This vignette, produced on 2017-12-14, documents the sources of thermodynamic data in CHNOSZ version 1.1.3-7. Running data(thermo) creates the default database (thermo$obigt) in the R session.

The sections below correspond to CSV data files that are stored in the extdata/OBIGT package directory and read by data(thermo) (except for Optional Data). In each section, the primary references (ref1 in thermo$obigt) are listed in chronological order. Any secondary references (ref2) are listed with bullet points. Each reference is followed by the number of species, and a note (from thermo$refs). Symbols show whether the data were present in the earliest of the sprons92.dat (ø), slop98.dat (*), slop07.dat (†), or slop15.dat (‡) datafiles for the SUPCRT92 package.

Any additional comments are placed at the beginning of the sections. Abbreviations used below are: Cp (heat capacity), GHS (standard Gibbs energy, enthalpy, entropy), HKF (Helgeson-Kirkham-Flowers equations), V (volume), T (temperature), P (pressure).

Recent additions (late 2017)

Sources of data

Use the tabs below to select a section for viewing. Select “All at once” to show all sections.

Aqueous species

H2O (3)

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) (default) or using the IAPWS-95 equations (Wagner and Pruß, 2002) or the Deep Earth Water (DEW) model (Sverjensky et al., 2014).

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). The formation reaction of the proton can be expressed as ½H2,(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. Puigdomenech et al., 1997). Therefore, the “element” of positive charge (Z) has zero thermodynamic properties except for an entropy, S°Tr, that is negative one-half that of H2,(g). The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by e- = -Z, is opposite that of Z.**

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; Shock and Helgeson, 1988). 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.^^

**Likewise, GEM-Selektor defines “independent components” to be stoichiometric units usually consisting of elements and charge; the latter, which is named Zz 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).

^^ Relatedly, charged amino acid sidechain groups have a charge that is tabulated as zero, because other values would be incompatible with group additivity of cations and anions (which have derivatives of the omega parameter (ω) in the revised HKF equations of state that are not opposites of each other) to give a neutral species (for which the derivatives of ω are taken to be zero) (cf. Dick et al., 2006).

Inorganic (855)

ZnCl4-2 was present in sprons92.dat but not in slop98.dat or later files, and is not included in CHNOSZ.

Shock and Helgeson (1988) – 59 ionic species (ø)

Shock et al. (1989) – 14 inorganic neutral species (ø)

Haas et al. (1995) – 249 complexes of rare earth elements (*)

  • slop98.dat – 88 “Corrected values based on data from Haas et al. (1995) (*)

McCollom and Shock (1997) – 3 MgSO4, NaSO4-, and HCl (*)

  • slop98.dat – 3 “Data and parameters as used by McCollom and Shock (1997).” (*)

Everett L. Shock, Sassani, and Betz (1997) – 15 uranium species (*)

Sverjensky et al. (1997) – 108 metal complexes (*)

  • slop15.dat – 1 Zn(Ac)3-: “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of Sverjensky et al. (1997).” (‡)

  • CHNOSZ – 1 AuCl4- renamed to AuCl4-3

Everett L. Shock, Sassani, Willis, et al. (1997) – 252 inorganic ions and hydroxide complexes (*)

  • Sassani and Shock (1998) – 1 Rh+3 (*)

Sassani and Shock (1998) – 61 platinum-group ions and complexes (*)

Murphy and Shock (1999) – 38 actinides (†)

Schulte et al. (2001) – 10 AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6

Accornero et al. (2010) – 45 metal-chromate complexes

CHNOSZ – 1 pseudo-H4SiO4; GHS and HKF parameters calculated as shown in the vignette, Regressing thermodynamic data

Organic (752)

Shock and Helgeson (1990) – 47 organic species (ø)

  • slop15.dat – 3 hexanol, heptanol, and octanol: “Minor differences in Gibbs energy, entropy, omega, a1, a2, a3, a4 and c1 values compared to Shock and Helgeson (1990).” (‡)

Shock (1992) – 4 diglycine, alanylglycine, leucylglycine, and diketopiperazine

  • CHNOSZ – 4 dipeptides not included in slop files after slop98.dat

Shock (1993) – 2 ethylacetate and acetamide (*)

Shock and Koretsky (1993) – 113 metal-acetate complexes (*)

  • slop15.dat – 32 “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements.” (‡)

Shock and McKinnon (1993) – 3 CO, HCN, urea (*)

Schulte and Shock (1993) – 10 aldehydes (*)

  • slop15.dat – 1 formaldehyde: “Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of Schulte and Shock (1993).” (‡)

Shock and Koretsky (1995) – 226 metal-organic acid complexes (*)

  • slop98.dat – 6 “These data were used in Shock and Koretsky (1995), but were not tabulated in the paper.” (*)

  • slop15.dat – 55 “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements.” (‡)

Shock and Koretsky (1995) – 54 alanate, glycinate and their complexes not included in later slop files. (*)

  • CHNOSZ – 2 alanate and glycinate: GHS as used by Dick et al. (2006)

  • CHNOSZ – 52 metal-amino acid complexes: GHS were recalculated by adding the differences between values from Amend and Helgeson (1997) and Dick et al. (2006) for alanate or glycinate to the properties of the complexes reported by Shock and Koretsky (1995).

