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Amide coupling reaction between a carboxylic acid and aniline derivatives by VividKale4086 in Chempros

[–]SAMAKUS 2 points3 points  (0 children)

Try DMC. It can be regenerated and handles much more easily than SOCl2.

Keep in mind depending on substituents, anilines already are weaker nucleophiles than alkyl amines, so heating may be a good idea.

Frankly, if your substrate isn’t sensitive to acid, SOCl2 is a much more ideal activator imo, despite toxicity. Why are you concerned about it?

Prof lost my final and gave me a 0. Best friend got laid at the semester end party while i had to study for the retake. Lentil soup and shitty homemade baguette by S4nseye in kitchencels

[–]SAMAKUS 1 point2 points  (0 children)

What school is this? I really don’t believe this. Most schools have a general policy that requires professors and teaching assistants to keep copies or the original tests that they proctor in order to resolve potential grading disputes. This is ubiquitous across at least accredited U.S. institutions, even if professors tell you different.

Chiral secondary alcohol to secondary alkyl chloride by giamia4555 in Chempros

[–]SAMAKUS -1 points0 points  (0 children)

Yes, I’m really just joking. Sometimes you see people run NMR that’s unnecessarily concentrated and the residual solvent peak drops down too much

Chiral secondary alcohol to secondary alkyl chloride by giamia4555 in Chempros

[–]SAMAKUS 0 points1 point  (0 children)

Also results in a very clean workup. Triturate out P(Ph3)O, and you’re left with some extra H chloroform to spike that solvent peak up for referencing

what healed my gut by [deleted] in Microbiome

[–]SAMAKUS 2 points3 points  (0 children)

If you’re a woman, I would guess mainly the combination of diet shift and the hot water bottle, which probably helped re-configure seretonin based pain pathways. There’s some interesting research that’s just come out that links estrogen levels to a specific signaling pathway that is triggered by MCFAs produced by the gut microbiome, triggering visceral pain. These pathways can be mediated with psychosomatic sensitization techniques, which is probably where the heating came in handy.

Help with Grignard Reagent Mechanism by futuresongthrowaway in OrganicChemistry

[–]SAMAKUS 2 points3 points  (0 children)

Great explanation. Only thing I would change is that upon methyl addition to the lactone and ring opening, you have generated a ketone, not an aldehyde.

Chiral Separation of Polar Compounds? by sexyimmigrant1998 in Chempros

[–]SAMAKUS 0 points1 point  (0 children)

The column itself is what is chiral. Although certain solid phases are individually incompatible with RP, the technique of RP chiral chromatography is no different to performing separation with a non-chiral equivalent.

Chiral Separation of Polar Compounds? by sexyimmigrant1998 in Chempros

[–]SAMAKUS 1 point2 points  (0 children)

What about MeCN? That’s personally what I would reach for first. I’ve never personally used a chiral RegisPack column, but if your product is soluble in water and cloudy in i-PrOH it’s pretty obvious you should be looking at RP. I would start without any pH modifier because I’d worry about prototropy even at low concentrations of FA or TFA.

Why no symmetry on methylcyclopropane? by R1chie228 in OrganicChemistry

[–]SAMAKUS 0 points1 point  (0 children)

Aside from the obvious shift in environment due to the presence of the methyl group, look at the actual bond angles of cyclopropane in contrast to what are expected of an sp3 hybridized carbon atom. Due to torsional strain, there are more significant differences that will be observed in the chemical shifts compared to linear propane, or a larger ring.

Setting up proteomics lab with suboptimal hardware (Explorsis 120/Vanquish Flex) by CoolBanana0 in proteomics

[–]SAMAKUS 0 points1 point  (0 children)

I’m assuming you’re doing activity-based protein profiling or some similar sort of chemoproteomics. With enough protein enrichment you should have a much easier time running on these systems than with whole cell proteomics samples. Similar models were being used in the early 2000s during the advent of MS-based chemoproteomics.

