Rue extraction - multiple pH peaks and other questions

[Jagube]

I'm doing my first Rue extraction and I've been on it for a week or so (not counting the cooking time). The starting material was 190g of seeds. I had bioassayed these seeds in their raw and tea form (that's why it's 190g and not 200) and they seem extremely potent... 2 grams was quite strong and entheogenic on its own, so I'm hoping for a good yield.

After the first basification it turned green (brown in poor light, but green in daylight and under a day-white LED light), not milky. I wonder if this is this normal? Maybe I cooked it for too long and extracted stuff that's not extracted by shorter boils, or it wasn't filtered enough.

Now I'm nearing the end of it and I'm doing the final basification, with pH-based separation of harmine and harmaline.

I'm quite confused by the pH changes with sodium carbonate added.

I'm using a pH pen and I'm not sure if it's calibrated well - I have reasons to suspect its readings are 0.3 pH lower than what they should be (so a reading of 7 may actually indicate pH 7.3). But for the sake of brevity for the rest of this post / thread I'll use the readings of my pH pen as if they were accurate (so when I say the pH was 7 I mean it read 7) - unless stated otherwise.

I first raised the pH to 8.7, let it settle and collected the crashed out solids - presumably harmine.

Then I proceeded to raise the pH further and this is where things got weird. I know there are supposed to be pH peaks, as when the harmine and harmaline are converted into freebase the pH drops. But I got *lots* of peaks, not just two... more like 10.

I was aiming to bring the pH to 10.3, as that's the highest I'd managed to get in previous sample basifications... there seemed to be a resistance line around that level.

During the process of adding sodium carb and stirring, the pH would reach something in the upper 9's and suddenly drop to the lower 8s or even upper 7s. It did that several times.
And when it reached 10.2 (light at the end of the tunnel :lol: ) and I got all excited, upon adding more sodium carb it suddenly dropped to 7.2, which is lower than my tap water. That drove me crazy.

After adding what must have been hundreds of grams of sodium carb (in 2 liters of liquid) I finally managed to bring it up to 10.3 and I'm waiting for this to settle. I wonder if this is sufficiently high to freebase most of the harmaline, or did I add to much sodium carb and will my precipitate be mostly sodium carb?

And one more question: the The Tao of Rue Extraction references Easy Caapi Vine Alkaloid Extraction Guide for final cleanup, which says:

Add about 200ml water to the precipitate, stir, and allow to settle again. Remove and reserve liquid. Repeat this step one more time.
Before removing the liquid the third time, check its pH. It should be somewhere between 7 and 8. If the solution is still very alkaline, you haven’t removed enough NaOH and must do additional rinses. Repeat until pH is between 7 and 8.

Is there a risk that by adding water and lowering the pH, some of the freebase harmalas may be converted back into salts, dissolve in the water and result in a loss when the liquid is discarded? Or do they remain 100% as freebase until the pH drops below 7 or some other low number?

To generalize this: I've read that harmaline doesn't start turning into freebase until the pH reaches 9.8. But it seems once its fb, it needs the pH lowered significantly before it converts back into salt form? So there are two pH thresholds for conversion, depending on which direction you're going: salt->fb (up) or fb->salt (down)? Does that mean there are also two pKa values - an 'up' pKa and a 'down' pKa, or is there only one pKa that applies in both directions?

Thanks

 

[blue.magic]

There are many variables that can play a role.

I assume you used acetic acid, which is monoprotic and should generate single pH step during titration. This may not be the case with other acids, such as citric or phosphoric. Your vinegar may contain other acids as well (just guessing) explaining the multiple pH stepping.

Sodium carbonate converts to sodium bicarbonate in presence of water, becoming a weaker base over time. This should be a slow process, maybe not so in a warm/hot solution?

Make sure your sodium carbonate has been stored in dry conditions - it can pick up moisture and weaken - you then need to bake it to get sodium carbonate back.

As for the separation, aim for pH 7.0 and collect almost pure harmine, then aim for more precise separation. I think "Phlux's Telepathine Tek" discusses this in detail.

Even more details on titration harmalas and observed peaks are described here. The document contains detailed experimental method and results confirmed by observing crystals under microscope.

Make sure to stir your solution well until pH settles at a certain value. Since you use lots of solution (2 liters), it will take considerable time until everything mixes and reacts.

Consider reducing the amount of solution, this will also help removing finer impurities by filtering. Impurities may also play some role, producing the weird behavior you observe.

I have a pH pen calibrated to 0.01 precision and also observe pH behaving weirdly - if only I can plot the pH values in a graph, that would be interesting.

