bluuebunny/crossref_metadata_2025 huggingface dataset:
The metzincins — Topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a super family of zinc‐peptidases
Authors: Stöcker Walter , Grams Frank , Reinemer Peter , Bode Wolfram , Baumann Ulrich , Gomis‐Rüth Franz‐Xaver , Mckay David B.
Published: June 2010

The three‐dimensional structures of the zinc endopeptidases human neutrophil collagenase, adamalysin II from rattle snake venom, alkaline proteinase from Pseudomonas aeruginosa, and astacin from crayfish are topologically similar, with respect to a five‐stranded β‐sheet and three α‐helices arranged in typical sequential order. The four proteins exhibit the characteristic consensus motif HEXXHXXGXXH, whose three histidine residues are involved in binding of the catalytically essential zinc ion. Moreover, they all share a conserved methionine residue beneath the active site metal as part of a superimposable “Met‐turn.” This structural relationship is supported by a sequence alignment performed on the basis of topological equivalence showing faint but distinct sequential similarity. The alkaline proteinase is about equally distant (26% sequence identity) to both human neutrophil collagenase and astacin and a little further away from adamalysin II (17% identity). The pairs astacin/adamalysin II, astacin/human neutrophil collagenase, and adamalysin II/human neutrophil collagenase exhibit sequence identities of 16%, 14%, and 13%, respectively. Therefore, the corresponding four distinct families of zinc peptidases, the astacins, the matrix metalloproteinases (matrixins, collagenases), the adamalysins/reprolysins (snake venom proteinases/reproductive tract proteins), and the serralysins (large bacterial proteases from Serratia, Erwinia, and Pseudomonas) appear to have originated by divergent evolution from a common ancestor and form a superfamily of proteolytic enzymes for which the designation “metzincins” has been proposed. There is also a faint but significant structural relationship of the metzincins to the thermolysin‐like enzymes, which share the truncated zinc‐binding motif HEXXH and, moreover, similar topologies in their N‐terminal domains.
Structural diversity in a conserved cholera toxin epitope involved in ganglioside binding
Authors: Shoham Menachem , Scherf Tali , Anglister Jacob , Levitt Michael , Merritt Ethan A. , Hol Wim G.J.
Published: June 2010

Cholera is a widespread disease for which there is no efficient vaccine. A better understanding of the conformational rearrangements at the epitope might be very helpful for the development of a good vaccine. Cholera toxin (CT) as well as the closely related heat‐labile toxin from Escherichia coli (LT) are composed of two subunits, A and B, which form an oligomeric assembly AB5. Residues 50–64 on the surface of the B subunits comprise a conserved loop (CTP3), which is involved in saccharide binding to the receptor on epithelial cells. This loop exhibits remarkable conformational plasticity induced by environmental constraints. The crystal structure of this loop is compared in the free and receptor‐bound toxins as well as in the crystal and solution structures of a complex with TE33, a monoclonal antibody elicited against CTP3. In the toxins this loop forms an irregular structure connecting a β‐strand to the central α‐helix. Ser 55 and Gin 56 exhibit considerable conformational variability in the five subunits of the unliganded toxins. Saccharide binding induces a change primarily in Ser 55 and Gin 56 to a conformation identical in all five copies. Thus, saccharide binding confers rigidity upon the loop. The conformation of CTP3 in complex with TE33 is quite different. The amino‐terminal part of CTP3 forms a β‐turn that fits snugly into a deep binding pocket on TE33, in both the crystal and NMR‐derived solution structure. Only 8 and 12 residues out of 15 are seen in the NMR and crystal structures, respectively. Despite these conformational differences, TE33 is cross‐reactive with intact CT, albeit with a thousandfold decrease in affinity. This suggests a different interaction of TE33 with intact CT.
Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions
Authors: Siddiqui Asim S. , Barton Geoffrey J.
Published: June 2010

An algorithm is presented for the fast and accurate definition of protein structural domains from coordinate data without prior knowledge of the number or type of domains. The algorithm explicitly locates domains that comprise one or two continuous segments of protein chain. Domains that include more than two segments are also located.

The algorithm was applied to a nonredundant database of 230 protein structures and the results compared to domain definitions obtained from the literature, or by inspection of the coordinates on molecular graphics. For 70% of the proteins, the derived domains agree with the reference definitions, 18% show minor differences and only 12% (28 proteins) show very different definitions. Three screens were applied to identify the derived domains least likely to agree with the subjective definition set. These screens revealed a set of 173 proteins, 97% of which agree well with the subjective definitions.

