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Entropy
Kinds of Entropy Terms modified by Entropy Selected AbstractsMORE ON MINIMAL ENTROPY,HELLINGER MARTINGALE MEASUREMATHEMATICAL FINANCE, Issue 1 2006Tahir Choulli This paper extends our recent paper (Choulli and Stricker 2005) to the case when the discounted stock price process may be unbounded and may have predictable jumps. In this very general context, we provide mild necessary conditions for the existence of the minimal entropy,Hellinger local martingale density and we give an explicit description of this extremal martingale density that can be determined by pointwise solution of equations in depending only on the local characteristics of the discounted price process S. The uniform integrability and other integrability properties are investigated for this extremal density, which lead to the conditions of the existence of the minimal entropy,Hellinger martingale measure. Finally, we illustrate the main results of the paper in the case of a discrete-time market model, where the relationship of the obtained optimal martingale measure to a dynamic risk measure is discussed. [source] Reaction of H + ketene to formyl methyl and acetyl radicals and reverse dissociationsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 1 2003Jongwoo Lee Thermochemical properties for reactants, intermediates, products, and transition states important in the ketene (CH2CO) + H reaction system and unimolecular reactions of the stabilized formyl methyl (C·H2CHO) and the acetyl radicals (CH3C·O) were analyzed with density functional and ab initio calculations. Enthalpies of formation (,Hf°298) were determined using isodesmic reaction analysis at the CBS-QCI/APNO and the CBSQ levels. Entropies (S°298) and heat capacities (Cp°(T)) were determined using geometric parameters and vibrational frequencies obtained at the HF/6-311G(d,p) level of theory. Internal rotor contributions were included in the S and Cp(T) values. A hydrogen atom can add to the CH2 -group of the ketene to form the acetyl radical, CH3C·O (Ea = 2.49 in CBS-QCI/APNO, units: kcal/mol). The acetyl radical can undergo ,-scission back to reactants, CH2CO + H (Ea = 45.97), isomerize via hydrogen shift (Ea = 46.35) to form the slight higher energy, formyl methyl radical, C·H2CHO, or decompose to CH3 + CO (Ea = 17.33). The hydrogen atom also can add to the carbonyl group to form C·H2CHO (Ea = 6.72). This formyl methyl radical can undergo , scission back to reactants, CH2CO + H (Ea = 43.85), or isomerize via hydrogen shift (Ea = 40.00) to form the acetyl radical isomer, CH3C·O, which can decompose to CH3 + CO. Rate constants are estimated as function of pressure and temperature, using quantum Rice,Ramsperger,Kassel analysis for k(E) and the master equation for falloff. Important reaction products are CH3 + CO via decomposition at both high and low temperatures. A transition state for direct abstraction of hydrogen atom on CH2CO by H to form, ketenyl radical plus H2 is identified with a barrier of 12.27, at the CBS-QCI/APNO level. ,Hf°298 values are estimated for the following compounds at the CBS-QCI/APNO level: CH3C·O (,3.27), C·H2CHO (3.08), CH2CO (,11.89), HC·CO (41.98) (kcal/mol). © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 20,44, 2003 [source] Spatial prediction of categorical variables with the Bayesian Maximum Entropy approach: the Ooypolder case studyEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2004D. D'Or Summary Categorical variables such as water table status are often predicted using the indicator kriging (IK) formalism. However, this method is known to suffer from important limitations that are most frequently solved by ad hoc solutions and approximations. Recently, the Bayesian Maximum Entropy (BME) approach has proved its ability to predict categorical variables efficiently and in a flexible way. In this paper, we apply this approach to the Ooypolder data set for the prediction of the water table classes from a sample data set. BME is compared with IK using global as well as local criteria. The inconsistencies of the IK predictor are emphasized and it is shown how BME permits avoiding them. [source] Spectral entropy monitoring allowed lower sevoflurane concentration and faster recovery in childrenACTA ANAESTHESIOLOGICA SCANDINAVICA, Issue 7 2010S. R. CHOI Background: Anesthetic titration using spectral entropy monitoring reduces anesthetic requirements and shortens recovery in adult surgical patients. This study was performed to evaluate the effect of entropy monitoring on end-tidal sevoflurane concentration and recovery characteristics in pediatric patients undergoing sevoflurane anesthesia. Methods: Seventy-eight children (aged 3,12 years) scheduled for a tonsillectomy and/or an adenoidectomy were randomly divided into one of two groups: standard practice (Standard) or entropy-guided (Entropy). In the Standard group, sevoflurane was adjusted to maintain the heart rate and systolic blood pressure (BP) within 20% of the baseline values. In the Entropy group, sevoflurane was adjusted to achieve a state entropy of 40,50. We compared the entropy values, end-tidal sevoflurane concentration