extdata {CHNOSZ}

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 cpetc contain experimental and calculated thermodynamic and environmental data:

• PM90.csv Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Temperature in °C 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 anintro 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 eos-regress for examples that use these files.

• SC10_Rainbow.csv Values of temperature (°C), pH and logarithms of activity of CO₂, H₂, NH₄⁺, 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 anintro 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 anintro for an example that uses this file.

• rubisco.csv UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL of reference for growth temperature, from Dick, 2014. See rank.affinity and the vignette anintro for examples that use 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").

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

• EF-Tu.aln consists of aligned sequences (394 amino acids) of elongation factor Tu (EF-Tu). The sequences correspond to those taken from UniProtKB for ECOLI (Escherichia coli), THETH (Thermus thermophilus) and THEMA (Thermotoga maritima), and reconstructed ancestral sequences taken from Gaucher et al., 2003 (maximum likelihood bacterial stem and mesophilic bacterial stem, and alternative bacterial stem). See read.fasta for an example that uses this file.

• rubisco.fasta Sequences of Rubisco obtained from UniProt (see Dick, 2014). See the vignette anintro for an example that uses this file.

• 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"}.

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 adds contain additional thermodynamic data and group additivity definitions:

• 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, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. Geochim. Cosmochim. Acta 67, 613–629. doi:10.1016/S0016-7037(02)01141-9

Amend, J. P. and Helgeson, H. C. (1997) Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. Part 1. L-α-amino acids. J. Chem. Soc., Faraday Trans. 93, 1927–1941. doi:10.1039/A608126F

Bazarkina, E. F., Zotov, A. V. and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1–1000 bar and 25°C. Geol. Ore Deposits 52, 167–178. doi:10.1134/S1075701510020054

Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na₂O-K₂O-CaO-MgO-FeO-Fe₂O₃-Al₂O₃-SiO₂-TiO₂-H₂O-CO₂. J. Petrol. 29, 445-522. doi:10.1093/petrology/29.2.445

Berman, R. G. and Aranovich, L. Ya. (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-Al₂O₃-TiO₂-SiO₂. Contrib. Mineral. Petrol. 126, 1-24. doi:10.1007/s004100050233

Dick, J. M. (2014) Average oxidation state of carbon in proteins. J. R. Soc. Interface 11, 20131095. doi:10.1098/rsif.2013.1095

Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J. A., Lachaize, C., Veuthey, A.-L., Gasteiger, E. and Bairoch, A. (2003) Automatic annotation of microbial proteomes in Swiss-Prot. Comput. Biol. Chem. 27, 49–58. doi:10.1016/S1476-9271(02)00094-4

Gaucher, E. A., Thomson, J. M., Burgan, M. F. and Benner, S. A (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425(6955), 285–288. doi:10.1038/nature01977

Helgeson, H. C., Delany, J. M., Nesbitt, H. W. and Bird, D. K. (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, R. H. and 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. doi:10.1006/jcht.1996.0011

Hnědkovský, L. and Wood, R. H. (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. 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, D. E. and Amend, J. P. (2019) The energetics of fermentation in natural settings. Geomicrobiol. J. 36, 492–505. doi:10.1080/01490451.2019.1573278

Merino, E. (1975) Diagenesis in teriary 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. doi:10.1016/0016-7037(75)90085-X

Privalov, P. L. and Makhatadze, G. I. (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. doi:10.1016/S0022-2836(05)80198-6

Richard, L. and Helgeson, H. C. (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. doi:10.1016/S0016-7037(97)00345-1

Robie, R. A. and Hemingway, B. S. (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. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10, 161–192. doi:10.1111/j.1468-8123.2010.00277.x

Shock, E. L. and Koretsky, C. M. (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. doi:10.1016/0016-7037(95)00058-8

Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (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. doi:10.1039/FT9928800803

Shock, E. L. and Schulte, M. D. (1998) Organic synthesis during fluid mixing in hydrothermal systems. J. Geophys. Res. 103, 28513–28527. doi:10.1029/98JE02142

Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J.-M. and Pronk, J. T. (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. doi:10.1074/jbc.M410573200

Tutolo, B. M., Kong, X.-Z., Seyfried, W. E., Jr. and Saar, M. O. (2014) Internal consistency in aqueous geochemical data revisited: Applications to the aluminum system. Geochim. Cosmochim. Acta 133, 216–234. doi:10.1016/j.gca.2014.02.036