bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small‐angle neutron scattering investigation of structural changes in nafion membranes induced by swelling with various solvents
Authors: Young Sandra K. , Trevino S. F. , Beck Tan Nora C. 
Published: October 2004

AbstractThe structure of Nafion‐117 perfluorosulfonate ionomer membranes was investigated with small‐angle neutron scattering techniques. Structural changes induced by the swelling of the membranes with water, alcohols, and dipolar, aprotic solvents were monitored at solvent‐swelling levels ranging from approximately 2 vol % to greater than 50 vol %. Membranes swollen up to approximately 50 vol % solvent exhibited two scattering maxima, one known to be associated with ionic regions of the membrane structure and one known to be associated with correlation distances between crystalline regions in the membrane structure. The positions of both maxima shifted toward lower scattering vector values as the solvent content in the membrane increased. The shift in the position of both maxima was linearly related to the solvent volume fraction in the membrane. The Bragg spacings corresponding to both the ionic‐feature scattering maximum and the crystalline‐feature scattering maximum were plotted versus the solvent volume fraction in the membranes, and the data fit with linear regression. The slopes associated with the curves of the spacing versus the solvent volume fraction were greater for the crystalline‐feature spacing than for the ionic‐feature spacing for all solvents other than water; this was indicative of preferential segregation of nonaqueous solvents into regions of the structure not directly associated with the ionic scattering maximum. © 2002 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 387–400, 2002; DOI 10.1002/polb.10092
Morphological study on water‐borne conducting polyaniline‐poly(ethylene oxide) blends
Authors: Wang Yanju , Wang Xianhong , Li Ji , Zhang Hongfang , Mo Zhishen , Jing Xiabin , Wang Fosong 
Published: October 2004

AbstractConducting polyaniline‐poly(ethylene oxide) blends were prepared from their aqueous solutions. The blends displayed an electrical conductivity percolation threshold as low as 1.83 wt % of polyaniline loading. As demonstrated by scanning electron microscopy, polarized optical microscopy, and wide‐angle X‐ray diffraction studies, the conducting polyaniline took a fibrillar morphology in the blend, and it existed only in the amorphous phase of poly(ethylene oxide). A three‐phase model combining morphological factors instead of a two‐phase model was proposed to explain the low‐conductivity percolation threshold. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 605–612, 2002; DOI 10.1002/polb.10114
Interaction parameters of crystalline/crystalline polypropylene/poly(butene‐1) blends: Effect of molecular fractionation
Authors: Shieh Yeong‐Tarng , Lee Mao‐Song , Chen Show‐An 
Published: October 2004

AbstractCompatibility of crystalline/crystalline polypropylene (PP)/poly(butene‐1) (PB‐1) blends was investigated via the method of equilibrium melting temperature depression followed by determining the polymer–polymer interaction parameter (χ) using the Nishi–Wang equation. The composition variation of the equilibrium melting temperatures of blends (T) was determined with the Hoffman–Weeks plot. The T and its variation with the blend composition depended on the crystallization temperature range. The morphological effect of the blend composition was not a contribution factor for the T depressions of PP and PB‐1 in the blends. The interplay of the dilution effect and molecular fractionation effect of the amorphous component on crystallization of the crystalline component in the blends governed the relation of T with the blend composition. The calculated χ values were negative depending on the blend composition. The negative χ values suggested that PP and PB‐1 in the amorphous region were compatible. The composition variation of the χ values was attributed to the molecular fractionation effect during crystallization. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 638–648, 2002; DOI 10.1002/polb.10125
Cystic fibrosis: Keeping it in the family*
Authors: Crowley Suzanne , Bush Andrew 
Published: October 2004

AbstractNearly all men with cystic fibrosis (CF) are infertile, although assisted conception has allowed an increasing number of women with CF to become pregnant. We report on the case of a couple investigated for infertility who conceived a child with CF. The father had previously undergone a laparotomy for meconium peritonitis as a neonate, and the mother had recently been given a diagnosis of asthma. Both parents fulfilled the United States Cystic Fibrosis Foundation diagnostic criteria for cystic fibrosis. We discuss the mild CF phenotype and the impact of the diagnosis on this family. Pediatr Pulmonol. 2002; 33:158–161. © 2002 Wiley‐Liss, Inc.
Effects of intrabronchial foreign body retention
Authors: Yildizeli Bedrettin , Zonüzi Ferzat , Yüksel Mustafa , Kodalli Nihat , Çakalağaoğlu Fulya , Küllü Sevgi 
Published: October 2004

