bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamic and structural properties of methanol–water solutions using nonadditive interaction models
Authors: Zhong Yang , Warren G. Lee , Patel Sandeep 
Published: December 2007

AbstractWe study bulk structural and thermodynamic properties of methanol–water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P‐FQ potential for water–water interactions, and the CHARMM‐based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol–methanol and methanol–water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self‐diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol–water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol–water gas‐phase interaction energy for the lowest‐energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P‐FQ water are predicted to be −5.6 ± 0.2 kcal/mol, in respectable agreement with the experimental value of −5.1 kcal/mol. With respect to solution microstructure, the present cluster analysis suggests that the microscale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bipercolating network structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
An improved pairwise decomposable finite‐difference Poisson–Boltzmann method for computational protein design
Authors: Vizcarra Christina L. , Zhang Naigong , Marshall Shannon A. , Wingreen Ned S. , Zeng Chen , Mayo Stephen L. 
Published: December 2007

AbstractOur goal is to develop accurate electrostatic models that can be implemented in current computational protein design protocols. To this end, we improve upon a previously reported pairwise decomposable, finite difference Poisson–Boltzmann (FDPB) model for protein design (Marshall et al., Protein Sci 2005, 14, 1293). The improvement involves placing generic sidechains at positions with unknown amino acid identity and explicitly capturing two‐body perturbations to the dielectric environment. We compare the original and improved FDPB methods to standard FDPB calculations in which the dielectric environment is completely determined by protein atoms. The generic sidechain approach yields a two to threefold increase in accuracy per residue or residue pair over the original pairwise FDPB implementation, with no additional computational cost. Distance dependent dielectric and solvent‐exclusion models were also compared with standard FDPB energies. The accuracy of the new pairwise FDPB method is shown to be superior to these models, even after reparameterization of the solvent‐exclusion model. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Time‐averaged predictions of folded and misfolded peptides using a reduced physicochemical model
Authors: Clarke Oliver J. , Parker Martin J. 
Published: December 2007

AbstractEnergy‐based methods for calculating time‐averaged peptide structures are important for rational peptide design, for defining local structure propensities in large protein chains, and for exploring the sequence determinants of amyloid formation. High‐end methods are currently too slow to be practicable, and will remain so for the foreseeable future. The challenge is to create a method that runs quickly on limited computer resources and emulates reality sufficiently well. We have developed a simplified off‐lattice protein model, incorporating semi‐empirical physicochemical potentials, and combined it with an efficient Monte Carlo method for calculating time‐averaged peptide structures. Reasonably accurate predictions are found for a set of small α‐helical and β‐hairpin peptides, and we demonstrate a potential application in measuring local structure propensities in protein chains. Time‐averaged structures have also been calculated for a set of small peptides known to form β‐amyloid fibrils. The simulations were of three interacting peptides, and in each case the time‐averaged structure describes a three‐stranded β‐sheet. The performance of our method in measuring the propensities of small peptides to self‐associate into possible prefibrillar species compares favorably with more detailed and CPU‐intensive approaches. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Complete basis set limit ofAb initiobinding energies and geometrical parameters for various typical types of complexes
Authors: Min Seung Kyu , Lee Eun Cheol , Lee Han Myoung , Kim Dong Young , Kim Dongwook , Kim Kwang S. 
Published: December 2007

