bluuebunny/crossref_metadata_2025 huggingface dataset:
DFT study of the Jahn–Teller impurity Rh2+ in octahedral symmetry
Authors: Barriuso M. T. , García Fernández P. , Aramburu J. A. , Moreno M.
Published: December 2002

Density functional calculations on clusters involving up to 87 atoms have been carried out for exploring the Jahn–Teller effect in NaCl: Rh2+. Due to the flexibility of density functional theory (DFT) methodology, calculations have first been performed for a ground state described by the (3z2 − r2)0.5(x2 − y2)0.5 configuration at different values of the Qθ(≈3z2 − r2) distortion. This electronic configuration allows one to extract the angular frequency, ωE, and anharmonic parameter, A3, corresponding to a hypothetical Rh2+ ion without orbital degeneracy. The calculation on an 87‐atom cluster indicates that ligands have undergone a 10% inward relaxation whereas the first Na+ ions along <100> directions experience a small outward relaxation. The latter fact is related to the additional positive charge created through the Na+ → Rh2+ substitution. Calculations at different Qθ(≈3z2 − r2) distortions for a ground state described by (3z2 − r2)1 and (x2 − y2)1 configurations have also been carried out and reveal that: (1) the energy minimum for the former electronic configuration corresponds to an elongated octahedron lying ≈200 cm−1 below the minimum associated with (x2 − y2)1 configuration displaying a compressed D4h geometry; (2) the calculated ratio EJT/ℏωE where EJT is the Jahn–Teller energy is found to be equal to 7.5, stressing that the Jahn–Teller effect in NaCl: Rh2+ is strong. These conclusions concur with available experimental findings. The current calculations reasonably account for the two crystal‐field transitions and the charge transfer band detected through magnetic circular dichroism up to 4.1 eV. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 2003
DFT‐based solution to the gap problem of antiferromagnetic transition metal oxides and parent compounds of high‐Tc superconductors
Authors: Fritsche L. , Pérez‐Jiménez A. J. , Reinert T.
Published: December 2002

Currently used approximations to the exchange‐correlation potential in density functional theory (DFT) are known to fail in describing the properties of certain compounds, of which we discuss here only two examples: CoO and stoichiometric La2CuO4. Both materials are insulating and antiferromagnetic. A DFT calculation on CoO yields antiferromagnetic order, but Co‐associated magnetic moments that are by ∼1 μB smaller than the experimental value, and one obtains the electronic structure of a metal. The latter applies also to La2CuO4, and, in contrast to the experiment, the calculation does not even yield nonzero moments associated with the Cu atoms. We exploit the fact that approximate exchange‐correlation potentials lead necessarily to spin‐dependent densities that differ from the exact ones. We therefore derive modified Kohn–Sham (KS) equations in which the effective potentials depend on the exact spin densities rather than on the standard KS densities. If the latter are modified by adding small (spin‐up, spin‐down) portions that individually integrate to zero within the lattice unit cell and do not change the total charge density, the inconsistencies with the experiment can be removed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Exchange‐correlation energies and correlation holes for some two‐ and four‐electron atoms along a nonlinear adiabatic connection in density functional theory
Authors: Pollet R. , Colonna F. , Leininger T. , Stoll H. , Werner H.‐J. , Savin A.
Published: December 2002

The adiabatic connection procedure of density functional theory has been applied to two‐ and four‐electron atomic systems by following a nonlinear path that leads from the noninteracting Kohn–Sham reference system to the physical one. We have calculated the exchange and correlation energies as the interaction strength is increased, as well as the densities of the corresponding correlation holes. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
MIKA: Multigrid‐based program package for electronic structure calculations
Authors: Torsti T. , Heiskanen M. , Puska M. J. , Nieminen R. M.
Published: December 2002

A general real‐space multigrid‐based program package MIKA (Multigrid Instead of the K‐spAce) for the self‐consistent solution of the Kohn–Sham equations appearing in the state‐of‐the‐art electronic structure calculations is described. The most important part of the method is the multigrid solver for the Schrödinger equation. Our choice is the Rayleigh quotient multigrid method (RQMG), which applies directly to the minimization of the Rayleigh quotient on the finest level. Coarse correction grids can be used because there is in principle no need to represent the states on the coarse levels. The RQMG method is generalized for the simultaneous solution of all the states of the system using a penalty functional to keep the states orthogonal. Special care has been taken to optimize the iterations toward the self‐consistency and run the code in parallel computer architectures. The scheme has been implemented in multiple geometries. We show examples from electronic structure calculations employing nonlocal pseudopotentials and/or the jellium model. The RQMG solver is also applied for the calculation of positron states in solids. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Thickness‐dependent interface magnetism of Fe/Cr/Fe trilayers
Authors: Man'kovsky S. V. , Baldomir D. , Pereiro M.
Published: December 2002

