Chemical Forums
Chemistry Forums for Students => Organic Chemistry Forum => Topic started by: curiouscat on August 18, 2013, 02:29:53 AM
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Just for fun (motivated by another thread) I decided to list some things that irritate me in Chemistry / Chem. Eng. papers. Please take this in a fun spirit, perhaps a flippant look at our profession. PS. I'm not immune to committing some of these myself.
Would love list additions to the list, critiques, opinions from others. (Mods: I hope this isn't too off topic?)
1. Reporting both a high selectivity and high conversion in the abstract. ( They forgot to mention that at 15% conversion they got 95% selectivity & they got 95% conversion but then selectivity was only 15% )
2. Almost complete conversion of acetaldehyde were observed. (Only when we used a 10x stoichiometric excess of other reactant)
3. Very high selectivity to desired product were observed. (We were working with 0.5 % aq. solutions)
4. Reporting concentrations as GC Area percents. Ughh.
5. This offers a novel renewable route to motor fuels. (Starting from oil extracted from salmon or some such exotic feedstock 10x the price of diesel )
6. Both high conversion and selectivity were observed. In the same experiment. (But we had to load ~50% of reactor mass with precious Ru catalyst. Yes, stirring was a bit problematic but we swapped in a larger motor.)
7. Very High selectivities make our route a promising route versus current industrial processes that operate at 70% selectivity. (Our dilution factors / low conversions mean that they'll need reactors the size of a Goodyear blimp and recycle lines the size of Hoover Dam water pipes, but that's ok. Oh, and our Catalyst Loadings will mean the plant will rival Fort Knox at precious metals. )
8. We got amazingly high concentrations of desired product in the organic phase. (Material balance? What's that? )
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One I don't like is when someone comes up with a new wonder reagent and says it it general for all substrates. Then you look at their tabulated examples which are usually restricted to the simple aromatics they had in the stock room and a few simple alkanes or the like. But point wonder reagent at something a bit more complicated and it fails miserably.
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Some of my pet peeves are:
Reports such as "the desired product was obtained in 6% yield and purified by column chromatography"; no your desired product is a byproduct of the reaction you choose and you just used loads of time and solvent to get enough out for the next step and now expect somebody else to figure out how to actually make that key intermediate in your "brilliant" new synthesis.
Anything that quotes 17hr reflux, stirred at room temp for 48hrs, dried for 3 days etc etc. Yeah but what does it really need to work?
"NMR of the resulting reaction mass indicated the target molecule had been formed" excellent and what was the yield and could it be isolated?
Any new process that uses ethyl acrylate; yes its a cheap monomer but it stinks so bad a lot of companies (ours included) refuse to handle it. If you're new product is guaranteed to have sales of >1000T per year by year 2 great it will pay for the investment. If not it will not get past the cost of scale up facilities. Anyone who thinks they can guarantee sales >1000T by years 2 for a new product is a deluded fool.
Any new process that uses TDI; yes its a cheap isocyanate but its volatility and toxicity means it has to be handled in a closed system. Investment as per the above.
Any new process that uses a chlorinated solvent, carbon tet in particular but the rest of them cost a lot to deal with and sooner or later will get banned as well.
Any new process that uses benzene for the obvious reasons
Any new process that uses diethyl ether it's just too flamable.
Any new process that uses THF as I just can not stand the smell of it anymore.
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Any new process that uses a chlorinated solvent, carbon tet in particular but the rest of them cost a lot to deal with and sooner or later will get banned as well.
Any new process that uses benzene for the obvious reasons
Any new process that uses diethyl ether it's just too flamable.
All true, but for the western hemisphere. Visit a small / medium scale plant in China, India etc. and you'll see benzene, chlorinated solvents etc. quite merrily and rampantly in use. :)
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Anything that quotes 17hr reflux, stirred at room temp for 48hrs, dried for 3 days etc etc. Yeah but what does it really need to work?
You would hate some of my papers.... ;D One has "was stirred for nine days at rt" because I was on vacation. ;D
peeves
Anything with hydrazine or pyridine.
Any synthesis with a yield of <20 mgs
Any synthesis where I need to evaporate a large volume of aqueous solution that is near saturated with inorganic salt.... 6h later...
"The methanol water solution was evaporated" (oh god the bumping)
"was recrystallized" how hard is it to include the solvent system? Similarly, "purified by column chromatography" without the solvent mixture being included.
synthesis uses a large molar excess of cyanogen azide..."the reaction was evaporated"...IT HAD TO GO SOMEWHERE :o :o
Old Russian papers where the reaction scheme is the entire detail of the synthesis and you need to figure out again all the reaction and workup conditions.
