bluuebunny/crossref_metadata_2025_split huggingface dataset:
The quest for the best nonpolarizable water model from the adaptive force matching method
Authors: Akin‐Ojo Omololu , Wang Feng 
Published: August 2010

AbstractThe recently introduced adaptive force matching (AFM) method is used to develop a significantly improved pair‐wise nonpolarizable potential for water. A rigid version of the potential is also presented to enable larger time steps for biological simulations. In this work, it is demonstrated that the AFM method can be used to systematically assess the importance of each functional term during the construction of a force field. For a water potential, it is established that a single off‐atom charge center (M) in the plane of water outperforms two out‐of‐plane charge sites for reproducing intermolecular forces. The four‐site pair‐wise nonpolarizable force field developed in this work rivals some of the most sophisticated polarizable models in terms of reproducing accurate ab initio forces. The force fields are parameterized to perform best in the temperature range from 0 to 40°C. Equilibrium and dynamical properties calculated with the flexible and rigid force fields are in good agreement with experimental results. For the flexible model, the agreement improves when path integral simulation is performed. These force fields provide high‐quality results at a very low computational cost and are thus well suited to atomistic scale biological simulations. The AFM method provides a mechanism for selecting important terms in force field expressions and is a very promising tool for producing accurate force fields in condensed phases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Discovery of new β‐D‐galactosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening
Authors: Abdula Ahmed Mutanabbi , Khalaf Reema Abu , Mubarak Mohammad S. , Taha Mutasem O. 
Published: August 2010

AbstractGlycosidases, including β‐D‐galactosidase, are involved in a variety of metabolic disorders, such as diabetes, viral or bacterial infections, and cancer. Accordingly, we were prompted to find new β‐D‐galactosidase inhibitors. Towards this end, we scanned the pharmacophoric space of this enzyme using a set of 41 known inhibitors. Genetic algorithm and multiple linear regression analyses were used to select an optimal combination of pharmacophoric models and physicochemical descriptors to yield self‐consistent and predictive quantitative structure‐activity relationship (QSAR). Five pharmacophores emerged in the QSAR equations suggesting the existence of more than one binding mode accessible to ligands within β‐D‐galactosidase pocket. The successful pharmacophores were complemented with strict shape constraints in an attempt to optimize their receiver‐operating characteristic curve profiles. The validity of the QSAR equations and the associated pharmacophoric models were experimentally established by the identification of several β‐D‐galactosidase inhibitors retrieved via in silico search of two structural databases: the National Cancer Institute list of compounds and our in house built structural database of established drugs and agrochemicals. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Effect of ligand binding on the intraminimum dynamics of proteins
Authors: Alakent Burak , Baskan Sena , Doruker Pemra 
Published: August 2010

AbstractEffects of ligand binding on protein dynamics are studied via molecular dynamics (MD) simulations on two different enzymes, dihydrofolate reductase (DHFR) and triosephosphate isomerase (TIM), in their unliganded (free) and liganded states. Domain motions in MD trajectories are analyzed by collectivities and rotation angles along the principal components (PCs). DHFR in the free state has well‐defined domain rotations, whereas rotations are slightly damped in the binary complex with nicotinamide adenine dinucleotide phosphate (NADPH), and remarkably distorted in the presence of NADP+, showing that NADP+ is solely responsible for the loss of correlation of the domains in DHFR. Although mean square fluctuations of MD simulations in the same PC subspaces are similar for different ligation states, linear stochastic time series models show that backbone flexibility along the first five PCs is decreased upon NADPH and NADP+ binding in subpicosecond scale. This shows that mobility of the protein along the PCs is closely related with intraminimum dynamics, and alterations in ligation states may change the intraminimum dynamics significantly. Low vibrational frequencies of the alpha‐carbon atoms of DHFR are determined from the time series models of a larger number of low indexed PCs, and it is found that number of modes in the lowest frequencies is reduced upon ligand binding. A similar result is obtained for TIM in the unliganded and dihydroxyacetone phosphate bound states. We suggest that stochastic time series modeling is a promising method to be used in determining subtle perturbations in protein dynamics. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Synthesis of novel functionalized 4‐aza‐2,3‐didehydropodophyllotoxin derivatives with potential antitumor activity
Authors: Kumar Ajay , Alegria Antonio E. 
Published: August 2010

