[CHNOSZ-commits] r384 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 7 07:43:10 CET 2019
Author: jedick
Date: 2019-02-07 07:43:08 +0100 (Thu, 07 Feb 2019)
New Revision: 384
Added:
pkg/CHNOSZ/demo/glycinate.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
add metal-glycinate complexes from Azadi et al., 2019 and demo/glycinate.R
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/DESCRIPTION 2019-02-07 06:43:08 UTC (rev 384)
@@ -1,6 +1,6 @@
Date: 2019-02-07
Package: CHNOSZ
-Version: 1.1.3-91
+Version: 1.1.3-92
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/R/examples.R 2019-02-07 06:43:08 UTC (rev 384)
@@ -27,8 +27,8 @@
}
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
- "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "mosaic",
- "copper", "solubility", "gold", "wjd", "bugstab", "Shh", "saturation",
+ "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "glycinate",
+ "mosaic", "copper", "solubility", "gold", "wjd", "bugstab", "Shh", "saturation",
"adenine", "DEW", "lambda", "TCA", "go-IU", "bison"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/data/refs.csv 2019-02-07 06:43:08 UTC (rev 384)
@@ -42,7 +42,7 @@
JUN92,"C. de Capitani",1992,"JUN92.bs database supplied with Theriak/Domino software","data as listed in `JUN92.bs` data file",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
-Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",https://doi.org/10.1016/0016-7037(92)90392-V
+Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine; not present in slop files after slop98.dat",https://doi.org/10.1016/0016-7037(92)90392-V
ZS92,"C. Zhu and D. A. Sverjensky",1982,"Geochim. Cosmochim. Acta 56, 3435-3467","F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of @ZS92; heat capacity and volume parameters from `berman.dat`.",https://doi.org/10.1016/0016-7037(92)90390-5
Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5
Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5
@@ -61,7 +61,7 @@
DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,http://dx.doi.org/10.1016/0016-7037(95)00403-3
AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
AH97b.1,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","alanate and glycinate GHS",https://doi.org/10.1039/A608126F
-AH97b.2,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","glycine and glycinium GHS",https://doi.org/10.1039/A608126F
+AH97b.2,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","glycine, glycinium, and methionine GHS",https://doi.org/10.1039/A608126F
DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
@@ -126,6 +126,7 @@
DLH06.3,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","glycine, [Gly], and [UPBB] HKF parameters",https://doi.org/10.5194/bg-3-311-2006
DLH06.4,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","methionine HKF parameters",https://doi.org/10.5194/bg-3-311-2006
DLH06.5,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","triglycine Cp, V, and HKF c1, c2, omega parameters",https://doi.org/10.5194/bg-3-311-2006
+DLH06.6,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336","[Gly], [Met], and [UPBB]",https://doi.org/10.5194/bg-3-311-2006
LMR06,"D. Langmuir et al.",2006,"Geochim. Cosmochim. Acta 70, 2942-2956","scorodite and amorphous ferric arsenate: G",https://doi.org/10.1016/j.gca.2006.03.006
MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186","coquimbite, ferricopiapite, and rhomboclase",https://doi.org/10.1127/0935-1221/2006/0018-0175
Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, Univ. of California","glutathione, cystine, and cystine sidechain",
@@ -171,9 +172,10 @@
