bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution
Authors: Fragaki Georgia , Stefanaki Irine , Dais Photis , Mikros Emmanuel 
Published: October 2008

AbstractPhase‐sensitive nuclear Overhauser enhancement spectroscopy (NOESY) experiments, 3J couplings and computational molecular modeling (MM2* and MMFF force fields) were employed to examine the conformational properties of verrucarin A in chloroform solutions. The MMFF force field calculations resulted in a family of 12 low‐energy structures along with their populations, the latter being determined by the NMR analysis of molecular flexibility in solution(NAMFIS) deconvolution analysis. The concluded model was capable of reproducing successfully the experimental NOESY cross‐peak volumes and the proton‐coupling constants. Among the 12 conformers, the one which was similar to the structure of verrucarin A in the solid state was the predominant accounting for 75% of the total relative population, although other low‐energy conformations contributed to a lesser degree in order to explain the experimental data. Copyright © 2008 John Wiley & Sons, Ltd.
Structural elucidation of propargylated products of 3‐substituted‐1,2,4‐triazole‐5‐thiols by NMR techniques
Authors: Chaudhary Preeti M. , Chavan Sayalee R. , Kavitha M. , Maybhate Shailaja P. , Deshpande Sunita R. , Likhite Anjali P. , Rajamohanan P. R. 
Published: October 2008

AbstractPropargylation of 3‐substituted‐1,2,4‐triazole‐5‐thiols, which predominantly exist as their thione tautomers, was carried out with the view to synthesize different heterocycles and study their biological activity. Three different products namely, a mono S‐propargyl and two S,N‐dipropargyl regioisomers, arising from N1/N2 substitution, were isolated and characterized. Unambiguous structural elucidation of the regioisomers of S,N‐dipropargyl derivatives was achieved by means of 13C1H HMBC technique. The proportion of the regioisomers was found to vary with the substituent on the 1,2,4‐triazole thiols. No product corresponding to N4 substitution was isolated from any of the reactions carried out. Copyright © 2008 John Wiley & Sons, Ltd.
Complete 1H and 13C NMR spectral assignment of benzo[d]isothiazole derivatives and of an isoindole isoster
Authors: Incerti Matteo , Acquotti Domenico , Vicini Paola 
Published: October 2008

AbstractThe complete 1H and 13C NMR assignments of the novel compound methyl 2‐amino‐3‐(benzo[d]isothiazol‐3‐yl)propanoate (1), of 3‐amino‐5‐methylbenzo[d]isothiazole (2) and N‐(t‐butyloxycarbonyl)‐2‐aminobenzo[d]isothiazol‐3(2H)‐one (3) and of the desulfurated isostere of 3, N‐(t‐butyloxycarbonyl)‐2‐aminoisoindolin‐1‐one (4), using 1D and 2D NMR techniques, including COSY, INADEQUATE, HSQC, and HMBC experiments are reported. Copyright © 2008 John Wiley & Sons, Ltd.
Real time HR–MAS NMR: application in reaction optimization, mechanism elucidation and kinetic analysis for heterogeneous reagent catalyzed small molecule chemistry
Authors: Roy Abhijeet Deb , Jayalakshmi K. , Dasgupta Somnath , Roy Raja , Mukhopadhyay Balaram 
Published: October 2008

AbstractA novel application of in situ 1H high‐resolution magic angle spinning (HR–MAS) NMR technique for real‐time monitoring of H2SO4‐silica promoted formation of 2, 2‐disubstituted quinozolin‐4(3H)‐ones is reported. The detailed NMR spectroscopic data led to elucidation of the mechanism, reaction optimization, kinetics and quantitative analysis of the product accurately and efficiently. The translation of the optimized parameters obtained by 1H HR–MAS NMR in the wet laboratory provided similar results. It is proposed that 1H HR‐MAS has a potential utility for optimization of various organic transformations in solid supported catalyzed reactions. Copyright © 2008 John Wiley & Sons, Ltd.
The efficacy of the bioadhesive patches containing licorice extract in the management of recurrent aphthous stomatitis
Authors: Moghadamnia A. A. , Motallebnejad M. , Khanian M. 
Published: October 2008

