bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of secreted frizzled related protein 1, a Wnt antagonist, in brain, kidney, and skeleton is dispensable for normal embryonic development
Authors: Trevant Brune , Gaur Tripti , Hussain Sadiq , Symons John , Komm Barry S. , Bodine Peter V.N. , Stein Gary S. , Lian Jane B.
Published: May 2008

Secreted frizzled related protein‐1 (sFRP1), an antagonist of Wnt signaling, regulates cell proliferation, differentiation and apoptosis and negatively regulates bone formation. The spatial and temporal pattern of endogenous sFRP1 expression and loss‐of‐function were examined in the sFRP1‐LacZ knock‐in mouse (sFRP1−/−) during embryonic development and post‐natal growth. β‐gal activity representing sFRP1 expression is robust in brain, skeleton, kidney, eye, spleen, abdomen, heart and somites in early embryos, but sFRP1 gene inactivation in these tissues did not compromise normal embryonic and post‐natal development. Kidney histology revealed increased numbers of glomeruli in KO mice, observed after 5 years of breeding. In the skeleton, we show sFRP1 expression is found in relation to the mineralizing front of bone tissue during skeletal development from E15.5 to birth. Trabecular bone volume and bone mineral density in the sFRP1−/− mouse compared to WT was slightly increased during post‐natal growth. Calvarial osteoblasts from newborn sFRP1−/− mice exhibited a 20% increase in cell proliferation and differentiation at the early stages of osteoblast maturation. sFRP1 expression was observed in osteoclasts, but this did not affect osteoclast number or activity. These findings have identified functions for sFRP1 in kidney and bone that are not redundant with other sFRPs. In summary, the absence of major organ abnormalities, the enhanced bone formation and a normal life span with no detection of spontaneous tumors suggests that targeting sFRP1 can be used as a therapeutic strategy for increasing bone mass in metabolic bone disorders or promoting fracture healing by modulating Wnt signaling. J. Cell. Physiol. 217: 113–126, 2008. © 2008 Wiley‐Liss, Inc.
Introducing metallocene into a triazole peptide conjugate reduces its off‐rate and enhances its affinity and antiviral potency for HIV‐1 gp120
Authors: Gopi Hosahudya , Cocklin Simon , Pirrone Vanessa , McFadden Karyn , Tuzer Ferit , Zentner Isaac , Ajith Sandya , Baxter Sabine , Jawanda Navneet , Krebs Fred C. , Chaiken Irwin M.
Published: May 2008

In this work, we identified a high affinity and potency metallocene‐containing triazole peptide conjugate that suppresses the interactions of HIV‐1 envelope gp120 at both its CD4 and co‐receptor binding sites. The ferrocene‐peptide conjugate, HNG‐156, was formed by an on‐resin copper‐catalysed [2 + 3] cycloaddition reaction. Surface plasmon resonance interaction analysis revealed that, compared to a previously reported phenyl‐containing triazole conjugate HNG‐105 (105), peptide 156 had a higher direct binding affinity for several subtypes of HIV‐1 gp120 due mainly to the decreased dissociation rate of the conjugate‐gp120 complex. The ferrocene triazole conjugate bound to gp120 of both clade A (92UG037‐08) and clade B (YU‐2 and SF162) virus subtypes with nanomolar KD in direct binding and inhibited the binding of gp120 to soluble CD4 and to antibodies that bind to HIV‐1YU‐2 gp120 at both the CD4 binding site and CD4‐induced binding sites. HNG‐156 showed a close‐to nanomolar IC50 for inhibiting cell infection by HIV‐1BaL whole virus. The dual receptor site antagonist activity and potency of HNG‐156 make it a promising viral envelope inhibitor lead for developing anti‐HIV‐1 treatments. Copyright © 2008 John Wiley & Sons, Ltd.
Predicting linear B‐cell epitopes using string kernels
Authors: EL‐Manzalawy Yasser , Dobbs Drena , Honavar Vasant
Published: May 2008

The identification and characterization of B‐cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production. Therefore, computational tools for reliably predicting linear B‐cell epitopes are highly desirable. We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using fivefold cross‐validation on a homology‐reduced data set of 701 linear B‐cell epitopes, extracted from Bcipep database, and 701 non‐epitopes, randomly extracted from SwissProt sequences. Based on the results of our computational experiments, we propose BCPred, a novel method for predicting linear B‐cell epitopes using the subsequence kernel. We show that the predictive performance of BCPred (AUC = 0.758) outperforms 11 SVM‐based classifiers developed and evaluated in our experiments as well as our implementation of AAP (AUC = 0.7), a recently proposed method for predicting linear B‐cell epitopes using amino acid pair antigenicity. Furthermore, we compared BCPred with AAP and ABCPred, a method that uses recurrent neural networks, using two data sets of unique B‐cell epitopes that had been previously used to evaluate ABCPred. Analysis of the data sets used and the results of this comparison show that conclusions about the relative performance of different B‐cell epitope prediction methods drawn on the basis of experiments using data sets of unique B‐cell epitopes are likely to yield overly optimistic estimates of performance of evaluated methods. This argues for the use of carefully homology‐reduced data sets in comparing B‐cell epitope prediction methods to avoid misleading conclusions about how different methods compare to each other. Our homology‐reduced data set and implementations of BCPred as well as the APP method are publicly available through our web‐based server, BCPREDS, at: http://ailab.cs.iastate.edu/bcpreds/. Copyright © 2008 John Wiley & Sons, Ltd.
Determination of apparent decomposition threshold energies of lithium adducts of acylglycerols using tandem mass spectrometry and a novel derived effective reaction path length approach
Authors: Ham Bryan M. , Cole Richard B.
Published: May 2008

