Good morning everyone. I'm wondering if it's possible to process lab data (statistics, spectra...) in a Linux environment instead of a Windows one. Are there reliable alternatives to common windows-exclusive softwares? Have you got any experience to share?

Hi guys, I’m trying to analyze a 2D spectrum right now and both axes are showing the proton spectrum. How do I change the second axis (vertical) to show the C13 spectrum?

Thanks!

Can someone explain me how can I color the volume under the points of a 3d scatter graph? I need it to represent plate reader optical measures. Thanks in advance

I have aromatic compound with only a couple of phenolic OH groups as functional groups and I would like to purify a small amount (100-ish mg) using column chromatography. To get an idea of what solvent(s) to use, I'm trying TLC to get an idea, but the compound is hardly visible after staining with PMA. To the TLC plate on the photo I dipped with a ridiculous amount of compound, hence the tailing. The eluent here is pure acetone. The blue line is the solvent front.

What would you do / try / change? Which solvent(s) and which staining reagent? I also tried KMnO4, but I dont see anything from that.

https://preview.redd.it/bharqku8g14e1.jpg?width=582&format=pjpg&auto=webp&s=d3f6469abd2e6157ce8ffbb000adcf6843ed458e

I know a reaction on Friday is not the wisest choice but I have to leave it until Monday and I’m using a schlenk line. What should I do so it’s safe to leave for the weekend without contaminating the reaction? Can I leave the argon line on low? I know it’s expensive. Ughh. Thank you for the help in advance!

So I'm trying to increase my overall yield for this reaction to perform a bis-hydrodeamination. My compound in question is highly halogenated and thus is susceptible to degradation/undesired products from radical mechanisms. Currently I have successfully performed the reaction in a THF/Water setup with NaNO2, HCl, and H3PO3. I've had yields as high as 61% but on scale-up taking yields at 25%. Additions have been slow and cold (0C) the entire process. I am going to switch solvents from THF to DMF due to actually seeing a facile method that demonstrated hydrodeamination just in the presence of THF with the formation of the diazonium salt. Any suggestions?

Hey Chempros!

I am currently running a synthesis and every time I try to protect an alcohol in my compound with TBDMSCl I get pretty horrendous yields around 20-30% I was just wondering what you might all recommend for this to help up my yields.

From What I have seen, silylation of alcohols proceeds best in DCM, but my starting material is too polar to dissolve in DCM and so I have been doing the reaction in DMF. I do 2.5 equivalents imidazole, 1.2 eq of TBDMSCl and I leave it at RT overnight. Still the best yield I have gotten is 35% The issue is that because my compound is so polar, when I do my extraction with DCM, I just lose all my unreacted starting material into the aqueous phase.

Thank you all in advance for the help here!

Edit: Dumb me forgot to add the pic of the pattern, so here's it: https://imgur.com/a/N9mCtIX

Not my first botched attempt at growing single crystal by slow evaporation, but it's the first time I've seen the solid crashed out forming a pattern like this.

Has anyone ever seen something similar? What could have caused this pattern to form?

Side note: People who synthesize complexes, do you have any motto or tricks when it comes to growing XRD-quality crystals?

I've only been doing lab work for a year, and I feel like:

Crystallization success = 20% good solvent choice

• 5% undisturbed container
• 25% favourable ambient condition
• 50% pure random luck?? Super tricky.

I'd like to a condensation reaction on a small scale (~20 mg total, 0.02 mmol of each SM). Normally I'd use a Dean-Stark with a toluene/DMSO solvent system (DMSO to dissolve SMs) but obviously this won't work well at this scale. I was thinking of using ground molecular sieves but I'm wondering if the DMSO will also be absorbed. Does anybody have any experience on this scale? Thank you

I am using scifinder to get the reaction conditions but my structure that I want to synthesize got zero result as drawn. What can I do to get the retro synthetic procedure?

Hi guys, I'm a Biochemist involved in biotransformation and molecular biology experiments. I needed a few suggestions for chemical resistant (as I deal with solvents) Centrifuges and rotors. We are planning to buy a new Centrifuge and would appreciate any suggestions in that regard.

Requirements: Chemical resistant rotors for 1.5-2.0 ml vials and 15ml/50ml conical tubes (falcon tubes), who's rpm can reach upto 10,000 (better if it reaches more than that) for vials and 8000 rpm for the falcon tubes.

Location: India.