CHNOSZ.1,"J. M. Dick",2017,"CHNOSZ package documentation","GHS (T<sub>r</sub>) of the phase that is stable at 298.15 K was combined with H<sub>tr</sub> and the Cp coefficients to calculate the metastable GHS (T<sub>r</sub>) of the phases that are stable at higher temperatures.",http://chnosz.net
CHNOSZ.3,"J. M. Dick",2017,"CHNOSZ package documentation","metal-amino acid complexes: GHS were recalculated by adding the differences between values from @SK95 and @AH97b for alanate or glycinate to the properties of the complexes reported by @SK95.",http://chnosz.net
CHNOSZ.5,"J. M. Dick",2017,"CHNOSZ package documentation","AuCl4- renamed to AuCl4-3",http://chnosz.net
-CHNOSZ.6,"J. M. Dick",2017,"CHNOSZ package documentation","dipeptides not included in slop files after slop98.dat",http://chnosz.net
CHNOSZ.7,"J. M. Dick",2017,"CHNOSZ package documentation","charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99",http://chnosz.net
CHNOSZ.8,"J. M. Dick",2017,"CHNOSZ package documentation","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.",http://chnosz.net
+CHNOSZ.9,"J. M. Dick",2019,"CHNOSZ package documentation","recalculated values of Cp (those in @AKAE19 appear to be calculated using wrong sign on ω) and enthalpy (using ΔG=ΔH-TΔS and the entropies of the elements)",http://chnosz.net
+CHNOSZ.10,"J. M. Dick",2019,"CHNOSZ package documentation","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: replace Ti with Tl",http://chnosz.net
LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine HKF parameters",https://doi.org/10.1016/j.jct.2017.04.005
DEW17,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","other data from Aqueous Species Table in spreadsheet (see detailed references there)",http://www.dewcommunity.org
DEW17.1,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for ions",http://www.dewcommunity.org
@@ -184,3 +186,4 @@
DEW17.103,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaCl: revised with new predicted a1 for complex species",http://www.dewcommunity.org
DEW17.104,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","propanoate: Revised a1 from new delVn correlation for -1 ions",http://www.dewcommunity.org
BDat17.1,"D. A. Sverjensky et al.",2017,"berman.dat file in SUPCRT92b.zip on the DEW website","antigorite: "Oct. 21, 2016: Revised volume coefficients consistent with @HDR06 and @YIY+14 "",http://www.dewcommunity.org/resources.html
+AKAE19,"M. R. Azadi et al.",2019,"Fluid Phase Equilib. 480, 25-40","metal-glycinate complexes",https://doi.org/10.1016/j.fluid.2018.10.002
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/demo/00Index 2019-02-07 06:43:08 UTC (rev 384)
@@ -10,6 +10,7 @@
buffer Minerals and aqueous species as buffers of hydrogen fugacity
protbuff Chemical activities buffered by thiol peroxidases or sigma factors
yeastgfp Subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams
+glycinate Divalent and monovalent metal-glycinate complexes
mosaic Eh-pH diagram for iron oxides, sulfides and carbonate with two sets of changing basis species
copper Another example of mosaic(): complexation of copper with glycine species
solubility Solubility of calcite and CO2(gas) as a function of pH
Added: pkg/CHNOSZ/demo/glycinate.R
===================================================================
--- pkg/CHNOSZ/demo/glycinate.R (rev 0)
+++ pkg/CHNOSZ/demo/glycinate.R 2019-02-07 06:43:08 UTC (rev 384)
@@ -0,0 +1,67 @@
+# CHNOSZ/demo/glycinate.R
+# plot logK of metal-glycinate complexes
+# 20190207
+
+# divalent metals
+di <- c("Cu+2", "Ni+2", "Co+2", "Mn+2", "Zn+2", "Cd+2")