AbstractUsing basis‐set extrapolation schemes for a given data set, we evaluated the binding energies and geometries at the complete basis set (CBS) limit at the levels of the second order Møller–Plesset perturbation theory (MP2) and the coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)]. The systems include the hydrogen bonding (water dimer), aromatic interaction (benzene dimer), π–H interaction (benzene–water), cation–water, anion–water, π–cation interaction (cation–benzene), and π–anion interaction (anion–triazine). One extrapolation method is to exploit both BSSE‐corrected and BSSE‐uncorrected binding energies for the aug‐cc‐pVNZ (N= 2, 3, 4, …) basis set in consideration that both binding energies give the same CBS limit (CBSB). Another CBS limit (CBSC) is to use the commonly known extrapolation approach to exploit that the electron correlation energy is proportional toN−3. Since both methods are complementary, they are useful for estimating the errors and trend of the asymptotic values. There is no significant difference between both methods. Overall, the values of CBSCare found to be robust because of their consistency. However, for smallN(in particular, forN= 2, 3), CBSis found to be slightly better for water–water interactions and cation–water and cation–benzene interactions, whereas CBSis found to be more reliable for bezene–water and anion–water interactions. We also note that the MP2 CBS limit value based onN= 2 and 3 combined with the difference between CCSD(T) and MP2 atN= 2 would be exploited to obtain a CCSD(T)/CBS value for aromatic–aromatic interactions and anion–π interactions, but not for cationic complexes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Computational studies on the dimers and the thermal dimerization of norbornadiene
Authors: Wu Yong , Xue Ying , Kim Chan Kyung 
Published: December 2007

AbstractIn this study, 14 norbornadiene (NBD) dimers and the thermal dimerization mechanism were studied using the hybrid density functional theory (B3LYP) and the second‐order multiconfigurational perturbation theory (CASPT2). In the process of dimerization, the biradical stationary points were located using the unrestricted, broken‐spin, symmetry approach. The pathways were divided into eight parts to aid the analysis of their mechanisms. Our results indicated that the process for the formation of the cage‐like heptacyclo[6.6.0.0.2, 60.3, 130.4, 1105, 9.010, 14] tetradecane (HCTD, D14) is highly exothermic (92.15 kcal/mol), indicating that D14 is the most stable NBD dimer. However, the formation of D14 is very difficult to achieve kinetically because of a higher barrier in the thermal dimerization. On the contrary, the formation of exo‐cis‐exo (D5) is kinetically favorable, but thermodynamically unfavorable at higher temperature. Therefore, the combination of both thermodynamic and kinetic factors indicated that the formation of exo‐exo (D9), which resembles the product of the pseudo‐Diels‐Alder addition, is most likely in the NBD dimerization. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Microbial growth reduction in sewage sludge by stirred ball mill disintegration and estimation by respirometry
Authors: Lajapathi Rai Chockalingam , Mueller Johannes , Struenkmann Georg , Gangadhar Rao Paruchuri 
Published: December 2007

AbstractBACKGROUND: Excess biomass generation in wastewater treatment plants is an unavoidable byproduct of the degradation process. Treatment and disposal of sewage sludge from wastewater treatment plants accounts for about half or even up to 60% of the total operating cost. The present study focuses on the reduction of excess sludge generation by engineering the microbes through mechanical energy inputs by means of stirred ball milling.RESULTS: The significant achievement of this study is microbial growth reduction of up to 89% at an applied specific energy of 15301 kJ kg−1. The degree of disintegration of microbial cells was substantiated by estimating the degree of inactivation (DDO), degree of soluble chemical oxygen demand (COD) release (DDCOD), particle size and microscopic examination. The effect of disintegration on sludge microbial growth reduction is proved by respirometric studies.CONCLUSIONS: Sludge disintegration employing stirred ball milling is proved to be a worthwhile pretreatment process for reducing the sludge microbial growth in activated sludge treatment processes. Copyright © 2007 Society of Chemical Industry
Evaluation of glycosylation and malonylation patterns in flavonoid glycosides during LC/MS/MS metabolite profiling
Authors: Kachlicki P. , Einhorn J. , Muth D. , Kerhoas L. , Stobiecki M. 
Published: December 2007

