Showing papers in "International Journal of Molecular Sciences in 2006"
TL;DR: In this article, the authors present a summary of the principal synthetic considerations pertaining to good practice in the polymerization aspects of molecular imprinting, and is primarily aimed at researcher familiar with molecular imprintings methods but with little or no prior experience in polymer synthesis.
Abstract: Hongyuan Yan and Kyung Ho Row* Center for Advanced Bioseparation Technology, Department of Chemical Engineering, Inha University, 253 Yonghyun-Dong, Nam-Ku, Incheon, 402–751, Korea * Corresponding author. E-mail: rowkho@inha.ac.kr Received: 12 April 2006 / Accepted: 27 June 2006 / Published: 29 June 2006 Abstract: Molecularly imprinted polymers (MIP) exhibiting high selectivity and affinity to the predetermined molecule (template) are now seeing a fast growing research. However, optimization of the imprinted products is difficult due to the fact that there are many variables to consider, some or all of which can potentially impact upon the chemical, morphological and molecular recognition properties of the imprinted materials. This review present a summary of the principal synthetic considerations pertaining to good practice in the polymerization aspects of molecular imprinting, and is primarily aimed at researcher familiar with molecular imprinting methods but with little or no prior experience in polymer synthesis. The synthesis, characteristic, effect of molecular recognition and different preparation methods of MIP in recent few years are discussed in this review, unsolved problems and possible developments of MIP were also been briefly discussed. Keywords: molecularly imprinted polymer, special molecular recognition, synthetic approach 1. Molecular Imprinting Technology Molecular imprinting technology is a rapidly developing technique for the preparation of polymers having specific molecular recognition properties for a given compound, its analogues or for a single enantiomer [1-3]. Synthesis of MIP is a relatively straightforward and inexpensive procedure. In short, the molecularly imprinted polymer is prepared by mixing the template molecule with functional monomers, cross-linking monomers and a radical initiator in a proper solvent, most often an aprotic and non polar solvent. Subsequently, this pre-polymerization mixture is irradiated with UV light or
447 citations
TL;DR: This review summarises the state-of-the-art methodologies used for designing homogeneous catalysts and optimising reaction conditions (e.g. choosing the right solvent), and assesses the use of molecular modelling tools, from descriptor models based on semiempirical and molecular mechanics calculations, to 2D topological descriptors and graph theory methods.
Abstract: This review summarises the state-of-the-art methodologies used for designing homogeneous catalysts and optimising reaction conditions (e.g. choosing the right solvent). We focus on computational techniques that can complement the current advances in high-throughput experimentation, covering the literature in the period 1996-2006. The review assesses the use of molecular modelling tools, from descriptor models based on semiempirical and molecular mechanics calculations, to 2D topological descriptors and graph theory methods. Different techniques are compared based on their computational and time cost, output level, problem relevance and viability. We also review the application of various data mining tools, including artificial neural networks, linear regression, and classification trees. The future of homogeneous catalysis discovery and optimisation is discussed in the light of these developments.
70 citations
TL;DR: In this article, several ionic liquids were applied as catalysts for the synthesis of cyclicurethanes from amino alcohols and pressurized CO2 in the presence of alkali metal compounds as promoters.
Abstract: Several ionic liquids were applied as catalysts for the synthesis of cyclicurethanes from amino alcohols and pressurized CO2 in the presence of alkali metalcompounds as promoters. A comparative study was made for the catalytic performanceusing different ionic liquids, substrates, promoters, and pressures. The optimum catalyticsystem was BMIM-Br promoted by K2CO3, which, for 1-amino-2-propanol, produced cyclicurethane in 40% yield with a smaller yield of substituted cyclic urea and no oligomericbyproducts. For other amino alcohols, cyclic urethanes, cyclic ureas, and/or undesiredbyproducts were produced in different yields depending on the substrates used. Possiblereaction mechanisms are proposed.
42 citations
TL;DR: A review of methods for separating and analysing imidazolium-and pyridinium-type ionic liquids in aqueous matrices using high performance liquidchromatography (HPLC) and capillary electrophoresis (CE) is presented in this article.
Abstract: Interest in ionic liquids for their potential in different chemical processes isconstantly increasing, as they are claimed to be environmentally benign – excellent, non-volatile solvents for a wide range of applications. The wide applicability of thesecompounds also demands reliable, relatively simple and reproducible analytical techniques.These methods must be applicable not only to different technical or natural matrices but alsoto the very low concentrations that are likely to be present in biological and environmentalsystems. In this review, therefore, methods for separating and analysing imidazolium- andpyridinium-type ionic liquids in aqueous matrices using high performance liquidchromatography (HPLC) and capillary electrophoresis (CE) are examined. The techniquesfor identifying ionic liquids are meant primarily to track the concentrations of ionic liquidsas residues not only in products and wastes but also in biological or environmental samples.The application of hyphenated techniques in this field is intended to selectively separate thequaternary entity from other cationic and non-ionic species present in the matrix, and toenable its fine-scale quantification. Nowadays, methods developed for cation analysis arebased mostly on reversed-phase high-performance liquid chromatography, ionchromatography, ion-pair chromatography and capillary electrophoresis, where variousbuffered mobile phases are used.
37 citations
TL;DR: In this paper, the behavior of 1-butyl-3-methylimidazolium chloride has been investigated by Raman spectroscopy as a function of hydrostatic pressure.