Shock (1995) – 77 carboxylic acids (*)

  • slop15.dat – 2 adipic acid and n-dodecanoate: “Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of Shock (1995).” (‡)

  • slop15.dat – 1 n-octanoate: “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of Shock (1995).” (‡)

Dale et al. (1997) – 10 alkylphenols (*)

Haas and Shock (1999) – 6 chloroethylene species (†)

Prapaipong et al. (1999) – 162 metal-dicarboxylate complexes (†)

  • slop07.dat – 1 corrected charge of Pu(Oxal)+2 (†)

  • CHNOSZ – 4 charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by Prapaipong et al. (1999)

Plyasunov and Shock (2001) – 11 aqueous nonelectrolytes (†)

Schulte and Rogers (2004) – 12 alkane thiols (†)

Hawrylak et al. (2006) – 2 methyldiethanolamine and methyldiethanolammonium chloride HKF parameters

Schulte (2010) – 7 organic sulfides

Dick et al. (2013) – 6 phenanthrene and methylphenanthrene isomers

Biotic (302)

Amend and Helgeson (1997) – 29 amino acids GHS (†)

  • Dick et al. (2006) – 29 amino acids HKF parameters (†)

Amend and Plyasunov (2001) – 10 carbohydrates (†)

  • slop07.dat – 10 high-temperature HKF parameters from Amend and Plyasunov (2001) (†)

LaRowe and Harold C. Helgeson (2006a) – 138 nucleic-acid bases, nucleosides, and nucleotides (†)

  • Lowe et al. (2017) – 1 adenine HKF parameters

LaRowe and Harold C. Helgeson (2006a) – 4 citric acid and citrate

  • Canovas and Shock (2016) – 4 citric acid species HKF a1–a4 parameters

LaRowe and Harold C. Helgeson (2006b) – 32 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP (†)

Dick et al. (2006) – 40 amino acid, protein, and organic groups (‡)

  • LaRowe and Dick (2012) – 1 methionine sidechain GHS

  • CHNOSZ – 1 Incorrect values of HKF a1–a4 parameters for [-CH2NH2] were printed in Table 6 of Dick et al. (2006); corrected values are used here. (‡)

Dick et al. (2006) – 1 amino acids HKF parameters (†)

  • LaRowe and Dick (2012) – 1 methionine GHS (‡)

Dick et al. (2006) – 20 Gly-X-Gly tripeptides

Dick (2007) – 4 glutathione, cystine, and cystine sidechain

Canovas and Shock (2016) – 24 citric acid cycle metabolites

Solids

Inorganic (296)

Chamosite,7A and witherite were present in sprons92.dat but not in slop98.dat or later files, and are not included in CHNOSZ.

The source of parameters used here for goethite is different from that in the slop files (Shock, 2009).

Helgeson et al. (1978) – 235 data for minerals (n = 167) and phase transitions (ø)

  • Kelley (1960) – 1 larnite Cp (ø)

  • Pankratz and King (1970) – 2 bornite and chalcopyrite (ø)

  • Robie et al. (1978) – 4 dickite, fluorphlogopite, halloysite, and pyrope (ø)

  • Plummer and Busenberg (1982) – 2 aragonite and calcite (ø)

  • Wagman et al. (1982) – 1 manganosite (ø)

  • Helgeson (1985) – 2 ferrosilite and siderite (ø)

  • sprons92.dat – 24 Ca-bearing minerals; “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

  • slop98.dat – 1 daphnite; “Gf and Hf from Saccocia and Seyfried (1993) TMM” (*)

  • CHNOSZ – 68 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 3 chlorargyrite, rutile, and titanite (ø)

  • Pankratz (1970) – 1 chlorargyrite (ø)

  • Bowers and Helgeson (1983) – 1 rutile (ø)

  • sprons92.dat – 1 titanite: Bowers and Helgeson (1983) + “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

Robie et al. (1978) – 4 iron (ø)

  • Kelley (1960) – 1 iron Cp (ø)

  • CHNOSZ – 3 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Wagman et al. (1982) – 1 MgSO4

Jackson and Helgeson (1985) – 5 Sn minerals (ø)

  • CHNOSZ – 1 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Parker and Khodakovskii (1995) – 1 melanterite

Robie and Hemingway (1995) – 1 gypsum GHS

  • Kelley (1960) – 1 gypsum Cp

McCollom and Shock (1997) – 3 sulfur (*)

  • slop98.dat – 3 “Data and parameters as used by McCollom and Shock (1997).” (*)

Everett L. Shock, Sassani, and Betz (1997) – 1 uraninite (*)

Everett L. Shock, Sassani, Willis, et al. (1997) – 2 zincite and litharge (*)

