THERM: a computer code for estimating thermodynamic properties for species important to combustion and reaction modeling

A computer package has been developed called THERM, an acronym for THermodynamic property Estimation for Radicals and Molecules. THERM is a versatile computer code designed to automate the estimation of ideal gas phase thermodynamic properties for radicals and molecules important to combustion and reaction-modeling studies. Thermodynamic properties calculated include heat of formation and entropies at 298 K and heat capacities from 300 to 1500 K. Heat capacity estimates are then extrapolated to above 5000 K, and NASA format polynomial thermodynamic property representations valid from 298 to 5000 K are generated. This code is written in Microsoft Fortran version 5.0 for use on machines running under MSDOS. THERM uses group additivity principles of Benson and current best values for bond strengths, changes in entropy, and loss of vibrational degrees of freedom to estimate properties for radical species from parent molecules. This ensemble of computer programs can be used to input literature data, estimate data when not available, and review, update, and revise entries to reflect improvements and modifications to the group contribution and bond dissociation databases. All input and output files are ASCII so that they can be easily edited, updated, or expanded. In addition, heats of reaction, entropy changes, Gibbs free-energy changes, and equilibrium constants can be calculated as functions of temperature from a NASA format polynomial database.     

JESS, A joint expert speciation system-I. Raison d'être

JESS is a new computer package for modelling chemical systems in solution and performing numerical analyses on associated experimental data. It was developed to solve problems requiring specialist knowledge of chemical speciation. It currently comprises over 150 programs, 1200 subroutines and 120,000 lines of Fortran code. The main reasons for the development of JESS, and the principles which underpin it, are described. Subsequent papers detail the major facilities which JESS now provides.     

The salting coefficient and size of alkylamines in saline media at different temperatures: estimation from Pitzer equations and the mean spherical approximation

The renewed theoretical interest in the proton transfer associated to the amino group together with the scarcity of acid-base studies of amines in moderate to concentrated saline media focussed our attention on the study of the basicities of some alkylamines, namely monomethyl, dimethyl and trimethylamine, in aqueous saline solutions of KCl at various temperatures.

A non-conventional analysis of stoichiometric equilibrium constants versus ionic strength data is carried out. On one hand, Pitzer’s model is easily applied to calculate the salting coefficient and the thermodynamic equilibrium constant of the alkylamines. On the other hand, the mean spherical approximation has the advantage over the Debye–Hückel based theories that it can account for effects produced by species of different sizes. Here, it is applied to predict the dependence of the salting behavior on the size of the alkylamines.     

Luminescence kinetics and association equilibria of lanthanide ions in aqueous solutions

Luminescence life time measurement can be used under certain conditions to determine the thermodynamic constants of complex formation between the luminescent (central ion) and ligand. The basic equations correlating the life time and the equilibria constants were derived for two cases: the time for establishing the thermodynamic equilibrium is much shorter than the life time of the excited state of the central ion; and the time for establishing the equilibrium and the life time are of the same order of magnitude.     

Dynamics of hydrogen bond complexes in polymer melts

The dynamics of hydrogen bond complex formation between functional groups which are attached to a polymer chain, is studied in the molten state. The concentration of complexes in the thermodynamic equilibrium is distorted by the application of a large oscillatory strain in the nonlinear viscoelastic regime. The relaxation back to the thermodynamic equilibrium is studied as a function of the temperature in the linear viscoelastic regime. From the mechanical response the kinetic analysis can be performed using a modified Doi-Edwards theory. Using the equilibrium constants obtained from IR-spectroscopy, the rate constants for complex formation and decomplexation are obtained. The temperature dependence is equivalent to the temperature dependence of the zero shear viscosity which implies that complex formation is a diffusion-controlled process.     

