bluuebunny/crossref_metadata_2025_split huggingface dataset:
New targets of Arabidopsis thioredoxins revealed by proteomic analysis
Authors: Marchand Christophe , Le Maréchal Pierre , Meyer Yves , Miginiac‐Maslow Myroslawa , Issakidis‐Bourguet Emmanuelle , Decottignies Paulette 
Published: July 2004

AbstractProteomics was used to search for putative thioredoxin (TRX) targets in leaves of the model plant, Arabidopsis thaliana. About forty different proteins have been found to be reduced by TRX, after TRX itself has been specifically reduced by its NADPH‐dependent reductase. Twenty‐one of the identified proteins were already known or recently proposed to be TRX‐dependent and nineteen of the proteins were new potential targets. The identified proteins are involved in a wide variety of processes, including the Calvin cycle, metabolism, photosynthesis, folding, defense against oxidative stress and amino acid synthesis. Two proteins from the glycine cleavage complex were also identified as putative TRX targets, and a new role can be postulated in leaves for TRX in defense against herbivores and/or pathogens.
A human proteome project with a beginning and an end
Authors: Humphery‐Smith Ian 
Published: July 2004

AbstractResearch activities centered on the ensemble of and individual human proteins have taken on numerous guises, some of which fall under the banner of what could be defined as a Human Proteome Project (HPP). However, the latter has yet to take‐on the apparent global focus of its predecessor, the Human Genome Project. The reasons for this are both financial and technical. The disparate properties afforded to each protein by a 20‐letter code render a single unifying approach difficult to implement, while the current limit of analytical detection has yet to deliver an entire proteome for even the simplest of microbes. The situation is complicated further by the fact that low abundance proteins dominate within any living cell. Thus, enhancement of signal‐to‐noise ratio by affinity ligands becomes of paramount importance if whole‐organism proteomics is to be realized. The generation of such ligands (molecules exhibiting desirable affinity and selectivity for target) could provide the necessary focus and a task list with a definable beginning and end. Such a finite task list is considered essential if an HPP might one day deliver global coverage on a scale seen currently for the total DNA sequence of some 200 living organisms.
The influence of phonon drag by diffusion carrier flux on the photoacoustic effect in semiconductors
Authors: Konin A. 
Published: July 2004

AbstractA theory of the photoacoustic effect in semiconductors is developed for the region of fundamental absorption, taking into account phonon drag by the electron–hole pair diffusion flux. The temperature on the illuminated surface of a semiconductor is calculated in a general form. It is shown that the phase–frequency characteristics of the variable temperature on the illuminated surface depend essentially on the drag coefficient, sample thickness and light wavelength. The method of phonon‐defect collision frequency determination is proposed. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of temperature on the product of bulk modulus and volume thermal expansion coefficient, and its application to the thermal expansion of MgO and other minerals
Authors: Fang Ming‐xing , Ye Pin , Yan Zu‐tong 
Published: July 2004

AbstractA particularly simple two‐parameter relation for the variation of the product of bulk modulus and volume thermal expansion coefficient of solids with changing temperature has been found. The relation, although empirical, fits all minerals tested. We used this relation for the isobaric equation of state and compared with other equations of state. The excellent results show that it can be successfully applied to study the temperature behavior of minerals from room temperature to high temperature. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Diffusion in silicon and the predictive power of ab‐initio calculations
Authors: Windl Wolfgang 
Published: July 2004

AbstractIn a recent paper, Leung et al. [Phys. Rev. Lett. 83, 2351 (1999)] reported a theoretical study where they calculated the formation energy for a neutral silicon self‐interstitial to be 4.9 eV using the diffusion quantum Monte Carlo (DMC) method, 50% (30%) higher than the LDA (GGA) result of “usual” ab‐initio calculations. In this paper, we show that gap and finite‐size corrections that have been proposed in the past might be able to explain this difference, as long as the defect levels for point defects are well known. We show that B‐interstitial systems are more difficult in that sense, which seriously questions the generality of the approach. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crystallization in hafnia‐ and zirconia‐based systems
Authors: Ushakov S. V. , Navrotsky A. , Yang Y. , Stemmer S. , Kukli K. , Ritala M. , Leskelä M. A. , Fejes P. , Demkov A. , Wang C. , Nguyen B.‐Y. , Triyoso D. , Tobin P. 
Published: July 2004