+# divalent metals with one glycinate
+di1 <- c("Cu(Gly)+", "Ni(Gly)+", "Co(Gly)+", "Mn(Gly)+", "Zn(Gly)+", "Cd(Gly)+")
+# divalent metals with two glycinates
+di2 <- c("Cu(Gly)2", "Ni(Gly)2", "Co(Gly)2", "Mn(Gly)2", "Zn(Gly)2", "Cd(Gly)2")
+# monovalent metals
+mo <- c("Au+", "Ag+", "Na+", "Tl+", "Cu+")
+# monovalent metals with one glycinate
+mo1 <- c("Au(Gly)", "Ag(Gly)", "Na(Gly)", "Tl(Gly)", "Cu(Gly)")
+# monovalent metals with two glycinates
+mo2 <- c("Au(Gly)2-", "Ag(Gly)2-", "Na(Gly)2-", "Tl(Gly)2-", "Cu(Gly)2-")
+
+# set the temperature values
+T <- seq(0, 150, 10)
+# calculate the logKs using data from Azadi et al., 2019
+# doi:10.1016/j.fluid.2018.10.002
+logK_di1 <- logK_di2 <- logK_mo1 <- logK_mo2 <- list()
+for(i in 1:length(di1)) logK_di1[[i]] <- subcrt(c(di[i], "glycinate", di1[i]), c(-1, -1, 1), T = T)$out$logK
+for(i in 1:length(di2)) logK_di2[[i]] <- subcrt(c(di[i], "glycinate", di2[i]), c(-1, -2, 1), T = T)$out$logK
+for(i in 1:length(mo1)) logK_mo1[[i]] <- subcrt(c(mo[i], "glycinate", mo1[i]), c(-1, -1, 1), T = T)$out$logK
+for(i in 1:length(mo2)) logK_mo2[[i]] <- subcrt(c(mo[i], "glycinate", mo2[i]), c(-1, -2, 1), T = T)$out$logK
+
+# calculate the logKs for divalent metals using data from Shock and Koretsky, 1995
+# doi:10.1016/0016-7037(95)00058-8
+add.obigt("OldAA")
+logK_di1_SK95 <- logK_di2_SK95 <- list()
+for(i in 1:length(di1)) logK_di1_SK95[[i]] <- subcrt(c(di[i], "glycinate", di1[i]), c(-1, -1, 1), T = T)$out$logK
+for(i in 1:length(di2)) logK_di2_SK95[[i]] <- subcrt(c(di[i], "glycinate", di2[i]), c(-1, -2, 1), T = T)$out$logK
+data(thermo)
+
+# set up the plots
+layout(matrix(1:6, byrow = TRUE, nrow = 2), widths = c(2, 2, 1))
+par(mar = c(4, 3.2, 2.5, 0.5), mgp = c(2, 1, 0), las = 1, cex = 0.8)
+xlab <- axis.label("T")
+ylab <- axis.label("logK")
+
+# first row: divalent metals
+matplot(T, sapply(logK_di1, c), type = "l", lwd = 2, lty = 1, xlab = xlab, ylab = ylab)
+matplot(T, sapply(logK_di1_SK95, c), type = "l", lwd = 2, lty = 2, add = TRUE)
+legend(-5, 7.7, c("Azadi et al., 2019", "Shock and Koretsky, 1995"), lty = c(1, 2), bty = "n", cex = 1)
+mtext(expression(M^"+2" + Gly^"-" == M*(Gly)^"+"), line = 0.5)
+matplot(T, sapply(logK_di2, c), type = "l", lwd = 2, lty = 1, xlab = xlab, ylab = ylab)
+matplot(T, sapply(logK_di2_SK95, c), type = "l", lwd = 2, lty = 2, add = TRUE)
+legend(-5, 14, c("Azadi et al., 2019", "Shock and Koretsky, 1995"), lty = c(1, 2), bty = "n", cex = 1)
+mtext(expression(M^"+2" + 2*Gly^"-" == M*(Gly)[2]), line = 0.5)
+plot.new()
+par(xpd = NA)
+legend("right", as.expression(lapply(di, expr.species)), lty = 1, col = 1:6, bty = "n", cex = 1.2, lwd = 2)
+
+# add overall title
+text(0, 1, "metal-\nglycinate\ncomplexes", cex = 1.3, font = 2)
+par(xpd = FALSE)
+
+# second row: monovalent metals
+matplot(T, sapply(logK_mo1, c), type = "l", lwd = 2, lty = 1, xlab = xlab, ylab = ylab)
+mtext(expression(M^"+" + Gly^"-" == M*(Gly)), line = 0.5)
+matplot(T, sapply(logK_mo2, c), type = "l", lwd = 2, lty = 1, xlab = xlab, ylab = ylab)
+mtext(expression(M^"+" + 2*Gly^"-" == M*(Gly)[2]^"-"), line = 0.5)
+plot.new()
+par(xpd = NA)
+legend("right", as.expression(lapply(mo, expr.species)), lty = 1, col = 1:5, bty = "n", cex = 1.2, lwd = 2)
+par(xpd = FALSE)
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/inst/NEWS 2019-02-07 06:43:08 UTC (rev 384)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-91 (2019-02-07)
+CHANGES IN CHNOSZ 1.1.3-92 (2019-02-07)
---------------------------------------
BUG FIXES
@@ -101,6 +101,9 @@
limits for calcite, dolomite, magnesite, and brucite in the
H2O-CO2-CaO-MgO-SiO2 system.