The algorithm represents a practical domain identification tool that can be run routinely on the entire structural database. Adjustment of parameters also allows smaller compact units to be identified in proteins.
On the lack of coordination between protein folding and flavin insertion in Escherichia coli for flavocytochrome b2 mutant forms Y254L and D282N
Authors: Gondry Muriel , Diêp Lê K.H. , Lederer Florence , Manson Forbes D.C. , Reid Graeme A. , Chapman Stephen K. , Scott Mathews F.
Published: June 2010

Wild‐type flavocytochrome b2 (L‐lactate dehydrogenase) from Saccharotnyces cerevisiae, as well as a number of its point mutants, can be expressed to a reasonable level as recombinant proteins in Escherichia coli (20–25 mg per liter culture) with a full complement of prosthetic groups. At the same expression level, active‐site mutants Y254L and D282N, on the other hand, were obtained with an FMN/heme ratio significantly less than unity, which could not be raised by addition of free FMN. Evidence is provided that the flavin deficit is due to incomplete prosthetic group incorporation during biosynthesis. Flavin‐free and holo‐forms for both mutants could be separated on a Blue‐Trisacryl M column. The far‐UV CD spectra of the two forms of each mutant protein were very similar to one another and to that of the wild‐type enzyme, suggesting the existence of only local conformational differences between the active holo‐enzymes and the nonreconstitutable flavin‐free forms. Selective proteolysis with chymotrypsin attacked the same bond for the two mutant holo‐enzymes as in the wild‐type one, in the protease‐sensitive loop. In contrast, for the flavin‐free forms of both mutants, cleavage occurred at more than a single bond. Identification of the cleaved bonds suggested that the structural differences between the mutant flavin‐free and holo‐forms are located mostly at the C‐terminal end of the barrel, which carries the prosthetic group and the active site. Altogether, these findings suggest that the two mutations induce an alteration of the protein‐folding process during biosynthesis in E. coli; as a result, the synchrony between folding and flavin insertion is lost. Finally, a preliminary kinetic characterization of the mutant holo‐forms showed the Km value for lactate to be little affected; kcat, values fell by a factor of about 70 for the D282N mutant and of more than 500 for the Y254L mutant, compared to the wild‐type enzyme.
Investigation of a side‐chain‐side‐chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy
Authors: Hammen Philip K. , Klevit Rachel E. , Martin Scholtz J. , William Anderson J. , Bruce Waygood E.
Published: June 2010

Anomalous NMR behavior of the hydroxyl proton resonance for Ser 31 has been reported for histidine‐containing protein (HPr) from two microorganisms: Escherichia coli and Staphylococcus aureus. The unusual slow exchange and chemical shift exhibited by the resonance led to the proposal that the hydroxyl group is involved in a strong hydrogen bond. To test this hypothesis and to characterize the importance of such an interaction, a mutant in which Ser 31 is replaced by an alanine was generated in HPr from Escherichia coli. The activity, stability, and structure of the mutant HPr were assessed using a reconstituted assay system, analysis of solvent denaturation curves, and NMR, respectively. Substitution of Ser 31 yields a fully functional protein that is only slightly less stable (ΔΔGfolding = 0.46 ± 0.15 kcal mor−1) than the wild type. The NMR results confirm the identity of the hydrogen bond acceptor as Asp 69 and reveal that it exists as the gauche− conformer in wild‐type HPr in solution but exhibits conformational averaging in the mutant protein. The side chain of Asp 69 interacts with two main‐chain amide protons in addition to its interaction with the side chain of Ser 31 in the wild‐type protein. These results indicate that removal of the serine has led to the loss of all three hydrogen bond interactions involving Asp 69, suggesting a cooperative network of interactions. A complete analysis of the thermodynamics was performed in which differences in side‐chain hydrophobicity and conformational entropy between the two proteins are accounted for. This analysis, performed in the context of information afforded by the NMR studies, indicates that this network of interactions contributes ca. 4–5 kcal mol−1 to the conformational free energy of wild‐type HPr.
Covalent control of 6‐phosphofructo‐2‐kinase/fructose‐2,6‐bisphosphatase: Insights into autoregulation of a bifunctional enzyme
Authors: Kurland Irwin J. , Pilkis Simon J.
Published: June 2010

The hepatic bifunctional enzyme, 6‐phosphofructo‐2‐kinase/fructose‐2,6‐bisphosphatase (6PF‐2‐K/Fru‐2,6‐P2ase), E.C. 2–7–1–105/E.C. 3–1–3–46, is one member of a family of unique bifunctional proteins that catalyze the synthesis and degradation of the regulatory metabolite fructose‐2,6‐bisphosphate (Fru‐2,6‐P2). Fru‐2,6‐P2 is a potent activator of the glycolytic enzyme 6‐phosphofructo‐1‐kinase and an inhibitor of the gluconeogenic enzyme fructose‐1,6‐bisphosphatase, and provides a switching mechanism between these two opposing pathways of hepatic carbohydrate metabolism. The activities of the hepatic 6PF‐2‐K/Fru‐2,6‐P2ase isoform are reciprocally regulated by a cyclic AMP‐dependent protein kinase (cAPK)‐catalyzed phosphorylation at a single NH2‐terminal residue, Ser‐32. Phosphorylation at Ser‐32 inhibits the kinase and activates the bisphosphatase, in part through an electrostatic mechanism. Substitution of Asp for Ser‐32 mimics the effects of cAPK‐catalyzed phosphorylation. In the dephosphorylated homodimer, the NH2‐ and COOH‐terminal tail regions also have an interaction with their respective active sites on the same subunit to produce an autoregulatory inhibition of the bisphosphatase and activation of the kinase. In support of this hypothesis, deletion of either the NH2‐ or COOH‐terminal tail region, or both regions, leads to a disruption of these interactions with a maximal activation of the bisphosphatase. Inhibition of the kinase is observed with the NH2‐truncated forms, in which there is also a diminution of cAPK phosphorylation to decrease the Km for Fru‐6‐P. Phosphorylation of the bifunctional enzyme by cAPK disrupts these autoregulatory interactions, resulting in inhibition of the kinase and activation of the bisphosphatase. Therefore, effects of cyclic AMP‐dependent phosphorylation are mediated by a combination of electrostatic and autoregulatory control mechanisms.
Quantitative approaches to utilizing mutational analysis and disulfide crosslinking for modeling a transmembrane domain
Authors: Lee Geoffrey F. , Hazelbauer Gerald L.
Published: June 2010