Abstract: 1 Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974, Taiwan 2 Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan 3 Institute of Atomic and Molecular Sciences, Academia Sinica, P. O. Box 23-166, Taipei 106, Taiwan 4 Department of Chemistry, National Taiwan University, Taipei 106, Taiwan * Author to whom correspondence should be addressed. E-mail: hcchang@mail.ndhu.edu.tw; Fax: +886-3-8633570; Phone: +886-3-8633585 Received: 7 September 2006, in revised form: 29 September 2006 / Accepted: 16 October 2006 / Published: 25 October 2006 Abstract: The behavior of 1-butyl-3-methylimidazolium chloride has been investigated by Raman spectroscopy as a function of hydrostatic pressure. Under ambient pressure two rotational isomers (GA and AA forms) of the 1-butyl-3-methylimidazolium cation coexist in the ionic liquid state. As the supercooled liquid was compressed from ambient to 0.9 GPa, the contribution of the GA conformer decreases in intensity as the pressure was elevated. A new high pressure phase is formed above the pressure of 1.5 GPa. This new high pressure phase of 1-butyl-3-methylimidazolium chloride arises from perturbed GA conformer, i.e., distorted Crystal 2. Crystal 1 form (AA form) is known as a thermodynamically stable form under ambient pressure. Nevertheless, crystal 1 form is switched to a metastable state under the condition of high pressure. Keywords: Raman spectroscopy, High pressure, 1-Butyl-3-methylimidazolium chloride.
35 citations
TL;DR: Using electronic absorption spectra and thin layer chromatography, the reaction of 2,2-diphenyl-1-picrylhydrazyl (DPPH) with O2•−, HO•, HO •, HO− and HOO− anions and freeradicals revealed the formation of the para-nitro- and para-hydroxy-derivatives of DPPH fragmentation products (diphenylamine, tetraphenylhydrazine) as discussed by the authors.
Abstract: Using electronic absorption spectra and thin layer chromatography, the reactionof 2,2-diphenyl-1-picrylhydrazyl (DPPH) with O2•–, HO•, HO–, and HOO– anions and freeradicals revealed the formation of the para-nitro- and para-hydroxy-derivatives of 2,2-diphenyl-1-picrylhydrazine (DPPH-H) and of DPPH fragmentation products(diphenylamine, tetraphenylhydrazine). The reaction of DPPH with the O2•– anion-radical(from KO2 in benzene solution at room temperature in the presence of 18-crown-6 ether) ispseudo-first-order during the first 25 minutes.
34 citations
TL;DR: Results show that EGCG can block alcohol-induced gut leakiness, reduce endotoxemia, and inhibit inflammatory factors expressions in the liver, thereby ameliorates alcohol- induced liver injury.
Abstract: Endotoxemia is a common event in alcoholic liver disease. Elevated intestinalpermeability is the major factor involved in the mechanism of alcoholic endotoxemia andthe pathogenesis of alcoholic liver disease. This study examined the effect ofepigallocatechin-3-gallate (EGCG) on alcohol-induced gut leakiness, and explored therelated mechanisms involved in its protection against alcohol-induced liver injury in rats.Four groups of female Sprague-Dawley rats were studied. Alcohol and alcohol/EGCGgroups rats received fish oil along with alcohol daily via gastrogavage for 6 weeks, anddextrose and dextrose/EGCG groups rats were given fish oil along with isocaloric dextroseinstead of alcohol. The dextrose/EGCG and alcohol/EGCG groups received additionaltreatment of EGCG (100mg.kg-1 body weight) daily intragastrically by gavage. Intestinalpermeability was assessed by urinary excretion of lactulose and mannitol (L/M ratio). Liverinjury was evaluated histologically and by serum alanine aminotransferase (ALT). Plasmaendotoxin and serum tumor necrosis factor-α (TNF-α) levels were assayed; livermalondialdehyde (MDA) contents determined. CD14 and inflammatory factors, such asTNF-α, cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) mRNAs inthe liver were analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR). Ratsgiven fish oil plus alcohol had gut leakiness (L/M ratio was increased), which wasassociated with both endotoxemia and liver injury. The above responses were accompaniedby increased CD14, TNF-α, COX-2 and iNOS mRNA expressions in the liver. EGCGsupplementation partly blocked the gut leakiness, reduced endotoxemia and lipidperoxidation, and blunted the elevated expressions of CD14, TNF-α, COX-2 and iNOS, allof which were associated with improved liver injury. These results show that EGCG can block alcohol-induced gut leakiness, reduce endotoxemia, and inhibit inflammatory factors expressions in the liver, thereby ameliorates alcohol-induced liver injury.
28 citations
TL;DR: Assuming the in vitro conditions for the enzyme-catalyzed reactions, the basic Michaelis-Menten description is modified in a logistic (mathematical) manner such that the inherent limitations that appear in the previous method are removed.