Abstract
magnified image Novel arylamino alcohols were synthesized and these alcohols were used to prepare 12 novel N‐(2‐hydroxy‐ethyl)‐2,3‐didehydroazapodophyllotoxins, in one step, by simple reflux in ethanol. Isolated yields in the range of 50–70% were obtained. J. Heterocyclic Chem., (2010).
A novel and short synthesis of naturally occurring 5‐(3′‐indolyl)oxazoles
Authors: Kumar Dalip , Sundaree Swapna , Patel Gautam , Kumar Anil 
Published: August 2010

Abstract
magnified image A novel, concise, and convenient synthesis of 5‐(3′‐indolyl)oxazoles using relatively benign reagent [hydroxy(2,4‐dinitrobenzenesulfonyloxy)iodo]benezene has been described. The advantages of this procedure include operational simplicity, good yield, and avoidance of the use of toxic metal. J. Heterocyclic Chem., (2010).
Design and synthesis of novel methylene‐bis‐fused pyrazoles as biologically active molecules
Authors: Reddy Ch. Sanjeeva , Srinivas A. , Sunitha M. , Nagaraj A. 
Published: August 2010

Abstract
magnified image A series of novel methylene‐bis‐fused pyrazoles 12a, 12b, 12c, 12d and methylene‐bis‐2‐(4‐methylsulfonyl)‐phenyl substituted fused pyrazoles 15a, 15b, 15c, 15d have been synthesized by the reaction of methylene‐bis‐aryl‐6‐hydroxymethylene‐2‐cyclohexenones 10 with hydrazine hydrate or (4‐methylsulfonyl)‐phenyl hydrazine 13. Chemical structures of all the newly synthesized compounds were elucidated by their IR, 1H NMR, 13C NMR, and MS spectral data. The compounds 15a, 15b, 15c, 15d were evaluated for their cyclooxygenase‐2 (COX‐2) inhibitory activity, and the compound 15b showed appreciable COX‐2 inhibition and selectivity. Further, all the new compounds were screened for their antimicrobial activity against Gram‐positive, Gram‐negative bacteria, and fungi. Amongst the screened compounds, 12c, 15a, and 15b were found to be the most active against almost all the test bacteria. The compound 15b displayed notable antibacterial activity against Bacillus subtilis (ATCC 6633), Staphylococcus aureus (ATCC 6538p), Micrococcus luteus (IFC 12708), Proteus vulgaris (ATCC 3851), and Salmonella typhimurium (ATCC 14028), equal to that of ampicillin. Similarly, these compounds also showed potent antifungal activity against Candida albicans (ATCC 10231), Aspergillus fumigatus (HIC 6094), Trichophyton rubrum (IFO 9185), and Trichophyton mentagrophytes (IFO 40996). J. Heterocyclic Chem., (2010).
Synthesis, structures, and herbicidal activity of isoxazole derivatives
Authors: Zhou Yuhan , Chen Yanhui , Miao Weirong , Qu Jingping 
Published: August 2010

Abstract
magnified image The several novel 3‐substituted phenyl isoxazole derivatives were prepared from substituted phenyl‐butan‐1,3‐dione. Their structures were confirmed by element analysis, IR, MS, and 1H NMR. X‐ray structure analysis indicated that the dihedral angles of the phenyl ring with the isoxazole ring in compounds 4a and 4b were 19.46° and 49.18°, respectively. Preliminary bioassay showed that the title compounds had good activity to various weeds, and 4a exhibited almost the same activity with 4b. This was different from the former works, which showed that the big dihedral angle of the phenyl ring with the heterocyclic moiety was necessary for high‐herbicidal activity. J. Heterocyclic Chem., (2010).
HPLC/ESI‐MSn and ESI‐MS studies on the Aconitum alkaloids in three Chinese medicinal herbs
Authors: Liu Wenlong , Pi Zifeng , Wang Xiye , Song Fengrui , Liu Shuying 
Published: August 2010

