bluuebunny/crossref_metadata_2025_split huggingface dataset:
Force‐field parameters for the simulation of tetrahedral intermediates of serine hydrolases
Authors: Otte Nikolaj , Bocola Marco , Thiel Walter 
Published: June 2008

AbstractCHARMM force‐field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6‐31G*) interaction energies of complexes between water and the model compound 1,1‐dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6‐311+G*//B3LYP/6‐31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6‐31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Relation between chemical bonding and exchange coupling approaches to the description of ordering in itinerant magnets
Authors: Samolyuk German D. , Miller Gordon J. 
Published: June 2008

AbstractTwo different approaches to explain and predict the types of magnetic ordering in the 3d metal series and their compounds are reviewed. According to the crossing theorem of Heine and Samson, the effective exchange coupling changes sign from negative (antiferromagnetic ordering) in the middle of 3d band to positive (ferromagnetic ordering) for the nearly empty or nearly filled d band cases. On the other hand, the analytical properties of the Crystal Orbital Hamilton Population, which is a measure of chemical bonding, predict only one crossing at the center of the band in the region of nonbonding states. Thus intermetallic compounds with Fermi energies falling within metal–metal nonbonding states are ordered antiferromagnetically whereas they order ferromagnetically when the Fermi levels fall within antibonding states. The general character of these dependencies is demonstrated for various examples containing the magnetically active 3d metals, examples that include the bcc metals, Heusler alloys, and a series of novel quaternary intermetallic borides. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions
Authors: Sakharov Dmitri V. , Lim Carmay 
Published: June 2008

AbstractThe question whether molecular dynamics (MD) simulations can yield reliable structural and dynamical properties of metalloproteins depend on the accuracy of the force field, i.e., the potential energy function (PEF) and associated parameters modeling the interactions of the metal ion of interest with water and protein ligands. Previously, we had developed a CTPOL PEF for protein simulations of Zn2+ bound to Cys− and/or His0 that includes charge transfer and local polarization effects as well as metal van der Waals parameters that reproduce the structural and thermodynamical properties of 22 dications. Here, we evaluate if the CTPOL PEF and the new metal parameters (referred to as the CTPOLa force field) can be applied to proteins containing polynuclear metal‐binding sites and heavy toxic metal ions, using the CdZn2‐Cys9 β‐domain of rat liver metallothionein‐2 and the Hg2+‐bound 18‐residue peptide from MerP as test systems. Using the CTPOLa force field, simulations of the β‐domain of rat liver metallothionein‐2 totaling 19 ns could preserve the experimentally observed CdZn2–Cys9 complex geometry and overall protein structure, whereas simulations neglecting charge transfer and local polarization effects could not. However, the CTPOLa force field cannot reproduce the experimentally observed linear bicoordination of Hg2+ in the MerP peptide without adding an angular restraint to the CTPOL PEF to correct the angle distribution about Hg2+. Thus, the force fields presented herein for the group IIB metal ions can be applied to simulation studies of proteins containing polynuclear metal‐binding sites and heavy metal ions in aqueous solution. PEF neglecting charge transfer and local polarization effects in conjunction with vdW parameters adjusted to reproduce the structural and thermodynamical properties of only the metal ion in question could not yield an accurate representation of the metal‐binding site and overall protein structure. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs
Authors: Chen Ke , Jiang Yingfu , Du Li , Kurgan Lukasz 
Published: June 2008

AbstractA computational model, IMP‐TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best‐performing existing models, IMP‐TYPE reduces the error rates of these methods by 19 and 34% for two out‐of‐sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP‐TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature‐based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Lipase‐catalyzed synthesis of polylactic acid: an overview of the experimental aspects
Authors: Lassalle V L , Ferreira M L 
Published: June 2008

AbstractBACKGROUND: Enzymes have received increasing attention as biocatalysts. The poly(lactic) acid (PLA) has been widely employed in biomedical applications and PLA synthesis by a ‘green route’ is of particular interest. Here the aim is to prepare PLA using lipases, focusing on optimization of the procedure. The effects of the type and concentration of lipase, type of reaction, solvent, and time on the recovery of solid polyester, conversion rate and molecular weight have been explored. Pseudomonas cepacia (PCL), Porcine pancreatic lipase (PPL) and immobilized CAL‐B were used as biocatalysts.RESULTS: CAL‐B was the most effective biocatalyst, with 60% LA conversion and 55% recovered solid polymer; PCL and PPL gave rise to poor recovery of polymer. A novel thermal treatment was successfully employed to enhance the molecular weight Mn of PLA.CONCLUSIONS: This work offers a set of optimal conditions to synthesize PLA as a function of the lipase used. Information of this nature is currently not available in the literature, thus the findings here are a valuable tool for any researcher in this topic and a state‐of‐the‐art contribution in terms of the best biocatalyst and the best conditions for PLA synthesis. Copyright © 2008 Society of Chemical Industry
HPTLC/DESI‐MS imaging of tryptic protein digests separated in two dimensions
Authors: Pasilis Sofie P. , Kertesz Vilmos , Van Berkel Gary J. , Schulz Michael , Schorcht Susanne 
Published: June 2008

