bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative energies of conformations and sulfinyl oxygen‐induced pentacoordination at silicon in 4‐bromo‐ and 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide: A computational study
Authors: Freeman Fillmore , Shainyan Bagrat A. 
Published: August 2005

AbstractThe equilibrium geometries and relative energies of the chair, twist, and boat conformations ofcis‐ andtrans‐4‐bromo‐4‐silathiacyclohexane 1‐oxide and 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide have been calculated at the B3LYP/6‐311G(d,p) and MP2/6‐311+G(d,p) theoretical levels. The axial (SO) chair conformers of the sulfoxides are of lower energy than the chair conformers of the corresponding equatorial (SO) sulfoxides. The chair conformer of the axial (SO)trans‐4‐bromo‐4‐silathiacyclohexane 1‐oxide is only 0.10 kcal/mol more stable than the corresponding 1,4‐boat conformer which is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The 1,4‐boat structure of equatorial (SO)trans‐4‐bromo‐4‐silathiacyclohexane 1‐oxide is a transition state and is 5.77 kcal/mol higher in energy than the respective chair conformer. The 1,4‐boat conformer of axial (SO) 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide is also stabilized by transannular coordination of the sulfinyl oxygen and silicon, but it is 4.31 kcal/mol higher in energy than the corresponding chair conformer. The relatively lower stability of the 1,4‐boat conformer of 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide may be due to repulsive interactions of the axial halogen and sulfinyl oxygen atom. The relative energies of the conformers and transition states are discussed in terms of hyperconjugative interactions, orbital interactions, nonbonded interactions, and transannular sulfinyl oxygen‐silicon coordination. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Table‐CI with macroconfiguration approach for describing electronic states of molecules in intense radiation fields
Authors: Khait Yuriy G. , Hoffmann Mark R. 
Published: August 2005

AbstractModifications to the recently introduced table‐driven multireference configuration interaction (CI) approach that uses macroconfigurations necessary for the efficient construction of electronic Floquet states are described. Adiabatic electronic Floquet states have recently shown promise as simplifying the description of the electronic structure of molecules in intense radiation fields. The algorithm for the table‐driven multireference CI approach that uses macroconfigurations for the calculation of electronic energies needs two principal modifications to extend use to the calculation of Floquet states. First, it must be possible to calculate electronic states of several irreducible representations of the molecular point group simultaneously. Second, matrix elements of the electronic dipole operator are required. It is demonstrated that the modifications that enable these capabilities are possible and in fact do not lessen the high computational efficiency of the energy algorithm. The modifications are described in sufficient detail, with appropriate formulas, to facilitate implementation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Structural connotations of bioactivity in a series of organophosphinates
Authors: King James W. , Molnar Stephen P. 
Published: August 2005

AbstractPretreatment before exposure is one of the options for temporarily protecting persons liable to exposure to toxic organophosphorus compounds in agricultural or warfare situations. It is known that organophosphinates interact with neuronal cholinesterases, but that the latter may spontaneously reactivate in time. Before that reactivation, the enzyme is protected against comlexation with organophosphates. In this study, geometrically optimized unitary molecular indices, i.e., the molecular transforms, FTm, FTe, and FTc, indicating general, electronic, and charge properties, respectively, and the analogous normalized molecular moments, Mn, Me, and Mc, were calculated for a number of phosphinates. These indices were subsequently used in correlation trials with spontaneous reactivation percentages at specific elapsed times, as well as in clustering procedures, to evaluate the effect of structure variations on the reactivation percentages. The results of these studies are discussed, as is the effect of the octanol/water partition coefficient on the noted bioactivity. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Pyridine adsorbed on H‐Faujasite zeolite: Electrostatic effect of the infinite crystal lattice calculated from a point charge representation
Authors: Injan Natcha , Pannorad Narong , Probst Michael , Limtrakul Jumras 
Published: August 2005