AbstractAconitum lipo‐alkaloids (LDAs) peaks in the previous HPLC studies have shown overlapping behavior, making it impossible to identify the total retention behavior of LDAs. The structural diversity of LDAs in Radix Aconiti, Radix Aconiti Kusnezoffii and Radix Aconiti Lateralis Preparata makes it difficult to synthesize and quantify each of them. Therefore, this study has been devoted to develop a HPLC/ESI‐MSn method with good resolution of Aconitum alkaloids especially LDAs and then set up a fast ESI‐MS SIM method to quantify the total contents of specific skeleton LDAs in the three herbs via in‐source CID and the capability of mass separation. As a result, the retention behavior of LDAs was summarized based on an optimized chromatographic separation; 32 alkaloids from the three herbs of Aconitum genus were separated and identified according to their fragmentation pathways by using HPLC/ESI‐MSn. In addition, a fast quantitative analysis ESI‐MS SIM method was successfully applied to the quantification of the total contents of specific skeleton LDAs in the three herbs.
Use of kinetic plots for the optimization of the separation time in ultra‐high‐pressure LC
Authors: Eeltink Sebastiaan , Decrop Wim M. C. , Steiner Frank , Ursem Mario , Cabooter Deirdre , Desmet Gert , Kok Wim Th. 
Published: August 2010

AbstractThe kinetic‐plot approach, in which experimental t0 and N‐values are extrapolated to the performance at maximum system pressure by increasing the column length, was validated by coupling 250×3 mm columns packed with 3 μm particles. The extra‐column volume introduced by coupling columns could be neglected with respect to the peak volumes. Plate numbers of up to 132 000 were experimentally achieved by coupling four columns. The maximum deviation between the experimental and predicted plate numbers was 7% for two coupled columns, and decreasing to 0.1% for four coupled columns. Kinetic plots were used to find the conditions to separate a critical pair, with a preset value for the effective plate number, in the shortest possible time. For high‐efficiency separations yielding 100 000 effective plates, the optimum critical‐pair retention factor was around 4.5. Kinetic plots are presented to find the optimal column length to obtain the fastest possible 100 000 effective‐plate separation, taking into account the effect of mobile‐phase viscosity on column pressure, and consequently the optimum column length.
Surface runoff and soil erosion estimation using the SWAT model in the Keleta Watershed, Ethiopia
Authors: Tibebe D. , Bewket W. 
Published: August 2010

AbstractThis study evaluates surface runoff generation and soil erosion rates for a small watershed (the Keleta Watershed) in the Awash River basin of Ethiopia by using the Soil and Water Assessment Tool (SWAT) model. Calibration and validation of the model was performed on monthly basis, and it could simulate surface runoff and soil erosion to a good level of accuracy. The simulated surface runoff closely matched with observed data (derived by hydrograph separation). Surface runoff generation was generally high in parts of the watershed characterized by heavy clay soils with low infiltration capacity, agricultural land use and slope gradients of over 25 per cent. The estimated soil loss rates were also realistic compared to what can be observed in the field and results from previous studies. The long‐term average soil loss was estimated at 4·3 t ha−1 y−1; most of the area of the watershed (∼80 per cent) was predicted to suffer from a low or moderate erosion risk (<8 t ha−1 y−1), and only in ∼1·2 per cent of the watershed was soil erosion estimated to exceed 12 t ha−1 y−1. Expectedly, estimated soil loss was significantly correlated with measured rainfall and simulated surface runoff. Based on the estimated soil loss rates, the watershed was divided into four priority categories for conservation intervention. The study demonstrates that the SWAT model provides a useful tool for soil erosion assessment from watersheds and facilitates planning for a sustainable land management in Ethiopia. Copyright © 2010 John Wiley & Sons, Ltd.
Rotating frame spin lattice relaxation in a swine model of chronic, left ventricular myocardial infarction
Authors: Witschey Walter R. T. , Pilla James J. , Ferrari Giovanni , Koomalsingh Kevin , Haris Mohammed , Hinmon Robin , Zsido Gerald , Gorman Joseph H. , Gorman Robert C. , Reddy Ravinder 
Published: August 2010

AbstractT1ρ relaxation times were quantified in a swine model of chronic, left ventricular myocardial infarction. It was found that there were low frequency relaxation mechanisms that suppress endogenous contrast at low spin‐lock amplitudes and in T2‐weighted images. A moderate amplitude spin‐locking pulse could overcome these relaxation mechanisms. Relaxation dispersion data were measured over a range of RF field amplitudes, and a model was formulated to include dipole–dipole relaxation modulated by molecular rotation and an apparent exchange mechanism. These techniques may find some use in the clinic for the observation of chronic, left ventricular cardiac remodeling. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Analysis of carbon nanotube chiralities obtained from a bimetallic Co‐Mo catalyst
Authors: Fouquet Martin , Hofmann Stephan , Thomsen Christian , Robertson John 
Published: August 2010

