[CHNOSZ-commits] r664 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Apr 7 06:19:47 CEST 2021 

Author: jedick
Date: 2021-04-07 06:19:46 +0200 (Wed, 07 Apr 2021)
New Revision: 664

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
   pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
Log:
Recalculate parameters for some species from LA16


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2021-03-22 23:43:04 UTC (rev 663)
+++ pkg/CHNOSZ/DESCRIPTION	2021-04-07 04:19:46 UTC (rev 664)
@@ -1,6 +1,6 @@
-Date: 2021-03-22
+Date: 2021-04-07
 Package: CHNOSZ
-Version: 1.4.0-33
+Version: 1.4.0-34
 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/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2021-03-22 23:43:04 UTC (rev 663)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2021-04-07 04:19:46 UTC (rev 664)
@@ -38,9 +38,9 @@
       \item \samp{OBIGT/Berman_cr.csv}: Use standard abbreviations for hematite
       (Hem) and magnetite (Mag).
 
-      \item \samp{OBIGT/organic_aq.csv}: Add properties of aqueous fatty acids
-      and saccharides and add associated \samp{demo/E_coli.R} (Gibbs energy of
-      biomass synthesis in \emph{E. coli}, after
+      \item \samp{OBIGT/organic_aq.csv}: Add properties of aqueous fatty acids,
+      saccharides, and other species, and add associated \samp{demo/E_coli.R}
+      (Gibbs energy of biomass synthesis in \emph{E. coli}, after
       \href{https://doi.org/10.1038/ismej.2015.227}{LaRowe and Amend, 2016}).
 
       \item \samp{OBIGT/inorganic_aq.csv}: Add properties of aqueous Nb and Ta

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv	2021-03-22 23:43:04 UTC (rev 663)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv	2021-04-07 04:19:46 UTC (rev 664)
@@ -192,7 +192,7 @@
 "succinic acid",NA,C4H6O4,aq,Sho95,NA,1992-02-28,cal,-177800,-218000,62.3,53.3,82.44,12.9872,22.7109,-0.5623,-3.7178,51.074,0.305,-0.1744,0
 "glutaric acid",NA,C5H8O4,aq,Sho95,NA,1992-02-28,cal,-176780,-223440,73.2,64.1,98.98,15.2749,27.8946,-1.7361,-3.9321,60.3712,1.3721,-0.1021,0
 "adipic acid",NA,C6H10O4,aq,Sho95,SLOP16.4,1998-06-02,cal,-175740,-229750,81.3,80.1,115.15,17.5058,32.9525,-2.8895,-4.1412,73.6536,2.9529,-0.0484,0
-"pimelic acid",NA,C7H12O4,aq,Sho95,NA,1998-06-02,cal,-172380,-253720,89.1,98,131.93,19.8194,38.1932,-4.0727,-4.3578,88.4361,4.7214,0.0033,0
+"pimelic acid",NA,C7H12O4,aq,Sho95,NA,1998-06-02,cal,-172380,-233720,89.1,98,131.93,19.8194,38.1932,-4.0727,-4.3578,88.4361,4.7214,0.0033,0
 "suberic acid",NA,C8H14O4,aq,Sho95,NA,1992-06-16,cal,-168490,-237760,95.1,122.6,146,21.7582,42.5872,-5.0703,-4.5395,108.4636,7.1519,0.0431,0
 "azelaic acid",NA,C9H16O4,aq,Sho95,NA,1992-06-16,cal,-163660,-240700,101.6,143.8,161.8,23.9348,47.5253,-6.2031,-4.7436,125.8045,9.2464,0.0862,0
 "sebacic acid",NA,C10H18O4,aq,Sho95,NA,1992-06-16,cal,-161240,-246000,108.3,165,177.6,26.1119,52.4558,-7.3146,-4.9474,143.1573,11.341,0.1306,0
@@ -692,6 +692,6 @@
 N-acetylglucosamine,NA,C8H15NO6,aq,LA16,NA,2021-03-16,J,-918200,-1329000,358.2,NA,NA,144.1,40.5,36.1,-33.7,570,-58.6,0.8,0
 "N-acetylmuramic acid",NA,C11H17NO8,aq,LA16,NA,2021-03-16,J,-1272400,-1789500,485.4,NA,NA,185.8,57.1,64.7,-48,685,-55.7,0.3,0
 ethanolamine,NA,C2H7NO,aq,LA16,NA,2021-03-16,J,-138300,-281000,173.2,NA,NA,47.7,26.4,52.4,-18.3,218,-6.7,-1,0
-"diaminopimelic acid",NA,C7H14N2O4,aq,LA16,NA,2021-03-16,J,-673500,-925900,347.2,NA,NA,59.7,145.2,-10.5,-13.3,215,-6.6,-0.4,0
-putrescine,NA,C4H12N2,aq,LA16,NA,2021-03-16,J,48200,-99500,140.5,NA,NA,52.4,33.5,65.6,-25.4,242,8.8,-0.8,0
-spermidine,NA,C7H19N3,aq,LA16,NA,2021-03-16,J,114900,-170500,248.7,NA,NA,96.2,61,127.5,-49.8,420,19.2,-1.4,0
+"diaminopimelic acid",NA,C7H14N2O4,aq,LA16,OBIGT.9,2021-04-07,J,-644060,-977667,436.9,111.5,142.7,92.1,131.5,-37.7,12.2,276.1,-72.5,1.9,0
+putrescine,NA,C4H12N2,aq,LA16,OBIGT.9,2021-04-07,J,77630,-151478,230.2,268,93.9,83.1,26,38.6,-9.5,321.9,-29.4,-0.6,0
+spermidine,NA,C7H19N3,aq,LA16,OBIGT.9,2021-04-07,J,144361,-222539,338.4,378.6,147.4,130.8,38.8,67,-15.6,465.6,-46.7,-0.8,0