Abstract: 1 Laboratory of Computational and Structural Physical Chemistry, Chemistry Department, West University of Timi soara, Pestalozzi Street No.16, Timi soara, RO-300115, Romania E-mails: mvputz@cbg.uvt.ro or mv_putz@yahoo.com 2 Laboratory of Biochemistry, Chemistry Department, West University of Timi soara, Pestalozzi Street No.16, Timi soara, RO-300115, Romania E-mails: lacramaanamaria@yahoo.com and vostafe@cbg.uvt.ro * Author to whom correspondence should be addressed. Received: 30 August 2006 / Accepted: 18 October 2006 / Published: 2 November 2006 Abstract: Assuming the in vitro conditions for the enzyme-catalyzed reactions, the basic Michaelis-Menten description is modified in a logistic (mathematical) manner such that the inherent limitations that appear in the previous method are removed. Beside its generality, the reliability of the present approach is proved through applications on the competitive multi- and bi- substrate enzyme catalyses. Keywords: Michaelis-Menten mechanism, W-Lambert function, Logistic function, multi-substrate kinetics, and fully competitive inhibition. 1. Introduction According to Charles Darwin’s famous paradigm of evolution, the principle of natural selection prescribes “the survival of the fittest” [1]. With the advent of the general theory of models in biology [2], as genomic, proteomic, and metabolomic scales are approached, the fitting concept resembles the equation of the net production of the species “ i” [3]: X i fi
26 citations
TL;DR: In this article, three new QSSPR models (poset-average, cluster-expansion, and splinoid poset) were proposed for the correlation of the octanol/water partition coefficient (log Kow) and the soil-sarcption coefficient of chlorophenols.
Abstract: Due to their widespread use in bactericides, insecticides, herbicides, andfungicides, chlorophenols represent an important source of soil contaminants. Theenvironmental fate of these chemicals depends on their physico-chemical properties. In theabsence of experimental values for these physico-chemical properties, one can use predictedvalues computed with quantitative structure-property relationships (QSPR). As analternative to correlations to molecular structure we have studied the super-structure of areaction network, thereby developing three new QSSPR models (poset-average, cluster-expansion, and splinoid poset) that can be applied to chemical compounds which can behierarchically ordered into a reaction network. In the present work we illustrate these posetQSSPR models for the correlation of the octanol/water partition coefficient (log Kow) and thesoil sorption coefficient (log KOC) of chlorophenols. Excellent results are obtained for allQSSPR poset models to yield: log Kow, r = 0.991, s = 0.107, with the cluster-expansionQSSPR; and log KOC, r = 0.938, s = 0.259, with the spline QSSPR. Thus, the poset QSSPRmodels predict environmentally important properties of chlorophenols.
24 citations
TL;DR: In this article, the feasibility of replacing a given anaesthetic by similar ones in the composition of a complex drug is studied based on information entropy and principal component analysis (PCA).
Abstract: 1 Institut Universitari de Ciencia Molecular, Universitat de Valencia, Edifici d'Instituts de Paterna, P. O. Box 22085, E-46071 Valencia, Spain. http://www.uv.es/~uiqt/index.htm. Tel. +34 963 544 431, Fax +34 963 543 274 2 Departamento de Ciencias Experimentales, Facultad de Ciencias Experimentales, Universidad Catolica de Valencia San Vicente Martir, Guillem de Castro-106, E-46003 Valencia, Spain * Author to whom correspondence should be addressed. E-mail: francisco.torrens@uv.es Received: 16 December 2005 / Accepted: 26 January 2006 / Published: 31 January 2006 Abstract: Algorithms for classification are proposed based on criteria ( information entropy and its production). The feasibility of replacing a given anaesthetic by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using characteristic chemical properties of different portions of their molecules. Many classification algorithms are based on information entropy. When applying these procedures to sets of moderate size, an excessive number of results appear compatible with data, and this number suffers a combinatorial explosion. However, after the equipartition conjecture , one has a selection criterion between different variants resulting from classification between hierarchical trees. According to this conjecture, for a given charge or duty, the best configuration of a flowsheet is the one in which the entropy production is most uniformly distributed. Information entropy and principal component analyses agree. The periodic law of anaesthetics has not the rank of the laws of physics: (1) the properties of anaesthetics are not repeated; (2) the order relationships are repeated with exceptions. The proposed statement is: The relationships that any anaesthetic p has with its neighbour p + 1 are approximately repeated for each period. Keywords: periodic property, periodic table, periodic law, classification, information entropy, equipartition conjecture, principal component analysis, cluster analysis, local anaesthetic, procaine analogue.
24 citations
TL;DR: The specific rates of solvolysis of benzyl fluoroformate have been measured in several hydroxylic solvents at 25.0 °C as mentioned in this paper, and the determinations made were consistent with an addition-elimination (association-dissociation) mechanism, with addition rate-determining.
Abstract: The specific rates of solvolysis of benzyl fluoroformate have been measured inseveral hydroxylic solvents at 25.0 °C. For methanolysis, the solvent deuterium isotopeeffect and activation parameters were determined and activation parameters were alsodetermined for solvolyses in ethanol and 80% ethanol. For several of the binary hydroxylicsolvents, measurement of product ratios allowed selectivity values to be determined. Anextended Grunwald–Winstein treatment of the data led to sensitivities to changes in solventnucleophilicity and ionizing power. Comparison with previously determined specific ratesfor solvolysis of the chloroformate gave fluorine/chlorine rate ratios greater than unity. Allof the determinations made were consistent with an addition–elimination (association–dissociation) mechanism, with addition rate-determining.
TL;DR: The principle of substance stability is applicable to all biological systems as discussed by the authors and it boils down for different temporal hierarchies to the following: duringthe formation (self-assembly) of the most thermodynamically stable structures at the highest hierarchical level (j), e.g., the supramolecular level, in accordance with the second law,Nature spontaneously uses predominantly the (available for the given local part of the biological system) least thermodynamic stable structures belonging to a lower level (i.e., the molecular level).