The transmembrane domain of chemoreceptor Trg from Escherichia coli contains four transmembrane segments in its native homodimer, two from each subunit. We had previously used mutational analysis and sulfhydryl cross‐linking between introduced cysteines to obtain data relevant to the three‐dimensional organization of this domain. In the current study we used Fourier analysis to assess these data quantitatively for periodicity along the sequences of the segments. The analyses provided a strong indication of α‐helical periodicity in the first transmembrane segment and a substantial indication of that periodicity for the second segment. On this basis, we considered both segments as idealized α‐helices and proceeded to model the transmembrane domain as a unit of four helices. For this modeling, we calculated helical crosslinking moments, parameters analogous to helical hydrophobic moments, as a quantitative way of condensing and utilizing a large body of crosslinking data. Crosslinking moments were used to define the relative separation and orientation of helical pairs, thus creating a quantitatively derived model for the transmembrane domain of Trg. Utilization of Fourier transforms to provide a quantitative indication of periodicity in data from analyses of transmembrane segments, in combination with helical crosslinking moments to position helical pairs should be useful in modeling other transmembrane domains.
A phage display system for studying the sequence determinants of protein folding
Authors: Gu Hongdi , Yi Qian , Bray Susan T. , Riddle David S. , Baker David , Shiau Andrew K.
Published: June 2010

We have developed a phage display system that provides a means to select variants of the IgG binding domain of peptostreptococcal protein L that fold from large combinatorial libraries. The premise underlying the selection scheme is that binding of protein L to IgG requires that the protein be properly folded. Using a combination of molecular biological and biophysical methods, we show that this assumption is valid. First, the phage selection procedure strongly selects against a point mutation in protein L that disrupts folding but is not in the IgG binding interface. Second, variants recovered from a library in which the first third of protein L was randomized are properly folded. The degree of sequence variation in the selected population is striking: the variants have as many as nine substitutions in the 14 residues that were mutagenized. The approach provides a selection for “foldedness” that is potentially applicable to any small binding protein.
Incorporation of pairwise interactions into the Lifson‐Roig model for helix prediction
Authors: Shalongo William , Stellwagen Earle
Published: June 2010

The helix/coil equilibrium of a peptide in solution can be modulated by a variety of side‐chain interactions that are not incorporated into the standard statistical mechanical models for prediction of peptide helical content. In this report, we describe a recursive formulation of the Lifson‐Roig model that facilitates incorporation of specific pairwise side‐chain interactions as well as nonspecific individual side‐chain capping interactions. Application of this extended model to a series of host/guest peptides indicates that the apparent AG value for a pairwise apolar interaction is dependent upon the spacing and orientation but not the sequential location of the participating residues. The apparent AG values for such interactions are about 40% greater than the corresponding apparent ΔΔG values obtained from difference measurements.
Domains in folding of model proteins
Authors: Abkevich V.I. , Gutin A.M. , Shakhnovich E.I.
Published: June 2010

By means of Monte Carlo simulation, we investigated the equilibrium between folded and unfolded states of lattice model proteins. The amino acid sequences were designed to have pronounced energy minimum target conformations of different length and shape. For short fully compact (36‐mer) proteins, the all‐or‐none transition from the unfolded state to the native state was observed. This was not always the case for longer proteins. Among 12 designed sequences with the native structure of a fully compact 48‐mer, a simple all‐or‐none transition was observed in only three cases. For the other nine sequences, three states of behavior — the native, denatured, and intermediate states — were found. The contiguous part of the native structure (domain) was conserved in the intermediate state, whereas the remaining part was completely unfolded and structureless. These parts melted separately from each other.
Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins
Authors: Mocz Gabor
Published: June 2010

Fuzzy cluster analysis has been applied to the 20 amino acids by using 65 physicochemical properties as a basis for classification. The clustering products, the fuzzy sets (i.e., classical sets with associated membership functions), have provided a new measure of amino acid similarities for use in protein folding studies. This work demonstrates that fuzzy sets of simple molecular attributes, when assigned to amino acid residues in a protein's sequence, can predict the secondary structure of the sequence with reasonable accuracy. An approach is presented for discriminating standard folding states, using near‐optimum information splitting in half‐overlapping segments of the sequence of assigned membership functions. The method is applied to a nonredundant set of 252 proteins and yields ˜73% matching for correctly predicted and correctly rejected residues with ˜60% overall success rate for the correctly recognized ones in three folding states: α‐helix, β‐strand, and coil. The most useful attributes for discriminating these states appear to be related to size, polarity, and thermodynamic factors. Van der Waals volume, apparent average thickness of surrounding molecular free volume, and a measure of dimensionless surface electron density can explain ˜95% of prediction results. Hydrogen bonding and hydrophobicity indices do not yet enable clear clustering and prediction.
De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology
Authors: Evans John Spencer , Chan Sunney I. , Mathiowetz Alan M. , Goddard William A.
Published: June 2010

We tested the dihedral probability grid Monte Carlo (DPG‐MC) methodology to determine optimal conformations of polypeptides by applying it to predict the low energy ensemble for two peptides whose solution NMR structures are known: integrin receptor peptide (YGRGDSP, Type II β‐turn) and S3 α‐helical peptide (YMSEDELKAAEAAFKRHGPT).