AbstractFlavonoid conjugates constitute several classes of plant phenolic secondary metabolites including many isomeric compounds differing in the hydroxylation pattern and substitution of their rings with different groups such as alkyls, acyls or sugars. These compounds occur in plant tissues mainly as glycosides and in many cases it is necessary to have reliable and detailed information concerning the structure of these natural products. Our results were obtained using leaf extracts of Arabidopsis thaliana and Lupinus angustifolius in which different glycosides of flavones, flavonols and isoflavones are present. Analysis of collision‐induced dissociation (CID)/MS/MS spectra of protonated [M + H]+, sodiated [M + Na]+ or deprotonated [M − H]− molecules recorded during HPLC runs may bring needed information in this respect. However, registration of mass spectra of [M + Na]+ ions with a good efficiency is possible only after post‐column addition of a sodium acetate solution to the LC column eluate. The retention of sodium cation on the saccharidic parts of the molecule is observed after the CID fragmentation. In many cases, the location of this cation on the glycan attached to C‐3 hydroxyl group of flavonol led to assignment of its structure. Additionally, the determination of the structure of the aglycone and of the sequence of the glycan part was made possible through the CID data obtained from the [M + H]+ and [M − H]− ions. CID spectra show a different order of sugar elimination from hydroxyl groups at C‐3 and C‐7 in flavonol glycosides isolated from A. thaliana leaves and give sufficient information to discriminate flavonoid O‐diglycosides from flavonoid di‐O‐glycosides. Copyright © 2007 John Wiley & Sons, Ltd.
Binding constant determination of high‐affinity protein–ligand complexes by electrospray ionization mass spectrometry and ligand competition
Authors: Wortmann Arno , Jecklin Matthias C. , Touboul David , Badertscher Martin , Zenobi Renato 
Published: December 2007

AbstractWe describe an approach for the determination of binding constants for protein–ligand complexes with electrospray ionization mass spectrometry, based on the observation of unbound ligands competing for binding to a protein target. For the first time, dissociation constants lower than picomolar could be determined with good accuracy by electrospray ionization mass spectrometry. The presented methodology relies only on the determination of signal intensity ratios for free ligands in the low mass region. Therefore, all the advantages of measuring low masses with mass spectrometry, such as high resolution are preserved. By using a reference ligand with known binding affinity, the affinity of a second ligand can be determined. Since no noncovalently bound species are observed, assumptions about response factors are not necessary. The method is validated with ligands binding to avidin and applied to ligands binding to p38 mitogen‐activated protein kinase. Copyright © 2007 John Wiley & Sons, Ltd.
Effects of Graptopetalumparaguayense extract on tert‐ butylhydroperoxide‐induced oxidative stress
Authors: Chou Su‐Tze , Chung Yun‐Chin , Teng Kai‐Yun , Yeh Jan‐Ying 
Published: December 2007

AbstractBACKGROUND: Graptopetalum paraguayense E. Walther is used in folk medicine to lower blood pressure, protect liver function and relieve pain and infection. The effect and mechanism of its 50% ethanolic extract (GE50) were investigated in tert‐butylhydroperoxide (t‐BHP)‐induced Wistar rats. The serum was analysed for aspartate aminotransferase (AST) and alanine aminotransferase (ALT) activities while the tissue cytosols were analysed for lipid peroxidation, antioxidant level and enzyme activities.RESULTS: The liver was the primary target organ while the heart appeared to be the least responsive organ for t‐BHP treatment among the three tissues investigated. t‐BHP treatment increased serum AST and ALT activities, which are indicators of liver toxicity, while GE50 pretreatment reduced t‐BHP‐induced liver damage. t‐BHP treatment induced lipid peroxidation in the liver and brain but not in the heart. GE50 pretreatment prevented t‐BHP‐induced lipid peroxidation by maintaining superoxide dismutase (SOD) activity as well as glutathione (GSH) and vitamin C levels in the liver and vitamin E level in the brain. Although t‐BHP treatment did not induce lipid peroxidation in the heart, it caused a decrease in antioxidant level. GE50 pretreatment prevented the t‐BHP‐induced decrease in vitamin C level in the heart.CONCLUSION: GE50 pretreatment in rats protects the liver and brain from possible damage by t‐BHP‐induced lipid peroxidation. Copyright © 2007 Society of Chemical Industry
Protection of deoxyribose and DNA from degradation by using aqueous extracts of several wild plants
Authors: Gião Maria S , González‐Sanjosé M L , Muñiz Pilar , Rivero‐Pérez M D , Kosinska Monika , Pintado Manuela E , Malcata F Xavier 
Published: December 2007