  • Helgeson et al. (1978) – 1 litharge S, V, and Cp parameters (ø)

  • slop98.dat – 1 zincite and litharge; “These data were used in Everett L. Shock, Sassani, Willis, et al. (1997), but were not tabulated in the paper.” (*)

Sassani and Shock (1998) – 15 platinum-group solids (*)

Stoffregen et al. (2000) – 3 jarosite, natroalunite, and natrojarosite

Amend and Shock (2001) – 3 selenium and molybdenite (†)

Mercury et al. (2001) – 8 polymorphs of ice

Juraj Majzlan, Grevel, et al. (2003) – 3 goethite, lepidocrocite, and maghemite GHS

  • Juraj Majzlan, Lang, et al. (2003) – 3 goethite, lepidocrocite, and maghemite Cp

Majzlan et al. (2004) – 1 hydronium jarosite

Majzlan et al. (2006) – 3 coquimbite, ferricopiapite, and rhomboclase

Grevel and Majzlan (2009) – 4 kieserite, starkeyite, hexahydrite, and epsomite

Organic (479)

Tardy et al. (1997) – 5 humic acid, microflora, and plants

Helgeson et al. (1998) – 59 organic molecules and groups

Helgeson et al. (1998) – 20 amino acids (‡)

  • LaRowe and Dick (2012) – 4 updated and corrected parameters for cysteine, glycine, leucine, and methionine (‡)

Richard and Helgeson (1998) – 311 organic molecules and groups

Richard (2001) – 8 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006a) – 19 nucleic-acid bases, nucleosides, and nucleotides

LaRowe and Harold C. Helgeson (2006b) – 9 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP

Helgeson et al. (2009) – 5 kerogens

Richard and Gaona (2011) – 13 organic iodine compounds

LaRowe and Dick (2012) – 30 4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins (‡)

Berman (86)

This file gives the identifiying information for minerals whose properties are calculated using the formulation of Berman (1988). To distinguish these minerals from the original set of mineral data in CHNOSZ (based on the compliation of Helgeson et al., 1978), the physical states are listed as cr_Berman. The actual data are stored separately, as CSV files in extdata/Berman/*.csv. To see the equations in use, run demo(lambda) to calculate properties of the lambda transition in quartz (Berman, 1988); the Berman equations are also used in demo(DEW) and demo(go-IU).

Berman (1988) – 67 minerals

  • Berman (1990) – 2 almandine and ilmenite: modified H and/or S

  • Sverjensky et al. (1991) – 9 G and H revisions for K- and Al-bearing silicates

  • Sverjensky et al. (1991) – 1 phlogopite: H and S modified by Berman (1990), followed by G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

  • berman.dat (2017) – 1 antigorite: “Oct. 21, 2016: Revised volume coefficients consistent with Hilairet et al. (2006) and Yang et al. (2014)

Berman (1990) – 1 annite

  • Sverjensky et al. (1991) – 1 annite: G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

Evans (1990) – 2 glaucophane and pumpellyite

  • JUN92.bs (1992) – 2 data as listed in JUN92.bs data file

Zhu and Sverjensky (1992) – 10 F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of Zhu and Sverjensky (1992); heat capacity and volume parameters from berman.dat.

Delgado Martín and Soler i Gil (2010) – 5 hedenbergite, andradite, ferro-actinolite, grunerite, and ilvaite

Facq et al. (2014) – 1 aragonite; source of data: berman.dat

Liquids

Organic (532)

Helgeson et al. (1998) – 186 organic molecules and groups

Richard and Helgeson (1998) – 231 organic molecules and groups

Richard (2001) – 67 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006b) – 2 pyridine and piperidine

Richard (2008) – 17 alkenes

Richard and Gaona (2011) – 29 organic iodine compounds

Gases

Inorganic (17)

Wagman et al. (1982) – 2 gases GHS (†)

  • Amend and Shock (2001) – 2 NO and N2O (†)

Wagman et al. (1982) – 15 gases GHS (ø)

  • Kelley (1960) – 15 gases Cp (ø)

Organic (266)

Shock (1993) – 2 carbon monoxide and ethylene (*)

Dale et al. (1997) – 4 phenol, and cresol isomers (*)

Dale et al. (1997) – 6 dimethylphenol isomers

Helgeson et al. (1998) – 153 organic molecules and groups

Richard (2001) – 62 organic sulfur compounds

Richard and Gaona (2011) – 39 organic iodine compounds

Optional Data

These files contain optional data updates that replace and/or may be inconsistent with other entries in the default database. Use e.g. add.obigt('SUPCRTBL') to load the data.

DEW (199)

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. The data here were taken from the May 2017 version of the DEW spreadsheet (Dew Model, 2017). The following species are present in the spreadsheet, but are not listed in DEW_aq.csv 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.

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.

