extdata: Extra data

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

Extra data

Description

The files in the subdirectories of extdata provide additional thermodynamic data and other data to support the examples in the package documentation and vignettes. See thermo for a description of the files in extdata/OBIGT, which are used to generate the thermodynamic database.

Details

Files in Berman contain thermodynamic data for minerals using the Berman formulation:

• Ber88_1988.csv contains thermodynamic data for minerals taken from Berman (1988).

• Other files with names like xxx_yyyy.csv contain thermodynamic data from other sources; xxx in the filename corresponds to the reference in thermo$OBIGT and yyyy gives the year of publication. Berman uses these data for the calculation of thermodynamic properties at specified \P and \T, which are then available for use in subcrt. If there are any duplicated mineral names in the files, only the most recent data are used, as determined by the year in the file name. Following conventions used SUPCRT92 (see Helgeson et al., 1978), the names of sanidine and microcline were changed to K-feldspar,high and K-feldspar,low (by using the same names in all data files, loading the optional SUPCRT92 data file updates these minerals rather than makes new ones).

• sympy.R is an R script that uses rSymPy to symbolically integrate Bermans's equations for heat capacity and volume to write experessions for enthalpy, entropy and Gibbs energy.

• The testing directory contains data files based on Berman and Aranovich (1996). These are used to demonstrate the addition of data from a user-supplied file (see Berman).

Files in protein contain protein sequences and amino acid compositions for proteins.

• rubisco.csv UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL for growth temperature reference, from Dick, 2014. See rank.affinity and demo{"rubisco_ZC"} for examples that use this file.

• rubisco.fasta Sequences of Rubisco obtained from UniProt.

• rubisco_aa.fasta Amino acid compositions of Rubisco.

• POLG.csv Amino acid compositions of a few proteins used for some tests and examples. These are various subunits of the Poliovirus type 1 polyprotein (POLG_POL1M in UniProt).

• TBD+05.csv lists genes with transcriptomic expression changes in carbon limitation stress response experiments in yeast (Tai et al., 2005).

• TBD+05_aa.csv has the amino acid compositions of proteins coded by those genes. The last two files are used in demo{"rank.affinity"}.

• Cas has scripts and data files for amino acid compositions of CRISPR associated (Cas) proteins.

  • ‘Cas_uniprot.csv’: class, subtype, organism, locus tag, gene names, and effector proteins from Makarova et al. (2020); UniProt IDs found by searching databases.

  • ‘download.R’: script to download sequences in FASTA format from UniProt and UniParc.

  • ‘mkaa.R’: script to calculate amino acid compositions from FASTA files.

  • ‘Cas_aa.csv’: amino acid compositions generated by above script.

Files in taxonomy contain taxonomic data files:

• names.dmp and nodes.dmp are excerpts of NCBI taxonomy files (https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz, accessed 2010-02-15). These files contain only the entries for Escherichia coli K-12, Saccharomyces cerevisiae, Homo sapiens, Pyrococcus furisosus and Methanocaldococcus jannaschii (taxids 83333, 4932, 9606, 186497, 243232) and the higher-ranking nodes (genus, family, etc.) in the respective lineages. See taxonomy for examples that use these files.

Files in misc contain miscellaneous data:

• PM90.csv Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Temperature in \degC is in the first column, and heat capacities of the proteins in J mol^{-1} K^{-1} in the remaining columns. See ionize.aa and the vignette \viglinkanintro for examples that use this file.

• RH95.csv Heat capacity data for iron taken from Robie and Hemingway, 1995. Temperature in Kelvin is in the first column, heat capacity in J K^{-1} mol^{-1} in the second. See subcrt for an example that uses this file.

• SOJSH.csv Experimental equilibrium constants for the reaction NaCl(aq) = Na+ + Cl- as a function of temperature and pressure taken from Fig. 1 of Shock et al., 1992. See demo("NaCl") for an example that uses this file.

• HWM96_V.csv, HW97_Cp.csv Apparent molar volumes and heat capacities of \CH4, \CO2, \H2S, and \NH3 in dilute aqueous solutions reported by Hnědkovský et al., 1996 and Hnědkovský and Wood, 1997. Units are Kelvin, MPa, J/K/mol, and cm3/mol. See demo("AD"), EOSregress and the vignette \viglinkeos-regress for examples that use these files.

• SC10_Rainbow.csv Values of temperature (\degC), pH and logarithms of activity of \CO2, \H2, \NH4plus, \H2S and \CH4 for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010. See the vignette \viglinkanintro for an example that uses this file.

• SS98_Fig5a.csv, SS98_Fig5b.csv Values of logarithm of fugacity of \O2 and pH as a function of temperature for mixing of seawater and hydrothermal fluid, digitized from Figs. 5a and b of Shock and Schulte, 1998. See the vignette \viglinkanintro for an example that uses this file.

• bluered.txt Blue - light grey - red color palette, computed using colorspace::diverge_hcl(1000, c = 100, l = c(50, 90), power = 1). This is used by ZC.col.

• AD03_Fig1?.csv Experimental data points digitized from Figure 1 of Akinfiev and Diamond, 2003, used in demo("AD").

• TKSS14_Fig2.csv Experimental data points digitized from Figure 2 of Tutolo et al., 2014, used in demo("aluminum").

• Mer75_Table4.csv Values of log(aK+/aH+) and log(aNa+/aH+) from Table 4 of Merino, 1975, used in demo("aluminum").

• BZA10.csv contains supplementary thermodynamic data taken from Bazarkina et al. (2010). The data can be added to the database in the current session using add.OBIGT. See add.OBIGT for an example that uses this file.

