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Mechanistic Interpretation (mechanistic + interpretation)
Selected AbstractsFactors controlling the carbon isotope fractionation of tetra- and trichloroethene during reductive dechlorination by Sulfurospirillum ssp. and Desulfitobacterium sp. strain PCE-SFEMS MICROBIOLOGY ECOLOGY, Issue 1 2007Danuta Cichocka Abstract Carbon stable isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE) was investigated during reductive dechlorination. Growing cells of Sulfurospirillum multivorans, Sulfurospirillum halorespirans, or Desulfitobacterium sp. strain PCE-S, the respective crude extracts and the abiotic reaction with cyanocobalamin (vitamin B12) were used. Fractionation of TCE (,C=1.0132,1.0187) by S. multivorans was more than one order of magnitude higher than values previously observed for tetrachloroethene (PCE) (,C=1.00042,1.0017). Similar differences in fractionation were observed during reductive dehalogenation by the close relative S. halorespirans with ,C=1.0046,1.032 and ,C=1.0187,1.0229 for PCE and TCE respectively. TCE carbon isotope fractionation (,C=1.0150) by the purified PCE-reductive dehalogenase from S. multivorans was more than one order of magnitude higher than fractionation of PCE (,C=1.0017). Carbon isotope fractionation of TCE by Desulfitobacterium sp. strain PCE-S (,C=1.0109,1.0122) as well as during the abiotic reaction with cyanocobalamin (,C=1.0154) was in a similar range to previously reported values for fractionation by mixed microbial cultures. In contrast with previous results with PCE, no effects due to rate limitations, uptake or transport of the substrate to the reactive site could be observed during TCE dechlorination. Our results show that prior to a mechanistic interpretation of stable isotope fractionation factors it has to be carefully verified how other factors such as uptake or transport affect the isotope fractionation during degradation experiments with microbial cultures. [source] Interpretation of the temperature dependence of equilibrium and rate constantsJOURNAL OF MOLECULAR RECOGNITION, Issue 5 2006Donald J. Winzor Abstract The objective of this review is to draw attention to potential pitfalls in attempts to glean mechanistic information from the magnitudes of standard enthalpies and entropies derived from the temperature dependence of equilibrium and rate constants for protein interactions. Problems arise because the minimalist model that suffices to describe the energy differences between initial and final states usually comprises a set of linked equilibria, each of which is characterized by its own energetics. For example, because the overall standard enthalpy is a composite of those individual values, a positive magnitude for ,Ho can still arise despite all reactions within the subset being characterized by negative enthalpy changes: designation of the reaction as being entropy driven is thus equivocal. An experimenter must always bear in mind the fact that any mechanistic interpretation of the magnitudes of thermodynamic parameters refers to the reaction model rather than the experimental system For the same reason there is little point in subjecting the temperature dependence of rate constants for protein interactions to transition-state analysis. If comparisons with reported values of standard enthalpy and entropy of activation are needed, they are readily calculated from the empirical Arrhenius parameters. Copyright © 2006 John Wiley & Sons, Ltd. [source] Jonathan Edwards and the Language of Nature: The Re-Enchantment of the World in the Age of Scientific ReasoningJOURNAL OF RELIGIOUS HISTORY, Issue 1 2002Avihu Zakai For a long time Jonathan Edwards (1703-58) was thought of more as a preacher of hellfire and revival than as a theologian, and rather as a Calvinist theologian than a philosopher of importance, and he was dismissed accordingly. Yet Edwards was more than a hellfire preacher, more than a theologian. This New England divine was one of the rare individuals anywhere to recognize and answer the challenges posed to traditional Christian belief by the emergence of new modes of thought in early modern history - the new ideas of the scientific thought and the Enlightenment. His force of mind is evident in his exposition of the poverty of mechanical philosophy, which radically transformed the traditional Christian dialectic of God's utter transcendence and divine immanence by gradually dimin-ishing divine sovereignty with respect to creation, providence, and redemption, thus leading to the disenchantment of the world. Edwards constructed a teleological and theological alternative to the prevailing mechanistic interpretation of the essential nature of reality, whose ultimate goal was the re-enchantment of the world by reconstituting the glory of God's majestic sovereignty, power, and will within the order of creation. [source] Are Mechanistic and Statistical QSAR Approaches Really Different?MOLECULAR INFORMATICS, Issue 6-7 2010MLR Studies on 158 Cycloalkyl-Pyranones Abstract Two parallel approaches for quantitative structure-activity relationships (QSAR) are predominant in literature, one guided by mechanistic methods (including read-across) and another by the use of statistical methods. To bridge the gap between these two approaches and to verify their main differences, a comparative study of mechanistically relevant and statistically relevant QSAR models, developed on a case study of 158 cycloalkyl-pyranones, biologically active on inhibition (Ki) of HIV protease, was performed. Firstly, Multiple Linear Regression (MLR) based models were developed starting from a limited amount of molecular descriptors which were widely proven to have mechanistic interpretation. Then robust and predictive MLR models were developed on the same set using two different statistical approaches unbiased of input descriptors. Development of models based on Statistical I method was guided by stepwise addition of descriptors while Genetic Algorithm based selection of descriptors was used for the Statistical II. Internal validation, the standard error of the estimate, and Fisher's significance test were performed for both the statistical models. In addition, external validation was performed for Statistical II model, and Applicability Domain was verified as normally practiced in this approach. The relationships between the activity and the important descriptors selected in all the models were analyzed and compared. It is concluded that, despite the different type and number of input descriptors, and the applied descriptor selection tools or the algorithms used for developing the final model, the mechanistical and statistical approach are comparable to each other in terms of quality and also for mechanistic interpretability of modelling descriptors. Agreement can be observed between these two approaches and the better result could be a consensus prediction from both the models. [source] Estimation of Aqueous-Phase Reaction Rate Constants of Hydroxyl Radical with Phenols, Alkanes and AlcoholsMOLECULAR INFORMATICS, Issue 11-12 2009Ya-nan Wang Abstract A quantitative structure activity relationship (QSAR) model was developed for the aqueous-phase hydroxyl radical reaction rate constants (kOH) employing quantum chemical descriptors and multiple linear regressions (MLR). The QSAR development followed the OECD guidelines, with special attention to validation, applicability domain (AD) and mechanistic interpretation. The established model yielded satisfactory performance: the correlation coefficient square (R2) was 0.905, the root mean squared error (RMSE) was 0.139, the leave-many-out cross-validated QLMO2 was 0.806, and the external validated QEXT2 was 0.922 log units. The AD of the model covering compounds of phenols, alkanes and alcohols, was analyzed by Williams plot. The main molecular structural factors governing kOH are the energy of the highest occupied molecular orbital (EHOMO), average net atomic charges on hydrogen atoms (), molecular surface area (MSA) and dipole moment (,). It was concluded that kOH increased with increasing EHOMO and MSA, while decreased with increasing and ,. [source] Kinetic modeling of cellulosic biomass to ethanol via simultaneous saccharification and fermentation: Part II.BIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009Experimental validation using waste paper sludge, anticipation of CFD analysis Abstract A kinetic model of cellulosic biomass conversion to ethanol via simultaneous saccharification and fermentation (SSF) developed previously was validated experimentally using paper sludge as the substrate. Adsorption parameters were evaluated based on the data obtained at various values for fractional cellulose conversion. The adsorption model was then combined with batch SSF data to evaluate the cellulose hydrolysis parameters. With the parameters evaluated for the specific substrate, the discrete model was able to predict SSF successfully both with discrete addition of cellulase only and with discrete feeding of substrate, cellulase, and media. The model tested in this study extends the capability of previous SSF models to semi-continuous feeding configurations, and invites a mechanistic interpretation of the recently observed trend of increasing conversion with decreasing feeding frequency [Fan et al. (2007a) Bioprocess Biosyst Eng 30(1):27,34]. Our results also support the feasibility and utility of determining adsorption parameters based on data obtained at several conversions, particularly when the model is to be applied to extended reaction times rather than only initial hydrolysis rates. The revised model is considerably more computationally efficient than earlier models, and appears for many conditions to be within the capability of simulation using computational fluid dynamics. Biotechnol. Bioeng. 2009;102: 66,72. © 2008 Wiley Periodicals, Inc. [source] Controllable Synthesis of Nickel Hydroxide and Porous Nickel Oxide Nanostructures with Different MorphologiesCHEMISTRY - A EUROPEAN JOURNAL, Issue 16 2008Lihong Dong Dr. Abstract ,-Ni(OH)2 nanobelts, nanowires, short nanowires, and ,-Ni(OH)2 nanoplates have been successfully prepared in high yields and purities by a convenient hydrothermal method under mild conditions from very simple systems composed only of NaOH, NiSO4, and water. It has been found that the ratio of NaOH to NiSO4 not only affects the morphology of the Ni(OH)2 nanostructures, but also determines whether the product is of the ,- or ,-crystal phase. A notable finding is that porous NiO nanobelts were produced after exposure of the Ni(OH)2 products to an electron beam for several minutes during transmission electron microscopy (TEM) observations. Another unusual feature is that rectangular nanoplates with many gaps were obtained. Furthermore, porous NiO nanobelts, nanowires, and nanoplates could also be obtained by annealing the as-prepared Ni(OH)2 products. A sequence of dissolution, recrystallization, and oriented attachment-assisted self-assembly of