Sciencemadness Discussion Board - how much of a history does glassware keep?

how much of a history does glassware keep?

coppercone - 21-5-2018 at 11:22

Assuming you do a reasonable job keeping your glassware clean, how much of a history does it keep with previous reactions?

I imagine things like ground glass joints to be pretty bad.

I am interested in analytical chemistry and I wonder how much can be picked up by various methods as contamination.

Say you do some kind of reaction, then you wash the flask out with soap water, then do something like a ether or acetone flush, so it looks basically brand new. I understand the solvents might leave a residue ,but how much can you flush out of the previous ?

PPM levels of residue? PPB? More? Less?

How about after something like a plasma clean?

I am wondering how much residue is left, particularly if similar reactions are done. I can imagine something like being interested in what side products occur in a particular reaction (so the reaction mechanism can possibly be modified to avoid them)... you are left with a problem if you previously did a reaction that had side products similar to those that you may be questioning the generation of from you reaction of interest.

It would be helpful to me if I knew what kind of machinery can resolve what kind of history and what kind of cleaning can clean things up enough. I am interested in very small things.

Are there situations in professional research chemistry where they will buy or make brand new glassware just to verify a particular reaction?

I assume the worst offender would be the glass frit and then the ground glass joint.

Also contamination might act catalytically and modify the outcome of certain reactions.

Where do the theoretical limits of detection lie?

All I can think to do is to do some kind of calculation like the type used in homeopathic medicine... but how accurate will it be? Do things get trapped in some kind of micro fissures or something on the glass surface? (i.e. you are supposed to bake glass for a long fucking time before using it for moistureless reactions, way more then I would have thought necessary based on my understandings of things... people say like you need to bake stuff for 2 hours, I would have thought like 5 minutes is complete overkill unless I read it somewhere. It makes me think that everything is completely filthy.

Are there some kind of common analysis methods to verify glassware is clean, like optically some how? i.e. scanning it to look for something like thin films, etc... so you can have a reasonable sanity check. Other then careful visual inspection. special light source, laser, polarization?

[Edited on 21-5-2018 by coppercone]

aga - 21-5-2018 at 11:47

I think it was Magpie who once suggested dousing your glassware with phenolpthalein, then clean it using a dilute NaOH solution.

You'll soon see the bits you missed.

Fundamentally, glassware is as clean as you can make it, which is orders of magnitude greater than the purity of anything that you can synthesize in that glassware.

Do some chemistry and find out.

[Edited on 21-5-2018 by aga]

Rogueasset - 21-5-2018 at 12:41

Depends what you are synthesising. Hot soapy water followed by acetone then dcm get out most organics. If that fails then organics will be oxidised by things like piranha or chromic mixture (dispose of waste properly) then hot soapy water acetone dcm in that order and straight into the drying cupboard. Rinsing method is important, hold upside down over appropriate waste bottle and direct wash bottle into base of rbf or beaker.

If you are going into work up and then purification steps anyway and you have followed the above , I doubt you will have a issues with reaction vessel residues.

phlogiston - 21-5-2018 at 12:46

I use an extremely sensitive ICP-MS at work (concentrations in 'ppb' range are routine. Sometimes we need to measure in the ppt range). It can detect all kinds of metals that glass was previously exposed to (even after it passed through our industrial dish washer (actually, that machine contributes a number of elements itself too)), or that are part of the glass's chemistry (forget about using borosilicate glass if you need to measure small quantities of boron).
We don't usually know or care enough to find out exactly how the metals stick to the glass. I doubt they are in cracks. I rather think they migrate into the glass a few nanometers only to be released into solutions slowly with time. Perhaps some metals are coordinated at 'active sites' on the glass. Who knows.
We work around it by using plastic disposable tubes/pipette tips etc that we know are clean (ie. do not contain appreciable levels of the metals we are interested in), and we use those whenever possible. We avoid glass. If we absolutely need to use certain glassware, we test it to make sure it is clean and then wash it ourselves (i.e. not leave the task to the guy with the dishwasher), typically with dilute nitric acid.

[Edited on 21-5-2018 by phlogiston]

Sigmatropic - 21-5-2018 at 12:57

Are there situations in professional research chemistry where they will buy or make brand new glassware just to verify a particular reaction?