But in my experience, even as little as 250 ml of solution needs some time and mixing until you get a correct pH reading. The pH meter itself needs some time until enough liquid permeates the glass electrode (probe).

Maybe heating the solution will help speed things up, just never exceed the range allowed by your pH meter (mine measures accurately only up to 50 degrees centigrade).

Also 2 litres of solution for ~200 grams of harmalas is too much. I can easily get by with 400 ml for freebasing and 700-800 ml for crystallization (so there is enough room for xtals to grow).

 

[Jagube]

I assume you used acetic acid

I used distilled vinegar.

Sodium carbonate converts to sodium bicarbonate in presence of water, becoming a weaker base over time. This should be a slow process, maybe not so in a warm/hot solution?

The solution was still hot (coming from re-dissolving my crystals in hot water) for the first (harmine) precipitation and cold for the second one.

Make sure your sodium carbonate has been stored in dry conditions - it can pick up moisture and weaken - you then need to bake it to get sodium carbonate back.

Thanks for pointing that out. It's fresh and hasn't been stored for long. Now I know to store it in a cupboard in the house and not in the shed.

As for the separation, aim for pH 7.0 and collect almost pure harmine, then aim for more precise separation.

Wow, I wouldn't have thought any harmine at all would have converted at pH 7.0.
Will check out Phlux's tek. I had seen the other paper on zenodo.

It's possible that my solution wasn't mixed well, the pH meter would often swing.

Consider reducing the amount of solution, this will also help removing finer impurities by filtering.

I didn't know what volume would be best, that's one useful piece of information the teks on the Wiki often don't state. I guess one develops an intuition after a while, but for a newbie it's a wild guess. My reasoning was a large volume would mean less losses, so it could only be a good thing.

Also 2 litres of solution for ~200 grams of harmalas is too much. I can easily get by with 400 ml for freebasing and 700-800 ml for crystallization (so there is enough room for xtals to grow).

I used less water for crystallization - the reasoning here was I wanted to make sure all alks crystallized. One of the Manske cycles turned out completely useless as all the liquid in the solution was soaked up by the forming crystals and I ended up with a crystal 'cake' with no liquid to pour off. The weight of that cake was much higher than the weight of my previous Manske cycle's crystals and I wonder how that's possible, as the added salt alone couldn't have accounted for the entire weight gain... maybe some water got trapped in the cake.

Will take note of your volume suggestions.

Update:
My second-base solution has settled into 4 layers, starting from the bottom: off-white solids (presumably harmine + harmaline), darker solids (presumably harmine + harmaline + impurities), green liquid, and a very thin layer of floating solids at the top (undissolved sodium carbonate?).

 

[blue.magic]

I didn't know what volume would be best, that's one useful piece of information the teks on the Wiki often don't state. I guess one develops an intuition after a while, but for a newbie it's a wild guess. My reasoning was a large volume would mean less losses, so it could only be a good thing.

Yes. Even the same tek can work great for one and not well for the other. It's wise to stick with one tek as you did and then optimize according to your working conditions, available chemicals, utensils etc.

I used less water for crystallization - the reasoning here was I wanted to make sure all alks crystallized. One of the Manske cycles turned out completely useless as all the liquid in the solution was soaked up by the forming crystals and I ended up with a crystal 'cake' with no liquid to pour off. The weight of that cake was much higher than the weight of my previous Manske cycle's crystals and I wonder how that's possible, as the added salt alone couldn't have accounted for the entire weight gain... maybe some water got trapped in the cake.

That happened to me in the past as well, especially when I scaled the extraction to 200-250 grams. You will find the right volume by practice.

I am using suction filtering with a large vintage Buchner funnel so the cake quickly deflates while the water gets sucked out of it. This allows me to dump over a liter of solution in the funnel and dry it at the same time. Then I simply scrape the crystals, wash the filter paper in clean water to salvage any harmalas stuck in the filter.

Of course if you prefer decanting, then you need more volume so you are probably doing it correctly.

You can sometime crash more crystals by adding excess salt to the filtered liquid or freebase the leftovers and re-Manske them in small amount of liquid.

Maybe you can also use glass funnel with a cotton plug, the crystals will collect on the cotton, you replace the container and dissolve the crystals with hot water - they will pass through the cotton.

Well you will find your best method - be creative

 

[Jees]

* Perform your reactions at room temp.

* If you don't want sodcarb to end as a powder among your crystals, then pre-dissolve the sodcarb and use that liquid to base.

* It's better to have clean white/beige crystals (doing enough A/B's and/or manskes) before trying to separate harmine from harmaline. Was that the case?