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2021-03-22 23:43:04 UTC (rev 663)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv	2021-04-07 04:19:46 UTC (rev 664)
@@ -202,7 +202,7 @@
 SHA14.3,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","Fitted to @HP97 data with a<sub>1</sub> pred. from the sum of the ions and used to predict the volume",https://doi.org/10.1016/j.gca.2013.12.019
 SHA14.4,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","BO<sub>2</sub><sup>-</sup>: revised a<sub>1</sub>-a<sub>4</sub> using delkappan for BO<sub>2</sub><sup>-</sup> instead of B(OH)<sub>4</sub><sup>-</sup> used by @SH88; @SSWS97",https://doi.org/10.1016/j.gca.2013.12.019
 PD15,"G. S. Pokrovski and J. Dubessy",2015,"Earth Planet. Sci. Lett. 411, 298-309","trisulfur radical ion",https://doi.org/10.1016/j.epsl.2014.11.035
-LA16,"D. E. LaRowe and J. P. Amend",2016,"ISME J. 10, 1285-1295","fatty acids and saccharides",https://doi.org/10.1038/ismej.2015.227
+LA16,"D. E. LaRowe and J. P. Amend",2016,"ISME J. 10, 1285-1295","fatty acids, saccharides, and other species",https://doi.org/10.1038/ismej.2015.227
 SLOP16.1,"E. L. Shock et al.",2016,"slop16.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",https://doi.org/10.5281/zenodo.2630820
 SLOP16.2,"E. L. Shock et al.",2016,"slop16.dat computer data file","Zn(Ac)<sub>3</sub><sup>-</sup>: "Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements. See footnote h in table 2 of @SSH97."",https://doi.org/10.5281/zenodo.2630820
 SLOP16.3,"E. L. Shock et al.",2016,"slop16.dat computer data file","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 @SS93."",https://doi.org/10.5281/zenodo.2630820
@@ -225,6 +225,7 @@
 OBIGT.6,"J. M. Dick",2019,"OBIGT database in CHNOSZ","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
 OBIGT.7,"J. M. Dick",2019,"OBIGT database in CHNOSZ","Tl(Gly) and Tl(Gly)<sub>2</sub><sup>-</sup>: change Ti to Tl",http://chnosz.net
 OBIGT.8,"J. M. Dick",2019,"OBIGT database in CHNOSZ","GHS recalculated by adding difference from SiO<sub>2</sub> [@SSH97] to updated values for SiO<sub>2</sub> [@AS04]",http://chnosz.net
+OBIGT.9,"J. M. Dick",2021,"OBIGT database in CHNOSZ","diaminopimelic acid, putrescine and spermidine: parameters recalculated to account for a missing [-CH2NH2] group in the group additivity equations",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
 DEW17.01,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(acetic acid, glycine, methanol, propanoic acid, propanol: parameters in DEW spreadsheet are the same as in @PS01)",http://www.dewcommunity.org
 DEW17.02,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","(ethanol: parameters in DEW spreadsheet are different from @PS01; no comment provided)",http://www.dewcommunity.org

Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2021-03-22 23:43:04 UTC (rev 663)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv	2021-04-07 04:19:46 UTC (rev 664)
@@ -136,7 +136,6 @@
 "OBIGT",1013,"Ce(Ac)2+","aq","cal",,,567
 "OBIGT",1041,"urea","aq","cal",-23.26,23.32,
 "OBIGT",1054,"propanoic acid","aq","cal",1.42,,
-"OBIGT",1073,"pimelic acid","aq","cal",,,-19931
 "OBIGT",1077,"formate","aq","cal",1.96,,
 "OBIGT",1079,"propanoate","aq","cal",1.68,,
 "OBIGT",1086,"n-decanoate","aq","cal",-1.93,,
@@ -240,9 +239,6 @@
 "OBIGT",1567,"heptose","aq","J",,,-75027
 "OBIGT",1571,"N-acetylmuramic acid","aq","J",,,-38589
 "OBIGT",1572,"ethanolamine","aq","J",,,4598
-"OBIGT",1573,"diaminopimelic acid","aq","J",,,108258
-"OBIGT",1574,"putrescine","aq","J",,,108157
-"OBIGT",1575,"spermidine","aq","J",,,108263
 "OBIGT",1584,"cysteinate","aq","cal",-1,,
 "OBIGT",1610,"glucose","aq","cal",1.11,,
 "OBIGT",1638,"guanine","aq","cal",-4.26,,

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