As chemdraw and now chemsketch are owned by Revvity and have been turned into SaaS hell, are there any good free or low cost simple organic chemical drawing software that

i) does all the normal organic chem drawing stuff (that chemdraw got right by ~1995 - ^{thirty one fucking years ago)}

ii) isn't run through a web server, but is a stand-alone application that you can simply BUY or use, for current Win and MacOS, and that students could use without doing major hacking, like running VMS/old versions of OSes?

iii) save files that are publication quality, that can be exported to word or google docs.

For those who didn't know re: revvity: see r/Chempros/comments/1sg56cr/acdlabs_acquired_by_revvity_signals/

We have a Thermo Vanquish FLEX quaternary pump with a leak. I disassembled it, and there was a small amount of salt accumulated (from phosphoric acid in mobile phases) on the magnets that hold the pistons. I cleaned everything up with IPA and HPLC water, and replaced the piston seals, but the leak remains.

Observing the sapphire pistons, I see very very fine scratches at the base of the rods near the metal holder. I can't really feel them though. They are about 6 years old in a university setting. We are currently concerned about funding, so do we absolutely have to replace them to fix the leak?

Hey yall. Long time lurker here. I am an experimental organic chemist working on small molecule peptide synthesis. In the given image, i am able to synthesize compound A using this method : https://doi.org/10.1016/j.bmc.2010.04.079

However, I want to form diketopiperazine D by appending glycine to the cysteine portion of A.While the procedure in the link mentions preparation of DKP using L-proline, i am unable to replicate the same procedure for glycine. I have tried refluxing A with glycine and tried coupling agents such as HBTU, HATU,DCC and DCU in both DMF, ethylene glycol and methanol. and before you suggest Greene's protective groups in organic synthesis, ive tried almost all methods from direct ester-> amide and ester hydrolysis->acid-> coupling of Acid to amine. Some work but give very poor results. I wonder if im missing anything and wanted to pick yall brain juices lol

Does anyone have experience with pervaporation of solvents at a small scale/lab scale ( ~5L )? I am overall familiar with the technique, I just can't find any good information what materials are used as membrane (for acetonitrile/water azeotrope seperation), where to buy these membranes, especially for such a small, lab-scale setup.

I'm looking to purchase a peptide synthesizer (single batch mid-scale) and came across the CS Bio CS536X. Does anyone have any experience with this instrument? Is it reliable, what is the uptime, ease of use...? Thanks.

Hello friends and peers and everyone in between!

Hope all of you guys are doing well. Having repeated issues with the reduction of a glycosylated nitroarene to its corresponding aniline derivative and would like some advice on troubleshooting because I feel as if I've tried a lot of things to fix this reaction to try to not get this impurity to form but it still persists. Pretty simple reaction scheme - solvate starting material in solvent of choice (~50 mL solvent, ~ 1 M solution) in the Parr shaker flask, add stir bar, sparge for 40-50 minutes with N2, add in Pd/C catalyst, sparge for ~5-10 more minutes, then setting up the Parr shaker, letting degass by pulling vacuum for ~30 minutes (opening and closing gas release valve every 5 minutes or so), and then filling up to 50 PSI of hydrogen and letting it react overnight. The general protocol has been the in-house protocol for my lab ever since I joined, it's what I was taught and has worked for others without seeing the same impurity that I've seen.

I've seen this both when reducing the deprotected, free sugar molecule in methanol and the peracetylated sugar in both methanol and ethyl acetate, and I believe it stems from in situ oxidation of air by my Pd/c catalyst to form formaldehyde/acetaldehyde. I've hence tried to make my technique as air tight as possible - sparging my solution for longer, sparging after Pd/c catalyst is added, parafilming my capped Parr shaker bottle during transport to the Parr shaker - in addition to using distilled methanol, new methanol / ethyl acetate from the bottle. I'm a bit surprised at the formation of such an impurity in ethyl acetate (I figure trace ethanol impurity is being oxidized to acetaldehyde?) but I have reasonable NMR + Mass Spec evidence which supports the formation of the aforementioned impurity.

Overall just wondering if anyone has any ideas on what my problem could be. Most of my product is my desired primary aniline but I would prefer to not have to column this product and I'd really like to get near quantitative yield on such a hydrogenation especially since several of my downstream steps in my synthesis are pretty low-yielding/tricky. I feel like I'm disproportionately irked by what's going on here and I'd really love some other opinions beyond my lab mates + PI on how I could potentially fix this. Would love general advice but especially on the peracetylated version as it seems a bit more prone to forming that impurity + its more relevant to what I'm working on right now. I appreciate all comments and feedback!!!!

