bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of common structural features of binding sites in galactose‐specific proteins
Authors: Sujatha M.S. , Balaji Petety V.
Published: February 2004

Galactose‐binding proteins characterize an important subgroup of sugar‐binding proteins that are involved in a variety of biological processes. Structural studies have shown that the Gal‐specific proteins encompass a diverse range of primary and tertiary structures. The binding sites for galactose also seem to vary in different protein‐galactose complexes. No common binding site features that are shared by the Gal‐specific proteins to achieve ligand specificity are so far known. With the assumption that common recognition principles will exist for common substrate recognition, the present study was undertaken to identify and characterize any unique galactose‐binding site signature by analyzing the three‐dimensional (3D) structures of 18 protein‐galactose complexes. These proteins belong to 7 nonhomologous families; thus, there is no sequence or structural similarity across the families. Within each family, the binding site residues and their relative distances were well conserved, but there were no similarities across families. A novel, yet simple, approach was adopted to characterize the binding site residues by representing their relative spatial dispositions in polar coordinates. A combination of the deduced geometrical features with the structural characteristics, such as solvent accessibility and secondary structure type, furnished a potential galactose‐binding site signature. The signature was evaluated by incorporation into the programCOTRANto search for potential galactose‐binding sites in proteins that share the samefoldas the known galactose‐binding proteins.COTRANis able to detect galactose‐binding sites with a very high specificity and sensitivity. The deduced galactose‐binding site signature is strongly validated and can be used to search for galactose‐binding sites in proteins. PROSITE‐type signature sequences have also been inferred for galectin and C‐type animal lectin‐likefoldfamilies of Gal‐binding proteins. Proteins 2004;55:44–65. © 2004 Wiley‐Liss, Inc.
Structural analysis of disease‐causing mutations in the P‐subfamily of forkhead transcription factors
Authors: Banerjee‐Basu Sharmila , Baxevanis Andreas D.
Published: February 2004

Mutations in a number of forkhead transcription factors are associated with the development of inherited diseases in humans. Two closely related genes, FOXP2 and FOXP3, are implicated in two completely different human disorders. A point mutation in the forkhead domain of FOXP2 (R553H) is responsible for a severe speech and language disorder, while a series of missense mutations distributed over the forkhead domain of FOXP3 cause a fatal disorder called IPEX, characterized by immune dysregulation, polyendocrinopathy, and enteropathy. Homology model building techniques were used to generate atomic structures of FOXP2 and FOXP3, using the solution structures of the forkhead domain of the adipocyte‐transcription factor FREAC‐11 and AFX as templates. The impact of these disease‐causing missense mutations on the three‐dimensional structure, stability, and surface electrostatic charge distribution of the forkhead domains is examined here. The missense mutations R553H in FOXP2 and R397W in FOXP3 dramatically alter the electrostatic potentials of the molecular surface of their respective forkhead domains. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Recovering the true targets of specific ligands by virtual screening of the protein data bank
Authors: Paul Nicodéme , Kellenberger Esther , Bret Guillaume , Müller Pascal , Rognan Didier
Published: February 2004

The Protein Data Bank (PDB) has been processed to extract a screening protein library (sc‐PDB) of 2148 entries. A knowledge‐based detection algorithm has been applied to 18,000 PDB files to find regular expressions corresponding to either protein, ions, co‐factors, solvent, or ligand atoms. The sc‐PDB database comprises high‐resolution X‐ray structures of proteins for which (i) a well‐defined active site exists, (ii) the bound‐ligand is a small molecular weight molecule. The database has been screened by an inverse docking tool derived from the GOLD program to recover the known target of four unrelated ligands. Both the database and the inverse screening procedures are accurate enough to rank the true target of the four investigated ligands among the top 1% scorers, with 70–100 fold enrichment with respect to random screening. Applying the proposed screening procedure to a small‐sized generic ligand was much less accurate suggesting that inverse screening shall be reserved to rather selective compounds. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Trehalose–protein interaction in aqueous solution
Authors: Lins Roberto D. , Pereira Cristina S. , Hünenberger Philippe H.
Published: February 2004

A variety of sugars are known to enhance the stability of biomaterials. Trehalose, a nonreducing disaccharide composed of two α, α(1 → 1)‐linked D‐glucopyranose units, appears to be one of the most effective protectants. Both in vivo and in vitro, trehalose protects biostructures such as proteins and membranes from damage due to dehydration, heat, or cold. However, despite the significant amount of experimental data on this disaccharide, no clear picture of the molecular mechanism responsible for its stabilizing properties has emerged yet. Three major hypotheses (water–trehalose hydrogen‐bond replacement, coating by a trapped water layer, and mechanical inhibition of the conformational fluctuations) have been proposed to explain the stabilizing effect of trehalose on proteins. To investigate the nature of protein–trehalose–water interactions in solution at the molecular level, two molecular dynamics simulations of the protein lysozyme in solution at room temperature have been carried out, one in the presence (about 0.5 M) and one in the absence of trehalose. The results show that the trehalose molecules cluster and move toward the protein, but neither completely expel water from the protein surface nor form hydrogen bonds with the protein. Furthermore, the coating by trehalose does not significantly reduce the conformational fluctuations of the protein compared to the trehalose‐free system. Based on these observations, a model is proposed for the interaction of trehalose molecules with a protein in moderately concentrated solutions, at room temperature and on the nanosecond timescale. Proteins 2004;55:177–186. © 2004 Wiley‐Liss, Inc.
Solution structure of the ubiquitin‐binding domain in Swa2p from Saccharomyces cerevisiae
Authors: Chim Nicholas , Gall Walter E. , Xiao Jing , Harris Mark P. , Graham Todd R. , Krezel Andrzej M.
Published: February 2004