Electronic structure and magnetic properties of FeN/Cr3/FeN bcc(100) trilayers (N is the number of atomic layers) are studied on the basis of ab initio calculations performed within the framework of the density functional theory in the local spin density approximation, using the full‐potential LAPW method in slab geometry. According to our calculations, the magnetic moment of a surface Fe layer increases monotonically from 2.45 μB for N = 1 to 2.92 μB for N = 3 and practically does not change at further increase of the Fe film thickness. However, the magnetic moment in the interface Fe layer changes nonmonotonically with the Fe film thickness increase and is close to the surface value at N = 5 and 7. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Properties of simple metals beyond the local density approximation of density functional theory
Authors: Almeida L. M. , Fiolhais Carlos , Causà M.
Published: December 2002

We calculated lattice parameters, binding energies, bulk moduli, and phase stabilities of some simple metals: Li, Be, Na, Mg, and Al. Our ab initio all‐electron calculations were done within the framework of density functional theory using the Crystal‐98 program. The accuracy of different functionals for exchange and correlation energies that go beyond the local density approximation (LDA) was tested. The recent metageneralized gradient approximation proposed from Perdew et al. (Phys Rev Lett 1999, 82, 2544) gives lattice parameters that are better than the LDA values but not always better than the results of generalized gradient approximation. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Realizations of the noninteracting kinetic energy functional enhancement factor through local‐scaling transformations: Atoms
Authors: Ludeña Eduardo V. , Karasiev Valentin V. , Echevarría Lorenzo
Published: December 2002

Within the framework of the local‐scaling version of density functional theory, we deal with the problem of constructing approximate forms for the noninteracting kinetic energy functional Ts[ρ]. For this purpose, we resort to density‐dependent orbitals generated by means of local‐scaling transformations. We examine the use of different types of initial orbital sets for the generation of the density‐dependent orbitals and, in particular, analyze the realization of the enhancement factor in terms of locally scaled plane waves, orthogonal polynomials (Laguerre), and generalized Slater‐type orbitals. Application to the Na and Al atoms shows the feasibility of representing the enhancement factor in closed form, in particular when generalized Slater‐type orbitals are used. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Is the vanadium(001) surface magnetic? Pseudopotential toward all‐electron calculations
Authors: Robles R. , Izquierdo J. , Vega A. , Balbás L. C.
Published: December 2002

The spin polarization of the vanadium(001) surface is studied by means of first‐principles generalized gradient approximation (GGA) calculations within the linear combination of atomic orbitals (LCAO) code Siesta and the norm‐conserving pseudopotentials of Troullier–Martins. Whereas the conventional valence 4s23d3 pseudopotential, including nonlinear core corrections (NLCC), leads to a high surface polarization for the 7‐, 9‐, and 15‐layer (001) films of V (with and without relaxation), treating explicitly as valence electrons, the semicore 3p6 state we obtain is a considerable reduction of the magnetic moment at the surface, which became nonmagnetic for the relaxed 15‐layer film, in agreement with recent all‐electron GGA first‐principles calculations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Self‐consistent solution of Dyson's equation up to second order for closed‐ and open‐shell atomic systems
Authors: Peirs K. , Van Neck D. , Waroquier M.
Published: December 2002

Green's function techniques offer new methods based upon perturbation theory to study many‐body systems. The computational cost in these schemes is substantially higher than in density functional theory (DFT), but they offer a clear picture of the nature of correlations included in the calculations. In this way, a connection between the Green's function scheme and DFT can learn more about the underlying mechanisms of the latter. Therefore, we need the correlated density of some carefully selected systems. In this work, a numerical scheme is presented to solve the Dyson equation up to second order self‐consistently for a few closed‐shell (He, Be, Ne, Mg, and Ar) and open‐shell (B, C, N, O, and F) atoms in coordinate space. A detailed discussion is held on the reproduction of total binding energies, ionization energies, electron affinities, and spectral strength distributions. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
First principles calculations of the formation energy of Cr/Al vacancies in spinel‐type MgCr2O4 and MgAl2O4
Authors: Moriwake Hiroki , Tanaka Isao , Oba Fumiyasu , Koyama Yukinori , Adachi Hirohiko
Published: December 2002

Quantitative analysis of the formation energy of Cr vacancy in MgCr2O4 was made by first principles calculation. A 56‐atom supercell was employed and relaxation of atoms within the second‐nearest‐neighbor shell of the vacancy was taken into account. The formation energy was calculated as a function of the atomic chemical potential of Cr. Theoretical formation energy of Cr vacancy in MgCr2O4 shows negative values in the case of the oxidation limit of MgCr2O4, in good agreement with experimental results showing abundance of Cr vacancies when annealed in air. On the other hand, the formation energy of the Al vacancy in MgAl2O4 under the same condition is as large as 4.76 eV. This also corresponds well to the experimental fact that Al vacancy does not form alone in MgAl2O4 in air. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Optical excitations of Si by time‐dependent density functional theory based on exact‐exchange Kohn–Sham band structure
Authors: Kim Yong‐Hoon , Städele Martin , Görling Andreas
Published: December 2002

