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[3] diagram (1 variable)

## Don't show: data(thermo)
thermo$obigt: 1809 aqueous, 3368 total species
## End(Don't show) ### 1-D diagrams: logarithms of activities ## Aqueous sulfur species (after Seewald, 1997 and 2001) basis("CHNOS+")
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 69 -3 aq H2O 0 2 0 1 0 0 1 0 liq NH3 0 3 1 0 0 0 68 -4 aq H2S 0 2 0 0 1 0 70 -7 aq O2 0 0 0 2 0 0 3095 -80 gas H+ 0 1 0 0 0 1 3 -7 aq
basis("pH", 5)
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 69 -3 aq H2O 0 2 0 1 0 0 1 0 liq NH3 0 3 1 0 0 0 68 -4 aq H2S 0 2 0 0 1 0 70 -7 aq O2 0 0 0 2 0 0 3095 -80 gas H+ 0 1 0 0 0 1 3 -5 aq
species(c("H2S", "S2-2", "S3-2", "S2O3-2", "S2O4-2", "S3O6-2", "S5O6-2", "S2O6-2", "HSO3-", "SO2", "HSO4-"))
CO2 H2O NH3 H2S O2 H+ ispecies logact state name 1 0 0 0 1 0.0 0 70 -3 aq H2S 2 0 -1 0 2 0.5 -2 53 -3 aq S2-2 3 0 -2 0 3 1.0 -2 54 -3 aq S3-2 4 0 -1 0 2 2.0 -2 26 -3 aq S2O3-2 5 0 -1 0 2 2.5 -2 1072 -3 aq S2O4-2 6 0 -2 0 3 4.0 -2 1077 -3 aq S3O6-2 7 0 -4 0 5 5.0 -2 1079 -3 aq S5O6-2 8 0 -1 0 2 3.5 -2 1076 -3 aq S2O6-2 9 0 0 0 1 1.5 -1 23 -3 aq HSO3- 10 0 -1 0 1 1.5 0 78 -3 aq SO2 11 0 0 0 1 2.0 -1 25 -3 aq HSO4-
a <- affinity(O2=c(-50, -15), T=325, P=350)
energy.args: temperature is 325 C energy.args: pressure is 350 bar energy.args: variable 1 is log_f(O2) at 128 values from -50 to -15 subcrt: 17 species at 598.15 K and 350 bar (wet)
e <- equilibrate(a, loga.balance=-2)
balance: coefficients are moles of H2S in formation reactions equilibrate: balancing coefficients are 1 2 3 2 2 3 5 2 1 1 1 equilibrate: logarithm of total moles of H2S (from loga.balance) is -2
diagram(e, ylim=c(-30, 0), legend.x="topleft") title(main=paste("Aqueous sulfur speciation, 325 degC, 350 bar\n", "After Seewald, 1997"))

Image diagram1

 

# try it with and without the loga.balance argument (total activity of # the balanced quantity, in this case H2S aka sulfur) ## Degrees of formation of ionized forms of glycine ## After Fig. 1 of Aksu and Doyle, 2001 basis("CHNOS+")
C H N O S Z ispecies logact state CO2 1 0 0 2 0 0 69 -3 aq H2O 0 2 0 1 0 0 1 0 liq NH3 0 3 1 0 0 0 68 -4 aq H2S 0 2 0 0 1 0 70 -7 aq O2 0 0 0 2 0 0 3095 -80 gas H+ 0 1 0 0 0 1 3 -7 aq
species(ispecies <- info(c("glycinium", "glycine", "glycinate")))
info.character: found glycine(aq), also available in cr CO2 H2O NH3 H2S O2 H+ ispecies logact state name 1 2 1 1 0 -1.5 1 1517 -3 aq glycinium 2 2 1 1 0 -1.5 0 1516 -3 aq glycine 3 2 1 1 0 -1.5 -1 592 -3 aq glycinate
a <- affinity(pH=c(0, 14))
energy.args: temperature is 25 C energy.args: pressure is Psat energy.args: variable 1 is pH at 128 values from 0 to 14 subcrt: 9 species at 298.15 K and 1 bar (wet)
e <- equilibrate(a)
balance: coefficients are moles of CO2 in formation reactions equilibrate: balancing coefficients are 2 2 2 equilibrate: logarithm of total moles of CO2 is -2.22184874961636
diagram(e, alpha=TRUE, lwd=1) title(main=paste("Degrees of formation of aqueous glycine species\n", "after Aksu and Doyle, 2001"))

Image diagram2

 

## Degrees of formation of ATP species as a function of ## temperature, after LaRowe and Helgeson, 2007, Fig. 10b # to make a similar diagram, activity of Mg+2 here is set to # 10^-4, which is different from LH07, who used 10^-3 total molality basis(c("CO2", "NH3", "H2O", "H3PO4", "O2", "H+", "Mg+2"), c(999, 999, 999, 999, 999, -5, -4))
C H Mg N O P Z ispecies logact state CO2 1 0 0 0 2 0 0 69 999 aq NH3 0 3 0 1 0 0 0 68 999 aq H2O 0 2 0 0 1 0 0 1 999 liq H3PO4 0 3 0 0 4 1 0 73 999 aq O2 0 0 0 0 2 0 0 67 999 aq H+ 0 1 0 0 0 0 1 3 -5 aq Mg+2 0 0 1 0 0 0 2 9 -4 aq
species(c("HATP-3", "H2ATP-2", "MgATP-2", "MgHATP-"))
CO2 NH3 H2O H3PO4 O2 H+ Mg+2 ispecies logact state name 1 10 5 -4 3 -7.5 -3 0 1666 -3 aq HATP-3 2 10 5 -4 3 -7.5 -2 0 1667 -3 aq H2ATP-2 3 10 5 -4 3 -7.5 -4 1 1723 -3 aq MgATP-2 4 10 5 -4 3 -7.5 -3 1 1724 -3 aq MgHATP-
a <- affinity(T=c(0, 120, 25))
energy.args: pressure is Psat energy.args: variable 1 is T at 25 values from 273.15 to 393.15 K subcrt: 11 species at 25 values of T and P (wet)
e <- equilibrate(a)
balance: coefficients are moles of CO2 in formation reactions equilibrate: balancing coefficients are 10 10 10 10 equilibrate: logarithm of total moles of CO2 is -1.39794000867204
diagram(e, alpha=TRUE) title(main=paste("Degrees of formation of ATP species,\n", "pH=5, log(aMg+2)=-3. After LaRowe and Helgeson, 2007"), cex.main=0.9)

Image diagram3

 


next up previous
Next: [4] diagram (2 variables) Up: CHNOSZ examples Previous: equil.boltzmann