+- Add demo/glycinate.R showing logK of complexation of glycinate with
+ divalent and monovalent metals.
+
THERMODYNAMIC DATA
- The Berman data (Berman, 1988 and later additions) have replaced the
@@ -170,9 +173,13 @@
ions), and diketopiperazine, [Gly] and [UPBB] groups from Kitadai,
2014.
+- Add data for metal-glycinate complexes from Azadi et al., 2019,
+ superseding Shock and Koretsky, 1995.
+
- For reproducing previous calculations, superseded data for [Gly] and
[UPBB], as well as [Met] (earlier superseded by LaRowe and Dick,
- 2012), have been moved to OBIGT/OldAA.csv.
+ 2012), and metal-glycinate complexes have been moved to
+ OBIGT/OldAA.csv.
DIAGRAMS
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv 2019-02-07 06:43:08 UTC (rev 384)
@@ -1,14 +1,14 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-alanylglycine,NA,C5H10N2O3,aq,Sho92,CHNOSZ.6,28.Feb.92,-116730,-186110,50.7,60.3,95.22,14.6503,21.164,12.0751,-3.6538,54.7374,0.7979,-0.4278,0
-leucylglycine,NA,C8H16N2O3,aq,Sho92,CHNOSZ.6,27.Aug.06,-110620,-202660,72.6,118.8,145.34,21.3967,34.6501,13.1805,-4.2113,98.6389,6.4783,-0.7594,0
-diglycine,NA,C4H8N2O3,aq,Sho92,CHNOSZ.6,28.Feb.92,-117020,-175640,54.2,38,76.27,12.0393,15.9447,11.6466,-3.4381,36.349,-1.3673,-0.4808,0
-diketopiperazine,NA,C4H6N2O2,aq,Sho92,CHNOSZ.6,28.Feb.92,-57440,-99300,53.5,17,76.73,12.1058,16.0764,11.6608,-3.4435,19.5904,-3.4064,-0.4702,0
-glycine,Gly,C2H5NO2,aq,"AH97b.2 [S07]","DLH06.1 [S07]",25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0
-glycinium,Gly+,C2H6NO2+,aq,"AH97b.2 [S07]","DLH06.1 [S07]",25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0
-methionine,Met,C5H11NO2S,aq,AH97b,DLH06,25.Aug.06,-120120,-178520,62.36,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
-[Gly],NA,H,aq,"DLH06 [S15]",NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0
-[Met],NA,C3H7S,aq,DLH06,NA,25.Aug.06,-35245,-59310,40.38,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
-[UPBB],NA,C2H2NO,aq,"DLH06 [S15]",NA,25.Aug.06,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0
+alanylglycine,NA,C5H10N2O3,aq,Sho92 [S98],NA,28.Feb.92,-116730,-186110,50.7,60.3,95.22,14.6503,21.164,12.0751,-3.6538,54.7374,0.7979,-0.4278,0
+leucylglycine,NA,C8H16N2O3,aq,Sho92 [S98],NA,27.Aug.06,-110620,-202660,72.6,118.8,145.34,21.3967,34.6501,13.1805,-4.2113,98.6389,6.4783,-0.7594,0
