is developed. This scheme consistently uses a two-parameter Coulomb-attenuating-method (CAM)-like decomposition of the electron-electron interaction for both exchange and correlation in order to combine Hartree-Fock exchange and second-order Møller-Plesset (MP2) correlation with a density functional. The RSDH scheme relies on an exact theory which is presented in some detail. Several semi-local approximations are developed for the short-range exchange-correlation density functional involved in this scheme. After finding optimal values for the two parameters of the CAM-like decomposition, the RSDH scheme is shown to have a relatively small basis dependence and to provide atomization energies, reaction barrier heights, and weak intermolecular interactions globally more accurate or comparable to range-separated MP2 or standard MP2. The RSDH scheme represents a new family of double hybrids with minimal empiricism which could be useful for general chemical applications.

Magnetism and transport properties of layered rare-earth cobaltates Ln{sub 0.3}CoO{sub 2}

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

Knížek, K., E-mail: knizek@fzu.cz; Novák, P.; Jirák, Z.

2015-05-07

The ab-initio (GGA+U) electronic structure calculations of layered cobaltates Ln{sub 0.3}CoO{sub 2} (Ln = La, Pr, Nd) prepared by ionic exchange from Na{sub 0.90}CoO{sub 2} precursors have been performed. The data are used for numerical modeling of Seebeck coefficient within Boltzmann transport theory using BoltzTraP program [G. K. H. Madsen and D. J. Singh, Comput. Phys. Commun. 175, 67 (2006)], as well as for determination of the crystal field split levels of rare-earth ions using a method based on a transformation of Bloch states into the basis of Wannier functions [P. Novák et al., Phys. Rev. B 87, 205139 (2013)]. An overallmore » agreement with observed magnetism and transport properties is obtained. In particular, the high p-type thermopower is well reproduced in a broad temperature range, but instead of theoretical linear decrease down to the lowest temperatures, the real systems exhibit an anomalous change of Seebeck sign, which might be related to the change of bare metallic carriers into the polaronic ones.« less

Magnetic exchange in {Gd(III)-radical} complexes: method assessment, mechanism of coupling and magneto-structural correlations.

PubMed

Gupta, Tulika; Rajeshkumar, Thayalan; Rajaraman, Gopalan

2014-07-28

Density functional studies have been performed on ten different {Gd(III)-radical} complexes exhibiting both ferro and antiferromagnetic exchange interaction with an aim to assess a suitable exchange-correlation functional within DFT formalism. This study has also been extended to probe the mechanism of magnetic coupling and to develop suitable magneto-structural correlations for this pair. Our method assessments reveal the following order of increasing accuracy for the evaluation of J values compared to experimental coupling constants: B(40HF)LYP < BHandHLYP < TPSSH < PW91 < PBE < BP86 < OLYP < BLYP < PBE0 < X3LYP < B3LYP < B2PLYP. Grimme's double-hybrid functional is found to be superior compared to other functionals tested and this is followed very closely by the conventional hybrid B3LYP functional. At the basis set front, our calculations reveal that the incorporation of relativistic effect is important in these calculations and the relativistically corrected effective core potential (ECP) basis set is found to yield better Js compared to other methods. The supposedly empty 5d/6s/6p orbitals of Gd(III) are found to play an important role in the mechanism of magnetic coupling and different contributions to the exchange terms are probed using Molecular Orbital (MO) and Natural Bond Orbital (NBO) analysis. Magneto-structural correlations for Gd-O distances, Gd-O-N angles and Gd-O-N-C dihedral angles are developed where the bond angles as well as dihedral angle parameters are found to dictate the sign and strength of the magnetic coupling in this series.

Multi-Paradigm Multi-Scale Simulations for Fuel Cell Catalysts and Membranes

DTIC Science & Technology

2006-01-01

transfer studies on model systems. . Applying newly developed density functionals QM ( X3LYP ) for estimating the thermodynamics and kinetic energy...Density functional theory methods We have used many QM methods to probe chemical reaction mechanisms and find that the B3LYP and X3LYP [6] flavors of DFT...carried out QM calculations on the surface reactivity of the Pt and PtRu anode catalysts. This QM uses a new ab initio DFT-GGA method ( X3LYP ) [6

Adsorption and Electronic Structure of Sr and Ag Atoms on Graphite Surfaces: a First-Principles Study

NASA Astrophysics Data System (ADS)

Luo, Xiao-Feng; Fang, Chao; Li, Xin; Lai, Wen-Sheng; Sun, Li-Feng; Liang, Tong-Xiang

2013-06-01

The adsorption behaviors of radioactive strontium and silver nuclides on the graphite surface in a high-temperature gas-cooled reactor are studied by first-principles theory using generalized gradient approximation (GGA) and local density approximation (LDA) pseudo-potentials. It turns out that Sr prefers to be absorbed at the hollow of the carbon hexagonal cell by 0.54 eV (GGA), while Ag likes to sit right above the carbon atom with an adsorption energy of almost zero (GGA) and 0.45 eV (LDA). Electronic structure analysis reveals that Sr donates its partial electrons of the 4p and 5s states to the graphite substrate, while Ag on graphite is a physical adsorption without any electron transfer.

Projector Augmented Wave formulation of orbital-dependent exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Xu, Xiao; Holzwarth, N. A. W.

2012-02-01

The use of orbital-dependent exchange-correlation functionals within electronic structure calculations has recently received renewed attention for improving the accuracy of the calculations, especially correcting self-interaction errors. Since the Projector Augmented Wave (PAW) methodootnotetext P. Bl"ochl, Phys. Rev. B 50, 17953 (1994). is an efficient pseudopotential-like scheme which ensures accurate evaluation of all multipole moments of direct and exchange Coulomb integrals, it is a natural choice for implementing orbital-dependent formalisms. Using Fock exchange as an example of an orbital-dependent functional, we developed the formulation and numerical implementation of the approximate optimized effective potential formalism of Kreiger, Li, and Iafrate (KLI)ootnotetext J. B. Krieger, Y. Li, and G. J. Iafrate Phys. Rev. A 45, 101 (1992). within the PAW method, comparing results with the analogous Hartree-Fock treatment.ootnotetext Xiao Xu and N. A. W. Holzwarth, Phys. Rev. B 81, 245105 (2010); 84, 155113 (2011). Test results are presented for ground state properties of two well-known materials -- diamond and LiF. This formalism can be extended to treat orbital-dependent functionals more generally.

Hyperfine field, electric field gradient, quadrupole coupling constant and magnetic properties of challenging actinide digallide

NASA Astrophysics Data System (ADS)

Khan, Sajid; Yazdani-Kachoei, M.; Jalali-Asadabadi, S.; Ahmad, Iftikhar

2017-12-01

In this paper, we explore the structural and magnetic properties as well as electric field gradient (EFG), hyperfine field (HFF) and quadrupole coupling constant in actinide digallide AcGa2 (Ac = U, Np, Pu) using LDA, GGA, LDA+U, GGA+U and hybrid functional with Wu-Cohen Generalized Gradient approximation HF-WC. Relativistic effects of the electrons are considered by including spin-orbit coupling. The comparison of the calculated structural parameters and magnetic properties with the available experimental results confirms the consistency and hence effectiveness of our theoretical tools. The calculated magnetic moments demonstrate that UGa2 and NpGa2 are ferromagnetic while PuGa2 is antiferromagnetic in nature. The EFG of AcGa2 is reported for the first time. The HFF, EFG and quadrupole coupling constant in AcGa2 (Ac = U, Np, Pu) are mainly originated from f-f and p-p contributions of Ac atom and p-p contribution of Ga atom.

Role of exact exchange in thermally-assisted-occupation density functional theory: A proposal of new hybrid schemes.

PubMed

Chai, Jeng-Da

2017-01-28

We propose hybrid schemes incorporating exact exchange into thermally assisted-occupation-density functional theory (TAO-DFT) [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)] for an improved description of nonlocal exchange effects. With a few simple modifications, global and range-separated hybrid functionals in Kohn-Sham density functional theory (KS-DFT) can be combined seamlessly with TAO-DFT. In comparison with global hybrid functionals in KS-DFT, the resulting global hybrid functionals in TAO-DFT yield promising performance for systems with strong static correlation effects (e.g., the dissociation of H 2 and N 2 , twisted ethylene, and electronic properties of linear acenes), while maintaining similar performance for systems without strong static correlation effects. Besides, a reasonably accurate description of noncovalent interactions can be efficiently achieved through the inclusion of dispersion corrections in hybrid TAO-DFT. Relative to semilocal density functionals in TAO-DFT, global hybrid functionals in TAO-DFT are generally superior in performance for a wide range of applications, such as thermochemistry, kinetics, reaction energies, and optimized geometries.

On the exchange-hole model of London dispersion forces

NASA Astrophysics Data System (ADS)

Ángyán, János G.

2007-07-01

First-principles derivation is given for the heuristic exchange-hole model of London dispersion forces by Becke and Johnson [J. Chem. Phys. 122, 154104 (2005)]. A one-term approximation is used for the dynamic charge density response function, and it is shown that a central nonempirical ingredient of the approximate nonexpanded dispersion energy is the charge density autocorrelation function, a two-particle property, related to the exchange-correlation hole. In the framework of a dipolar approximation of the Coulomb interaction around the molecular origin, one obtains the so-called Salem-Tang-Karplus approximation to the C6 dispersion coefficient. Alternatively, by expanding the Coulomb interaction around the center of charge (centroid) of the exchange-correlation hole associated with each point in the molecular volume, a multicenter expansion is obtained around the centroids of electron localization domains, always in terms of the exchange-correlation hole. In order to get a formula analogous to that of Becke and Johnson, which involves the exchange-hole only, further assumptions are needed, related to the difficulties of obtaining the expectation value of a two-electron operator from a single determinant. Thus a connection could be established between the conventional fluctuating charge density model of London dispersion forces and the notion of the "exchange-hole dipole moment" shedding some light on the true nature of the approximations implicit in the Becke-Johnson model.