AbstractDesorption electrospray ionization mass spectrometry (DESI‐MS) was demonstrated as a method to detect and identify peptides from two‐dimensional separations of cytochrome c and myoglobin tryptic digests on ProteoChrom HPTLC Cellulose sheets. Data‐dependent tandem mass spectra were acquired during lane scans across the TLC plates. Peptides and the corresponding proteins were identified using a protein database search software. Two‐dimensional distributions of identified peptides were mapped for each separated protein digest. Sequence coverages for cytochrome c and myoglobin were 81 and 74%, respectively. These compared well with those determined using the more standard HPLC/ESI‐MS/MS approach (89 and 84%, respectively). Preliminary results show that use of more sensitive instrumentation has the potential for improved detection of peptides with low Rf values and improvement in sequence coverage. However, less multiple charging and more sodiation were seen in HPTLC/DESI‐MS spectra relative to HPLC/ESI‐MS spectra, which can affect peptide identification by MS/MS. Methods to increase multiple charging and reduce the extent of sodiation are currently under investigation. Published in 2008 by John Wiley & Sons, Ltd.
Low LC‐MS/MS detection of glycopeptides released from pmol levels of recombinant erythropoietin using nanoflow HPLC‐chip electrospray ionization
Authors: Groleau Paule Emilie , Desharnais Philippe , Coté Linda , Ayotte Christiane 
Published: June 2008

AbstractThe test used by anti‐doping laboratories to detect the misuse of recombinant erythropoietin (rhEPO) is based on its different migration pattern on isoelectric focusing (IEF) gel compared with the endogenous human erythropoietin (hEPO) that can possibly be explained by structural differences. While there is definitely a need to identify those differences by LC‐MS/MS, the extensive characterization that was achieved for the rhEPO was never performed on human endogenous EPO because its standard is not available in sufficient amount. The goal of this study was to develop an analytical method to detect pmol amounts of N‐linked and O‐linked glycopeptides of the recombinant hormone as a model. Using a nanoflow HPLC‐Chip electrospray ionization/ion trap mass spectrometer, the diagnostic ion at m/z 366 of oligosaccharides was monitored in the product ion spectra to identify the four theoretical glycosylation sites, Asn24, Asn38, Asn83 and Ser126, respectively, on glycopeptides 22–37, 38–55, 73–96 and 118–136. With 3 pmol of starting material applied on Chip, only the desialylated N‐glycopeptides 22–37 and 38–55/38–43 could be observed, and of all the glycan isoforms, those with the smaller structures were predominantly detected. While the preservation of the sialic acid moieties decreased the detection of all the N‐glycopeptides, it allowed a more extensive characterization of the O‐linked glycopeptide 118–136. The technique described herein provides a mean to detect glycopeptides from commercially available pharmaceutical preparations of rhEPO with the sensitivity required to analyze pmol amounts of hEPO, which could ultimately lead to the identification of structural differences between the recombinant and the human forms of the hormone. Copyright © 2008 John Wiley & Sons, Ltd.
Hair analysis of anabolic steroids in connection with doping control—results from horse samples
Authors: Anielski P. 
Published: June 2008

AbstractDoping control of anabolic substances is normally carried out with urine samples taken from athletes and horses. Investigation of alternative specimens, e.g. hair samples, is restricted to special cases, but can also be worthwhile, in addition to urine analysis. Moreover, hair material is preferred in cases of limited availability or complicated collection of urine samples, e.g. from horses.In this work, possible ways of interpretation of analytical results in hair samples are discussed and illustrated by practical experiences. The results demonstrate the applicability of hair analysis to detect anabolic steroids and also to obtain further information about previous abuse. Moreover, the process of incorporation of steroids into hairs is described and the consequences on interpretation are discussed, e.g. on the retrospective estimation of the application date.The chosen examples deal with the detection of the anabolic agent testosterone propionate. Hair samples of an application study, as well as a control sample taken from a racing horse, were referred to. Hair material was investigated by a screening procedure including testosterone, nandrolone and several esters (testosterone propionate, phenylpropionate, decanoate, undecanoate, cypionate; nandrolone decanoate, dodecanoate and phenylpropionate; limits of detection (LODs) between 0.1 and 5.0 pg/mg). Confirmation of testosterone propionate (LOD 0.1 pg/mg) was carried out by an optimised sample preparation. Trimethylsilyl (TMS) and tert‐butyl dimethylsilyl derivatives were detected by gas chromatography–high‐resolution mass spectrometry (GC‐HRMS) and gas chromatography–tandem mass spectrometry (GC‐MS/MS). Copyright © 2008 John Wiley & Sons, Ltd.
Seasonal variability in the response of the airflow characteristics to the changes in the macro‐scale westerly flow intensity over Europe, 1971–2000
Authors: Marosz Michal 
Published: June 2008