Shock and Helgeson (1988) – 2 ionic species

  • Sverjensky et al. (2014) – 2 revisions for BO(OH) and BO2-

Shock and Helgeson (1990) – 3 formic acid, formate, and propanoate

  • DEW model (2017) – 1 revised with new predicted a1 for ions

  • DEW model (2017) – 1 revised with new predicted a1 for complex species

  • DEW model (2017) – 1 propanoate: Revised a1 from new delVn correlation for -1 ions

Pokrovskii and Helgeson (1995) – 2 aluminum species

  • Sverjensky et al. (2014) – 2 revisions for AlO2- and HAlO2

Ho and Palmer (1997) – 1 KOH

  • Sverjensky et al. (2014) – 1 Fitted to Ho and Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume

Plyasunov and Shock (2001) – 2 acetic acid, propanoic acid, and methane

  • DEW model (2017) – 1 methane: revised with new predicted a1 for complex species

Facq et al. (2014) – 3 CO2, CO3-2, and HCO3-

Sverjensky et al. (2014) – 2 SiO2 and Si2O4

DEW model (2017) – 184 other data from Aqueous Species Table in spreadsheet (see detailed references there)

  • DEW model (2017) – 1 acetate: revised January 26th, 2016; new a1 value from complexes and organics correlation.

  • DEW model (2017) – 1 MgCl+: revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions

  • DEW model (2017) – 1 NaCl: revised with new predicted a1 for complex species

SUPCRTBL (97)

SUPCRTBL is a modification and data update for the SUPCRT92 package (Zimmer et al., 2016). Data for SiO2(aq) were updated to reflect the higher observed solubility of quartz compared to the SUPCRT92 dataset, and other aqueous species and minerals relevant to environmental geochemistry were added. The data provided in CHNOSZ were taken from the original references cited below or, where indicated, from spronsbl.dat (downloaded here; file dated 2016-03-01).

NOTE 1: The SUPCRTBL modifications apply the Holland and Powell (2011) equations and dataset for minerals, which are not available in CHNOSZ. Instead, as an alternative to the default dataset of Helgeson et al. (1978), CHNOSZ offers the dataset of Berman (1988) (see the Solids / Berman section of this vignette). NOTE 2: The minerals listed below are represented in the compilation of Zimmer et al. (2016) by constant volume and, where available, a 4-term heat capacity equation that, unlike the complete Holland and Powell formulation, is compatible with CHNOSZ. NOTE 3: Although Zimmer et al. (2016) remark that properties of HSiO3- were recalculated, the values in spronsbl.dat are identical to those in Sverjensky et al. (1997). Those data are not included here (they are part of the default database of CHNOSZ).

Run demo(go-IU) for some examples.

Robie et al. (1978) – 1 gibbsite GHS

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Ball and Nordstrom (1991) – 1 arsenopyrite: G

  • Zimmer et al. (2016) – 1 data listed in spronsbl.dat

Hemingway et al. (1991) – 1 bohemite

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Stefánsson (2001) – 1 aqueous H4SiO4

Tagirov and Schott (2001) – 17 aqueous Al species

  • Diakonov et al. (1996) – 1 NaAl(OH)4

Nordstrom and Archer (2003) – 8 As oxide and sulfide minerals

  • Zimmer et al. (2016) – 1 As(α): V listed in spronsbl.dat

Nordstrom and Archer (2003) – 10 aqueous As oxides and sulfides

Apps and Spycher (2004) – 1 aqueous SiO2

  • Zimmer et al. (2016) – 1 data listed in spronsbl.dat

Zhu et al. (2005) – 2 barium arsenate and barium hydrogen arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Langmuir et al. (2006) – 2 scorodite and amorphous ferric arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Marini and Accornero (2007) – 52 metal-arsenate and metal-arsenite complexes

  • Marini and Accornero (2010) – 52 corrected values

Zimmer et al. (2016) – 1 dawsonite GHS

  • Ferrante et al. (1976) – 1 dawsonite Cp (value at 25 °C as listed by Bénézeth et al. (2007); not present in spronsbl.dat)

All at once

Aqueous species

H2O (3)

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) (default) or using the IAPWS-95 equations (Wagner and Pruß, 2002) or the Deep Earth Water (DEW) model (Sverjensky et al., 2014).

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). The formation reaction of the proton can be expressed as ½H2,(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. Puigdomenech et al., 1997). Therefore, the “element” of positive charge (Z) has zero thermodynamic properties except for an entropy, S°Tr, that is negative one-half that of H2,(g). The standard entropy of the aqueous electron, which is a solely a pseudospecies defined by e- = -Z, is opposite that of Z.**

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; Shock and Helgeson, 1988). 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.^^

**Likewise, GEM-Selektor defines “independent components” to be stoichiometric units usually consisting of elements and charge; the latter, which is named Zz 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).

^^ Relatedly, charged amino acid sidechain groups have a charge that is tabulated as zero, because other values would be incompatible with group additivity of cations and anions (which have derivatives of the omega parameter (ω) in the revised HKF equations of state that are not opposites of each other) to give a neutral species (for which the derivatives of ω are taken to be zero) (cf. Dick et al., 2006).