We calculate the imaginary part of the frequency‐dependent dielectric function of bulk silicon by applying time‐dependent density functional theory (TDDFT) based on the exact‐exchange (EXX) Kohn–Sham (KS) band structure and the adiabatic local‐density approximation (ALDA) kernel. The position of the E2 absorption peak calculated with the EXX band structure at the independent‐particle level is in excellent agreement with experiments, which demonstrate the good quality of EXX “KS quasiparticles.” The excitonic E1 peak that is missing at the independent‐particle level remains absent if two‐particle interaction effects are taken into account within the ALDA to TDDFT, demonstrating the incapability of the ALDA kernel to describe excitonic effects. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Density functional calculation of photoabsorption in metal clusters using an exchange‐correlation potential with correct asymptotic behavior
Authors: Torres M. B. , Balbás L. C.
Published: December 2002

The exchange‐correlation potential with the correct −1/r asymptotic behavior proposed by Parr and Ghosh (Phys Rev A 1995, 51, 3564) is used here to study the linear response to external fields of (1) neutral and charged sodium clusters, and (2) doped clusters of the type NanPb (n = 4, 6, 16). Our results for the photoabsorption cross section are compared with experiments, when available, and with previous density functional theory calculations using local and nonlocal functionals. The calculated static polarizabilities and plasmon frequencies are in better agreement with experiments than were previous calculations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Nonlocal WDA functional capable of describing the image potential of a metallic surface
Authors: García‐González P. , Alvarellos J. E. , Chacón E. , Tarazona P.
Published: December 2002

It is known that the exchange‐correlation (XC) potential vXC obtained using the nonlocal weighted density approximation (WDA) does not yield the image behavior −1/4z outside a metal surface. This limitation might be due to the fact that the WDA is based on an isotropic scaling of the electron pair correlation function. In this work we present a WDA scheme based on an anisotropic scaling for the pair correlation function showing that, in this case, the potential vXC has the correct imagelike decay. This new scheme does not entail a significant additional effort if compared with the standard WDA method. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Ferromagnetic instabilities in atomically thin lithium and sodium wires
Authors: Bergara A. , Neaton J. B. , Ashcroft N. W.
Published: December 2002

Using density functional theory, the ground‐state structural, electronic, and magnetic properties of monoatomic lithium and sodium chains with low average density are investigated. A metallic, zigzag ground‐state structure is predicted, but, most interestingly, stable equilibria for chains under tension are predicted to be ferromagnetic, which can be traced to exchange effects arising from occupation of the second subband as a function of the interatomic distance. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Two‐dimensional electron gas: Correlation energy versus density and spin polarization
Authors: Gori‐Giorgi Paola , Attaccalite Claudio , Moroni Saverio , Bachelet Giovanni B.
Published: December 2002

We propose a simple analytic representation of the correlation energy ϵc for the two‐dimensional electron gas, as a function of the density parameter rs and the spin polarization ζ. This new parametrization includes most of the known high‐ and low‐density limits and fits our new fixed‐node diffusion Monte Carlo simulations, performed for a wide range of electron densities (1 ≤ rs ≤ 40) and spin‐polarization states (0 ≤ ζ ≤ 1). In this way we provide a reliable local‐spin‐density energy functional for two‐dimensional systems. The corresponding correlation potential is discussed and compared with previous models. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Many‐fermion systems: Differential equations and kinetic energy functionals for different confining potentials
Authors: Howard I. A. , March N. H.
Published: December 2002

Determination of the kinetic energy functional is one of the central problems in the density functional theory of a many‐fermion system. We consider several many‐fermion systems to be characterized by simple confining potentials: the harmonic oscillator potential in one and three dimensions, the Coulomb potential, and the potential V(x) = −Uosech2(x/L). We discuss for each of these cases the differential equation that determines the fermion density in the given potential, and the corresponding kinetic energy density. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
First‐principles study of inter‐nitrogen interaction energy of Cu(100)‐ c(2 × 2)N surface
Authors: Yoshimoto Yoshihide , Tsuneyuki Shinji
Published: December 2002

Effective interaction energy among nitrogen atoms on Cu(100)‐c(2 × 2)N surface was obtained by a density functional plane‐wave pseudopotential calculation. For efficient calculation of metallic systems, a preconditioning method for the local potential in self‐consistent field iteration was proposed. Attractive interaction energy among nitrogen atoms consistent with a high‐temperature STM experiment was obtained. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Ab initio calculations of magnetic properties of Fe–Cr trilayer as a function of ferromagnetic slab thickness
Authors: Pereiro M. , Baldomir D. , Man'kovsky S. , Arias J.
Published: December 2002

Most of the articles devoted to giant magnetoresistance phenomenon take into account only the thickness variation of the spacer. Within this work, we study the magnetic behavior of the trilayer system Fe/Cr/Fe (0 0 1) after changing the thickness of the magnetic layers (Fe layers) and keeping the spacer constant (Cr layers). The calculations were done at the ab initio level by means of density functional theory, solving the Kohn–Sham equations with the full‐potential linearized augmented plane wave method. These results show an oscillatory behavior of magnetic moment per atom as a function of the iron monolayers number. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Excitation energies of molecules by time‐dependent density functional theory based on effective exact exchange Kohn–Sham potentials
Authors: Della Sala Fabio , Görling Andreas
Published: December 2002