AbstractUnrecognized bronchial foreign bodies (Fbs) cause irreversible changes in the airways. However, the exact course of these changes is not well‐known. We developed an animal model of bronchial obstruction to radiologically and histopathologically assess the development of postobstructive pulmonary changes. A piece of peanut was placed in the airways of 21 rabbits through a 2.5‐mm rigid bronchoscope. Animals were divided into three groups (groups I–III) that were sacrificed on day 3,10, and 30 after Fb placement, respectively.Prior to sacrifice, since there were no differences between the groups prior to Fb placement, computerized tomography (CT) of the lung was taken, and the lungs were harvested for histologic analysis under light microscope. In group I, leukocyte infiltration around the bronchial wall (P = 0.0003) and edema (P = 0.0384) around the alveolar septa were the predominant histological findings. The CT scan was normal. In group II and group III, increased amounts of mononuclear cells and macrophage infiltration around the bronchial wall were observed (P = 0.0008, P = 0.0409, respectively). There were no differences in presence of granuloma formation, emphysema, atelectasis, or thickness of alveolar septa among the three groups. The CT scan of group II showed consolidations plus minimal bronchial dilatation in the involved lung of the rabbits (P not significant). Bronchial cartilage destruction was seen in 4 out of 7 rabbits in group III (P = 0.0071).We conclude that 30‐day retention of intrabronchial peanut caused bronchial cartilage destruction and fibrosis that were attributed as bronchiectatic changes in the airways of the lung parenchyma. Therefore, any case with suspected foreign body aspiration should be treated immediately to prevent possible irreversible changes of the lungs. Pediatr Pulmonol. 2002; 33:362–367. © 2002 Wiley‐Liss, Inc.
A clade of trypsins found in cold‐adapted fish
Authors: Roach Jared C. 
Published: October 2004

AbstractA clade of trypsins, known as group III, is identified by phylogenetic analysis. These trypsins occur in fish that spend all or part of their lives at temperatures near 0°C and may represent extreme psychrophilic enzymes. A principal component analysis of amino acid compositions distinguishes group III from mesophilic trypsins, as do molecular trees and multidimensional scaling of molecular sequence distances. The primary sequences of group III trypsins, in conjunction with the known structures of mesophilic trypsins, permit insight into function and mechanisms of cold adaption. The techniques employed are broadly applicable to phylogenies characterized by a markedly different, or “fast‐evolving,” clade. An updated lactate dehydrogenase molecular tree illustrates an additional fast‐evolving clade. Proteins 2002;47:31–44. © 2002 Wiley‐Liss, Inc.
Protein–protein docking of electron transfer complexes: Cytochromecoxidase and cytochromec
Authors: Flöck Dagmar , Helms Volkhard 
Published: October 2004

AbstractElectron transferring protein complexes form only transiently and the crystal structures of electron transfer protein–protein complexes involving cytochromeccould so far be determined only for the pairs of yeast cytochromecperoxidase (CcP) with iso‐1‐cytochromec(iso‐1‐cytc) and with horse heart cytochromec(cytc). This article presents models from computational docking for complexes of cytochromecoxidase (COX) fromParacoccus denitrificanswith horse heart cytochromec, and with its physiological counterpart cytochromec552 (c552). Initial docking is performed with the FTDOCK program, which permits an exhaustive search of translational and rotational space. A filtering procedure is then applied to reduce the number of complexes to a manageable number. In a final step of structural and energetic refinement, the complexes are optimized by rigid‐body energy minimization with the molecular mechanics package CHARMM. This methodology was first tested on the CcP:iso‐1‐cytccomplex, in which the complex with the lowest CHARMM energy has an RMSD from the crystal structure of only 1.8 Å (Cαcarbon atoms). Notably, the crystal conformation has an even lower energy. The same procedure was then applied to COX:cytcand COX:c552. The lowest‐energy COX:cytccomplex is very similar to a docking model previously described for the complex of bovine cytochromecoxidase with horse heart cytochromec. For the COX:c552 complex, cytochromec552 is found in two different orientations, depending on whether it is docked against COX from a two‐subunit or from a four‐subunit crystal structure, respectively. Both conformations are discussed critically in the light of the available experimental data. Proteins 2002;47:75–85. © 2002 Wiley‐Liss, Inc.
Ab initio prediction of protein structure using LINUS
Authors: Srinivasan Rajgopal , Rose George D. 
Published: October 2004