The SWA2/AUX1 gene has been proposed to encode the Saccharomyces cerevisiae ortholog of mammalian auxilin. Swa2p is required for clathrin assembly/dissassembly in vivo, thereby implicating it in intracellular protein and lipid trafficking. While investigating the 287‐residue N‐terminal region of Swa2p, we found a single stably folded domain between residues 140 and 180. Using binding assays and structural analysis, we established this to be a ubiquitin‐associated (UBA) domain, unidentified by bioinformatics of the yeast genome. We determined the solution structure of this Swa2p domain and found a characteristic three‐helix UBA fold. Comparisons of structures of known UBA folds reveal that the position of the third helix is quite variable. This helix in Swa2p UBA contains a bulkier tyrosine in place of smaller residues found in other UBAs and cannot pack as close to the second helix. The molecular surface of Swa2p UBA has a mostly negative potential, with a single hydrophobic surface patch found also in the UBA domains of human protein, HHR23A. The presence of a UBA domain implicates Swa2p in novel roles involving ubiquitin and ubiquitinated substrates. We propose that Swa2p is a multifunctional protein capable of recognizing several proteins through its protein–protein recognition domains. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
Authors: Zacharias Martin
Published: February 2004

Most current docking methods to identify possible ligands and putative binding sites on a receptor molecule assume a rigid receptor structure to allow virtual screening of large ligand databases. However, binding of a ligand can lead to changes in the receptor protein conformation that are sterically necessary to accommodate a bound ligand. An approach is presented that allows relaxation of the protein conformation in precalculated soft flexible degrees of freedom during ligand–receptor docking. For the immunosuppressant FK506‐binding protein FKBP, the soft flexible modes are extracted as principal components of motion from a molecular dynamics simulation. A simple penalty function for deformations in the soft flexible mode is used to limit receptor protein deformations during docking that avoids a costly recalculation of the receptor energy by summing over all receptor atom pairs at each step. Rigid docking of the FK506 ligand binding to an unbound FKBP conformation failed to identify a geometry close to experiment as favorable binding site. In contrast, inclusion of the flexible soft modes during systematic docking runs selected a binding geometry close to experiment as lowest energy conformation. This has been achieved at a modest increase of computational cost compared to rigid docking. The approach could provide a computationally efficient way to approximately account for receptor flexibility during docking of large numbers of putative ligands and putative docking geometries. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Conserved spatially interacting motifs of protein superfamilies: Application to fold recognition and function annotation of genome data
Authors: Bhaduri Anirban , Ravishankar R. , Sowdhamini R.
Published: February 2004

Limitations in techniques for the elucidation of protein function have led to an increasing gap between the annotated proteins and those encoded in a genome. The functional selection and three‐dimensional structural constraints of proteins in nature often relate to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. We identify spatially interacting conserved regions, or motifs, within protein superfamilies that are critical for structure and/or function. A search in sequence databases using these descriptors as additional constraints is an approach to identifying putative additional members of superfamilies. Such constrained searches have been tested against proteins of known structure to demonstrate high percentage specificity (93) with a low error rate of 0.0004. This approach has been compared with other sensitive sequence search methods (e.g., PSI‐BLAST, HMMsearch, and IMPALA). It has been extended to analyze the distribution of 11 superfamilies in 93 genomes, including the human genome. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Extreme free energy of stabilization of Taq DNA polymerase
Authors: Schoeffler Allyn J. , Joubert Allison M. , Peng Fenggang , Khan Farheen , Liu Chin‐Chi , LiCata Vince J.
Published: February 2004

