Thermodynamic data sets

Thermodynamic databases are the primarily source of information of all geochemical modeling programs. Basically, it is possible to create one s own thermodynamic dataset with almost any program. However, it is a considerable effort and requires great care. Normally one accesses already existing data sets. 

With the help of appropriate filters it is also possible to create a partial data set out of the standard data set. Especially when a huge number of analyses have to be calculated - as with a coupled model (transport plus reaction) - CPU-time can be saved with a reduced data set. However, it must be verified that the partial data set yields comparable results to the original data set. 

3 additionally considered in MESTTEQ.dat cyanide, cyanate, benzoate, para-acetate, isophthalate, diethylamine, n-butylamine, methylamine, dimethylamine, tributylphosphate, hexylamine, ethylenediamine, n-propylamine, isopropylamine, trimethylamine, citrate, NTA, EDTA, propanoate, butanoate, isobutyrate, 2-methylpyridine, trimethylpyridine, 4-methylpyridine, formate, isovalerate, valerate, acetate, tartrate, glycine, salicylate, glutamate, phthalate 

4 additionally considered in LLNL.dat acetate, ethylene, orthophthalate 

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Holland TJB, Powell R (1998) An internally consistent thermodynamic data set for phases of petrological interest. J Metamorphic Geology 16 309-343... 

Representative heats of formation predicted by the ECP/BAC-MP4 method are given in Table 1 (the complete published [88] thermodynamic data set used in the analyses below is available online [91]). Data are shown for a range of compoimds, including tetravalent, trivalent, and divalent coordination at tin. Values for the reference compounds SnCU, SnH4, and Sn(CH3)4 are also given. Finally, heats of formation for atoms and groups needed to calculate reaction enthalpies are given. These results are used in the analysis below to identify potential reaction pathways for MBTC and its decomposition products. 

Holland TJB, Powell R (1998) An internally consistent thermodynamic data set for phases of petrological interest. J Metamorph Geol 16 309-343 Horneck G, Baumstark-Khan C (eds) (2002) Astrobiology the Quest for the Conditions of Life. Springer, Berlin Heidelberg New York Hubbard WB, Podolak M, Stevenson DJ (1995) The interior of Neptune. In Cruikshank DP (ed) Neptune and Triton. University of Arizona Press, Tucson, pp 109-140... 

The most common approach used by geochemical modeling codes to describe the water-gas-rock-interaction in aquatic systems is the ion dissociation theory outlined briefly in chapter 1.1.2.6.1. However, reliable results can only be expected up to ionic strengths between 0.5 and 1 mol/L. If the ionic strength is exceeding this level, the ion interaction theory (e.g. PITZER equations, chapter 1.1.2.6.2) may solve the problem and computer codes have to be based on this theory. The species distribution can be calculated from thermodynamic data sets using two different approaches (chapter 2.1.4) ... 

However, the most common sources of different results are both based on the approach used for the calculation of the activity coefficient (chapter 1.1.2.6) and the thermodynamic data sets themselves (chapter 2.1.4), which provide the respective program with the fundamental geochemical information of each single species. The thermodynamic databases available partly use severely differing data with different solubility products, different species, minerals and reaction equations. Nordstrom et al (1979, 1990), Nordstrom Munoz (1994), Nordstrom (1996, 2004) discuss this inconsistency of thermodynamic datasets in detail. For some species, for which stability constants have been published, not even the existence of the respective species has been proved doubtless, as can been shown in the following example. 

That had been already known since 1985 (Robins 1985), but has never been changed in the above cited thermodynamic data sets (Zhu Merkel 2001). 

Additionally, thermodynamic data are yielded by laboratory tests under defined boundary conditions (temperature, ionic strength) that apply to natural, geogenic circumstances only to a limited extent, e.g. for uranium thermodynamic data sets were derived from nuclear research that deals with uranium concentrations in the range of 0.1 mol/L. But in natural aquatic systems, concentrations are in the range of nmol/L. 