Density-to-Potential Inversions to Guide Development of Exchange-Correlation Approximations at Finite Temperature

NASA Astrophysics Data System (ADS)

Jensen, Daniel; Wasserman, Adam; Baczewski, Andrew

The construction of approximations to the exchange-correlation potential for warm dense matter (WDM) is a topic of significant recent interest. In this work, we study the inverse problem of Kohn-Sham (KS) DFT as a means of guiding functional design at zero temperature and in WDM. Whereas the forward problem solves the KS equations to produce a density from a specified exchange-correlation potential, the inverse problem seeks to construct the exchange-correlation potential from specified densities. These two problems require different computational methods and convergence criteria despite sharing the same mathematical equations. We present two new inversion methods based on constrained variational and PDE-constrained optimization methods. We adapt these methods to finite temperature calculations to reveal the exchange-correlation potential's temperature dependence in WDM-relevant conditions. The different inversion methods presented are applied to both non-interacting and interacting model systems for comparison. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94.

Neutrinoless ββ decay mediated by the exchange of light and heavy neutrinos: the role of nuclear structure correlations

NASA Astrophysics Data System (ADS)

Menéndez, J.

2018-01-01

Neutrinoless β β decay nuclear matrix elements calculated with the shell model and energy-density functional theory typically disagree by more than a factor of two in the standard scenario of light-neutrino exchange. In contrast, for a decay mediated by sterile heavy neutrinos the deviations are reduced to about 50%, an uncertainty similar to the one due to short-range effects. We compare matrix elements in the light- and heavy-neutrino-exchange channels, exploring the radial, momentum transfer and angular momentum-parity matrix element distributions, and considering transitions that involve correlated and uncorrelated nuclear states. We argue that the shorter-range heavy-neutrino exchange is less sensitive to collective nuclear correlations, and that discrepancies in matrix elements are mostly due to the treatment of long-range correlations in many-body calculations. Our analysis supports previous studies suggesting that isoscalar pairing correlations, which affect mostly the longer-range part of the neutrinoless β β decay operator, are partially responsible for the differences between nuclear matrix elements in the standard light-neutrino-exchange mechanism.

Some Fundamental Issues in Ground-State Density Functional Theory: A Guide for the Perplexed.

PubMed

Perdew, John P; Ruzsinszky, Adrienn; Constantin, Lucian A; Sun, Jianwei; Csonka, Gábor I

2009-04-14

Some fundamental issues in ground-state density functional theory are discussed without equations: (1) The standard Hohenberg-Kohn and Kohn-Sham theorems were proven for a Hamiltonian that is not quite exact for real atoms, molecules, and solids. (2) The density functional for the exchange-correlation energy, which must be approximated, arises from the tendency of electrons to avoid one another as they move through the electron density. (3) In the absence of a magnetic field, either spin densities or total electron density can be used, although the former choice is better for approximations. (4) "Spin contamination" of the determinant of Kohn-Sham orbitals for an open-shell system is not wrong but right. (5) Only to the extent that symmetries of the interacting wave function are reflected in the spin densities should those symmetries be respected by the Kohn-Sham noninteracting or determinantal wave function. Functionals below the highest level of approximations should however sometimes break even those symmetries, for good physical reasons. (6) Simple and commonly used semilocal (lower-level) approximations for the exchange-correlation energy as a functional of the density can be accurate for closed systems near equilibrium and yet fail for open systems of fluctuating electron number. (7) The exact Kohn-Sham noninteracting state need not be a single determinant, but common approximations can fail when it is not. (8) Over an open system of fluctuating electron number, connected to another such system by stretched bonds, semilocal approximations make the exchange-correlation energy and hole-density sum rule too negative. (9) The gap in the exact Kohn-Sham band structure of a crystal underestimates the real fundamental gap but may approximate the first exciton energy in the large-gap limit. (10) Density functional theory is not really a mean-field theory, although it looks like one. The exact functional includes strong correlation, and semilocal approximations often overestimate the strength of static correlation through their semilocal exchange contributions. (11) Only under rare conditions can excited states arise directly from a ground-state theory.

Investigating the Psychometric Properties of the ACEI Global Guidelines Assessment, Third Edition (GGA) in Nine Countries

ERIC Educational Resources Information Center

Hardin, Belinda J.; Bergen, Doris; Busio, Dionne Sills; Boone, William

2017-01-01

The Third Edition of the ACEI Global Guidelines Assessment (GGA) was evaluated for its effectiveness as an international assessment tool for use by early childhood educators to develop, assess, and improve program quality worldwide. This expanded study was conducted in nine countries [People's Republic of China (2 sites), Guatemala, India, Italy,…

Short-range second order screened exchange correction to RPA correlation energies

NASA Astrophysics Data System (ADS)

Beuerle, Matthias; Ochsenfeld, Christian

2017-11-01

Direct random phase approximation (RPA) correlation energies have become increasingly popular as a post-Kohn-Sham correction, due to significant improvements over DFT calculations for properties such as long-range dispersion effects, which are problematic in conventional density functional theory. On the other hand, RPA still has various weaknesses, such as unsatisfactory results for non-isogyric processes. This can in parts be attributed to the self-correlation present in RPA correlation energies, leading to significant self-interaction errors. Therefore a variety of schemes have been devised to include exchange in the calculation of RPA correlation energies in order to correct this shortcoming. One of the most popular RPA plus exchange schemes is the second order screened exchange (SOSEX) correction. RPA + SOSEX delivers more accurate absolute correlation energies and also improves upon RPA for non-isogyric processes. On the other hand, RPA + SOSEX barrier heights are worse than those obtained from plain RPA calculations. To combine the benefits of RPA correlation energies and the SOSEX correction, we introduce a short-range RPA + SOSEX correction. Proof of concept calculations and benchmarks showing the advantages of our method are presented.

Short-range second order screened exchange correction to RPA correlation energies.

PubMed

Beuerle, Matthias; Ochsenfeld, Christian

2017-11-28

Direct random phase approximation (RPA) correlation energies have become increasingly popular as a post-Kohn-Sham correction, due to significant improvements over DFT calculations for properties such as long-range dispersion effects, which are problematic in conventional density functional theory. On the other hand, RPA still has various weaknesses, such as unsatisfactory results for non-isogyric processes. This can in parts be attributed to the self-correlation present in RPA correlation energies, leading to significant self-interaction errors. Therefore a variety of schemes have been devised to include exchange in the calculation of RPA correlation energies in order to correct this shortcoming. One of the most popular RPA plus exchange schemes is the second order screened exchange (SOSEX) correction. RPA + SOSEX delivers more accurate absolute correlation energies and also improves upon RPA for non-isogyric processes. On the other hand, RPA + SOSEX barrier heights are worse than those obtained from plain RPA calculations. To combine the benefits of RPA correlation energies and the SOSEX correction, we introduce a short-range RPA + SOSEX correction. Proof of concept calculations and benchmarks showing the advantages of our method are presented.

Bond breaking and bond formation: how electron correlation is captured in many-body perturbation theory and density-functional theory.

PubMed

Caruso, Fabio; Rohr, Daniel R; Hellgren, Maria; Ren, Xinguo; Rinke, Patrick; Rubio, Angel; Scheffler, Matthias

2013-04-05

For the paradigmatic case of H(2) dissociation, we compare state-of-the-art many-body perturbation theory in the GW approximation and density-functional theory in the exact-exchange plus random-phase approximation (RPA) for the correlation energy. For an unbiased comparison and to prevent spurious starting point effects, both approaches are iterated to full self-consistency (i.e., sc-RPA and sc-GW). The exchange-correlation diagrams in both approaches are topologically identical, but in sc-RPA they are evaluated with noninteracting and in sc-GW with interacting Green functions. This has a profound consequence for the dissociation region, where sc-RPA is superior to sc-GW. We argue that for a given diagrammatic expansion, sc-RPA outperforms sc-GW when it comes to bond breaking. We attribute this to the difference in the correlation energy rather than the treatment of the kinetic energy.

Biofuel combustion. Energetics and kinetics of hydrogen abstraction from carbon-1 in n-butanol by the hydroperoxyl radical calculated by coupled cluster and density functional theories and multistructural variational transition-state theory with multidimensional tunneling.

PubMed

Alecu, I M; Zheng, Jingjing; Papajak, Ewa; Yu, Tao; Truhlar, Donald G

2012-12-20

Multistructural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT) is employed to calculate thermal rate constants for hydrogen-atom abstraction from carbon-1 of n-butanol by the hydroperoxyl radical over the temperature range 250-2000 K. The M08-SO hybrid meta-GGA density functional was validated against CCSD(T)-F12a explicitly correlated wave function calculations with the jul-cc-pVTZ basis set. It was then used to compute the properties of all stationary points and the energies and Hessians of a few nonstationary points along the reaction path, which were then used to generate a potential energy surface by the multiconfiguration Shepard interpolation (MCSI) method. The internal rotations in the transition state for this reaction (like those in the reactant alcohol) are strongly coupled to each other and generate multiple stable conformations, which make important contributions to the partition functions. It is shown that neglecting to account for the multiple-structure effects and torsional potential anharmonicity effects that arise from the torsional modes would lead to order-of-magnitude errors in the calculated rate constants at temperatures of interest in combustion.