We have examined the chemical denaturations of the Klentaq and Klenow large‐fragment domains of the Type 1 DNA polymerases from Thermus aquaticus (Klentaq) and Escherichia coli (Klenow) under identical solution conditions in order to directly compare the stabilization energetics of the two proteins. The high temperature stability of Taq DNA polymerase is common knowledge, and is the basis of its use in the polymerase chain reaction. This study, however, is aimed at understanding the thermodynamic basis for this high‐temperature stability. Chemical denaturations with guanidine hydrochloride report a folding free energy (ΔG) for Klentaq that is over 20 kcal/mol more favorable than that for Klenow under the conditions examined. This difference between the stabilization free energies of a homologous mesophilic–thermophilic protein pair is significantly larger than generally observed. This is due in part to the fact that the stabilization free energy for Klentaq polymerase, at 27.5 kcal/mol, is one of the largest ever determined for a monomeric protein. Large differences in the chemical midpoints of the unfolding (Cm) and the dependences of the unfolding free energy on denaturant concentration in the transition region (m‐value) between the two proteins are also observed. Measurements of the sedimentation coefficients of the two proteins in the native and denatured states report that both proteins approximately double in hydrodynamic size upon denaturation, but that Klentaq expands somewhat more than Klenow. Proteins 2004;00:000–000. © 2004 Wiley‐Liss, Inc.
Reorganization in apo‐ and holo‐β‐lactoglobulin upon protonation of Glu89: Molecular dynamics and pKa calculations
Authors: Eberini Ivano , Baptista António M. , Gianazza Elisabetta , Fraternali Franca , Beringhelli Tiziana
Published: February 2004

Molecular dynamics (MD) simulations starting from crystallographic data allowed us to directly account for the effects of the protonation state of Glu89 on the conformational stability of apo‐ and holo‐β‐lactoglobulin (BLG). In apo‐BLG simulations starting from the protonated crystal structure, we observe a long‐lived H‐bond interaction between the protonated Glu89 and Ser116. This interaction, sequestering the proton from the aqueous medium, explains a pKhalf value evaluated at pH 7.3 by continuum electrostatics/Monte Carlo computation on MD data, using linear response approximation. A very large root‐mean‐square deviation (RMSD; 5.11 Å) is observed for the EF loop between protonated and unprotonated apo‐BLG. This results from a quite different orientation of the EF loop that acts either as a closed or as an open lid above the protein calyx. Proton exchange by Glu89 in apo‐ but not in holo‐BLG is associated with a reorganization energy of 4.7 kcal/mol. A 3‐ns MD simulation starting from the crystal structure of protonated apo‐BLG, but considering the Glu89 as unprotonated, shows the progressive opening of the lid giving rise to the Tanford transition. In both holo‐BLG forms, the lid is most probably held in place by hydrophobic interactions of amino acid side‐chains of the EF loop with the palmitate hydrocarbon tail. Proteins 2004;00:000–000. © 2004 Wiley‐Liss, Inc.
Why does the Ras switch “break” by oncogenic mutations?
Authors: Shurki Avital , Warshel Arieh
Published: February 2004

The elucidation of the structure of the RasGAP complex provides what is perhaps the most detailed link between protein structure and cancer causing mutations. In particular, it is known that mutations of Gln 61 destroy the GTPase activity of the complex, locks the cell in its ON state and thus, can cause cancer. It is entirely unclear however, why this specific mutation is so important. The present work uncovers the elusive role of Gln 61 by computer simulation of the GTPase reaction in Ras, RasGAP and of their mutants. Simulations of the effects of mutations of Gln 61 reproduce the corresponding observed changes in activation energies and allow us to analyze the energy contributions to these effects. It is found that Gln 61 does not operate in a direct chemical way nor by a direct electrostatic or steric interaction with the transition state (TS). Instead, oncogenic mutations of Gln 61 lead to the destruction of the exquisitely preorganized catalytic configuration of the active site of the RasGAP complex. This “allosteric” effect causes a major reduction in the electrostatic stabilization of the TS. Our findings have general relevance to other proteins that control signal transduction processes. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Selection and affinity maturation of IgNAR variable domains targeting Plasmodium falciparum AMA1
Authors: Nuttall Stewart D. , Humberstone Karen S. , Krishnan Usha V. , Carmichael Jennifer A. , Doughty Larissa , Hattarki Meghan , Coley Andrew M. , Casey Joanne L. , Anders Robin F. , Foley Michael , Irving Robert A. , Hudson Peter J.
Published: February 2004

The new antigen receptor (IgNAR) is an antibody unique to sharks and consists of a disulphide‐bonded dimer of two protein chains, each containing a single variable and five constant domains. The individual variable (VNAR) domains bind antigen independently, and are candidates for the smallest antibody‐based immune recognition units. We have previously produced a library of VNAR domains with extensive variability in the CDR1 and CDR3 loops displayed on the surface of bacteriophage. Now, to test the efficacy of this library, and further explore the dynamics of VNAR antigen binding we have performed selection experiments against an infectious disease target, the malarial Apical Membrane Antigen‐1 (AMA1) from Plasmodium falciparum. Two related VNAR clones were selected, characterized by long (16‐ and 18‐residue) CDR3 loops. These recombinant VNARs could be harvested at yields approaching 5mg/L of monomeric protein from the E. coli periplasm, and bound AMA1 with nanomolar affinities (KD= ∼2 × 10−7 M). One clone, designated 12Y‐2, was affinity‐matured by error prone PCR, resulting in several variants with mutations mapping to the CDR1 and CDR3 loops. The best of these variants showed ∼10‐fold enhanced affinity over 12Y‐2 and was Plasmodium falciparum strain‐specific. Importantly, we demonstrated that this monovalent VNAR co‐localized with rabbit anti‐AMA1 antisera on the surface of malarial parasites and thus may have utility in diagnostic applications. Proteins 2004;00:000–000. © 2004 Wiley‐Liss, Inc.
Inter‐residue and solvent‐residue interactions in proteins: A statistical study on experimental structures
Authors: Chelli Riccardo , Gervasio Francesco Luigi , Procacci Piero , Schettino Vincenzo
Published: February 2004