An exchange‐only approach to calculate both valence and Rydberg excitation energies within time‐dependent density functional theory is presented. The ground‐state Kohn–Sham (KS) orbitals and eigenvalues are evaluated using an effective exact‐exchange KS potential, the localized Hartree–Fock potential. The exchange correlation kernel is taken into account within the adiabatic exchange‐only local density approximation. Results for the nitrogen molecule, ethylene, and benzene are presented. The calculated excitation energies exhibit the same accuracy as those obtained using various empirically parameterized asymptotically corrected exchange correlation KS potential although no empirical parameters are used and correlation is completely neglected. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Density functional theory from the extreme limits of correlation
Authors: Seidl Michael
Published: December 2002

Density functional perturbation theory for the correlation energy Ec[ρ] is equivalent to the Taylor expansion of the coupling‐constant integrand Wα[ρ] around its weak‐interaction limit α → 0. While this theory appears to diverge for many systems of interest (atoms, molecules, etc.), the opposite limit α → ∞ of strong interaction (which is mathematically simple) appears to provide just the missing information. Only the two leading terms of the perturbation expansion in the weak‐interaction limit are required for an accurate prediction of Ec[ρ] if they are extrapolated properly to the strong‐interaction limit. This interaction‐strength interpolation is demonstrated here for the helium atom, where the strong‐interaction limit can be treated rigorously. For general systems with more than two electrons, simple explicit approximations to that limit are available. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Exchange correlation energy as a function of the orbital occupancies: Implementation on first principles local orbital methods
Authors: Pou P. , Oszwałdowski R. , Vázquez H. , Pérez R. , Flores F. , Ortega J.
Published: December 2002

We introduce a local density formalism, where the total energy of the system is obtained as a function of the orbital occupancies {nμσ}. The exchange energy, EX is written in terms of the electrostatic interaction between a charge nμσ and its hole (1 − nμσ), while the correlation energy is analyzed by means of a Hubbard Hamiltonian using a dynamic field approximation. Once the exchange correlation energy is obtained as an explicit function of the {nμσ}, our orbital occupancy method is completely defined. Our approach is then applied to bulk diamond, Si, and zinc‐blende GaN, as well as the benzene molecule. The results obtained show that this approach offers an interesting alternative to the well‐established density functional theory methods based on the electron density ρ($\vec{r}$
). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Time‐dependent density functional theory as a foundation for a firmer understanding of sum‐over‐states density functional perturbation theory: “Loc.3” approximation
Authors: Fadda Elisa , Casida Mark E. , Salahub Dennis R.
Published: December 2002

Sum‐over‐states density functional perturbation theory (SOS‐DFPT) (Malkin, V. G.; Malkina, O. L.; Casida, M. E.; Salahub, D. R. J Am Chem Soc 1994, 116, 5898) has been successful as a method for calculating nuclear magnetic resonance (NMR) chemical shifts. The key to this success is the introduction of an ad hoc correction to the excitation energies represented by simple orbital energy differences in uncoupled density functional theory. It has been suggested (Jamorski, C.; Casida, M. E.; Salahub, D. R. J Chem Phys 1996, 104, 5134) that the good performance of this methodology could be partly explained by the resemblance of the corrected excitation energy to the orbital energy difference given by time‐dependent density functional theory (TDDFT). In fact, according to exact (wave function) time‐dependent perturbation theory, both magnetic and electric perturbations may be described using essentially the same simple SOS expression. However in adiabatic TDDFT, with no explicit relativistic or current density functional dependence, the functional is approximate and so the magnetic and electric SOS expressions are different. Because TDDFT (neglecting relativistic and current density functional dependence) is formally exact for electric perturbations but not magnetic perturbations and because the two SOS expressions should have the same form, we propose that the SOS expression for electric perturbations should also be used for magnetic perturbations. We then go on to realize our theory by deriving a “Loc.3” approximation that is explicitly designed by applying the electric field SOS expression to magnetic fields within the two‐level model and Tamm–Dancoff approximation. Test results for 13 small organic and inorganic molecules show that the Loc.3 approximation performs at least as well as the “Loc.1” and “Loc.2” approximations of SOS‐DFPT. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Dual transformation for non‐Born–Oppenheimer time‐dependent density functional theory
Authors: Ohta Y. , Maki J. , Nagao H. , Kono H. , Fujimura Y.
Published: December 2002

We developed a dual transformation method that is applicable to multicomponent density functional theory. The model of a multicomponent system is chosen to be H. The energy and the geometry of the ground state are calculated by using the finite difference method based on multicomponent density functional theory. The results obtained were compared with those obtained from the Born–Oppenheimer approximation and those obtained by exact treatment. The real‐time dynamics of H are also demonstrated. The results obtained are discussed and compared with the exact solution. The importance of the dynamic correlation effect between nuclei and an electron is clearly shown. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Magnetism and energetics of the 4d bimetallic cluster Pd6Ru6
Authors: Bromley S. T. , Catlow C. R. A.
Published: December 2002