Apparent decomposition threshold energies for the fragmentation pathways of lithiated acylglycerols were experimentally determined by collisional activation in a quadrupole‐hexapole‐quadrupole (QhQ) mass spectrometer. A previously developed ‘derived effective reaction path length’ approach for predicting bond dissociation energies (BDEs) of simple dissociations of electrostatic complexes such as alkali metal adducts (Li+), or halide adducts (Cl−) of acylglycerols, was extended to predict covalent bond apparent decomposition threshold energies of lithium adducts of a mono‐acylglycerol, a 1,2‐diacylglycerol, and a 1,3‐diacylglycerol. The ability of the model to treat relatively large ionic systems (e.g. more than 100 atoms) represents a huge advantage of this approach. The model's calculated apparent decomposition threshold energies (Ea) are used in conjunction with the method of energy‐resolved mass spectrometry, employing breakdown graphs, to give a more complete quantitative description of the fragmentation processes. Calculated Ea values allowed ranking of the 1,2‐diacylglycerol as more reactive than the 1,3‐diacylglycerol; the mono‐acylglycerol was ranked the least reactive. The method was applied to the low molecular weight product ions generally associated with the hydrocarbon series CnH2n+1+, where two separate pathways are deduced as contributing to the production of the abundant m/z 81 fragment ion. The favored ranking of the neutral losses of fatty acyl substituents for the 1,2‐diacylglycerol was determined as: loss of lithium fatty acetate > loss of fatty acid > loss of fatty acyl chain as ketene. For the 1,3‐diacylglycerol, the descending order of ease of neutral loss was: loss of fatty acyl ketene > loss of lithium fatty acetate > loss of fatty acid. The results of this study demonstrate that the newly developed method is general in nature, and it can be used for the measurement of covalent bond decomposition threshold energies, as well as for the previously documented electrostatic (noncovalent) bond energies. Copyright © 2008 John Wiley & Sons, Ltd.
Fragmentation patterns of newly isolated cassane butenolide diterpenes and differentiation of stereoisomer by tandem mass spectrometry
Authors: Kanojiya Sanjeev , Yadav Prem P.
Published: May 2008

Different stereoisomers of active molecules often cause different physiological responses and hence pose a challenge for their identification. This study involves perceptive fragmentation behavior of newly isolated cassane butenolides, caesalpinolide A [1] and caesalpinolide B [2] (epimeric at the hemiketal position) by tandem MS. The electrospray ionization‐mass spectrometry (ESI‐MS)/collision‐induced dissociation (CID; ESI‐MS2 and ESI‐IT‐MSn) were investigated. The effect of orientations of hemiketal hydroxyl at C‐12 was clearly observed in the mass spectrum. Tandem mass spectra of 1, 1A or 2, 2A show stereospecific fragmentation resulting in significant abundance dissimilarity of [MH − H2O]+ as well as differences in fragmentation pathway. Both of these pathways seem to be influenced by the stereochemistry of the molecule. The differentiation can be clearly visualized from the [M + H − H2O]+/[M + H]+ ratio of the two isomers where β‐isomer 2 was found to be five times higher than that of α‐isomer 1 in full scan liquid chromatography‐electrospray ionization mass spectrometry(LC‐ESI‐MS). In high‐energy CID, the mass fingerprint of 1, 2, 1A, and 2A was found to be different from one anothers. Copyright © 2008 John Wiley & Sons, Ltd.
A Green's function‐based method for the transient analysis of plane waves obliquely incident on lossy and dispersive planar layers
Authors: Antonini Giulio
Published: May 2008

This paper presents a new methodology for the transient analysis of plane waves obliquely incident on a planar lossy and dispersive layer. The proposed model is based on the Sturm–Liouville problem associated with the propagation equations. Green's function is calculated in a series form and the open‐end impedance matrix is obtained as the sum of infinite rational functions. This form permits an easy identification of poles and residues. Furthermore, the knowledge of poles leads to the development of a model order reduction technique by selecting only the dominant poles of the system. The pole–residue representation is converted into a state‐space model that can be easily interfaced with ordinary differential equation solvers. The numerical results confirm the effectiveness of the proposed modeling technique. Copyright © 2008 John Wiley & Sons, Ltd.
Composite versus single sampling of spent irrigation water to assess the microbiological status of sprouting mung bean beds
Authors: McEgan Rachel , Lee Susan , Schumacher Bengt , Warriner Keith
Published: May 2008

BACKGROUND: Spent irrigation water testing has been recommended in sprouted seed production to detect the presence of pathogens. However, because of the heterogeneous distribution of contamination within batches of sprouted seed, taking single samples of spent irrigation water may return false‐negative results. The following evaluated whether spent irrigation water collected from multiple points provided a more representative assessment of the microbiological status of the sprouting mung bean bed compared to when single samples were taken.

RESULTS: Generic Escherichia coli or Aeromonas was recovered in one and 10 of the 160 sprout samples taken from 32 sprouting mung bean batches, respectively. Composite spent irrigation water samples tested positive for generic E. coli on 19 occasions compared to 12 when single samples were taken. Mesophilic Aeromonas was detected in 13 composite spent irrigation water samples which compared to eight single samples. The prevalence of either target bacterium in composite spent irrigation water samples was not significantly (P > 0.05) different compared to when a single sample was collected.