A large set of protein structures resolved by X‐ray or NMR techniques has been extracted from the Protein Data Bank and analyzed using statistical methods. In particular, we investigate the interactions between side chains and the interactions between solvent and side chains, pointing out on the possibility of including the solvent as part of a knowledge‐based potential. The solvent‐residue contacts are accounted for on the basis of the Voronoi's polyhedron analysis. Our investigation confirms the importance of hydrophobic residues in determining the protein stability. We observe that in general hydrophobic‐hydrophobic interactions and, more specifically, aromatic‐aromatic contacts tend to be increasingly distally separated in the primary sequence of proteins, thus connecting distinct secondary structure elements. A simple relation expressing the dependence of the protein free energy by the number of residues is proposed. Such a relation includes both the residue‐residue and the solvent‐residue contributions. The former is dominant for large size proteins, whereas for small sizes (number of residues less than 100) the two terms are comparable. Gapless threading experiments show that the solvent‐residue knowledge‐based potential yields a significant contribution with respect to discriminating the native structure of proteins. Such contribution is important especially for proteins of small size and is similar to that given by the most favorable residue‐residue knowledge‐based potential referring to hydrophobic‐hydrophobic interactions such as isoleucine‐leucine. In general, the inclusion of the solvent‐residue interaction produces a relevant increase of the free energy gap between the native structures and decoys. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Enzyme family classification by support vector machines
Authors: Cai C.Z. , Han L.Y. , Ji Z.L. , Chen Y.Z.
Published: February 2004

One approach for facilitating protein function prediction is to classify proteins into functional families. Recent studies on the classification of G‐protein coupled receptors and other proteins suggest that a statistical learning method, Support vector machines (SVM), may be potentially useful for protein classification into functional families. In this work, SVM is applied and tested on the classification of enzymes into functional families defined by the Enzyme Nomenclature Committee of IUBMB. SVM classification system for each family is trained from representative enzymes of that family and seed proteins of Pfam curated protein families. The classification accuracy for enzymes from 46 families and for non‐enzymes is in the range of 50.0% to 95.7% and 79.0% to 100% respectively. The corresponding Matthews correlation coefficient is in the range of 54.1% to 96.1%. Moreover, 80.3% of the 8,291 correctly classified enzymes are uniquely classified into a specific enzyme family by using a scoring function, indicating that SVM may have certain level of unique prediction capability. Testing results also suggest that SVM in some cases is capable of classification of distantly related enzymes and homologous enzymes of different functions. Effort is being made to use a more comprehensive set of enzymes as training sets and to incorporate multi‐class SVM classification systems to further enhance the unique prediction accuracy. Our results suggest the potential of SVM for enzyme family classification and for facilitating protein function prediction. Our software is accessible at http://jing.cz3.nus.edu.sg/cgi‐bin/svmprot.cgi. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Design Vulnerability Analysis and Design Improvement by Using Warranty Data
Authors: Yang Kai , Cekecek Ethem
Published: February 2004

Continuous improvement in reliability is one of the key factors to success in the world automobile market. Good reliability can only be achieved through good design and manufacturing practice. Manufacturers want to allocate their limited resources to improvement in such a way that they can get the highest benefits. The warranty claims database contains more information than any other test for the reliability of products in actual use. Assisted by a design vulnerability index derived from the axiomatic design principle, warranty data can be used to identify the areas of the product such that the improvement of these areas will maximize the gain in reliability improvement. In this paper, we provide a methodology of utilizing warranty data to prioritize design improvement efforts based on design vulnerability and the feedback from warranty data. The methodology is illustrated with an example case. Copyright © 2004 John Wiley & Sons, Ltd.
Determining Thermal Test Requirements for Automotive Components
Authors: Aldridge Dustin S.
Published: February 2004

Component thermal response is dependent upon numerous factors including the atmospheric temperature, heat sinks and sources, vehicle use time, etc. The number of significant thermal cycles and time at temperature for many components will be related to the number of times the engine is started. This paper provides a methodology to determine the number of significant thermal cycles and time at temperature a product will experience in 10 years which will depend upon engine starts. These calculations provide the basis for an accelerated test requirement to qualify the product based upon customer usage measurements. Because of the trace ability and linkage, the methodology is more marketable to internal and external customers, and less likely to be questioned or arbitrarily overruled. It also enables relative severity assessments for historical customer requirements compared with field needs. Copyright © 2004 John Wiley & Sons, Ltd.
Accelerated Reliability Qualification in Automotive Testing
Authors: Porter Alex
Published: February 2004