* The very first basing has so much impurities in the liquid that it is normal to see no real "milk", but as soon as you are doing more A/B's and/or manskes, it should turn "milk" when basing.

*

...Even more details on titration harmalas and observed peaks are described here. ...

Please do not confuse a pH depressions as described by Van Der Sypt with any pH dance you observe. To illustrate: a VDS pH depression is linked to a component. If Jagube speaks of 10 spikes we already know this is not separating 10 components. We must avoid misinterpretations in these matters and I realize that VDS himself has add to the confusion himself by completely condemning the classic pKa separation tek, and postulating that his observed mechanics are the-one-and-only. E.g. he hasn't even bordered the circumstantial parameters where his mechanics apply and where not. In Jagube's case the volume of liquid is too large, the concentration too low for any {component specific pH depression} to occur. In those cases the classic pKa related separation is the only way.

Jagube's spikes are imho chemical dynamics while the soup has not reached a new equilibrium, nothing to ponder about. Personally I haven't used sodcarb to base rue soup.

* Important correction:
concerning the classic pKa related separation: Phlux telepatine tek does not suggest to aim for pH 7 to get your harmaline, but to respect the 8.75:

...To separate the two one can take advantage of the difference in their pKa values.
The pKa value of a substance is the pH at which half of the substance is in freebase form and the other half in salt form.
Harmine - pKa=7.7
Harmaline - pKa=9.8
According to Infundibulum(The Nexus) the best pH to precipitate harmine is at pH 8.75 because at this pH one will in theory get at around 92% harmine and 8% harmaline.

It is my limited experience that this a fine route where VDS pH depressions (circumstances) do not occur.
I won't say it is impossible @ pH 7 as in only one case I was able to get all my harmaline at pH 7 but I had to make extra conditions in a VDS compliant situation.

* Jagube yes washing your alks to pH 7 will sure cost you harmaline, you will see that the lower your pH gets, the more colored your wash water becomes, that is harmaline starting to dissolve in the wash water. It's the guys basing with lye that need to wash better than those that base with sodcarb. I work with lye a lot, but for this purpose I like to make the final end base with sodcarb so lesser washing is needed. I've also suspected the crystals to stay whiter with sodcarb. The FB derived with lye I thought it turned red-ish sooner when preserved.

Til here
Sorry for the nagging

 

[blue.magic]

I am not sure about the layers. They form if the freebasing is not complete or if there are impurities - I add a bit more base, mix, and suddenly I have just two layers formed (brown to yellow water and tan-colored harmalas).

Oh one more thing: I never grind the seeds - just do 3-4 cookings. I once ground the exhausted seeds to see how much extra alkaloids I get by that and all I got was a milky suspension that is super hard to filter.

So now I just cook the whole seeds, filter with cotton, reduce, filter again and then it's reasonably pure.

First run is cotton, second is with paper filter and final run is with Celite.

You also don't have to worry about losses if you wash the container say 2 times after pouring it.

 

[blue.magic]

I've read about the pH 7 separation at some subforum by Phlux. It was before he wrote the Telepathine Tek so I though he included that... but no... sorry for mis-information.

I was too lazy to read the actual paper from start to end and assumed Jagube did proper titration observing these peaks. But this is probably just pH pertuberations before the solution is completely mixed and reacted.

So don't take my word for it - just throwing in the best I know. Maybe it's better to leave it for the experts here.

 

[Loveall]

It is very ironic that VDS condemned the pKa approximation as "chemically incorrect" in his paper and then turns around and gives an absolute pH separation algorithm.

Truth is that the precipitation point will depend on many things like Jees said and the Nexus has been consistent in saying that pKa use is only a first order approximation. I would add that salting in effects matter a lot and I believe Sakkadelic has already shown that by minimizing trace salt amounts precipitation will occur earlier in the pH sweep.

At the end of the day rue extractions contain many factors. They do tend to behave a certain way, but simple approximations such as pKa can end up being off by quite a bit due to the presence of many compounds affecting the ionic strength.

And don't forget to enjoy the mystery that is rue extraction. It is a beautiful thing. I ask the seeds for permission to extract their magic, I truly think that helps.

 

[Jees]

It is very ironic that VDS condemned the pKa approximation as "chemically incorrect" in his paper and then turns around and gives an absolute pH separation algorithm...

I think it is best to see it as all people bringing out their findings, and together we come to a broader picture. I'm so grateful that VDS brought his separation algorithm to start with, I had never heard or read of those mechanisms. There was also not one single cross reference mentioned here from another source that speaks of what he did and google gives nothing, we are truly privileged. Too bad that the VDS thread got swollen so hard in trying to get grips on it, not very pleasant for new people I guess.

bue.magic, in the end I'm quite sure my own perceptions are prone to correction also and I invite any remark to do so. We only have momentarily truths I guess.