A density functional investigation into the energetics and magnetism of a novel 4d transition metal cluster possessing an equal number of “open‐shell” Ru atoms and “closed‐shell” Pd atoms is presented. The two atom types give rise to a potentially rich spectrum of low‐energy geometric cluster structures and corresponding cluster wavefunctions. The cluster's structure is based on experimental data for a denuded highly symmetric (D3d) organometallic cluster and then optimized, allowing for energy‐lowering structural symmetry breaking, to a C2h configuration. The cluster wavefunction is then is calculated for high and low multiplicities with and without employing the natural structural symmetry of the cluster. Of particular interest is the magnetism of the cluster and the extent of 4d spin polarization of the Pd atoms by the Ru atoms in the cluster. We find that the energetically favored state of the cluster has high multiplicity with significant spin density carried by the Pd atoms. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Association simulation by a metallic Car–Parrinello dynamics
Authors: Kawamoto Syuhei , Oda Tatsuki , Hamada Ikutaro
Published: December 2002

We implemented a metallic Car–Parrinello dynamics in which the additional dynamics of the pseudo‐eigenvalue matrix and the two‐thermostat scheme are combined. Molecular dynamics with the new scheme allows us simultaneously to treat the level crossing at the Fermi level and to access the trajectory in which the system evolves just above the Born–Oppenheimer surface. We applied the scheme to associations between Si‐clusters in which there are some degenerate levels at the Fermi level. In the association of two Si dimers, the energy levels of the Kohn–Sham orbitals, which are estimated from temporal Hamiltonian matrixes, evolve reasonably with showing level crossings. We discussed scopes of this new dynamics. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Transcorrelated self‐consistent calculation for electronic systems with variational Monte Carlo method
Authors: Umezawa Naoto , Tsuneyuki Shinji
Published: December 2002

We propose a new approach to calculate the electronic states for strongly correlated systems. Our calculation is based on the transcorrelated method, in which the eigen value problem of the original Hamiltonian is transformed to that of an effective Hamiltonian. The effective Hamiltonian, the so‐called “transcorrelated Hamiltonian” is obtained through a similarity transformation of the original Hamiltonian with aid to a Jastrow factor that represents the correlation effects. A single Slater determinant is assumed as a trial function and both the Slater determinant and the two‐body Jastrow factor are optimized self‐consistently by minimizing the variance of the transcorrelated Hamiltonian. The so‐called “variational Monte Carlo” (VMC) method is adopted to overcome the time‐consuming calculation of the variance. We found that this method gives remarkably good results for heliumlike two‐electron systems (H−, He, Li+, Be2+), and we reproduced about 90% of their respective correlation energies, despite using the simplest Jastrow factor. We also display results for three‐ and four‐electron systems (Li, Be). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Possible spin configurations and magnetism in BaCoO3 perovskite
Authors: López Cacheiro J. , Iglesias M. , Pardo V. , Baldomir D. , Arias J. E.
Published: December 2002

The electronic structure, spin densities, and band structure of the perovskite BaCoO3 have been obtained using the spin‐polarized density functional theory within the generalized‐gradient approximation and the full‐potential linearized augmented plane wave method, adding local orbitals to the basis set. Different spin configurations were estimated using the fixed‐spin–moment method. The ground state that results after a partial geometry optimization to reduce the internal forces on the structure is magnetic with the Co ions in a low‐spin state. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Development of the exact exchange scheme using a basis set framework
Authors: Fernández J. J. , Tablero C. , Wahnón P.
Published: December 2002

A combination of the exact exchange (EXX) scheme for the approximation of the exchange term within the density functional theory is presented. For this task we have developed it and implemented in the atom code program. As will be discussed in this article, the use of this approach has the advantages of using a simple, but efficient, calculation numerical code and the refinement of the EXX method for the exchange part within the Khon–Sham formalism. We present the development of the EXX theory within an atomic scheme for energy calculations. Results for several atomic systems are presented. We found a remarkable improvement in the energies of all the systems studied compared with the local density approximation and generalized gradient approximation approaches. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
AddRemove: A new link model for use in QM/MM studies
Authors: Swart Marcel
Published: December 2002

The division of a system under study in a quantum mechanical (QM) and a classical system in QM/MM molecular mechanical calculations is sometimes very natural, but a problem arises in the case of bonds crossing the QM/MM boundary. A new link model that uses a capping (link) atom to satisfy the valences of the quantum chemical system is presented, with the position of the capping atom depending on the positions of the real atoms involved in the link bond. Using this method no degrees of freedom for the capping atom are introduced. Moreover, the introduction of this artificial atom is corrected for by subtracting the classical MM interactions with the real QM system it would have if it were a classical atom. That is, the capping atoms are added and removed. The new model has been tested on three amino acid residues and shows a clear improvement over other link models (as represented by the Integrated Molecular Orbital and Molecular Model (IMOMM)/ADF implementation). The average absolute deviation for the Cα–Cβ bond distance, as obtained when comparing the full QM and QM/MM results, is around 0.75 pm. The IMOMM model predicts distances for the Cα–Cbackbone and Cα–Nbackbone bonds, with an average absolute deviation of 2.3–2.8 and 5.3–5.5 pm, respectively; this is an increase by a factor of 3.1–4.0 and 7.1–7.3 compared with the Cα–Cβ bond. For the new AddRemove model, the average absolute deviations are 1.0–1.2 and 0.6–0.9 pm, respectively, for the Cα–Cbackbone and Cα–Nbackbone bonds; compared with the Cα–Cβ bond, this indicates only a slight change, with a factor of 1.3–1.6 and 0.8–1.2, respectively. The new AddRemove model therefore performs much better and is shown to be a substantial improvement over the IMOMM model. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Fimbrial control of bidirectional synaptic plasticity of medial perforant path‐dentate transmission
Authors: Nakao Kazuhito , Ikegaya Yuji , Yamada Maki K. , Nishiyama Nobuyoshi , Matsuki Norio
Published: December 2002