Abstract: The principle of substance stability – the feedback principle – is applicable to allbiological systems. It boils down for different temporal hierarchies to the following: duringthe formation (self-assembly) of the most thermodynamically stable structures at the highesthierarchical level (j), e.g., the supramolecular level, in accordance with the second law,Nature spontaneously uses predominantly the (available for the given local part of thebiological system) least thermodynamically stable structures belonging to a lower level, forexample, the molecular level (j-1). The principle can be also applied to understructurehierarchical levels of any temporal hierarchy. It helps in understanding the causes of cancerformation and the origin of some other diseases.
TL;DR: In this paper, the specific rates of solvolysis of 1-adamantyl bromide and 1 -adamantsyl iodide in 1, 1,1,1.3,3, 3,3-hexafluoro-2-propanol-water mixtures, in conjunction with reported values in 80% ethanol, have led to additional YBr and YI solvent ionizing power values.
Abstract: Determinations of the specific rates of solvolysis of 1-adamantyl bromide and 1-adamantyl iodide in 1,1,1,3,3,3-hexafluoro-2-propanol-water mixtures, in conjunction withearlier reported values in 80% ethanol, have led to additional YBr and YI solvent ionizingpower values. These new values will be especially important in avoiding multicollinearitywhen the extended Grunwald-Winstein equation (extended by addition of a term involvingsolvent nucleophilicity) is used to correlate solvent-induced changes in the specific rates ofsolvolyses involving a bromide or iodide ion leaving group.
TL;DR: Curvularia eragrostidis, a causal agent of head blight on the weed (Digitariasanguinalis), did not cause disease on the turfgrass Festuca arundinacea, but differentextracellular esterase isoenzymes were detected in saprophytic and parasitic phases during fungal germination.
Abstract: Curvularia eragrostidis, a causal agent of head blight on the weed (Digitariasanguinalis), did not cause disease on the turfgrass Festuca arundinacea. Differentextracellular esterase isoenzymes were detected in saprophytic and parasitic phases duringthe fungal germination. The epicuticular waxes of D. sanguinalis were more efficient toinduce the secretion of esterases from the fungus than that of F. arundinacea, but were morerapidly degraded by the fungal enzymes. Component analysis indicated that the epicuticularwaxes from D. sanguinalis were mostly composed of alcohols, with 54.3% being 9,12-Octadecadien-1-ol. The main component of F arundinacea waxes was alkyl compounds,with 49.8% being olefin, 9-Tricosence. More long-chained esters were found in D.sanguinalis waxes, which were easier to be digested than those in F. arundinacea waxes byextreacellular esterases of the fungus. Epicuticular waxes play a role in varyingpathogenicity of C. eragrostidis on D. sanguinalis and F arundinacea.
TL;DR: An extensive QSAR study performed upon a largeseries of 79 HEPT ligands using the MTD and HyperChem molecular modeling methods shows that there are three 3D molecular zones important for the anti-HIV biological activity of the HEPt ligands under study.
Abstract: 1 Chemistry Department, West University of Timi soara, Pestalozzi Street No.16, Timi soara, RO-300115, Romania; E-mails: mvputz@cbg.uvt.ro and cori_mam@yahoo.com 2 Clinic of Preventive Cardiology and Cardiovascular Rehabilitation, University of Medicine and Pharmacy “Victor Babe s” Timi soara, B-dul C.D. Loga 49, RO-300020, Romania; E-mail: duda.seiman@cardiologie.ro 3 Faculty of Pharmacy, University of Medicine and Pharmacy “Victor Babe s” Timi soara, Bd. Eftimie Murgu No. 2, Timi soara, RO-300041, Romania; Email: ddragos@umft.ro, dciubotariu@mail.dnttm.ro 4 Faculty of Chemistry, “Politehnica” University Ti mi soara, Pia Ńa Victoriei no. 2, Timi soara, RO-300006, Romania; Email: medeleanu@chem.utt.ro 5 Institute of Chemistry “Coriolan Dr agulescu” of the Romanian Academy, Bd. Mihai Viteazul No. 24, RO-300223, Timisoara, Romania; Email: vcareja@acad-tim.utt.ro * Author to whom correspondence should be addressed. Received: 07 November 2006 / Accepted: 20 November 2006 / Published: 29 November 2006 Abstract: Molecular modeling and MTD methods are useful tools to assess both qualitative (SAR) and quantitative (QSAR) chemical structure-biological activity relationships. The 1-[(2-hydroxiethoxi)-methyl]-6-(phenylthio)thymine congeners (HEPT ligands) show in vitro anti-viral activity against the type-1 human immunodeficiency virus (HIV-1), which is the etiologic agent of AIDS. This work shows an extensive QSAR study performed upon a large series of 79 HEPT ligands using the MTD and HyperChem molecular modeling methods. The studied HEPT ligands are HIV reverse-transcriptase inhibitors. Their geometries were optimized and conformational analysis was carried out to build the hypermolecule, which allowed applying the MTD method. The hypermolecule was used for space mapping of the receptor’s interaction site. The obtained results show that there are three 3D molecular zones important for the anti-HIV biological activity of the HEPT ligands under study.
TL;DR: Quantitative structure-activity relationships (QSARs) for benz[a]anthracene (BA) mutagens using 73 descriptors were searched and each strain exhibited its own characteristic descriptors.