AbstractBACKGROUND: Aqueous extracts of 48 herbal plants were obtained via alternative extraction protocols, and were assayed for their capacity to protect deoxyribose and DNA itself from degradation (or, conversely, for their capacity to promote DNA degradation), using electrophoresis as analytical tool.RESULTS: For a given (constant) volume of extract, deoxyribose protection ranged from 14.13 ± 1.35% (mean ± SD) inhibition by dwarf mallow powder infusion, up to 106.51 ± 15.93% inhibition by avocado powder infusion. DNA protection was tested at two extract concentrations, and was slightly greater at the higher concentration. Pro‐oxidant effects were essentially absent.CONCLUSION: The anti‐oxidative roles of plants upon deoxyribose and DNA displayed by our experimental results were rather promising with regards to practical applications of those plants, viz. as ingredients in the formulation of nutraceutical beverages and/or foods. Copyright © 2007 Society of Chemical Industry
Plant neurobiology and green plant intelligence: science, metaphors and nonsense
Authors: Struik Paul C , Yin Xinyou , Meinke Holger 
Published: December 2007

AbstractThis paper analyses the recent debates on the emerging science of plant neurobiology, which claims that the individual green plant should be considered as an intelligent organism. Plant neurobiology tries to use elements from animal physiology as elegant metaphors to trigger the imagination in solving complex plant physiological elements of signalling, internal and external plant communication and whole‐plant organisation. Plant neurobiology proposes useful concepts that stimulate discussions on plant behaviour. To be considered a new science, its added value to existing plant biology needs to be presented and critically evaluated. A general, scientific approach is to follow the so‐called ‘parsimony principle’, which calls for simplest ideas and the least number of assumptions for plausible explanation of scientific phenomena. The extent to which plant neurobiology agrees with or violates this general principle needs to be examined. Nevertheless, innovative ideas on the complex mechanisms of signalling, communication, patterning and organisation in higher plants are badly needed. We present current views on these mechanisms and the specific role of auxins in regulating them. Copyright © 2007 Society of Chemical Industry
Differential effect of organic cultivation on the levels of phenolics, peroxidase and capsidiol in sweet peppers
Authors: del Amor Francisco M , Serrano‐Martínez Ana , Fortea Isabel , Núñez‐Delicado Estrella 
Published: December 2007

AbstractBACKGROUND: Coincident with the changes in agricultural practices from conventional to organic, changes in the nutrient composition of fresh fruits and vegetables have been identified. The levels of peroxidase, total phenolics content, and capsidiol activity in organic as compared with conventional sweet pepper fruit were examined in this study. In order to avoid interferences of environmental factors on the studied parameters, the sweet peppers were grown (organically and conventionally) in a greenhouse under the same soil and climate conditions.RESULTS: Peroxidase was partially purified using the Triton X‐114 method and both organic and conventional peppers had the same isoenzymatic form. However, peroxidase activity in organic sweet peppers was higher than in conventional ones, in both maturity stages studied. The level of total phenolics compunds was also higher in organic than in conventional sweet peppers. With respect to the capsidiol activity, expressed as inhibition of fungus growth, it was not affected by the cultivation method at the green mature stage. However, at the red mature stage, organic sweet peppers showed higher capsidiol activity than those grown under the conventional system.CONCLUSION: Sweet peppers grown under organic culture have a maturity‐related response, with high levels of phenolic compounds, and peroxidase and capsidiol activity that contribute to disease resistance in organic farming. Copyright © 2007 Society of Chemical Industry
Simultaneous determination of iridoids, phenolic acids, flavonoids, and saponins in Flos Lonicerae and Flos Lonicerae Japonicae by HPLC‐DAD‐ELSD coupled with principal component analysis
Authors: Chen Chun‐Yun , Qi Lian‐Wen , Li Hui‐Jun , Li Ping , Yi Ling , Ma Hong‐Liang , Tang Dan 
Published: December 2007