Lesions of the fimbria‐fornix (FF) tract cause profound impairments of cognitive ability in animals. Our previous study showed that spatial performance correlates with long‐term potentiation (LTP) of the dentate gyrus (DG), but not of the CA1 region, in rats with bilateral FF lesions, suggesting that FF lesions selectively inhibited LTP in the DG. The cortical input to the DG is anatomically and physiologically divided into two types of afferents, i.e., the medial perforant path (MPP) and the lateral perforant path (LPP), which show distinct synaptic properties. To elucidate the difference in the FF modulation of these two inputs, field responses were recorded from MPP‐ or LPP‐DG synapses in anesthetized rats. MPP‐DG synapses of rats with FF lesions displayed neither LTP in response to theta‐burst stimulation nor long‐term depression (LTD) in response to low‐frequency burst stimulation. In contrast to the MPP, LPP‐DG synapses showed normal LTP in rats with FF lesions. The low‐frequency burst stimulation could not induce LTD at LPP‐DG synapses in either intact or FF‐lesioned rats. These results suggest that the FF pathway selectively supports the mechanisms of bidirectional synaptic plasticity at MPP‐DG synapses. This study provides new insights into external control of information processing in the hippocampus. Synapse 47:163–168, 2003. © 2002 Wiley‐Liss, Inc.
Visualization of α5 subunit of GABAA/benzodiazepine receptor by [11C]Ro15‐4513 using positron emission tomography
Authors: Maeda Jun , Suhara Tetsuya , Kawabe Kouichi , Okauchi Takashi , Obayashi Shigeru , Hojo Junko , Suzuki Kazutoshi
Published: December 2002

Although [11C]Ro15‐4513 and [11C]flumazenil both bind to the central benzodiazepine (BZ) receptors, the distributions of the two ligands are not identical in vivo. Moreover, the in vivo pharmacological properties of [11C]Ro15‐4513 have not been thoroughly examined. In the present study, we examined the pharmacological profile of [11C]Ro15‐4513 binding in the monkey brain using positron emission tomography (PET). [11C]Ro15‐4513 showed relatively high accumulation in the anterior cingulate cortex, hippocampus, and insular cortex, with the lowest uptake being observed in the pons. Accumulation in the cerebral cortex was significantly diminished by the BZ antagonist flumazenil (0.1 mg/kg, i.v.), but not that in the pons. Using the pons as a reference region, the specific binding of [11C]Ro15‐4513 in most of the cerebral cortex including the limbic regions clearly revealed two different affinity sites. On the other hand, specific binding in the occipital cortex and cerebellum showed only a low affinity site. Zolpidem with affinity for α1, α2, and α3 subunits of GABAA/BZ receptor fully inhibited [11C]Ro15‐4513 binding in the occipital cortex and cerebellum, while only about 23% of the binding was blocked in the anterior cingulate cortex. Diazepam with affinity for α1, α2, α3, and α5 subunits inhibited the binding in all brain regions. Since Ro15‐4513 has relatively high affinity for the α5 subunit in vitro, these in vivo bindings of [11C]Ro15‐4513 can be interpreted as the relatively high accumulation in the fronto‐temporal limbic regions representing binding to the GABAA/BZ receptor α5 subunit. Synapse 47:200–208, 2003. © 2002 Wiley‐Liss, Inc.
Real‐time imaging of the surface topography of living yeast cells by atomic force microscopy
Authors: Ahimou François , Touhami Ahmed , Dufrêne Yves F.
Published: December 2002

Atomic force microscopy (AFM) was used to image the surface topography of living Saccharomyces cerevisiae cells at high resolution and to monitor enzyme digestion of the cell wall in real time. Apart from the presence of bud scars, the surface of native cells imaged in aqueous solution was homogeneous and smooth. Topographic images of the surface were recorded to a lateral resolution of 2 nm without significant modification of the surface morphology. Successive images of single cells were collected at fixed time intervals following addition of protease and amyloglucosidase solutions. Protease caused a progressive increase of surface roughness. Large depressions surrounded by protruding edges, ∼50 nm in height, were formed and attributed to the erosion of the mannoprotein outer layer. By contrast, no modification of the cell surface was noted upon addition of amyloglucosidase, which was consistent with the cell wall biochemical composition. These results indicate that AFM is a complementary tool to electron microscopy in that it allows the surface of living cells to be explored directly in real time. Copyright © 2002 John Wiley & Sons, Ltd.
The role of the GATA factors Gln3p, Nil1p, Dal80p and the Ure2p on ASP3 regulation in Saccharomyces cerevisiae
Authors: Oliveira Edna M. M. , Martins Adriana S. , Carvajal Elvira , Bon Elba P. S.
Published: December 2002