AbstractCalculations on cluster models of infinite systems require less computational effort and are technically simpler than periodic calculations, but they neglect, among other contributions, the effect of long‐range electrostatic interaction from the infinite crystal lattice. In the case of zeolites, such contributions can be important for adsorption processes and surface reactions. We test a simple method for including this effect into the calculation by generating a finite number of point charges placed on the lattice sites. These point charges reproduce the infinite electrostatic potential at the chemically important region of the zeolite. We apply this method to the adsorption of pyridine on H‐Faujasite zeolite. The embedding method gives an adsorption energy of −42.8 kcal/mol, which agrees well with the experimental value of −43.1 ± 1 kcal/mol. Without the electrostatic effect of the crystal field, the value is ∼9 kcal/mol higher. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Quantification of isomers from a mixture of twelve heparin and heparan sulfate disaccharides using tandem mass spectrometry
Authors: Behr Jonathan R. , Matsumoto Yuri , White Forest M. , Sasisekharan Ram 
Published: August 2005

AbstractHeparin/heparan sulfate‐like glycosaminoglycans (HSGAGs) have been implicated in clinically relevant processes such as hemostasis, infection, development, and cancer progression, through their interactions with proteins. Electrospray ionization mass spectrometry (ESI‐MS) and tandem mass spectrometry (MSn) were combined to identify and quantify 12 HSGAG disaccharides that can be generated by enzymatic depolymerization with heparin lyases. This technique includes free amine‐containing disaccharides that had previously been observed in MSn but not quantified. Our methods use diagnostic product ions from MSn spectra of up to three isomeric disaccharides at once, and up to three sequential stages of MSn in tandem, for the quantitative analysis of the relative percentage of each of these isomers. The isomer quantification was validated using mock mixtures and showed acceptable accuracy and precision. These methods may be applied to the quantification of other isomers by MSn. While each of the 12 disaccharides alone had a linear response to an internal standard in the MS1 spectra, the individual response factors did not remain constant when the concentrations of the other 11 disaccharides in the mixtures fluctuated, due to competition for electrospray ionization. The absolute concentration of one fluctuating isomer was determined out of a constant mixture of the other disaccharides. The rapid, accurate, and sensitive quantification of all isomeric disaccharides may contribute to the eventual sequencing of longer saccharides by MSn, enabling the elucidation of the structure‐function relationships of HSGAGs. Copyright © 2005 John Wiley & Sons, Ltd.
Characterization of oligosaccharide moieties of intact glycoproteins by microwave‐assisted partial acid hydrolysis and mass spectrometry
Authors: Lee Bao‐Shiang , Krishnanchettiar Sangeeth , Lateef Syed Salman , Lateef Nabila Salman , Gupta Shalini 
Published: August 2005

AbstractA method, which utilizes microwave‐assisted partial acid hydrolysis and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS), to elucidate oligosaccharide composition of intact glycoproteins is presented here. Glycoproteins, such as ribonuclease B, avidin, α1‐acid glycoprotein, and fetuin, are used as model systems to demonstrate this technique. Partial cleavage of oligosaccharides from whole intact glycoproteins with trifluoroacetic acid was observed after a short exposure to microwaves. Due to the high‐resolution mass spectra obtained by MALDI‐TOFMS from glycoproteins with molecular weights less than 20 kDa, the compositions of oligosaccharides are readily derived for ribonuclease B and avidin. The data agree with the proposed oligosaccharide structures of ribonuclease B (five glycoforms) and avidin (eight glycoforms). Larger glycoproteins such as α1‐acid glycoprotein (many glycoforms) and fetuin (many glycoforms) exhibited only broad peaks with no glycoform resolution. Nevertheless, this method can be used successfully for analysis of glycoproteins with molecular weights greater than 20 kDa to determine the presence or absence of glycosylation. Copyright © 2005 John Wiley & Sons, Ltd.
Characterization of carotenoids and carotenoid esters in red pepper pods (Capsicum annuum L.) by high‐performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry
Authors: Schweiggert Ute , Kammerer Dietmar R. , Carle Reinhold , Schieber Andreas 
Published: August 2005