Magnetic interactions in a quasi-one-dimensional antiferromagnet Cu(H{sub 2}O){sub 2}(en)SO{sub 4}

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

Sýkora, Rudolf, E-mail: rudolf.sykora@vsb.cz; Legut, Dominik

A theoretical ab-initio investigation of exchange interaction between Cu atoms in an insulating antiferromagnet Cu(H{sub 2}O){sub 2}(en)SO{sub 4}, en = C{sub 2}H{sub 8}N{sub 2}, is reported. While the previous experimental studies described the system's magnetism to be quasi-two-dimensional, our results, based on a mapping of the system onto an effective Heisenberg model, rather support a quasi-one-dimensional character with the exchange coupling between the Cu atoms being propagated mainly along a zigzag line lying in the crystal's bc plane and connecting the Cu atoms through the N atoms. Further, the direction of magnetic moments on the Cu atoms is suggested to be nearlymore » along the crystal's a axis. A check of the change in the exchange constants induced either by external pressure or by various values of U in the GGA + U approximation is made. Finally, based on experimental values of positions of broad maxima in magnetic-susceptibility and specific-heat curves and using theoretical expressions available in the literature a relevant value of the U parameter and related expected value of the electronic gap are estimated to be about 5 eV and 2 eV, respectively.« less

Ab initio calculation of pentacene-PbSe hybrid interface for photovoltaic applications.

PubMed

Roy, P; Nguyen, Thao P

2016-07-21

We perform density functional theory (DFT) quantum chemical calculations for the pentacene-PbSe hybrid interface at both molecular and crystal levels. At the interface, the parallel orientation of pentacene on the PbSe surface is found to be the most favorable, analogous to a pentacene-gold interface. The molecule-surface distance and the value of charge transfer from one pentacene molecule to the PbSe surface are estimated at around 4.15 Å and 0.12 e(-) respectively. We found that, standard-LDA/GGA-PBE/hybrid/meta-GGA xc-functionals incorrectly determine the band gaps of both pentacene and PbSe and leads to a failed prediction of the energy alignment in this system. So, we use a relativistic G0W0 functional and accurately model the electronic properties of pentacene and PbSe in both bulk material and near the interface. An energy shift of 0.23 eV, due to the difference in work function at the interface was supplemented after a detailed analysis of the electrostatic potential. The highest occupied molecular orbital level of pentacene is 0.01 eV above PbSe while the lowest unoccupied molecular orbital of pentacene lies 1.70 eV above PbSe, allowing both electrons and holes to transfer along the donor-acceptor junction. Our results provide additional insights into the electronic structure properties of the pentacene-PbSe heterojunction and establish it as a promising and efficient candidate for photovoltaic applications.

Adaptation of the projector-augmented-wave formalism to the treatment of orbital-dependent exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Xu, Xiao; Holzwarth, N. A. W.

2011-10-01

This paper presents the formulation and numerical implementation of a self-consistent treatment of orbital-dependent exchange-correlation functionals within the projector-augmented-wave method of Blöchl [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.50.17953 50, 17953 (1994)] for electronic structure calculations. The methodology is illustrated with binding energy curves for C in the diamond structure and LiF in the rock salt structure, by comparing results from the Hartree-Fock (HF) formalism and the optimized effective potential formalism in the so-called KLI approximation [Krieger, Li, and Iafrate, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.45.101 45, 101 (1992)] with those of the local density approximation. While the work here uses pure Fock exchange only, the formalism can be extended to treat orbital-dependent functionals more generally.

Discontinuity of the exchange-correlation potential and the functional derivative of the noninteracting kinetic energy as the number of electrons crosses integer boundaries in Li, Be, and B.

PubMed

Morrison, Robert C

2015-01-07

Accurate densities were determined from configuration interaction wave functions for atoms and ions of Li, Be, and B with up to four electrons. Exchange-correlation potentials, Vxc(r), and functional derivatives of the noninteracting kinetic energy, δK[ρ]/δρ(r), obtained from these densities were used to examine their discontinuities as the number of electrons N increases across integer boundaries for N = 1, N = 2, and N = 3. These numerical results are consistent with conclusions that the discontinuities are characterized by a jump in the chemical potential while the shape of Vxc(r) varies continuously as an integer boundary is crossed. The discontinuity of the Vxc(r) is positive, depends on the ionization potential, electron affinity, and orbital energy differences, and the discontinuity in δK[ρ]/δρ(r) depends on the difference between the energies of the highest occupied and lowest unoccupied orbitals. The noninteracting kinetic energy and the exchange correlation energy have been computed for integer and noninteger values of N between 1 and 4.

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit

NASA Astrophysics Data System (ADS)

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-01

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Møller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit.

PubMed

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-14

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Moller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

Concerted hydrogen atom exchange between three HF molecules

NASA Technical Reports Server (NTRS)

Komornicki, Andrew; Dixon, David A.; Taylor, Peter R.

1992-01-01

We have investigated the termolecular reaction involving concerted hydrogen exchange between three HF molecules, with particular emphasis on the effects of correlation at the various stationary points along the reaction. Using an extended basis, we have located the geometries of the stable hydrogen-bonded trimer, which is of C(sub 3h) symmetry, and the transition state for hydrogen exchange, which is of D(sub 3h) symmetry. The energies of the exchange reation were then evaluated at the correlated level, using a large atomic natural orbital basis and correlating all valence electrons. Several correlation treatments were used, namely, configration interaction with single and double excitations, coupled-pair functional, and coupled-cluster methods. We are thus able to measure the effect of accounting for size-extensivity. Zero-point corrections to the correlated level energetics were determined using analytic second derivative techniques at the SCF level. Our best calculations, which include the effects of connected triple excitations in the coupled-cluster procedure, indicate that the trimer is bound by 9 +/- 1 kcal/mol relative to three separate monomers, in excellent agreement with previous estimates. The barrier to concerted hydrogen exchange is 15 kcal/mol above the trimer, or only 4.7 kcal/mol above three separated monomers. Thus the barrier to hydrogen exchange between HF molecules via this termolecular process is very low.

First principle study of structural, electronic and fermi surface properties of aluminum praseodymium

NASA Astrophysics Data System (ADS)

Shugani, Mani; Aynyas, Mahendra; Sanyal, S. P.

2018-05-01

We present a structural, Electronic and Fermi surface properties of Aluminum Praseodymium (AlPr) using First-principles density functional calculation by using full potential linearized augmented plane wave (FP-LAPW) method within generalized gradient approximation (GGA). The ground state properties along with electronic and Fermi surface properties are studied. It is found that AlPr is metallic and the bonding between Al and Pr is covalent.

Revealing the optoelectronic and thermoelectric properties of the Zintl quaternary arsenides ACdGeAs{sub 2} (A = K, Rb)

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

Azam, Sikander; Khan, Saleem Ayaz; Goumri-Said, Souraya, E-mail: Souraya.Goumri-Said@chemistry.gatech.edu

Highlights: • Zintl tetragonal phase ACdGeAs{sub 2} (A = K, Rb) are chalcopyrite and semiconductors. • Their direct band gap is suitable for PV, optolectronic and thermoelectric applications. • Combination of DFT and Boltzmann transport theory is employed. • The present arsenides are found to be covalent materials. - Abstract: Chalcopyrite semiconductors have attracted much attention due to their potential implications in photovoltaic and thermoelectric applications. First principle calculations were performed to investigate the electronic, optical and thermoelectric properties of the Zintl tetragonal phase ACdGeAs{sub 2} (A = K, Rb) using the full potential linear augmented plane wave method andmore » the Engle–Vosko GGA (EV–GGA) approximation. The present compounds are found semiconductors with direct band gap and covalent bonding character. The optical transitions are investigated via the dielectric function (real and imaginary parts) along with other related optical constants including refractive index, reflectivity and energy-loss spectrum. Combining results from DFT and Boltzmann transport theory, we reported the thermoelectric properties such as the Seebeck’s coefficient, electrical and thermal conductivity, figure of merit and power factor as function of temperatures. The present chalcopyrite Zintl quaternary arsenides deserve to be explored for their potential applications as thermoelectric materials and for photovoltaic devices.« less

On the molecular structure, vibrational spectra, HOMO-LUMO, molecular electrostatic potential, UV-Vis, first order hyperpolarizability, and thermodynamic investigations of 3-(4-chlorophenyl)-1-(1yridine-3-yl) prop-2-en-1-one by quantum chemistry calculations

NASA Astrophysics Data System (ADS)

Rahmani, Rachida; Boukabcha, Nourdine; Chouaih, Abdelkader; Hamzaoui, Fodil; Goumri-Said, Souraya

2018-03-01

A recent experimental study has allowed synthesis of a new organic nonlinear optical material 3-(4-chlorophenyl)-1-(pyridin-3-yl)prop-2-en-1-one(CPP) with a high second harmonic generation efficiency. We apply density functional theory (DFT, GGA and B3LYP) and Hartree-Fock (HF) methods to calculate the vibrational wavenumbers. They are assigned with by using the potential energy distribution method. The calculated first hyperpolarizability of the title compound is comparable with the reported values of similar derivatives and 25 times that of the standard NLO material urea. The HOMO-LUMO calculations lead to consider GGA-PBE as the best functional to determine the electronic band gap of CPP molecule. We complete this study with assignment of the vibrational modes and perform a comparison with the experimental results. The analysis of MEP map shows that the most reactive site of the CPP molecule is the site containing the oxygen atom. Furthermore, because of the enhancement of molecular vibration within the CPP molecule, the thermodynamic parameters are increasing with the increase of temperature. The FTIR, Raman and NMR spectra are calculated using DFT approach and corroborate the experimental available data.

First Principles Study of Electronic Band Structure and Structural Stability of Al2C Monolayer and Nanotubes

NASA Astrophysics Data System (ADS)

Pramchu, S.; Jaroenjittichai, A. P.; Laosiritaworn, Y.

