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Author: Subject: Real chemistry is dying out, why?
jamit
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[*] posted on 16-1-2013 at 00:38


... for the home chemist you really can't go too microscale into the mg. This is especially true for synthesis of compounds. If its just to see the chemical reaction or observe a physical property, then doing it in mg sample is fine -- examples would include the diffusion of KMnO4 or test for chloride ion using silver nitrate.

However, I do lots of experiments with my kids and so we work in 1g-100g batches mainly because we're doing lots of synthesis. Plus like Woelen, we like to make and purify and finally collect our final product for storage in 20ml vials.



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[*] posted on 16-1-2013 at 03:12


Quote: Originally posted by bfesser  

kristofvagyok, are you trolling us, or are you really as ignorant as you're making yourself out to be?

What's cheaper, 1 gram of chamazulene, or 5 kg of it? A 5L beaker, or a case of 5 mL beakers?

Basically, what I'm saying is; your 'argument' is idiotic and uninformed.
Thanks!

The price between 1g chamazulene and 5kg chamazulene is not that big. 1g chamazulene is usually made on a small scale extraction while 5kg is made on an industrial scale what is always cheap, almost the cheapest. So the price difference between that two is not big as the difference should be.

E.G.: carbon nanotubes was 20USD/kg price from the manufacturer 5 years ago...

Quote: Originally posted by kmno4  
ps. mg-scale procedures are very often not scalable to multi-gram preparations; besides, some procedures and yields exist only on paper and no-one is able to confirm them.
-I would agree with this, because often (almost always) this happens.



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[*] posted on 16-1-2013 at 11:28


Quote: Originally posted by kristofvagyok  
The price between 1g chamazulene and 5kg chamazulene is not that big. 1g chamazulene is usually made on a small scale extraction while 5kg is made on an industrial scale what is always cheap, almost the cheapest. So the price difference between that two is not big as the difference should be.


My post was meant to challenge you to actually look up the prices and do the calculations. Go ahead, do them. Show them clearly here.

Also, I highly doubt the purity of whatever sludge that was in your beaker matches that of whatever (analytical standard grade) commercially available product you arbitrarily chose to compare to.




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[*] posted on 16-1-2013 at 13:06


Economy of scale is not the same thing as saying its cheaper to work on a larger scale. If you wish to make a gram of compound, the overall cost of a gram from a 500g batch is obviously going to cheaper than a gram from a single gram reaction. However, the overhead for the larger scale reaction is of course much larger, as is the cost of the glassware and equipment required (compare say a benchtop buchi with a 20L process one...).

And then theres the sad fact of chemistry: Not every reaction works as described, especially not on the first attempt. Reactions that give no or little product (with tedious isolation in the latter case) are obviously money going down the drain, and time wasted too (especially after you have to wash all the glass from the reaction too!). I routinely perform the reaction using a gram or two before scaling up. This way you can assess how the reaction works (and identify any exotherms/gas evolutions) before commiting time, money and material to the preparation of a main batch.
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[*] posted on 16-1-2013 at 13:18


I've carelessly tried some micro scale type procedures(not 1mg but 100mg's). And I'm with woelen in that the loss on a filter just makes it not worth the time or investment. That "oh cool if I breath to hard I will lose my entire yield" feeling isn't one I enjoy. Or "could I drip some solvent in to a melting point capillary to get this back" :D. Or "is that scraped cellulose from the filter paper, or my product"...

On the flip-side if I go macro the conditions change and the waste can be a real burden(home-chemist). Volume of solvents and as Dr. Bob said silica gel go up almost exponentially. Some procedures are just awful, using 2 liters of solvent to pull a gram of material(end product). Let alone doing that on a 10 gram scale, simply no point in either experiments. Also large-scale has a lot more risk, runaways are more fierce, more risk for exposure, more fumes, etc. At home it's just not comfortable and not really all that fruitful. I'd rather do a 1/20th a mole 5 times then a 1/4th a mole off the bat in many scenarios. It's no short-cut for someone who loves being in the lab enough to live in one hehehe.

For home experimentation which is the only side of chemistry I have an opinion on other then academic(student), there's a happy medium. Go too small, and what's the point, go to big and what a mess. 5-10 grams is what I like to work with. 50-250mL flasks feel right in my hand. I don't even own a 1 liter flask. For tricky procedures and new chemicals I stay in the millimole scale. For more basic chemicals and or reactions I don't mind doing 1/5-1/3 a mole(acidifying sodium benzoate). For really basic chemicals(nitric acid preparation etc), the only real limit is the glass-ware size, how much I need, and how long do I want to sit by a distillation, and do I have a container and location to store it safely.

I probably just reiterated a lot of what other people said, oh well, hahaha.

[Edited on 16-1-2013 by smaerd]




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17-1-2013 at 09:42
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[*] posted on 18-1-2013 at 10:46


Wow. I do reactions much more scaled-up than you gentlemen, apparently. I *do* have a 1-liter flask, and am almost always using it for something or other. Reactions I do are almost always 50-500g, and I simply don't have the patience for going smaller.



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[*] posted on 18-1-2013 at 14:27


I feel that small scale reactions are good for testing and trying out some kind of possible route to a chemical, especially if you have no clue what yield you might get or if it will work; otherwise you'd be wasting a lot of chemicals. On the other hand when I'm doing something that I know works and gives good yield than I usually work on a scale that I like, maybe 50-100g... Only other reason to work on a very small scale is to prove a point like oxidation states of a metal.
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[*] posted on 18-1-2013 at 14:56


This topic is not what I planned about, sorry for that.