DPG‐MC involves importance sampling, local random stepping in the vicinity of a current local minima, and Metropolis sampling criteria for acceptance or rejection of new structures. Internal coordinate values are based on side‐chain‐specific dihedral angle probability distributions (from analysis of high‐resolution protein crystal structures). Important features of DPG‐MC are: (1) Each DPG‐MC step selects the torsion angles (ϕ, ψ, χ) from a discrete grid that are then applied directly to the structure. The torsion angle increments can be taken as S = 60, 30, 15, 10, or 5°, depending on the application. (2) DPG‐MC utilizes a temperature‐dependent probability function (P) in conjunction with Metropolis sampling to accept or reject new structures.

For each peptide, we found close agreement with the known structure for the low energy conformational ensemble located with DPG‐MC. This suggests that DPG‐MC will be useful for predicting conformations of other polypeptides.
A putative FAD‐binding domain in a distinct group of oxidases including a protein involved in plant development
Authors: Mushegian Arcady R. , Koonin Eugene V.
Published: June 2010

Using methods for database screening with individual protein sequences and alignment blocks, a conserved domain is delineated in a group of proteins including several FAD‐dependent oxidases. Two motifs within this domain resemble phosphate‐binding loops and may be directly involved in FAD binding. These motifs can be readily distinguished from previously described nucleotide‐binding sites using a method for database screening with position‐dependent weight matrices derived from alignment blocks. Unexpectedly, this group of known and predicted FAD‐dependent oxidases includes the product of the DIMINUTO gene, which is involved in Arabidopsis development, and its homologues from man and Mycobacterium leprae.
Explicit solvent dynamics and energetics of HIV‐1 protease flap opening and closing
Authors: Sadiq S. Kashif , De Fabritiis Gianni
Published: June 2010

An accurate description of the conformational dynamics of the β‐hairpin flaps of HIV‐1 protease is of central importance in elucidating the functional recognition of the enzyme by ligands. Using all‐atom molecular dynamics simulations in explicit solvent, with a total of 461 trajectories of ∼50 ns each, we report the closed, semiopen, open, and wide‐open flap conformation of the free wild‐type protease. The free energy of flap opening and closing from the semiopen state is 0.9 ± 0.2 and 2.4 ± 0.4 kcal/mol, respectively. The mean relaxation time of opening is ∼8 ns, in good agreement with NMR data. The explicit solvent simulations quantitatively confirm the hypothesis that the semiopen state is the dominant population in the free protease whilst fast flap tip fluctuations lead frequently to an open state. More pronounced flap rearrangements lead to a rare wide‐open state with the catalytic site completely exposed to the solvent. The structures of the different flap conformations provided herein are of general interest for improved drug design of HIV‐1 protease, in particular, the wide‐open conformation could be favored by the large Gag and GagPol polyprotein chains. Strategies that take into account multiple flap‐gating mechanisms may lead to more effective inhibitors. Proteins 2010. © 2010 Wiley‐Liss, Inc.
TEM analysis of (Ni,Fe)Si2 precipitates in Si
Authors: Langkau Sabine , Wagner Gerald , Kloess Gert , Heuer Matthias
Published: June 2010

The present article provides evidence that Fe impurity atoms in silicon can be gathered by NiSi2 precipitates at temperatures near RT via solid‐state diffusion. Mixtures of silicon and silicide grains, resulting from annealing at 800–900 °C, were analysed. High supersaturation (about 1019–1020 atoms/cm3) of metal impurities in Si was achieved locally by incorporation of nickel and iron atoms from silicide grains into silicon grains during ion milling for TEM specimen preparation. Consequently, particles with local densities of 1013–1014 precipitates/cm3 and average volumes of 10−18–10−16 cm3 formed via diffusion and precipitation. Precipitates with an irregular octahedra shape and platelet‐like habit were found at dislocations. Less frequently, precipitates with a regular octahedra shape were observed in undisturbed matrix. HRTEM images and SAD patterns demonstrate that all precipitates have NiSi2 structure. Ni contents were detected for all precipitates by EDX analysis, but accumulated amounts of Fe could only be proven for some precipitates at dislocations. Quantitative EDX‐analysis revealed Fe/(Fe + Ni) ratios between 16 and 30 at% for these ternary precipitates.
Parasitic resistance analysis of pseudovertical structure diamond Schottky barrier diode
Authors: Kumaresan R. , Umezawa H. , Shikata S.
Published: June 2010