AbstractThis study evaluated the efficacy of licorice bioadhesive hydrogel patches to control the pain and reduce the healing time of recurrent aphthous ulcer.This study was carried out in three episodes of ulcers: in the first episode of ulcer, all 15 patients were asked to record their baseline individual pain level by a visual analog scale. In the second and third episodes, comparative and consecutive subjective and objective evaluations of the bioadhesive were done. The effects of the following variables were investigated: (1) VAS pain score for 5 consecutive days, (2) profile of aphthous ulcers on days 3 and 5, (3) time to complete relief of pain and healing of the ulcers, (4) diameter of the lesions and necrotic zone.A significant reduction in VAS was recorded following application of the licorice patches on days 2, 3, 4 and 5 compared with the no‐treatment group (p < 0.001). Licorice patches caused a significant reduction in the diameter of the inflammatory halo and necrotic center compared with the placebo group (p = 0.03).According to the results of this study, licorice bioadhesive can be effective in the reduction of pain and of the inflammatory halo and necrotic center of aphthous ulcers. Copyright © 2008 John Wiley & Sons, Ltd.
Impact of initial condition uncertainties on the predictability of heavy rainfall in the Mediterranean: a case study
Authors: Argence Sébastien , Lambert Dominique , Richard Evelyne , Chaboureau Jean‐Pierre , Söhne Nathalie 
Published: October 2008

AbstractThis study explores the predictability of a heavy rainfall event that struck North Africa on 9 and 10 November 2001. This case is a paradigm of Mediterranean extreme events characterized by the presence of a deep upper‐level trough associated with an intense cyclone which developed over the Western Mediterranean basin. Using the French non‐hydrostatic mesoscale model MESO‐NH, numerical experiments starting from various initial atmospheric states were conducted to assess the impact of initial condition uncertainties on the precipitation and cloud cover forecast. To generate a set of perturbed atmospheric states, a simple date‐shifting initialization method was used. Two sets of simulations were run, using lateral boundaries and initial conditions derived from both the French operational global assimilation system Action de Recherche Petite Echelle Grande Echelle (ARPEGE) and the European Centre for Medium‐Range Weather Forecasts (ECMWF) system. Initial perturbations applied to the upper‐level trough propagated and intensified throughout the simulation, leading to some discrepancy in the forecast of the low‐level cyclone. While it was found that the upper‐level trough and the surface cyclone controlled the location of the overall precipitation pattern, the predictability of smaller‐scale features such as localized heavy rainfall was directly related to specific mesoscale structures. The low‐level jet associated with the surface cyclone and the location and the intensity of the surface‐low both impact upon the triggering and the sustainment of the convective cells. In consequence, small‐scale perturbations of these mesoscale features led to large errors in the precipitation forecast, especially in the Algiers area. Copyright © 2008 Royal Meteorological Society
Degradation of the insecticides thiamethoxam and imidacloprid by zero‐valent metals exposed to ultrasonic irradiation in water medium: electrospray ionization mass spectrometry monitoring
Authors: Lopes Renata P. , de Urzedo Ana P. F. M. , Nascentes Clésia C. , Augusti Rodinei 
Published: October 2008

AbstractThe degradation of thiamethoxam (1) and imidacloprid (2), prototype neonicotinoid insecticides bearing a characteristic N‐NO2 moiety in their structures, promoted by a number of zero‐valent metals (Fe, Sn, Zn) upon ultrasonic irradiation in acidic aqueous solution (pH 2) was investigated. It was verified that thiamethoxam (1) and imidacloprid (2) are quickly and almost completely consumed under these experimental conditions (degradation >90% after a reaction time of 30 min) and that ultrasonic irradiation strongly enhances the degradation rate for both insecticides, especially when zinc and tin are employed. Based on the results from electrospray ionization mass (and tandem mass) spectrometry in the positive ion mode, degradation routes for both insecticides, comprising an initial NO2 → NH2 reduction, were proposed. In addition, products from the dehydrochlorination of imidacloprid were also found to be formed under these conditions. Copyright © 2008 John Wiley & Sons, Ltd.
Binding studies of nNOS‐active amphibian peptides and Ca2+ calmodulin, using negative ion electrospray ionisation mass spectrometry
Authors: Pukala Tara L. , Urathamakul Thitima , Watt Stephen J. , Beck Jennifer L. , Jackway Rebecca J. , Bowie John H. 
Published: October 2008