AbstractA method, HPLC coupled with diode‐array and evaporative light scattering detectors (HPLC‐DAD‐ELSD), was newly developed to evaluate the quality of Flos Lonicerae (FL) and Flos Lonicerae Japonicae (FLJ), through a simultaneous determination of multiple types of bioactive components. By employing DAD, the detection wavelengths were set at 240 nm for the determination of iridoids, 330 nm for phenolic acids, and 360 nm for flavonoids, respectively. While ELSD, connected in series after DAD, was applied to the determination of saponins. This assay was fully validated with respect to precision, repeatability, and accuracy. Moreover, principal component analysis (PCA) was used for the similarity evaluation of different samples, and it was proven straightforward and reliable to differentiate FL and FLJ samples from different origins. For PCA, two principal components have been extracted. Principal component 1 (PC1) influences the separation between different sample sets, capturing 54.598% variance, while principal component 2 (PC2) affects differentiation within sample sets, capturing 12.579% variance. In conclusion, simultaneous quantification of bioactive components by HPLC‐DAD‐ELSD coupled with PCA would be a well‐acceptable strategy to differentiate the sources and to comprehensively control the quality of the medicinal plants FL and FLJ.
Pore structural characteristics, size exclusion properties and column performance of two mesoporous amorphous silicas and their pseudomorphically transformed MCM‐41 type derivatives
Authors: Bayram‐Hahn Zöfre , Grimes Brian A. , Lind Anna M. , Skudas Romas , Unger Klaus K. , Galarneau Anne , Iapichella Julien , Fajula François 
Published: December 2007

AbstractHighly ordered mesoporous silicas such as, mobile composition of matter, MCM‐41, MCM‐48, and the SBA‐types of materials have helped to a large extent to understand the formation mechanisms of the pore structure of adsorbents and to improve the methods of pore structural characterization. It still remains an open question whether the high order, the regularity of the pore system, and the narrow pore size distribution of the materials will lead to a substantial benefit when these materials are employed in liquid phase separation processes. MCM‐41 type 10 μm beads are synthesized following the route of pseudomorphic transformation of highly porous amorphous silicas. Highly porous silicas and the pseudomorphically transformed derivatives are characterized by nitrogen sorption at 77 K and by inverse size‐exclusion chromatography (ISEC) employing polystyrene standards. Applying the network model developed by Grimes, we calculated the pore connectivity nT of the materials. The value of nT varies between the percolation threshold of the lattice and values of nT > 10, the latter being the limiting value above which the material can be considered to be almost infinitely connected such that the ISEC behavior of the material calculated with the pore network model is the same when calculated with a parallel pore model which assumes an infinite connectivity. One should expect that the pore connectivity is reflected in the column performance, when these native and unmodified materials are packed into columns and tested with low molecular weight analytes in the Normal Phase LC mode. As found in a previous study on monolithic silicas and highly porous silicas, the slope of the plate height (HETP) – linear velocity (u) curve decreased significantly with enhanced pore connectivity of the materials. First results on the pseudomorphically transformed MCM‐41 type silicas and their highly porous amorphous precursors showed that (i) the transformation did not change the pore connectivity (within the limits detectable by ISEC) from the starting material to the final product and (ii) the slope of the HETP versus u curve for dibutylphtalate did not change significantly after the pseudomorphic transformation.