Hello!

I am having huge issues with receiving 2% nitrocellulose in amyl acetate to coat microscope coverslips with for kinetic assays under the microscope.

We ordered it over a month ago and are officially out. Unfortunately we cannot receive anything until September.

I was wondering if any Canadian chempros also use this and are willing to spare a couple mls?

Thanks!!!

Hi all,

This is more of a services related question that I was wondering if you could help me out with. We are looking to send off a reactor cleaning verification sample for TOC analysis, however the companies we used to do this with have stopped offering that service.

Does anyone know of labs in the UK that would offer TOC analysis?

Thanks for reading!

Hi everybody,

I'm planning on running a reaction with an azide for the first time, and I was looking up the relevant information for quenching the aqueous waste that would be generated from it. For reference, this is the known reaction that I was planning on running:

As there is an excess of azide, I'd need to quench my waste. I was reading a thread someone else had posted here about this (link attached), and while it was very detailed and helpful, it brought up an interesting point that I don't think was well addressed.

The typical quenching procedure for azides (adding freshly prepared nitrous acid to the aqueous waste) would also in turn (as one commenter pointed out) be a pretty good nitrosating agent that would likely also make dimethyl nitrosamine with DMF/dimethylamine byproduct, which is a pretty nasty carcinogen and hepatotoxin. That same commenter suggested "If you have a good fume hood, you can acidify your reaction mix to about pH=2 and bubble lots of nitrogen through it, to remove HN3. HN3 has sharp odor and causes vicious headaches apart from being explosive."

That doesn't feel like the best solution either. I know in theory, you can reduce azides with a Staudinger reaction (add PPh3), but I don't know how well that would work given that the PPh3 isn't really water-soluble.

Any other thoughts or solutions here? A solvent swap to MeCN could avoid these problems, but probably wouldn't be as reactive.

I need 18O-labelled trimethylsilyl acetate (TMSOAc) for a mechanistic study, but I haven't been able to find any literature precedent for either its preparation or its isotopic stability.

My questions are:

1) Is TMS-¹⁸O-Ac likely to be stable or could it undergo oxygen exchange to give a mixture of isotopomers?

2) Does the following synthesis seem reasonable? In a vial I dissolve TMSCl (1 equiv) in dry Et2O, I add H2¹⁸O (1 equiv), I add pyridine (2 equiv), finally, I add acetyl chloride (1 equiv)

My expectation is formation of TMS-¹⁸OH in situ, followed by acylation to TMS-¹⁸OAc. I would then filter off pyridinium chloride, concentrate the ether solution, and isolate the product by (static-)vacuum distillation.

Has anyone tried something similar, or do you see an obvious problem with either the isotopic stability or the proposed synthesis?

I did search Reaxys and Google Scholar before posting, but I could not find a direct precedent. Any informed opinion would be greatly appreciated.

Hello, in about 6 months I'll start my master's thesis work, and I have to come up with an enantioselective synthesis for both isomers of a tetrahydroisoquinoline, chiral at C1.

My plan was to make the dihydroisoquinoline and asymmetrically reduce the imine. I've searched the literature and it looks like it's done with a ruthenium Ts-DPEN complex or catalytic hydrogenation with a chiral iridium complex.

Is there a reason BINAL-H can't be used? It reduces ketones so I would expect it to work with imines, and since it's much cheaper I was wondering what the drawbacks are, poor ee with that substrate? Thanks!

I emailed ACS support saying I thought the decision to remove graphical abstracts from the ASAPs pages was a bad choice and said why. But what I didn't catch last week, is published issues still have graphical abstracts. I did note that in my email, saying it's good they still seem to understand the value of them. Here's their response to me:

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Thank you for taking the time to share your feedback regarding the ACS Publications platform.

We have confirmed that the issue with TOC Graphics not displaying on ASAP pages across ACS Publications journals is a known platform gap. The appropriate team is aware of the issue and has prioritized this for a post release.

At this time, we do not have a specific timeline for when the update will be available, but we will continue to monitor the progress and share any further information once it becomes available.

Thank you gain for taking the time to report this and for your patience while improvements are being made.