2017-09-01

We used density functional theory (DFT) based on generalized gradient approximation (GGA) and hybrid functional (HSE06) to investigate band gap and structural stability of Al2C monolayer and nanotubes. From the results, both GGA and HSE06 band gaps of Al2C monolayer agree well with previously reported data. For the Al2C nanotubes, we found that their band gaps are more sensitive to the size and the chirality than that of the widely studied SiC2 nanotubes, indicating the Al2C nanotubes may have higher band gap tuning capabilities (with varying diameter size and chirality) compared with those of SiC2 nanotubes. We have also discovered a desirable direct band gap in the case of (n,0) nanotubes, although Al2C monolayer band gap is indirect. The calculated strain energy reveals that (n,0) nanotubes constructed by wrapping up Al2C monolayer consume less energy than (0,n) nanotubes. Thus, (n,0) nanotubes is easier to synthesize than (0,n) nanotubes. This discovery of direct band gap in (n,0) Al2C nanotubes and their adjustable band gap suggests them as promising sensitizer for enhancing power conversion efficiency of excitonic solar cells.

The role of the van der Waals interactions in the adsorption of anthracene and pentacene on the Ag(111) surface

NASA Astrophysics Data System (ADS)

Morbec, Juliana M.; Kratzer, Peter

2017-01-01

Using first-principles calculations based on density-functional theory (DFT), we investigated the effects of the van der Waals (vdW) interactions on the structural and electronic properties of anthracene and pentacene adsorbed on the Ag(111) surface. We found that the inclusion of vdW corrections strongly affects the binding of both anthracene/Ag(111) and pentacene/Ag(111), yielding adsorption heights and energies more consistent with the experimental results than standard DFT calculations with generalized gradient approximation (GGA). For anthracene/Ag(111) the effect of the vdW interactions is even more dramatic: we found that "pure" DFT-GGA calculations (without including vdW corrections) result in preference for a tilted configuration, in contrast to the experimental observations of flat-lying adsorption; including vdW corrections, on the other hand, alters the binding geometry of anthracene/Ag(111), favoring the flat configuration. The electronic structure obtained using a self-consistent vdW scheme was found to be nearly indistinguishable from the conventional DFT electronic structure once the correct vdW geometry is employed for these physisorbed systems. Moreover, we show that a vdW correction scheme based on a hybrid functional DFT calculation (HSE) results in an improved description of the highest occupied molecular level of the adsorbed molecules.

Optimization of an exchange-correlation density functional for water

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

Fritz, Michelle; Fernández-Serra, Marivi; Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-3800

2016-06-14

We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem, constrains the optimized functional not to depart unphysically from existing ab initio functionals. The resulting functional maximizes the probability of being the “correct” parameterization of a given functional form, in the sense of Bayes theory. The application of DPPS to water sheds new light on why density functional theory has performed rather poorly for liquid water, on what improvements are needed, and onmore » the intrinsic limitations of the generalized gradient approximation to electron exchange and correlation. Finally, we present tests of our water-optimized functional, that we call vdW-DF-w, showing that it performs very well for a variety of condensed water systems.« less

Novel density functional methodology for the computation of accurate electronic and thermodynamic properties of molecular systems and improved long-range behavior

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

Kafafi, S.A.

1998-12-10

A novel general purpose density functional methodology for the computation of accurate electronic and thermodynamic properties of molecules and improved long-range behavior is reported. Assuming the separability of the exchange (E{sub x}) and correlation (E{sub c}) contributions to the total exchange-correlation energy functional (E{sub xc}), the E{sub x} term consists of a hybrid mixture of 37.5% Hartree-Fock exchange and the appropriate local spin density exchange using the adiabatic connection formula. He demonstrated that E{sub x} and its corresponding potential V{sub x} [=dE{sub x}/d{rho}(r)] have the proper asymptotic limits at r = 0 and r {r_arrow} {infinity}, E{sub c} consists ofmore » the Vosko, Wilk, and Nusair formula for the free-electron gas correlation energy and a generalized gradient approximation term with one adjustable parameter. V{sub c} [=dE{sub c}/d{rho}(r)] was shown to obey the r {r_arrow} {infinity} limit of the corresponding potential derived from exact atomic exchange-correlation computations; namely, V{sub c} is proportional to r{sup {minus}4}. Most importantly, he demonstrated that, at r values where dispersion forces are operating, V{sub c} is proportional to 1/r{sup n} (n = 4, 6, 8, {hor_ellipsis}). The reported method was denoted by K2-BVWN because it used two adjustable parameters in its formulation. The K2-BVWN scheme scales as N{sup 3}, where N is the number of basis functions, compared to {approximately}N{sup 7} for Gaussian-2 (G2) ab initio theory and related methods, {approximately}N{sup 5} for Barone`s mPW1,3PW, and {approximately}N{sup 4} for Becke`s three-parameter density functional approaches. The G2 data set complemented by the reported molecular systems investigated in this work was recommended as a critical test for evaluating novel ab initio and density functional methodologies. The K2-BVWN method has been implemented in the Gaussian series of programs.« less

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

Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole

Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we showmore » that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B₃N₃H₆) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.« less

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

Al-Hamdani, Yasmine S.; Michaelides, Angelos, E-mail: angelos.michaelides@ucl.ac.uk; Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ

Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we showmore » that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B{sub 3}N{sub 3}H{sub 6}) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.« less

Newtype single-layer magnetic semiconductor in transition-metal dichalcogenides VX2 (X = S, Se and Te)

NASA Astrophysics Data System (ADS)

Fuh, Huei-Ru; Chang, Ching-Ray; Wang, Yin-Kuo; Evans, Richard F. L.; Chantrell, Roy W.; Jeng, Horng-Tay

2016-09-01

We present a newtype 2-dimensional (2D) magnetic semiconductor based on transition-metal dichalcogenides VX2 (X = S, Se and Te) via first-principles calculations. The obtained indirect band gaps of monolayer VS2, VSe2, and VTe2 given from the generalized gradient approximation (GGA) are respectively 0.05, 0.22, and 0.20 eV, all with integer magnetic moments of 1.0 μB. The GGA plus on-site Coulomb interaction U (GGA + U) enhances the exchange splittings and raises the energy gap up to 0.38~0.65 eV. By adopting the GW approximation, we obtain converged G0W0 gaps of 1.3, 1.2, and 0.7 eV for VS2, VSe2, and VTe2 monolayers, respectively. They agree very well with our calculated HSE gaps of 1.1, 1.2, and 0.6 eV, respectively. The gap sizes as well as the metal-insulator transitions are tunable by applying the in-plane strain and/or changing the number of stacking layers. The Monte Carlo simulations illustrate very high Curie-temperatures of 292, 472, and 553 K for VS2, VSe2, and VTe2 monolayers, respectively. They are nearly or well beyond the room temperature. Combining the semiconducting energy gap, the 100% spin polarized valence and conduction bands, the room temperature TC, and the in-plane magnetic anisotropy together in a single layer VX2, this newtype 2D magnetic semiconductor shows great potential in future spintronics.

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

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

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

2012-01-11

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

Fundamental gaps with approximate density functionals: The derivative discontinuity revealed from ensemble considerations

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

Kraisler, Eli; Kronik, Leeor

2014-05-14

The fundamental gap is a central quantity in the electronic structure of matter. Unfortunately, the fundamental gap is not generally equal to the Kohn-Sham gap of density functional theory (DFT), even in principle. The two gaps differ precisely by the derivative discontinuity, namely, an abrupt change in slope of the exchange-correlation energy as a function of electron number, expected across an integer-electron point. Popular approximate functionals are thought to be devoid of a derivative discontinuity, strongly compromising their performance for prediction of spectroscopic properties. Here we show that, in fact, all exchange-correlation functionals possess a derivative discontinuity, which arises naturallymore » from the application of ensemble considerations within DFT, without any empiricism. This derivative discontinuity can be expressed in closed form using only quantities obtained in the course of a standard DFT calculation of the neutral system. For small, finite systems, addition of this derivative discontinuity indeed results in a greatly improved prediction for the fundamental gap, even when based on the most simple approximate exchange-correlation density functional – the local density approximation (LDA). For solids, the same scheme is exact in principle, but when applied to LDA it results in a vanishing derivative discontinuity correction. This failure is shown to be directly related to the failure of LDA in predicting fundamental gaps from total energy differences in extended systems.« less

Density-functional theory based on the electron distribution on the energy coordinate

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki

2018-03-01

We developed an electronic density functional theory utilizing a novel electron distribution n(ɛ) as a basic variable to compute ground state energy of a system. n(ɛ) is obtained by projecting the electron density n({\\boldsymbol{r}}) defined on the space coordinate {\\boldsymbol{r}} onto the energy coordinate ɛ specified with the external potential {\\upsilon }ext}({\\boldsymbol{r}}) of interest. It was demonstrated that the Kohn-Sham equation can also be formulated with the exchange-correlation functional E xc[n(ɛ)] that employs the density n(ɛ) as an argument. It turned out an exchange functional proposed in our preliminary development suffices to describe properly the potential energies of several types of chemical bonds with comparable accuracies to the corresponding functional based on local density approximation. As a remarkable feature of the distribution n(ɛ) it inherently involves the spatially non-local information of the exchange hole at the bond dissociation limit in contrast to conventional approximate functionals. By taking advantage of this property we also developed a prototype of the static correlation functional E sc including no empirical parameters, which showed marked improvements in describing the dissociations of covalent bonds in {{{H}}}2,{{{C}}}2{{{H}}}4 and {CH}}4 molecules.

Quantum dust magnetosonic waves with spin and exchange correlation effects

NASA Astrophysics Data System (ADS)

Maroof, R.; Mushtaq, A.; Qamar, A.

2016-01-01

Dust magnetosonic waves are studied in degenerate dusty plasmas with spin and exchange correlation effects. Using the fluid equations of magnetoplasma with quantum corrections due to the Bohm potential, temperature degeneracy, spin magnetization energy, and exchange correlation, a generalized dispersion relation is derived. Spin effects are incorporated via spin force and macroscopic spin magnetization current. The exchange-correlation potentials are used, based on the adiabatic local-density approximation, and can be described as a function of the electron density. For three different values of angle, the dispersion relation is reduced to three different modes under the low frequency magnetohydrodynamic assumptions. It is found that the effects of quantum corrections in the presence of dust concentration significantly modify the dispersive properties of these modes. The results are useful for understanding numerous collective phenomena in quantum plasmas, such as those in compact astrophysical objects (e.g., the cores of white dwarf stars and giant planets) and in plasma-assisted nanotechnology (e.g., quantum diodes, quantum free-electron lasers, etc.).