and recovery times between groups. Results: During maintenance of anesthesia, the entropy and BP values were higher in the Entropy group (P<0.05). The end-tidal sevoflurane concentration during maintenance was lower in the Entropy group (2.2 (0.3) vol%) compared with the Standard group (2.6 (0.4) vol%) (P<0.05). Recovery times were faster in the Entropy group (P<0.05). Conclusions: Compared with standard practice, we found that entropy-guided anesthetic administration was associated with a reduced sevoflurane concentration and a slightly faster emergence and recovery in 3,12-year-old children. [source] Entropy-based metrics in swarm clusteringINTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 9 2009Bo Liu Ant-based clustering methods have received significant attention as robust methods for clustering. Most ant-based algorithms use local density as a metric for determining the ants' propensities to pick up or deposit a data item; however, a number of authors in classical clustering methods have pointed out the advantages of entropy-based metrics for clustering. We introduced an entropy metric into an ant-based clustering algorithm and compared it with other closely related algorithms using local density. The results strongly support the value of entropy metrics, obtaining faster and more accurate results. Entropy governs the pickup and drop behaviors, while movement is guided by the density gradient. Entropy measures also require fewer training parameters than density-based clustering. The remaining parameters are subjected to robustness studies, and a detailed analysis is performed. In the second phase of the study, we further investigated Ramos and Abraham's (In: Proc 2003 IEEE Congr Evol Comput, Hoboken, NJ: IEEE Press; 2003. pp 1370,1375) contention that ant-based methods are particularly suited to incremental clustering. Contrary to expectations, we did not find substantial differences between the efficiencies of incremental and nonincremental approaches to data clustering. © 2009 Wiley Periodicals, Inc. [source] Rate and product studies in the solvolyses of methanesulfonic anhydride and a comparison with methanesulfonyl chloride solvolyses,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2007Dennis N. Kevill Abstract The specific rates of solvolysis of methanesulfonic anhydride have been measured conductometrically at ,10,°C in 41 solvents. Use of the extended Grunwald,Winstein equation, with the NT scale of solvent nucleophilicity and the YOTs scale of solvent ionizing power, leads to sensitivity to changes in solvent nucleophilicity (, value) of 0.95 and a sensitivity to changes in solvent ionizing power (m value) of 0.61, with a multiple correlation coefficient (R) of 0.973. Product selectivity values (S) in binary hydroxylic solvents favor alcohol attack in EtOH,H2O (a value of 1.2 in 90% EtOH rising to 4.0 in 40% EtOH) and in MeOH,H2O (a value of 3.7 in 90% MeOH rising to 6.0 in 50% MeOH). In 2,2,2,-trifluoroethanol,H2O, the S values are much lower at about 0.1. Entropy of activation values are appreciably negative. Literature values for the specific rates of solvolysis of methanesulfonyl chloride have been extended to fluoroalcohol-containing solvents (titrimetric method) and, at 45.0,°C, for an overall 43 solvents values are obtained (using NT and YC1 scales) of 1.20 for , and of 0.52 for m (R,=,0.969). It is proposed that both substrates solvolyze by an SN2 pathway. Copyright © 2007 John Wiley & Sons, Ltd. [source] A semantic entropy metricJOURNAL OF SOFTWARE MAINTENANCE AND EVOLUTION: RESEARCH AND PRACTICE, Issue 4 2002Letha H. Etzkorn Abstract This paper presents a new semantically-based metric for object-oriented systems, called the Semantic Class Definition Entropy (SCDE) metric, which examines the implementation domain content of a class to measure class complexity. The domain content is determined using a knowledge-based program understanding system. The metric's examination of the domain content of a class provides a more direct mapping between the metric and common human complexity analysis than is possible with traditional complexity measures based on syntactic aspects (software aspects related to the format of the code). Additionally, this metric represents a true design metric that can measure complexity early in the life cycles of software maintenance and software development. The SCDE metric is correlated with analyses from a human expert team, and is also compared to syntactic complexity measures. Copyright © 2002 John Wiley & Sons, Ltd. [source] Relative Importance of Intrinsic, Extrinsic, and Anthropic Factors in the Geomorphic Zonation of the Trinity River, Texas,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 4 2010Jonathan D. Phillips Phillips, Jonathan D., 2010. Relative Importance of Intrinsic, Extrinsic, and Anthropic Factors in the Geomorphic Zonation of the Trinity River, Texas. Journal of the American Water Resources Association (JAWRA) 46(4): 807-823. DOI: 10.1111/j.1752-1688.2010.00457.x Abstract:, The Trinity River, Texas, was characterized according to its geologic framework, valley width and confinement, slope, sinuosity, channel-floodplain connectivity, and