I've heard of a company manufacturing a drug (I believe it was ritonavir), as in on the market, for a year or so when all of a sudden they got a different polymorph of the drug. Same drug, same purity but a different crystal structure with different dissolution properties resulting in a lower bioavailability. This in turn caused them to temporarily withdraw the drug from the market. They tried cleaning the plant thoroughly but could not obtain the original polymorph. I heard they resorted to building a new plant (!) and obtained the original polymorph for about 6 months at which point the new polymorph appeared again.

So here is a case where an impurity, the new polymorph, was acting catalytically and disrupting the outcome of the process. Apparently no amount of cleaning could resolve this but it leaves me thinking that you cannot get something completely clean once it's used. And they weren't talking about just the glassware, no the building too.

Normally I would assume that such low level impurities have no influence on the outcome of reactions but crystallization really is black magic.

I couldn't find the reference I was looking for and may be mistaken about the identity of the drug. If anybody knows this story more specifically then please correct me.

[Edited on 21-5-2018 by Sigmatropic]

aga - 21-5-2018 at 13:09

New or used glassware - there are always contaminants.

In an Amateur Setting (certainly mine) the glassware cleanliness is less relevant than the size of the bugs that get into everything.

Pros would certainly need to take into account the glass manufacture material/melt/cleaning processes to stay in their game.

As far as i recall, SM is about Amateur Chemistry.

Clean or dirty glass, likely you'll end up somewhere in the ballpark.

To know exactly would be very hard, 'cos you'd have to do the experiment at least once and have it tested by someone who had the right equipment and knew what they were doing.

Finding those people is increasingly difficult.

DavidJR - 21-5-2018 at 13:21

Quote: Originally posted by Sigmatropic

Are there situations in professional research chemistry where they will buy or make brand new glassware just to verify a particular reaction?

I've heard of a company manufacturing a drug (I believe it was ritonavir), as in on the market, for a year or so when all of a sudden they got a different polymorph of the drug. Same drug, same purity but a different crystal structure with different dissolution properties resulting in a lower bioavailability. This in turn caused them to temporarily withdraw the drug from the market. They tried cleaning the plant thoroughly but could not obtain the original polymorph. I heard they resorted to building a new plant (!) and obtained the original polymorph for about 6 months at which point the new polymorph appeared again.

So here is a case where an impurity, the new polymorph, was acting catalytically and disrupting the outcome of the process. Apparently no amount of cleaning could resolve this but it leaves me thinking that you cannot get something completely clean once it's used. And they weren't talking about just the glassware, no the building too.

Normally I would assume that such low level impurities have no influence on the outcome of reactions but crystallization really is black magic.

I couldn't find the reference I was looking for and may be mistaken about the identity of the drug. If anybody knows this story more specifically then please correct me.

[Edited on 21-5-2018 by Sigmatropic]

Very interesting!

Attachment: Ritonavir_An_Extraordinary_Example_of_Conformational_Polymorphism.pdf (464kB)
This file has been downloaded 698 times

Attachment: Elucidation_of_crystal_form_diversity_of_the_HIV_protease_inhibitor_ritonavir_by_high-throughput_crystallization.pdf (385kB)
This file has been downloaded 417 times

coppercone - 21-5-2018 at 14:03

That's precisely what I am interested in.

https://www.youtube.com/watch?v=opfwmesQgys

Keep those stories coming. The bit about ritonavir is kind of like a chemistry ghost story but it is very interesting.

zed - 21-5-2018 at 16:34

Prions, which should be much more fragile than simple molecules, cannot be reliably removed from contaminated surfaces.

Brain electrodes once used on "Mad cow" type patients, transmitted disease to later patients, despite extensive cleaning and sterilization efforts. Chemical treatment and autoclaving, are not enough.

Likewise, when you have a facility where crystallizations are going awry, you might have to bag it, and go elsewhere. Crap. You might need to hire a completely new crew, and thereby cut all ties to the contaminated facility.

coppercone - 21-5-2018 at 17:36

I thought you can boil prion soaked stuff in NaOH 50% for like an hour to clean it?

i read about it, fuck that, throw that shit in a pit of molten metal like the fucking terminator

They need to make neurosurgical instruments cheaper so people dont attempt to clean em

[Edited on 22-5-2018 by coppercone]

weilawei - 22-5-2018 at 05:15

Quote:

The only thing to do was to keep the peroxide in a tank made of something that didn’t catalyze its decomposition (very pure aluminum was best) and to keep it clean. The cleanliness required was not merely surgical — it was levitical. Merely preparing an aluminum tank to hold peroxide was a project, a diverting ceremonial that could take days. Scrubbing, alkaline washes, acid washes, flushing, passivation with dilute peroxide — it went on and on. And even when it was successfully completed, the peroxide would still decompose slowly; not enough to start a runaway chain reaction, but enough to build up an oxygen pressure in a sealed tank, and make packaging impossible.

