[3] diagram (lines)

## Don't show: data(thermo)
thermo$obigt: 1911 aqueous, 3588 total species
## End(Don't show) ## calculate the equilibrium logarithm of activity of a ## basis species in different reactions basis("CHNOS")
C H N O S ispecies logact state CO2 1 0 0 2 0 1576 -3 aq H2O 0 2 0 1 0 1 0 liq NH3 0 3 1 0 0 66 -4 aq H2S 0 2 0 0 1 67 -7 aq O2 0 0 0 2 0 3316 -80 gas
species(c("ethanol", "lactic acid", "deoxyribose", "ribose"))
CO2 H2O NH3 H2S O2 ispecies logact state name 1 2 3 0 0 -3.0 890 -3 aq ethanol 2 3 3 0 0 -3.0 1104 -3 aq lactic acid 3 5 5 0 0 -5.5 1681 -3 aq deoxyribose 4 5 5 0 0 -5.0 1680 -3 aq ribose
a <- affinity(T=c(0, 150))
energy.args: pressure is Psat energy.args: variable 1 is T at 128 values from 273.15 to 423.15 K subcrt: 9 species at 128 values of T and P (wet)
diagram(a, what="O2", legend.x="topleft", col=rev(rainbow(4)), lwd=2) title(main="Equilibrium logfO2 for 1e-3 mol/kg of CO2 and ... ")

Image diagram1

 

### 1-D diagrams: logarithms of activities ## 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 1576 -3 aq H2O 0 2 0 1 0 0 1 0 liq NH3 0 3 1 0 0 0 66 -4 aq H2S 0 2 0 0 1 0 67 -7 aq O2 0 0 0 2 0 0 3316 -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 1624 -3 aq glycinium 2 2 1 1 0 -1.5 0 1623 -3 aq glycine 3 2 1 1 0 -1.5 -1 1122 -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: from moles of CO2 in formation reactions equilibrate: n.balance is 2 2 2 equilibrate: loga.balance is -2.22184874961636 equilibrate: using reaction method
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 1576 999 aq NH3 0 3 0 1 0 0 0 66 999 aq H2O 0 2 0 0 1 0 0 1 999 liq H3PO4 0 3 0 0 4 1 0 70 999 aq O2 0 0 0 0 2 0 0 65 999 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 1763 -3 aq HATP-3 2 10 5 -4 3 -7.5 -2 0 1764 -3 aq H2ATP-2 3 10 5 -4 3 -7.5 -4 1 1820 -3 aq MgATP-2 4 10 5 -4 3 -7.5 -3 1 1821 -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: from moles of CO2 in formation reactions equilibrate: n.balance is 10 10 10 10 equilibrate: loga.balance is -1.39794000867204 equilibrate: using reaction method
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