Surface complexion with zwitterionic Amino acids

[A.Schneidt]

Hello all!

I'm a master student and mostly self taught on phreeqc, so forgive me if I'm making some "obvious" mistakes.

Simplifying somewhat, I have some pieces of iron saponite clay with small amounts organics in them, and want to model how these organics (mostly amino acids) become available when put in various different solutions. These amino acids can exist in multiple forms based on the pH of the solution, going from negatively to positively charged. Importantly, they can also exist as zwitterions, where they are dipoles but have no total charge. To start with I'm just working with Glycine and Glutamate.

What I did first is find some Langmuir isotherms for the exchange of Glycine and Glutamate with Na+ Homoionic saponite, and then I used example 19 from the handbook and calculated a log_k. Phreeqc has the zwitterions in built (very helpful), and the initial amino acids should be in the saponite has zwitterions. I then tried two seperate methods.

First, I tried using "SURFACE" because exchange could really only use ions and my amino acids were (for phreeqc at least, they are in reality dipoles) uncharged. I defined some charged surfaces, since the saponite interlayer should be (at least slightly) charged. I saw on some forums that you should use donnan, so I did that. Nevertheless, I don't think this is a good way of doing what I want to.

Code: [Select]

SOLUTION_MASTER_SPECIES

Glycine                 Glycine- 1       74.07   74.07
Glutamate Glutamate-2 1.0 145.115 145.115

SOLUTION_SPECIES

# From the MINTEQ database

Glycine- = Glycine-
        log_k   0
        delta_h 0       kcal
Glycine- + H+ = H(Glycine)
        log_k   9.78
        delta_h 0       kcal
        -gamma  0       0.07
Glycine- + 2H+ = H2(Glycine)+
        log_k   12.12
        delta_h 0       kcal
        -gamma  0       0.07

Glutamate-2 = Glutamate-2
log_k 0
H+ + Glutamate-2 = H(Glutamate)-
log_k 9.96
delta_h -41.0032 kJ
-gamma 0 0
2H+ + Glutamate-2 = H2(Glutamate)
log_k 14.26
delta_h -43.5136 kJ
-gamma 0 0
3H+ + Glutamate-2 = H3(Glutamate)+
log_k 16.42
delta_h -46.8608 kJ
-gamma 0 0

PHASES

Saponite-Fe-Fe #From core11, Neveu et al., 2017
(H(Glycine))0.000029272(H2(Glutamate))0.000003825Fe3.175Al.35Si3.65O10(OH)2 + 7.4 H+ = 0.35 Al+3 + 3.175 Fe+2 + 3.65 SiO2 + 4.7 H2O + 0.000029272 H(Glycine) + 0.000003825 H2(Glutamate)
log_k 18.9359
-analytic 5.762e1 -1.630e-1 0 0 0 1.099e-4
# Range 0-300
-Vm 142.672
# Extrapol supcrt92
# Ref Catalano13

Fix_H+
H+ = H+
log_k 0.0

SOLUTION 1 Pure water (t=25, pH=7)
pH 7
temp 25 # Celcius
Na 0.00001 charge
Cl 0.00001
-water 0.004 #kg, 4ml.
END

USE solution 1
EQUILIBRIUM_PHASES 1 # Changes the pH to 2, 7 or 12 using HCl or NaOH from a pool of 10 moles.
Fix_H+ -7 HCl 10.0
SAVE solution 1
END

SURFACE_MASTER_SPECIES
Surf_x Surf_x-

SURFACE_SPECIES

Surf_x- = Surf_x-
log_k 0.0
Surf_x- + H(Glycine)= Surf_xH(Glycine)-
log_k 8.4440
Surf_x- + H2(Glutamate) = Surf_xH2(Glutamate)-
log_k 7.9177

USE solution 1
EQUILIBRIUM_PHASES 1 (t=25, pH=7)
Saponite-Fe-Fe 0.0 0.00008882 #Mol

SURFACE 1 (t=25, pH=7)
-equilibrate with solution 1
Surf_x(H(Glycine))0.000029272(H2(Glutamate))0.000003825- Saponite-Fe-Fe equilibrium_phase 1 0.0001
-donnan

Phreeqc doesn't like it when I define Glycine and glutamate on the same surface seperately (like below) and I could only get it to run like above.