Products must come to market quickly, be more reliable and cost less. The problem is that statistical measures take time. There is a clear need for actionable information about the robustness or durability of a product early in the development process. In a Failure Mode Verification Test (FMVT), the analysis is not statistical but is designed to check two assumptions. First, that the design is capable of producing a viable product for the environments applied. Second, that a good design and fabrication of the product would last for a long period of time under all of the stresses that it is expected to see and would accumulate stress damage throughout the product in a uniform way. Testing a product in this way leads to three measures of the product's durability: (1) design maturity, the ratio between time to first failure and the average time between failures after the first failure; (2) technological limit, the time under test at which fixing additional failures would not provide a significant improvement in the life of the product; and (3) failure mode histogram, which indicates the repeatability of failures in a product. Using techniques like FMVT can provide a means of breaking the tyranny of statistics over durability and reliability testing in a competitive business climate. Copyright © 2004 John Wiley & Sons, Ltd.
Modelling Feasible Design Regions Using Lattice‐based Kernel Methods
Authors: Bates R. A. , Wynn H. P.
Published: February 2004

Reliability, robustness and general performance are key indicators when attempting to improve the design of existing engineering systems. The search for an improved design is conducted in the space of all possible designs, referred to as the design space. Often when searching this space, infeasible or unsafe regions are encountered, perhaps because particular combinations of parameter values are not physically possible. Such regions need to be avoided during optimization to ensure that any new design is itself feasible. In addition, when considering the reliability and robustness of a design, it may be important to know how far a feasible design is from any boundary. Indeed, it may be the case that such distances are directly related to the reliability and robustness of the design and it may, therefore, be useful to model the boundary between feasible and infeasible regions. This paper proposes the use of Hilbert bases as a method of identifying points in the design space that are close to, or on, the feasible boundary and then uses this information to model the boundary by defining positive definite kernels on new spaces such as hyperspheres. In this way it is possible to model whole surfaces as opposed to single functions. Copyright © 2004 John Wiley & Sons, Ltd.
Reliability Improvement of a Diesel Engine Using the FMETA Approach
Authors: Arcidiacono G. , Campatelli G.
Published: February 2004

This paper provides a way to deal with issues related to design for reliability using axiomatic design (AD). A theoretical approach is studied, starting from the traditional theory of AD, in order to help designers to optimize the product's reliability using a structured approach. The aim of this work is to introduce a new method that is able to assess the product reliability using the support of the AD methodology combined with other methods, e.g. FMEA and FTA. The approach developed is called failure mode and effect tree analysis (FMETA). FMETA allows the designer to find the most critical characteristic of the product from a reliability point of view and provides the designer with a set of possible changes. The core of this work is the development of a reliability tree, used to evaluate both the RPN for the component of the product and to find the reliability relation useful for the following optimization. The reliability tree is born from the combined use of AD, FMEA and FTA. This method has been validated by an application to an automotive heavy‐duty diesel engine. Copyright © 2004 John Wiley & Sons, Ltd.
Electronic structure and molecular orbital study of the first excited state of the high‐efficiency blue OLED material bis(2‐methyl‐8‐quinolinolato)aluminum(III) hydroxide complex from ab initio and TD‐B3LYP
Authors: Gao Hong‐Ze , Su Zhong‐Min , Qin Chun‐Sheng , Mo Ri‐Gen , Kan Yu‐He
Published: February 2004

Bis(2‐methyl‐8‐quinolinolato)aluminum(III) hydroxide complex (AlMq2OH) is used in organic light‐emitting diodes (OLEDs) as an electron transport material and emitting layer. By means of ab initio Hartree–Fock (HF) and density functional theory (DFT) B3LYP methods, the structure of AlMq2OH was optimized. The frontier molecular orbital characteristics and energy levels of AlMq2OH have been analyzed systematically to study the electronic transition mechanism in AlMq2OH. For comparison and calibration, bis(8‐quinolinolato)aluminum(III) hydroxide complex (Alq2OH) has also been examined with these methods using the same basis sets. The lowest singlet excited state (S1) of AlMq2OH has been studied by the singles configuration interaction (CIS) method and time‐dependent DFT (TD‐DFT) using a hybrid functional, B3‐LYP, and the 6‐31G* basis set. The lowest singlet electronic transition (S0 → S1) of AlMq2OH is π → π* electronic transitions and primarily localized on the different quinolate ligands. The emission of AlMq2OH is due to the electron transitions from a phenoxide donor to a pyridyl acceptor from another quinolate ligand including C → C and O → N transference. Two possible electron transfer pathways are presented, one by carbon, oxygen, and nitrogen atoms and the other via metal cation Al3+. The comparison between the CIS‐optimized excited‐state structure with the HF ground‐state structure indicates that the geometric shift is mainly confined to the one quinolate and these changes can be easily understood in terms of the nodal patterns of the highest occupied and lowest unoccupied molecular orbitals. On the basis of the CIS‐optimized structure of the excited state, TD‐B3‐LYP calculations predict an emission wavelength of 499.78 nm. An absorption wavelength at 380.79 nm on the optimized structure of B3LYP/6‐31G* was predicted. They are comparable to AlMq2OH 485 and 390 nm observed experimentally for photoluminescence and UV‐vis absorption spectra of AlMq2OH solid thin film on quartz, respectively. Lending theoretical corroboration to recent experimental observations and supposition, the reasons for the blue‐shift of AlMq2OH were revealed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
On Ehrenfest's theorem
Authors: Sahni Viraht
Published: February 2004