Inorganic (855)

ZnCl4-2 was present in sprons92.dat but not in slop98.dat or later files, and is not included in CHNOSZ.

Shock and Helgeson (1988) – 59 ionic species (ø)

Shock et al. (1989) – 14 inorganic neutral species (ø)

Haas et al. (1995) – 249 complexes of rare earth elements (*)

  • slop98.dat – 88 “Corrected values based on data from Haas et al. (1995) (*)

McCollom and Shock (1997) – 3 MgSO4, NaSO4-, and HCl (*)

  • slop98.dat – 3 “Data and parameters as used by McCollom and Shock (1997).” (*)

Everett L. Shock, Sassani, and Betz (1997) – 15 uranium species (*)

Sverjensky et al. (1997) – 108 metal complexes (*)

  • slop15.dat – 1 Zn(Ac)3-: “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of Sverjensky et al. (1997).” (‡)

  • CHNOSZ – 1 AuCl4- renamed to AuCl4-3

Everett L. Shock, Sassani, Willis, et al. (1997) – 252 inorganic ions and hydroxide complexes (*)

  • Sassani and Shock (1998) – 1 Rh+3 (*)

Sassani and Shock (1998) – 61 platinum-group ions and complexes (*)

Murphy and Shock (1999) – 38 actinides (†)

Schulte et al. (2001) – 10 AsH3, CF4, CH3F, Cl2, ClO2, N2O, NF3, NO, PH3, and SF6

Accornero et al. (2010) – 45 metal-chromate complexes

CHNOSZ – 1 pseudo-H4SiO4; GHS and HKF parameters calculated as shown in the vignette, Regressing thermodynamic data

Organic (752)

Shock and Helgeson (1990) – 47 organic species (ø)

  • slop15.dat – 3 hexanol, heptanol, and octanol: “Minor differences in Gibbs energy, entropy, omega, a1, a2, a3, a4 and c1 values compared to Shock and Helgeson (1990).” (‡)

Shock (1992) – 4 diglycine, alanylglycine, leucylglycine, and diketopiperazine

  • CHNOSZ – 4 dipeptides not included in slop files after slop98.dat

Shock (1993) – 2 ethylacetate and acetamide (*)

Shock and Koretsky (1993) – 113 metal-acetate complexes (*)

  • slop15.dat – 32 “Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements.” (‡)

Shock and McKinnon (1993) – 3 CO, HCN, urea (*)

Schulte and Shock (1993) – 10 aldehydes (*)

  • slop15.dat – 1 formaldehyde: “Entropy corrected to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote i in table 2 of Schulte and Shock (1993).” (‡)

Shock and Koretsky (1995) – 226 metal-organic acid complexes (*)

  • slop98.dat – 6 “These data were used in Shock and Koretsky (1995), but were not tabulated in the paper.” (*)

  • slop15.dat – 55 “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements.” (‡)

Shock and Koretsky (1995) – 54 alanate, glycinate and their complexes not included in later slop files. (*)

  • CHNOSZ – 2 alanate and glycinate: GHS as used by Dick et al. (2006)

  • CHNOSZ – 52 metal-amino acid complexes: GHS were recalculated by adding the differences between values from Amend and Helgeson (1997) and Dick et al. (2006) for alanate or glycinate to the properties of the complexes reported by Shock and Koretsky (1995).

Shock (1995) – 77 carboxylic acids (*)

  • slop15.dat – 2 adipic acid and n-dodecanoate: “Gibbs free energy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote y in table 4 of Shock (1995).” (‡)

  • slop15.dat – 1 n-octanoate: “Enthalpy corrected to be compatible with the equation ΔG=ΔH-TΔS for the formation reaction from elements. See footnote ab in table 4 of Shock (1995).” (‡)

Dale et al. (1997) – 10 alkylphenols (*)

Haas and Shock (1999) – 6 chloroethylene species (†)

Prapaipong et al. (1999) – 162 metal-dicarboxylate complexes (†)

  • slop07.dat – 1 corrected charge of Pu(Oxal)+2 (†)

  • CHNOSZ – 4 charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by Prapaipong et al. (1999)

Plyasunov and Shock (2001) – 11 aqueous nonelectrolytes (†)

Schulte and Rogers (2004) – 12 alkane thiols (†)

Hawrylak et al. (2006) – 2 methyldiethanolamine and methyldiethanolammonium chloride HKF parameters

Schulte (2010) – 7 organic sulfides

Dick et al. (2013) – 6 phenanthrene and methylphenanthrene isomers

Biotic (302)

Amend and Helgeson (1997) – 29 amino acids GHS (†)

  • Dick et al. (2006) – 29 amino acids HKF parameters (†)

Amend and Plyasunov (2001) – 10 carbohydrates (†)

  • slop07.dat – 10 high-temperature HKF parameters from Amend and Plyasunov (2001) (†)

LaRowe and Harold C. Helgeson (2006a) – 138 nucleic-acid bases, nucleosides, and nucleotides (†)