AbstractThe aim of the research was to identify the seasonal variability of correlation between the air motion characteristics and common zonal circulation index (Rossby's Index). Air flow characteristics comprised divergence and vorticity. The spatial coverage of the research was the so called Euro‐Atlantic Region covering parts of North Atlantic and Europe (40W–40E, 35N–75N). Temporal extent was 1971–2000 thus matching the latest WMO normal period. The data used was the components of the wind vector (u—zonal component, v—meridional component) and geopotential heights (hgt) from NCEP/NCAR Reanalysis. The response of the vorticity field is apparent and the greatest variability is noted at 1000 hPa. The mid and upper levels in the troposphere reveal quite homogenous response of vorticity to the macro‐scale forcing. The response of the divergence field is also apparent though more complex in the vertical profile of the troposphere. The analysis of correlation was followed by the description of annual as well as seasonal shape of vorticity and divergence fields in the extremes of Rossby Index. Copyright © 2008 Royal Meteorological Society
How business‐education partnerships are building a diverse science and technology workforce: Lessons from Bayer
Authors: Molnar Attila 
Published: June 2008

AbstractThe CEO of Bayer Corporation proposes business‐education partnerships in K–12 schools as a necessary action for building a stronger, diverse pipeline of future science and technology workers—and science‐literate customers. Bayer and other companies bring much more than money to the table, and the success stories prove the power of volunteerism, education reform, and raising public awareness. The author makes the case for business involvement in K–12 education; describes Bayer's signature partnership program, Making Science Make Sense; and discusses resources Bayer has developed for other interested companies, including a compendium of the programs most successful in closing science achievement gaps for girls and minorities, and a forum that brought companies together with the programs' leaders to learn what such partnerships entail and can achieve © 2008 Wiley Periodicals, Inc.
Accelerating executive transitions at The Home Depot
Authors: Joyce Leslie W. 
Published: June 2008

AbstractThe Home Depot accelerates “speed to competency” for new executives through a variety of processes and tools tailored to different types of transitions. The approaches focus on the early days of the transition, engage key stakeholders in the process, and emphasize organizational realities, including what it really takes to make it at The Home Depot. The author discusses research into the factors common to successful transitions in the company; the company's acceleration framework; two different approaches, for role‐based transitions in the field and context‐based transitions at headquarters; and other tools for supporting executives new to the company and/or their roles. © 2008 Wiley Periodicals, Inc.
Microsoft implements readiness as a strategic force
Authors: Grosse Dustin 
Published: June 2008

AbstractThe success of Microsoft's global product launches and solutions for a huge, diverse customer base hinges upon readiness in the field. To make workforce readiness a strategic lever, field training is aligned with business objectives, the role, and the task, and delivered to highly mobile communities at the right time, in the right place, and on the right device. The Sales, Marketing, and Services Group Readiness group builds its training offerings on three pillars of content development: an operating model that aligns priorities across businesses, regions, and customer segments; strong partnerships with business groups and subject matter experts; and metrics for assessing results. © 2008 Wiley Periodicals, Inc.
Nonlinear multigrid for the solution of large‐scale Riccati equations in low‐rank and ℋ︁‐matrix format
Authors: Grasedyck L. 
Published: June 2008

AbstractThe algebraic matrix Riccati equation AX+XAT−XFX+C=0, where matrices A, B, C, F ∈ ℝn × n are given and a solution X ∈ ℝn × n is sought, plays a fundamental role in optimal control problems. Large‐scale systems typically appear if the constraint is described by a partial differential equation (PDE). We provide a nonlinear multigrid algorithm that computes the solution X in a data‐sparse, low‐rank format and has a complexity of 𝒪(n), subject to the condition that F and C are of low rank and A is the finite element or finite difference discretization of an elliptic PDE.We indicate how to generalize the method to ℋ︁‐matrices C, F and X that are only blockwise of low rank and thus allow a broader applicability with a complexity of 𝒪(nlog(n)p), p being a small constant. The method can also be applied to unstructured and dense matrices C and X in order to solve the Riccati equation in 𝒪(n2). Copyright © 2008 John Wiley & Sons, Ltd.
Convolution quadrature method‐based symmetric Galerkin boundary element method for 3‐d elastodynamics
Authors: Kielhorn L. , Schanz M. 
Published: June 2008