flow regime, leading to the identification of 18 hinge points along the 638 km study area where major transitions in two or more criteria occur. These, and effects of human agency, avulsions, and sea level rise, delineate 21 river styles or zones. Each zone was evaluated with respect to dominant factors determining its geomorphological characteristics: geology/lithology, tectonics, Holocene sea level rise, meandering, cutoffs and other lateral channel changes, avulsions, valley constrictions by alluvial terraces, and paleomeander depressions. Direct human influences (a large impoundment and water withdrawals) are also evident. Entropy of the relationships between these controls and the geomorphological zones shows that all the controls are significant, and each accounts for 4-15% of the total entropy. Geologic controls, lateral channel changes, and constriction by terraces are the three most influential controls, illustrating that controls on river morphology include extrinsic boundary conditions, active process-form interrelationships, and inherited features. Extrinsic and intrinsic controls each account for about a third of the entropy, but the latter includes antecedent features as well as active channel dynamics, underscoring the importance of historical contingency even in alluvial rivers. [source] GEOSTATISTICAL ESTIMATION OF HORIZONTAL HYDRAULIC CONDUCTIVITY FOR THE KIRKWOOD-COHANSEY AQUIFER,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 1 2004Vikram M. Vyas ABSTRACT: The Kirkwood-Cohansey aquifer has been identified as a critical source for meeting existing and expected water supply needs for southern New Jersey. Several contaminated sites exist in the region; their impact on the aquifer has to be evaluated using ground water flow and transport models. Ground water modeling depends on availability of measured hydrogeologic data (e.g., hydraulic conductivity, for parameterization of the modeling runs). However, field measurements of such critical data have inadequate spatial density, and their locations are often clustered. The goal of this study was to research, compile, and geocode existing data, then use geostatistics and advanced mapping methods to develop a map of horizontal hydraulic conductivity for the Kirkwood-Cohansey aquifer. Spatial interpolation of horizontal hydraulic conductivity measurements was performed using the Bayesian Maximum Entropy (BME) Method implemented in the BMELib code library. This involved the integration of actual measurements with soft information on likely ranges of hydraulic conductivity at a given location to obtain estimate maps. The estimation error variance maps provide an insight into the uncertainty associated with the estimates, and indicate areas where more information on hydraulic conductivity is required. [source] Danckwerts Revisited , The Use of Entropy to Define Scale and Intensity of SegregationMACROMOLECULAR THEORY AND SIMULATIONS, Issue 2 2009Marco Camesasca Abstract Rényi statistical entropy as a means to quantify mixing in two-dimensional binary systems is presented. The use of Rényi entropies in defining the scale and intensity of segregation for mixing quality determination is analyzed. Finally, the relationship between the mixing process and the structures generated in the system is explored by using the Rényi entropy as an easy and computationally efficient method to calculate the system spectrum of fractal dimensions. [source] Quantifying Fluid Mixing with the Shannon EntropyMACROMOLECULAR THEORY AND SIMULATIONS, Issue 8 2006Marco Camesasca Abstract Summary: We introduce a methodology to quantify the quality of mixing in various systems, including polymeric ones, by adapting the Shannon information entropy. For illustrative purposes we use particle advection of two species in a two-dimensional cavity flow. We compute the entropy by using the probability of finding a suitable chosen group/complex of particles of a given species, at a given location. By choosing the size of the group to be in direct proportion to the overall concentration of the components in the mixture we ensure that the entropic measure is maximized for the case of perfect mixing, that is, when at each location the component concentration is equal to the corresponding overall component concentrations. The scale of observation role in evaluating mixing is analyzed using the entropic methodology. We also illustrate the effect of initial conditions on mixing in a laminar system, typical in operations involving polymers. [source] Surprising Effects on the Conformational Entropy due to Nonrandom Distributions of Local Conformations Along Unperturbed ChainsMACROMOLECULAR THEORY AND SIMULATIONS, Issue 7 2006Wayne L. Mattice Abstract Summary: Nonrandomness in the distribution of rotational isomeric states along a flexible unperturbed chain reduces its conformational entropy. Pairwise interdependence of the bonds is a necessary, but not sufficient, condition for a significant reduction. The reduction in conformational entropy from this source can be as severe as a factor of three. It is generally more severe for isotactic chains than for the syndiotactic chains constructed