AbstractCrystallization of hafnia and zirconia and their alloys with silica and lanthana was studied in bulk and thin film samples by thermal analysis, X‐ray diffraction and electron microscopy. Crystallization temperatures of hafnia and zirconia increase by more than 300 °C with increase of surface/interface area of the amorphous phase. Crystallization temperatures of zirconia and hafnia alloys with silica and lanthana increase with dopant content and exceed 900 °C for 50 mol% SiO2 and LaO1.5. Energies for tetragonal HfO2 and ZrO2 interfaces with amorphous silica were derived from their crystallization enthalpies from silicates as 0.25 ± 0.08 and 0.13 ± 0.07 J/m2, respectively. The crystallization pathways in bulk powders and films of zirconia and hafnia can be interpreted as resulting from thermodynamic stabilization by the surface energy term of tetragonal and amorphous phases over monoclinic. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High‐pressure polymorphism in phosphorus nitrides
Authors: Dong Jianjun , Kinkhabwala A. A. , McMillan P. F. 
Published: July 2004

AbstractBased on first‐principles density functional calculations, we have investigated the high‐pressure polymorphism of phosphorus nitrides (P3N5). In addition to the recently‐determined α and γ phases, our study predicts three new meta‐stable high pressure phases existing in the 5 to 35 GPa range, with structures related to the Al2SiO5 mineral polymorphs sillimanite, andalusite, and kyanite, and a new thermodynamically stable phase with a structure related to V3O5, that should form above 35.5 GPa. All these phases contain octahedrally coordinated phosphorus. By providing new insights on the different P–N bonding coordination within different pressure ranges and on the structural connection between isoelectronic oxides and nitrides, our predictive theoretical study will serve as a guideline for future experiments to explore synthesis of novel dense main group nitrides under high‐pressure conditions. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigations of conductance of photochromic switching molecules
Authors: Speyer Gil , Li Jun , Sankey Otto F. 
Published: July 2004

AbstractRecent experimental work has confirmed a dramatic conductance enhancement of more than two orders of magnitude after the optical switching between two molecular isomers of a dithienylethene‐derivative on gold. To determine which dithienylethene‐derivative may be the optimal candidate for use as an optical molecular switch, it is necessary to understand the nature of the conductance switching. To this end, a variety of theoretical tools were employed to study the critical aspects of this unique metal‐molecule‐metal junction. A plane wave based density functional method revealed marked differences between the two isomers with regard to the line‐up of the molecular states and the contact states. A local orbital based density functional method was used to generate a tractable Hamiltonian for a Landauer based transport calculation. Three different derivatives are analyzed to determine which may be an appropriate candidate in a molecular electronic device. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crystalline oxides on semiconductors: a future for the nanotransistor
Authors: Buongiorno Nardelli M. , Walker F. J. , McKee R. A. 
Published: July 2004

AbstractIn this paper we will broadly review the promises and advantages that crystalline‐oxides‐on‐semiconductors will bring to semiconductor technology. The central issue in the epitaxial oxide semiconductor system is the role of the interface. Preparation of the semiconductor surface is essential to successful, high quality, crystalline oxide formation. Furthermore, the chemical nature of the surface then controls such fundamental properties of the system as band offsets, band bending and transport. Drawing on recent accomplishments in determining key features in the structural and electronic properties of prototype Si/(Sr,Ba)O interfaces [R. A. McKee, F. J. Walker, M. Buongiorno Nardelli, W. A. Shelton, and G. M. Stocks, Science 300, 1726 (2003)], we will then illustrate how high‐performance simulations combined with experiments have been able to characterize an interface phase whose structure‐specific chemical bonding is fundamental in determining the properties of the semiconductor/crystalline oxide system. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Analytic–numerical approach to calculate electronic nonadiabatic coupling terms: Study of the C2H molecule and the H2 + H system
Authors: Vibók Á. , Halász G. , A. M. Mebel  , Hu S. , Baer M. 
Published: July 2004