CONCLUSIONS: Sampling spent irrigation water from multiple points under sprouting mung bean beds does not significantly increase the probability of detecting contamination, if present. The findings of the study should be considered when devising sampling plans for spent irrigation water testing in bean sprout production. Copyright © 2008 Society of Chemical Industry
Extrusion cooking of barley flour and process parameter optimization by using response surface methodology
Authors: Altan Aylin , McCarthy Kathryn L , Maskan Medeni
Published: May 2008

BACKGROUND: The nutritional profile of barley places it in a prime position for development of a new extruded–expanded snack food with health benefits. It was therefore the aim to investigate the effect of extrusion processing variables on system parameters (specific mechanical energy, die pressure and die melt temperature) and physical properties (expansion, bulk density, texture and color) of barley flour extrudates and to optimize processing conditions for production of extruded snack food from barley flour by response surface methodology.

RESULTS: Barley flour with 219.7 g kg−1 moisture content was extruded at different die temperatures (140–160 °C) and screw speeds (150–200 rpm) through a co‐rotating twin‐screw extruder. The system parameters as well as product responses were mainly dependent on temperature, whereas the screw speed imparted a lesser effect. Extrudates produced under extrusion conditions of 160 °C, 150 and 200 rpm and at 164 °C and 150 rpm had higher preference levels of appearance, taste, texture and overall acceptability than that of other selected extrudates for sensory analysis. The optimal conditions for minimum bulk density and desired textural characteristics and color of extrudates correspond to a temperature of 156 °C and screw speed of 166 rpm.

CONCLUSION: The results suggested that use of barley flour in extruded snack products offers a desirable variation in diet and can take advantage of the nutritional quality of barley. Copyright © 2008 Society of Chemical Industry
Establishing native plants on newly‐constructed and older‐reclaimed sites along West Virginia highways
Authors: Skousen J.G. , Venable C.L.
Published: May 2008

Many state highway departments in the USA must use native plants for revegetating roadsides. We conducted two field studies in West Virginia to assess native plant establishment under two different conditions. On newly‐constructed sites, native species were seeded alone or combined with non‐native species. On older roadsides, native species were seeded in disturbed existing vegetation. In the first study, we used four seed mixtures comprised of seeds of native and non‐native species, and two N‐P‐K fertilizer treatments at three newly‐constructed sites. Native, warm‐season grasses were slow to establish and only contributed 25 per cent cover in some plots after three years. Indiangrass (Sorghastrum nutans [L.] Nash), big bluestem (Andropogon gerardii Vitman), Brown‐Eyed Susan (Rudbeckia triloba L.), and wild senna (Cassia hebecarpa Fernald) were the only seeded native species found. Fertilizer at 150 kg ha−1 of 10‐20‐10 showed little influence on increasing plant cover. In the second study, we disturbed three different‐aged established stands of vegetation composed of tall fescue (Festuca arundinacea Screb.) and crownvetch (Coronilla varia L.) by mowing, herbicide, or tillage, and native plants were seeded with and without fertilizer. Native cover was <10 per cent in all plots during the first year, but greatly increased by the second year to as much as 45 per cent in tilled plots, indicating that disturbance was necessary for natives to become important contributors within 2 years. Only switchgrass (Panicum virgatum L.), little bluestem (Andropogon scoparius Vitman), partridge pea (Chamaecrista fasciculate Michx.), and Brown‐Eyed Susan were observed in plots. Fertilizer at 300 kg ha−1 of 10‐20‐10 did not increase native plant cover on these sites. Based on our results, introducing or increasing the cover of native species along roadsides requires (1) reducing competition from non‐native species, and (2) longer time periods for these slower‐establishing species to be observed. Copyright © 2008 John Wiley & Sons, Ltd.
Impacts of land use/cover change on soil properties in the Mediterranean region of northwestern Jordan
Authors: Khresat Sa'eb , Al‐Bakri Jawad , Al‐Tahhan Ragheb
Published: May 2008

This study was carried out to evaluate the effects of deforestation on physical and chemical properties of soils under native forest in the Mediterranean region of northwestern Jordan. Land use/cover maps of 1953, 1978 and 2002 were interpreted and analysed within GIS to quantify the shift from forest to rainfed cultivation. Six sites were sampled in a non‐changed forest and in cultivated fields, three for each. Different soil properties of texture, bulk density, organic matter, total nitrogen, pH, cation exchange capacity (CEC), phosphorous and potassium were analysed. Results showed that many forests were changed into cultivated lands at a rate more than the reforestation. Subsequently, adverse effects on the studied physical and chemical properties were observed. The most affected properties were particle size distribution, bulk density of surface soil and subsoil. Organic matter and CEC decreased in cultivated soil as compared to the forest soil. Cultivated soils were found to exhibit a significantly lower status in physical and chemical soil properties as compared to forest soils. This general decline in the soil physical and chemical properties, in turn, contributed to soil erosion, reduction of soil fertility and land degradation.