Assessing exchange-correlation functionals for elasticity and thermodynamics of α -ZrW2O8 : A density functional perturbation theory study

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; Gordon, Margaret E.; Bryan, Charles R.

2018-04-01

Elastic and thermodynamic properties of negative thermal expansion (NTE) α -ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ∼ 2 % with PBEsol and ∼ 6 % with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be CP0 = 192.2 and 193.8 J mol-1K-1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

Ab initio study on half-metallic, electronic and thermodynamic attributes of LaFeO3

NASA Astrophysics Data System (ADS)

Tariq, Saad; Saad, Saher; Jamil, M. Imran; Sohail Gilani, S. M.; Mahmood Ramay, Shahid; Mahmood, Asif

2018-03-01

By using the density functional theory (DFT) the systematic study of the structural, electronic and thermodynamic properties of lanthanum ferrite (LaFeO3) has been conducted. The elastic stability criterion and structural tolerance factor reveal that LaFeO3 exists in the cubic phase and is found to be stable under the ambient conditions. In electronic properties, the optical spectrum of the compound has been found to fall in the range of 488 to 688nm which has been calculated from the electronic band gap values by using the PBE-GGA and mBJ-GGA techniques. The light between 488 to 688nm would cause the valence electrons to jump in the conduction band showing the photoconductivity. The pronounced half-metallic character has been discussed by using the projected electronic density of states. The ferromagnetic response has been observed which may be attributed to the Fe-O bonding situation. The compound exhibits ductile, indirect band gap and half-metallic traits in the bulk phase. We expect the compound to be felicitous for the novel spintronic applications.

Electronic structure of lanthanide scandates

NASA Astrophysics Data System (ADS)

Mizzi, Christopher A.; Koirala, Pratik; Marks, Laurence D.

2018-02-01

X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and density functional theory calculations were used to study the electronic structure of three lanthanide scandates: GdSc O3,TbSc O3 , and DySc O3 . X-ray photoelectron spectra simulated from first-principles calculations using a combination of on-site hybrid and GGA +U methods were found to be in good agreement with experimental x-ray photoelectron spectra. The hybrid method was used to model the ground state electronic structure and the GGA +U method accounted for the shift of valence state energies due to photoelectron emission via a Slater-Janak transition state approach. From these results, the lanthanide scandate valence bands were determined to be composed of Ln 4 f ,O 2 p , and Sc 3 d states, in agreement with previous work. However, contrary to previous work the minority Ln 4 f states were found to be located closer to, and in some cases at, the valence band maximum. This suggests that minority Ln 4 f electrons may play a larger role in lanthanide scandate properties than previously thought.

Mitochondria-targeting nanomedicine: An effective and potent strategy against aminoglycosides-induced ototoxicity.

PubMed

Zhou, Shuang; Sun, Yanhui; Kuang, Xiao; Hou, Shanshan; Yang, YinXian; Wang, Zhenjie; Liu, Hongzhuo

2018-04-21

We report a proof-of-concept for the development of mitochondria-targeting nanoparticles (NPs) loaded with geranylgeranylacetone (GGA) to protect against a wide range of gentamicin-induced ototoxicity symptoms in a zebrafish model. The polymeric NPs were functionalized with a mitochondrial-homing peptide (d‑Arg‑Dmt‑Orn‑Phe‑NH 2 ) and exhibited greater mitochondrial uptake and lower gentamicin uptake in hair cells via mechanotransduction (MET) channels and tuned machinery in the hair bundle than the ordinary NPs did. Blockade of MET channels rapidly reversed this effect, indicating the reversible responses of hair cells to the targeting NPs were mediated by MET channels. Pretreatment of hair cells with mitochondria-targeting GGA-loaded NPs exhibited a superior acute or chronic protective efficacy against subsequent exposure to gentamicin compared with unmodified formulations. Mitochondrial delivery regulating the death pathway of hair cells appeared to cause the therapeutic failure of untargeted NPs. Thus, peptide-directed mitochondria-targeting NPs may represent a novel therapeutic strategy for mitochondrial dysfunction-linked diseases. Copyright © 2018 Elsevier B.V. All rights reserved.

Density functional study on redox energetics of LaMO{sub 3−δ} (M=Sc–Cu) perovskite-type oxides

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

Pishahang, Mehdi, E-mail: Mehdi.Pishahang@sintef.no; Erik Mohn, Chris; Stølen, Svein

2016-01-15

This study evaluates the redox energetics of LaMO{sub 3−δ} (M=Sc–Cu) perovskite-type oxides via generalized gradient approximation (GGA) to DFT. Two different approaches to redox energetics of oxygen deficient perovskites of strongly non-stoichiometric (δ=0.5) and dilute defect limits (δ→0) are studied. In the first approach the enthalpies of oxidation are calculated using the stoichiometric end-compounds of LaMO{sub 3} and LaMO{sub 2.5}. The most common structures for the reduced lanthanides and strontides similar to the ones experimentally reported for SrMnO{sub 2.5}, SrFeO{sub 2.5}, and LaNiO{sub 2.5} are considered. The second approach to the oxidation enthalpies termed (δ→0) follow the trend observed experimentally.more » This approach represents the experimental conditions of the measured oxygen enthalpies, and is hampered less by the artificial features due to spurious self-interaction errors in GGA.« less

First-principles calculation of electronic and optical properties of graphene like ZnO (G-ZnO)

NASA Astrophysics Data System (ADS)

Farooq, Rabia; Mahmood, Tariq; Anwar, Abdul Waheed; Abbasi, Ghadah Niaz

2016-02-01

Semiconductor metal oxides are favorable for their exotic properties like wide band gap, transparency, enhanced charge mobility, and strong luminescence at room temperature. These properties have put metal oxides under limelight, especially ZnO has earned a renowned position in emanate industry for transparent electrodes, electronics, super-capacitors, photo-voltaic cells, gas-sensors, and many more. ZnO is not only environmental friendly but also a highly stable and cheap photo catalytic source naturally available in high abundance. First principles calculation is performed to study optoelectronic properties of ZnO. Geometry optimization of graphene like ZnO (G-ZnO) is preformed using generalized gradient approximation along with hybrid functional (GGA-PBE and GGA-PBE + U) to calculate various structural and electronic parameters of G-ZnO. Employing Hubbard (U) parameter improved band gap and c/a ratio calculation as 1.245 eV and 1.613 respectively; also dielectric constant is calculated as 4.58 (U = 15 eV) which is in accordance with the available experimental data.

Theoretical investigation of the magnetoelectric properties of Bi2NiTiO6

NASA Astrophysics Data System (ADS)

Patra, Lokanath; Ravindran, P.

2018-04-01

We report the first principle investigations on the structural, electronic, magnetic and ferroelectric properties of a Pb free double perovskite multiferroic Bi2NiTiO6 using density functional theory within the general gradient approximation (GGA) and GGA+U method. Our results show that Bi2NiTiO6 will be an insulator with G-type magnetic ordering in its ground state with Ni2+ in a high spin state and a spin moment of 1.741μB. The paraelectric phase stabilizes in nonmagnetic state with Ni2+ in low spin configuration showing that spin state transition plays an important role in strong magnetoelectric coupling in Bi2NiTiO6. The bonding characteristics of the constituents are analyzed with the help of partial density of states and Born effective charges. The presence of Ti ions at Ni sites suppresses the disproportionation observed in case of BiNiO3 and results in a noncentrosymmetric crystal structure. The coexistence of Bi 6s lone pair and Ti4+ d0 ions which brings covalency produces a polarization of 32 µCcm-2.

Bonding in the first-row diatomic molecules within the local spin-density approximation

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

Painter, G.S.; Averill, F.W.

1982-08-15

The Hohenberg-Kohn-Sham density-functional equations in the local spin-density approximation (LSDA) have been solved with essentially no loss of accuracy for dimers of the first row of the Periodic Table with the use of a fully-self-consistent spin-polarized Gaussian-orbital approach. Spectroscopic constants (binding energies, equilibrium separations, and ground-state vibrational frequencies) have been derived from the calculated potential-energy curves. Intercomparison of results obtained using the exchange-correlation functionals of Slater (scaled exchange or X..cap alpha..), Gunnarsson and Lundqvist (GL), and Vosko, Wilk, and Nusair (VWN) permits assessment of the relative merits of each and serves to identify general shortcomings in the LSDA. Basic trendsmore » are similar for each functional, but the treatment of the spin dependence of the exchange-correlation energy in the GL and VWN functionals yields a variation of the binding energy across the series which is more systematic than that in the X..cap alpha.. approximation. Agreement between the present results and those of Dunlap, Connolly, and Sabin in the X..cap alpha.., approximation confirms the accuracy of the variational charge-density-fit procedure used in the latter work. The refinements in correlation treatment within the VWN functional are reflected in improvements in binding energies which are only slight for most dimers in the series. This behavior is attributed to the error remaining in the exchange channel within the LSDA and demonstrates the necessity for self-interaction corrections for more accurate binding-energy determinations. Within the current LSDA, absolute accuracies of the VWN functional for the first-row dimers are within 2.3 eV for binding energies, 0.07 a.u. for bond lengths, and approx.200 cm/sup -1/ for vibrational frequencies.« less

Simple iterative construction of the optimized effective potential for orbital functionals, including exact exchange.

PubMed

Kümmel, Stephan; Perdew, John P

2003-01-31

For exchange-correlation functionals that depend explicitly on the Kohn-Sham orbitals, the potential V(xcsigma)(r) must be obtained as the solution of the optimized effective potential (OEP) integral equation. This is very demanding and has limited the use of orbital functionals. We demonstrate that instead the OEP can be obtained iteratively by solving the partial differential equations for the orbital shifts that exactify the Krieger-Li-Iafrate approximation. Unoccupied orbitals do not need to be calculated. Accuracy and efficiency of the method are shown for atoms and clusters using the exact-exchange energy. Counterintuitive asymptotic limits of the exact OEP are presented.

