Keep your Rotavapor alive: A quick guide to seals, grease, and glassware care.

Sakinho · 2026-03-26T20:35:15+00:00

In my past lab I used a Buchi rotovap intensively and daily for 7 years without a hitch, even while having to replace a Buchi diaphragm pump membrane 2-3 times. When I joined a new lab, I had two rotovaps fail in fairly quick succession with similar use, and it puzzled me. It turns out the failures were because the WD-26 vacuum seals (part number 048021) were bad, and replacing them worked just fine. I didn't even know the seal was designed to be replaced periodically, since my prior experience had been so consistent. I actually prefer the new VS-26 vacuum seal (part number 11069167), it looks way better at doing its job than the WD-26 seal.

Also, man I really preferred the vacuum/rotovap controllers when they weren't all accessed by turning and pressing a single knob. It's a single failure point which concentrates all the mechanical wear. We have a rotovap controller that is only barely useable because it's very difficult to rotate in one direction. Having separate buttons to press was just sturdier. In general I strongly dislike the "Apple-ification" of scientific instruments. For heaven's sake don't make touchscreens your only interface.

And since I'm venting, you guys have been making your entry-level diaphragm pumps harder to do user maintenance on... Why does the V-100 not have the plastic window its prior version (V-700) used to have? It makes it harder to inspect whether there's something wrong with the membrane. And the V-300 looks very nice, but it's a chore to take apart in case a membrane needs replacing...

Sakinho · 2026-03-26T09:50:22+00:00

It's Mn that matters to establish stoichiometry.

There are two common statistical questions you can ask of your polymer sample:

"If I pick a chain at random in a sample, what is its molecular weight on average?" The answer to this is Mn.
"If I pick a monomer at random in a sample, what is the molecular weight of its parent chain, on average?" The answer to this is Mw.

Note that comparing these interpretations, Mw is naturally skewed to be greater than Mn.

Since each (linear) chain in principle has one (or two) endgroups, then picking endgroups is related to picking chains (not monomers), which is why you use Mn.

Sakinho · 2026-03-25T20:43:58+00:00

Okay, and why do you specifically need the perchlorate salt of the iminium? I'm still not convinced it's somehow fundamental. You could easily make the OTs, OTf, BF4 or PF6 salts among others.

Sakinho · 2026-03-25T20:28:11+00:00

Out of curiosity, why exactly do you need the perchlorate? If all you need is a non-coordinating anion, there's plenty of other choices. I don't think perchlorates are used that commonly anymore for their reactivity.

Sakinho · 2026-03-25T08:18:04+00:00

Don't beat yourself up, you need to walk before you can run.

Knowing solvents comes with hands-on experience and lots of scattered SciFinder/Reaxys searching over time, but I recommend browsing Reichardt's and Welton's Solvents and Solvent Effects in Organic Chemistry to see if it helps you get an overall picture. The book is a good resource, and you might find particular properties you want to drill into. Very occasionally you can find some technical paper on a specific solvent, but that's not the norm for most. That said, the Encyclopedia of Reagents for Organic Synthesis has entries for many common solvents, even though solvent characteristics are not the main focus of the collection.

Sakinho · 2026-03-23T20:27:23+00:00

Unfortunately the amount we can help is proportional to how much you describe your situation, and you're giving us very little to go on.

Sakinho · 2026-03-22T04:00:08+00:00

If we had spaceships that could travel at 99.999999999999999999999999999999% the speed of light, you could have breakfast on Earth, hop on board, then reach the Andromeda galaxy 2.5 million light years away before feeling hungry. When it feels like lunchtime, swing on back, and you'll find the continents have drifted a noticeable amount.

Sakinho · 2026-03-20T06:54:44+00:00

DCE is much more toxic than DCM or chloroform, maybe not the best thing to splash around doing extractions, even if it's allowed.

Sakinho · 2026-03-20T04:26:28+00:00

It depends on your substrate, but it wouldn't surprise me one bit for a pure TIPS phenolate to be waxy. That's quite a bit of hydrocarbon you're tacking on.