AbstractAmphibian peptides which inhibit the formation of nitric oxide by neuronal nitric oxide synthase (nNOS) do so by binding to the protein cofactor, Ca2+calmodulin (Ca2+CaM). Complex formation between active peptides and Ca2+CaM has been demonstrated by negative ion electrospray ionisation mass spectrometry using an aqueous ammonium acetate buffer system. In all cases studied, the assemblies are formed with a 1:1:4 calmodulin/peptide/Ca2+ stoichiometry. In contrast, the complex involving the 20‐residue binding domain of the plasma Ca2+ pump C20W (LRRGQILWFRGLNRIQTQIK‐OH) with CaM has been shown by previous two‐dimensional nuclear magnetic resonance (2D NMR) studies to involve complexation of the C‐terminal end of CaM. Under identical conditions to those used for the amphibian peptide study, the ESI complex between C20W and CaM shows specific 1:1:2 stoichiometry. Since complex formation with the studied amphibian peptides requires Ca2+CaM to contain its full complement of four Ca2+ ions, this indicates that the amphibian peptides require both ends of the CaM to effect complex formation. Charge‐state analysis and an H/D exchange experiment (with caerin 1.8) suggest that complexation involves Ca2+CaM undergoing a conformational change to a more compact structure. Copyright © 2008 John Wiley & Sons, Ltd.
Fractional mass filtering as a means to assess circulating metabolites in early human clinical studies
Authors: Tiller Philip R. , Yu Sean , Bateman Kevin P. , Castro‐Perez Jose , Mcintosh Ian S. , Kuo Yushin , Baillie Thomas A. 
Published: October 2008

AbstractRecent changes in the regulatory environment have led to a need for new methods to assess circulating human drug metabolites in early clinical studies with respect to their potential toxicological impact. The specific goals of such studies are to determine if the metabolites present in human plasma following administration of a drug candidate also are observed in plasma from the animal studies employed for preclinical toxicological evaluation, and to estimate corresponding exposure margins (animal:human) for the major metabolites. Until recently, the accepted best practice for the characterization of circulating drug metabolites utilized liquid chromatography/tandem mass spectrometry (LC/MS/MS)‐based methodologies, in conjunction with authentic chemical standards, for the detection and quantitative analyses of metabolites predicted from both animal studies and experiments with human liver preparations in vitro. While this approach is satisfactory for anticipated biotransformation products, metabolites that were not expected to circulate in human plasma frequently escape detection. Current accurate mass instruments enable the use of the technique of fractional mass filtering to detect both expected and unexpected metabolites in a rapid, less resource‐intensive and more robust manner. Application of this technology to several clinical development programs at Merck Research Laboratories has demonstrated the value of fractional mass filtering in the assessment of circulating drug metabolites in early clinical trials. Copyright © 2008 John Wiley & Sons, Ltd.
Mass spectrometry for the characterization of unsulfated chondroitin oligosaccharides from 2‐mers to 16‐mers. Comparison with hyaluronic acid oligomers
Authors: Volpi Nicola , Zhang Zhenqing , Linhardt Robert J. 
Published: October 2008

AbstractThis study reports for the first time the complete liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) and tandem mass spectrometry (MS/MS) analyses performed in negative ion mode of saturated unsulfated chondroitin oligosaccharides up to 16‐mers and comparison with hyaluronic acid (HA) oligomers differing only in the nature of the hexosamine residue. MS/MS of the chondroitin disaccharide on the singly charged precursor at m/z 396.1 afforded a glycosidic cleavage C1 product ion at m/z 192.9. In the tetrasaccharide, C2 (m/z 396.0) and C3 (m/z 572.0) product anions were generated by glycosidic cleavage. A C5 [M–2H]2− product ion at m/z 475.1 was generated by the glycosidic cleavage of the hexasaccharide, and a C7 ion (m/z 664.6, charge state of −2) was produced from the octasaccharide. The same fragmentation pattern of deprotonated oligomers was observed for the largest oligosaccharides, from 10‐ to 16‐mers. There has been no previous report of MS/MS spectra for unsulfated chondroitin oligomers of these sizes. Unsulfated saturated chondroitin oligosaccharides with x‐mer units and larger than a tetrasaccharide dissociate to almost exclusively form CX–1‐type ions. Saturated HA oligomers also afforded the same fragmentation pattern as deprotonated oligomers by ESI‐MS and MS/MS analyses. Thus, under the experimental conditions used in the current study, we were unable to distinguish between unsulfated chondroitin and HA. Copyright © 2008 John Wiley & Sons, Ltd.
Thermal formation of mixed‐metal inorganic complexes at atmospheric pressure
Authors: Peng Wen‐Ping , Goodwin Mike P. , Chen Hao , Cooks R. Graham , Wilker Jonathan 
Published: October 2008