 

[Jagube]

My alks were not very pure before attempting the separation.

My motivation for the separation is:

- I'd like to bioassay harmine and harmaline separately, to get a better idea of their effects in (relative) isolation. I know the effects of Rue tea and Caapi tea (hundreds of experiences) and would like to better understand which alkaloids contribute to which effects.

- Once the extraction is complete, I'm planning a zinc reduction of the harmaline to obtain THH, so again I can bioassay it.

- The whole thing (rue extraction, separation of harmaline / harmine and zinc reduction) is a proof of concept, to develop a protocol to obtain a product from rue that mimics Caapi.

So purity is not that critical, as long as the impurities don't bulk up the final product too much. Also I'm not that interested in smoking or using it sublingually (other than to satisfy my curiosity). And perfect separation is not critical either. Even if one powder is 80% harmine / 20% harmaline, and the other is 20% harmine / 80% harmaline, it's enough of a separation to be able to bioassay both and get a rough idea of the difference. In the long run separation shouldn't be necessary as the zinc reduction on 1:1 harmine to harmaline (rue's natural ratio) should theoretically yield a 1:1 harmine to THH (caapi's natural ratio).

Now the precipitate collected from my pH 10.3 basification is much lighter in color and several times larger in volume than the first (pH 8.7). I'm guessing a lot of it must be sodium carbonate?

I don't want to lose too much harmaline in the cleanup stage and I'm thinking maybe it's better not to clean up until *after* the zinc reduction, because:

- I've read somewhere the proposition (unconfirmed) that the pKa of THH is 6.9. If that's indeed the case, the cleanup of THH should result in smaller losses than the cleanup of harmaline.
- The vinegar used in the zinc reduction should neutralize the sodium carb anyway.

Is my thinking correct or am I missing something?

 

[Loveall]

It is very ironic that VDS condemned the pKa approximation as "chemically incorrect" in his paper and then turns around and gives an absolute pH separation algorithm...

I think it is best to see it as all people bringing out their findings, and together we come to a broader picture. I'm so grateful that VDS brought his separation algorithm to start with, I had never heard or read of those mechanisms. There was also not one single cross reference mentioned here from another source that speaks of what he did and google gives nothing, we are truly privileged. Too bad that the VDS thread got swollen so hard in trying to get grips on it, not very pleasant for new people I guess.

bue.magic, in the end I'm quite sure my own perceptions are prone to correction also and I invite any remark to do so. We only have momentarily truths I guess.

Wise words Jees. Thank you.

 

[blue.magic]

Now the precipitate collected from my pH 10.3 basification is much lighter in color and several times larger in volume than the first (pH 8.7). I'm guessing a lot of it must be sodium carbonate?

Maybe you can wash it with cold water several times to remove the undissolved sodium carbonate.

I did water washings of the freebase until the water was clear enough (light yellow), but not sure if that can lead to a loss of product (at least I haven't observed any loss visually).

 

[Jagube]

I'm doing the washing and every wash seems to increase the volume of the precipitate. Looks like it's becoming more and more fluffy.

I was also surprised that the first wash of my pH 8.7 precipitate had pH 10.4. I would have thought that adding tap water would have *decreased* the pH, not increased it.

 

[Jees]

Potential CO2? You've worked with vinegar + sodcarb, the formed CO2 can hold the pH lower. Poring your precips at 8.7 trough a coffee filter, that action in and on itself is enough to drive off potential CO2 away from the crystals. We've seen that happening before. Important is that the separation happened at the right pH (8.7) no matter the constitution of the liquid, CO2 or not, so you should be good.

 

[Jagube]

Thanks guys, here are my yields from 191g Rue:

1st precipitate at pH 8.7: 7.1g (quite dark tan - impurities?)
2nd precip at pH 9.3-9.6: 6.1g (light tan)
3rd precip at pH 11: 1.2g (very light tan)

Total yield: 14.4g, or ~7.5%

Bioassays to follow

 

[Infundibulum]

I'm doing the washing and every wash seems to increase the volume of the precipitate. Looks like it's becoming more and more fluffy.

I was also surprised that the first wash of my pH 8.7 precipitate had pH 10.4. I would have thought that adding tap water would have *decreased* the pH, not increased it.

Alkaloids are alkaline (= they raise the pH) and are named alkaloids due to their propensity to make the water basic.

So in clean, unbuffered water it is normal that an alkaloid preparation will have a pH >7