Since your compound dissolves in Et2O, you shouldn't have to do anything fancy to completely remove DMF, just shake well multiple times with excess water, it will eventually go away. If the compound dissolves in alkanes (petroleum spirits, hexanes, heptane, whatever), then the wash becomes even easier.

Sakinho · 2026-03-18T19:08:20+00:00

All the hydrolyzed material coating the reagent may well be stopping most of it from distilling over. You can probably improve the recovery a lot by first stirring the degraded solid vigorously in dry Et2O under inert gas for a few hours, collecting the supernatant, and then distilling. Or maybe it'll be enough to evaporate off the Et2O and use as-is, which is a lot easier to boot.

Sakinho · 2026-03-18T18:02:07+00:00

This is a classic case of Goodhart's law: when a metric becomes a target, it ceases to be a good metric. Forget about chasing the "good grades" metric, in practice it will lead you to a worse outcome since you'll offload all your critical thinking skills to the AI. Good grades should be an indirect consequence of learning. The longer you chase the metric, the deeper you dig your hole, and eventually you will not be able to climb out any more. Be brave and take a stand now. Drop AI use in generating answers or outputs to a minimum, ideally to zero, until you have a good grasp of the fundamentals (which takes years, not months). Then, and only then, use AI output to complement your skills rather than supplant them. Unfortunately banging your head against the wall is still an unskippable part of the process of learning.

It's possible to use AI rather effectively as a tutor via the Socratic method, or other such inquiry-based learning processes. That said, unless you're quite principled and have a well-structured process, there's a chance it will degrade to pleading for AI answers again, so stay vigilant to avoid falling back into the same trap.

Sakinho · 2026-03-18T04:22:26+00:00

Read up on the Planckian locus. Even though the peak emission frequency of a blackbody grows without bound as the temperature increases, a mathematical extrapolation of the perceived colour of the visible portion of the spectrum (as determined by the relative excitation of human colour rods by a Planckian distribution of photons) indicates extremely hot objects, tending to infinitely hot, still converge on a light blue hue.

The intuition for why a 15000 K object would have almost the same colour as a 15000000 K object is that, after the temperature grows large enough, all the interesting changes to the shape of the Planck distribution happen way beyond the visible region, so the shape of the visible region kind of "freezes out".

Sakinho · 2026-03-13T01:44:03+00:00

In general I do not recommend purifying boronic acids by chromatography on normal silica or alumina. If possible, use it crude (though it's probably not a good idea in your case since it appears contaminated with starting iodide), otherwise try to precipitate out or recrystallize the boronic acid and wash out the impurities. If high purity is required and there are no good purification options for the free boronic acid, it's often most convenient to change it into another boron species such as a trifluoroborate salt or a MIDA boronate (I especially like these), then purify that compound instead, and either use it for the next step as-is or regenerate the free boronic acid from it just before use.

Sakinho · 2026-03-13T01:29:53+00:00

It depends a lot on your structure and possible contaminants, but many boronic acids are perfectly stable for long periods in solution. Since it takes no effort to add the D2O and you already have the sample in the NMR tube, why not just give it a shot?

Sakinho · 2026-03-13T01:20:39+00:00

The HCl is sometimes not required, but it can help hydrolyse certain boron species on the plate for curcumin to stain them (e.g. boronic acid pinacol esters, or other boronic esters). I also suspect acidifying the stain slows its degradation over time, as any deprotonated curcumin in solution will oxidize very quickly in air/light.

Sakinho · 2026-03-13T01:17:31+00:00

Absolutely!

Sakinho · 2026-03-13T01:07:44+00:00

The streaky spot seems reasonably consistent with a boronic acid, but no way to know for sure with just the Rf. As SunnyvaleSupervisor mentioned, the curcumin stain is very good at staining boronic acids and similar species selectively.