AbstractAtmospheric‐pressure thermal desorption ionization (APTDI), a new variant on older ionization methods, is employed to generate gas‐phase ions from inorganic and organometallic compounds. The method is compared to conventional electrospray ionization (ESI) of these compounds and found in most cases examined to yield simpler mass spectra which are useful in the characterization of the pure compounds. Cluster formation, however, is prominent in these spectra and mixtures of V(IV)O(salen), Ni(II)(salen) and Co(II)(salen) show mixed‐metal cluster ions. This makes APTDI a way to prepare gas‐phase ions which contain multiple selected metal atoms and ligands. Such mixed‐metal complexes can be mass‐selected and structurally characterized by tandem mass spectrometry. Strong contrasts are evident in the dissociation behavior of homonuclear and heteronuclear metal clusters, the latter showing accompanying redox processes. The chemical reactivity accompanying collision‐induced dissociation (CID) of some of the mixed‐metal clusters is typified by the protonated species H+[NiVO(salen)], which undergoes a formal oxidation process (hydrogen atom loss) to give the molecular radical cation of Ni(salen). This ionization method may provide a new route to unique inorganic compounds on surfaces through soft landing of appropriate cluster ions. The contrasting behavior of the ESI and APTDI processes is evident in the salens where ESI shows simple Bronsted acid/base chemistry, no mixed‐metal clusters and no redox chemistry. Copyright © 2008 John Wiley & Sons, Ltd.
A computational approach to characterizing bond linkages of glycan isomers using matrix‐assisted laser desorption/ionization tandem time‐of‐flight mass spectrometry
Authors: Sheng Quanhu , Mechref Yehia , Li Yixue , Novotny Milos V. , Tang Haixu 
Published: October 2008

AbstractGlycans commonly exhibit variations in their branching structures and glycosidic bond linkages, in addition to their sequence variation. These glycan features are known to be highly correlated with their biological functions. It is relatively straightforward to deduce the composition and sequence of monosaccharides of a glycan from its tandem mass spectra. However, the characterization of the linkage types of each glycosidic bond is still analytically challenging. In this paper, we present a rank‐based discriminative model to differentiate between two types of glycosidic linkages (namely, 1‐4 and 1‐6) based on the cross‐ring fragmentation patterns of the corresponding glycans observed under high‐energy collision‐induced dissociation (CID). To train our models, we acquired tandem mass spectra for three groups of both native and permethylated linear oligoglucoses using a matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI/TOF/TOF) instrument. Based on a 5‐fold cross‐validation, the prediction accuracies of our model for native glycans are determined to be about 88.4% and 92.9% for 1‐6 and 1‐4 linkages, respectively. The accuracies determined for permethylated glycans are slightly lower, but comparable: 85.6% and 89.0% for 1‐6 and 1‐4 linkages, respectively. Our method is implemented as a web‐hosted utility, thus making it readily accessible to the public which can be accessed through http://ggdb.informatics.indiana.edu:8080/glycanview. Copyright © 2008 John Wiley & Sons, Ltd.
A non‐covalent dimer formed in electrospray ionisation mass spectrometry behaving as a precursor for fragmentations
Authors: Pan Hefeng 
Published: October 2008

AbstractA non‐covalent‐bonded dimer was detected in the positive ion electrospray ionisation (ESI) mass spectra of a synthetic impurity. In tandem mass spectrometry (MS/MS) experiments using collision‐induced dissociation (CID), the ion was found to behave as a [M+H]+‐type precursor ion for fragmentation until MS5. The dimer was probably formed through multi‐hydrogen bonds over a proton bridge. When the fragmentation occurred at the center of the bridge, the dimer was broken apart to give monomer fragments at MS6. However, no corresponding deprotonated dimer [2M–H]− was found in the negative ion ESI spectra. The dimer was extremely stable, and it could still be observed when a fragmentation voltage of up to 50 V was applied in the ionisation source. The formation of the non‐covalent dimer was also found to be instrument‐dependent, but independent of sample concentration. Accurate mass measurements of the [2M+H]+ and [M+H]+ ions, and their MSn product ions, provided the basis for assessing the fragmentation mechanism proposed for [2M+H]+. The fragmentation pathway was also illustrated for the deprotonated molecule [M–H]−. Copyright © 2008 John Wiley & Sons, Ltd.
Summary of ISO/TC 201 standard: XXXIII, ISO 18115:2001/Amd. 2:2007—Surface Chemical Analysis—Vocabulary—Amendment 2
Authors: Seah M. P. 
Published: October 2008