  • Lowe et al. (2017) – 1 adenine HKF parameters

LaRowe and Harold C. Helgeson (2006a) – 4 citric acid and citrate

  • Canovas and Shock (2016) – 4 citric acid species HKF a1–a4 parameters

LaRowe and Harold C. Helgeson (2006b) – 32 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP (†)

Dick et al. (2006) – 40 amino acid, protein, and organic groups (‡)

  • LaRowe and Dick (2012) – 1 methionine sidechain GHS

  • CHNOSZ – 1 Incorrect values of HKF a1–a4 parameters for [-CH2NH2] were printed in Table 6 of Dick et al. (2006); corrected values are used here. (‡)

Dick et al. (2006) – 1 amino acids HKF parameters (†)

  • LaRowe and Dick (2012) – 1 methionine GHS (‡)

Dick et al. (2006) – 20 Gly-X-Gly tripeptides

Dick (2007) – 4 glutathione, cystine, and cystine sidechain

Canovas and Shock (2016) – 24 citric acid cycle metabolites

Solids

Inorganic (296)

Chamosite,7A and witherite were present in sprons92.dat but not in slop98.dat or later files, and are not included in CHNOSZ.

The source of parameters used here for goethite is different from that in the slop files (Shock, 2009).

Helgeson et al. (1978) – 235 data for minerals (n = 167) and phase transitions (ø)

  • Kelley (1960) – 1 larnite Cp (ø)

  • Pankratz and King (1970) – 2 bornite and chalcopyrite (ø)

  • Robie et al. (1978) – 4 dickite, fluorphlogopite, halloysite, and pyrope (ø)

  • Plummer and Busenberg (1982) – 2 aragonite and calcite (ø)

  • Wagman et al. (1982) – 1 manganosite (ø)

  • Helgeson (1985) – 2 ferrosilite and siderite (ø)

  • sprons92.dat – 24 Ca-bearing minerals; “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

  • slop98.dat – 1 daphnite; “Gf and Hf from Saccocia and Seyfried (1993) TMM” (*)

  • CHNOSZ – 68 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Robie et al. (1978) – 3 chlorargyrite, rutile, and titanite (ø)

  • Pankratz (1970) – 1 chlorargyrite (ø)

  • Bowers and Helgeson (1983) – 1 rutile (ø)

  • sprons92.dat – 1 titanite: Bowers and Helgeson (1983) + “Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca2+ and CO32- (Shock and Helgeson, 1988) together with the solubilities of calcite and aragonite reported by Plummer and Busenberg (1982) (ø)

Robie et al. (1978) – 4 iron (ø)

  • Kelley (1960) – 1 iron Cp (ø)

  • CHNOSZ – 3 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Wagman et al. (1982) – 1 MgSO4

Jackson and Helgeson (1985) – 5 Sn minerals (ø)

  • CHNOSZ – 1 GHS (Tr) of the phase that is stable at 298.15 K was combined with Htr and the Cp coefficients to calculate the metastable GHS (Tr) of the phases that are stable at higher temperatures.

Parker and Khodakovskii (1995) – 1 melanterite

Robie and Hemingway (1995) – 1 gypsum GHS

  • Kelley (1960) – 1 gypsum Cp

McCollom and Shock (1997) – 3 sulfur (*)

  • slop98.dat – 3 “Data and parameters as used by McCollom and Shock (1997).” (*)

Everett L. Shock, Sassani, and Betz (1997) – 1 uraninite (*)

Everett L. Shock, Sassani, Willis, et al. (1997) – 2 zincite and litharge (*)

  • Helgeson et al. (1978) – 1 litharge S, V, and Cp parameters (ø)

  • slop98.dat – 1 zincite and litharge; “These data were used in Everett L. Shock, Sassani, Willis, et al. (1997), but were not tabulated in the paper.” (*)

Sassani and Shock (1998) – 15 platinum-group solids (*)

Stoffregen et al. (2000) – 3 jarosite, natroalunite, and natrojarosite

Amend and Shock (2001) – 3 selenium and molybdenite (†)

Mercury et al. (2001) – 8 polymorphs of ice

Juraj Majzlan, Grevel, et al. (2003) – 3 goethite, lepidocrocite, and maghemite GHS

  • Juraj Majzlan, Lang, et al. (2003) – 3 goethite, lepidocrocite, and maghemite Cp

Majzlan et al. (2004) – 1 hydronium jarosite

Majzlan et al. (2006) – 3 coquimbite, ferricopiapite, and rhomboclase

Grevel and Majzlan (2009) – 4 kieserite, starkeyite, hexahydrite, and epsomite

Organic (479)

Tardy et al. (1997) – 5 humic acid, microflora, and plants

Helgeson et al. (1998) – 59 organic molecules and groups

Helgeson et al. (1998) – 20 amino acids (‡)

  • LaRowe and Dick (2012) – 4 updated and corrected parameters for cysteine, glycine, leucine, and methionine (‡)

