examples: Run Examples from the Documentation
In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

examples

R Documentation

Run Examples from the Documentation

Description

Run the examples contained in each of the documentation topics.

Usage

  examples(save.png = FALSE)
  demos(which = c("sources", "protein.equil", "affinity", "NaCl",
    "density", "ORP", "ionize", "buffer", "protbuff",
    "glycinate", "mosaic", "copper", "arsenic", "solubility", "gold",
    "contour", "sphalerite", "minsol", "Shh", "saturation",
    "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum", "AD",
    "comproportionation", "Pourbaix", "E_coli", "yttrium", "rank.affinity"),
    save.png = FALSE)

Arguments

`save.png`	logical, generate PNG image files for the plots?
`which`	character, which example to run

Details

examples runs all the examples in the help pages for the package. example is called for each topic with ask set to FALSE (so all of the figures are shown without prompting the user).

demos runs all the demos in the package. The demo(s) to run is/are specified by which; the default is to run them in the order of the list below.

sources: Cross-check the reference list with the thermodynamic database
protein.equil: Chemical activities of two proteins in metastable equilibrium (Dick and Shock, 2011)
affinity: Affinities of metabolic reactions and amino acid synthesis (Amend and Shock, 1998, 2001)
NaCl: Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992)
density: Density of \H2O, inverted from IAPWS-95 equations (rho.IAPWS95)
ORP: Temperature dependence of oxidation-reduction potential for redox standards
ionize: ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
buffer: Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995)
protbuff: Chemical activities buffered by thiol peroxidases or sigma factors
glycinate: Metal-glycinate complexes (Shock and Koretsky, 1995; Azadi et al., 2019)
mosaic: Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965)
copper: Another example of mosaic: complexation of Cu with glycine (Aksu and Doyle, 2001)
arsenic: Another example of mosaic: Eh-pH diagram for the system As-O-H-S (Lu and Zhu, 2011)
solubility: Solubility of calcite (cf. Manning et al., 2013) and \CO2 (cf. Stumm and Morgan, 1996)
gold: Solubility of gold (Akinfiev and Zotov; 2001; Stef\aacutensson and Seward, 2004; Williams-Jones et al., 2009)
contour: Gold solubility contours on a log fO2 - pH diagram (Williams-Jones et al., 2009)
sphalerite: Solubility of sphalerite (Akinfiev and Tagirov, 2014)
minsol: Solubilities of multiple minerals
dehydration: \logK
of dehydration reactions; SVG file contains tooltips and links
Shh: Affinities of transcription factors relative to Sonic hedgehog (Dick, 2015)
saturation: Equilibrium activity diagram showing activity ratios and mineral saturation limits (Bowers et al., 1984)
adenine: HKF regression of heat capacity and volume of aqueous adenine (Lowe et al., 2017)
DEW: Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b)
lambda: Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988)
potassium: Comparison of thermodynamic datasets for predicting mineral stabilities (Sverjensky et al., 1991)
TCA: Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016)
aluminum: Reactions involving Al-bearing minerals (Zimmer et al., 2016; Tutolo et al., 2014)
carboxylase: Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase
AD: Dissolved gases: Henry's constant, volume, and heat capacity (Akinfiev and Diamond, 2003)
comproportionation: Gibbs energy of sulfur comproportionation (Amend et al., 2020)
Pourbaix: Eh-pH diagram for Fe-O-H with equisolubility lines (Pourbaix, 1974)
E_coli: Gibbs energy of biomass synthesis in E. coli (LaRowe and Amend, 2016)
rank.affinity: Affinity ranking for proteins in yeast nutrient limitation (data from Tai et al., 2005)
yttrium: logB.to.OBIGT fits at 800 and 1000 bar and Y speciation in NaCl solution at varying pH (Guan et al., 2020)

For either function, if save.png is TRUE, the plots are saved in png files whose names begin with the names of the help topics or demos.

Two of the demos have external dependencies and are not automatically run by demos. ‘⁠dehydration⁠’ creates an interactive SVG file; this demo depends on RSVGTipsDevice, which is not available for Windows. ‘⁠carboxylase⁠’ creates an animated GIF; this demo requires that the ImageMagick convert commmand be available on the system (tested on Linux and Windows).

‘⁠carboxylase⁠’ animates diagrams showing rankings of calculated chemical activities along a combined \T and \logaH2 gradient, or makes a single plot on the default device (without conversion to animated GIF) if a single temperature (T) is specified in the code. To run this demo, an empty directory named ‘⁠png⁠’ must be present (as a subdirectory of the R working directory). The proteins in the calculation are 24 carboxylases from a variety of organisms. There are 12 ribulose phosphate carboxylase and 12 acetyl-coenzyme A carboxylase; 6 of each type are from nominally mesophilic organisms and 6 from nominally thermophilic organisms, shown as blue and red symbols on the diagrams. The activities of hydrogen at each temperature are calculated using \log a_{\mathrm{H_{2}}_{\left(aq\right)}}=-11+3/\left(40\times T\left(^{\circ}C\right)\right); this equation comes from a model of relative stabilities of proteins in a hot-spring environment (Dick and Shock, 2011).

Warning

The discontinuities apparent in the plot made by the NaCl demo illustrate limitations of the "g function" for charged species in the revised HKF model (the 355 \degC boundary of region II in Figure 6 of Shock et al., 1992). Note that SUPCRT92 (Johnson et al., 1992) gives similar output at 500 bar. However, SUPCRT does not output thermodynamic properties above 350 \degC at \Psat; see Warning in subcrt.

