bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractSum‐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

AbstractWe 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

AbstractA 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

AbstractWe 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

AbstractWe 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

AbstractThe 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

AbstractA 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

AbstractThe 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

AbstractLesions 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

AbstractAlthough [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

AbstractAtomic 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

AbstractThe 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

AbstractA 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

AbstractWe 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

AbstractWe 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

AbstractLipomyces 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.