from the same monomer. Surprising effects are sometimes seen, such as the nearly identical reductions in conformational entropy for polydimethylsiloxane, a very flexible chain, and for poly(methyl methacrylate), a much stiffer chain. Fractional difference in conformational entropy due to nonrandomness versus probability of helix in helix-coil transition. [source] Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate changeMOLECULAR ECOLOGY, Issue 17 2010VICTORIA L. SORK Abstract Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971,2000) and future (2070,2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions. [source] Doppler broadening of annihilation radiation spectroscopy study using Richardson-Lucy, Maximum Entropy and Huber methodsPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 10 2007D. P. Yu Abstract The Richardson-Lucy, Maximum Entropy and Huber regularization methods are popularly used in solving ill-posed inverse problems. This paper considers the use of these three methods in the deconvoluting DBARS (Doppler Broadening of Annihilation Radiation Spectroscopy) data. As DBARS data have a constant background on the high-energy side and a long exponential tail on the low-energy side, we check the different deconvolution schemes paying specific attention to the quality of the deconvolution at the peak and tail positions. Comparison of the three methods is made by testing on Monte-Carlo simulated data both in terms of the deconvoluted quality and computational resources required. Finally, we apply these methods to experimental DBARS data taken on polycrystalline metal samples. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Entropy,enthalpy compensation: Fact or artifact?PROTEIN SCIENCE, Issue 3 2001Kim Sharp Abstract The phenomenon of entropy,enthalpy (S-H) compensation is widely invoked as an explanatory principle in thermodynamic analyses of proteins, ligands, and nucleic acids. It has been suggested that this compensation is an intrinsic property of either complex, fluctuating, or aqueous systems. The questions examined here are whether the observed compensation is extra-thermodynamic (i.e., reflects anything more than the well-known laws of statistical thermodynamics) and if so, what does it reveal about the system? Compensation is rather variably defined in the literature and different usages are discussed. The most precise and interesting one, which is considered here, is a linear relationship between ,H and ,S for some series of perturbations or changes in experimental variable. Some recent thermodynamic data on proteins purporting to show compensation is analyzed and shown to be better explained by other causes. A general statistical mechanical model of a complex system is analyzed to explore whether and under what conditions extra-thermodynamic compensation can occur and what it reveals about the system. This model shows that the most likely behavior to be seen is linear S-H compensation over a rather limited range of perturbations with a compensation temperature Tc = d,H/d,S within 20% of the experimental temperature. This behavior is insensitive to the details of the model, thus revealing little extra-thermodynamic or causal information about the system. In addition, it will likely be difficult to distinguish this from more trivial forms of compensation in real experimental systems. [source] Evaluation of an Entropy-Based Combustion Model using Stochastic ReactorsCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 7 2008J. Leicher Abstract The entropy transport concept (ETC) presented in this paper is a novel approach to describe reaction systems such that the dynamic behavior of a chemical system can be reproduced with a minimum in independent parameters. It is shown that, for adiabatic conditions, the mixture fraction and the reaction entropy are sufficient to describe combustion processes without significant loss of information. Entropy is used as a measure of the reaction progress in this context. In order to evaluate the applicability of the ETC for combustion modeling in turbulent systems, the entropy transport concept was implemented into a stochastic reactor model. For several test cases, the results of this ETC-based reactor were compared with a reactor that directly integrates the species transport equations. [source] ChemInform Abstract: Estimation of the Excess Entropy of Mixing and the Excess Heat Capacity of Liquid Alloys.CHEMINFORM, Issue 16 2001V. T. Witusiewicz Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Addressing Association Entropy by Reconstructing Guanidinium Anchor Groups for Anion Binding: Design, Synthesis, and Host,Guest Binding Studies in Polar and Protic SolutionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2008Vinod Abstract The bicyclic hexahydropyrimidino[1,2a]pyrimidine cationic scaffold has a well-known capacity to bind a variety of oxoanions (phosphates, carboxylates, squarates, phosphinates). Based on this feature, the parent host was supplemented with sec -carboxamido substituents to generate compounds 1,3 in an effort to improve the anion-binding affinity and selectivity and to learn about the role and magnitude of entropic