AbstractCarotenoids and carotenoid esters were extracted from red pepper pods (Capsicum annuum L.) without saponification. Among the 42 compounds detected, 4 non‐esterified, 11 mono‐ and 17 diesters were characterized based on their retention times, UV/Vis spectra and their fragmentation patterns in collision‐induced dissociation experiments in atmospheric pressure chemical ionization mass spectrometry (APCI‐MS). Positive and negative ion mode measurements were used for the characterization of major and minor carotenoids and their esters. Capsanthin esterified with lauric, palmitic and myristic acids represented the predominant compounds in the red pepper extracts. Additionally, three β‐cryptoxanthin and one zeaxanthin monoester were tentatively identified in red pepper pods for the first time. Furthermore, the specific fragmentation patterns of capsanthin‐laurate‐myristate and capsanthin‐myristate‐palmitate were used for the distinction of both regioisomers. The results obtained from LC‐DAD‐APCI‐MSn experiments demonstrated that the carotenoid profile of red pepper pods is considerably more complex than considered hitherto. Copyright © 2005 John Wiley & Sons, Ltd.
An evaluation of the performance of porous polymer monolith assisted electrospray
Authors: Lee Stephen Shu Hang , Douma Michelle , Koerner Terry , Oleschuk Richard D. 
Published: August 2005

AbstractA novel electrospray interface, which has distinct advantages over conventional pulled silica emitters, has been developed. This novel interface can be easily fabricated by forming a porous polymer monolith (PPM) at the end of a fused‐silica capillary that facilitates a stable electrospray over a wide range of flow rates with only a modest increase in back‐pressure. A comparison was made between the PPM‐assisted electrospray and a commercial nanosprayer in terms of sensitivity, stability and robustness. A PPM‐filled electrospray tip produced a day‐to‐day signal variation of 23% relative standard deviation (RSD) over a 3‐day period when spraying a 1.0 µM test peptide solution. Furthermore, three different capillaries fabricated by the same process produced a signal variation of 17% RSD, indicating that the fabrication process shows good reproducibility. The multiple flow paths of the PPM function to split the flow and reduce clogging. Even following the accumulation of debris after prolonged use, a stable spray could still be generated with the PPM‐filled capillary while the commercial nanosprayer ceased to function properly. In terms of sensitivity, PPM‐assisted electrospray showed an enhancement in sensitivity at infusion flow rates between 100 to 1000 nL/min while commercial nanosprayers performed slightly better at flow rates below 100 nL/min. A sample purification step can be combined with the PPM‐assisted sprayer, using the PPM as a stationary phase to desalt and preconcentrate samples prior to mass spectrometric detection. Copyright © 2005 John Wiley & Sons, Ltd.
Accelerated throughput metabolic route screening in early drug discovery using high‐resolution liquid chromatography/quadrupole time‐of‐flight mass spectrometry and automated data analysis
Authors: Mortishire‐Smith Russell J. , O'Connor Desmond , Castro‐Perez Jose M. , Kirby Jane 
Published: August 2005

AbstractThe resource investment required to characterise the metabolic fate of a compound is relatively large, meaning that within a drug discovery environment relatively few compounds are characterised in depth. Rate‐limiting steps include the setting up of a complex array of mass spectrometry experiments and the subsequent analysis of the large data sets produced. We describe here a strategy for the evaluation of metabolic routes using full‐scan high‐resolution liquid chromatography/quadrupole time‐of‐flight mass spectrometry (LC/QToFMS) with automated data analysis using Metabolynx™, a commercially available software package. Data from several structurally diverse compounds taken from the literature illustrate that, with careful setting of key parameters, this approach is able to indicate the presence of a wide range of metabolites with only a limited requirement for manual intervention. Copyright © 2005 John Wiley & Sons, Ltd.
In vivo metabolism for the hydroxylation of FK778 to the metabolite M3 in humans studied by enantioselective liquid chromatography/tandem mass spectrometry
Authors: Chen Yu‐Luan , Akhtar Shahzad , Murai Hidetsugu , Kobayashi Masakazu 
Published: August 2005