Dimension Concepts and Reduced Dimensions in Toxicological QShAR Databases as Tools for Data Quality Assessment

The dimensions of databases can be defined based on a variety of concepts, ranging from the standard tools of principal component analysis to context-biased approaches. The effective dimensions of databases, in particular the effective dimensions involving continua such as electron density data, provide a set of important tools for database comparisons and for the evaluation of some aspects of database quality. The problems associated with database comparisons and database mergers, such as those occurring in the process of database unification in the actual merger of two pharmaceutical companies, provide challenging tasks and opportunities for data science. Some of the tools for effective dimension reduction and dimension expansion are reviewed in the context of database quality control and conditions for database compatibility are presented. A common misconception affecting data sampling techniques for data quality evaluation is discussed and methods for circumventing the associated sampling errors are described.     

Les différentes voies de modélisation macroscopique du procédé de dépôt de SiC par voie gazeuse

The different macroscopic modelling routes and chemical databases are reviewed for the growth of silicon carbide from the vapour phase in the Si-C-H-Ar system. Theses databases have been built up by experts over many years through the critical assessment of primary experimental data and ab-initio calculations. The thermodynamic modelling route addresses several important issues with respect to vapour deposition techniques. This approach is a useful tool in understanding the complex chemistry involved during the growth, but should be used with careful attention to the assumptions underlying the application. The transport modelling approach extends the previous analysis to dynamical systems. It is based on the conservation equations for momentum and heat transfer combined with mass transfer including thermodiffusion and chemical reactions based on thermodynamic and kinetic data. In addition to empirical, lumped chemical kinetic models, we propose a new modelling route linking transfers models with local thermochemical equilibrium (LTCE) computations. The modelling results have been validated with the help of the SiC sublimation technique for the transfer-LTCE concept, and of the chemical vapour deposition technique for lumped chemistry models. The simulated results allow the quantification of the different modelling proposals.     

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation

To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling. However, Hg speciation modeling is often hindered by a lack of reliable thermodynamic constants. Although computational chemistry (e.g., density functional theory [DFT]) can generate these constants, methods for directly coupling DFT and speciation modeling are not available. Here, we combine computational chemistry and continuum-scale modeling with curated online databases to ameliorate the problem of unreliable inputs to Hg speciation modeling. Our AQUA-MER databases and web server ( https://aquamer.ornl.gov ) provides direct speciation results by combining web-based interfaces to a speciation calculator, databases of thermodynamic constants, and a computational chemistry toolkit to estimate missing constants. Although Hg is presented as a concrete use case, AQUA-MER can also be readily applied to other elements. © 2019 Wiley Periodicals, Inc.     

SPECA: a program for the calculation of thermodynamic equilibrium constants from spectrophotometric data

A computer program called SPECA and written in compiled BASIC (Microsoft QuickBasic Ver. 4.5) has been written for the calculation of thermodynamic constants in solution equilibria studies from spectrophotometric measurements. In order to calculate the thermodynamic constants it is necessary to introduce different theories to estimate the activity coefficients of the system involved under investigation. In this version of the program the equations proposed in the models of Debye-Hückel. Specific Interaction Theory (SIT) or the Modified's Bromley Theory can be chosen. To achieve its purpose, the program uses absorbance and activity or free concentration data of one of the components, normally H(+), and it is not limited with respect to the number of components that can be studied. Minimization of the error square sum in the absorbance, which can be absolute or relative, is carried out using the Levenberg-Marquardt-Nash algorithm at three different levels: equilibrium constants in the first level, molar absorptivities in the second and interaction coefficients in the third for those systems using the SIT or the Modified Bromley's Theories.     

Chemical bonding and the equilibrium composition of Grignard reagents in ethereal solutions

A thorough analysis of the electronic structure and thermodynamic aspects of Grignard reagents and its associated equilibrium composition in ethereal solutions is performed. Considering methylmagnesium halides containing fluorine, chlorine, and bromine, we studied the neutral, charged, and radical species associated with their chemical equilibrium in solution. The ethereal solvents considered, tetrahydrofuran (THF) and ethyl ether (Et(2)O), were modeled using the polarizable continuum model (PCM) and also by explicit coordination to the Mg atoms in a cluster. The chemical bonding of the species that constitute the Grignard reagent is analyzed in detail with generalized valence bond (GVB) wave functions. Equilibrium constants were calculated with the DFT/M06 functional and GVB wave functions, yielding similar results. According to our calculations and existing kinetic and electrochemical evidence, the species R(?), R(-), (?)MgX, and RMgX(2)(-) must be present in low concentration in the equilibrium. We conclude that depending on the halogen, a different route must be followed to produce the relevant equilibrium species in each case. Chloride and bromide must preferably follow a "radical-based" pathway, and fluoride must follow a "carbanionic-based" pathway. These different mechanisms are contrasted against the available experimental results and are proven to be consistent with the existing thermodynamic data on the Grignard reagent equilibria.     