AbstractThe boundary integral equations in 3‐d elastodynamics contain convolution integrals with respect to the time. They can be performed analytically or with the convolution quadrature method. The latter time‐stepping procedure's benefit is the usage of the Laplace‐transformed fundamental solution. Therefore, it is possible to apply this method also to problems where analytical time‐dependent fundamental solutions might not be known.To obtain a symmetric formulation, the second boundary integral equation has to be used which, unfortunately, requires special care in the numerical implementation since it involves hypersingular kernel functions. Therefore, a regularization for closed surfaces of the Laplace‐transformed elastodynamic kernel functions is presented which transforms the bilinear form of the hypersingular integral operator to a weakly singular one. Supplementarily, a weakly singular formulation of the Laplace‐transformed elastodynamic double layer potential is presented. This results in a time domain boundary element formulation involving at least only weakly singular integral kernels.Finally, numerical studies validate this approach with respect to different spatial and time discretizations. Further, a comparison with the wider used collocation method is presented. It is shown numerically that the presented formulation exhibits a good convergence rate and a more stable behavior compared with collocation methods. Copyright © 2008 John Wiley & Sons, Ltd.
On the heat of formation of nitromethane
Authors: Bumpus John A. , Willoughby Patrick H. 
Published: June 2008

AbstractTwo experimental values (−19.3 ± 0.3 and −17.8 ± 0.1 kcal/mol) for the gas phase heat of formation (δfH) (298k) of nitromethane have been reported. Although these values differ by only 1.5 kcal/mol, substantially greater differences in theoretical and experimental results occur when these differing values are used to calculate thermodynamic properties. This is especially evident when these two values for the δfH of nitromethane are used to calculate thermodynamic properties of polynitro compounds. For example, when density functional theory (DFT) is coupled with the use of isodesmic reactions, the ΔfH of octanitrocubane is calculated to be 160.6 or 172.6 kcal/mol, depending on which value is used. It should also be appreciated that several computational theories depend upon having access to reliable experimental data for testing and development. We have examined this discrepancy using several computational models and several levels of theory. Our results coupled with a comprehensive review of the literature support the lower (−19.3 ± 0.3 kcal/mol) experimental value. This is problematic because the higher value (−17.8 ± 0.1 kcal/mol) has been used in the development and/or testing of several semiempirical quantum mechanical models as well as ab initio Gaussian theory (G2 and G3). Copyright © 2008 John Wiley & Sons, Ltd.
Influence of charge carrier mobility on the performance of organic solar cells
Authors: Deibel Carsten , Wagenpfahl Alexander , Dyakonov Vladimir 
Published: June 2008

AbstractThe power conversion efficiency of organic solar cells based on donor–acceptor blends is governed by an interplay of polaron pair dissociation and bimolecular polaron recombination. Both processes are strongly dependent on the charge carrier mobility, the dissociation increasing with faster charge transport, with raised recombination losses at the same time. Using a macroscopic effective medium simulation, we calculate the optimum charge carrier mobility for the highest power conversion efficiency, for the first time accounting for injection barriers and a reduced Langevin‐type recombination. An enhancement of the charge carrier mobility from 10–8 m2/V s for state of the art polymer–fullerene solar cells to about 10–6 m2/V s, which yields the maximum efficiency, corresponds to an improvement of only about 20% for the given parameter set. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An augmented system approach to static output‐feedback stabilization with ℋ︁∞ performance for continuous‐time plants
Authors: Shu Zhan , Lam James 
Published: June 2008

AbstractThis paper revisits the static output‐feedback stabilization problem of continuous‐time linear systems from a novel perspective. The closed‐loop system is represented in an augmented form, which facilitates the parametrization of the controller matrix. Then, new equivalent characterizations on stability and ℋ︁∞ performance of the closed‐loop system are established in terms of matrix inequalities. On the basis of these characterizations, a necessary and sufficient condition with slack matrices for output‐feedback stabilizability is proposed, and an iteration algorithm is given to solve the condition. An extension to output‐feedback ℋ︁∞ control is provided as well. The effectiveness and merits of the proposed approach are shown through several examples. Copyright © 2008 John Wiley & Sons, Ltd.