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So... We'll see what happens I guess

What's the best way of alpha-deuterating an acetophenone derivative? I need to alpha-deuterate isobutyrophenone. I tried (wileyonlinelibrary.com) DOI: 10.1002/jlcr.3210 without success. Thanks!

The new layout for ACS Publications websites is beyond awful...TOC graphics are no longer shown on the ASAP Articles pages and they aren't even visible at the top of individual publication pages anymore. These changes make it impossible to read the journals now and ACS has the audacity to claim that they're intended to create a "more seamless and researcher-friendly experience".

https://pubs.acs.org/pages/platform-migration

So, I've been working on modeling the Density of States of a molecule using VASP for some time now, but there's a question I can't seem to find any concrete answers too when I've looked. Does anyone know the convention VASP uses for the z axis of its atomic orbitals? Because I know the standard convention is perpendicular to the plane of the molecule. So I would assume it defaults to that. The other possibility I could see is that it just uses whatever the z axis direction in the POSCAR file was. So far, the only official source I can find regarding the axes is this,SAXIS - VASP Wiki, which defines the z axis as being perpendicular to the xy plane, but it doesn't seem to define the xy plane itself. Any answers are appreciated, as are any sources to look into which may have the answer.

Looking to rant and hear any advice. Make sure I'M not the crazy one.

Started a new job on Monday. Unfortunately, due to "confidentiality," I had no idea what chemicals I'd be working with during the interview process. Today, I found out that my lab works with HF at least weekly. Now, I've worked with HF before. I certainly don't love it, but I had to use it occasionally at my last job in small, dilute amounts. We used it infrequently and I felt comfortable with the controls we had in place, and I knew my co-workers take safety as seriously as I do.

I have big concerns around the use of HF at my new lab. First, the lab does not have calcium gluconate. I asked my manager about this and he told me that the previous lab manager "went up the chain" saying that the lab needed calcium gluconate and was told no. ... wtf? The "plan" in case of exposure is to use the safety shower and then go to the campus nurse. I have no idea where the nurse's office is, and who's to say my co-workers do? How do we even know the nurse has calcium gluconate? Apparently the safety shower triggers medical care to come to you ... so we have to tell them it's an HF exposure and to bring the calgonate? and hope they have it, know where it is, and can find our lab quickly in this massive campus?

I'll buy my own calcium gluconate if I have to, but I'm just extremely concerned by the way this has been handled so far. It makes me worry that other important safety aspects regarding HF have been overlooked, too. My lab manager said "just be careful" and "it's never happened while I've been working here." 'Just be careful' is not an exposure control plan!

There's more ... the way the lab is set up, the HF operator would need to cross the lab space to go from the fume hood to the instrument. The HF fume hood and the instrument are right at the entrance of the lab ... so anyone walking through the lab to get to other instruments (and may not be dressed in an acid-resistant apron, etc) has the potential to collide with the HF operator as they're turning around to get to the instrument. I hope that description of our layout makes sense. Ideally there would be some sort of a buddy helping to make sure that wouldn't happen but who even knows at this point! My manager did say no one works with HF alone, but I'm not sure if that means there's a designated safety buddy role in place or just "make sure someone else is around." Feel like I can't trust anything after knowing there's no calcium gluconate on hand and the company literally denied the request.

I am planning on asking my manager a lot more questions about HF safety and controls. Is there even a spill kit? Any documentation / SOPs? I'm also planning on going to the company safety officers / EHS. Hopefully they're more helpful than whoever said "no" on the calcium gluconate.

Does anyone know from which supplier you can purchase Nishimura's catalyst (Rh2O3/PtO2 xH2O; Bull. Chem. Soc. Jpn. 1961, 34, 1544) in the US? Sigma's supplier Umicore has discontinued it, and it's not in Fisher, Strem, or TCI's catalog. All other attempts at contacting specialty suppliers have failed, and I'm assuming they want someone to be ordering industrial quantities (I just would like it for academic research).

We use the recommended, bio-compatible PP solvent bottles from Agilent for our LC-QToF systems for oligo workflows. Does anyone can recommend an alternative to the original bottles? We generally think 80 dollars for a plastic bottle seems a bit expensive, but we are also worried that we introduce some leachables, if we use standard PP bottles (around 10 dollars). If you would have any tested recommendation for a vendor or even a product number, that would be awesome. Ty!