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And the icing on the cake:
http://www.nrcresearchpress.com/doi/abs/10.1139/v69-606#.UhFBRVKhzD4
"hey lets distill 10g of mixed primary explosives"
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"was recrystallized" how hard is it to include the solvent system? Similarly, "purified by column chromatography" without the solvent mixture being included.
^This one drives me mad.
"Neutralized with conc HCl/50% NaOH" - Really? You can reliably hit pH 7 using very strong, concentrated acids/bases?
"NaBH4 was quenched with water" - no it wasn't, water is a perfectly good solvent to conduct NaBH4 reductions
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"Neutralized with conc HCl/50% NaOH" - Really? You can reliably hit pH 7 using very strong, concentrated acids/bases?
with ph paper as your endpoint determination as well as larger scale, sure you can ;)
Forgot one of my worst general peeves: extraction solvent volume of over a litre. Mass of compound within? 100mgs. poor scaleup :(
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My pet peeves are more related to presentation and analysis of results than actual usefulness of content. Many times I read articles and find myself asking how this ever got through peer review. Experimental details vague or wholly absent, poor proof-reading and grammatical errors, references that don't actually have anything to do with what they've been referenced for, questionable data analysis procedures (my ultimate favorite: a linear fit through two points, or a polynomial fit through three), complete disregard of statistics (something that is endemic to academic science: e.g., calling something 'significantly larger/smaller' without actually having any statistical basis to do so), poor quality figures, and so forth.
On other pet peeve I have, and I know this is pretty stupid: article titles framed as questions. I hate this practice with a passion, though I'd be hard pressed to explain why.
@408
LOL, I had a number of published syntheses where the final yield was ~20 mg or sometimes less. In my defense, though, as a spectroscopist this was usually about 1000x what I needed to do my experiments.
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complete disregard of statistics (something that is endemic to academic science: e.g., calling something 'significantly larger/smaller' without actually having any statistical basis to do so), poor quality figures, and so forth.
You think applied science / industry are better with statistics? :)
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One I don't like is when someone comes up with a new wonder reagent and says it it general for all substrates. Then you look at their tabulated examples which are usually restricted to the simple aromatics they had in the stock room and a few simple alkanes or the like. But point wonder reagent at something a bit more complicated and it fails miserably.
@disco:
You having a rich industrial experience, a question:
What were the lowest concentrations of reactants you remember using in any of your commercial (or almost commercial) processes?
I keep coming across low conc. synthesis: e.g.
"The following general procedure was used for the aldol condensation. First, 4-nitrobenzaldehyde (76 mg, 0.5 mmol) was dissolved in acetone (10 mL), and the respective catalyst was added (0.05 mmol total amines and/or acids)"
That's effectively <1% conc. of reactant. I'm wondering if this is not too odd for you pharma guys etc. With my petro / commodities background these are bizarrely low conc. to me. Absolutely unworkable for any viable process.
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"was recrystallized" how hard is it to include the solvent system? Similarly, "purified by column chromatography" without the solvent mixture being included.
Sometimes the crystallisation solvent system is given as "aqueous methanol" or "a mixture of DCM and hexane". Very helpful, thanks!
Or another favourite of mine, "a seed crystal was added". I don't have any seed crystals because I am trying to make this compound!
I am currently in day 394 of "protracted standing" waiting for crystallisation to occur from a patent method. It is an ongoing joke, I intend to leave it in the lab with a message to call me when it does and hope that crystals form before I shuffle off this mortal coil.
@curiouscat
When I was working in industry I had to aim for 1:5 reagent to solvent ratio. All costings were calculated in litre hours.
This can be a nuissance for compounds with very low solubility if it's a low temperature reaction but as we made large amounts of low value materials this was the only way to do it.
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@curiouscat
When I was working in industry I had to aim for 1:5 reagent to solvent ratio. All costings were calculated in litre hours.
This can be a nuissance for compounds with very low solubility if it's a low temperature reaction but as we made large amounts of low value materials this was the only way to do it.
Thanks! 1:5 is at the practical limit I can imagine. That or anything beyond seems just too expensive from a solvent handling / distillation / solvent losses etc. Of course, most products I've handled are below $30/kg so perhaps for more expensive products high dilutions are ok?
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It depends on the cost of your feed material. If higher dilutions are unavoidable then this drives the cost up.
I usually worked at 1:10 in the lab so up to about 50g just because representative external cooling can be difficult to achieve until you get onto pilot scale. I had a 5 Lt reactor which was reasonable for 250g of material and that is when we would start trying to reduce the solvent down.