Thermal stability of mullite RMn₂O₅ (R  =  Bi, Y, Pr, Sm or Gd): combined density functional theory and experimental study.

PubMed

Li, Chenzhe; Thampy, Sampreetha; Zheng, Yongping; Kweun, Joshua M; Ren, Yixin; Chan, Julia Y; Kim, Hanchul; Cho, Maenghyo; Kim, Yoon Young; Hsu, Julia W P; Cho, Kyeongjae

2016-03-31

Understanding and effectively predicting the thermal stability of ternary transition metal oxides with heavy elements using first principle simulations are vital for understanding performance of advanced materials. In this work, we have investigated the thermal stability of mullite RMn2O5 (R  =  Bi, Pr, Sm, or Gd) structures by constructing temperature phase diagrams using an efficient mixed generalized gradient approximation (GGA) and the GGA  +  U method. Simulation predicted stability regions without corrections on heavy elements show a 4-200 K underestimation compared to our experimental results. We have found the number of d/f electrons in the heavy elements shows a linear relationship with the prediction deviation. Further correction on the strongly correlated electrons in heavy elements could significantly reduce the prediction deviations. Our corrected simulation results demonstrate that further correction of R-site elements in RMn2O5 could effectively reduce the underestimation of the density functional theory-predicted decomposition temperature to within 30 K. Therefore, it could produce an accurate thermal stability prediction for complex ternary transition metal oxide compounds with heavy elements.

Effect of on-site Coulomb interaction on electronic and transport properties of 100% spin polarized CoMnVAs

NASA Astrophysics Data System (ADS)

Bhat, Tahir Mohiuddin; Gupta, Dinesh C.

2017-08-01

The structural, electronic, magnetic and transport properties of a new quaternary Heusler alloy CoMnVAs have been investigated by employing generalized gradient approximation (GGA), modified Becke-Johnson (mBJ) and GGA with Hubbard U correction (GGA + U). The alloy is energetically more stable in ferromagnetic Y1 type structure. Elastic parameters reveal high anisotropy and ductile nature of the material. CoMnVAs shows half-metallic ferromagnet character with 100% spin polarization at Fermi level with band gap of 0.55 eV in the minority spin state. The alloy also possesses high electrical conductivity and Seebeck coefficients with 15 μVK-1 at room temperature, achieving a figure of merit of 0.65 at high temperatures. The high degree of ductility, 100% spin polarization and large Seebeck coefficient, makes it an attractive candidate to be used in spin voltage generators and thermoelectric materials.

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene.

PubMed Central

Koch, K S; Gleiberman, A S; Aoki, T; Leffert, H L; Feren, A; Jones, A L; Fodor, E J

1995-01-01

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the STMS are expressed variably in the 3' untranslated regions (3'UTRs) of two 'Groups' of PIGR-encoded hepatic mRNAs (pIg-R) during liver regeneration. STMS elements include neighboring constant regions (a 60-bp d[GA]-rich tract with a chi-like octamer, followed by 15 tandem d[GGA] repeats) that merge directly with 36 or 39 tandem d[GAA] repeats (Fisher or Wistar strains, respectively) interrupted by d[AA] between their 5th-6th repeat units. The Wistar STMS is flanked upstream by two regions of nearly contiguous d[CA] or d[CT] repeats in the 3' end of intron 8; and downstream, by a 283 bp 'unit' containing several inversions at its 5' end, and two polyadenylation signals at its 3' end. The 283 nt unit is expressed in Group 1 pIg-R mRNAs; but it is absent in the Group 2 family so that their GAA repeats merge with their poly A tails. In contrast to genomic sequence, GGA triplet repeats are amplified (n > or = 24-26), whereas GAA triplet repeats are truncated variably (n < or = 9-37) and expressed uninterruptedly in both mRNA Groups. These results suggest that 3' end processing of the rat PIGR gene may involve misalignment, slippage and premature termination of RNA polymerase II. The function of this unusual processing and possible roles of chi-like octamers in quiescent or extrahepatic tissues are discussed. Images PMID:7739889

Electronic structure, magnetism, and optical properties of Fe2SiO4 fayalite at ambient and high pressures: A GGA+U study

NASA Astrophysics Data System (ADS)

Jiang, Xuefan; Guo, G. Y.

2004-04-01

The electronic structure, magnetism, and optical properties of Fe2SiO4 fayalite, the iron-rich end member of the olivine-type silicate, one of the most abundant minerals in Earth’s upper mantle, have been studied by density-functional theory within the generalized gradient approximation (GGA) with the on-site Coulomb energy U=4.5 eV taken into account (GGA+U). The stable insulating antiferromagnetic solution with an energy gap ˜1.49 eV and a spin magnetic moment of 3.65μB and an orbital magnetic moment of 0.044μB per iron atom is obtained. It is found that the gap opening in this fayalite results mainly from the strong on-site Coulomb interaction on the iron atoms. In this band structure, the top of valence bands consists mainly of the 3d orbitals of Fe2 atoms, and the bottom of the conduction bands is mainly composed of the 3d orbitals of Fe1 atoms. Therefore, since the electronic transition from the Fe2 3d to Fe1 3d states is weak, significant electronic transitions would appear only about 1 eV above the absorption edge when Fe-O orbitals are involved in the final states. In addition, our band-structure calculations can explain the observed phenomena including redshift near the absorption edge and the decrease of the electrical resistivity of Fe2SiO4 upon compression. The calculated Fe p partial density of states agree well with Fe K-edge x-ray absorption spectrum. The calculated lattice constants and atomic coordinates for Fe2SiO4 fayalite in orthorhombic structure are in good agreement with experiments.

A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

PubMed

Hirano, Toshiyuki; Sato, Fumitoshi

2014-07-28

We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

Exchange interaction between the triplet exciton and the localized spin in copper-phthalocyanine.

PubMed

Wu, Wei

2014-06-14

Triplet excitonic state in the organic molecule may arise from a singlet excitation and the following inter-system crossing. Especially for a spin-bearing molecule, an exchange interaction between the triplet exciton and the original spin on the molecule can be expected. In this paper, such exchange interaction in copper-phthalocyanine (CuPc, spin-½) was investigated from first-principles by using density-functional theory within a variety of approximations to the exchange correlation, ranging from local-density approximation to long-range corrected hybrid-exchange functional. The magnitude of the computed exchange interaction is in the order of meV with the minimum value (1.5 meV, ferromagnetic) given by the long-range corrected hybrid-exchange functional CAM-B3LYP. This exchange interaction can therefore give rise to a spin coherence with an oscillation period in the order of picoseconds, which is much shorter than the triplet lifetime in CuPc (typically tens of nanoseconds). This implies that it might be possible to manipulate the localized spin on Cu experimentally using optical excitation and inter-system crossing well before the triplet state disappears.

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.

Screened hybrid density functionals for solid-state chemistry and physics.

PubMed

Janesko, Benjamin G; Henderson, Thomas M; Scuseria, Gustavo E

2009-01-21

Density functional theory incorporating hybrid exchange-correlation functionals has been extraordinarily successful in providing accurate, computationally tractable treatments of molecular properties. However, conventional hybrid functionals can be problematic for solids. Their nonlocal, Hartree-Fock-like exchange term decays slowly and incorporates unphysical features in metals and narrow-bandgap semiconductors. This article provides an overview of our group's work on designing hybrid functionals for solids. We focus on the Heyd-Scuseria-Ernzerhof screened hybrid functional [J. Chem. Phys. 2003, 118, 8207], its applications to the chemistry and physics of solids and surfaces, and our efforts to build upon its successes.

Exact Time-Dependent Exchange-Correlation Potential in Electron Scattering Processes

NASA Astrophysics Data System (ADS)

Suzuki, Yasumitsu; Lacombe, Lionel; Watanabe, Kazuyuki; Maitra, Neepa T.

2017-12-01

We identify peak and valley structures in the exact exchange-correlation potential of time-dependent density functional theory that are crucial for time-resolved electron scattering in a model one-dimensional system. These structures are completely missed by adiabatic approximations that, consequently, significantly underestimate the scattering probability. A recently proposed nonadiabatic approximation is shown to correctly capture the approach of the electron to the target when the initial Kohn-Sham state is chosen judiciously, and it is more accurate than standard adiabatic functionals but ultimately fails to accurately capture reflection. These results may explain the underestimation of scattering probabilities in some recent studies on molecules and surfaces.

Importance of the Kinetic Energy Density for Band Gap Calculations in Solids with Density Functional Theory.

PubMed

Tran, Fabien; Blaha, Peter

2017-05-04

Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke-Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke-Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Combined therapy with gas gangrene antitoxin and recombinant human soluble thrombomodulin for Clostridium perfringens sepsis in a rat model.

PubMed

Hifumi, Toru; Nakano, Daisuke; Chiba, Joe; Takahashi, Motohide; Yamamoto, Akihiko; Fujisawa, Yoshihide; Kawakita, Kenya; Kuroda, Yasuhiro; Nishiyama, Akira

2018-01-01

Cases of Clostridium perfringens septicemia, such as liver abscess, often develop a rapidly progressive intravascular hemolysis and coagulation; the mortality rate with current standard care including antibiotics and surgery is high. Herein, we firstly investigated the effects of gas gangrene antitoxin (GGA) (antitoxin against C. perfringens) and recombinant human soluble thrombomodulin (rTM) on the hemolysis, coagulation status, inflammatory process, and mortality in α-toxin-treated rats. Male 11-week-old Sprague Dawley rats were randomly divided into five groups: control group, α-toxin group, GGA group, rTM group, and combined GGA and rTM (combination group). After α-toxin injection, mortality and platelet counts, and hemolysis were observed for 6 h. The fibrin/fibrinogen degradation products (FDP), and plasma high-mobility group box 1 (HMGB1) were also measured at 6 h. The combination group demonstrated 100% survival compared with 50% survival in the α-toxin group and demonstrated significantly improved hemolysis, platelet counts, and lactate levels compared with those in the α-toxin group (p < .01). The FDP and HMGB1 levels in the combination therapy group were significantly lower than those in the α-toxin group (p < .05). Combination therapy with GGA and rTM administration is applicable as adjunct therapy for fatal C. perfringens sepsis. Copyright © 2017 Elsevier Ltd. All rights reserved.