AbstractThis International Standard adds a further 87 terms to this Vocabulary series, many for secondary ion mass spectrometry, elastic peak electron spectroscopy and reflected electron energy loss spectroscopy, together with 76 acronyms for scanned probes, 33 definitions of scanned probe techniques, 6 terms for contact mechanics and 147 terms for concepts in scanned probe analysis. This brings the total number of terms and acronyms to over 750 in these documents. The terms cover words or phrases used in describing the samples, instruments and theoretical concepts involved in surface chemical analysis. Copyright © 2008 John Wiley & Sons, Ltd.
Etching characteristics of GaN by plasma chemical vaporization machining
Authors: Nakahama Yasuji , Kanetsuki Norio , Funaki Takeshi , Kadono Masaru , Sano Yasuhisa , Yamamura Kazuya , Endo Katsuyoshi , Mori Yuzo 
Published: October 2008

AbstractA high‐quality bulk gallium nitride (GaN) substrate, which is suitable for high‐quality homoepitaxial growth, is indispensable for realizing high‐performance GaN devices. With improvement in the quality of the bulk GaN substrate, the removal of subsurface damage induced during surface polishing has become increasingly necessary. To remove the subsurface damage from the bulk GaN substrate, a chemical finishing method that does not produce further damage is required. We applied plasma chemical vaporization machining (CVM) to remove the subsurface damage from the bulk GaN substrate. In this study, we investigated the etching characteristics of GaN by plasma CVM applying atmospheric pressure Cl2/He plasma. The maximum removal rate in the depth direction by plasma CVM was 9100 nm/min, which is seven times greater than that of reactive ion etching (RIE). The activation energy in plasma CVM was estimated to be 2.1 kcal/mol, which is 1.75 times greater than that in RIE. It is supposed that some of the energy required for the removal reaction in RIE is supplied by ion bombardment, but plasma CVM depends on only a chemical reaction without high‐energy ion collision. This result suggests that plasma CVM is a finishing method that causes less subsurface damage than RIE. Copyright © 2008 John Wiley & Sons, Ltd.
Long-term peritoneal dialysis and encapsulating peritoneal sclerosis in children
Authors: Honda Masataka , Warady Bradley A. 
Published: October 2008

AbstractEncapsulating peritoneal sclerosis (EPS) is the most serious complication of long-term peritoneal dialysis (PD), with a mortality rate that exceeds 30%. There have been many reports of the incidence of EPS being strongly correlated to the duration of PD. Patients on PD for longer than 5 years, and especially those receiving this treatment for more than 8 years, should undergo careful and repeated surveillance for risk factors associated with the development of EPS. The development of ultrafiltration failure, a high dialysate/plasma creatinine ratio, as determined by the peritoneal equilibration test, peritoneal calcification, a persistently elevated C-reactive protein level, and severe peritonitis in patients on PD for longer than 8 years are signals that should prompt the clinician to consider terminating PD as a possible means of preventing the development of EPS. The impact of the newer, biocompatible PD solutions on the incidence of EPS has not yet been determined.
Expression and Characterization of CYP51, the Ancient Sterol 14‐demethylase Activity for Cytochromes P450 (CYP), in the White‐Rot Fungus Phanerochaete chrysosporium
Authors: Warrilow Andrew , Ugochukwu Cynthia , Lamb David , Kelly Diane , Kelly Steven 
Published: October 2008

AbstractPhanerochaete chrysosporium was the first fungal genome to exhibit more than one hundred cytochrome P450 (CYP) genes for a fungus within its genome (~150). It can metabolize lignocellulose and a wide range of environmental xenobiotics including many carcinogens and pollutants where cytochromes P450 may be involved. In the present paper we describe the heterologous expression and characterization of an ancestral CYP form, sterol 14α‐demethylase (CYP51—EC1.14.13.70), from this organism. CYP51 was cloned from a cDNA library and expressed in both Escherichia coli, where it exhibited high affinity for azole antifungals, and Saccharomyces cerevisiae. Proof of function was observed by complementation of a conditional knock‐down mutant of yeast CYP51. The CYP51 gene was found to be 1,956 bases long and contained 7 exons and 6 introns coding for a polypeptide 550 amino acids long (62 kDa). The CYP51 protein exhibited high affinity (kd 0.25–0.45 μM) for azole antifungal compounds.