Progress toward an internally consistent and reliable thermodynamic data set for geochemical calculations is a tedious, slow, and poorly supported enterprise. For some applications, a smaller but consistent subset of data is sufficient. Some... 

The data sets WATEQ4F.dat, MINTEQ.dat, PHREEQC.dat and LLNL.dat are automatically installed with the program PHREEQC and can be chosen from the menu item Calculations/File under Database File. The internal structure of these thermodynamic data sets has already been explained in great detail in chapter... 

One can even combine this damped atom-atom dispersion correction to the LC hybrid functionals. The (oB97X functional has been modified to include dispersion correction to create the (j)B97X-D functional. Performance of this functional is significantly better than dispersion-corrected standard functionals, like B3LYP-D, and improves performance in the G3/05 thermodynamic data set by 0.6 kcalmol over (OB97-X. 

This chapter presents the chemical thermodynamic data set for selenium species which has been selected in this review. Table lll-l contains the reeommended thermodynamic data of the selenium species, Table III-2 the recommended thermodynamic data of chemical equilibrium reactions by which the selenium compounds and complexes are formed, and Table III-3 the temperature coefficients of the heat capacity data of Table lll-lwhere available (see Appendix E for additional selenium data, cf. Section 11.7). 

Tables 7.1 and 7.2 are copied directly from the thermodynamic compilation of Robie, Hemingway and Fisher (1978), abbreviated as RHF. Many of the other standard thermodynamic data sets discussed later in this chapter are arranged in a similar fashion. We can now begin to examine some of the features of these tables a little more closely. First, we have just observed that A/ G° and Ay H° for the formation of 02(g) from the elements is zero at all temperatures because this is just the difference between the G (or H) of oxygen and the G (or H) of the elements making up oxygen, which is the same thing. We have not yet defined the equilibrium constant K (see Chapter 13), but for completeness we should point out that it is 1.0 and log IT = 0 for the reaction for the formation of oxygen from itself, giving us another column of zeros. Note too that the entropy of 02(g), S°t, given in Table 7.1 is not equal to zero at any temperature shown these are absolute entropies, not entropies of formation from the elements, as discussed in Chapter 6 and again later in this chapter. Table 7.1 is typical of data tables for the elements.

It has long been known that the solubilities of sulfide ore minerals in hydrothermal fluids results from the complexation of metals such as Cu, Zn and Fe by Cl and HS ligands (Seward and Barnes 1997). Complexation of heavy metals such as As, Pb and Cd by mineral surfaces controls the mobility of such metals in the environment. Geochemists need to have a reliable thermodynamic data set to predict mineral solubilities and metal sorption reactions. Such data are found by fitting measured solubilities and sorption isotherms to a set of stability constants for aqueous and surface complexes. However, fits to experimental data are often non-unique and depend on the speciation model an independent way to determine the nature of metal complexes in aqueous solutions and on mineral surfaces is needed. 

In the present system, CuO powder is dispersed in the reaction solution. When the pH of the reaction solution is 9 and the temperature is 298 K, the activity of Cu + aquo ion is calculated to be about 7.5 x lOii using the thermodynamic data shown in Table 1 (Criss Cobble, 1964 Kubaschewski Alcock, 1979 Latimer 1959 Stull Prophet, 1971). This value itself does not have a precise meaning the calculated value of the activity of Cu2+ aquo ion can be significantly affected by an experimental error of thermodynamic data, e.g. the standard entropy of CuO. Normally, this value just indicates that CuO does not dissolve into the solution in a practical sense. However using this value, one can calculate other important thermodynamic values such as the oxidation-reduction (redox) pxjtential of Cu +ZCu redox pair in this reaction system using the same thermodynamic data set. 

The progress of adiabatic biocalorimetry in the last ten years has enabled us to gain insight into a new field of nucleic acid-conformation-transitions. Besides the canonical B-DNA helix to coil transitions of the linear DNA sequences we have evaluated the conformational changes of a series of new secondary structures and gained access to a complete thermodynamic data set for all linear sequences as function of two fundamental system parameters, namely the net GC content of the given sequence and the counter ion concentration. 

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