+diglycine,NA,C4H8N2O3,aq,Sho92 [S98],NA,28.Feb.92,-117020,-175640,54.2,38,76.27,12.0393,15.9447,11.6466,-3.4381,36.349,-1.3673,-0.4808,0
+diketopiperazine,NA,C4H6N2O2,aq,Sho92 [S98],NA,28.Feb.92,-57440,-99300,53.5,17,76.73,12.1058,16.0764,11.6608,-3.4435,19.5904,-3.4064,-0.4702,0
+glycine,Gly,C2H5NO2,aq,AH97b.2,DLH06.1,25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0
+glycinium,Gly+,C2H6NO2+,aq,AH97b.2,DLH06.1,25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0
+methionine,Met,C5H11NO2S,aq,AH97b.2,DLH06.1,25.Aug.06,-120120,-178520,62.36,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
+[Gly],NA,H,aq,DLH06.6,NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0
+[Met],NA,C3H7S,aq,DLH06.6,NA,25.Aug.06,-35245,-59310,40.38,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
+[UPBB],NA,C2H2NO,aq,DLH06.6,NA,25.Aug.06,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0
alanate,NA,C3H6NO2-,aq,"SK95.1 [S98]",AH97b.1,3.Sep.06,-75360,-121470,30.71,17.8,61.88,10.6281,17.3648,0.6505,-3.4968,12.685,-4.1859,1.17,-1
glycinate,NA,C2H4NO2-,aq,"SK95.1 [S98]",AH97b.1,3.Sep.06,-77610,-114190,30.07,-6.6,43.77,8.1592,11.7696,1.921,-3.2655,12.9389,-4.1859,1.1975,-1
Ca(Gly)+,NA,Ca(C2H4NO2)+,aq,"SK95.1 [S98]",CHNOSZ.3,3.Sep.06,-211570,-240519,34.375,59.3,32.6,6.2431,7.4595,2.8241,-3.0873,41.4246,9.0464,0.0543,1
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv.xz 2019-02-07 06:43:08 UTC (rev 384)
@@ -1,4 +1,4 @@
-ý7zXZ æÖ´F ! t/å£à¢ò0] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù ¦cL; ù"ß“<²ëbï¨gò;ø¥K䇥Šfœ‘1Æw?oz†ÆCþaì]IØŽ¨Ý5i‡*U9œ—X‘×0wã±t GƒØꪥáýA¢æ‰Yo|Û¥XQ$š{ÃÏ16¦\O¯]x¡˜t % È~ žA2Ké¹¾2õ
+ý7zXZ æÖ´F ! t/å£à¯u4 ] 7Iýúb‹¿ñ9²¶Ë¦¨•TB;qý"½qù ¦cL; ù"ß“<²ëbï¨gò;ø¥K䇥Šfœ‘1Æw?oz†ÆCþaì]IØŽ¨Ý5i‡*U9œ—X‘×0wã±t GƒØꪥáýA¢æ‰Yo|Û¥XQ$š{ÃÏ16¦\O¯]x¡˜t % È~ žA2Ké¹¾2õ
MöÜØëÏuÛ2CŒûÄíl,Úó̉ßÿß ðõë>I“,t¿bßPK“ä7t(emA-PÄQÀ]Æå ›·8Ó.fø|šöÛ©–V[ŒÖ΃è=ÍñK¸®ŸÿVTmÚ~vwÓ
æ2/ ѺWaÓás¼-×ú‚¢Îp÷lVsýáêÕH˜¬ßuÔ˜ÑÍ ´%²XFöîk#ÅéêÁ£‹èÿ»+ÒÇ(ë¬m5’St5”FaÉa˜jNч8®à€>zÄÑ°3MwS%Ò°ÛÚøî+Ú3x¨Ù`cw`¤; $ˆ (‘ú¼ý˜‘P„> ’ºµ•>ò1b¿ºòQAÊáîÈç?>6o©=Ñ-¥((äŠpNÚÊÄiéä¹ÒVOL·A®˜ï9 c»E3ñÂXPœ ¸ ¾¼kjsÌóíÔ¢Y!&oÀªw(Ò•3³+ƒ"îÕÖÈ–ò; ±£R6eWë’Î![˼îör¿O>O»<¹‡ÕÆË&œÔºYÙ ² r |¸¡à‘kzí:$’6"&x´½{D71Ÿt\Z’²8dwï>*ˆh\t½”€tyï‚)BÿîêÂn<ç9lÓN!3ŒÏÙz ' ú}Üí±nVº,0uVeå ÈÜ›¼¤
j ò–˜×Þ|Bƒ´d^7&KK¾-
@@ -88,4 +88,11 @@
úÚ±^Vö¤4‡-o¬ ½”K{¸´ÚÝÅ÷1<7É
cŒO_´®2Á¾ƒ &r.w
ü ÷³èÀ#F5ÕV<ùËzñŠ\>¶v}8…â@ò™t·é°§a…±Ñ ¿Ò'@½µ;å÷?e3¬ÂžF±@m}Æ+/¦ºu*…|0Õ]ãM×=Õ¾Ù; eu+ËŸ]åÔ%âÞÙü®!d"ý϶¶À˜.Ë úô€8… —î‰nŒÒžè)«®DÀMñ?