AbstractThe Curl equations (Baer, M. Chem Phys Lett 1975, 35, 112) are applied to calculate the nonadiabatic coupling terms, τij, subject to ab initio boundary conditions. As an example we consider a two‐state, planar system characterized by two (polar) coordinates, θ and q, and treat the corresponding components of τ, namely, τθ(q, θ) and τq(q, θ). The main difficulty that we encounter is that the vectorial Curl equation supplies, for this case, only one differential equation although we have two unknown functions. To overcome this difficulty we employ a gauge transformation that leads to a divergence equation—the missing equation. Next, the two Curl–divergence equations are treated with the aim of forming two decoupled second‐order differential equations for the two components of a vector potential A(q, θ) [which is related to τ(q, θ) through a gauge transformation], namely, one for Aθ(q, θ) [related to τθ(q, θ)] and one for Aq(q, θ) [related to τq(q, θ)]. The main achievement of the theory is a relation, for a given q1, between the Fourier coefficients of τq(q, θ) and those of τθ(q, θ). This approach is applied to three cases: an analytic model and two ab initio treatments—one for the C2H molecule and one for the H + H2 molecular system. In all three cases encouraging agreements were obtained between the ab initio‐calculated values of τq(q, θ) values and the ones that follow from the present approach. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Double‐electron capture processes in charge transfer reactions
Authors: Tergiman Y. S. , Bacchus‐Montabonel M. C. 
Published: July 2004

AbstractDouble‐electron capture processes may be important in some collisions of multiply charged ions with atomic or molecular targets and have thus to be taken into account carefully. An illustration of these mechanisms is presented in parallel with single‐electron capture on two examples involving the quadruply charged ions B4+ and N4+ in collision with a helium target. A complete ab initio molecular treatment of the potential energy curves and couplings followed by a semiclassic collision dynamics has been performed for these systems. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Density functional theory study of point defects in the SiSiO2 system and in substoichiometric titanium dioxide TiO2−x
Authors: Capron N. , Boureau G. 
Published: July 2004

AbstractDensity functional theory allows us now to calculate structural and energetic quantities related to nonstoichiometric oxides. Using as examples solutions of oxygen in silicon, substoichiometric titanium dioxide TiO2−x, and vacancies in silica, we show that, despite severe requirements in terms of computational effort, these calculations give insights into the nature of defects and their contribution to the macroscopic properties of nonstoichiometric oxides. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Tight‐binding parameterization of transition and noble metal clusters
Authors: Fortunelli Alessandro , Velasco Ana Marìa 
Published: July 2004

AbstractThe possibility of a tight‐binding (TB) parameterization of transition metal (TM) and noble metal clusters is investigated. An original procedure is proposed that allows one to derive the values of orthogonal‐TB matrix elements reproducing the exact one‐electron spectrum from an analysis of first‐principles density functional calculations. The procedure is applied to selected small metals clusters: Ni2, Pt2, Au2, Pt3, Ni13, Pt13, and Au13. Ni, Pt, and Au are taken as examples of first‐row TM and third‐row transition and noble metals. The diatomic molecules are chosen as the simplest examples of TM clusters, Pt3 allows one to compare closed‐shell and spin‐symmetry‐broken configurations, and the 13‐atom clusters are representative of larger systems. With respect to the current TB parameterizations, it is found that the p‐orbitals lie at higher energies (especially for third‐row TMs) than usually assumed, the diagonal matrix elements among d‐functions also depend on the bond directionality, and an s‐orbital relaxation effect is present for third‐row elements (especially Pt). The validity of the TB approach is substantially confirmed, as well as the possibility of a TB treatment of transition and noble metal clusters, provided that these effects are taken into account (e.g., more than one s‐orbital should be included in the TB parameterization for platinum). © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Theoretical study of hydrogenation of thiouracils and their base pairs with adenine
Authors: Eriksson Leif A. , Kryachko Eugene S. , Nguyen Minh T. 
Published: July 2004