Diamond Schottky barrier diodes (SBDs) in pseudovertical configuration were fabricated and analysed. Temperature and diode size dependence analysis of forward I–V characteristics showed an increase in current with increasing diode size, and temperature, along with a decrease in device series‐resistance (RS). It was revealed that device RS consisted of two major factors: primarily significant resistance arising from p+ layer [$R_{({\rm p}^{ + } )} $], and the other from p− layer [$R_{({\rm p}^{ - } )} $]. High temperature characteristics of SBDs in varying size exhibited a saturating limitation in the increase of forward current with increasing diode size, because the decrease in device series resistance (RS) is mainly by $R_{({\rm p}^{ - } )} $ part, whereas $R_{({\rm p}^{ + } )} $ is same irrespective of diode size, and forms to be parasitic resistance of device structure. Curve fitting analysis of experimental RS with our proposed model for $R_{({\rm p}^{ + } )} $ of varying p+ layer thickness revealed that, parasitic resistance originating from p+ layer can be decreased by increasing its thickness, towards achieving high current transport.
Noncatalytic synthesis of carbon‐nitride nanocolumns by dc magnetron sputtering
Authors: Shalaev R. V. , Ulyanov A. N. , Prudnikov A. M. , Shin G. M. , Yoo S. I. , Varyukhin V. N.
Published: June 2010

Carbon‐nitride nanocolumns were produced without catalyst metal by dc magnetron sputtering of a graphite target in pure N2 gas at pressure of 26.0 Pa on a quartz glass substrate kept at ∼200 °C. The nitrogen/carbon ratio in nanocolumns equals 0.18. Scanning electron microscopy shows that films represent dense nanostructure with columns ∼70–80 nm in diameter. The main fraction of the nitrogen is sp2‐coordinated by carbon and enters into the graphene layers as substitutional atoms; the other fraction of the nitrogen facilitates a cross‐linking between the graphene layers through sp3‐coordinated carbon.
Influence of bias voltage on the structure and deposition mechanism of diamond‐like carbon films produced by RF (13.56 MHz) CH4 plasma
Authors: Ouchabane M. , Salah H. , Herrmann M. , Tabet N. , Henda K. , Touchrift B. , Kechouane M.
Published: June 2010

Plasma enhanced chemical vapour deposition technique (PECVD) was used to grow diamond‐like carbon films using pure methane gas plasma. Structural, optical and mechanical properties of the obtained a‐C:H films were investigated as a function of bias voltage in the range 120–270 V, using different techniques. Elastic recoil detection analysis (ERDA) was employed to determine the hydrogen content and Fourier transform infrared spectroscopy (FTIR) was used to analyse the absorption of optically active hydrogen in the deposited films. The relative concentrations of sp2 and sp3 groups were determined from fitting of both X‐ray photoelectron spectroscopy (XPS) and FTIR spectra. Mechanical hardness and optical transmission were determined using nanoindentation and spectrophotometry, respectively. The results showed that the structure and properties of the films formed strongly depended on the applied bias voltage. In the range of energy considered the growth of the films was governed by a competition between both chemical and physical processes, with a dominance of physical process (subplantation) above 240 V, the energy at which more than 90% sp3 hybridization was obtained. Nanoindentation tests revealed hardness and Young's modulus of the films ranging from 12–15 and 116–155 GPa, respectively. The optical gap values deduced from the optical transmission spectra varied between 1.13 and 1.60 eV.
Analysis of the multistage phase separation reaction in Fe–25 at%Co–9 at%Mo
Authors: Eidenberger Elisabeth , Schober Michael , Schmoelzer Thomas , Stergar Erich , Staron Peter , Leitner Harald , Clemens Helmut
Published: June 2010

Differential scanning calorimetry (DSC) has been used to characterize the phase reactions during age hardening of a Fe–25 at%Co–9 at%Mo alloy. The heat of reaction which can be accounted for the development of the hardening phase was further analyzed on the basis of the Kissinger method and a fit based on the JMA model. Additionally, the precipitation sequence was studied byin situsmall‐angle neutron scattering (SANS) as well asin situX‐ray diffraction (XRD) to gain knowledge on the chemistry and crystallography of the prevailing phases. As direct imaging techniques 3D atom probe (3DAP) and high‐resolution transmission electron microscopy (HRTEM) were used. The combination of these methods revealed that hardening in the investigated alloy starts with spinodally formed Mo‐rich clusters followed by precipitation of the intermetallic µ‐phase (Fe,Co)7Mo6.
Density functional theory study of the structure and energetics of negatively charged oligopyrroles
Authors: Dai Yafei , Chowdhury Sugata , Blaisten‐Barojas Estela
Published: June 2010

First‐principles calculations are used to investigate the electronic properties of negatively charged n‐pyrrole oligomers with n = 2–18. Chains of neutral oligomers are bent, whereas the negatively charged oligomers become almost planar due to accumulation of negative charge at the end monomers. Isomers of short oligomers (n < 6) display negative electron affinity although the corresponding anions are energetically stable. For longer oligomers with n ≥ 6, the electron affinity is small and positive, slowly increasing with oligopyrrole length. Doping of 12‐pyrrole with lithium atoms shows that negative oxidation states are possible due to electron transfer from dopant to oligomer at locations close to dopant. These 12‐pyrrole regions support extra negative charge and exhibit a local structural change from benzenoid to quinoid structure in the CC backbone conjugation. Comparison between neutral and doped polypyrrole (PPy) indicates that doped polymers displays a substantial depletion of the band gap energy and the appearance of dopant‐based bands in the gap for a 50% per monomer doping level. It is predicted that Li‐doped PPy is not metallic. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Solvent polarity and dopant effect on the electronic structure of the emeraldine salt
Authors: Romanova Julia , Madjarova Galia , Tadjer Alia , Gospodinova Natalia
Published: June 2010