Please help. Thank you! Appreciate any suggestions.

hello all, i'm not the most familiar with synthesis, but i'm having to do some for a surface project i am working on. my grignard reagent is intended to be MgClDecane, and it is to react with a THP protected chlorobenzylmercaptan.

to create my grignard reagent, i added Mg, chlorodecane, and Br (to catalyze) in dry THF. i attempted several methods to activate the Mg (crush, mortar and pestle, dry stir) and i lacked any traditional activators. Br was the only thing i attempted that resulted in any reaction, and i had tried adding Br before and after chlorodecane, but the reagent looked the same regardless. i tried this a few times with different bottles of anhydrous THF and got the same result.

as for the rest of the reaction, it is chlorobenzylmercaptan with Ni(dppp)Cl2 (as a catalyst) in dry THF with the grignard added. the solution before adding the grignard is clear and afterwards, it is a cyan/baby blue which appears to have precipitate. at this point, i have been unable to take NMR to confirm that i got what i was hoping for. since i am a student on break, i will have to wait about a week to go back in, so while i am away, i wanted to prepare for contingencies (if applicable) and better understand why the solution was that blue color.

I’m sure many of you have experience fixing the nasty snot emulsion/precipitate that aluminum hydroxide makes after a DIBAL type quench. I am using Rochelle’s salt to try and fix it since acetic acid ends up creating more waste water from the neutralization after. If I can make this work then I would cut out about half our waste water.

I have seen varying information on the time it actually takes to work, from a coffee break to overnight. What was your experience time-wise? I would like to use it in the interest of creating less waste water, but if it is more feasible to stick with my faster but messier AcOH cleanup then I will.

I am using a 10% molar excess of Rochelle’s, maybe I need to go higher on that number. The temperature is sensitive since it is in methylene chloride, I am limited on how much I can heat it up.

I'm in my postdoc and looking ahead to employment. I've seen news of Pfizer laying off people in recent months. Is that going to continue into next year and beyond? With the post-Covid reduction in the demand for covid vaccines, not to mention whatever Donald Trump and RFK Jr is going to do to the FDA, NIH, and the industry in general, I'm worried about my job prospects.

Hello all,

I’m brand new to crystallization and trying to develop a process to crystallize some low purity material.

I found a solvent (acetone) that the compound is fully soluble in at 30C. I then added anti solvent (MTBE) until the solution was slightly cloudy. I then cooled the solution until it was opaque, which did not occur until -10C

I then went to filter the solution and tested the filtrates by HPLC. I had no solids from the filtration, and all of my compound was in the filtrates.

Can anyone give me some pointers on what I’m doing wrong?

Hi guys, were doing a glucose chemistry project and Im having several issues I hope someone here might help me with:

Im trying to make benzyl glucose following several literature protocols Chem. Commun., 2010,46, 6066-6068 Carbohydrate Research, 2010, vol. 345, # 9, p. 1225 - 1229 and others

Basicaly, its all the same: slurry glucose in benzyl alcohol, add acid catalyst (be it ptsa, AcCl, HCl...) heat to some temperature - between 50 and 80 for some time (3-48 hours) and isolate.

The thing is, im strugling with isolation of the product. The first paper describes a column which kinda works but they dont comment on how they get rid of the benzyl alcohol. I did try to distill it away but I end up with caramell like substance that is only poorly soluble. Another procedure calls for pouring it into ether and filter away but while I got some white precipitate, again one big chunk of caramel is formed as well.

I could use different procedure but that is more steps and they are low yielding in general (ie. benzylate glucose peracetate but thats only 40% yield or use bromo-glucose tetraacetate but yields are similarly low)

I dont necesairly need a benzyl protecting group there but its preffered since I can globaly deprotect in one step. The aim is to make glucose with position 4 free for reactions. If you have any insights/ideas/hints/experience im listening. Thanks

also, before you ask: No I cant buy it since aim for some 13C6 glucose derivatives in gram quantities

Hello everyone,

I have no knowledge of EPR and recently carried out EPR of my samples to understand the formation of free radicals after high energy sterilization. I plotted the graph and it shows nothing but noisy data before sterilization, but after sterilization is shows peaks. I tried reading few papers and understood that, presence of free radicals with g value of 2.0023 indicated paramagnetic species.

In other samples, even before sterilization i can see peaks.

Can anyone please help me interpret this data.

Before saying just buy it fresh, I'm doing a PhD in New Zealand and while previously it was a quick (8 month...) wait to get a bottle from Sigma Aldrich (that was already 30% lithium hydride), we can't get it in via shipping anymore due to updated regulations.

I've stupidly managed to make it a critical part of my synthesis route beforehand and have about half the data I need for a nice publication before running out of our remaining stock. Have screened some other options (activated n-BuLi mixtures - which are much more accessible - like schlossers base/TMEDA) but have had no luck. So yeah I understand making it is stupid for anyone in a first world country (irony), but pretty desperate here.