Ehrenfest's theorem for a system of electrons in a time‐dependent external force is the quantal analogue to Newton's second law of motion for interacting classical particles. The theorem is in terms of the averaged force and position of the electrons. Here we draw the quantal analogue to the equation of motion for the individual classical particle and thereby describe the internal forces experienced by each electron and the evolution of these forces with time. This explanation is based on the description of Schrödinger theory in terms of fields and their quantal sources. The quantum mechanical average of the internal fields and their averaged torques, taken over all the electrons, vanish as they must. However, unlike classical physics, the vanishing of the averaged internal fields cannot be attributed solely to Newton's third law but is additionally a consequence of quantum mechanics. The field perspective thus leads to a new derivation of Ehrenfest's theorem. Furthermore, the theorem can be expressed in terms of the response of the electrons to the external field as described by a field representative of the electronic current density. In addition, the vanishing of the averaged torque of the internal fields leads to a quantal torque–angular momentum equation analogous to that of classical physics. The structure of the internal fields is demonstrated for both a ground and an excited state of the analytically solvable Hooke's atom. The concept of the internal field is extended via quantal density functional theory to the S system of noninteracting Fermions with density equivalent to that of the Schrödinger theory of electrons. By invoking Ehrenfest's theorem and the quantal torque–angular momentum relationship, sum rules for the S system are derived. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Oxidative polymerization of 5 amino,1,10‐phenanthroline: A theoretical study
Authors: Mora M. A. , Galicia Laura , Mora‐Ramirez M. A.
Published: February 2004

The molecular and electronic structures of 5‐amino‐1,10‐phenanthroline and its monoprotonated and diprotonated species were obtained from ab initio quantum mechanical calculations with unrestricted Hartree–Fock (HF) and Møller–Plesset perturbation theories. The analysis of the net atomic charges and the total spin densities show three possible sites for the monomeric coupling in the polymerization process. The minimal energy conformation for the different kinds of coupling in the formation of the dimers was obtained. The studies were extended to the HF/6‐311 + G(2d,p)//B3LYP (Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar)/6‐31G(d) level of theory to obtain theoretical nuclear magnetic resonance spectra to study the number and kinds of species involved in the protonation mechanism. Theoretical and experimental nuclear magnetic resonance spectra are in excellent agreement. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Variational principles for bound states of Schrödinger and Dirac equations allowing the use of discontinuous trial functions
Authors: Szmytkowski Radosław , Bielski Sebastian
Published: February 2004

We present systematic constructions of variational principles for energies of bound states of the Schrödinger and Dirac equations. The principles allow the use of discontinuous trial functions. The method employed is based on a generalized Lagrange procedure. Relationships between our variational principles and those available in the literature are established. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Generalized population analysis of three‐center two‐electron bonding
Authors: Ponec Robert , Cooper David L.
Published: February 2004

Modern valence bond theory, in its spin‐coupled (SC) form, is used to assess the utility of generalized population analysis, using correlated density matrices, for identifying patterns of three‐center two‐electron bonding in B2H6, B3H, and CH2Li2. The effect on the relevant three‐center indices of including electron correlation, via the SC method, is assessed by means of comparison with analogous Hartree–Fock values. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Impacts of different weed cutting practices on macrophyte species diversity and composition in a Danish stream
Authors: Baattrup‐Pedersen Annette , Riis Tenna
Published: February 2004

Various effects of stream management on biotic communities have been suggested on the basis of observations and investigations in regularly managed streams throughout Europe, but only very sparse information is available about if and how stream management can be combined with maintaining a natural and diverse stream flora. Our study was carried out to investigate how weed cutting practice and frequency can affect macrophyte communities to provide knowledge for future decisions regarding management in streams. We chose an experimental approach and applied four different weed cutting practices (cutting full width, central channel, diagonal channels and no cutting) and frequencies within one stream reach for four years. We found only very limited changes over the four years in overall macrophyte diversity parameters following different management practices and there were no changes in macrophyte diversity parameters either as a function of the weed cutting frequency or method applied. In contrast we found directional changes in macrophyte composition following frequent cuttings of either the whole stream channel or a less comprehensive cutting of only one central channel for four years. In both cases the macrophyte communities changed towards a more Ranunculus dominated community while Potamogeton natans became less important in the community. This change seemed to reflect a higher tolerance of Ranunculus towards disturbance. On the basis of these results, we recommend that the management frequency in streams is limited and, if several cuttings are needed to prevent bank over‐flow, cutting in several narrow channels is preferable to cutting in one central channel as directional changes in plant communities are avoided. Copyright © 2003 John Wiley & Sons, Ltd.
Effect of mixing patterns and light dose on growth of Anabaena circinalis in a turbid, lowland river
Authors: Westwood Karen J. , Ganf George G.
Published: February 2004