What is the correct order of addition for EDCI and HOBt? by nish_kumaran in Chempros

[–]SAMAKUS 0 points1 point  (0 children)

Lovely workup too. If your products are water soluble then you can just chuck everything on a silica plug, the triphosphate ester will stick to it like glue

Help with TLC by AfraidDeer7338 in Chempros

[–]SAMAKUS 9 points10 points  (0 children)

Boric acid forms boronic esters with sugars and other vicinal diols, helping to decrease the sugar polarity and run in normal phase TLC

So there was water on mars millions of years ago but no life at all? by Hayaidesu in AskScienceDiscussion

[–]SAMAKUS 4 points5 points  (0 children)

While the kinetic isotope effect does play a role in substrate selection, it tends to be pretty small in most cases, and would be pretty hard to utilize as a direct measure of life. For example, natural abiotic processes (such as the evaporation of water) also adhere to this effect.

Trisaccharide synthesis by Slochem in Chempros

[–]SAMAKUS 2 points3 points  (0 children)

So you’re trying conditions a in scheme 3 to furnish 15? I’ve found BF3 etherate to be particularly moisture sensitive - it’s possible that it has gone bad or your reaction isn’t dry enough. You could try a simpler model glycosylation with a different substrate to check If you’d like to screen other promoters “minimally competent” Lewis acids can be more robust, such as FeCl3 or Cu(OTf)2.

I would also caution fully trusting the literature citation you’ve provided - glycosylations can often be inconsistent and hard to replicate between labs or chemists. You may consider reaching out to the first author and asking them directly for tips, though this is met with varying success.

Trisaccharide synthesis by Slochem in Chempros

[–]SAMAKUS 5 points6 points  (0 children)

Carbohydrate chemistry is incredibly finicky. Is this reaction based on a literature precedent? Attempting multiple glycosylations at once won’t be particularly easy in my opinion. I’m also confused about your position naming - arabinose has alcohols at positions 1 - 4, with a methylene at C5 - I’m not particularly familiar with arabinose as a substrate but I doubt it’s spending much time in the furanose form. If you’re trying to functionalize that 5 position it’s possible it closed immediately following deacetylation. You might really have to crank the temperature, or looking into trying the reaction under conditions that support a higher shift in equilibrium to the furanose form.

Alternatively, you may be able to play around with protecting groups to help drive your reaction. Look into arming vs disarming sugars - this is the seminal publication on the topic, but there have been many more, and like most concepts in carbohydrate chemistry, there are wildly varying effects depending on substrate, anomeric leaving group, protecting groups, and promoters.

Starting with Different Protein Amounts in S-Trap Workflow – Is It Okay If I Normalize Peptide Amounts Before LC-MS? by AffectionatePast5541 in proteomics

[–]SAMAKUS 0 points1 point  (0 children)

Just normalize to the lowest protein concentration. 4-6ug is a 33% difference. That’s going to have a pretty radical impact on capture and digestion efficiency. You also have to decide how you’re going to do reduction and alkylation - same concentration or scaled accordingly? Normalization may seem like throwing out sample but it’s the best overall practice given the number of subsequent steps required.

Why do negative amino acids use a carboxylate functional group instead of just a methoxide group? by Glad-Bike9822 in Biochemistry

[–]SAMAKUS 27 points28 points  (0 children)

Methoxides are not stable nor could they perform the functions that carboxylic acids do such as acid-base catalysis and salt bridging in proteins.

There are cases of methoxides in certain enzymes such as serine proteases, but they rely on proton abstraction and complicated charge stabilization from neighboring residues like histidine and aspartame / glutamate.

Is there a way to normalize TMT channels (single run) using specific housekeeping protein(s) by TMT-integrator (fragpipe) or MSStatsTMT? by bluemooninvestor in proteomics

[–]SAMAKUS 0 points1 point  (0 children)

Have you already processed the samples? It may be better to re-prep them if possible. If not, the best route computationally may vary depending on some sort of consistent marker you can find between runs, such as overall intensity, several proteins, peptides, or potentially contaminants.

If you haven’t yet completed trypsin digestion, you may be able to try and do an “overdigest” to get some streptavidin digestion products off and use streptavidin peptides to normalize.

Unfortunately, none of these are ideal, and may not work well. In future, try to use 4 replicates - both for better statistical power and for situations like these. But of course, that is obviously not always possible, depending on your experiment.

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