Richard and Helgeson (1998) – 311 organic molecules and groups

Richard (2001) – 8 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006a) – 19 nucleic-acid bases, nucleosides, and nucleotides

LaRowe and Harold C. Helgeson (2006b) – 9 Mg-complexed adenosine nucleotides (ATP), NAD, and NADP

Helgeson et al. (2009) – 5 kerogens

Richard and Gaona (2011) – 13 organic iodine compounds

LaRowe and Dick (2012) – 30 4-hydroxyproline, 5-hydroxylysine, 4 dipeptides, and sidechain and backbone groups in proteins (‡)

Berman (86)

This file gives the identifiying information for minerals whose properties are calculated using the formulation of Berman (1988). To distinguish these minerals from the original set of mineral data in CHNOSZ (based on the compliation of Helgeson et al., 1978), the physical states are listed as cr_Berman. The actual data are stored separately, as CSV files in extdata/Berman/*.csv. To see the equations in use, run demo(lambda) to calculate properties of the lambda transition in quartz (Berman, 1988); the Berman equations are also used in demo(DEW) and demo(go-IU).

Berman (1988) – 67 minerals

  • Berman (1990) – 2 almandine and ilmenite: modified H and/or S

  • Sverjensky et al. (1991) – 9 G and H revisions for K- and Al-bearing silicates

  • Sverjensky et al. (1991) – 1 phlogopite: H and S modified by Berman (1990), followed by G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

  • berman.dat (2017) – 1 antigorite: “Oct. 21, 2016: Revised volume coefficients consistent with Hilairet et al. (2006) and Yang et al. (2014)

Berman (1990) – 1 annite

  • Sverjensky et al. (1991) – 1 annite: G and H revision for K-bearing silicates (after Sverjensky et al., 1991)

Evans (1990) – 2 glaucophane and pumpellyite

  • JUN92.bs (1992) – 2 data as listed in JUN92.bs data file

Zhu and Sverjensky (1992) – 10 F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of Zhu and Sverjensky (1992); heat capacity and volume parameters from berman.dat.

Delgado Martín and Soler i Gil (2010) – 5 hedenbergite, andradite, ferro-actinolite, grunerite, and ilvaite

Facq et al. (2014) – 1 aragonite; source of data: berman.dat

Liquids

Organic (532)

Helgeson et al. (1998) – 186 organic molecules and groups

Richard and Helgeson (1998) – 231 organic molecules and groups

Richard (2001) – 67 organic sulfur compounds

LaRowe and Harold C. Helgeson (2006b) – 2 pyridine and piperidine

Richard (2008) – 17 alkenes

Richard and Gaona (2011) – 29 organic iodine compounds

Gases

Inorganic (17)

Wagman et al. (1982) – 2 gases GHS (†)

  • Amend and Shock (2001) – 2 NO and N2O (†)

Wagman et al. (1982) – 15 gases GHS (ø)

  • Kelley (1960) – 15 gases Cp (ø)

Organic (266)

Shock (1993) – 2 carbon monoxide and ethylene (*)

Dale et al. (1997) – 4 phenol, and cresol isomers (*)

Dale et al. (1997) – 6 dimethylphenol isomers

Helgeson et al. (1998) – 153 organic molecules and groups

Richard (2001) – 62 organic sulfur compounds

Richard and Gaona (2011) – 39 organic iodine compounds

Optional Data

These files contain optional data updates that replace and/or may be inconsistent with other entries in the default database. Use e.g. add.obigt('SUPCRTBL') to load the data.

DEW (199)

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. The data here were taken from the May 2017 version of the DEW spreadsheet (Dew Model, 2017). The following species are present in the spreadsheet, but are not listed in DEW_aq.csv 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.

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.

Shock and Helgeson (1988) – 2 ionic species

  • Sverjensky et al. (2014) – 2 revisions for BO(OH) and BO2-

Shock and Helgeson (1990) – 3 formic acid, formate, and propanoate

  • DEW model (2017) – 1 revised with new predicted a1 for ions

  • DEW model (2017) – 1 revised with new predicted a1 for complex species

  • DEW model (2017) – 1 propanoate: Revised a1 from new delVn correlation for -1 ions

Pokrovskii and Helgeson (1995) – 2 aluminum species

  • Sverjensky et al. (2014) – 2 revisions for AlO2- and HAlO2

Ho and Palmer (1997) – 1 KOH

  • Sverjensky et al. (2014) – 1 Fitted to Ho and Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume

Plyasunov and Shock (2001) – 2 acetic acid, propanoic acid, and methane

  • DEW model (2017) – 1 methane: revised with new predicted a1 for complex species

Facq et al. (2014) – 3 CO2, CO3-2, and HCO3-

Sverjensky et al. (2014) – 2 SiO2 and Si2O4

DEW model (2017) – 184 other data from Aqueous Species Table in spreadsheet (see detailed references there)

  • DEW model (2017) – 1 acetate: revised January 26th, 2016; new a1 value from complexes and organics correlation.