Abstract: Quantitative structure-activity relationships (QSARs) for benz[a]anthracene (BA)mutagens using 73 descriptors were searched. The mutagenicity data was obtained fromAmes assays for Mycobacterium vanbaalenii, Mycobacterium gilvum and Mycobacteriumflavescens strains. These data were fitted using a mutagenicity-cytotoxicity competitionmodel which defines the mutagenic potencies of BA metabolites, and include oxides,phenols, quinones, and dihydrodiols. The QSAR equations were derived using the moleculardescriptor set (charged partial surface area, spatial, thermodynamic and electronicdescriptors) and semi-empirical energetic and charge descriptors. Genetic functionapproximation was used to reduce and fit independent variables, including linear- andquadratic-based functions. Multiple QSAR equations were generated and a separate QSARequation was chosen and evaluated for each strain using conventional r2, F-test, and cross-validated r2. Each strain exhibited its own characteristic descriptors.
TL;DR: The results showed that strain GK24 is an aerobic, thermophilic, cellulolytic eubacterium which belongs to the group T. thermophilus, and a three-dimensional model of the endocellulase, Tc Cel5A, was generated based on known crystal structures and carried out a flexible cellotetraose docking study.
Abstract: 1 Systems Microbiology Research Center, KRIBB, Daejeon 305-806, Korea 2 Department of Biomicrosystem Technology, Korea University, Seoul 136-701, Korea 3 Department of Chemical and Biological Engineering, Korea University, Seoul 136-701, Korea * Author to whom correspondence should be addressed. Tel: +82-42-860-4135; Fax: +82-42-860-4597; E-mail address: dikim@kribb.re.kr Received: 20 November 2006 / Accepted: 14 December 2006 / Published: 18 December 2006 Abstract: The genome of T. caldophilus GK24 was recently sequenced and annotated as 14 contigs, equivalent to 2.3 mega basepairs (Mbp) of DNA. In the current study, we identified a unique 13.7 kbp DNA sequence, which included the endocellulase gene of T. caldophilus GK24, which did not appear to be present in the complete genomic sequence of the closely related species T. thermophilus HB27 and HB8. Congo-red staining revealed a unique phenotype of cellulose degradation by strain GK24 that was distinct from other closely related Thermus strains. The results showed that strain GK24 is an aerobic, thermophilic, cellulolytic eubacterium which belongs to the group T. thermophilus . In order to understand the mechanism of production of cellobiose in T. caldophilus GK24, a three-dimensional model of the endocellulase, Tc Cel5A, was generated based on known crystal structures. Using this model, we carried out a flexible cellotetraose docking study. Keywords: Endocellulase, Thermus caldophilus GK24, Glycosyl hydrolase family 5, Homology modeling, Molecular dynamics, Congo-red staining
TL;DR: A novel modified suspension polymerization method for the production of superparamagnetic poly ( methacrylate divinylbenzene) ( PMA-DVB) microbeads, with amino groups on their surface after simple modifications, which was proved to be a better method compared to the ELISA.
Abstract: Superparamagnetic polymers (SPMP) microbead was an excellent form for nanosized magnetic particles less than 10nm to realize their potential applications in many fields. We developed a novel modified suspension polymerization method for the production of superparamagnetic poly ( methacrylate divinylbenzene) ( PMA-DVB) microbeads, with amino groups on their surface after simple modifications. We applied these SPMP microbeads to establish a sandwich enzyme chemiluminence immuno (ECLIA) procedure of detecting the free hCG beta in serum. It was proved to a better method compared to the ELISA, since it need half of the sample volume, simpler protocols, and the time it need was shortened from 2 hours to 1 hour. The detection limit was 0.22 mIU.m(-1), one order lower than the ELISA assay. Its linear range was between 0.45 - 185.2 mIU.m(-1). And in the detections of clinical serum samples, the related coefficient between the two methods' results was 0.955.
TL;DR: It was concluded that the damage effect of ascorbate was reduced by Zinc-Hydroxybenzoite and the intensity of bands were changed at the different concentrations of the metal complex.
Abstract: Zinc-Hydroxybenzoite ([Zn (H20)6] (p-HO-C6H4COO)22H20) complex which wassynthesized and characterized by instrumental methods and the DNA samples which hadbeen isolated from cattle were allowed to interact at 37 oC for different time periods. Theinteraction of genomic DNA with this complex has been followed by agarose gelelectrophoresis at 50 V for 2 h. When DNA samples were allowed to interact with this metalcomplex, it was found that band intensities changed with the concentrations of the complex.In the result of interaction between this complex and genomic DNA samples, it wasdetermined that the intensities of bands were changed at the different concentrations of thecomplex. The brightness of the bands was increased and mobility of the bands wasdecreased, indicating the occurrence of increased covalent binding of the metal complexwith DNA. In this study it was concluded that the damage effect of ascorbate was reducedby Zinc-Hydroxybenzoite.
TL;DR: In this paper, an energy-partitioning quest for the origin of the barrier to the internal rotation of two iso-structuralmolecules, hydrogen peroxide, H2O2, and fluorine peroxide is performed.