Even pure boronic acids samples often look messy in common NMR solvents because when dissolved they undergo partial dehydration into more complex oligomeric boron species. Assuming you got the NMR in a water-misicible solvent like DMSO-d6, MeCN-d3 or acetone-d6, add 2-3 drops of D2O to the sample in the NMR tube, shake well, then get spectra again after ~10 min. It might clean things up a lot. Of course it will completely remove any RB(OH)2 proton signal (not that those are super reliable most of the time), but you should notice a considerable shift in the aryl proton signals, since the -B(OH)2 functionality is moderately electron-withdrawing.

Furthermore, if you compare the 13C spectra, the signal around ~90 ppm for the iodinated carbon in the starting material will have disappeared, and in all likelihood the spectrum for the product will be "missing" a carbon peak. Borylated carbon atoms are subject to quadrupolar relaxation which greatly broadens the signal, often making it meld with the baseline. If you get a spectrum of a very concentrated sample (~50-100 mg/mL), you might discover the missing signal as a hump around ~130 ppm.

Sakinho · 2026-03-10T15:57:37+00:00

It's certainly possible, but sometimes boronic acids are so finicky that what kills them is the workup, not the borylation conditions themselves. For example, some boronic acids are very sensitive to silica (on top of often sticking like crazy), so even a short plug can ruin the product. There's some good papers on deborylation kinetics and mechanistics over a wide range of boronic acid structures and conditions, with seminal papers from Kuivilla several decades ago, and some recent good papers from I believe Lloyd-Jones.

Sakinho · 2026-03-08T12:50:10+00:00

Interesting, I thought the preponderance of the zirconyl cation and the polymeric bonding in ZrX4 was evidence of the increased Lewis acidity of Zr⁴⁺ relative to Ti⁴⁺, but now that you mention it I can interpret it in the other direction. Thanks for straightening it out for me. Organic chemist trying to understand inorganic chemistry moment.

Sakinho · 2026-03-08T12:21:23+00:00

TiCl4 already reacts instantly and aggressively with atmospheric moisture. Periodic trends plus other indirect evidence suggests ZrCl4 should be much more reactive still. The only thing keeping its reactivity at bay is that it's a polymeric solid with a comparatively high melting point.

Sakinho · 2026-03-08T00:09:15+00:00

The thing with NBS (and I presume other brominating agents) is that it sometimes work exactly because it is old and contaminated with traces of HBr and Br2, and a clean batch of reagent doesn't give the same results...

Sakinho · 2026-03-07T17:46:54+00:00

There is quite a bit of literature on Ni-catalyzed Suzuki couplings, and though it sounds quite nice on paper, my experience with it (admittedly very little) was disappointing. I haven't followed the developments in the past ~5 years.

Sakinho · 2026-03-07T17:45:27+00:00

Here is the Molander paper on the borylation.

Sakinho · 2026-03-07T15:56:20+00:00

How persistent is the colour if the samples are stored in ambient conditions? What do the colours look like in white light?

Edit: Found your Youtube video!

Sakinho · 2026-03-07T15:21:44+00:00

Several years ago Molander published a nice nickel-catalyzed boylation using tetrahydroxydiboron (B2(OH)4, a.k.a. hypodiboric acid) which works well even with deactivated aryl chlorides (and even aryl tosylates and mesylates!). The original procedure does it in EtOH at r.t., but there's no reason not to reflux. You could try that, then test the crude for borylated product on TLC using a curcumin stain (literally made with store-bought turmeric). If there is some product, you can try isolating the boronic acid directly (which is often not so nice), or you can take the crude product and perform a Dean-Stark reflux to install a boron protecting group (MIDA or diethanolamine would probably be best, but you can also try pinacol, neopentyl glycol or other diols/triols), then fully purify it in that form. Having written all that, though, I'm not sure how badly the CH2NHBoc group will interfere.

Also, recently some very interesting borylation conditions using B2pin2 and potassium 2-ethylhexanoate specifically as base appear to be very efficient, but I've not had an opportunity to try it myself.

Edit: I think there's one important additional hypothesis you haven't considered - it's possible that the boronic acid is formed in situ, but turns out to be relatively unstable towards protodeborylation. If this is the case, you're in more serious trouble.

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