There is an urgent need to improve soil quality by developing sustainable land use practices to reduce the rate of soil degradation and to ensure long‐term sustainability of the farming system in the study area and in similar biophysical settings. Copyright © 2008 John Wiley & Sons, Ltd.
Soil microbiochemical properties as indicators for success of heathland restoration after military disturbance
Authors: Heitkamp F. , Glatzel S. , Michalzik B. , Fischer E. , Gerold G.
Published: May 2008

Decline of heathlands in Central Europe raises the question of successful restoration of degraded heathlands. We examined the impact of different restoration techniques on soil microbial biomass carbon (Cmic) and nitrogen (Nmic) and enzyme activity on an abandoned military training site in the Lüneburger Heaths. The aim was to determine which technique resulted in typical heathland soil conditions. The training site was in use for about 50 years. Vegetation and soils were degraded in large areas. Restoration actions were: (1) spreading of heath plaggen (sods, containing the organic layer and a few centimetres mineral soil), (2) spreading of heath plaggen and grass seeds (Festuca filiformis Pourr.), (3) spreading of F. filiformis‐seeds and (4) succession (episodical tree removal). Ten years after restoration, we measured pH, bulk density, abundance of roots, soil organic carbon (SOC), nitrogen (Nt), phosphorus (Pt), Cmic, Nmic and acid phosphatase activity (AcP) in the first 10 cm of the mineral soil. Four restoration treatments were compared with one reference site. The reference site is heathland located near the training site, where no military actions took place.

At all disturbed sites, bulk density and pH proved to be higher than on the reference site. Relative to the reference site, SOC storage reached from 37 to 91 per cent, regeneration of Nt was slightly lower. In contrast to the advanced development of SOC and Nt, the regeneration of Cmic and Nmic was much lower (15–44 per cent). The succession site showed a low pool of SOC, Nt, Cmic and Nmic, but microbial ratios indicated a less disturbed C‐ and N‐cycle. AcP pronounced differences in nutrient demand between disturbed sites and reference. On this base, recommendations for restoration management were given. Copyright © 2008 John Wiley & Sons, Ltd.
Social and ecological trade offs in combating land degradation: the case of invasion by a woody shrub (Euryops Floribundus) at Macubeni, South Africa
Authors: Shackleton C. M. , Gambiza J.
Published: May 2008

Woody plant invasions, either of alien or indigenous species, are deemed to result in loss of ecosystem goods and services in many areas throughout the world, resulting in significant degradation and economic costs. Invasion of Euryops floribundus, a species indigenous to South Africa, is perceived to have reduced the grazing available for domestic livestock. Consequently, a programme of manual eradication has been implemented to improve the grazing resource and provide jobs for poverty alleviation. However, there is potential for a conflict of interest as our study shows that almost all households rely on Euryops for fuel and at times fencing material, whereas only a minority of households own livestock. Moreover, comparison of invaded and non‐invaded sites indicated that the invaded sites harbour greater plant species richness and higher grass culm density per unit area of grass cover, as well as higher forb and litter cover. While invaded sites had lower grass cover, overall plant cover was no different between invaded and non‐invaded sites. Multivariate analysis indicated no obvious differentiation in community composition between invaded and non‐invaded areas, suggesting stronger drivers of community composition other than Euryops invasion presumed to be facilitated by the effects of high livestock densities. Overall, our study suggests that the clearing operation may well benefit from a better understanding of the social needs, perceptions of degradation by the various stakeholders and ecological dynamics of the area, especially local reliance on the resources, and the dynamics of the invasion, particularly its extent, rate of spread and susceptibility for re‐invasion in the cleared areas. Copyright © 2008 John Wiley & Sons, Ltd.
Soil microbial biomass C and N changes in relation to forest conversion in the Northwestern Turkey
Authors: Kara Ö. , Bolat İ.
Published: May 2008

Tree species differ in their effect on soil development and nutrient cycling. Conversion of beech coppice to pine plantations can alter soil physical and chemical properties, which in turn may have significant impacts on soil microbial biomass C and N (Cmic, Nmic). The major objective of this study was to evaluate soil quality changes associated with the forest conversion in humid NW Turkey. Results from this study showed that levels of soil organic carbon (Corg), total nitrogen (Nt), moisture, Cmic and Nmic under beech coppice were consistently higher but levels of pH, CaCO3 and EC were lower compared to pine plantation. Differences between the forest stands in Cmic and Nmic were mainly related to the size of the Corg stores in soil and to tree species. In addition, high level of CaCO3 is likely to reduce pools of soil organic C and possibly even microbial biomass C and N in pine forests. The average Cmic:Nmic ratios were higher in soils under beech coppice than pine plantation, while Cmic:Corg and Nmic:Nt percentages were similar in both forest types. These results revealed the differences in microbial community structure associated with different tree species and the complex interrelationships between microbial biomass, soil characteristics, litter quantity and quality. Copyright © 2008 John Wiley & Sons, Ltd.
Insights into virus capsid assembly from non‐covalent mass spectrometry
Authors: Morton Victoria L. , Stockley Peter G. , Stonehouse Nicola J. , Ashcroft Alison E.
Published: May 2008

The assembly of viral proteins into a range of macromolecular complexes of strictly defined architecture is one of Nature's wonders. Unraveling the details of these complex structures and the associated self‐assembly pathways that lead to their efficient and precise construction will play an important role in the development of anti‐viral therapeutics. It will also be important in bio‐nanotechnology where there is a plethora of applications for such well‐defined macromolecular complexes, including cell‐specific drug delivery and as substrates for the formation of novel materials with unique electrical and magnetic properties. Mass spectrometry has the ability not only to measure masses accurately but also to provide vital details regarding the composition and stoichiometry of intact, non‐covalently bound macromolecular complexes under near‐physiological conditions. It is thus ideal for exploring the assembly and function of viruses. Over the past decade or so, significant advances have been made in this field, and these advances are summarized in this review, which covers the literature up to the end of 2007. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 575–595, 2008
Phytochemical analysis of the Southern Australian marine alga, Plocamium mertensii using HPLC‐NMR
Authors: Dias Daniel , Urban Sylvia
Published: May 2008

Introduction: Over the last decade HPLC‐NMR has become a robust analytical technique that has been applied to a wide range of studies, particularly plant extracts. There have been only a few applications of the use of HPLC‐NMR to profile marine natural product extracts and no studies involving marine algae. The marine alga selected for this study belongs to the genus Plocamium, which is a well known source of polyhalogenated monoterpenes.