AbstractThe purpose of the present work is to employ theoretical chemical tools to explore the subtle features of the hydrogenation of uracil and its related thioderivatives. The reactions of hydrogenation are followed for the free uracil, 2‐thiouracil, 4‐thiouracil, and 2,4‐dithiouracil as well as for adenine–thiouracil base pairs. It is shown for the first time that, in contrast to the hydrogenation pathways to the carbon atoms C5 and C6 of the studied molecules, characterized by the transition states, the hydrogenations at the sulphur atoms for thiouracils are barrierless and thus the latter are the kinetically most favorable pathways for hydrogenation. As also shown, these features are retained under the hydrogenation of the adenine–thiouracil base pairs. The present study clearly demonstrates that the base pairing destruction is the key radiation‐induced lesion in the adenine–4‐thiouracil and adenine–2,4‐dithiouracil base pairs when the hydrogen radical H·, as one of the primary radiation products, resides at the sulphur atom S4. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Rotational and alignment effects in a wave packet calculation for the Cl + H2 reaction
Authors: Skouteris Dimitris , Laganà Antonio , Capecchi Gabriella , Werner Hans‐Joachim 
Published: July 2004

AbstractTime‐dependent quantum mechanical calculations have been carried out for a total angular momentum J = 0 to determine the distribution among product rovibrational states for the reaction Cl + H2 using product Jacobi coordinates. Calculations have been performed for the ground vibrational state of H2 (v = 0) and its rotational states j = 0–3. Moreover, calculations for the negative parity block of the J = 1, j = 1, K = 1 state have been carried out to get a picture of the geometry of approach dependence of reactivity. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
First‐principles calculation of formation energy of neutral point defects in perovskite‐type BaTiO3
Authors: Moriwake Hiroki 
Published: July 2004

AbstractQuantitative analysis of the formation energy of neutral point defects in perovskite‐type BaTiO3 was carried out by first‐principles calculation. A 40‐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 the constituent atoms. The theoretical formation energy of the O vacancy in BaTiO3 shows negative values in the case of the reduction limit of BaTiO3, which is in good agreement with experimental results showing an abundance of O vacancies when annealed in reducing atmosphere and n‐type electrical conduction. On the other hand, the formation energies of the Ba vacancy and Ti vacancy in BaTiO3 even under the oxidizing condition are as large as 2.21 and 5.65 eV, respectively. This also well corresponds to the experimental fact that the Ba and Ti vacancies are not formed alone in BaTiO3. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Computations of the catalytic effects in the stone–wales fullerene isomerizations: N and CN agents
Authors: Slanina Zdenĕk , Uhlík Filip , Adamowicz Ludwik , Lee Shyi‐Long 
Published: July 2004

AbstractThe Stone–Wales rearrangement has long been considered as a plausible, albeit hypothetical, mechanism for fullerene annealing and isomerizations. In the view of a recently applied new catalyst, KCN, for incorporation of noble gases in fullerenes, the CN radical is studied here computationally as a possible catalytic species acting in kinetics of the Stone–Wales fullerene transformation, and a possible role of K+ is also investigated. The computations are performed on the PM3‐optimized bowl‐shaped model C34H12 to which the CN radical is attached by its C or N atom. The activation energies are evaluated at the UPM3, UHF/6‐31G*, UB3LYP/6‐31G*, ROB3LYP/6‐31G*, ROHF/6‐31G**, and ROB3LYP/6‐31G** levels. However, the reduction of the kinetic barrier owing to the catalyst action is modest so that a free N atom, neutral or charged, still remains a more efficient option. Effects of negatively charged CN species and of K+ are also found insufficient. Small amounts of nitrogen are indeed always present during fullerene synthesis, especially from He gas. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Distributed Gaussian basis sets: Variationally optimized s‐type sets for the open‐shell systems HeH and BeH
Authors: Glushkov V. N. , Wilson S. 
Published: July 2004