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0016-7037(02)01141-9")}

Akinfiev, N. N. and Tagirov, B. R. (2014) Zn in hydrothermal systems: Thermodynamic description of hydroxide, chloride, and hydrosulfide complexes. Geochem. Int. 52, 197–214. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1134/S0016702914030021")}

Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. Geochem. Int. 39, 990–1006.

Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. J. Electrochem. Soc. 148, B51–B57.

Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. Science 281, 1659–1662. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1126/science.281.5383.1659")}

Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiol. Rev. 25, 175–243. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0168-6445(00)00062-0")}

Amend, J. P., Aronson, H. S., Macalady, J. and LaRowe, D. E. (2020) Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. Environ. Microbiol. 22, 1971–1976. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/1462-2920.14982")}

Azadi, M. R., Karrech, A., Attar, M. and Elchalakani, M. (2019) Data analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes. Fluid Phase Equilib. 480, 25-40. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.fluid.2018.10.002")}

Berman, R. G. (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")}

Bowers, T. S., Jackson, K. J. and Helgeson, H. C. (1984) Equilibrium Activity Diagrams for Coexisting Minerals and Aqueous Solutions at Pressures and Temperatures to 5 kb and 600\degC, Springer-Verlag, Berlin, 397 p. https://www.worldcat.org/oclc/11133620

Canovas, P. A., III and Shock, E. L. (2016) Geobiochemistry of metabolism: Standard state thermodynamic properties of the citric acid cycle. Geochim. Cosmochim. Acta 195, 293–322. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2016.08.028")}

Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLOS One 6, e22782. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pone.0022782")}

Dick, J. M. (2015) Chemical integration of proteins in signaling and development. bioRxiv. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/015826")}

Garrels, R. M. and Christ, C. L. (1965) Solutions, Minerals, and Equilibria, Harper & Row, New York, 450 p. https://www.worldcat.org/oclc/517586

Guan, Q., Mei, Y., Etschmann, B., Testemale, D., Louvel, M. and Brugger, J. (2020) Yttrium complexation and hydration in chloride-rich hydrothermal fluids: A combined ab initio molecular dynamics and in situ X-ray absorption spectroscopy study. Geochim. Cosmochim. Acta 281, 168–189. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2020.04.015")}

Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\degC. Comp. Geosci. 18, 899–947. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/0098-3004(92)90029-Q")}

LaRowe, D. E. and Amend, J. P. (2016) The energetics of anabolism in natural settings. ISME J. 10, 1285–1295. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ismej.2015.227")}

Lowe, A. R., Cox, J. S. and Tremaine, P. R. (2017) Thermodynamics of aqueous adenine: Standard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from T = 278.15 K to 393.15 K. J. Chem. Thermodyn. 112, 129–145. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.jct.2017.04.005")}

Lu, P. and Zhu, C. (2011) Arsenic Eh–pH diagrams at 25\degC and 1 bar. Environ. Earth Sci. 62, 1673–1683. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s12665-010-0652-x")}

Manning, C. E., Shock, E. L. and Sverjensky, D. A. (2013) The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: Experimental and theoretical constraints. Rev. Mineral. Geochem. 75, 109–148. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.2138/rmg.2013.75.5")}

Pourbaix, M. (1974) Atlas of Electrochemical Equilibria in Aqueous Solutions, NACE, Houston, TX and CEBELCOR, Brussels. https://www.worldcat.org/oclc/563921897

Schulte, M. D. and Shock, E. L. (1995) Thermodynamics of Strecker synthesis in hydrothermal systems. Orig. Life Evol. Biosph. 25, 161–173. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/BF01581580")}

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. \Sexpr[results=rd]{tools:::Rd_expr_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 \degC and 5 kbar. J. Chem. Soc. Faraday Trans. 88, 803–826. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1039/FT9928800803")}

Stef\aacutensson, A. and Seward, T. M. (2004) Gold(I) complexing in aqueous sulphide solutions to 500\degC at 500 bar. Geochim. Cosmochim. Acta 68, 4121–4143. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2004.04.006")}

Stumm, W. and Morgan, J. J. (1996) Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters, John Wiley & Sons, New York, 1040 p. https://www.worldcat.org/oclc/31754493

Sverjensky, D. A., Harrison, B. and Azzolini, D. (2014a) Water in the deep Earth: The dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200 \degC. Geochim. Cosmochim. Acta 129, 125–145. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2013.12.019")}

Sverjensky, D. A., Hemley, J. J. and D'Angelo, W. M. (1991) Thermodynamic assessment of hydrothermal alkali feldspar-mica-aluminosilicate equilibria. Geochim. Cosmochim. Acta 55, 989-1004. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/0016-7037(91)90157-Z")}

Sverjensky, D. A., Stagno, V. and Huang, F. (2014b) Important role for organic carbon in subduction-zone fluids in the deep carbon cycle. Nat. Geosci. 7, 909–913. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ngeo2291")}

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. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.gca.2014.02.036")}

Williams-Jones, A. E., Bowell, R. J. and Migdisov, A. A. (2009) Gold in solution. Elements 5, 281–287. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.2113/gselements.5.5.281")}

Zimmer, K., Zhang, Y., Lu, P., Chen, Y., Zhang, G., Dalkilic, M. and Zhu, C. (2016) SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Comp. Geosci. 90, 97–111. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cageo.2016.02.013")}