-D‹’×EŸÓ;y9Ô Ë.¡Å—¹‡‡ Üäo;[Ùì¹5K‰äVæÜÍ4Y (å^|…È`¦Á•¡`žå¢Æö3ë {IƒÓ¹ú,Î:©½w?WÈOpÈ÷Ì-1Æøb^¬½ü×Å=ú Ô²áOÈ*ŒYmEUu§ãŽ˜ÿ«ýÝÝ\ EÁ`¾ÁZt8g“¿5nåÒ×1ýò˜ Mg#˜·lÅ .œÉšnë‘ŽÐÈ+ pOYEâvàÅf°íu4uV}J–i×›èE¹w¼y`ömß÷Ã9ma¢iø½šÄÐÝo›¾R»>¤&f7Ö¼;»úЬÉå=lïHØ¡³&E…Ò&L —(ľËûL†4É¡½»(¦dƒ£½IºÎN-/Eï‚bƒ9†Ý:ôädÑŽ 6Dl ÊóØŠÓ"_;o’ž™s¦wq½™vµ0‚_Û¥?_%è WÉñ’ñ– ³`óÅ +M¸÷±Ägû YZ
\ No newline at end of file
+D‹’×EŸÓ;y9Ô Ë.¡Å—¹‡‡ Üäo;[Ùì¹5K‰äVæÜÍ4Y (å^|…È`¦Á•¡`žå¢Æö3ë {IƒÓ¹ú,Î:©½w?WÈOpÈ÷Ì-1Æøb^¬½ü×Å=ú Ô²áOÈ*ŒYmEUu§ãŽ˜ÿ«ýÝÝ\ EÁ`¾ÁZt8g“¿5nåÒ×1ýò˜ Mg#˜·lÅ .œÉšnë‘ŽÐÈ+ pOYEâvàÅf°íu4uV}J–i×›èE¹w¼y`ömß÷Ã9ma¢iø½šÄÐÝo›¾R»>¤&f7Ö¼;»úЬÉå=lïHØ¡³&E…Ò&L —(ľËûL†4É¡½»(¦dƒ£½IºÎN-/Eï‚bƒ9†Ý:ôädÑŽ 6Dl ÊóØŠÓ"_;o’ž™s¦wq½™vµ0‚_Û¥Cm{ßê¶)PiTë
+UÃÍ°-‹*˧]Ãœd]=ù¶ WP
+«#§½Í5}x$Š®?˜£bûAkòÞæ9±ê‘È4ýͪµôsä§GbAióͼ²ÅŒ Im»‡to±ñsQú3~$Ñ?€“²½tOä+Øu#FkŠ:¥áÝé <0jXÒóÉ‹P(ùØý2fõþ½Ÿ!F’å‰Ê‚ß!äÅÏñ‹áÇ» âÁ‹—֪ܯ†½lÆœ¸tE¬Æ‹\¯¾†¯%Ø©Ç]ÿÁ[fa¾˜wû™sì}]tŒù5zw—tªV?åäNÅ-ÄÊ¿8ØT;Eõo/R ¢| Iyó¯Oßžö¾‡å6Y°Äf?€þgÏÅœ%JjÕyý˓жö°IÄ®{(1FÛ•ª§×p_pŸ8iyEÐgõ&¨u_š³2²³Ç}’Ú£‘â„.ýÀ/]¨ ©V‘Ó`DFj˜nÓ[ûPÅ6!€YÜت³Æ,<Û™_ÁxMò𪮠#‚´;QTÍÖ¡ñ‡Y k㻓Í2œ˜5~-$-µSº˜¥
+·`ú‚
+¿;†Ì!®zÖûò{¢çÿ>ú}C¾=¢ñ&:Õ:Âãµ}Búx²$“Á¤‡FËè˜fèÆqwY¡©!ò ^çúPœaÑ
+2æÈ ˆÙJö¨½HÊp¾¿ø€}ölð}p¾4Pù ²Úß؃î¬h,½¸˜VPn«i.ìÛsyM ’˜£÷@*å¤~€ò¥˜œ´§ qe'½GÏ€ã/]¼viZÖ`q”ð¶aC,Þµ¸tÒ[°Bg{aìž-ŧÂü«B*‘<½ªãX) w;q1 “RâÊž"™íSêDçÅ'O´Rj(iª¢Ì“A Öäf¼¢æð\Ä žºÙˆ¾ýÝg1‘|pFÎ Ž
+¸V´äXãß‹³ˆÂ*Ëy—gÔ¯/»&E\2CçûÓÂuƒðï
+¡BJ–vÊŽX ªß ¨½ *‹È ºª|m§>_^i줆=E÷êÎ.°L TfçV9¾ QÊò'e’§[OëÁ̶ók<ÙwœkZ 'õ®#ñ2*w‚¸_c߀nè('˜Aè ](6½ùÙå©ÞÛ¬ Tg~Ô®¸nö,0Ф¢Æžƒ½¤66Ä!¨M FÀÈ;9L7òW£œ¤ˆ™†EŽoè "™3HY²ºÔtQ®Mã"‚&f#’· \6ã±åOã”YÆÕ:G=î-MÁrÿ,™A¾ãA-ÍÔwV8[…pQò¶ÞR×8(ñÝ ’Õ¥RâuÆIcLvÙ¿¸b1>x£yçÔ3Ø<$ ÛÏÒf_ŒÊ·š¡Dð‹>k<¥ ´ îªèÏ ºhöÞ ëjDZÄgû YZ
\ No newline at end of file
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/man/examples.Rd 2019-02-07 06:43:08 UTC (rev 384)
@@ -15,8 +15,8 @@
examples(save.png = FALSE)
demos(which = c("sources", "protein.equil", "affinity", "NaCl",
"density", "ORP", "revisit", "findit", "ionize", "buffer",
- "protbuff", "yeastgfp", "mosaic", "copper", "solubility",
- "gold", "wjd", "bugstab", "Shh", "saturation",
+ "protbuff", "yeastgfp", "glycinate", "mosaic", "copper",