So before reworking my entire route, can anyone recommend a lab scale method for making, filtering, and storing a 1.0-2.0 M solution? Obvoiusly fairly adept at standard shlenk technquies at this stage, but my main concerns are around any specialised glassware needed - no clue what frit sizes or anything would be needed to remove precipitates via a shlenkfrit or something, and any recommended storage solutions (shlenk bomb?). Luckily do have access to a glassblower so if theres anything needed it can likely be made.

Thanks!

has anyone here recently ordered a 100g bottle of this from sigma and if so did it come with a sureseal cap or without. supervisor is convinced its sureseal but there’s no indication either way on the product page and i’ve seen TiCl4 packaged without a sureseal so im not so convinced ..

not really thrilled with the idea of finding out only upon opening the bottle

Let's say, a routine 400 MHz for routine use in a chem department?

edit: Apparently in Switzerland it is 290k incl VAT. https://www.simap.ch/en/project-detail/a6d82b80-709c-4146-9336-eb7b9fd6483f?lot-id=cb0fee4a-e9e7-4b09-9279-6d8846384410 But from others I heard more like 450k for Bruker 400. Is there competition? I heard Varian is long gone.

I am an undergraduate chemistry student about to start the advanced-level inorganic chemistry lab rotation, which involves working under inert gas conditions and using a glovebox, among other techniques. Our professor briefly covered safety protocols, including what to avoid and which chemicals should never be combined, but the explanation was very rushed. He also mentioned the risk of oxygen condensation when working with inert gas, emphasizing that this must be avoided, but he did not explain how to prevent such situations. To ensure my safety, I am looking for reliable resources where I can learn more about safety measures and best practices for working in an inorganic chemistry lab. I would really appreciate your help

Hello chempros.
I am a PhD student who does not belong directly to materials or chemistry, but I have a project in hand in which we have made some measurements on a synchrotron and I am having problems when analysing the results, because I am an outsider. To summarise briefly, we have measured a metallic sample with a thickness of about 50 microns on a synchrotron. One more detail that might be relevant is the size of the beam, about 50x10 microns. The main idea was to measure a sample, wait some time (months) and measure it again to evaluate its evolution. The data collection I think went quite well. Each sample was analysed completely, which gave for example in one case a spectrogram matrix of 200x501 positions, making a total of 100200 analysed points (other samples need not be discussed yet). From these 100200 points, air (background) was also measured. In the first picture, you can see the result of the sum of all spectra in 1d (left) and on the right the 2d intensity. So far so good, I hope. I've been trying to clean up the data a bit and doing a few things. One of them, for example, is to try to adjust the baseline, which you can see in the second image. I have used the drPLS method on each spectrum individually (of the 100200 points) in a script, and I have done this to avoid doing it on the sum of all, as I think it would lose detail (in my opinion). Obviously it's a script that takes about 11 hours to run, but I think it works pretty well. My problems start now.

1d sum to the left, no baseline correction. 2d in the right.

Baseline correction using drPLS. This is only one point. You can see it is not perfect, specially in q around 3.4-3.5

Being an outsider in this world, I have no idea what is expected of an analysis like this to be published in a journal. Besides, I don't think I'm doing everything as I should and the analysis is probably not the most correct one. So, now that you have the context, I ask for help from this community.

• What are common practices/free software/techniques to analyse this data in a correct way. I am talking about normalization, baseline correction, etc.
• I can do a comparison point by point, it is doable, I have time and resources and I have detected the shift in between measurements (a few pixels in x and y), but what is the best practice in here. DISCLAIMER: There was also a shift in q values that I empirically corrected. We think is due to sample-to-detector distance. I simply computed the shift, that was linear and then, more or less now first measurement vs the second one are almost aligned, but not perfectly aligned of course. Any suggestion on how to do this better???

Shift in q

Empirically corrected one

• As you can see, there are some differences in between the samples, but not super big ones, and probably the central part difference comes from the baseline correction. The problem here is that these comparisons are based on the sum of all sample. Individually assessing pixel by pixel I can see differences in some peaks, the problem is that the sum of all spectrums "erase" or "hidden" these differences, so comparing the sums is interesting, yet not useful.
• I have also detected a small shift in peaks in between reference databases and the data. Again, empirically corrected, and is a shift of around 0.032. Why this is happening and what can I do?

https://preview.redd.it/w5ze6dl4g73e1.png?width=1113&format=png&auto=webp&s=46871fa466900eafbc51b31666037ab65eaf7f7f

I will edit the post with more details if you ask for them, but as for now I think is enough and I have a lot of questions there. Thanks a lot for the help in advance.