Abstract: In order to understand the structure-property relationship, SPR, an energy-partitioning quest for the origin of the barrier to the internal rotation of two iso-structuralmolecules, hydrogen peroxide, H2O2, and fluorine peroxide, F2O2 is performed. Thehydrogen peroxide is an important bio-oxidative compound generated in the body cells tofight infections and is an essential ingredient of our immune system. The fluorine peroxideis its analogue. We have tried to discern the interactions and energetic effects that entail thenonplanar skew conformation as the equilibrium shape of the molecules. The physicalprocess of the dynamics of internal rotation initiates the isomerization reaction and generatesinfinite number of conformations. The decomposed energy components faithfully display thephysical process of skewing and eclipsing as a function of torsional angles and hence aregood descriptors of the process of isomerization reaction of hydrogen peroxide (H2O2) anddioxygen difluoride (F2O2) associated with the dynamics of internal rotation. It is observedthat the one-center, two-center bonded and nonbonded interaction terms are sharply dividedin two groups. One group of interactions hinders the skewing and favours planar cis/transforms while the other group favours skewing and prefers the gauche conformation of themolecule. The principal energetic effect forcing the molecules into the nonplanar gaucheform is the variation “O–O’ bond energy with torsion in both the molecules. It isdemonstrated that the barrier is not a regional effect rather it is made by the conjoint actionof all one- and two-center bonding and nonbonding interactions comprising the entireframework of the molecule. The present study claims to reveal one amazing feature of non-bonded interactions. Computed results of nonbonding interactions demonstrate that thenature of interaction between two formally positively charged non-bonding H atoms (Hδ+ ----Hδ+ ) is not always repulsive and it is attractive as well; the nature of the non-bondinginteraction between formally negatively charged atom (‘O’) and formally positively charged(‘H’) atom, (Oδ−----Hδ+ ), is not always attractive but repulsive too; it is also demonstrated that the nature of the nonbonding interaction between strongly electronegative atoms, ( Fδ−-- --Fδ−), is not always repulsive and it may be attractive as well.
TL;DR: In this article, the photochemical properties of the ionic liquid (RTIL) 1-butyl-3-methylimidazolium hexafluorophosphate (bmim) and its binary mixed solutions with organic solvices (DMF and MeCN) were investigated by laser photolysis at an e xcitation wavelength of 355 nm, using anthraquinone (AQ) as a probe molecule.
Abstract: Photochemical properties of the ionic liquid (RTIL) 1-butyl-3-methylimidazolium hexafluorophosphate (bmim)(PF 6) and its binary mixed solutions with organic solve nt (DMF and MeCN) were investigated by laser photolysis at an e xcitation wavelength of 355 nm, using anthraquinone (AQ) as a probe molecule. It was indicated that the triplet excited state of AQ ( 3 AQ*) can abstract hydrogen from (bmim)(PF 6). Moreover, along with the change of the ratio of RTIL and organic solvent, th e reaction rate constant changes regularly. Critical points were observed at volume fraction VRTIL = 0.2 for RTIL/MeCN and V RTIL = 0.05 for RTIL/DMF. For both systems, before the cri tical point, the rate constant increases rapidly with increasing VRTIL ; however, it decreases obviously with VRTIL after the critical point. We conclude that the concentration dependence is dominant at lower VRTIL , while the viscosity and phase transformation are dominant at higher VRTIL for the effect of ionic liquid on the decay of rate constant.
TL;DR: Self-organizing molecular field analysis (SOMFA), a simple three-dimensionalquantitative structure–activity relationship (3D-QSAR) method is used to study the correlation between the molecular properties and the anti-inflammatory biological activities of a new series of Diarylimidazoles that act as selective COX-2 inhibitors.
Abstract: Self-organizing molecular field analysis (SOMFA), a simple three-dimensionalquantitative structure–activity relationship (3D-QSAR) method is used to study the correlationbetween the molecular properties and the anti-inflammatory biological activities of a new series of1,5-Diarylimidazoles that act as selective COX-2 inhibitors. The statistical results, cross-validated rCV2 (0.507) and non cross-validated r2 (0.546), show a satisfied predictive ability.
TL;DR: The location, formation and biosynthetic regulation of cellulases in C. hutchinsonii were demonstrated on different substrates, and apparently glucose or labile substrates such as cellobiose seem to repress the formation of CM-cellulase.
Abstract: 1 Florida A&M University, Environmental Sciences Institute, FSH Science Research Center, 1520 South Bronough Street, Tallahassee, FL 32307, USA. * Current address of author to whom correspondence should be addressed: University of Maryland School of Medicine, Department of Medical Research and Technology, 100 Penn Street, Baltimore, MD 21201, USA. Email: clouime@som.umaryland.edu, Phone: 410-706-7664, Fax: 410-706-0073. Received: 27 December 2006 / Accepted: 30 January 2006 / Published: 31 January 2006 Abstract: An analysis of the recently published genome sequence of Cytophaga hutchinsonii revealed an unusual collection of genes for an organism that can attack crystalline cellulose. Consequently, questions were being raised by cellulase scientists, as to what mechanism this organism uses to degrade its insoluble substrates. Cellulose, being a highly polymeric compound and insoluble in water, cannot enter the cell walls of microorganisms. Cellulose-degrading enzymes have therefore to be located on the surface of the cell wall or released extracellularly. The location of most cellulase enzymes has been studied. However, basic information on C. hutchinsonii cellulases is almost non-existent. In the present study, the location, formation and biosynthetic regulation of cellulases in C. hutchinsonii were demonstrated on different substrates. Various fractions isolated from C. hutchinsonii after cell rupture were assayed for carboxymethyl-cellulase activity (CMC). The cellulases were found to be predominantly cell-free during active growth on solka-flok, although 30% of activity was recorded on cell-bound enzymes. Relatively little CM-cellulase was formed when cells were grown on glucose and cellobiose. Apparently glucose or labile substrates such as cellobiose seem to repress the formation of CM-cellulase. These findings should provide some insight into possible hydrolysis mechanisms by C. hutchinsonii . Keywords: Cellulase, Cytophaga , Cell Adhesion, Enzyme Regulation and Suppression
TL;DR: In this paper, a quantum chemical study of the dipolecorrelation of the electronic structure of the molecule as a function of conformations generated following the normal modes of vibrations between the two extremeconformations, including the equilibrium one, has been performed.