AbstractA major active metabolite of malononitrilamide FK778 (an immunosuppressant under development) is labeled M3. Due to a chiral center created during in vivo metabolism, the exploration of enantiomer profiles in clinical samples is critical to the characterization of the immunosuppressive activity of M3. An enantioselective liquid chromatography method with detection by tandem mass spectrometry (LC/MS/MS) was developed for the resolution of M3 enantiomers. It was experimentally confirmed that no interconversion between the two enantiomers occurred during sample preparation. This new approach was applied to measure the enantioselectivity of the M3 metabolite in human plasma samples from kidney transplanted patients. The assay results of 91 in vivo human samples from three subjects showed a ratio of 57:43 for the (−)‐enantiomer (the 2nd eluter) vs. the (+)‐enantiomer (1st eluter), indicating that the enantiometabolism of FK778 through human enzymes is essentially non‐specific. Copyright © 2005 John Wiley & Sons, Ltd.
Software process commonality analysis
Authors: Ocampo Alexis , Bella Fabio , Münch Jürgen 
Published: August 2005

AbstractTo remain viable and thrive, software organizations must rapidly adapt to frequent and, often, rather far‐ranging changes to their operational context. These changes typically concern many factors, including the nature of the organization's marketplace in general, its customers' demands, and its business needs. In today's most highly dynamic contexts, such as web services development, other changes create additional, severe challenges. Most critical are changes to the technology in which a software product is written or which the software product has to control or use to provide its functionality. These product‐support technology changes are frequently relatively ‘small’ and incremental. They are, therefore, often handled by relatively ‘small’, incremental changes to the organization's software processes. However, the frequency of these changes is high, and their impact is elevated by time‐to‐market and requirements change demands. The net result is an extremely challenging need to create and manage a large number of customized process variants, collectively having more commonalities than differences, and incorporating experience‐based, proven ‘best practices’. This paper describes a tool‐based approach to coping with product‐support technology changes. The approach utilizes established capabilities such as descriptive process modeling and the creation of reference models. It incorporates a new, innovative, tool‐based capability to analyze commonalities and differences among processes. The paper includes an example‐based evaluation of the approach in the domain of Wireless Internet Services as well as a discussion of its potentially broader application. Copyright © 2005 John Wiley & Sons, Ltd.
A study of open source software evolution data using qualitative simulation
Authors: Smith Neil , Capiluppi Andrea , Ramil Juan F. 
Published: August 2005

AbstractSimulation modelling of growth trends and other empirical data from software systems can reveal the main drivers of software evolution and help improve understanding and management of the software evolution phenomenon. This article reports on the application of qualitative abstraction techniques to data from 25 open source software (OSS) systems. After justifying the use of qualitative simulation techniques for the software process domain, the article presents an analysis of the support from OSS‐derived data to previously developed qualitative simulation models, which were inspired by observations from the domain of proprietary systems. The analysis involved comparison of model output and qualitatively abstracted growth trends. The analysis also involved the comparison of the transitions in trends of functional size and complexity to those predicted by the models in a sub‐set of 21 systems for which complexity data was available. The results indicate that models are able to replicate some of the features in the data. This, in turn, suggests that the study of the relationship between size and complexity and its interaction via feedback loops has a role in explaining the long‐term evolutionary behaviour of OSS systems. This is not surprising since it is well known that the evolution of all type of real‐world software systems, proprietary and OSS, is driven by feedback from their stakeholders. Copyright © 2005 John Wiley & Sons, Ltd.
Managing the dynamics of mutual adaptation of technology and organisation in information systems development projects
Authors: Bygstad Bendik 
Published: August 2005