Quantum mechanical simulations of a variety of inorganic and organic emeraldine salts (doping agents HCl, HBr, H2SO4, MSA, BSA, and CSA) in bipolaron and polaron form with account of solvents of different polarity (chloroform, m‐cresol, and water) are reported for the first time. The models are based on tetramers, and the calculations are performed with the DFT method. The polarizable continuum model is used for the treatment of solute–solvent interaction. The effect of the different dopants and polarity of the solvents on the electronic structure and properties of the salts is evaluated and interpreted from the standpoint of the available experimental data. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Quantum‐chemical‐aided design of copolymers with tailored bandgaps and effective masses: The role of composition
Authors: Gil‐bernal Hernan , Zambrano Martha L. , Arce Julio C.
Published: June 2010

Extending a key observation made by Meyers et al. (Meyers et al., J Chem Phys, 1992, 97, 2750), a strategy for the systematic design of conducting polymers with tailor‐made bandgaps and carrier effective masses is described and quantum‐chemically implemented. Such strategy relies on the construction of alternating binary copolymers from well‐characterized parent polymers, in such a manner that those electronic parameters can be phenomenologically predicted from the composition of the copolymer. Illustrative calculations for three types of alternating copolymers built from five parent π‐conjugated polymers demonstrate the plausibility of the methodology and the internal consistency of its computational implementation. Specifically, it is shown that the bandgaps of copolymers built from parent monomers with similar chemical structures exhibit nearly linear behaviors as functions of composition, whereas the bandgaps of copolymers with dissimilar parent monomers exhibit nearly monotonic deviations from linearity. On the other hand, the electron and hole effective masses of copolymers with similar parent monomers do not show a significant dependence on composition, whereas for copolymers with dissimilar parent monomers these quantities also display nearly monotonic deviations from linearity. A qualitative rationalization of these trends in terms of the strengths of the inter‐parent–monomer interactions, which bears an intriguing resemblance to the behavior of the vapor pressure of binary solutions, is provided. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2522–2531, 2010
Quantitative structure property relationships to evaluate the photosensitizing capability in porphyrins and chlorins
Authors: Cárdenas‐Jirón Gloria I. , Santander‐Nelli Mireya , López Ramón , Menéndez María Isabel
Published: June 2010

The wavelength of the Q band (λQ) of sixteen compounds (porphyrins and chlorins) was related to eight descriptors (aromatic, electrostatic, and reactivity ones) by using quantitative structure property relationships (QSPR). These descriptors were calculated using density functional theory (DFT). No single linear regressions were found. So, our work demonstrates that λQ does not depend on a unique property; rather it is a multidimensional parameter. From twelve QSPR models obtained, four of them yielded regression coefficients over 0.8. In addition, the λQ values resulting from our QSPR models are closer to experiment than time dependent‐DFT calculated ones. It has been proved the power of QSPR models to reproduce and predict the λQ values for new porphyrin derivatives with potential capability to be used in Photodynamic Therapy. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
An ab initio quantum chemical characterization of structure and vibrational spectra of anthranilic acid
Authors: Maciel Bruna C. M. , Chaudhuri Puspitapallab
Published: June 2010

High‐level ab initio methods are used to analyze the electronic structure and vibrational spectra of the anthranilic acid or ortho‐aminobenzoic acid (o‐Abz), both in gas phase and aqueous solution. The geometries of the stationary points for the two lowest energy conformations (I and II) of o‐Abz are optimized at the MP2/6‐31++G** and MP2/aug‐cc‐pVDZ levels of theory. Conformation I is found to be more stable, less polar but more polarizable than conformation II. The same levels of calculation are used to obtain the harmonic vibrational frequencies. Polarizable continuum model method is used later to study the solvent effect on the structure and vibrational spectra of o‐Abz. Several electronic, electric, and thermodynamical properties are calculated and compared with the available experimental results and other theoretical calculations. The aqueous solution produces red‐shift for most of the vibrational frequencies but increases the intensity of vibrations for all modes of vibration of o‐Abz. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Theoretical study of the GemSin (m + n = 3) clusters
Authors: Ueno Leonardo T. , Kiohara Valéria O. , Ferrão Luiz F. A. , Marim Luiz R. , Roberto‐Neto Orlando , Machado Francisco B. C.
Published: June 2010