AbstractLINUS is an ab initio method for the prediction of protein structure based on simple physical principles. Here we report the performance of LINUS at CASP4, a communitywide experiment to predict protein structure in which participants are blinded to the structures they seek to predict. We submitted 13 predictions for this experiment. The best four are described in detail, together with an assessment of secondary structure prediction for the entire set. Coordinates for all predictions are available from the CASP web site (http://predictioncenter.llnl.gov). It should be emphasized that our use of the descriptor “ab initio” is unequivocal: the sole input into these simulations is the amino acid sequence. Proteins 2002;47:489–495. © 2002 Wiley‐Liss, Inc.
Emergence of highly designable protein‐backbone conformations in an off‐lattice model
Authors: Miller Jonathan , Zeng Chen , Wingreen Ned S. , Tang Chao 
Published: October 2004

AbstractDespite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino acid sequences for which they represent the unique lowest energy state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off‐lattice model. The highly designable conformations of a chain of 23 amino acids are identified and found to be remarkably insensitive to model parameters. Although some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix‐turn‐helix motifs, others do not resemble known folds and may be candidates for novel fold design. Proteins 2002;47:506–512. © 2002 Wiley‐Liss, Inc.
ConsDock: A new program for the consensus analysis of protein–ligand interactions
Authors: Paul Nicodème , Rognan Didier 
Published: October 2004

AbstractProtein‐based virtual screening of chemical libraries is a powerful technique for identifying new molecules that may interact with a macromolecular target of interest. Because of docking and scoring limitations, it is more difficult to apply as a lead optimization method because it requires that the docking/scoring tool is able to propose as few solutions as possible and all of them with a very good accuracy for both the protein‐bound orientation and the conformation of the ligand. In the present study, we present a consensus docking approach (ConsDock) that takes advantage of three widely used docking tools (Dock, FlexX, and Gold). The consensus analysis of all possible poses generated by several docking tools is performed sequentially in four steps: (i) hierarchical clustering of all poses generated by a docking tool into families represented by a leader; (ii) definition of all consensus pairs from leaders generated by different docking programs; (iii) clustering of consensus pairs into classes, represented by a mean structure; and (iv) ranking the different means starting from the most populated class of consensus pairs. When applied to a test set of 100 protein–ligand complexes from the Protein Data Bank, ConsDock significantly outperforms single docking with respect to the docking accuracy of the top‐ranked pose. In 60% of the cases investigated here, ConsDock was able to rank as top solution a pose within 2 Å RMSD of the X‐ray structure. It can be applied as a postprocessing filter to either single‐ or multiple‐docking programs to prioritize three‐dimensional guided lead optimization from the most likely docking solution. Proteins 2002;47:521–533. © 2002 Wiley‐Liss, Inc.
NADH interactions with WT‐ and S94A‐acyl carrier protein reductase from Mycobacterium tuberculosis: An ab initio study
Authors: Pantano Sergio , Alber Frank , Lamba Doriano , Carloni Paolo 
Published: October 2004

AbstractWe present an ab initio molecular dynamics study of the complex between acyl carrier protein reductase InhA from M. tuberculosis and isonicotinic acid hydrazide‐NADH. We focus on wild‐type (WT) InhA and a mutant causing drug resistance (S94A) for which structural information is available (Rozwarski et al., 1998;279:98–102; Dessen et al., 1995;267:1638–1641). Our calculations suggest that the water‐mediated H‐bond interactions between Ser94 side chain and NADH, present in WT InhA X‐ray structure, can be lost during the dynamics. This conformational change is accompanied by a structural rearrangement of Gly14. The calculated structure of WT is rather similar to the X‐ray structure of the S94A mutant in terms of geometrical parameters and chemical bonding. Further evidence for the mobility of Ser94 is provided by a 1‐ns‐long classical molecular dynamics on the entire protein. The previously unrecognized high mobility of Ser94 can provide a rationale of the small change in free binding energies on passing from WT to S94A InhA. Proteins 2002;47:62–68. © 2002 Wiley‐Liss, Inc.
Synthesis, crystal structure and herbicidal activity of mimics of intermediates of the KARI reaction
Authors: Wang Bao‐Lei , Duggleby Ronald G , Li Zheng‐Ming , Wang Jian‐Guo , Li Yong‐Hong , Wang Su‐Hua , Song Hai‐Bin 
Published: October 2004