nanowires into nanobelts is proposed as a plausible mechanistic interpretation for the formation of the observed structures. The method presented here possesses several advantages, including high yields, high purities, low cost, and environmental benignity. It might feasibly be scaled-up for industrial mass production. [source] Nitrobenzene toxicity: QSAR correlations and mechanistic interpretations,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2003Alan R. Katritzky Abstract The overall five-parameter QSAR correlation [ in terms of log(IGC50,1)] based on CODESSA-PRO methodology for the aquatic toxicity of 97 substituted nitrobenzenes to the ciliate Tetrahymena pyriformis supports previous conclusions that hydrophobicity and electrophilic reactivity control nitrobenzene toxicity. Correcting for the ionization of acidic species (picric and nitrobenzoic acids) improves the results: . Consideration of the total set of 97 compounds suggests two mechanisms of toxic action. A subset containing 43 compounds favorably disposed to reversible reduction of nitro group with respect to the single occupied molecular orbital energy, ESOMO correlated well with just four theoretically derived descriptors: . Another set of 49 substances predisposed to aromatic nucleophilic substitution modeled well () with five descriptors. Copyright © 2003 John Wiley & Sons, Ltd. [source] Exploitation of the complex chemistry of hindered amine stabilizers in effective plastics stabilization,JOURNAL OF VINYL & ADDITIVE TECHNOLOGY, Issue 3 2007J. Pospí Hindered amine stabilizers (HAS) remain a prominent class of stabilizers having a fortunate development with continuous interest in shaping the future properties of plastics: increase in polymer durability, application extension, reaching new effects. Commercial tests provided much information. Insufficient mechanistic interpretations of the complex effects of environmental factors (harshness of testing, penetration of radiation and oxygen, superposition of temperature, atmospheric impurities) and those of the microenvironment (morphology of the polymer matrix, physical relations of HAS,polymer, interference between HAS and other additives) are a drawback. Model experiments complement commercial studies and explain some phenomena. A careful transfer of information from model experiments must be done to avoid misinterpretation of mechanisms, particularly of the HAS regenerative cycle. A critical analysis of primary steps of the HAS activity mechanism in the polymer matrix based on HAS-related primary nitroxides, formation of their stationary concentration and concentration gradients influenced by polymer morphology, spatial competition between autoreactions, and oxidation of polymer-developed alkyl radicals and their scavenging by nitroxides (the key process of HAS efficiency) is outlined. Cyclic regeneration of nitroxides affected by the structure of the amino moiety in the HAS molecule, influence of acid environment, atmospheric ozone or singlet oxygen, cooperative mixtures of HAS with UV absorbers, combinations with additives increasing the thermal stabilization effect and improving color retention, assessment of the heat stabilization performance of HAS by proper testing, and influence of the molecular weight of HAS are mentioned together with examples of the chemical consumption of HAS in the final phases of their lifetime. lifetime. J. VINYL ADDIT. TECHNOL., 13:119,132, 2007. © 2007 Society of Plastics Engineers [source] A new crystal form of XT6 enables a significant improvement of its diffraction quality and resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2004Maya Bar Xylanases (1,4-,- d -xylan xylanhydrolases; EC 3.2.1.8) hydrolyze the 1,4-,- d -xylopyranosyl linkage of xylans. The detailed structural characterization of these enzymes is of interest for the elucidation of their catalytic mechanism and for their rational modification toward improved stability and specificity. An extracellular xylanase from Geobacillus stearothermophilus T-6 (XT6) has recently been cloned, overexpressed, purified and biochemically characterized. Previous crystallographic efforts resulted in a hexagonal crystal form, which subsequently proved to be of limited use for structural analysis, mainly because of its relatively poor diffraction quality and resolution. A systematic search for more suitable crystals of XT6 recently resulted in a new crystal form of this enzyme with significantly improved diffraction characteristics. The new crystals belong to a C -centred monoclinic crystal system (space group C2), with unit-cell parameters a = 121.5, b = 61.7, c = 89.1,Å, , = 119.7°. These crystals diffract X-rays to better than 1.5,Å resolution, showing a very clear diffraction pattern of relatively high quality. The crystals are mechanically strong and exhibit excellent radiation-stability when frozen under cold nitrogen gas. A full diffraction data set to 1.45,Å resolution (94.1% completeness, Rmerge = 7.0%) has been collected from flash-frozen crystals of the native enzyme at 95,K using synchrotron radiation. Crystals of the E159A/E265A catalytic double mutant of XT6 were found to be isomorphous to those of native XT6. They were used for a full measurement of 1.8,Å resolution diffraction data at 100,K (90.9% completeness; Rmerge = 5.0%). These data are currently being used for the high-resolution structure determination of XT6 and its mutant for mechanistic interpretations and rational introduction of thermostability. [source] | |||||||||||||