The role of Gln3p, Nil1p, Dal80p and Ure2p in the nitrogen regulation of ASP3, which codes for the periplasmic Saccharomyces cerevisiae asparaginase II, was investigated. Analysis of enzyme levels and mRNAASP3 in two wild‐type strains and gln3, nil1, gln3nil1, gln3ure2, nil1ure2, nil1dal80, ure2, dal80 and ure2dal80 mutant cells allowed the study of the qualitative and quantitative regulatory role of the GATA factors and Ure2p on ASP3 expression. The simultaneous presence of Gln3p and Nil1p is a required condition for full gene transcription. Enzyme activity doubled upon nitrogen starvation of either ammonium‐grown (possibly due to Nil2p/Deh1p derepression) or proline‐grown (due to Dal80p derepression) cells. The ure2 mutation increased enzyme levels five‐fold in fresh ammonium‐grown cells and ten‐fold in fresh proline‐grown cells. The combined effects of the ure2 mutation and nitrogen starvation on ammonium‐ or proline‐grown cells resulted in an overall 10–20‐fold enzyme activity increase, respectively, in comparison with the wild‐type cells. Copyright © 2002 John Wiley & Sons, Ltd.
Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae
Authors: Warringer Jonas , Blomberg Anders
Published: December 2002

A methodology for large‐scale automated phenotypic profiling utilizing quantitative changes in yeast growth has been tested and applied to the analysis of some commonly used laboratory strains. This yeast‐adjusted methodology is based on microcultivation in 350 µl liquid medium, where growth is frequently optically recorded, followed by automated extraction of relevant variables from obtained growth curves. We report that cultivation at this micro‐scale displayed overall growth features and protein expression pattern highly similar to growth in well aerated medium‐scale (10 ml) culture. However, differences were also encountered, mainly relating to the respiratory potential and the production of stress‐induced proteins. Quantitative phenotypic profiles for the laboratory yeast strains W303, FY1679 and CEN‐PK.2 were screened for in environmental arrays, including 98 different conditions composed of low, medium and high concentrations of 33 growth inhibitors. We introduce the concepts phenotypic indexrate and phenotypic indexstationary, which relate to changes in rate of growth and the stationary phase optical density increment, respectively, in a particular environment relative a reference strain. The laboratory strains presented selective phenotypic profiles in both phenotypic indexes and the two features appeared in many cases to be independent characteristics. We propose the utilization of this methodology in large‐scale screening of the complete collection of yeast deletion mutants. Copyright © 2002 John Wiley & Sons, Ltd.
Disruption of 12 ORFs located on chromosomes IV, VII and XIV of Saccharomyces cerevisiae reveals two essential genes
Authors: Volckaert Guido , Voet Marleen , Van der Schueren Jan , Robben Johan , Vanstreels Elisabeth , Vander Stappen Jacqueline
Published: December 2002

We describe the generation of null‐mutants of 12 open reading frames (ORFs), discovered during the systematic sequencing of the Saccharomyces cerevisiae genome. These ORFs are located on chromosome IV (YDL183c), on chromosome VII (YGL139w, YGL140c, YGL141w, YGR280c and YGR284c) or on chromosome XIV (YNL006w, YNR004w, YNR007c, YNR008w, YNR009w and YNR013c). Disruptants were generated using the PCR‐based short flanking homology (SFH) strategy in yeast strain FY1679. Tetrad analysis, following sporulation of the heterozygous disruptants, revealed that YGR280c and YNL006w are essential genes for vegetative yeast growth in rich medium. The lethality of the two genes was confirmed by gene complementation analysis. The protein encoded by YNL006w (LST8) is now known to be involved in transport of permeases from the Golgi to the plasma membrane. Basic phenotypic analyses were performed on haploid disruptants from both mating types of 10 non‐essential genes. One disruptant (YNR004w) revealed a slow growth rate on glucose‐minimal medium at 15° C. For each of the individual ORFs, a disruption cassette and the corresponding cognate gene were cloned into appropriate plasmids. Copyright © 2002 John Wiley & Sons, Ltd.
Analysis of the hypoxia‐induced ADH2 promoter of the respiratory yeast Pichia stipitis reveals a new mechanism for sensing of oxygen limitation in yeast
Authors: Passoth Volkmar , Cohn Marita , Schäfer Bernd , Hahn‐Hägerdal Bärbel , Klinner Ulrich
Published: December 2002