+ "solubility", "gold", "wjd", "bugstab", "Shh", "saturation",
"adenine", "DEW", "lambda", "TCA", "go-IU", "bison"),
save.png=FALSE)
}
@@ -43,6 +43,7 @@
\code{buffer} \tab * Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr
\code{protbuff} \tab Chemical activities buffered by thiol peroxidases or sigma factors \cr
\code{yeastgfp} \tab * Subcellular locations: \logfO2 - \logaH2O and \loga - \logfO2 diagrams (Dick, 2009) \cr
+ \code{glycinate} \tab * Divalent and monovalent metal-glycinate complexes (Azadi et al., 2019) \cr
\code{mosaic} \tab * Eh-pH diagram with two sets of changing basis species (Garrels and Christ, 1965) \cr
\code{copper} \tab * Another example of \code{\link{mosaic}}: complexation of Cu with glycine (Aksu and Doyle, 2001) \cr
\code{solubility} \tab * Solubility of calcite (cf. Manning et al., 2013) and \CO2 (cf. Stumm and Morgan, 1996) \cr
@@ -88,6 +89,8 @@
Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. \emph{FEMS Microbiol. Rev.} \bold{25}, 175--243. \url{https://doi.org/10.1016/S0168-6445(00)00062-0}
+Azadi, M. R., Karrech, A., Attar, M. and Elchalakani, M. (2019) Data analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes. \emph{Fluid Phase Equilib.} \bold{480}, 25-40. \url{https://doi.org/10.1016/j.fluid.2018.10.002}
+
Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
Bowers, T. S., Jackson, K. J. and Helgeson, H. C. (1984) \emph{Equilibrium Activity Diagrams for Coexisting Minerals and Aqueous Solutions at Pressures and Temperatures to 5 kb and 600\degC}, Springer-Verlag, Berlin, 397 p. \url{http://www.worldcat.org/oclc/11133620}
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2019-02-07 06:43:08 UTC (rev 384)
@@ -235,7 +235,7 @@
### `r setfile("SLOP98.csv")`
```{r SLOP98, results="asis", echo=FALSE}
-cat('These species, taken from the slop98 data file, were present in earlier versions of CHNOSZ but have been replaced by or are inconsistent with later updates. The data are kept here for comparative purposes. Use <span style="color:red">`add.obigt("SLOP98")`</span> to load the data.\n\n')