DFT-GGA errors in NO chemisorption energies on (111) transition metal surfaces

NASA Astrophysics Data System (ADS)

Huang, Xu; Mason, Sara E.

2014-03-01

We investigate whether well-known DFT-GGA errors in predicting the chemisorption energy (Echem) of CO on transition metal surfaces manifest in analogous NO chemisorption systems. While widely investigated in the case of CO/metal, analogous DFT-GGA errors have long been claimed to be absent in NO/metal chemisorption. Here, we provide theoretical evidence of systematic enhanced back-donation in NO/metal chemisorption at the DFT-GGA level. We use electronic structure analysis to show that the partially filled molecular NO 2π* orbital rehybridizes with the transition metal d-band to form new bonding and anti-bonding states. We relate the back-donation charge transfer associated with chemisorption to the promotion of an electron from the 5σ orbital to the 2π* orbital in the gas-phase NO G2Σ- ← X2Π excitation. We establish linear relationships between Echem and ΔEG ← X and formulate an Echem correction scheme in the style of Mason et al. [Physical Review B 69, 161401(R)]. We apply the NO Echem correction method to the (111) surfaces of Pt, Pd, Rh, and Ir, with NO chemisorption modeled at a coverage of 0.25 ML. We note that the slope of Echemvs. ΔEG ← X and the dipole moment depend strongly on adsorption site for each metal, and we construct an approximate correction scheme which we test using NO/Pt(100) chemisorption.

Spin-polarized Molecular Dynamics simulations of liquid iron silicate at high pressures.

NASA Astrophysics Data System (ADS)

Munoz Ramo, David; Stixrude, Lars

2010-05-01

Liquid iron silicate (Fe2SiO4) is an important component of natural silicate liquids appearing in Earth's interior. The effect of iron in the properties of these melts is a crucial issue, as it displays a high-spin to low-spin transition at high pressures which is accompanied by volume reduction and changes in the optical absorption spectrum. This phenomenon has a major influence on properties like the buoyancy or the thermal conductivity of the melt, and ultimately on the chemical and thermal evolution of our planet. Computer simulations using ab initio methods have proven to be a powerful approach to the study of liquid silicate systems[1,2], although not yet including Fe. In this paper, we report ab initio molecular dynamics studies of liquid iron silicate at high pressure (up to 400 GPa) and high temperatures (from 3000K to 6000K) that allow us to predict different properties of the system. We use the spin-polarized formalism and the GGA+U density functional for a better treatment of the iron magnetic moments in the system. Previous studies in the solid phase have shown that GGA predicts fayalite as a metal, while the introduction of U leads to a correct description of the band gap and the magnetic ordering of the system. We extend this analysis to the liquid phase. By means of these simulations we predict the liquid structure and thermodynamic properties of the liquid. We compute the theoretical Hugoniot for the system and find good agreement with values obtained from shock experiments [3]. Our calculations show large differences in the magnitude and orientation of the magnetic moments depending on the choice of functional; the GGA+U functional consistently provides larger values of the individual moments (about 1 unit larger) and of the total magnetization of the system. The high-spin to low-spin transition is predicted to take place at pressures from around 260GPa at 3000K to around 280GPa at 6000K in this iron-rich system. [1] N. P. de Koker, L. Stixrude, B. B. Karki, Geochim Cosmochim Acta 2008, 72, 1427. [2] B. B. Karki, D. Bhattarai, L. Stixrude, Phys. Rev. B 2007, 76, 104205. [3] G. Q. Chen, T. J. Ahrens, E. M. Stolper, Phys. Earth Planet. Inter. 2002, 134, 35.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

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

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Theoretical Study of Sodium Effect on the Gasification of Carbonaceous Materials with Carbon Dioxide.

PubMed

Calderón, Lucas A; Garza, Jorge; Espinal, Juan F

2015-12-24

The effect of sodium on the thermodynamics and kinetics of carbon gasification with carbon dioxide was studied by using quantum chemistry methods. Specifically, in the density functional context, two exchange-correlation functionals were used: B3LYP and M06. Some results obtained by these exchange-correlation functionals were contrasted with those obtained by the CCSD(T) method. It was found that density functional theory gives similar conclusions with respect to the coupled-cluster method. As one important conclusion we can mention that the thermodynamics of carbon monoxide desorption is not favored by the sodium presence. However, the presence of this metal induces: (a) an easier formation of one semiquinone group, (b) the dissociation of carbon dioxide, and (c) an increment on the CO desorption rate for one of the proposed pathways.

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Greathouse, Jeffery A.; ...

2018-03-15

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be Cmore » $$O\\atop{P}$$=192.2 and 193.8 J mol -1K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.« less

Optical properties of alkali halide crystals from all-electron hybrid TD-DFT calculations

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

Webster, R., E-mail: ross.webster07@imperial.ac.uk; Harrison, N. M.; Bernasconi, L.

2015-06-07

We present a study of the electronic and optical properties of a series of alkali halide crystals AX, with A = Li, Na, K, Rb and X = F, Cl, Br based on a recent implementation of hybrid-exchange time-dependent density functional theory (TD-DFT) (TD-B3LYP) in the all-electron Gaussian basis set code CRYSTAL. We examine, in particular, the impact of basis set size and quality on the prediction of the optical gap and exciton binding energy. The formation of bound excitons by photoexcitation is observed in all the studied systems and this is shown to be correlated to specific features ofmore » the Hartree-Fock exchange component of the TD-DFT response kernel. All computed optical gaps and exciton binding energies are however markedly below estimated experimental and, where available, 2-particle Green’s function (GW-Bethe-Salpeter equation, GW-BSE) values. We attribute this reduced exciton binding to the incorrect asymptotics of the B3LYP exchange correlation ground state functional and of the TD-B3LYP response kernel, which lead to a large underestimation of the Coulomb interaction between the excited electron and hole wavefunctions. Considering LiF as an example, we correlate the asymptotic behaviour of the TD-B3LYP kernel to the fraction of Fock exchange admixed in the ground state functional c{sub HF} and show that there exists one value of c{sub HF} (∼0.32) that reproduces at least semi-quantitatively the optical gap of this material.« less

In silico screening of the chicken genome for overlaps between genomic regions: microRNA genes, coding and non-coding transcriptional units, QTL, and genetic variations.

PubMed

Zorc, Minja; Kunej, Tanja

2016-05-01

MicroRNAs (miRNAs) are a class of non-coding RNAs involved in posttranscriptional regulation of target genes. Regulation requires complementarity between target mRNA and the mature miRNA seed region, responsible for their recognition and binding. It has been estimated that each miRNA targets approximately 200 genes, and genetic variability of miRNA genes has been reported to affect phenotypic variability and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes could therefore represent biomarkers for phenotypic traits in livestock animals. In our previous study, we collected polymorphisms within miRNA genes in chicken. In the present study, we identified miRNA-related genomic overlaps to prioritize genomic regions of interest for further functional studies and biomarker discovery. Overlapping genomic regions in chicken were analyzed using the following bioinformatics tools and databases: miRNA SNiPer, Ensembl, miRBase, NCBI Blast, and QTLdb. Out of 740 known pre-miRNA genes, 263 (35.5 %) contain polymorphisms; among them, 35 contain more than three polymorphisms The most polymorphic miRNA genes in chicken are gga-miR-6662, containing 23 single nucleotide polymorphisms (SNPs) within the pre-miRNA region, including five consecutive SNPs, and gga-miR-6688, containing ten polymorphisms including three consecutive polymorphisms. Several miRNA-related genomic hotspots have been revealed in chicken genome; polymorphic miRNA genes are located within protein-coding and/or non-coding transcription units and quantitative trait loci (QTL) associated with production traits. The present study includes the first description of an exonic miRNA in a chicken genome, an overlap between the miRNA gene and the exon of the protein-coding gene (gga-miR-6578/HADHB), and the first report of a missense polymorphism located within a mature miRNA seed region. Identified miRNA-related genomic hotspots in chicken can serve researchers as a starting point for further functional studies and association studies with poultry production and health traits and the basis for systematic screening of exonic miRNAs and missense/miRNA seed polymorphisms in other genomes.

Heat transfer and flow friction correlations for perforated plate matrix heat exchangers

NASA Astrophysics Data System (ADS)

Ratna Raju, L.; Kumar, S. Sunil; Chowdhury, K.; Nandi, T. K.

2017-02-01

Perforated plate matrix heat exchangers (MHE) are constructed of high conductivity perforated plates stacked alternately with low conductivity spacers. They are being increasingly used in many cryogenic applications including Claude cycle or Reversed Brayton cycle cryo-refrigerators and liquefiers. Design of high NTU (number of (heat) transfer unit) cryogenic MHEs requires accurate heat transfer coefficient and flow friction factor. Thermo-hydraulic behaviour of perforated plates strongly depends on the geometrical parameters. Existing correlations, however, are mostly expressed as functions of Reynolds number only. This causes, for a given configuration, significant variations in coefficients from one correlation to the other. In this paper we present heat transfer and flow friction correlations as functions of all geometrical and other controlling variables. A FluentTM based numerical model has been developed for heat transfer and pressure drop studies over a stack of alternately arranged perforated plates and spacers. The model is validated with the data from literature. Generalized correlations are obtained through regression analysis over a large number of computed data.