The main objective of this study consists in providing reliable structures, harmonic vibrational frequencies, and relative electronic energies of Si3, GeSi2, Ge2Si, and Ge3 clusters using DFT, CCSD(T), CASSCF, and MP2 methods and extended basis sets. The CCSD(T) results are extrapolation to the complete basis set (CBS) limit. For Si3 cluster, the ground‐state is a singlet (1A1) and the lowest lying electronic state is triplet state (
$ ^{3}{\rm A}^{\prime}_{2}$) separated by 0.44 kcal mol−1 at the CCSD(T)/(CBS) limit. The ground‐states of GeSi2, Ge2Si, and Ge3 clusters are also singlet state with triplet states very close energetically. Computed equilibrium geometries and vibrational frequencies are compared with previous theoretical and experimental data. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Tracking the Footprints Puzzle: The problematic persistence of science‐as‐process in teaching the nature and culture of science
Authors: Ault Charles R. , Dodick Jeff
Published: June 2010

For many decades, science educators have asked, “In what ways should learning the content of traditional subjects serve as the means to more general ends, such as understanding the nature of science or the processes of scientific inquiry?” Acceptance of these ends reduces the role of disciplinary context; the “Footprints Puzzle” and Oregon's “Inquiry Scoring Guide” illustrate this point. In the Footprints Puzzle, students are challenged to distinguish observations from inferences to learn about the nature of science or the culture of science. Oregon's Inquiry Scoring Guide separates content knowledge from inquiry skills. Given long‐standing discredit of “the” scientific method, modern views emphasize the diversity of inquiry methods and explanatory ideals across disciplines. Paleontologists, for example, reconstruct the behavior of extinct beasts from fossil footprints using methods of inquiry responsive to this aim. Figuring out dinosaur locomotion depends upon making analogies to the limb structure and behavior of extant species. The history of the Footprints Puzzle demonstrates that an enduring adherence to “a process approach” obscures how conceptualization intertwines with methodology. A discipline's concepts themselves, such as “extinction” and “geologic time,” function as tools of inquiry in distinctive and productive ways. © 2010 Wiley Periodicals, Inc. Sci Ed 94:1092–1122, 2010
Sustainable development: a role for market information systems for non‐timber forest products
Authors: Yadav Manmohan , Misra Shekhar
Published: June 2010

The extraction and exploitation of non‐timber forest products (NTFP) has been one of the major causes of the degradation of forests in developing countries like India. The highly unorganized and secretive nature of intermediary operations leads to market imperfections that are usually to the disadvantage of the collectors and cultivators. This often leads to destructive and unsustainable harvesting techniques. We provide a possible solution based on a market information system (MIS) that can help to remove market imperfections by providing information related to demand and supply to collectors and cultivators. This can be helpful in promoting sustainable harvesting and also to policy‐makers and implementation agencies. A conceptual framework related to an MIS for medicinal and aromatic plants, a subset of NTFPs, is presented. The development of such MISs can not only help to reduce unsustainable harvesting techniques but also to improve the economic condition of some of the poorest people. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
Public participation in development of small infrastructure projects
Authors: Rojanamon Pannathat , Chaisomphob Taweep , Bureekul Thawilwadee
Published: June 2010

This article presents the benefits of public participation concerning social and environmental impacts in the development of an infrastructure project. A small hydropower project, which is situated in the Nan Province, Thailand, is selected as a case study. In this study, the public participation process comprised an interview questionnaire survey and a focus group discussion; 1550 questionnaires were used to collect the opinion of local people and stakeholders regarding the project's development. Citizen dialogue and focus group discussions were conducted to provide information and to collect details of the public's opinions, concerns, and needs. The results from the questionnaires were analyzed statistically and then illustrated on maps using the Geographic Information System technique. The results from the citizens' dialogue and the focus group discussion show the benefit of giving project information to local people and bringing the needs of all groups into consideration in planning, decision‐making, and the implementation of the project. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
Mediation of tropical forest interests through empowerment to locals by means of ecological indicators
Authors: Hermansen John Eilif
Published: June 2010

Globalization and global concerns for tropical moist forests have a strong impact on the ability of local, indigenous people who live either in or close to the forest and depend upon the quality of the ecosystem resources that the forest provides for the vital necessities of their daily life. This paper explores how tension between global and local interests arises. It investigates differences in the acquisition of knowledge about the forest ecosystem and suggests ways to mediate and negotiate between the interested parties. Catchment forest management at Mount Kilimanjaro, Tanzania is the reference case for this research. Methodologically, there are challenges connected to the different positions expressed in a ‘locals – globals’ discussion about forest ecosystem services and sustainability. Within this setting, the paper argues for an ecological mediation between locals and globals based on an actor‐network and stakeholder approach. In the conclusion, the paper suggests a framework for ecological methods, where ecological semantics can be a mediator between nature (ecology) and culture (society) to evolve a common understanding for environmental sustainability and valuation of ecosystem services. From this, another framework for mediating ecological indicators is developed to keep the elements of local versus global interest, nature versus society and epistemology versus ontology together in one system. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
Procrustes methods
Authors: Gower John C.
Published: June 2010

The basic Procrustes problem is to transform a matrix to in order to match a target matrix . Matching necessitates that and have the same number of rows identified with the same entities but the columns are unrestricted in type and number. Special cases discussed are when T is an orthogonal, projection, or direction‐cosine matrix. Sometimes, both matrices are transformed and size parameters referring to isotropic and various forms of anisotropic scaling may be incorporated. Procrustes methods may be generalized to cover K transformed matrices , in which case their average (the group average) is important. Applications are in shape analysis, image analysis, psychometrics etc. Copyright © 2010 John Wiley & Sons, Inc.