AbstractTwo mimics of the intermediate in the reaction catalyzed by ketol‐acid reductoisomerase (KARI) were synthesized. Their structures were established on the basis of elemental analyses, IR, 1H NMR and GC/mass detector. The crystal structure of compound 2 was found to be a substituted dioxane, formed by the condensation of two molecules. The two compounds showed some herbicidal activity on the basis of tests using rape root and barnyard grass growth inhibition. However, the herbicidal effect was weaker in greenhouse tests. Copyright © 2004 Society of Chemical Industry
Antifungal activity of limonoids from Khaya ivorensis
Authors: Abdelgaleil Samir AM , Hashinaga Fumio , Nakatani Munehiro 
Published: October 2004

AbstractChemical investigation of the diethyl ether extract of the stem bark of Khaya ivorensis A Chev (Meliaceae) afforded ten limonoids of angolensates, ring D‐opened limonoids and mexicanolides. The structures of the limonoids isolated were determined by comparison of their 1H and 13C NMR data with those reported in the literature. These compounds were evaluated for their antifungal activity against the plant pathogenic fungus Botrytis cinerea Pers. Methyl 6‐hydroxyangolensate and 3,7‐dideacetylkhivorin were also tested for their antifungal and antibacterial activities on several fungal and bacterial species. Methyl angolensate and 1,3,7‐trideacetylkhivorin displayed the highest antifungal activity against B cinerea, with respectively 62.8 and 64.0% mycelial growth inhibition at 1000 mg litre−1, and 73.3 and 68.6% mycelial growth inhibition at 1500 mg litre−1. 3,7‐Dideacetylkhivorin showed stronger antifungal and antibacterial activities than methyl 6‐hydroxyangolensate against all of the test fungi and bacteria except Penicillium expansum Link. This is the first report on the antifungal and antibacterial effects of these limonoids. Structure‐antifungal activity relationships of the limonoids isolated are discussed. Copyright © 2004 Society of Chemical Industry
Sorption in reconstituted waxes of homologous series of alcohol ethoxylates and n‐alkyl esters and their effects on the mobility of 2,4‐dichlorophenoxybutyric acid
Authors: Šimáňová Eva , Shi Tuansheng , Schönherr Jörg , Schreiber Lukas 
Published: October 2004

AbstractEquilibrium sorption of n‐alkyl esters (dimethyl suberate, diethyl suberate, diethyl sebacate, dibutyl suberate and dibutyl sebacate) and monodisperse alcohol ethoxylates (diethylene glycol, tetraethylene glycol, pentaethylene glycol, hexaethylene glycol and octaethylene glycol monododecyl ether) between the reconstituted cuticular waxes of Stephanotis floribunda Brongn (Madagascar jasmine) or Hordeum vulgare L (barley) leaves and an external aqueous receptor solution was determined. Logarithms of the wax/receptor partition coefficient (Kwax/rec) of the n‐alkyl esters increased linearly with the number of C‐atoms. With alcohol ethoxylates, log Kwax/rec decreased linearly with the number of ethylene oxide units. For both groups of compounds, Kwax/rec increased with increasing lipophilicity. The values of Kwax/rec in Stephanotis wax were between 5 and 16 times higher than in barley wax. It is argued that this difference was due to different chemical composition and crystallinity of the waxes. Mobility of [14C]2,4‐dichlorophenoxybutyric acid (2,4‐DB) in reconstituted Stephanotis and barley wax was increased by a factor of 2–8 by both n‐alkyl esters and alcohol ethoxylates. Effects on the mobility of 2,4‐DB were linearly related to the internal concentrations of n‐alkyl esters and alcohol ethoxylates in reconstituted Stephanotis or barley wax. At the same internal concentrations the effect of n‐alkyl esters on the mobility of 2,4‐DB in wax exceeded that of alcohol ethoxylates by between 1 and 2 orders of magnitude. Results are discussed in relation to formulating systemic pesticides. Copyright © 2004 Society of Chemical Industry
Use of promolecular ASA density functions as a general algorithm to obtain starting MO in SCF calculations
Authors: Amat Lluís , Carbó‐Dorca Ramon 
Published: October 2004