factors. Bicyclic guanidinium compounds were prepared by a convergent strategy via the corresponding tetraester 22 followed by catalytic amidation. Host,guest binding studies with isothermal titration calorimetry in acetonitrile probed the behavior of artificial hosts 1,3 in comparison with the tetraallylguanidinium compound 4 on binding p -nitrobenzoate, dihydrogenphosphate, and 2,2,-bisphenolcyclophosphate guests that showed enhanced affinities in the 105,106,M,1 range. Contrary to expectation, better binding emerges from more positive association entropies rather than from stronger enthalpic interactions (hydrogen bonding). In an NMR spectroscopy titration in DMSO, o -phthalate was sufficiently basic to abstract a proton from the guanidinium function, as confirmed by an X-ray crystal structure of the product. The novel carboxamide-appended anchor groups also bind carboxylates and phosphates, but not hydrogen sulfate in methanol with affinities in excess of 104,M,1. The energetic signature of the complexation in methanol is inverted with respect to acetonitrile solvent and shows a pattern of general ion pairing with strong positive entropies overcompensating endothermic binding enthalpies. This study provides an example of the fact that bona fide decoration of a parent guanidinium anchor function with an additional binding functionality may provide the desired enhancement of the host,guest affinity, yet for a different reason than that implemented by design as guided by standard molecular modeling. [source] Investigation of the stereodynamics of tris-(, -diimine),transition metal complexes by enantioselective dynamic MEKCELECTROPHORESIS, Issue 2 2009Sabrina Bremer Abstract Enantiomerization of octahedral tris(, -diimine),transition metal complexes was investigated by enantioselective dynamic MEKC. Varying both the transition metal ion (Fe2+, Fe3+, and Ni2+) and the bidentate diimine ligand (1,10-phenanthroline and 2,2,-bipyridyl), the enantiomer separations were performed either in a 100,mM sodium tetraborate buffer (pH 9.3) or in a 100,mM sodium tetraborate/sodium dihydrogenphosphate buffer (pH 8.0) both containing sodium cholate as chiral surfactant. The unified equation of dynamic chromatography was employed to determine apparent reaction rate constants from the electropherograms showing distinct plateau formation. Apparent activation parameters ,H, and ,S, were calculated from temperature-dependent measurements between 10.0 and 35.0°C in 2.5,K steps. It was found that the nature of the central metal ion and the ligand strongly influence the enantiomerization barrier. Surprisingly, complexes containing the 2,2,-bipyridyl ligand show highly negative activation entropies between ,103 and ,116,J (K,mol),1 while the activation entropy of tris(1,10-phenanthroline) complexes is positive indicating a different mechanism of interconversion. Furthermore, it was found that the Ni2+ complexes are stereostable under the conditions investigated here making them a lucent target as enantioselective catalysts. [source] A thermodynamics-based estimation model for adsorption of organic compounds by carbonaceous materials in environmental sorbentsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 6 2003Paul C. M. van Noort Abstract A model was developed to estimate Langmuir affinities for adsorption of low-polarity organic compounds from either water or air by carbonaceous sorbents. Sorption enthalpies and entropies provided the basic information for the description of sorption affinities in terms of the entropy of melting and either solubility in water or vapor pressure. For m -xylene, polycyclic aromatic hydrocarbons (PAHs) and chlorobenzenes on 10 different sorbents, 80% of the measured sorption affinities fall within a factor of four of the model estimates. Equations for the limiting distribution coefficients in terms of either octanol,air (KOA) or octanol,water partition (Kow) coefficients were derived from regressions of calculated affinities combined with an estimated relation between experimental Langmuir sorption capacities and Kow. Estimated soot,water distribution coefficients were within a factor of three of measured data for polychlorobiphenyls (PCBs) and lower molecular weight PAHs on automotive soot samples and captured the dependence of PCB distribution coefficients on the extent of ortho substitution. For higher molecular weight PAHs, sorption was underestimated. For soot in sediment,water distribution coefficients of PAHs and PCBs, estimated values captured both the trend of measured data with Kow and the dependence on sorbate planarity. Tentative application to aerosol,air distribution explained the observed independence of distribution coefficient,KOA relations for PCBs on the extent of ortho substitution and suggested nonequilibrium conditions for PAHs in comparison with recent measurements. [source] Discrete Cyanide-Bridged Mixed-Valence Co/Fe Complexes: Outer-Sphere Redox BehaviourEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 13 2003Paul V. Bernhardt Abstract The outer-sphere redox behaviour of a series of [LnCoIIINCFeII(CN)5], (Ln = n -membered pentadentate aza-macrocycle) complexes have been