Code: [Select]

SURFACE 1 (t=25, pH=7)
-equilibrate with solution 1
Surf_x(H(Glycine)) Saponite-Fe-Fe equilibrium_phase 0.0.000029272 0.0001
Surf_x(H2(Glutamate)) Saponite-Fe-Fe equilibrium_phase 0.000003825 0.0001
-donnan
This has several obvious issues, not the least of which that I think it's creating 1 mole surface per mole saponite, and so creating far more surfaces than there should be. And also that I'm having an extremely hard time finding any good inputs for specific area per mole. So I've started exploring using EXCHANGE instead. Since the langmuir isotherms were from Na homoionic saponite, I think I can simply use the log_k I calculated using them. The log_K for those describes the equilibrium between NaX and GlyX, so if phreeqc takes Na + X = NaX as 0, I should be able to get away with using those values for Gly + X = GlyX.

Code: [Select]

SOLUTION_MASTER_SPECIES

Glycine                 Glycine- 1       74.07   74.07
Glutamate Glutamate-2 1.0 145.115 145.115

SOLUTION_SPECIES

################### Glycine Species ###################
# From the MINTEQ database

Glycine- = Glycine-
        log_k   0
        delta_h 0       kcal
Glycine- + H+ = H(Glycine)
        log_k   9.78
        delta_h 0       kcal
        -gamma  0       0.07
Glycine- + 2H+ = H2(Glycine)+
        log_k   12.12
        delta_h 0       kcal
        -gamma  0       0.07

Glutamate-2 = Glutamate-2
log_k 0
H+ + Glutamate-2 = H(Glutamate)-
log_k 9.96
delta_h -41.0032 kJ
-gamma 0 0
2H+ + Glutamate-2 = H2(Glutamate)
log_k 14.26
delta_h -43.5136 kJ
-gamma 0 0
3H+ + Glutamate-2 = H3(Glutamate)+
log_k 16.42
delta_h -46.8608 kJ
-gamma 0 0

PHASES

Saponite-Fe-Fe #From core11, Neveu et al., 2017
(H(Glycine))0.000029272(H2(Glutamate))0.000003825Fe3.175Al.35Si3.65O10(OH)2 + 7.4 H+ = 0.35 Al+3 + 3.175 Fe+2 + 3.65 SiO2 + 4.7 H2O + 0.000029272 H(Glycine) + 0.000003825 H2(Glutamate)
log_k 18.9359
-analytic 5.762e1 -1.630e-1 0 0 0 1.099e-4
# Range 0-300
-Vm 142.672
# Extrapol supcrt92
# Ref Catalano13

Fix_H+
H+ = H+
log_k 0.0

EXCHANGE_SPECIES
H2(Glycine)+ + X- = H2(Glycine)X
log_k 8.4440
H3(Glutamate)+ + X- = H3(Glutamate)X
log_k 7.9177

SOLUTION 1 Pure water (t=25, pH=7)
pH 7
temp 25 # Celcius
Na 0.00001 charge
Cl 0.00001
-water 0.004 #kg, 4ml.
END

USE solution 1
EQUILIBRIUM_PHASES 1 # Changes the pH to 2, 7 or 12 using HCl or NaOH from a pool of 10 moles.
Fix_H+ -7 HCl 10.0
SAVE solution 1
END


USE solution 1
EQUILIBRIUM_PHASES 1 (t=25, pH=7)
Saponite-Fe-Fe 0.0 0.00008882 #Mol

EXCHANGE 1 (t=25, pH=7)
H(Glycine)X Saponite-Fe-Fe e 0.000029272
H2(Glutamate)X Saponite-Fe-Fe e 0.000003825
This looks a lot better (in my opinion), except for the fact that it's using the positively charged amino acids. For whatever reason I can define the zwitterions on the exchange positions in the EXCHANGE command despite the fact that this shouldn't be charge balanced. For Phreeqc, this really should be H(Glycine)X-, since H(Glycine) is not charged. Regardless, it hasn't shown me any errors yet, at least until I try to define the exchange under EXCHANGE_SPECIES at which point phreeqc rightfully doesn't accept the disappearance of the charge.