Anabaena circinalis is common in the lower Murray River, Australia, and may compromise water quality due to the release of toxins. The water is turbid and thermal structure may significantly affect light availability. An in situ experiment was designed to represent complete mixing, diurnal stratification and persistent stratification and test the effect on growth of A. circinalis. To represent the mixing treatments, cells were incubated in diffusion chambers that were adjusted to different positions in the water‐column throughout the day. Populations exposed to persistent stratification over six days grew significantly faster than the other treatments at a rate of 0.65 day−1. However, growth of the diurnally stratified populations was slower than (0.28 day−1), or similar to (0.40 day−1) the mixed population (0.40 day−1). Therefore, the growth of the subpopulations exposed to the euphotic zone was insufficient to counteract the slow growth of the majority that were confined to darkness during the stratified period. A relationship between growth rate (G) and average daily light dose (I) was constructed and growth rate at optimal light dose (Gmax), slope of linear section of G–I curve (α), and light dose where lines of Gmax and light‐limited portion of G–I curve intersect (Ik) were solved as 0.66 day−1, 0.12 day−1 (mol−1 m−2 day−1)−1 and 5.4 mol m−2 day−1, respectively. Using these parameters, a model was developed to predict possible differences in growth between diurnal and mixed populations under varying conditions of vertical light attenuation, mixed depth and incubation time. Copyright © 2003 John Wiley & Sons, Ltd.
A survey of methods for setting minimum instream flow standards in the Caribbean basin
Authors: Scatena F. N.
Published: February 2004

To evaluate the current status of instream flow practices in streams that drain into the Caribbean Basin, a voluntary survey of practising water resource managers was conducted. Responses were received from 70% of the potential continental countries, 100% of the islands in the Greater Antilles, and 56% of all the Caribbean island nations. Respondents identified ‘effluent discharges’, ‘downstream water quality’ and ‘existing extraction permits’ to be the most common sources of instream flow conflicts. In 75% of the countries, some type of ‘formal procedures’ exist for reviewing permit applications for freshwater extraction. In 82% of the countries, effluent discharge permits state the amount of effluent that can be discharged into a water body while only 69% require that surface water extraction permits explicitly state the quantity of water that can be extracted. In setting instream flow requirements, record low flow is used over 83% of the time. Freshwater fish were identified as the most important aquatic organism but no country ‘always’ considers the ecology or habitat requirements of aquatic species in their instream flow determinations and nearly 70% of the respondents indicated that multivariate, ecological‐based methods are ‘never’ used in their country. Survey responses also indicate there is a notable lack of public involvement during the issuing of water permits. Moreover, over 80% of the countries do not provide public announcements or hearings during the permit process. In summary, this survey indicates that while there is a widespread recognition of the need for instream flows, there is a general lack of regionally based information and public involvement regarding stream flow determination. Copyright © 2003 John Wiley & Sons, Ltd.
The importance of inshore areas for adult fish distribution along a free‐flowing section of the Danube, Austria
Authors: Hirzinger V. , Keckeis H. , Nemeschkal H. L. , Schiemer F.
Published: February 2004

This study analyses bank morphological parameters of inshore areas as significant qualifying criteria for the habitat of riverine fish in large rivers. The mesoscaled (1.04±0.35 km) spatial distribution of adult fish was studied along a 50 km stretch of a free‐flowing section of the Austrian Danube. Fish abundance at the inshore zone of the main channel was assessed every month from March 1992 to May 1993, applying stratified random sampling by electrofishing.

In order to calculate river morphological variables, a specific DOS application was programmed taking riverbank profiles, slope of the Danube and mean daily water level into account. The sampling sites by environmental variables were analysed by principal component analysis (PCA). PCA scores, together with the relative densities of each fish species in terms of their proportions per catch, were treated by a simple logistic regression. The different species exhibit specific patterns of statistical probability in terms of distribution and densities at distinct structural inshore types with regard to area, slope, habitat heterogeneity and connectivity parameters.