  • DEW model (2017) – 1 MgCl+: revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions

  • DEW model (2017) – 1 NaCl: revised with new predicted a1 for complex species

SUPCRTBL (97)

SUPCRTBL is a modification and data update for the SUPCRT92 package (Zimmer et al., 2016). Data for SiO2(aq) were updated to reflect the higher observed solubility of quartz compared to the SUPCRT92 dataset, and other aqueous species and minerals relevant to environmental geochemistry were added. The data provided in CHNOSZ were taken from the original references cited below or, where indicated, from spronsbl.dat (downloaded here; file dated 2016-03-01).

NOTE 1: The SUPCRTBL modifications apply the Holland and Powell (2011) equations and dataset for minerals, which are not available in CHNOSZ. Instead, as an alternative to the default dataset of Helgeson et al. (1978), CHNOSZ offers the dataset of Berman (1988) (see the Solids / Berman section of this vignette). NOTE 2: The minerals listed below are represented in the compilation of Zimmer et al. (2016) by constant volume and, where available, a 4-term heat capacity equation that, unlike the complete Holland and Powell formulation, is compatible with CHNOSZ. NOTE 3: Although Zimmer et al. (2016) remark that properties of HSiO3- were recalculated, the values in spronsbl.dat are identical to those in Sverjensky et al. (1997). Those data are not included here (they are part of the default database of CHNOSZ).

Run demo(go-IU) for some examples.

Robie et al. (1978) – 1 gibbsite GHS

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Ball and Nordstrom (1991) – 1 arsenopyrite: G

  • Zimmer et al. (2016) – 1 data listed in spronsbl.dat

Hemingway et al. (1991) – 1 bohemite

  • Zimmer et al. (2016) – 1 Cp parameters listed in spronsbl.dat

Stefánsson (2001) – 1 aqueous H4SiO4

Tagirov and Schott (2001) – 17 aqueous Al species

  • Diakonov et al. (1996) – 1 NaAl(OH)4

Nordstrom and Archer (2003) – 8 As oxide and sulfide minerals

  • Zimmer et al. (2016) – 1 As(α): V listed in spronsbl.dat

Nordstrom and Archer (2003) – 10 aqueous As oxides and sulfides

Apps and Spycher (2004) – 1 aqueous SiO2

  • Zimmer et al. (2016) – 1 data listed in spronsbl.dat

Zhu et al. (2005) – 2 barium arsenate and barium hydrogen arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Langmuir et al. (2006) – 2 scorodite and amorphous ferric arsenate: G

  • Zimmer et al. (2016) – 2 data listed in spronsbl.dat

Marini and Accornero (2007) – 52 metal-arsenate and metal-arsenite complexes

  • Marini and Accornero (2010) – 52 corrected values

Zimmer et al. (2016) – 1 dawsonite GHS

  • Ferrante et al. (1976) – 1 dawsonite Cp (value at 25 °C as listed by Bénézeth et al. (2007); not present in spronsbl.dat)

Total count of species

3588 of 3588 entries in thermo$obigt and 296 optional data entries are documented here.

References

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Amend JP, Helgeson HC. 1997. Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. Part 1. l-α-amino acids. Journal of the Chemical Society, Faraday Transactions 93(10): 1927–1941. doi: 10.1039/A608126F

Amend JP, Plyasunov AV. 2001. Carbohydrates in thermophile metabolism: Calculation of the standard molal thermodynamic properties of aqueous pentoses and hexoses at elevated temperatures and pressures. Geochimica et Cosmochimica Acta 65(21): 3901–3917. doi: 10.1016/S0016-7037(01)00707-4

Amend JP, Shock EL. 2001. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews 25(2): 175–243. doi: 10.1111/j.1574-6976.2001.tb00576.x

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Ball JW, Nordstrom DK. 1991. User’s manual for WATEQ4F, with revised thermodynamic data base and text cases for calculating speciation of major, trace, and redox elements in natural waters. Menlo Park, CA: U. S. Geological Survey. Report No.: 91-183. Available at https://pubs.er.usgs.gov/publication/ofr91183.

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Dick JM, Evans KA, Holman AI, Jaraula CMB, Grice K. 2013. Estimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature. Geochimica et Cosmochimica Acta 122: 247–266. doi: 10.1016/j.gca.2013.08.020

Dick JM, LaRowe DE, Helgeson HC. 2006. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences 3(3): 311–336. doi: 10.5194/bg-3-311-2006

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Langmuir D, Mahoney J, Rowson J. 2006. Solubility products of amorphous ferric arsenate and crystalline scorodite (FeAsO<sub>4</sub>·2H<sub>2</sub>O) and their application to arsenic behavior in buried mine tailings. Geochimica et Cosmochimica Acta 70(12): 2942–2956. doi: 10.1016/j.gca.2006.03.006

LaRowe DE, Dick JM. 2012. Calculation of the standard molal thermodynamic properties of crystalline peptides. Geochimica et Cosmochimica Acta 80: 70–91. doi: 10.1016/j.gca.2011.11.041

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