This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Multivariate Analysis

Statistical and Graphical Methods of Data Analysis > Dimension Reduction
Political Representation and its Mechanisms: A Dynamic Left–Right Approach for the United Kingdom, 1976–2006
Authors: Hakhverdian Armen
Published: June 2010

Some scholars use the ‘dynamic representation’ approach to test how much current policy changes reflect past public preferences. This article tests hypotheses derived from this approach in a left–right context for the United Kingdom from 1976 to 2006. This shows that government policy on the left–right scale shifts as public preferences change (‘rational anticipation’). Secondly, a public with right-wing preferences elects the Conservatives, who pursue right-wing policies in office (‘electoral turnover’). However, popular incumbents are less likely to adjust their policy position to the public. The Westminster system is criticized for its weak link between the rulers and the ruled, but dynamic representation on the left–right scale in the United Kingdom seems to have functioned admirably in this period.
ChineseTongas British Trust: Institutional Collisions and Legal Disputes in Urban Hong Kong, 1860s–1980s
Authors: CHUNG STEPHANIE PO-YIN
Published: June 2010

By the nineteenth century, with the advance of British colonial activities, British corporate laws had been transplanted to maritime Asia with varying degrees of vigour. In British Hong Kong, these laws often clashed with native customs. Through a reconstruction of the legal disputes found in urban Hong Kong, this paper discusses how British and Chinese business traditions interacted with each other during the late nineteenth and early twentieth centuries. Before assessing the historical implications and consequences of these legal decisions, this paper will also explore whether the Chinese institution oftongis compatible with British law in urban Hong Kong.
Allergic disease: understanding howin uteroevents set the scene
Authors: Prescott Susan L.
Published: June 2010

Events and exposures in pregnancy can have critical effects on fetal development with lasting implications for subsequent health and disease susceptibility. There is growing interest in how modern environmental changes influence fetal immune development and contribute to the recent epidemic of allergy and other immune disorders. Rising rates of allergic disease in early infancy, together with pre-symptomatic differences in immune function at birth, suggest that antenatal events play a predisposing role in the development of disease. A number of environmental exposures in pregnancy can modify neonatal immune function including diet, microbial exposure and maternal smoking, and there is emerging evidence from animal models that these factors may have epigenetic effects on immune gene expression and disease susceptibility. Furthermore, functional genetic polymorphisms also alter individual vulnerability to the effects of these environmental exposures, highlighting the complexity of gene–environmental interactions in this period. All these observations underscore the need for ongoing research to understand the pathogenesis and rising incidence of disease in the hope of better strategies to reverse this.
Default knowledge, time pressure, and the theory-theory of concepts
Authors: Blanchard Thomas
Published: June 2010

I raise two issues for Machery's discussion and interpretation of the theory-theory. First, I raise an objection against Machery's claim that theory-theorists take theories to be default bodies of knowledge. Second, I argue that theory-theorists' experimental results do not support Machery's contention that default bodies of knowledge include theories used in their own proprietary kind of categorization process.
Carving nature at its joints using a knife called concepts
Authors: Couchman Justin J. , Boomer Joseph , Coutinho Mariana V. C. , Smith J. David
Published: June 2010

That humans can categorize in different ways does not imply that there are qualitatively distinct underlying natural kinds or that the field of concepts splinters. Rather, it implies that the unitary goal of forming concepts is important enough that it receives redundant expression in cognition. Categorization science focuses on commonalities involved in concept learning. Eliminating “concept” makes this more difficult.
An additional heterogeneity hypothesis
Authors: Dove Guy
Published: June 2010

In this commentary, I make three points concerning Machery's response to neo-empiricism. First, his methodological critique fails to remove the threat that neo-empiricism poses to his conceptual eliminativism. Second, evidence suggests that there are multiple semantic codes, some of which are not perceptually based. Third, this representational heterogeneity thwarts neo-empiricism but also raises questions with respect to how we should “do without concepts.”
The faux, fake, forged, false, fabricated, and phony: Problems for the independence of similarity-based theories of concepts
Authors: Jacobson Anne J.
Published: June 2010

Some things in our environment are not what they seem, and they provide a challenge to theories of concepts that emphasize similarity. Section 1 of my commentary explores a dilemma this situation creates for Machery. Section 2 describes a more general problem for prototype and exemplar theories. Section 3 locates a place for similarity-based concepts, and indicates an alternative to Machery's thesis.
The function and representation of concepts
Authors: Khemlani Sangeet S. , Goodwin Geoffrey
Published: June 2010

Machery has usefully organized the vast heterogeneity in conceptual representation. However, we believe his argument is too narrow in tacitly assuming that concepts are comprised of only prototypes, exemplars, and theories, and also that its eliminative aspect is too strong. We examine two exceptions to Machery's representational taxonomy before considering whether doing without concepts is a good idea.
From conceptual representations to explanatory relations
Authors: Lombrozo Tania
Published: June 2010

Machery emphasizes the centrality of explanation for theory-based approaches to concepts. I endorse Machery's emphasis on explanation and consider recent advances in psychology that point to the “heterogeneity” of explanation, with consequences for Machery's heterogeneity hypothesis about concepts.