Abstract: In order to settle the issue of equivalence or non-equivalence of the two lone pairsof electrons on oxygen atom in water molecule, a quantum chemical study of the dipolecorrelation of the electronic structure of the molecule as a function of conformationsgenerated following the normal modes of vibrations between the two extremeconformations, C2v (∠HOH at 90o) and D∝h (∠HOH at 180o), including the equilibrium one,has been performed. The study invokes quantum mechanical partitioning of moleculardipoles into bond moment and lone pair moment and localization of delocalized canonicalmolecular orbitals, CMO’s into localized molecular orbitals, LMO’s. An earlier suggestion,on the basis of photoelectron spectroscopy, that one lone pair is in p-type and the other is ins-type orbital of O atom of water molecule at its equilibrium shape, and also the qualitative“Squirrel Ears” structure are brought under serious scrutiny. A large number ofconformations are generated and the charge density matrix, dipole moment of eachconformation is computed in terms of the generated canonical molecular orbitals, CMO’sand then Sinanoglu’s localization method is invoked to localize the CMO’s of eachconformation and the quantum mechanical hybridizations of all the bonds and lone pairs onO center are evaluated in terms of the localized molecular orbitals. Computed datademonstrate that the electronic structures i.e. two bond pairs and two lone pairs and itshybridization status of all conformations of water molecule are straightforward in terms ofthe LMO’s. It is further revealed that the pattern of orbital hybridization changescontinuously as a function of evolution of molecular shape. The close analysis of thegenerated LMO’s reveals that one lone pair is accommodated in a pure p orbital and anotherlone pair is in a hybrid orbital in almost all conformations. One more important result of the present study is that, with the physical process of structural evolution from close angular shape to the linear transition state, the length of the σ (O–H) decreases and its strength increases as a monotone function of reaction coordinates. The bond length is shortest and the strength is largest at the transition state of structural inversion. Result of structural effect of the present study during the evolution of molecular conformations is quite consistent with the result of a very refined calculation that one physically significant feature of force field that the stretching force constants at the linear geometry are considerably larger than their equilibrium counter parts. The variation of bond strength and the hybridization of s and p orbitals on O atom center to form the σ (O–H) bond as a function of evolution of conformations is in accordance with Coulson’s prediction. The total dipole moment of all conformations is partitioned into the contribution from bonds and lone pairs and correlated in terms of the computed hybridization in lone pairs. The analysis of the variation of dipole moment as a function of angular to linear structural evolution reveals that the dipole moment of H2O molecule is not due to the bond moments only but a significant contribution comes from a lone pair. It is strongly established that the dipole moment of water molecule at and around the equilibrium geometry is not due to the bond moments only and the major part of the molecular dipole comes from the contribution of lone pair electrons. This necessitates the accommodation of a lone pair of electrons in a hybrid orbital on O atom. The computed LMO’s webbed with partitioned molecular dipole reveal that one lone pair is in a pure p- type orbital and the other lone pair is in a hybrid of s and p, and not in a pure s type orbital as suggested on the basis of photoelectron spectra. The possibility of qualitative “Squirrel Ears” structure is also ruled out. The problem of equivalence or non-equivalence of the two lone pairs of the O atom in water seems to have been finally resolved by the present quantum chemical calculation. An attempt of locating the origin of barrier to the physical process of inversion of water molecule is made in terms of energy partitioning method. It is found that the dipole can be used as a descriptor for the elucidation of electronic structure of molecules.
TL;DR: Downregulation of the expression of GLUT1 was associated with the apoptosis induced bysodium butyrate in HT-29 cell line, and the concentration ofglucose had positive correlation with theexpression of bcl-x/l protein and negativecorrelation with the suicides induced by sodium butyrates.
Abstract: The regulation of glucose and sodium butyrate transporters(glucose transporter1-5 and Monocarboxylate transporter 1) and their relationship with cell apoptosis induced bysodium butyrate in colonic caner cell line HT-29 were studied. Cell apoptosis was detectedby flow cytometric assay. The expression of MCT1 and GLUT1-5 mRNA were detected byRT-PCR and the uptake of glucose was detected using 2-deoxy-[3H]glucose. The expressionof bax and bcl-x/l were detected by westernblot assay. We found that sodium butyrateinduced apoptosis in HT-29 cell line. The expression of GLUT1 mRNA, bcl-x/l, as well theuptake of glucose was inhibited by sodium butyrate. The expression of MCT1 and GLUT2,GLUT3, GLUT5 was not regulated by sodium butyrate. However, the concentration ofglucose had positive correlation with the expression of bcl-x/l protein and negativecorrelation with the apoptosis induced by sodium butyrate. All the results suggested thatdownregulation of the expression of GLUT1 was associated with the apoptosis induced bysodium butyrate in HT-29 cell line.
TL;DR: In this paper, a molecular quantitative model is constructed for a chemical reaction that might generate the elementary component of active streaming (AS) within the pure water phase, where a ballistic H+ may be released from H2O-H+ at a velocity of 10km/sec, carrying akinetic energy of 0.5 proton*volt.