studied as a function of pH and oxidising agent. All the dinuclear complexes show a double protonation process at pH , 2 that produces a shift in their UV/Vis spectra. Oxidation of the different non-protonated and diprotonated complexes has been carried out with peroxodisulfate, and of the non-protonated complexes also with trisoxalatocobaltate(III). The results are in agreement with predictions from the Marcus theory. The oxidation of [Fe(phen)3]3+ and [IrCl6]2, is too fast to be measured, although for the latter the transient observation of the process has been achieved at pH = 0. The study of the kinetics of the outer-sphere redox process, with the S2O82, and [Co(ox)3]3, oxidants, has been carried out as a function of pH, temperature, and pressure. As a whole, the values found for the activation volumes, entropies, and enthalpies are in the following margins, for the diprotonated and non-protonated dinuclear complexes, respectively: ,V, from 11 to 13 and 15 to 20 cm3 mol,1; ,S, from 110 to 30 and ,60 to ,90 J K,1 mol,1; ,H, from 115 to 80 and 50 to 65 kJ·mol,1. The thermal activation parameters are clearly dominated by the electrostriction occurring on outer-sphere precursor formation, while the trends found for the values of the volume of activation indicate an important degree of tuning due to the charge distribution during the electron transfer process. The special arrangement on the amine ligands in the isomer trans -[L14CoIIINCFeII(CN)5], accounts for important differences in solvent-assisted hydrogen bonding occurring within the outer-sphere redox process, as has been established in redox reactions of similar compounds. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Role of electrostatics in the interaction between plastocyanin and photosystem I of the cyanobacterium Phormidium laminosumFEBS JOURNAL, Issue 23 2002Beatrix G. Schlarb-Ridley The interactions between photosystem I and five charge mutants of plastocyanin from the cyanobacterium Phormidium laminosum were investigated in vitro. The dependence of the overall rate constant of reaction, k2, on ionic strength was investigated using laser flash photolysis. The rate constant of the wild-type reaction increased with ionic strength, indicating repulsion between the reaction partners. Removing a negative charge on plastocyanin (D44A) accelerated the reaction and made it independent of ionic strength; removing a positive charge adjacent to D44 (K53A) had little effect. Neutralizing and inverting the charge on R93 slowed the reaction down and increased the repulsion. Specific effects of MgCl2 were observed for mutants K53A, R93Q and R93E. Thermodynamic analysis of the transition state revealed positive activation entropies, suggesting partial desolvation of the interface in the transition state. In comparison with plants, plastocyanin and photosystem I of Phormidium laminosum react slowly at low ionic strength, whereas the two systems have similar rates in the range of physiological salt concentrations. We conclude that in P. laminosum, in contrast with plants in vitro, hydrophobic interactions are more important than electrostatics for the reactions of plastocyanin, both with photosystem I (this paper) and with cytochrome f[Schlarb-Ridley, B.G., Bendall, D.S. & Howe, C.J. (2002) Biochemistry41, 3279,3285]. We discuss the implications of this conclusion for the divergent evolution of cyanobacterial and plant plastocyanins. [source] Comparison of the specificity, stability and individual rate constants with respective activation parameters for the peptidase activity of cruzipain and its recombinant form, cruzain, from Trypanosoma cruziFEBS JOURNAL, Issue 24 2001Wagner A. S. Judice The Trypanosoma cruzi cysteine protease cruzipain contains a 130-amino-acid C-terminal extension, in addition to the catalytic domain. Natural cruzipain is a complex of isoforms, because of the simultaneous expression of several genes, and the presence of either high mannose-type, hybrid monoantennary-type or complex biantenary-type oligosacharide chains at Asn255 of the C-terminal extension. Cruzipain and its recombinant form without this extension (cruzain) were studied comparatively in this work. S2 to S2, subsite specificities of these enzymes were examined using four series of substrates derived from the internally quenched fluorescent peptide Abz-KLRFSKQ-EDDnp (Abz, ortho -aminobenzoic acid; EDDnp, N -(2,4-dinitrophenyl)-ethylenediamine). Large differences in the kinetic parameters were not observed between the enzymes; however, Km values were consistently lower for the hydrolysis of most of the substrates by cruzain. No difference in the pH,activity profile between the two enzymes was found, but in 1 m NaCl cruzipain presented a kcat value significantly higher than that of cruzain. The activation energy of denaturation for the enzymes did not differ significantly; however, a negative entropy value was observed for cruzipain denaturation whereas the value for cruzain was positive. We determined the individual rate constants (k1, substrate diffusion; k,1, substrate dissociation; k2, acylation; k3, deacylation) and the respective activation energies and entropies for