We introduced a reporter gene system into Pichia stipitis using the gene for the artificial green fluorescent protein (GFP), variant yEGFP. This system was used to analyse hypoxia‐dependent PsADH2 regulation. Reporter gene activity was only found under oxygen limitation on a fermentable carbon source. The promoter was not induced by oxygen limitation in the Crabtree‐positive yeast Saccharomyces cerevisiae. Promoter deletions revealed that a region of 15 bp contained the essential site for hypoxic induction. This motif was different from the known hypoxia response elements of S. cerevisiae but showed some similarity to the mammalian HIF‐1 binding site. Electrophoretic mobility shift assays demonstrated specific protein binding to this region under oxygen limitation. Similar to the S. cerevisiae heme sensor system, the promoter was induced by Co2+. Cyanide was not able to mimic the effect of oxygen limitation. The activation mechanism of PsADH2 also, in this respect, has similarities to the mammalian HIF‐1 system, which is inducible by Co2+ but not by cyanide. Thus, the very first promoter analysis in P. stipitis revealed a hitherto unknown mechanism of oxygen sensing in yeast. Copyright © 2002 John Wiley & Sons, Ltd.
Cloning and characterization of a second α‐amylase gene (LKA2) from Lipomyces kononenkoae IGC4052B and its expression in Saccharomyces cerevisiae
Authors: Eksteen Jeremy M. , Steyn Andries J. C. , Rensburg Pierre van , Cordero Otero Ricardo R. , Pretorius Isak S.
Published: December 2002

Lipomyces kononenkoae secretes a battery of highly effective amylases (i.e. α‐amylase, glucoamylase, isoamylase and cyclomaltodextrin glucanotransferase activities) and is therefore considered as one of the most efficient raw starch‐degrading yeasts known. Previously, we have cloned and characterized genomic and cDNA copies of the LKA1 α‐amylase gene from L. kononenkoae IGC4052B (CBS5608T) and expressed them in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Here we report on the cloning and characterization of the genomic and cDNA copies of a second α‐amylase gene (LKA2) from the same strain of L. kononenkoae. LKA2 was cloned initially as a 1663 bp cDNA harbouring an open reading frame (ORF) of 1496 nucleotides. Sequence analysis of LKA2 revealed that this ORF encodes a protein (Lka2p) of 499 amino acids, with a predicted molecular weight of 55 307 Da. The LKA2‐encoded α‐amylase showed significant homology to several bacterial cyclomaltodextrin glucanotransferases and also to the α‐amylases of Aspergillus nidulans, Debaryomyces occidentalis, Saccharomycopsis fibuligera and Sz. pombe. When LKA2 was expressed under the control of the phosphoglycerate kinase gene promoter (PGK1p) in S. cerevisiae, it was found that the genomic copy contained a 55 bp intron that impaired the production of biologically active Lka2p in the heterologous host. In contrast to the genomic copy, the expression of the cDNA construct of PGK1p–LKA2 in S. cerevisiae resulted in the production of biologically active α‐amylase. The LKA2‐encoded α‐amylase produced by S. cerevisiae exhibited a high specificity towards substrates containing α‐1,4 glucosidic linkages. The optimum pH of Lka2p was found to be 3.5 and the optimum temperature was 60 °C. Besides LKA1, LKA2 is only the second L. kononenkoae gene ever cloned and expressed in S. cerevisiae. The cloning, characterization and co‐expression of these two genes encoding these highly efficient α‐amylases form an important part of an extensive research programme aimed at the development of amylolytic strains of S. cerevisiae for the efficient bioconversion of starch into commercially important commodities. The nucleotide sequence of the LKA2 gene has been assigned GenBank Accession No. AF443872. Copyright © 2002 John Wiley & Sons, Ltd.
Studies of yeast Kluyveromyces lactis mutations conferring super‐secretion of recombinant proteins
Authors: Bartkevičiute Danguole , Sasnauskas Kestutis
Published: December 2002

We have isolated mutants responsible for a super‐secretion phenotype in Kluyveromyces lactis using the gene coding for a Bacillus amyloliquefaciens α‐amylase as a marker for secretion. These mutations defined two groups, dominant and recessive. The recessive mutant strain, which secreted the heterologous protein in five‐fold excess compared to the wild‐type strain, was used for the cloning of genes, restraining the super‐secreting phenotype. In screening for genes affecting super‐secreting phenotype, we found that multiple copies of 10 different independently isolated DNA sequences suppressed the super‐secreting phenotype. The first among the genes characterized, named KlSEL1 (‘secretion lowering’) showed homology to Saccharomyces cerevisiae ORF YML013w. The KlSEL1 gene is predicted to encode a polypeptide of 620 amino acid residues containing a putative transmembrane domain and UBX domain, characteristic for the ubiquitin‐regulatory proteins. We demonstrated that the disruption of the SEL1 orthologues in K. lactis and S. cerevisiae conferred the super‐secreting phenotype. SEL1 isolated from S. cerevisiae suppressed the super‐secretion phenotype in K. lactis klsel1 strain, likewise homologous KlSEL1. No other phenotypic features for strains lacking the SEL1 gene were noticed except for the S. cerevisiae mutant growth being notably slower than in a wt strain. No growth changes were observed in the K. lactis klsel1 mutant. The set of genes (suppressors of over‐secreting phenotype) could be attractive for further analysis of gene functions, super‐secreting mechanisms and construction of new strains. This collection could be useful for the expedient construction of reduced yeast genomes, optimized for heterologous protein secretion. The KlSEL1 gene has been assigned EMBL Accession No. AJ488285. Copyright © 2002 John Wiley & Sons, Ltd.