## `r setfile("H2O_aq.csv")` ```{r reflist, results="asis", echo=FALSE} used <- c(used, filerefs(csvfile)) ``` This file contains H₂O, *e*^-, and H⁺. The properties of H₂O are listed as NA; CHNOSZ calculates its properties using a Fortran subroutine taken from SUPRCT92 ([Johnson et al., 1992](https://doi.org/10.1016/0098-3004(92)90029-Q)) (default) or using the IAPWS-95 equations ([Wagner and Pruß, 2002](https://doi.org/10.1063/1.1461829)) or the Deep Earth Water (DEW) model ([Sverjensky et al., 2014](https://doi.org/10.1016/j.gca.2013.12.019)). By convention, the standard Gibbs energy of formation, entropy, and heat capacity of the aqueous proton (H⁺) are 0 at all *T* and *P* ([e.g. Cox et al., 1989](https://www.worldcat.org/oclc/18559968)). The formation reaction of the proton can be expressed as ½H_2,(*g*) + Z = H⁺, where Z is the "element" of positive charge. Because the conventional standard Gibbs energy of this reaction is 0 at all *T*, the standard entropy of the reaction is also constrained to be zero (cf. Denbigh, 1981; Puigdomenech et al., 1997). Therefore, the "element" of positive charge (Z) has zero thermodynamic properties except for an entropy, *S*°_{*T*_r}, that is negative one-half that of H_2,(*g*). The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by *e*^- = -Z, is opposite that of Z. Likewise, [GEM-Selektor](http://gems.web.psi.ch/) defines "independent components" to be stoichiometric units usually consisting of elements and charge; the latter, [which is named Zz](http://gems.web.psi.ch/tests/TestNaCl-dep.html) and has a standard molal entropy of -65.34 J/mol/K and heat capacity of -14.418 J/mol/K (negative one-half those of gaseous hydrogen), is negated in the formula of the fictive "aqueous electron" ([Kulik, 2006](https://doi.org/10.1016/j.chemgeo.2005.08.014)). Despite these considerations, the final column of the thermodynamic database (`thermo()$OBIGT`) lists a charge of "0" for both the aqueous proton and electron. Data in this this column are used in CHNOSZ only to specify the charge that is input to the "*g*-function" ([Tanger and Helgeson, 1988](https://doi.org/10.2475/ajs.288.1.19); [Shock and Helgeson, 1988](https://doi.org/10.1016/0016-7037(88)90181-0)). Setting it to zero prevents activation of the *g*-function, which would result in non-zero contributions to thermodynamic properties, conflicting with the conventions mentioned above. All other calculations in CHNOSZ obtain the elemental makeup, including the correct charge for the species, by parsing the chemical formulas stored in the database.

## `r setfile("organic_aq.csv")` Charged amino acid sidechain groups have a Z parameter that is tabulated as zero; their chemical formulas indicate the correct charge. Non-zero values of Z would yield derivatives of the omega parameter (ω) in the revised HKF equations of state for the cations and anions *that are not opposites of each other*. This would be incompatible with group additivity of cations and anions to give a neutral species, for which the derivatives of ω are taken to be zero (cf. [Dick et al., 2006](https://doi.org/10.5194/bg-3-311-2006)). ```{r reflist, results="asis", echo=FALSE} ```

## `r setfile("SUPCRT92.csv")` These minerals, taken from the SUPCRT92 database, were present in earlier versions of CHNOSZ but have since been superseded by data from @Ber88 (most minerals) or @RH95 (cassiterite). The thermodynamic properties and parameters are kept here as optional data for reproducing published calculations and making comparisons with newer data. The minerals here include all of the silicates and Al- and Ti-bearing minerals from @HDNB78, as well as calcite, dolomite, hematite, and magnetite. Use `add.OBIGT("SUPCRT92")` to load the data. **NOTE:** Other minerals from SUPCRT92, including native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate those in the Berman dataset, are still present in the default database (**inorganic_cr.csv**). ```{r optreflist, results="asis", echo=FALSE} optused <- c(optused, filerefs(csvfile)) ```

## `r setfile("SLOP98.csv")` These species, whose parameters were listed in or are otherwise linked to slop98.dat (or later versions) and were present in earlier versions of CHNOSZ, have been replaced by or are incompatible with species currently in the default database. The elements with updated data for at least some aqueous species include: HCl [@TZA97], Al [@TS01], Au, Ag, and Cu(I) [@AZ01; @AZ10], As [@NA03], REE [@MWW09], Cd [@BZA10], Co [@LBT+11], Pd [@TBZ+13], Zn [@AT14], Pt [@TBB15], Nb [@AKK+20], Ga and In [@HB24], and U [@MBA+24]. Use `add.OBIGT("SLOP98")` to load the data. **NOTE:** Other species listed in slop98.dat and later versions are still present in the default database. ```{r optreflist, results="asis", echo=FALSE} ```

## `r setfile("DEW.csv")` The Deep Earth Water (DEW) model extends the applicability of the revised HKF equations of state to 60 kbar. Accuracy of the thermodynamic calculations at these conditions is improved by revised correlations for the a₁ HKF parameter, as described by [Sverjensky et al. (2014)](https://doi.org/10.1016/j.gca.2013.12.019). The thermodynamic parameters for species were taken from the May 2017 and January 2019 versions of the DEW spreadsheet. The following species are present in the spreadsheet, but are not used here because the parameters are unchanged from the default database in CHNOSZ: B(OH)₃, Br^-, Ca⁺², Cl^-, Cs⁺, F^-, H⁺, H₂, He, I^-, K⁺, Kr, Li⁺, Mg⁺², Na⁺, Ne, O₂, Rb⁺, Rn, SO₄^-2. Besides using `add.OBIGT("DEW")` to load these data, you should also run `water("DEW")` to activate the DEW equations in CHNOSZ. See `demo(DEW)` for some examples. Most of the comments below were transcribed from the DEW spreadsheet. Comments in parentheses were added by JMD. ```{r optreflist, results="asis", echo=FALSE} ```

## `r setfile("testing")` These are optional data files used for testing purposes. Load the data with e.g. `add.OBIGT("GEMSFIT")`.

SiO2

Aqueous SiO₂ from @AS04 and HSiO₃^- modified to be consistent with it. This file also has H₄SiO₄ from an earlier publication [@Ste01] that is roughly consistent with the SiO₂ here. See `demo(aluminum)` and the vignette [*Regressing thermodynamic data*](eos-regress.html) for examples.

GEMSFIT

Internally consistent dataset for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl obtained with the [GEMSFIT](https://doi.org/10.1016/j.apgeochem.2014.10.013) package [@MWKH16;@MWKL17].

IGEM

Updates for Au and Cu complexes and SO₄^-2-bearing species from researchers at the Institute of Geology of Ore Deposits, Petrography, Mineralogy, and Geochemistry, Russian Academy of Sciences (IGEM RAS) [@AZ23;@TTA+23;@TAT+24;@TAZ24].

Sandia

Model for the Mg(OH)₂-MgCl₂-H₂O system at 25 to 150 °C from researchers at Sandia National Laboratories [@KBJ24].

Citations

```{r optreflist, results="asis", echo=FALSE} ```