Hey all,

I am trying to synthesize bimetallic nanoparticles using Pt and Ag. I have premade the silver nanoparticles and am adding platinum dropwise under heat with the goal of forming alloyed nanoparticles showing a UV-Vis shift, with additional platinum correlating to a greater shift to lower wavelengths and broader, shorter peaks. I have tried adding platinum in different concentrations, adjusting silver nanoparticle concentration, and with/without heat and reducing agent. So far, it seems like galvanic exchange is not occurring very rapidly. Peaks form, but are barely shifted, taller, and narrower and inconsistent shifting occurs across varying Pt concentration. For example, two samples containing lower and higher platinum will shift the same amount. Is there any way to see a better shift or to ensure that alloyed particles are forming? Right now, I am using 5mM AgNPs and dropwise adding varying volumes of PtNO3. Is coreduction the better option here?

Thanks.

The immediate availability of material safety documents is crucial in case of a lab emergency situation. The latest release V.2.4.0 of the open-source chemistry lab notebook Phoenix ELN now features the ability to attach safety documentation to reagents, solvents and auxiliaries.

This attachment is global, all future additions of the affected materials will contain the assigned safety documents by default, and will be at hand when you need them. See the safety documents help topic for more details. The installer for this latest release is accessible from GitHub.

https://preview.redd.it/0wuo7cazbn2e1.png?width=707&format=png&auto=webp&s=d2e1d172319cb1332719b4f347b1fe71f7eda391

I was doing a peptide coupling, and I am trying to figure out why my yield is so low (coupling boc protected tert leucine with L proline at 50 mmol scale). After stirring the mixture overnight, I noticed there was still proline left over, so I decided to heat the mixture to 60 degrees. Please correct me if I am wrong, but... When I heat it to 60 degrees, would it cause the Boc group to fall off the nitrogen? I know that when I stain TLC plates of my product with ninhydrin, if I heat the plate up, then the Boc group falls off and I see my product being stained. I was wondering if I am losing my dipeptide product because I am heating up the boc-protected dipeptide. The deprotection is probably not to a large extent, though, since I am getting 30% yield for my coupling reaction. I am considering using HBTU to see if the yield is better. Any thoughts on the matter would be appreciated. Also, idk why my mentor expects me to be able to column the crude mixture of a 50 mmol reaction using two 100-g silica columns on the biotage, when almost certainly I am overloading the column, but maybe it's a skill issue?

I have synthesised an extremely polar compound in DMF on just less than 100 mg scale. The base I used is sodium hydride (1 equivalent) and I used 2 ml DMF. Compound contains some amines, an amide and sulfonic acid moiety

My plan was to remove the DMF by adding toluene, then rotavap and repeat (this has worked well for me in the past at temperatures of around 50-55 degrees celcius) and then purify immediately using prep HPLC, without any quenching or work-up

I wanted to ask:

Will not quenching my reaction possibly cause issues further down the line? I also do not want to do a liquid-liquid extraction that involves water in any way as I will “lose” my product to the water layer.

Just not sure how best to proceed with all this. Open to better ideas

Dear pros,

I am looking at the virtual vault for pseudopotentials (https://nninc.cnf.cornell.edu/psplist.php?element=C) for carbon to conduct geometry optimisation for my hydrocarbon in SIESTA. As shown in the screengrab, it seems there is no pseudopotential available for GGA-BLYP. Is GGA-PBE pseudopotential for C and H appropriate for SIESTA calculations?

P.S. I am assuming that I have to use SIESTA-coded pseudopotentials.

https://preview.redd.it/9wgar1w0rf2e1.png?width=901&format=png&auto=webp&s=1fa73aace4a4107814ae952ce17f6963fb41b013

I just published in Chem. Eur. J. I’ve realised now that the final version is up that there’s two words in the main text with no space in between!

I’m pretty sure this occurred during proof revisions as the track changes made it so hard to see if the spaces were there or not.

Is it worth contacting the journal to fix? It’s still in Early View and not been assigned an issue.

Hi everyone,

I am trying to obtain a species that contains both a ketal and an amine. I have unsuccessfully tried ketalizing a ketone/amine substrate, and also unsuccessfully tried using an Sn2 to introduce the amine after ketalization.

My normal methods of ketalization are DST using toluene and PTSA, or using trimethyl orthoformate at RT in DCM with a drop of sulfuric acid.

I have seen a handful of literature examples using phthalimides as protecting groups for the amine to undergo a subsequent ketalization. Is this necessary, or is it possible to ketalize a ketone with an amine present? Has anybody had a successful approach?