+cat('These species, taken from the slop98 data file, were present in earlier versions of CHNOSZ but have been replaced by or are incompatible with later updates. The data are kept here for comparative purposes. Use <span style="color:red">`add.obigt("SLOP98")`</span> to load the data.\n\n')
```
```{r optreflist, results="asis", echo=FALSE}
@@ -243,7 +243,7 @@
### `r setfile("OldAA.csv")`
```{r OldAA, results="asis", echo=FALSE}
-cat('Data for these amino acids and related species were present in earlier versions of CHNOSZ but have been replaced by or are inconsistent with later updates [@Kit14]. The data are kept here to reproduce published calculations and for comparison with newer data. Use <span style="color:red">`add.obigt("OldAA")`</span> to load the data.\n\n')
+cat('Data for these amino acids and related species were present in earlier versions of CHNOSZ but have been replaced by or are incompatible with later updates [@LD12; @Kit14; @AKAE19]. The data are kept here to reproduce published calculations and for comparison with newer data. Use <span style="color:red">`add.obigt("OldAA")`</span> to load the data.\n\n')
```
```{r optreflist, results="asis", echo=FALSE}
Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib 2019-02-07 01:19:55 UTC (rev 383)
+++ pkg/CHNOSZ/vignettes/obigt.bib 2019-02-07 06:43:08 UTC (rev 384)
@@ -272,7 +272,6 @@
doi = {10.1007/s00239-014-9616-1},
issn = {0022-2844},
language = {English},
- publisher = {Springer US},
}
@Article{LD12,
@@ -1260,6 +1259,17 @@
url = {http://www.ingentaconnect.com/content/10.1127/0935-1221/2010/0022-2021},
}
+ at Article{AKAE19,
+ author = {M.R. Azadi and A. Karrech and M. Attar and M. Elchalakani},
+ journal = {Fluid Phase Equilibria},
+ title = {{D}ata analysis and estimation of thermodynamic properties of aqueous monovalent metal-glycinate complexes},
+ year = {2019},
+ volume = {480},
+ pages = {25--40},
+ doi = {10.1016/j.fluid.2018.10.002},
+ issn = {0378-3812},
+}
+
@Article{AZ10,
author = {Akinfiev, N. N. and Zotov, A. V.},
journal = {Geochemistry International},
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