Code: [Select]

EXCHANGE_SPECIES
H(Glycine) + X- = H(Glycine)X
log_k 8.4440
H2(Glutamate) + X- = H2(Glutamate)X
log_k 7.9177
This has left me with some questions. The first is if I can even use these log_K values, or if the ones I calculated using the langmuir isotherm are inherently incompatible with the way phreeqc models exchange? The second if there's some way to use exchange with a zwitterion/non charged species? What would be the most sensible path forward? Attempting to make it work as a SURFACE reaction or work around the EXCHANGE charge in some manner. Going through the manual I couldn't find anything, and despite the fact that this forum has massively helped me many times, I couldn't find anything here either.

I would be very thankful for any help. Have a wonderful day,
Alexander

[dlparkhurst]

A few too many questions for me to answer them all. Let's start with the SURFACE approach.

I would not include Glycine or Glutamate as part of the formula in the SURFACE definition. I think you should define the surface as follows with appropriate values for sites per mole and area per mole of sapronite. If you include Glycine and Glutamate in your SOLUTION 1, then PHREEQC will calculate the surface composition that will be in equilibrium with solution 1 (without changing the composition of solution 1).

Similarly, I don't see why you are including Glycine or Glutamate in the Saponite formula. I think you should precipitate pure saponite, which creates exchange sites, and then Glycine and Glutamate will sorb on the sites.

So, this is the way that I would set it up. You can change concentrations in SOLUTION, and, in general, I prefer to use a liter of solution; PHREEQC will work best when the volume of solution is about 1 L. I have left the solution as 4 mL.

If this script does not meet your needs, write another post and explain your position.

Code: [Select]

SOLUTION_MASTER_SPECIES
    Glycine       Glycine-         1     74.07           74.07
    Glutamate     Glutamate-2      1     145.115         145.115

SOLUTION_SPECIES
# From the MINTEQ database
Glycine- = Glycine-
    log_k     0
Glycine- + H+ = H(Glycine)
    log_k     9.78
    -gamma    0 0.07
Glycine- + 2H+ = H2(Glycine)+
    log_k     12.12
    -gamma    0 0.07
Glutamate-2 = Glutamate-2
    log_k     0
Glutamate-2 + H+ = H(Glutamate)-
    log_k     9.96
    delta_h   -41.0032 kJ
    -gamma    0 0
Glutamate-2 + 2H+ = H2(Glutamate)
    log_k     14.26
    delta_h   -43.5136 kJ
    -gamma    0 0
Glutamate-2 + 3H+ = H3(Glutamate)+
    log_k     16.42
    delta_h   -46.8608 kJ
    -gamma    0 0
END
SURFACE_MASTER_SPECIES
Surf_x Surf_x-
SURFACE_SPECIES
Surf_x- = Surf_x-
log_k 0.0
Surf_x- + H(Glycine)= Surf_xH(Glycine)-
log_k 8.4440
Surf_x- + H2(Glutamate) = Surf_xH2(Glutamate)-
log_k 7.9177
END
PHASES
Saponite-Fe-Fexxx #From core11, Neveu et al., 2017
(H(Glycine))0.000029272(H2(Glutamate))0.000003825Fe3.175Al.35Si3.65O10(OH)2 + 7.4 H+ = 0.35 Al+3 + 3.175 Fe+2 + 3.65 SiO2 + 4.7 H2O + 0.000029272 H(Glycine) + 0.000003825 H2(Glutamate)
log_k 18.9359
-analytic 5.762e1 -1.630e-1 0 0 0 1.099e-4
# Range 0-300
-Vm 142.672
# Extrapol supcrt92
# Ref Catalano13
Saponite-Fe-Fe
Fe3.175Al.35Si3.65O10(OH)2 + 7.4 H+ = 0.35 Al+3 + 3.175 Fe+2 + 3.65 SiO2 + 4.7 H2O
log_k 18.9359
-analytic 5.762e1 -1.630e-1 0 0 0 1.099e-4
# Range 0-300
-Vm 142.672
# Extrapol supcrt92
# Ref Catalano13
Fix_H+
H+ = H+
log_k 0.0
END
SOLUTION 1 Pure water (t=25, pH=7)
    temp      25
    pH        7
    pe        4
    redox     pe
    units     mmol/kgw
    density   1
    Cl        1e-05
    Glutamate 1
    Glycine   1
    Na        1e-05 charge
    -water    0.004 # kg
END
USE solution 1
EQUILIBRIUM_PHASES 1
    Fix_H+    -7 HCl       10
SAVE solution 1
END
EQUILIBRIUM_PHASES 1 (t=25, pH=7)
    Saponite-Fe-Fe 0 8.882e-05
END
SURFACE 1 (t=25, pH=7)
    -equilibrate with solution 1
    Surf_xH Saponite-Fe-Fe  equilibrium_phase 0.1    1
    -donnan 1e-08
END
USE solution 1
USE surface 1
USE equilibrium_phases 1
END