AbstractAll growth methods for single‐walled carbon nanotubes (SWNTs) usually result in a wide distribution of chiral indices (n,m). Bimetallic catalysts can narrow this distribution 1,2. Here we grow SWNTs by a Co‐Mo catalyst and measure the different chiral distributions for an array of growth parameters. A CoMo‐acetate solution as described by Miyauchi et al. 1 was used to prepare the catalyst. With chiral maps we find that the absolute diameter range for the SWNT is about 0.7–1.7 nm for all samples. Hereby metallic and semiconducting tubes favour different diameters and thus divide the full range in two intervals. Histogramms made for the chiral angle distribution of the assigned SWNT suggest that semiconducting tubes favour a chiral angle of 20°–25°.
Molecular and supramolecular templating of silica‐based nanotubes and introduction of metal nanowires
Authors: Gruber Sabine , Gottschlich Andreas , Scheel Hanne , Aresipathi Catherine , Bannat Inga , Zollfrank Cordt , Wark Michael 
Published: August 2010

AbstractIn this article, we describe the development and application of molecular and supramolecular templates for the fabrication silica nanotubes (NTs) and nanowires (NWs) and subsequent metallisation. In one first approach molecular templates such as nanofibres of [Pt(NH3)4](HCO3)2 salt crystals were used as templates. Pure silica as well as mixed silica/tin oxide NTs with incorporated Pt metal were synthesised. Tubular structures with lengths in the range of 2–5 µm and diameters between 50 and 800 nm were formed. Collaborative effects from templating crystals and a capping agent tetraethylorthosilicate are vital in obtaining Pt embedded SiO2/stannic oxide NTs. This simple approach incorporates as much as about 40 wt.% of Pt directly inside the NTs. Pt NWs form directly during heat treatment in air by an autoreduction of the templating nanofibres. These NWs exhibit diameters of 15–35 nm and lengths up to 2 µm. Biotemplates such as cellulose nanocrystals isolated from biological sources are efficient supramolecular templates for the fabrication of inorganic one‐dimensional structures. The fabrication of biotemplated silica NTs and NWs was performed via sol–gel processing. The biotemplated silica NTs and NWs exhibited diameters of around 15 nm and lengths up to 500 nm. Gold nanoparticles were deposited on the cellulose and SiO2 coated cellulose nanocrystals to form metal NWs. The gold nanoparticles formed a nearly closed gold shell using weak reducing agents. Transmission electron microscopy and UV–Vis absorption spectroscopy confirmed successful deposition of the metal particles on the SiO2 NWs. The fabrication of size‐controlled metal NWs using Pt‐derived molecular nanofibres and cellulose nanocrystals as supramolecular templates is of specific benefit for the design of metal NWs with various sizes and unique optical properties.
Measurement of Local Si‐Nanowire Growth Kinetics Using In situ Transmission Electron Microscopy of Heated Cantilevers
Authors: Kallesøe Christian , Wen Cheng‐Yen , Mølhave Kristian , Bøggild Peter , Ross Frances M. 
Published: August 2010

AbstractA technique to study nanowire growth processes on locally heated microcantilevers in situ in a transmission electron microscope has been developed. The in situ observations allow the characterization of the nucleation process of silicon wires, as well as the measurement of growth rates of individual nanowires and the ability to observe the formation of nanowire bridges between separate cantilevers to form a complete nanowire device. How well the nanowires can be nucleated controllably on typical cantilever sidewalls is examined, and the measurements of nanowire growth rates are used to calibrate the cantilever‐heater parameters used in finite‐element models of cantilever heating profiles, useful for optimization of the design of devices requiring local growth.
First‐Layer Effect in Graphene‐Enhanced Raman Scattering
Authors: Ling Xi , Zhang Jin 
Published: August 2010

AbstractGraphene as a substrate for enhancing Raman scattering, called graphene‐enhanced Raman scattering (GERS), has been reported in previous work. Herein, it is found that the “first‐layer effect”, which is widely used to explain the chemical‐enhanced mechanism in surface‐enhanced Raman scattering (SERS), exists in the GERS system. The Langmuir–Blodgett (LB) technique is used to construct mono‐ and multilayer ordered aggregates of protoporphyrin IX (PPP). Raman spectra of PPP with different layer numbers of the LB film on graphene are collected. The Raman signal from the first monolayer LB film of PPP has a larger contribution to the Raman enhancement than that from subsequent monolayers. Meanwhile, the Raman enhancement is dependent on the molecular configuration in contact with graphene, in which the functional group of PPP in direct contact with graphene has a stronger enhancement than other groups. These results reveal that GERS is strongly dependent on the distance between graphene and the molecule, which is convincing evidence that the Raman enhancement effect based on graphene belongs to the chemical‐enhanced mechanism. This discovery provides a convenient system for the study of the chemical‐enhanced mechanism and will benefit further understanding of SERS.
Silver nanoparticles‐modified films versus biomedical device‐associated infections
Authors: Cao Huiliang , Liu Xuanyong 
Published: August 2010