Perhaps we should clean them like this. Maybe wash them in ClF3 after?

[Edited on 22-5-2018 by weilawei]

Tsjerk - 22-5-2018 at 06:55

These guys reported a reassessment of there "palladium free" Suzuki couplings, the catalyst appeared to be palladium after all, at 50 ppb coming from there sodium carbonate. (50 nanogram per ml, pretty potent catalyst, corresponding with 200.000 reactions catalyzed per Pd atom in 5 minutes (20% yield).

Not that is has a whole lot to do with this threat, but I remembered this when reading about sub-detectable catalysts.

Attachment: arvela2005.pdf (187kB)
This file has been downloaded 531 times

zed - 25-5-2018 at 13:09

Some scientists were proposing that even incineration might not completely inactivate some prions.

Perhaps residual carbon in the "ashes" might provide a "template" or "stencil", that could
(if ingested) stick to healthy proteins, and serve as a jig, to encourage the manufacture of deadly new prions.

Not unlike molecular sieves, providing an inorganic scaffolding for "newly arrived" H2O molecules to nestle into, thereby replacing those, now long departed.

[Edited on 25-5-2018 by zed]

[Edited on 25-5-2018 by zed]

phlogiston - 25-5-2018 at 13:37

That is an interesting but extreme view, and I don't believe any credible evidence exists to substantiate that concern.
I would be confident that the WHO recommended procedures of treating surgical instruments with 1N NaOH and 1N of hypochlorite and autoclaving are good enough. I'd undergo brain surgery myself with instruments being treated thus.

unionised - 26-5-2018 at 03:32

Quote: Originally posted by phlogiston

I use an extremely sensitive ICP-MS at work (concentrations in 'ppb' range are routine. Sometimes we need to measure in the ppt range). It can detect all kinds of metals that glass was previously exposed to (even after it passed through our industrial dish washer (actually, that machine contributes a number of elements itself too)), or that are part of the glass's chemistry (forget about using borosilicate glass if you need to measure small quantities of boron).
We don't usually know or care enough to find out exactly how the metals stick to the glass. I doubt they are in cracks. I rather think they migrate into the glass a few nanometers only to be released into solutions slowly with time. Perhaps some metals are coordinated at 'active sites' on the glass. Who knows.
We work around it by using plastic disposable tubes/pipette tips etc that we know are clean (ie. do not contain appreciable levels of the metals we are interested in), and we use those whenever possible. We avoid glass. If we absolutely need to use certain glassware, we test it to make sure it is clean and then wash it ourselves (i.e. not leave the task to the guy with the dishwasher), typically with dilute nitric acid.

[Edited on 21-5-2018 by phlogiston]

And, in the interest of balance...
I worked in an organic chem analysis lab.
We avoided the use of plastic equipment because it leached phthalates and silicones etc into everything. There was also the problem of everything sticking to the plastic by "dissolving" into it.
If you really wanted to be sure the container was clean, you used glass.
From the organics point of view you can heat the glass to 400C in air for a while and be absolutely certain that it's clean.

Perhaps we can agree that PTFE is useful stuff.

coppercone - 26-5-2018 at 08:04

Can you also clean a frit that way?

How long do you keep stuff at 400C?

I am guessing you are just left with some kind of ash residue?

[Edited on 26-5-2018 by coppercone]

Tsjerk - 26-5-2018 at 09:20

As soon as you hit 400 degrees Celsius you are done, and it will probably leave some oxidized carbon polymers I guess.

unionised - 26-5-2018 at 11:47

Given a while, the carbon also burns off.
It's quicker if you rinse stuff with sulphuric acid, then heat it to boil off the acid- but the fumes are nasty.

How long it takes depends on how much stuff you are trying to remove (and yes, it will work with a frit, but you need to be sure it's borosilicate. Also the diffusion of air into the pores in the glass will be slow.