Abstract: Active streaming (AS) of liquid water is considered to generate and overcomepressure gradients, so as to drive cell motility and muscle contraction by hydrauliccompression. This idea had led to reconstitution of cytoplasm streaming and musclecontraction by utilizing the actin-myosin ATPase system in conditions that exclude acontinuous protein network. These reconstitution experiments had disproved a contractileprotein mechanism and inspired a theoretical investigation of the AS hypothesis, aspresented in this article. Here, a molecular quantitative model is constructed for a chemicalreaction that might generate the elementary component of such AS within the pure waterphase. Being guided by the laws of energy and momentum conservation and by the physicalchemistry of water, a vectorial electro-mechano-chemical conversion is considered, asfollows: A ballistic H+ may be released from H2O-H+ at a velocity of 10km/sec, carrying akinetic energy of 0.5 proton*volt. By coherent exchange of microwave photons during 10-10sec, the ballistic proton can induce cooperative precession of about 13300 electrically-polarized water molecule dimers, extending along 0.5 μm. The dynamic dimers rearrangealong the proton path into a pile of non-radiating rings that compose a persistent rowing-likewater soliton. During a life-time of 20 msec, this soliton can generate and overcome amaximal pressure head of 1 kgwt/cm2 at a streaming velocity of 25 μm/sec and intrinsicpower density of 5 Watt/cm3. In this view, the actin-myosin ATPase is proposed to catalyzestereo-specific cleavage of H2O-H+ , so as to generate unidirectional fluxes of ballisticprotons and water solitons along each actin filament. Critical requirements and evidentialpredictions precipitate consistent implications to the physical chemistry of water, enzymatichydrolysis and synthesis of ATP, trans-membrane signaling, intracellular transport, cellmotility, intercellular interaction, and associated electro-physiological function. Sarcomerecontraction is described as hydraulic compression, driven by the suction power of centrally-oriented AS. This hydraulic mechanism anticipates structural, biochemical, mechanical and energetic aspects of striated muscle contraction, leading to quantitative formulation of a hydrodynamic power-balance equation yielding a general force-velocity relation.
TL;DR: Wang et al. as discussed by the authors proposed an MCI-based quantitative structure-property relationship (QSPR) model for the estimation of the aqueous solubility of chlorinated hydrocarbons.
Abstract: Ying-Long Wang, Yang-Dong Hu *, Lian-Ying Wu and We i-Zhong An College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266003, People’s Republic of China * Author to whom correspondence should be addressed; E-mail: chem_ouc@yahoo.com.cn or ylong_wang@yahoo.com Received: 24 November 2005 / Accepted: 17 February 2006 / Published: 28 February 2006 Abstract: Correlation for estimation of the aqueous solubility (logSw) of chlorinated hydrocarbons molecules is proposed. The MCI based quantitative structure-property relationship (QSPR) model proposed is predictive and requires only three connectivity indices in the calculation. The correlation equation obtained which is based on a training set of 50 chlorinated hydrocarbons has a correlation coefficient of 0.9670 and a standard error of 0.44 log
TL;DR: In this article, a multiple linear regression analysis was performed on the quantitative structure-activity relationships (QSAR) of the triazoloquinazoline adenosine antagonists for human A3receptors.
Abstract: Multiple linear regression analysis was performed on the quantitative structure-activity relationships (QSAR) of the triazoloquinazoline adenosine antagonists for human A3receptors. The data set used for the QSAR analysis encompassed the activities of 33triazoloquinazoline derivatives and 72 physicochemical descriptors. A template moleculewas derived using the known molecular structure for one of the compounds when bound tothe human A2B receptor, in which the amide bond was in a cis-conformation. All the testcompounds were aligned to the template molecule. In order to identify a reasonable QSARequation to describe the data set, we developed a multiple linear regression program thatexamined every possible combination of descriptors. The QSAR equation derived from thisanalysis indicates that the spatial and electronic effects is greater than that of hydrophobiceffects in binding of the antagonists to the human A3 receptor. It also predicts that a largesterimol length parameter is advantageous to activity, whereas large sterimol widthparameters and fractional positive partial surface areas are nonadvatageous.
TL;DR: In this article, a sensitive and rapid method was developed for the determination of cAMP inLocusta migratoria manilensis Meyen by high-performance liquid chromatography withfluorescence detection.
Abstract: A sensitive and rapid method was developed for the determination of cAMP inLocusta migratoria manilensis Meyen by high-performance liquid chromatography withfluorescence detection. The cAMP was derivatized using chloroacetaldehyde and TBASbuffer/methanol was used as the mobile phase. A detection quantification of 40 fmol/mlcould be achieved when using fluorescence detection. An HPLC-MS method using DMHAas an ion-pair agent to analyze cAMP was also demonstrated. We studied the effect ofdopamine and other stimulants on cAMP levels from isolated locust central nervoussystems. The new method is well suited for the analysis of cAMP in small biologicalsamples.
TL;DR: The resonance structures of allyl-(5pyridin-2-yl-[1,3,4]-thiadiazol-2yl)-amine have been determined by means of its 1H- (100 MHz, 500 MHz) 13C- and 15N-NMRspectra and B3LYP/6-31G* computations.
Abstract: The resonance structures of allyl-(5-pyridin-2-yl-[1,3,4]-thiadiazol-2-yl)-aminehave been determined by means of its 1H- (100 MHz, 500 MHz) 13C- and 15N-NMRspectra and B3LYP/6-31G* computations. The tautomeric equilibrium of this compoundhas been observed in the 1H-NMR spectra (100 MHz).