[A.Schneidt]

Hello, thank you so much for your reply! I took a while to make sure I exhausted all my other ideas before I returned.

I don't think this script fits my needs. The amino acids I'm modelling arrive into the solution trapped inside of the clay saponite, trapped in the interlayer space. I'm specifically interested in the release of these amino acids through two major pathways. 1) The dissolution of the clay releases any and all amino acids inside, 2) The equilibrium between the solution and the clay interlayer spaces. Most of the amino acids (at the pH I'm working with) are dipoles/uncharged.

For that reason I think defining the amino acids already in solution would not work for me.

I'm modelling this all alongside some experimental work, which is why I chose for 4 mL water. If it works better in phreeqc it would not be much work to scale the phreeqc model so that the concentrations remain the same. Thank you!

[dlparkhurst]

Okay, I think I've got a better idea of your experiment. Below is a script that will run. I am not sure it is exactly what you need. I may not have the stoichiometry right, and I wonder what else is sorbed on the surface besides Glutamate and Glycine that will compete for sites. For example, you may want to add some amount of Surf_xH in the SURFACE definition, adjusting the number of sites accordingly. You will probably also adjust the equilibrium constants for the surface reactions.

Take a look and post your concerns for the next iteration.

Code: [Select]

SOLUTION_MASTER_SPECIES
    Glycine       Glycine-         1     74.07           74.07
    Glutamate     Glutamate-2      1     145.115         145.115

SOLUTION_SPECIES
# From the MINTEQ database
Glycine- = Glycine-
    log_k     0
Glycine- + H+ = H(Glycine)
    log_k     9.78
    -gamma    0 0.07
Glycine- + 2H+ = H2(Glycine)+
    log_k     12.12
    -gamma    0 0.07
Glutamate-2 = Glutamate-2
    log_k     0
Glutamate-2 + H+ = H(Glutamate)-
    log_k     9.96
    delta_h   -41.0032 kJ
    -gamma    0 0
Glutamate-2 + 2H+ = H2(Glutamate)
    log_k     14.26
    delta_h   -43.5136 kJ
    -gamma    0 0
Glutamate-2 + 3H+ = H3(Glutamate)+
    log_k     16.42
    delta_h   -46.8608 kJ
    -gamma    0 0
END
SURFACE_MASTER_SPECIES
Surf_x Surf_x-
SURFACE_SPECIES
Surf_x- = Surf_x-
log_k 0.0
Surf_x- + H(Glycine)= Surf_xH(Glycine)-
log_k 8.4440
Surf_x- + H2(Glutamate) = Surf_xH2(Glutamate)-
log_k 7.9177
END
PHASES
Saponite-Fe-Fe #From core11, Neveu et al., 2017
(H(Glycine))0.000029272(H2(Glutamate))0.000003825Fe3.175Al.35Si3.65O10(OH)2 + 7.4 H+ = 0.35 Al+3 + 3.175 Fe+2 + 3.65 SiO2 + 4.7 H2O + 0.000029272 H(Glycine) + 0.000003825 H2(Glutamate)
log_k 18.9359
-analytic 5.762e1 -1.630e-1 0 0 0 1.099e-4
# Range 0-300
-Vm 142.672
# Extrapol supcrt92
# Ref Catalano13
Fix_H+
H+ = H+
log_k 0.0
END
SOLUTION 1 Pure water (t=25, pH=7)
    temp      25
    pH        7
    pe        4
    redox     pe
    units     mmol/kgw
    density   1
    Cl        1e-05
    Na        1e-05 charge
    -water    0.004 # kg
END
END
EQUILIBRIUM_PHASES 1 (t=25, pH=7)
    Saponite-Fe-Fe 0 8.882e-05
END
SURFACE 1 (t=25, pH=7)
Surf_x(HGlycine)0.884430613(H2Glutamate)0.115569387  Saponite-Fe-Fe equilibrium_phase 0.000033097 0.0001
-donnan
END
USE solution 1
USE surface 1
USE equilibrium_phases 1
END


[A.Schneidt]

Hello!