hydrolysis of Abz-KLRFSKQ-EDDnp determining the temperature dependence of the Michaelis,Menten parameters kcat/Km and kcat as previously described [Ayala, Y.M. & Di Cera, E. (2000) Protein Sci.9, 1589,1593]. Differences between the two enzymes were clearly detected in the activation energies E1 and E,1, which are significantly higher for cruzipain. The corresponding ,S1 and ,S,1 were positive and significantly higher for cruzipain than for cruzain. These results indicate the presence of a larger energy barrier for cruzipain relating to substrate diffusion and dissociation, which could be related to the C-terminal extension and/or glycosylation state of cruzipain. [source] Dediazoniation of 1-naphthalenediazonium tetrafluoroborate in aqueous acid and in micellar solutionsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 6 2008Carlos Bravo-Diaz We have measured the rates and product yields of dediazoniation of 1-naphthalenediazonium (1ND) tetrafluoroborate in the presence and absence of sodium dodecyl sulfate (SDS) micellar aggregates by employing a combination of UV,vis spectroscopy and high-performance liquid chromatography (HPLC) measurements. Kinetic data were obtained by a derivatization procedure with product yields were determined by HPLC. HPLC chromatograms show that in aqueous acid and in micellar solutions only one dediazoniation product is formed in significant quantities, 1-naphthol (NOH), and the observed rate constants (kobs) are the same when 1ND loss is monitored spectrometrically and when NOH formation is monitored by HPLC. Activation parameters were obtained both in the presence and absence of SDS micellar aggregates. In both the systems, the enthalpies of activation are high and the entropies of activation are positive. The enthalpy of activation in the absence of SDS is very similar to that in the presence of SDS micelles, but the entropy of activation is lower by a factor of 4. As a consequence, SDS micelles speed up the thermal decomposition of 1ND and increase kobs by a factor of 1.5 when [SDS] = 0.02 M. In contrast, results obtained in the presence of complexing systems such as crown ethers and polyethers show significant stabilization of the parent arenediazonium ions. Kinetic and HPLC data are consistent with the heterolytic DN + AN mechanism that involves the rate-determining fragmentation of the arenediazonium ion into a very reactive phenyl cation that reacts competitively with available nucleophiles. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 301,309, 2008 [source] Thermodynamics and micellar properties of some surface active cobalt(III) metallosurfactants in nonaqueous mediumINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 1 2007K. Santhakumar The critical micelle concentration (CMC) of four kinds of metallosurfactants of the type halogeno(dodecyl/cetylamine)-bis(ethylenediamine)cobalt(III) has been studied in n -alcohol and in formamide at different temperatures by electrical conductivity method. Specific conductivity data (at 293,313 K) served for the evaluation of temperature-dependent CMC and the thermodynamic parameters such as standard Gibbs free energy changes (,G), enthalpies (,H), and entropies (,S) of micelle formation. CMCs have also been measured as a function of percentage concentration of alcohol added. It is suggested that alcohol addition leads to increase in formamide penetration into micellar interface that depends on the alcohol chain length. The results have been discussed in terms of increased hydrophobic effect (solvophobic interaction), dielectric constant of the medium, and the chain length of the alcohols, the surfactant in the solvent mixture. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 39: 22,31, 2007 [source] Reaction pathways of propene pyrolysisJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Yena Qu Abstract The gas-phase reaction pathways in preparing pyrolytic carbon with propene pyrolysis have been investigated in detail with a total number of 110 transition states and 50 intermediates. The structure of the species was determined with density functional theory at B3PW91/6-311G(d,p) level. The transition states and their linked intermediates were confirmed with frequency and the intrinsic reaction coordinates analyses. The elementary reactions were explored in the pathways of both direct and the radical attacking decompositions. The energy barriers and the reaction energies were determined with accurate model chemistry method at G3(MP2) level after an examination of the nondynamic electronic correlations. The heat capacities and entropies were obtained with statistical thermodynamics. The Gibbs free energies at 298.15 K for all the reaction steps were reported. Those at any temperature can be developed with classical thermodynamics by using the fitted (as a function of temperature) heat capacities. It was found that the most favorable paths are mainly in the radical attacking chain reactions. The chain was proposed with 26 reaction steps including two steps of the initialization of the chain to produce H and CH3 radicals. For a typical temperature (1200 K) adopted in the experiments, the highest energy barriers were found in the production of C3 to be 203.4 and 193.7 kJ/mol. The highest energy barriers for the production of C2 and C were found 174.1 and 181.4 kJ/mol, respectively. These results are comparable with the most recent experimental observation of the apparent activation energy 201.9 ± 0.6 or 137 ± 25 kJ/mol. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Accurate prediction of thermodynamic properties of alkyl peroxides by combining density functional theory calculation with least-square calibrationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2009Cun-Xi Liu Abstract Owing to the significance in kinetic modeling of the oxidation and combustion mechanisms of hydrocarbons, a fast and relatively accurate method was developed for the prediction of ,fH of alkyl peroxides. By this method, a raw ,fH value was calculated from the optimized geometry and vibration frequencies at B3LYP/6-31G(d,p) level and then an accurate ,fH value was obtained by a least-square procedure. The least-square procedure is a six-parameter linear equation and is validated by a leave-one out technique, giving a cross-validation squared correlation coefficient q2 of 0.97 and a squared correlation coefficient of 0.98 for the final model. Calculated results demonstrated that the least-square calibration leads to a remarkable reduction of error and to the accurate ,fH values within the chemical accuracy of 8 kJ mol,1 except (CH3)2CHCH2CH2CH2OOH which has an error of 8.69 kJ mol,1. Comparison of the results by CBS-Q, CBS-QB3, G2, and G3 revealed that B3LYP/6-31G(d,p) in combination with a least-square calibration is reliable in the accurate prediction of the standard enthalpies of formation for alkyl peroxides. Standard entropies at 298 K and heat capacities in the temperature range of 300,1500 K for alkyl peroxides were also calculated using the rigid rotor-harmonic oscillator approximation. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods,,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2008Vladimir Hnizdo Abstract Changes in the configurational entropies of molecules make important contributions to the free energies of reaction for processes such as protein-folding, noncovalent association, and conformational change. However, obtaining entropy from molecular simulations represents a long-standing computational challenge. Here, two recently introduced approaches, the nearest-neighbor (NN) method and the mutual-information expansion (MIE), are combined to furnish an efficient and accurate method of extracting the configurational entropy from a molecular simulation to a given order of correlations among the internal degrees of freedom. The resulting method takes advantage of the strengths of each approach. The NN method is entirely nonparametric (i.e., it makes no assumptions about the underlying probability distribution), its estimates are asymptotically unbiased and consistent, and it makes optimum use of a limited number of available data samples. The MIE, a systematic expansion of entropy in mutual information terms of increasing order, provides a well-characterized approximation for lowering the dimensionality of the numerical problem of calculating the entropy of a high-dimensional system. The combination of these two methods enables obtaining well-converged estimations of the configurational entropy that capture many-body correlations of higher order than is possible with the simple histogramming that was used in the MIE method originally. The combined method is tested here on two simple systems: an idealized system represented by an analytical distribution of six circular variables, where the full joint entropy and all the MIE terms are exactly known, and the R,S stereoisomer of tartaric acid, a molecule with seven internal-rotation degrees of freedom for which the full entropy of internal rotation has been already estimated by the NN method. For these two systems, all the expansion terms of the full MIE of the entropy are estimated by the NN method and, for comparison, the MIE approximations up to third order are also estimated by simple histogramming. The results indicate that the truncation of the MIE at the two-body level can be an accurate, computationally nondemanding approximation to the configurational entropy of anharmonic internal degrees of freedom. If needed, higher-order correlations can be estimated reliably by the NN method without excessive demands on the molecular-simulation sample size and computing time. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Thermodynamic calculations for molecules with asymmetric internal rotors.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2008Abstract The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Proton affinities of maingroup-element hydrides and noble gases: Trends across the periodic table, structural effects, and DFT validationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2006Marcel Swart Abstract We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15,17 and the noble gases, that is, group 18, and periods 1,6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1486,1493, 2006 [source] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||