AbstractAtomic shell approximation (ASA) constitutes a way to fit first‐order density functions to a linear combination of spherical functions. The ASA fitting method makes use of positive definite expansion coefficients to ensure appropriate probability distribution features. The ASA electron density is sufficiently accurate for the practical implementation of quantum similarity measures, as was proved in previous published work. Here, a new application of the ASA density formalism is analyzed, and employed to obtain an initial guess of the density matrix for SCF procedures. The number of cycles needed to assess the convergence criterion in electronic energy calculations appears comparable to or less than those obtained by other means. Several molecular structures of different classes, including organic systems and metal complexes, were chosen as representative test cases. In addition, an ASA basis set for atoms Sc‐Kr fitted to an ab initio 6‐311G basis set is also presented. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Hellmann–Feynman theorem near the threshold
Authors: Pupyshev Vladimir I. 
Published: October 2004

AbstractThe features of the spectrum structure are considered for situations where some parameter λ of the N‐electron Hamiltonian reaches the threshold value η under which the discrete energy level falls into the continuous spectrum. The electron density properties are also studied. It is proved that for a sequence of the wave functions converging in energy to the lower bound of the continuous spectrum as λ approaches η the corresponding sequence of the electron densities converges to the density of the (N − 1)‐electron ground state. The results generalize the Hellmann–Feynman theorem for the cases where only the one‐side energy derivatives exist or there is no limiting wave function. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
NANOPACK: Parallel codes for semiempirical quantum chemical calculations of large systems in the sp‐ and spd‐basis
Authors: Berzigiyarov Parvaz K. , Zayets Valentin A. , Ginzburg Ilya Ya. , Razumov Vladimir F. , Sheka Elena F. 
Published: October 2004

AbstractA parallel implementation of the conventionally used NDDO (MNDO, AM1, PM3, CLUSTER‐Z1) and modified NDDO‐WF (CLUSTER‐Z2) techniques for semiempirical quantum chemical calculations of large molecular systems in the sp‐ and spd‐basis, respectively, is described. The atom‐pair distribution of data over processors forms the basis of the parallelization. The technological aspects of designing scalable parallel calculations on supercomputers (using ScaLAPACK and MPI libraries) are discussed. The scaling of individual algorithms and the entire package was carried out for model systems with 894, 1920, and 2014 atomic orbitals. The package speed‐up provided by different multiprocessor systems involving a cluster of Intel PIII processors, Alpha‐21264‐processor‐built machine MBC‐1000M, and Cray‐T3E is analyzed. The effect of computer characteristics on the package performance is discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Unconventional consideration of the symmetry properties—New techniques and computer codes: Application for high‐temperature superconductors
Authors: Liverts E. Z. 
Published: October 2004

AbstractThe conventional technique for solving the equations of quantum chemistry is extended to the structures possessing certain symmetries. This proposal allows the release of unoccupied electronic states located lower than the ground‐state Fermi level of a specific system. Such states can be treated as “spectral holes.” Application of this technique, in particular, when calculating the electronic structure of the high‐temperature superconductor (HTSC) compound YBa2Cu3O7δ (0 ≤ δ ≤ 1) results in the following. For all versions of the examined charge distributions over a crystal lattice, spectral holes of high spatial localization are found. The “spatial spectral holes” are located mainly at the py‐orbitals of the apex oxygens. These orbitals overlap and form linear chains that are parallel to the known Cu(1)O chains, disappearing when δ is close to 1. One can suppose that the linear chains of the overlapping hole states form a “superconducting channel.” Some other parameters closely related to the critical characteristics of HTSC materials are also calculated. The calculations show that the superconducting channel is broken when the oxygen chain atoms O(1) are removed (δ > 0). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002