Large gradually sloping inshore areas are characterized by rheophilic Chondrostoma nasus, Leuciscus idus and Abramis ballerus, whereas eurytopic species do not show a consistent pattern. Heterogeneous stretches contain high proportions of Leuciscus cephalus, Abramis brama and Abramis ballerus. Connectivity discriminates strictly riverine species like Chondrostoma nasus from rheophilic species which require non‐channel habitat during their life history. Copyright © 2003 John Wiley & Sons, Ltd.
Patterns of channel adjustment to impoundment of the upper River Spey, Scotland (1942–2000)
Authors: Gilvear David J.
Published: February 2004

Over the last 30 years, understanding of how river channel morphology adjusts to upstream impoundment has been improved considerably with clearwater erosion close to the dam and aggradation downstream of unregulated tributary confluences being identified. In a UK context our understanding of channel response to impoundment has been based principally on analysis of a number of regulated rivers using a time–space substitution approach but the temporal pattern of channel change was not fully observed. This paper details channel change over almost six decades following impoundment of the River Spey, Scotland, primarily via the use of cartographic and aerial photographic evidence. Channel change initially involved the formation of tributary confluence bars followed by bench development and vegetation colonization and development on the benches and gravel bars. Sixty years after impoundment, the channel is still adjusting its form at distance from the dam to be in quasi‐ equilibrium with its regulated flow regime; indeed adjustment was most rapid between 1989 to 1995. This accelerated adjustment is due to the occurrence of a greater number of large and geomorphologically significant flood events in this period. Sediment supply limitation from unregulated tributaries will have stemmed the rate of narrowing and bench development prior to 1989. This spatial and temporal pattern of adjustment supports, for the most part, the model advocated by Petts (Progress in Physical Geography, 1979, Vol. 3, pp. 329–362). The wider implications of the channel change for river conservation and management are addressed. Copyright © 2003 John Wiley & Sons, Ltd.
Prospects for developing absorptive capacity through internal information provision
Authors: Lenox Michael , King Andrew
Published: February 2004

Theories of absorptive capacity propose that knowledge gained from prior experience facilitates the identification, selection, and implementation of related profitable practices. Researchers have investigated how managers may develop absorptive capacity by building internal knowledge stocks, but few have focused on the distribution of this knowledge within the firm and the role managers play in administering information to organizational subunits. In this paper, we explore the degree to which managers can develop absorptive capacity by directly providing information to agents in the organization that might potentially adopt a new practice. We find that the effectiveness of managerial information provision depends on the degree to which potential adopters have information from other sources. We find that information from previous adopters and past events reduces the effect of information provision, while experience with related practices amplifies it. Our research helps clarify when absorptive capacity may provide a sustained competitive advantage. Copyright © 2004 John Wiley & Sons, Ltd.
Emergent patterns of strategy, environment and performance in a transition economy
Authors: Davies Howard , Walters Peter
Published: February 2004

Insights from the resource dependence approach, dynamic fit, and strategic choice theories are used to explore the strategies adopted by Chinese enterprises, their settings, and the relationship between strategy, environment, and performance. Results from 959 firms indicate that respondents operating under ‘more marketized’ institutional settings tend to locate themselves in more munificent environments and place greater emphasis on meeting customer needs. Firms in China do not trade off one strategic direction against another, and certain strategy/environment coalignments have significant implications for performance. In particular, performance is better in more marketized and munificent environments and amongst firms who adopt an ‘aggressive’ strategic posture. Copyright © 2004 John Wiley & Sons, Ltd.
An assessment of the use of structural equation modeling in strategic management research
Authors: Shook Christopher L. , Ketchen David J. , Hult G. Tomas M. , Kacmar K. Michele
Published: February 2004

Structural equation modeling (SEM) is a powerful, yet complex, analytical technique. The use of SEM to examine strategic management phenomena has increased dramatically in recent years, suggesting that a critical evaluation of the technique's implementation is needed. We compared the use of SEM in 92 strategic management studies published in nine prominent journals from 1984 to 2002 to guidelines culled from methodological research. We found that the use and reporting of SEM often have been less than ideal, indicating that authors may be drawing erroneous conclusions about relationships among variables. Given these results, we offer suggestions for researchers on how to better deploy SEM within future inquiry. Copyright © 2004 John Wiley & Sons, Ltd.
The strategy/governance structure fit relationship: theory and evidence in franchising arrangements
Authors: Yin Xiaoli , Zajac Edward J.
Published: February 2004

Despite widespread recognition of the importance of strategy–structure fit, e.g., diversification and divisionalization, research has yet to address the possibility of similar fit issues for other structural forms of organization, such as the choice of franchised vs. company‐owned governance structures. In this study, we depart from the usual debates regarding the superiority of one governance structure over another and argue that performance differences between these two alternative governance structures may be attributable more to the matching of one structure with a correspondingly appropriate strategy. Specifically, we posit that stores will act in fit‐enhancing ways by pursuing strategies that are more congruent with their governance structure; i.e., that franchised stores, with their more flexible and decentralized structures, will be more likely to pursue strategies that emphasize flexibility and local adaptation, whereas company‐owned stores will tend to pursue strategies that emphasize predictability and control. We also argue that those stores acting in such a manner will enjoy subsequent performance benefits. We develop these ideas around strategy/governance structure fit and test our hypotheses using longitudinal data from over 6000 stores within one of the biggest U.S. restaurant chains from 1991 to 1997. Copyright © 2004 John Wiley & Sons, Ltd.