Scandium: Thermodynamic properties,chemical equilibria,and standard potentials

We have gathered, critically evaluated, calculated, and tabulated thermodynamic properties and related equilibrium constants and standard potentials for compounds and aqueous species of scandium. We have been explicit about sources of data so that interested readers can check the steps leading to tabulated thermodynamic quantities and thus form their own opinions about reliability and accuracy.     

Lanthanum: Thermodynamic properties,chemical equilibria,and standard potentials

We have gathered, critically evaluated, calculated, and tabulated thermodynamic properties and related equilibrium constants and standard potentials for inorganic compounds and aqueous species of lanthanum. We have been explicit about sources of data and our calculations so that interested readers can check the steps leading to tabulated thermodynamic quantities and thus form their own opinions about reliability and accuracy.     

Complete resolution of the ionization equilibria of 5-deoxypyridoxal in water-dioxane mixtures

We have used a potentiometric method to determine the thermodynamic equilibrium constants for the macroscopic ionization processes of 5-deoxypyridoxal (DPL) in water-dioxane mixtures (0-70% weight fraction in dioxane) at temperatures ranging from 10°C to 50°C. These data, together with previously published equilibrium constants for the tautomerism and hydration processes, have allowed us to resolve the complete microconstant system. We have also calculated the microscopic ionization equilibrium constants under all the experimental conditions. The changes of standard thermodynamic function for the macroscopic and microscopic ionization processes were obtained in various water-dioxane mixtures at 25°C. The values of a given microscopic pK with different solvents and temperatures fit very well to an equation which relates this magnitude with the thermodynamic parameters, the solvation of the components of the reaction, and a solvent parameter. We have obtained an interesting linear correlation between the thermodynamic parameters corresponding to all the microscopic ionizations of DPL and the net change of the solvation during the process: enthalpies correlate linearly for all the microscopic ionizations, while entropies do so for the phenols and pyridinium ions separately.     

Nickel Aqueous Speciation and Solubility at Ambient Conditions: A Thermodynamic Elegy

Summary.  This review reveals that, in contrast to the general opinion, the aqueous speciation of nickel is poorly known. Besides the fairly well established first hydrolysis constant, data are scarce and only poor estimates can be derived for higher Ni hydrolysis constants from a few solubility studies. The situation is even worse in the case of aqueous carbonate complexes. No reliable experimental study has been published so far and almost all numbers reported in thermodynamic databases are unacceptable estimates. In this review we scrutinise all these published estimates and propose expectation ranges of nickel carbonate complex stability through correlation with other known thermodynamic constants. Solubility constants for a few simple nickel solids are known or have been estimated from thermochemical data. However, none of these simple solids is of geochemical relevance at ambient conditions. Based on field evidence, classes of solids are identified which potentially govern nickel concentrations in ground and surface waters. Recent spectroscopic data indicate that magnesium clay minerals and layered double hydroxides are the most prominent candidates for nickel-bearing solids at ambient conditions. Corresponding author. E-mail: wolfgang.hummel@psi.ch Dedicated to the memory of Prof. Rolf Grauer Received January 14, 2003; accepted January 24, 2003 Published online May 15, 2003     

The binding of organic anions by polyvinylpyrrolidone: Determination of intrinsic binding constant and number of binding sites by competitive binding

