bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phytochemical analysis of the Southern Australian marine alga, Plocamium mertensii using HPLC‐NMR
Authors: Dias Daniel , Urban Sylvia 
Published: May 2008

AbstractIntroduction: 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

AbstractIn 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

AbstractA 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractThe 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

AbstractConcentration 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

AbstractThe 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

AbstractPlant 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

AbstractThe 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

AbstractThe 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

AbstractWe 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

AbstractThe 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

AbstractPlasmepsins 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.