Objective: To chemically profile the marine alga P. mertensii, using a combination of on‐line (HPLC‐NMR) and off‐line approaches.

Methodology: P. mertensii was extracted with 3:1 methanol–dichloromethane and subsequently partitioned into dichloromethane and methanol‐soluble fractions. The methanol partition was exclusively profiled by HPLC‐NMR (on‐flow, stop‐flow and time‐slice experiments) whilst the dichloromethane partition was investigated by conventional isolation and purification procedures.

Results: HPLC‐NMR analysis of the methanol partition partially identified the presence of the major compounds 7, 13, 27 and 37, the structures of which were unequivocally elucidated by off‐line characterisation of the dichloromethane partition. Two additional minor metabolites (3 and 8) present in the dichloromethane partition were only tentatively identified as these co‐occurred in a mixture with compounds 7 and 13. As a result of this study a number of chemical shift reassignments were made for compound 37.

Conclusion: This is one of the few reports describing the application of HPLC‐NMR to rapidly profile or dereplicate a marine organism and the first application of HPLC‐NMR to successfully profile the chemistry of a marine alga. Copyright © 2008 John Wiley & Sons, Ltd.
QSPR correlation for conductivities and viscosities of low‐temperature melting ionic liquids
Authors: Bini Riccardo , Malvaldi Marco , Pitner William R. , Chiappe Cinzia
Published: May 2008

In order to rationalize the physicochemical behaviour of ionic liquids (ILs), quantitative structure–property relationship (QSPR) models have been derived for the conductivity and viscosity of a class of ILs based on the bis(trifluoromethylsulphonyl)imide anion. Data obtained at two different temperatures were analysed to assess the consistency of the derived relationships. Satisfactory correlations were found for both properties, although the QSPR derived for viscosity was heavily temperature dependent. ILs containing nitrile‐functionalized cations could not be inserted into satisfactory QSPR. Copyright © 2008 John Wiley & Sons, Ltd.
A gemini amphiphilic phase transfer catalyst for dark singlet oxygenation
Authors: Borde Cédric , Nardello Véronique , Wattebled Laurent , Laschewsky André , Aubry Jean‐Marie
Published: May 2008

A new gemini surfactant phase transfer catalyst, namely diethyl‐ether‐α,ω‐bis‐(dimethyldodecylammonium molybdate) codified as 12‐EO‐12‐Mo, was prepared by anion exchange from the analogous gemini dichloride (12‐EO‐12‐Cl2). The physico‐chemical properties of these compounds such as Krafft temperature, critical micelle concentration, surface activity and binary water‐surfactant behavior were compared and the influence of the molybdate counterion was examined. Though both compounds are highly hydrophilic, the cmc of 12‐EO‐12‐Mo (0.4 mmol L−1) is about five times lower than of its dichloride analogue (2.2 mmol L−1). Moreover, 12‐EO‐12‐Mo exhibits an additional cubic liquid crystal phase between 53 and 64 wt%. The usefulness of 12‐EO‐12‐Mo as an amphiphilic phase transfer catalyst for the dark singlet oxygenation was demonstrated with the peroxidation of two typical organic substrates: α‐terpinene which reacts with 1O2 according to a [4 + 2] cycloaddition and the less reactive β‐citronellol, which provides two hydroperoxides according to the ene‐reaction. 12‐EO‐12‐Mo provides a simple reaction medium with only three components for the preparative peroxidation of hydrophobic substrates by chemically generated singlet oxygen. Copyright © 2008 John Wiley & Sons, Ltd.
Activation of double and triple bonds in C6 unsaturated hydrocarbons by the Ru(001) surface: an overview
Authors: Garcia Ana R. , Barros Ricardo B. , Ilharco Laura M.
Published: May 2008