We had one material what we could only prepare 100g in a 5 lt (1:25) reactor and that was after a lot of R&D to keep it from exceeding 0°C. It was a high value input material but as it was a specialist substance I think the added value was £1500 per kg for the reaction. This was a niche chemical of which we only ever made a few kg's which I suspect meant that it was an unusual case.
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We had one material what we could only prepare 100g in a 5 lt (1:25) reactor and that was after a lot of R&D to keep it from exceeding 0°C. It was a high value input material but as it was a specialist substance I think the added value was £1500 per kg for the reaction. This was a niche chemical of which we only ever made a few kg's which I suspect meant that it was an unusual case.
I think $2300/kg is the key detail. At that price, I can condone all sorts of exotic conditions including fantastic dilutions I guess. :)
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Well I didnt read that much papers but having 2 steps out of 4 with 100% yield both is quite surprising and suspicious. Not that It cant happen but when you get instead of nice Fe-TETA complex which is required for step 1 some crazy mixture of I dont realy know what three times in a row while following exact procedure it gets annoying.
The worst for me is, that I cant realy distinguish if it was my mistake or if they forgot to add some important detail in their paper..
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I'm really enjoying this thread. I'm just a student, so I can't contribute much, but I'm sure it will help me to not make these kind of mistakes in the future.
By the way, this would be kind of offtopic, but I want to ask if anyone could guide me to start reading some not so "advanced-level" papers that I could mostly understeand, since I just finished the second year of my Chemistry Degree. Any idea of where could I start? Most interest in Org Chem.
(If this is not the right place to ask, please let me know and I'll edit my post and go for another thread. If you see it appropriate, answer me by PM)
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I'm really enjoying this thread. I'm just a student, so I can't contribute much, but I'm sure it will help me to not make these kind of mistakes in the future.
By the way, this would be kind of offtopic, but I want to ask if anyone could guide me to start reading some not so "advanced-level" papers that I could mostly understeand, since I just finished the second year of my Chemistry Degree. Any idea of where could I start? Most interest in Org Chem.
(If this is not the right place to ask, please let me know and I'll edit my post and go for another thread. If you see it appropriate, answer me by PM)
My advice is, start anywhere just be willing to accept you might only understand, say, 10% of a typical paper. :)
Also, be willing to look up or simply google lots of phrases. Even now, I'm lucky if I grok 40% of most papers, the trick is to take away what you can and keep building on it.
PS. Review papers might be a good start. They are harder to understand than a textbook but easier than a typical paper.
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Agreed with curiouscat: reviews are good for people who want to start digesting some of the peer reviewed literature. Most journals now feature concise reviews that can be read in a single setting. Accounts of Chemical Research is also a nice journal where people can kind of offer birds' eye views of their own research. Another option is perspective or commentary articles, which are more geared toward people with general science backgrounds. Most journals now feature these as well, including the ACS journals and the Nature subject journals.
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Agreed with curiouscat: reviews are good for people who want to start digesting some of the peer reviewed literature. Most journals now feature concise reviews that can be read in a single setting. Accounts of Chemical Research is also a nice journal where people can kind of offer birds' eye views of their own research. Another option is perspective or commentary articles, which are more geared toward people with general science backgrounds. Most journals now feature these as well, including the ACS journals and the Nature subject journals.
One thing I really like about Nature / Sci. is their practice of shadowing most scholarly articles with a less technical commentary written by a different expert.
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So, where and how would you recommend me to look for and read papers or reviews? I prefer if its online or downloadable to a Kindle/eBook. I've chekced out that ACS website, and as I see 48 hours of access costs $35.00.. As I said I'm a student, 20 years old, and I can't spend much money freely, so it would be nice to be able to acces to some papers for free or paying a not so expensive suscription.
Also, any idea about what should I search to start? I know that like curiouscat said, I can start anywhere, but I'm totally lost...
Thank you so much
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You are student at college right? Go ask your teacher or ask in college library to get access to those papers. For individual its realy expensive but universities usualy pay for access to those databases so they can provide you with login / password or can tell you how to get into such database. Usualy, you will not have access to all papers (I can´t get about 20% of those I would like) but it can be solved via library for example.
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So, where and how would you recommend me to look for and read papers or reviews?
How about a good old library?
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I just find out that a SciFinder account that the gave us last year still works. Is that a good soure of papers? I think so.
Where would you start? Any recomendation of what to search?
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SciFinder will give you sources for the original literature and abstracts of the papers. You will still have to go retrieve the full information from a library.
You use it to find answers to specific questions and to do structure and/or substructure searches. So really unless you have something definite to look for it won't help you much.
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Any recomendation of what to search?
Lunar carbon.