Correlational and thermodynamic properties of finite-temperature electron liquids in the hypernetted-chain approximation.

PubMed

Tanaka, Shigenori

2016-12-07

Correlational and thermodynamic properties of homogeneous electron liquids at finite temperatures are theoretically analyzed in terms of dielectric response formalism with the hypernetted-chain (HNC) approximation and its modified version. The static structure factor and the local-field correction to describe the strong Coulomb-coupling effects beyond the random-phase approximation are self-consistently calculated through solution to integral equations in the paramagnetic (spin unpolarized) and ferromagnetic (spin polarized) states. In the ground state with the normalized temperature θ=0, the present HNC scheme well reproduces the exchange-correlation energies obtained by quantum Monte Carlo (QMC) simulations over the whole fluid phase (the coupling constant r s ≤100), i.e., within 1% and 2% deviations from putative best QMC values in the paramagnetic and ferromagnetic states, respectively. As compared with earlier studies based on the Singwi-Tosi-Land-Sjölander and modified convolution approximations, some improvements on the correlation energies and the correlation functions including the compressibility sum rule are found in the intermediate to strong coupling regimes. When applied to the electron fluids at intermediate Fermi degeneracies (θ≈1), the static structure factors calculated in the HNC scheme show good agreements with the results obtained by the path integral Monte Carlo (PIMC) simulation, while a small negative region in the radial distribution function is observed near the origin, which may be associated with a slight overestimation for the exchange-correlation hole in the HNC approximation. The interaction energies are calculated for various combinations of density and temperature parameters ranging from strong to weak degeneracy and from weak to strong coupling, and the HNC values are then parametrized as functions of r s and θ. The HNC exchange-correlation free energies obtained through the coupling-constant integration show reasonable agreements with earlier results including the PIMC-based fitting over the whole fluid region at finite degeneracies in the paramagnetic state. In contrast, a systematic difference between the HNC and PIMC results is observed in the ferromagnetic state, which suggests a necessity of further studies on the exchange-correlation free energies from both aspects of analytical theory and simulation.

Magnetocrystalline anisotropy in cobalt based magnets: a choice of correlation parameters and the relativistic effects

DOE PAGES

Nguyen, Manh Cuong; Yao, Yongxin; Wang, Cai-Zhuang; ...

2018-05-16

The dependence of the magnetocrystalline anisotropy energy (MAE) in MCo 5 (M = Y, La, Ce, Gd) and CoPt on the Coulomb correlations and strength of spin orbit (SO) interaction within the GGA + U scheme is investigated. A range of parameters suitable for the satisfactory description of key magnetic properties is determined. We show that for a large variation of SO interaction the MAE in these materials can be well described by the traditional second order perturbation theory. We also show that in these materials the MAE can be both proportional and negatively proportional to the orbital moment anisotropymore » (OMA) of Co atoms. Dependence of relativistic effects on Coulomb correlations, applicability of the second order perturbation theory for the description of MAE, and effective screening of the SO interaction in these systems are discussed using a generalized virial theorem. Finally, such determined sets of parameters of Coulomb correlations can be used in much needed large scale atomistic simulations.« less

Magnetocrystalline anisotropy in cobalt based magnets: a choice of correlation parameters and the relativistic effects

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

Nguyen, Manh Cuong; Yao, Yongxin; Wang, Cai-Zhuang

The dependence of the magnetocrystalline anisotropy energy (MAE) in MCo 5 (M = Y, La, Ce, Gd) and CoPt on the Coulomb correlations and strength of spin orbit (SO) interaction within the GGA + U scheme is investigated. A range of parameters suitable for the satisfactory description of key magnetic properties is determined. We show that for a large variation of SO interaction the MAE in these materials can be well described by the traditional second order perturbation theory. We also show that in these materials the MAE can be both proportional and negatively proportional to the orbital moment anisotropymore » (OMA) of Co atoms. Dependence of relativistic effects on Coulomb correlations, applicability of the second order perturbation theory for the description of MAE, and effective screening of the SO interaction in these systems are discussed using a generalized virial theorem. Finally, such determined sets of parameters of Coulomb correlations can be used in much needed large scale atomistic simulations.« less

libvdwxc: a library for exchange-correlation functionals in the vdW-DF family

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Kuisma, Mikael; Löfgren, Joakim; Pouillon, Yann; Erhart, Paul; Hyldgaard, Per

2017-09-01

We present libvdwxc, a general library for evaluating the energy and potential for the family of vdW-DF exchange-correlation functionals. libvdwxc is written in C and provides an efficient implementation of the vdW-DF method and can be interfaced with various general-purpose DFT codes. Currently, the Gpaw and Octopus codes implement interfaces to libvdwxc. The present implementation emphasizes scalability and parallel performance, and thereby enables ab initio calculations of nanometer-scale complexes. The numerical accuracy is benchmarked on the S22 test set whereas parallel performance is benchmarked on ligand-protected gold nanoparticles ({{Au}}144{({{SC}}11{{NH}}25)}60) up to 9696 atoms.

Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress.

PubMed

Van Goor, Angelica; Ashwell, Christopher M; Persia, Michael E; Rothschild, Max F; Schmidt, Carl J; Lamont, Susan J

2016-04-14

Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.

On the difference between the pyroxenes LiFeSi2O6 and LiFeGe2O6 in their magnetic structures and spin orientations

NASA Astrophysics Data System (ADS)

Lee, Changhoon; Hong, Jisook; Shim, Ji Hoon; Whangbo, Myung-Hwan

2014-03-01

The clinopyroxenes LiFeSi2O6 and LiFeGe2O6, crystallizing in a monoclinic space group P21/c, are isostructural and isoelectronic Their crystal structures are made up of zigzag chains of edge-sharing FeO6 octahedra containing high-spin Fe3 + ions, which run along the c direction. Despite this structural similarity, the two have quite different magnetic structures and spin orientations. In LiFeSi2O6 the Fe spins have a ferromagnetic coupling within the zigzag chains along c and such FM chains have an antiferromagnetic coupling along a. In contrast, in LiFeGe2O6, the spins have an AFM coupling within the zigzag chains along c and such FM chains have an ↑ ↑ ↓ ↓ coupling along a. In addition, the spin orientation is parallel to c in LiFeSi2O6, but is perpendicular to c in LiFeGe2O6. To explain these differences in the magnetic structure and spin orientation, we evaluated the spin exchange parameters by performing energy mapping analysis based on LDA +U and GGA +U calculations and also by evaluating the magnetocrystalline anisotropy energies in terms of GGA +U +SOC and LDA +U +SOC calculations. Our study show that the magnetic structures and spin orientations of LiFeSi2O6 and LiFeGe2O6 are better described by LDA +U and LDA +U +SOC calculations. This research was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education(2013R1A1A2060341).

Exchange interaction between the triplet exciton and the localized spin in copper-phthalocyanine

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

Wu, Wei, E-mail: wei.wu@ucl.ac.uk

2014-06-14

Triplet excitonic state in the organic molecule may arise from a singlet excitation and the following inter-system crossing. Especially for a spin-bearing molecule, an exchange interaction between the triplet exciton and the original spin on the molecule can be expected. In this paper, such exchange interaction in copper-phthalocyanine (CuPc, spin-1/2 ) was investigated from first-principles by using density-functional theory within a variety of approximations to the exchange correlation, ranging from local-density approximation to long-range corrected hybrid-exchange functional. The magnitude of the computed exchange interaction is in the order of meV with the minimum value (1.5 meV, ferromagnetic) given by themore » long-range corrected hybrid-exchange functional CAM-B3LYP. This exchange interaction can therefore give rise to a spin coherence with an oscillation period in the order of picoseconds, which is much shorter than the triplet lifetime in CuPc (typically tens of nanoseconds). This implies that it might be possible to manipulate the localized spin on Cu experimentally using optical excitation and inter-system crossing well before the triplet state disappears.« less

MicroRNAs-1614-3p gene seed region polymorphisms and association analysis with chicken production traits.

PubMed

Li, Hong; Sun, Gui-Rong; Tian, Ya-Dong; Han, Rui-Li; Li, Guo-Xi; Kang, Xiang-Tao

2013-05-01

In the present study, a total of 860 chickens from a Gushi-Anka F2 resource population were used to evaluate the genetic effect of the gga-miR-1614-3p gene. A novel, silent, single nucleotide polymorphism (SNP, +5 C>T) was detected in the gga-miR-1614-3p gene seed region through AvaII polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR products sequencing methods. Associations between the SNP and chicken growth, meat quality and carcass traits were performed by association analysis. The results showed that the SNP was significantly associated with breast muscle shear force and leg muscle water loss rate, wing weight, liver weight and heart weight (p<0.05), and highly significantly associated with the weight of the abdominal fat (p<0.01). The secondary structure of gga-miR-1614 and the free energy were altered due to the variation predicted by the M-fold program.

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

Sun, Jianwei; Yang, Zenghui; Peng, Haowei

The uniform electron gas and the hydrogen atom play fundamental roles in condensed matter physics and quantum chemistry. The former has an infinite number of electrons uniformly distributed over the neutralizing positively charged background, and the latter only one electron bound to the proton. The uniform electron gas was used to derive the local spin density approximation to the exchange-correlation functional that undergirds the development of the Kohn-Sham density functional theory. We show here that the ground-state exchange-correlation energies of the hydrogen atom and many other 1- and 2-electron systems are modeled surprisingly well by a different local spin densitymore » approximation (LSDA0). LSDA0 is constructed to satisfy exact constraints but agrees surprisingly well with the exact results for a uniform two-electron density in a finite, curved three-dimensional space. We also apply LSDA0 to excited or noded 1-electron densities, where it works less well. Furthermore, we show that the localization of the exact exchange hole for a 1- or 2-electron ground state can be measured by the ratio of the exact exchange energy to its optimal lower bound.« less