AbstractDistributed basis sets of s‐type Gaussian functions are determined by invoking the variation principle for the restricted open‐shell matrix Hartree–Fock ground states of the open‐shell molecular systems HeH and BeH for nuclear separations of 1.500 bohr and 2.500 bohr, respectively. The calculated energy expectation values supported by these distributed basis sets are compared with the energies obtained from finite difference open‐shell Hartree–Fock calculations. The restricted open‐shell matrix Hartree–Fock calculations are performed by means of the asymptotic method. The accuracy of the approximations to the energy expectation values supported by the distributed basis sets of s‐type Gaussian functions is comparable with that attained in previous studies of closed‐shell systems. The parameters, that is, the exponents and positions defining the variationally optimized distributed basis sets, are presented and discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Alternatives to multireference methods for the molecular electronic structure problem
Authors: Wilson S. 
Published: July 2004

AbstractThe development of robust many‐body methods for the molecular electronic structure problem with respect to multireference functions has attracted much attention over the past two decades. In recent years, multireference methods based on the Brillouin–Wigner expansion have been shown to overcome the intruder state problems which have plagued similar approaches based on the Rayleigh–Schrödinger series. However, there are some problems in molecular electronic structure theory, which may be handled by means of multireference methods, but can be treated by methods that avoid the use of multireference functions. We consider two examples of alternatives to multireference methods for the molecular electronic structure problem. The study of excited states having the same symmetry as the ground state or some lower lying excited state often involves the use of a multireference function. We describe an alternative procedure based on the generalized Rayleigh–Ritz variation principle. Gidopoulos, Glushkov, and Wilson have termed this the optimized trace method. The generalized Rayleigh–Ritz principle for the relativistic formulation of the molecular electronic structure problem is briefly also considered. Molecular dissociative processes are frequently described by quantum chemical methods based on multireference functions. Single‐reference Hartree–Fock methods usually provide a qualitatively incorrect description of such processes even in the simplest of molecules, H2. However, approximate single configuration wave functions constructed from nonorthogonal orbitals can often afford a useful approximation to bond‐breaking processes. Each occupied nonorthogonal orbital is then an eigenfunction of a different Fock‐like operator. Each of these Fock‐like operators supports a spectrum of M single particle states, where M is the size of the basis set, and only the lowest of these is occupied. We briefly consider the relativistic formulation of the molecular electronic structure problem based on approximations involving products of nonorthogonal functions within the Furry bound state interaction picture of quantum electrodynamics. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Calculation of states of an ion Fe3 in crystal FeBO3
Authors: Filippov D. A. , Nikiforov I. S. 
Published: July 2004

AbstractMethod of the calculation of the energy levels and wave function of the S‐state ions is presented. Using the second order of the perturbation theory, the split of the ground term 6S by the spin‐orbit interaction with higher states is determined. Energy levels and wave function of the ion Fe3+ in the crystalline field model is obtained. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
ONIOM study of one‐carbon unit transfer from imidazolidine to dUMP analogue
Authors: Qi C. S. , Feng D. C. , Cai Z. T. 
Published: July 2004

AbstractThe ONIOM quantum mechanics method is used in this article to study one‐carbon unit transfer from an imidazolidine to 6‐aminouracil derivates. The computation results show that this reaction can be completed via three paths, owing to the three different proton transfer modes. Each path experiences three processes of nucleophile attacking, proton transferring, and bond rupturing. The focus of discussion falls on the proton transfer process. By analyzing the calculation results, we find that the direct proton transfer is the preferable pathway. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Beispiele für verglaste Vertikalseilfassaden
Authors: Sobek Werner , Rehle Norbert 
Published: July 2004

AbstractVerglaste Fassaden, deren tragende Konstruktion ausschließlich aus vertikal verlaufenden vorgespannten Seilen oder Zugstangen besteht, eröffnen die Möglichkeit einer weitestgehenden Minimierung des Materialverbrauchs bei gleichzeitiger Maximierung der Transparenz. Durch ihre Konstruktionsweise bedingt, weisen diese Fassaden unter Horizontalbelastung große Verformungen auf, welche durch Einbau von Federpaketen und Stoppern beeinflußt werden können. Unterschiedliche Glashaltesysteme und unterschiedliche Glasarten, bis hin zu explosionssicheren Isolierverglasungen, sind mit der Konstruktionsweise möglich. Der Aufsatz beschreibt die Entwicklung und die Charakteristika derartiger Fassaden anhand einer Reihe ausgeführter Beispiele.