• OBIGT_check.csv contains the results of running check.OBIGT to check the internal consistency of entries in the default and optional datafiles.

• RH98_Table15.csv Group stoichiometries for high molecular weight crystalline and liquid organic compounds taken from Table 15 of Richard and Helgeson, 1998. The first three columns have the compound name, formula and physical state (‘⁠cr⁠’ or ‘⁠liq⁠’). The remaining columns have the numbers of each group in the compound; the names of the groups (columns) correspond to species in thermo$OBIGT. The compound named ‘⁠5a(H),14a(H)-cholestane⁠’ in the paper has been changed to ‘⁠5a(H),14b(H)-cholestane⁠’ here to match the group stoichiometry given in the table. See RH2OBIGT for a function that uses this file.

• SK95.csv contains thermodynamic data for alanate, glycinate, and their complexes with metals, taken from Amend and Helgeson (1997) and Shock and Koretsky (1995) as corrected in slop98.dat. These data are used in demo("copper") and demo("glycinate").

• LA19_test.csv contains thermodynamic data for dimethylamine and trimethylamine from LaRowe and Amend (2019) in energy units of both J and cal. This file is used in test-util.data.R) to check the messages produced by check.GHS and check.EOS.

References

Akinfiev NN, Diamond LW. 2003. Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. Geochim Cosmochim Acta 67: 613–629. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0016-7037(02)01141-9")}

Amend JP, Helgeson HC. 1997. Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. Part 1. L-\alpha-amino acids. J Chem Soc Faraday Trans 93: 1927–1941. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1039/A608126F")}

Bazarkina EF, Zotov AV, Akinfiev NN. 2010. Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1–1000 bar and 25°C. Geol Ore Deposits 52: 167–178. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1134/S1075701510020054")}

Berman RG. 1988. Internally-consistent thermodynamic data for minerals in the system Na\s2O-K\s2O-CaO-MgO-FeO-Fe\s2O\s3-Al\s2O\s3-SiO\s2-TiO\s2-H\s2O-CO\s2. J Petrol 29: 445–522. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/petrology/29.2.445")}

Berman RG, Aranovich LYa. 1996. Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-Al\s2O\s3-TiO\s2-SiO\s2. Contrib Mineral Petrol 126: 1–24. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s004100050233")}

Dick JM. 2014. Average oxidation state of carbon in proteins. J R Soc Interface 11: 20131095. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1098/rsif.2013.1095")}

Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJA, Lachaize C, Veuthey A-L, Gasteiger E, Bairoch A. 2003. Automatic annotation of microbial proteomes in Swiss-Prot. Comput Biol Chem 27: 49–58. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S1476-9271(02)00094-4")}

Helgeson HC, Delany JM, Nesbitt HW, Bird DK. 1978. Summary and critique of the thermodynamic properties of rock-forming minerals. Am J Sci 278-A: 1–229. https://www.worldcat.org/oclc/13594862

Hnědkovský L, Wood RH, Majer V. 1996. Volumes of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. J Chem Thermodyn 28: 125–142. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1006/jcht.1996.0011")}

Hnědkovský L, Wood RH. 1997. Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. J Chem Thermodyn 29: 731–747. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1006/jcht.1997.0192")}

Joint Genome Institute. 2007. Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M. https://img.jgi.doe.gov/

LaRowe DE, Amend JP. 2019. The energetics of fermentation in natural settings. Geomicrobiol J 36: 492–505. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/01490451.2019.1573278")}

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. 2020. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 18: 67–83. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41579-019-0299-x")}

Merino E. 1975. Diagenesis in tertiary sandstones from Kettleman North Dome, California. II. Interstitial solutions: distribution of aqueous species at 100°C and chemical relation to diagenetic mineralogy. Geochim Cosmochim Acta 39: 1629–1645. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/0016-7037(75)90085-X")}

Privalov PL, Makhatadze GI. 1990. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J Mol Biol 213: 385–391. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0022-2836(05)80198-6")}

Richard L, Helgeson HC. 1998. Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. Geochim Cosmochim Acta 62: 3591–3636. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0016-7037(97)00345-1")}

Robie RA, Hemingway BS. 1995. Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (10^5 Pascals) Pressure and at Higher Temperatures. U S Geol Surv Bull 2131, 461 p. https://www.worldcat.org/oclc/32590140

Shock E, Canovas P. 2010. The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10: 161–192. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1468-8123.2010.00277.x")}

Shock EL, Koretsky CM. 1995. Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. Geochim Cosmochim Acta 59: 1497–1532. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/0016-7037(95)00058-8")}

Shock EL, Oelkers EH, Johnson JW, Sverjensky DA, Helgeson HC. 1992. Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 °C and 5 kbar. J Chem Soc Faraday Trans 88: 803–826. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1039/FT9928800803")}

Shock EL, Schulte MD. 1998. Organic synthesis during fluid mixing in hydrothermal systems. J Geophys Res 103: 28513–28527. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1029/98JE02142")}

Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran J-M, Pronk JT. 2005. Two-dimensional transcriptome analysis in chemostat cultures: Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 280: 437–447. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1074/jbc.M410573200")}

Tutolo BM, Kong X-Z, Seyfried WE Jr, Saar MO. 2014. Internal consistency in aqueous geochemical data revisited: Applications to the aluminum system. Geochim Cosmochim Acta 133: 216–234. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2014.02.036")}

CHNOSZ documentation built on Dec. 18, 2025, 3:01 p.m.