Yes I think that works really well! With a little adjusting I think that's perfect. Thank you so much.

I do have one last question though. Since I'm working with a clay, and the amino acids (at least theoretically) are found in the interlayer, I was curious if using the "EXCHANGE" command would be more representative. Despite the amino acids not being charged, they do still find their way into the clay interlayers. So to compare with the SURFACE command I made this

Code: [Select]

SOLUTION_MASTER_SPECIES
    Glycine       Glycine-         1     74.07           74.07
    Glutamate     Glutamate-2      1     145.115         145.115

SOLUTION_SPECIES
# From the MINTEQ database
Glycine- = Glycine-
    log_k     0
Glycine- + H+ = H(Glycine)
    log_k     9.78
    -gamma    0 0.07
Glycine- + 2H+ = H2(Glycine)+
    log_k     12.12
    -gamma    0 0.07
Glutamate-2 = Glutamate-2
    log_k     0
Glutamate-2 + H+ = H(Glutamate)-
    log_k     9.96
    delta_h   -41.0032 kJ
    -gamma    0 0
Glutamate-2 + 2H+ = H2(Glutamate)
    log_k     14.26
    delta_h   -43.5136 kJ
    -gamma    0 0
Glutamate-2 + 3H+ = H3(Glutamate)+
    log_k     16.42
    delta_h   -46.8608 kJ
    -gamma    0 0

EXCHANGE_SPECIES

###################  Exchange Species ###################
# From MINTEQ and LLNL database.

Na+ + X- = NaX
        log_k   0.0
        -llnl_gamma  4.0     
H(Glycine) + X- = H(Glycine)X-
log_k 8.4440

H2(Glutamate) + X- = H2(Glutamate)X-
log_k 7.9177

PHASES
Saponite-Fe-Fe #From core11, Neveu et al., 2017
(H(Glycine))0.000029272(H2(Glutamate))0.000003825Fe3.175Al.35Si3.65O10(OH)2 + 7.4 H+ = 0.35 Al+3 + 3.175 Fe+2 + 3.65 SiO2 + 4.7 H2O + 0.000029272 H(Glycine) + 0.000003825 H2(Glutamate)
log_k 18.9359
-analytic 5.762e1 -1.630e-1 0 0 0 1.099e-4
# Range 0-300
-Vm 142.672
# Extrapol supcrt92
# Ref Catalano13
Fix_H+
H+ = H+
log_k 0.0
END
SOLUTION 1 Pure water (t=25, pH=7)
    temp      25
    pH        7
    pe        4
    redox     pe
    units     mmol/kgw
    density   1
    Cl        1e-05
    Na        1e-05 charge
    -water    0.004 # kg
END
END
EQUILIBRIUM_PHASES 1 (t=25, pH=7)
    Saponite-Fe-Fe 0 8.882e-05
END
EXCHANGE 1 (t=25, pH=2)
H(Glycine)X- Saponite-Fe-Fe e 0.000029272
H2(Glutamate)X- Saponite-Fe-Fe e 0.000003825
END
USE solution 1
USE EXCHANGE 1
USE equilibrium_phases 1
END
As I understand it, these should be relatively similar. Since the values for log_k come from exchange with homoionic Na clay, and the exchange log_k is relative to the exchange with sodium, I think I should be able to use the same log_K values. However, both come to a very different result, I think perhaps due to the other species exchanging into the interlayer whereas the surface version only allowed amino acids (until i define otherwise).

[dlparkhurst]

The main difference between EXCHANGE and SURFACE is that surfaces can have an accumulated charge, whereas with exchange, all sites are filed with counter ions resulting in a net charge of zero.

I think you understand the basics. I would be reluctant to use the exchange approach for the reasons you give--your ions are actually anions, which doesn't fit well to a cation exchange model, and you must have other ions to fill all the sites, so there is the added complication of competition. Of course there should be competition for the surface sites as well, but you can add competition as needed.

To me, the surface approach is simpler and more suitable.