Obviously, it's a lot better if you can get the glass pretty nearly clean first.

coppercone - 27-5-2018 at 07:29

Hmm, so the biggest problem is then metal ions?

Are there any in particular? Like magnesium for instance, used in grignards, wont it just go to inert MgO2?

Are there known troublemakers we should keep seperate glassware for?

zed - 30-5-2018 at 13:55

Seems like I remember a caution about heating Formic Acid, in glassware formerly exposed to Platinum. But, perhaps.... I am mis-remembering. It has been a long time since I vacuum distilled Formic Acid. Maybe never? Better check>

Yeah, I've vacuum distilled formic acid. Sometimes abruptly decomposes, for no apparent reason.

[Edited on 31-5-2018 by zed]

phlogiston - 31-5-2018 at 05:26

It is impossible to generalise what the 'biggest problem' is.
Whether there even is any problem in the first place depends on what you are trying to do.

In the opening post, you asked about analytical chemistry, but you also seem interested in contaminants that might interfere with organic synthesis.

Because analytical techniques can be highly sensitive, you are more likely to experience effects from contamination, especially if the contaminating species are similar to what you are trying to measure.
Some of the replies describe how metals and organic contamination presented problems in analyses. They are just examples, I'm sure there are countless more stories, and the replies you got so far are unlikely to be a good representation of glassware contamination problems in general.

LearnedAmateur - 31-5-2018 at 08:49

Quote: Originally posted by unionised

It's quicker if you rinse stuff with sulphuric acid, then heat it to boil off the acid- but the fumes are nasty.

I do this when I get charred crap in my flasks, works well for small amounts of staining and lumps which can’t be reached by mechanical scraping, although I don’t boil off the acid completely. I heat until white fumes are given off then pour it into a waste container when cooled, followed by a few rinses with water to remove the last of the particulates. Especially handy since I don’t have access to concentrated H2O2 for Piranha or enough nitric acid for cleaning purposes.

In general, I found this article, seems like it might come in handy for some:
https://www.sigmaaldrich.com/technical-documents/articles/la...

Edited for spelling

[Edited on 31-5-2018 by LearnedAmateur]

DavidJR - 31-5-2018 at 08:59

Quote: Originally posted by LearnedAmateur

Especially handy since I don’t have access to concentrated H2O2 for Pirhana or enough nitric acid for cleaning purposes.

I buy 12% H₂O₂ since that's the max allowed without an EPP licence, and in combination with some 91% sulphuric acid drain cleaner it works pretty well.

LearnedAmateur - 31-5-2018 at 10:21

I mean I’d buy some if I’d use it for multiple things, but I very rarely order reagents which would only have a single use, especially if I’m buying a few hundred grams or a litre at least. I simply don’t have a need for hydrogen peroxide in synthesis, whereas I have plenty of sulphuric acid (on my synthesis scale anyway) for instance because I use it for a lot of things, and have enough to spare for glassware cleaning.

kulep - 31-5-2018 at 10:34

35% H2O2 for pool sanitation tends to be quite cheap in some places (where it hasn't been banned)

DavidJR - 31-5-2018 at 10:46

Quote: Originally posted by LearnedAmateur

I mean I’d buy some if I’d use it for multiple things, but I very rarely order reagents which would only have a single use, especially if I’m buying a few hundred grams or a litre at least. I simply don’t have a need for hydrogen peroxide in synthesis, whereas I have plenty of sulphuric acid (on my synthesis scale anyway) for instance because I use it for a lot of things, and have enough to spare for glassware cleaning.

Hydrogen peroxide is extremely useful. It's also probably the cheapest and most ecologically-friendly oxidising agent other than air/oxygen gas.

Fulmen - 31-5-2018 at 12:30

Heat is probably the best choice for organics. I once worked at a lab analyzing among other things CHC and dioxin emissions using GC-MS. As I'm sure you can imagine these were extremely low concentrations, even after concentrating several liters of sample down to a few ml's of extract. All glassware in the lab was cleaned in a dishwasher with a very strong detergent, rinsed with distilled water and burned overnight at 400°C.
Must have cost a fortune as equipment routinely broke during the process. And we're not just talking beakers here, graduated flasks, pipettes, custom gas sampling equipment, soxhlet extractors, everything was treated this way.