The decomposition patterns of hexene and hexyne isomers on clean Ru(001), under ultra‐high vacuum, are overviewed and correlated with functionality and isomerism. The key surface intermediates and products were identified by reflection absorption infrared spectroscopy (RAIRS). The results evidence the relevant role of the unsaturation position over its nature. The effects of steric hindrance and geometrical isomerism are apparent only in the inhibition of some decomposition pathways. The RAIRS data show that 1‐hexene chemisorbs at low temperature (∼90 K) and coverage as a di‐σ complex, whereas 1‐hexyne forms a di‐σ/π complex. By thermal activation, both these species dehydrogenate (in C1), yielding hexylidyne [µ3‐η1‐C(CH2)4CH3], which further decomposes (at 280–290 K) into surface metallocycles, [Ru3C(CH2)4CH2‐Ru] and [Ru3C(CH2)4CRu3]. Eventually, at 300 K, complete CC bond breaking occurs, yielding just adsorbed methylidyne [µ3‐η1‐CH]. The hexene and hexyne isomers with the unsaturation between secondary carbons may follow two surface‐assisted decomposition mechanisms. At low temperatures, they adsorb as the corresponding alkyne di‐σ/π complex, which implies a rehybridization of the sp2 (or sp) carbons with reduction of the bond order, plus, for alkenes, dehydrogenation at the same carbons. These complexes decompose by breaking the CC bonds adjacent to the surface anchors: C1C2 and C3C4 in the case of the 2‐isomer, yielding methylidyne, ethyne di‐σ/π complex [µ3‐η2‐CHCH] and propylidyne [µ3‐η1‐CCH2CH3], and C2C3 and C4C5 in the 3‐isomer, with the formation of the ethyne di‐σ/π complex and ethylidyne [µ3‐η1‐CCH3]. The second decomposition path occurs upon direct adsorption at the reaction temperatures. It involves the scission of the multiple bond, with the formation of shorter chain alkylidynes: propylidyne (for 3‐hexyne and Z‐3‐hexene), ethylidyne and butylidyne [µ3‐η1‐C(CH2)2CH3] (for 2‐hexyne). The reactivity of Z‐2‐hexene revealed to be different, since no evidence was found for the second decomposition path. This was ascribed to a reduced accessibility of the double bond to the surface, due to a steric hindrance effect of the alkyl chain. The influence of geometrical isomerism was particularly clear in the decomposition of E‐3‐hexene, which has a remarkable stability. Copyright © 2008 John Wiley & Sons, Ltd.
Comparison of mechanistic models for correlation of activation energies of liquid‐phase addition of carbon‐centered radicals to terminal olefins
Authors: Poutsma Marvin L.
Published: May 2008

The performance of different models for the influence of enthalpy and polar effects on radical additions is compared for the extensive data set from the Fischer group, supplemented by additional data. The best correlations result from the Fischer–Radom (FR) model, but it also contains the largest number of adjustable radical‐dependent parameters not based on physical observables. Updating the literature values of $\Delta _f H$, IP, and EA that are inputs to the FR model led to some deterioration in the quality of the correlations; this is symptomatic of remaining deficiencies in the thermochemical databases. In contrast, the Lalevee–Allonas–Fouassier (LAF) model gives poorer correlation but this is in part compensated because it uses the same inputs but with no adjustable parameters. Hammett‐type models based on polar and radical substituent constants rather than on molecular properties of the reactants perform even more poorly. In all cases, poorer correlation, as judged by increasing sd(ΔE), is accompanied by a systematic bias to over‐predict the lower E values and under‐predict the higher ones. The enthalpy contribution in the FR and LAF models is expressed as a linear Evans–Polanyi dependence of E on ΔH. Replacement by nonlinear Marcus dependences does not significantly improve performance. An attempt to significantly reduce the number of adjustable parameters in the FR model by anchoring them to a base set applicable to all radicals, which is then modulated for spin delocalization based on observable ESR hyperfine constants in the initial and adduct radicals, showed modest success. Copyright © 2008 John Wiley & Sons, Ltd.
Kinetic study of nitrosation of guanidines
Authors: Fernández I. , Hervés P. , Parajó M.
Published: May 2008

The kinetics of the nitrosation reaction of three guanidines, dicyandiamide, N,N′‐dimethyl‐N″‐cyanoguanidine and guanidine have been studied. The nitrosation rate is first order with respect to both the guanidine and acid concentration. The absence of catalysis by nucleophilic anions, the observed general acid–base catalysis and the observed deuterium isotope effect lead us to propose mechanism for the nitrosation of guanidines similar to that which operates in the case of the amides and ureas, in which a slow proton transfer is the rate determining step. From this mechanism we were able to obtain the values of the rate constants for the nitrosation and denitrosation processes. The catalytic constants in presence of buffers were also obtained and the analysis of the Brönsted slopes suggests a process with a transition state more similar to reactants than products. Copyright © 2008 John Wiley & Sons, Ltd.
Computational study of the mechanism of thermal decomposition of xanthates in the gas phase (the Chugaev reaction)
Authors: Vélez Ederley , Quijano Jairo , Notario Rafael , Murillo Juliana , Ramírez Juan F.
Published: May 2008

A theoretical study on the mechanism of the thermal decomposition of a series of xanthates, O‐alkyl S‐methyl and S‐alkyl O‐methyl dithiocarbonates, has been carried out, and the alkyl groups being ethyl, isopropyl, and tert‐butyl. Kinetically, these xanthates can be classified in two groups: those where the oxygen atom is involved in the bonding changes of the transition state (properly the Chugaev reaction), and those where it is not, O‐alkyl S‐methyl and S‐alkyl O‐methyl dithiocarbonates, respectively. We have studied not only the thermal elimination reactions but also the other possible reactions such as the thione‐to‐thiol rearrangement and the nucleophilic substitution to give ethers or thioethers. Two possible mechanisms for the thermal elimination reactions, in one and in two steps, respectively, have been studied. Calculations were made at the MP2/6‐31G(d) level of theory, and the progress of the reactions has been followed by means of the Wiberg bond indices. Copyright © 2008 John Wiley & Sons, Ltd.
Kinetics and mechanism of the pyridinolysis of diaryl carbonates
Authors: Castro Enrique A. , Acuña Magdalena , Soto Claudia , Trujillo Carolina , Vásquez Bárbara , Santos José G.
Published: May 2008