The binding of 4′-dibutylaminoazobenzene-4-sulfonate (butyl orange, BO) and 1-amino-4-methylaminoanthraquinone-2-sulfonate (AQ) by crosslinked polyvinylpyrrolidone and the competition between BO and AQ for binding sites of the polymer were examined. The equilibrium data showed competitive binding. Thus the intrinsic binding constants and the number of binding sites can be evaluated easily and precisely by competitive binding. The thermodynamic parameters that accompained the binding were calculated from the intrinsic binding constant and its temperature-dependence. The thermodynamic data for BO showed that the binding process is athermal and stabilized entirely by the entropy term. The binding of BO to the polymer is entropically favorable as a result of the operation of the hydrophobic effect. In contrast, with AQ a favorable free energy for a dye-polymer complex formation is associated with a large negative enthalpy and a small entropy. Therefore it is likely that the binding of AQ occurs by energetic forces and that the large aromatic ring of the dye contributes to the binding energy. On the average, BO and AQ can bind to the crosslinked polymer to the extent of 1 dye/ca 73 basemol in 0.1M tris-acetate buffer, pH 7.0.     

Application of a single model to study the adsorption equilibrium of prednisolone on six carbonaceous materials

The knowledge of sorption processes of nonelectrolytes in solution by solid adsorbents implies the study of kinetics, equilibrium, and thermodynamic functions. However, quite frequently the equilibrium isotherms are studied by comparing them with those corresponding to the Giles et al. classification (1); these isotherms are also analyzed by fitting them to equations based on thermodynamic or kinetic criteria, and even to empirical equations. Nevertheless, information obtained is more coherent and satisfactory if the adsorption isotherms are fitted by using an equation describing the equilibrium isotherms according to the kinetic laws. These mentioned laws would determine each one of the unitary processes (one or more) which condition the global process. In this paper, an adsorption process of prednisolone in solution by six carbonaceous materials is explained according to a previously proposed single model, which allows to establish a kinetic law which fits satisfactorily most of C vs t isotherms (2). According to the above-mentioned kinetic law, equations describing sorption equilibrium processes have been deducted, and experimental data points have been fitted to these equations; such a fitting yields to different values of adsorption capacity and kinetic equilibrium constants for the different processes at several temperatures. However, in spite of their practical interest, these constants have no thermodynamic signification. Thus, the thermodynamic equilibrium constant (K) has been calculated by using a modified expression of the Gaines et al. equation (3). Global average values of the thermodynamic functions have also been calculated from the K values. Information related to variations of DeltaH and DeltaS with the surface coverage fraction was obtained by using the corresponding Clausius-Clapeyron equations.     

On equilibrium distributions and detailed balance relations in non-isothermal systems

The significance of the detailed balance principle and equilibrium solutions of the master equation is discussed from a thermodynamic point of view for isolated and isothermal systems. Starting from a master equation for all the time dependent degrees of freedom it is shown that the uniqueness of the equilibrium distribution as a stationary solution is ensured if the detailed rate constants are balanced with the aid of the distribution which maximizes the entropy subject to the thermodynamic constraints. This procedure should precede physical assumptions which simplify the original master equation, e.g. the assumption that rapidly relaxing modes can be described by canonical distribution functions.     

Reflections on the calculation and publication of potentiometrically-determined formation constants

Calculation and reporting procedures are described, which aim to improve the quality and comparability of published formation constant values obtained by glass-electrode potentiometry. Ways in which the processing of data by computer optimization programs can be standardized are the main concern, particularly in respect of improving the usefulness of equilibrium data through incorporation into large publically available databases. These recommendations may be particularly valuable to researchers beginning in this field as well as to those who determine formation constants only occasionally.     

Concentration and solvent effects on proline—p-benzoquinone complexes

Spectrophotometric studies have been used to show that the concentration of proline has a marked effect on its interaction with p-benzoquinone in pH 7 buffer. As the concentration is decreased, both the back reaction rate constant and the equilibrium constant increase whereas the entropy change decreases very rapidly. Similar effects are observed in a constant proline concentration but adding an increasing amount of dimethyl sulphoxide (DMSO). The extinction coefficient for the proline-p-benzoquinone complex is lower in the presence of DMSO. Extinction coefficients and equilibrium constants obtained by both Benesi—Hildebrand and Rose—Drago methods are identical. The interaction is shown to be first order with respect to each component and second order overall. The reaction is both temperature and dilution reversible. Rate constants and thermodynamic parameters have been calculated over a wide range of conditions.