AbstractA serious issue related to biomedical devices (BDs) is that of bacterial infections. BDs colonized by bacteria may cause infection or mortality. To prevent such infections, an effective strategy is to develop novel BDs with antibacterial abilities via various surface modification processes. Thus, plenty of silver nanoparticles (Ag NPs)‐modified films were brought forward to because of their potential applications in improving the antibacterial properties of BDs. This article reviews the difficulties in diagnosing and treating biomedical device‐associated infections as well as the state of arts in fabricating the Ag NPs‐modified films for antibacterial applications. In addition, the nanoeffect of silver particles and the cytotoxicity of Ag NPs are also discussed. It is clear that safe and durable Ag NPs‐modified films are more desirable for the BDs prone to bacteria. To further extend the investigations on controlling the toxicity path of Ag NPs to both bacteria and mammalian cells, developing novel green fabrication processes with more ‘cleaner’ (without accompaniment of ligands or reduction agents) Ag NPs should be the first mission for the material scientists to complete.WIREs Nanomed Nanobiotechnol2010 2 670–684This article is categorized under:Implantable Materials and Surgical Technologies > Nanomaterials and ImplantsNanotechnology Approaches to Biology > Nanoscale Systems in Biology
Polytype Transformations in the SO42– Containing Layered Double Hydroxides of Zinc with Aluminum and Chromium: The Metal Hydroxide Layer as a Structural Synthon
Authors: Radha Shivaramaiah , Antonyraj Churchil A. , Vishnu Kamath P. , Kannan Srinivasan 
Published: August 2010

AbstractSolid–solid inter‐polytype transformations are observed during the thermal dehydration of sulfate‐containing layered double hydroxides (LDHs). The metal hydroxide layer behaves as a “structural synthon” and the interconversion of polytypes of rhombohedral and hexagonal symmetries takes place by rigid translations of successive layers by (± 1/3, ± 2/3) relative to one another in the ab plane. These translations are selected among the many possible, as they preserve the coincidence of the symmetry elements of the individual layers and thereby conserve the threefold symmetry of the crystal across the inter‐polytype conversions. As a result, these transformations are enthalpically not expensive. These translations are facilitated at near ambient temperatures (30–60 °C) by the reversible dehydration of the LDH, which involves the deinsertion/insertion of water molecules within the restricted space of the interlayer region.
155Gd Mössbauer Spectroscopy on Intermetallics – An Overview
Authors: Pöttgen Rainer , Łątka Kazimierz 
Published: August 2010

Abstract155Gd Mössbauer spectroscopy on intermetallic compounds is a useful complementary spectroscopic tool for the determination of magnetic structures, since the high absorption cross‐section strongly hampers neutron diffraction experiments for compounds containing natural gadolinium. The recent trends applied to solid state chemistry and materials sciences for that spectroscopic technique are reviewed.
Covalent Bonds in α‐SnF2 Monitored by J‐Couplings in Solid‐State NMR Spectra
Authors: Bräuniger Thomas , Ghedia Stefan , Jansen Martin 
Published: August 2010

AbstractThe stable ambient‐temperature phase of tin(II) fluoride, α‐SnF2, was studied by 19F and 119Sn magic‐angle spinning (MAS) NMR spectroscopy. A large chemical shift anisotropy (CSA) is observed in the spectra of both nuclides, which is indicative of the presence of stereochemically active lone electron pair on tin. Symmetric satellite lines with low intensity have been detected in the 119Sn MAS spectra acquired under 19F decoupling, and are assigned to indirect J‐couplings between the magnetically active tin isotopes. The detection of J‐couplings is evidence for the existence of genuine covalent bonds in α‐SnF2, a fact which was deduced before from X‐ray crystallography, which revealed the presence of Sn–F distances smaller than the sum of the respective ionic radii.