The reactions of 4‐methylphenyl and 4‐chlorophenyl 4‐nitrophenyl carbonates (1 and 2, respectively), phenyl, 4‐methylphenyl, 4‐chlorophenyl, and 4‐nitrophenyl 2,4‐dinitrophenyl carbonates (3, 4, 5, and 6, respectively), and bis(2,4‐dinitrophenyl) carbonate (7) with a series of pyridines are studied kinetically at 25.0 °C in 44 wt% ethanol–water and an ionic strength of 0.2 M (KCl). The reactions are followed spectrophotometrically and under excess amine pseudo‐first‐order rate coefficients (kobs) are found. For all these reactions, plots of kobs versus free amine concentration at constant pH are linear, the slope (kN) being independent of pH. The Brønsted‐type plots (log kN vs. pKa of the conjugate acids of the pyridines) are all biphasic (linear portions at high and low pKa and a curvature in between). These plots are in accordance with a stepwise mechanism, through a zwitterionic tetrahedral intermediate (T±), and a change in the rate‐determining step from formation of T± to its breakdown to products, as the pyridine basicity decreases. Also studied are the effects of the leaving, non‐leaving, and electrophilic groups of the substrate, and of the amine nature, on the ${\rm p}K_{\rm a}^0 $ value (value at the center of curvature of the Brønsted‐type plots). Copyright © 2008 John Wiley & Sons, Ltd.
Concentration controlled multilevel self‐assembly of 3‐armed poly(ethylene glycol)‐b‐poly(ε‐caprolactone) block copolymers investigated by AFM
Authors: Guo Shengrong , Zhang Yaqiong
Published: May 2008

Concentration dependent morphology of 3‐armed poly(ethylene glycol)‐b‐poly(ε‐caprolactone) copolymer aggregates in aqueous system was investigated by atomic force microscopy (AFM). The AFM results show that, at a low concentration, 4 × 10−5 g/mL, spherical micelles occur, and unmicellized molecules are not distributed homogeneously in the copolymer aqueous solution. Unequal outspread clusters composed of wormlike aggregates are formed at a moderate copolymer concentration, 4 × 10−4 g/mL, those wormlike aggregates are orderly packed in the clusters. At a high concentration of 0.05 g/mL, the copolymer aqueous system is indeed a gel at room temperature, outspread clusters of wormlike aggregates join together to forma network structure. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1412–1418, 2008
Polyisobutylene: A most unusual polymer
Authors: Kunal K. , Paluch M. , Roland C. M. , Puskas J. E. , Chen Y. , Sokolov A. P.
Published: May 2008

The influence of molecular weight, M, on the fragility and fast dynamics in polyisobutylene (PIB) was studied using dielectric and mechanical relaxation spectroscopies, calorimetry, and Raman spectroscopy. The measurements indicate a decrease in fragility with increasing M for shorter chains, in the range of M where Tg is M‐dependent. Such behavior is not observed for other polymers and is at odds with traditional theoretical models that predict an increase in fragility with chain length. These results confirm the unusual character of PIB, as evident in various properties including extremely low gas permeability, a low fragility, and a segmental relaxation spectrum much broader than expected for a low‐fragility material. The reason for this anomalous behavior remains unclear, but might be related to the symmetric structure of the PIB repeat unit, together with comparable flexibility of both structural components, the backbone and side groups. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1390–1399, 2008
Novel insights on the mechanism of action of α‐amylase inhibitors from the plant defensin family
Authors: Pelegrini Patrícia B. , Lay Fung T. , Murad André M. , Anderson Marilyn A. , Franco Octavio L.
Published: May 2008

Plant defensins are small cysteine‐rich proteins commonly synthesized in plants, encoded by large multigene families. Most plant defensins that have been characterized to date show potent antifungal and/or bactericidal activities. This report describes VuD1, an unusual defensin that is able to inhibit insect‐pest α‐amylases. VuD1 was cloned from cowpea (Vigna unguiculata) seeds and expressed in a heterologous system. Inhibitory enzyme assays showed that VuD1 efficiently inhibits α‐amylases from the weevils Acanthoscelides obtectus and Zabrotes subfasciatus, caused low inhibition toward mammalian enzymes and was unable to inhibit the α‐amylases from Callosobruchus maculatus and Aspergillus fumigatus. To shed some light over the mechanism of action of VuD1, molecular modeling analyses were performed, revealing that the N‐terminus of the molecule is responsible for binding with the active site of weevil enzymes. Moreover, models of VuD1 and mammalian enzymes were also generated to elucidate the specificity mechanisms. The data presented herein suggests that this defensin has potential application in the development of transgenic plants for insect pest control. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron
Authors: Feng Yaping , Jernigan Robert L. , Kloczkowski Andrzej
Published: May 2008

The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices (Bagci et al., Proteins 2003;53:56–67; Raghunathan et al., Protein Sci 1997;6:2072–2083). In this work, instead of a lattice we use the regular polyhedron, the icosahedron, as the model to describe the orientational distribution of contacts in clusters derived from a high‐resolution protein dataset (522 protein structures with high resolution < 1.5 Å). We find that the order parameter (orientation function) measuring the angular overlap of directions in coordination clusters with directions of the icosahedron is 0.91, which is a significant improvement in comparison with the value 0.82 for the order parameter with the face‐centered cubic (fcc) lattice. Close packing tendencies and patterns of residue packing in proteins are considered in detail and a theoretical description of these packing regularities is proposed. Proteins 2008. © 2008 Wiley‐Liss, Inc.
HIV‐1 protease function and structure studies with the simplicial neighborhood analysis of protein packing method
Authors: Zhang Shuxing , Kaplan Andrew H. , Tropsha Alexander
Published: May 2008

The Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method was used to predict the effect of mutagenesis on the enzymatic activity of the HIV‐1 protease (HIVP). SNAPP relies on a four‐body statistical scoring function derived from the analysis of spatially nearest neighbor residue compositional preferences in a diverse and representative subset of protein structures from the Protein Data Bank. The method was applied to the analysis of HIVP mutants with residue substitutions in the hydrophobic core as well as at the interface between the two protease monomers. Both wild‐type and tethered structures were employed in the calculations. We obtained a strong correlation, with R2 as high as 0.96, between ΔSNAPP score (i.e., the difference in SNAPP scores between wild‐type and mutant proteins) and the protease catalytic activity for tethered structures. However, a weaker but significant correlation was obtained for nontethered structures. Our analysis identified residues both in the hydrophobic core and at the dimeric interface that are very important for the protease function. This study demonstrates a potential utility of the SNAPP method for rational design of mutagenesis studies and protein engineering. Proteins 2008. © 2008 Wiley‐Liss, Inc.
How general is the nucleation–condensation mechanism?
Authors: Nölting Bengt , Agard David A.
Published: May 2008

We investigate the structures of the major folding transition states of nine proteins by correlation of published Φ‐values with inter‐residue contact maps. Combined with previous studies on six proteins, the analysis suggests that at least 10 of the 15 small globular proteins fold via a nucleation–condensation mechanism with a concurrent build‐up of secondary and tertiary structure contacts, but a structural consolidation that is clearly nonuniformly distributed over the molecule and most intense in a single structural region suggesting the occurrence of a single folding nucleus. However, on average helix‐ and sheet‐forming residues show somewhat larger Φ‐values in the major transition state, suggesting that secondary structure formation is one important driving force in the nucleation–condensation in many proteins and that secondary‐structure forming residues tend to be more prominent in folding nuclei. We synthesize the combined information on these 10 of 15 proteins into a unified nucleation–condensation mechanism which also accounts for effects described by the framework, hydrophobic collapse, zipper, and funnel models. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Very fast prediction and rationalization of pKa values for protein–ligand complexes
Authors: Bas Delphine C. , Rogers David M. , Jensen Jan H.
Published: May 2008

The PROPKA method for the prediction of the pKa values of ionizable residues in proteins is extended to include the effect of non‐proteinaceous ligands on protein pKa values as well as predict the change in pKa values of ionizable groups on the ligand itself. This new version of PROPKA (PROPKA 2.0) is, as much as possible, developed by adapting the empirical rules underlying PROPKA 1.0 to ligand functional groups. Thus, the speed of PROPKA is retained, so that the pKa values of all ionizable groups are computed in a matter of seconds for most proteins. This adaptation is validated by comparing PROPKA 2.0 predictions to experimental data for 26 protein–ligand complexes including trypsin, thrombin, three pepsins, HIV‐1 protease, chymotrypsin, xylanase, hydroxynitrile lyase, and dihydrofolate reductase. For trypsin and thrombin, large protonation state changes (|n| > 0.5) have been observed experimentally for 4 out of 14 ligand complexes. PROPKA 2.0 and Klebe's PEOE approach (Czodrowski P et al. J Mol Biol 2007;367:1347–1356) both identify three of the four large protonation state changes. The protonation state changes due to plasmepsin II, cathepsin D and endothiapepsin binding to pepstatin are predicted to within 0.4 proton units at pH 6.5 and 7.0, respectively. The PROPKA 2.0 results indicate that structural changes due to ligand binding contribute significantly to the proton uptake/release, as do residues far away from the binding site, primarily due to the change in the local environment of a particular residue and hence the change in the local hydrogen bonding network. Overall the results suggest that PROPKA 2.0 provides a good description of the protein–ligand interactions that have an important effect on the pKa values of titratable groups, thereby permitting fast and accurate determination of the protonation states of key residues and ligand functional groups within the binding or active site of a protein. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Pepsinogen‐like activation intermediate of plasmepsin II revealed by molecular dynamics analysis
Authors: Friedman Ran , Caflisch Amedeo
Published: May 2008

Plasmepsins are pharmaceutically relevant aspartic proteases involved in haemoglobin degradation by the malaria causing parasites Plasmodium spp. They are translated as inactive proenzymes, with an elongated prosegment. On prosegment cleavage, plasmepsins undergo a series of hitherto unresolved conformational changes before becoming active. Here, the flexibility of plasmepsin and proplasmepsin and the activation process are investigated by multiple explicit water molecular dynamics simulations. The large N‐terminal displacement and the interdomain shift from the proenzyme structure to active plasmepsin are promoted by essential dynamics sampling. An intermediate, stabilized by electrostatic interactions between the catalytic dyad and the N‐terminus of mature plasmepsin, is observed along all activation trajectories. Notably, the stabilizing interactions in the activation intermediate of plasmepsin are similar to those in the X‐ray structure of pepsinogen. In particular, the catalytic aspartates act as hydrogen bond acceptors for the N‐terminal amino group and the Ser2 hydroxyl in plasmepsin, and the side chains of Lys36pro and Tyr9 in pepsinogen. The simulation results are used to suggest in vitro experiments to test the conformational transitions involved in the maturation of plasmepsin, and design small‐molecule inhibitors. Proteins 2008. © 2008 Wiley‐Liss, Inc.