AbstractThis article explores a strategy of mutual adaptation between the information system and the business process, facilitated by the iterative and incremental mechanisms of modern SW engineering frameworks. The concept of mutual adaptation implies that the real innovation of an information systems project is not the software, but the working solution after implementation. Too little is known about this phenomenon: What are the dynamics of mutual adaptation? To what extent is it possible to control? Which organisational mechanisms facilitate it? Should planned mutual adaptation be part of an information systems development project, or is it outside the reasonable scope of such projects?The article builds on a longitudinal case study from a large public auditing organisation that developed a new audit process in parallel with the construction of a new information system to support it. The project is described through seven iterations as it experiments with different organisational mechanisms to achieve mutual adaptation. The dynamics of mutual adaptation is described by a window of opportunity, where both the information system and the business process are malleable. Copyright © 2005 John Wiley & Sons, Ltd.
Intrauterine growth restriction and fetal body composition
Authors: Larciprete G. , Valensise H. , Di Pierro G. , Vasapollo B. , Casalino B. , Arduini D. , Jarvis S. , Cirese E. 
Published: August 2005

AbstractObjectiveTo assess the differences in fetal body compartments between fetuses with normal growth and those with reduced intrauterine growth, during the third trimester, through ultrasonographic determination of subcutaneous tissue thickness (SCTT).MethodsTwenty‐eight patients were enrolled into this case control study carried out at 30–31 weeks' gestation. Two study groups were matched for maternal age and pregestational body mass index: controls (n = 14) and intrauterine growth‐restricted (IUGR) fetuses (n = 14). Routine ultrasound‐derived biometric parameters (head circumference, abdominal circumference, femur length and humerus length) were measured. Additionally, the mid‐arm fat mass and lean mass (MAFM and MALM), the mid‐thigh fat mass and lean mass (MTFM and MTLM), the abdominal fat mass (AFM) and the subscapular fat mass (SSFM) were measured. The Mann–Whitney U‐test and Student's t‐test were used to compare the two groups.ResultsThe abdominal circumference and the humerus were significantly smaller in IUGR fetuses than in controls. Most of the SCTT values were different in the two groups. The SSFM (3.6 ± 1.1 vs. 2.6 ± 0.7 mm; P = 0.011), the AFM (5.1 ± 0.7 vs. 4 ± 1 mm; P = 0.01), the MAFM (3.5 ± 0.9 vs. 2.2 ± 0.8 cm2; P < 0.01) and MALM (2.1 ± 0.4 vs. 1.7 ± 0.5 cm2; P = 0.029) were all significantly greater in fetuses with normal development compared to those with growth restriction.ConclusionsDuring the third trimester, SCTT (with the exception of MTFM and MTLM) is reduced in fetuses with IUGR. Furthermore, MALM is lower in growth‐restricted fetuses, confirming that the parameters measured in this study are affected in IUGR fetuses. Our findings indicate that specific changes in fetal body compartments occur as a result of chronic metabolic impairment. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Less input same output: simplified approach for population size assessment in Lepidoptera
Authors: Nowicki Piotr , Richter Anett , Glinka Uta , Holzschuh Andrea , Toelke Ulrike , Henle Klaus , Woyciechowski Michal , Settele Josef 
Published: August 2005

AbstractWith the aim of creating a simplified sampling scheme that would retain the accuracy of standard mark–release–recapture (MRR) sampling, but at a greatly reduced cost, we analysed 23 capture–recapture data sets from spatially closed populations of six Lepidoptera species according to the constrained Cormack–Jolly–Seber models. Subsequently the relationships between the estimates of population parameters were investigated in order to develop a regression equation that would enable us to calculate seasonal population size without sampling the population throughout the entire flight period. The proportion of individuals flying at peak population was highly variable (CV=0.39), but the variation decreased considerably (CV=0.14) after different life span and flight period length were accounted for. Over 90% of the variance of this proportion was explained by the life span:flight period length ratio. Simulations of hypothetical sampling schemes proved that schemes covering the second and third quarter of the flight period performed much better than those restricted to the second quarter only. The accuracy of seasonal population size estimated with the regression equation developed was comparable for intensive schemes (daily sampling) and non‐intensive ones (sampling once in 2 or 3 days). We propose a simplified method of surveying butterfly populations that should be based on checking the presence of flying adults at the beginning and end of the flight period to assess its length, and MRR sampling covering its middle part, with intervals between capture days corresponding to the average life span of investigated butterflies.