My main question was that in published papers where research groups make chemistry from lot money, why do they publish reactions made on 1mmol scale, yield calculated by NMR/MS data and write down reactions what are impossible to scale up or to repeat. What's the reason for that?

Now if I go down to the library, start to read a recent published jornal (Tetrahedron, Synlett, Angewandte Chemie, ect) main part of the reactions are on mmol scale and only a few of these are reproducible. Why do they publish these things? Impact factor? If noone can reproduce the experiment than no impact factor will be gained.




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[*] posted on 18-1-2013 at 17:06


"...yield calculated by NMR/MS data...", or as a gross product % of area-sum by LC/GC. The answer? "Lazy".

O3




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[*] posted on 18-1-2013 at 17:41


Quote: Originally posted by kristofvagyok  

Quote: Originally posted by froot  
I would also suggest that it has much to do with the growing awareness of the health hazards from exposure to countless compounds. Smaller quantities are easier to crisis manage and dispose of without major expense. The newer school of thought: "if it's toxicity is unknown, then it's deadly" springs to mind which is not exactly in favour of old style bench top chemistry.


I work with benzene, CCl4, chlorine, bromine, brucine, several organic halogens, carcinogen stuffs and a lot "hazardous" material and I'm still alive. If everyone is a pussy to work with real reagents then I would suggest to don't work as a chemist. Chemistry is about hazardous materials, just don't be afraid from it and there will be no problem, according to my experiences.

And for the "new school thought", that if it's unknown it will kill you... No comment.


OK, an extreme example, let's assume you just have an accidentally large dose of H2S. But you are still breathing and otherwise feel OK. So your fine, right? Wrong, possibly dead wrong. Hydrogen sulfide has a delayed mortality profile, you may in fact be dead, a walking dead, but you just don't know it yet.

This is a parallel to other chemicals that facilitate your death to cancers, but because it doesn't kill you quickly, it does mean your OK.
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[*] posted on 18-1-2013 at 17:47


Yields look better when artificially boosted. Just like how Harvard gives more "A"s now, politicians all claim that they will cut your taxes and increase your benefits, and "in search of" ads always talk about romantic notions.

Human nature is that people want to do the least work, get the most credit, and look the best. If you have worked 5 years towards a PhD, and you think that your adviser will let you finally graduate if you just finish that paper and get it published, you might tend to make the work look as good as possible. I have tried to repeat work, tried to create new chemistry, and worked to publish as well. I have been published, as well as rejected, and sometimes the reasons for each are very unclear, so I can understand why people might think that yields matter to publishing. Some professors are quite notorious in demanding high yields, and if you are a tired graduate student, you might just make the yield work. I never had that particular problem, as my adviser was not as worried about yield in my project, much more about novel mechanism and creating lots of data.

But having to repeat others work has shown me that it is hard to 1) create knowledge 2) repeat others work, and 3) make sure that you are doing your work as well as the original author. I have seen people do a sloppy job of repeating a reaction and then be surprised that they got low yields, even through they used 1) non dry glassware 2) un-titrated base 3) very old reagents which were not checked in any manner 4) not been careful in addition speed or order of addition 5) and skipped steps in the work up. Conversely, there are some reactions which do not require as much care, and I have seen people get good yields with very little effort (my favorite kind of chemistry). So before you are critical of someones work, make sure that you are doing your work right.

The recheck on every reaction is what I like about Organic Syntheses and their verified reactions.

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[*] posted on 18-1-2013 at 20:12


Quote: Originally posted by kristofvagyok  
This topic is not what I planned about, sorry for that.

My main question was that in published papers where research groups make chemistry from lot money, why do they publish reactions made on 1mmol scale, yield calculated by NMR/MS data and write down reactions what are impossible to scale up or to repeat. What's the reason for that?

Now if I go down to the library, start to read a recent published jornal (Tetrahedron, Synlett, Angewandte Chemie, ect) main part of the reactions are on mmol scale and only a few of these are reproducible. Why do they publish these things? Impact factor? If noone can reproduce the experiment than no impact factor will be gained.


Are you serious? Chemistry is a science. Don't you know what science is!? You sound like you belong in engineering...




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[*] posted on 19-1-2013 at 09:46


Just out of curiosity, what do you kristofvagyok think about computational/physical chemistry?
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[*] posted on 19-1-2013 at 15:36


Quote: Originally posted by kavu  
Just out of curiosity, what do you kristofvagyok think about computational/physical chemistry?
It is useful if something useful is calculated e.g.: will a medicine molecule fit in the cyclodextrine and is it possible to put it in it or not and not even worth a try.

But when they calculate e.g.: the n+1-th metastable state of ice what could only exisist on X pressure and Z temperature and will probably never ever exist in real life... I think that's just waste of time.
Quote: Originally posted by bfesser  
You sound like you belong in engineering...
I am not an engineer, but I think that if something is not scaleable, not reproduceable and just good for gathering some impact factor than it is useless.



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[*] posted on 20-1-2013 at 02:20


You do realize that efficent applications require the study of simple and theoretical things at first? In order to screen the scope of reactions small scale experimentation is needed. These results can then be applied by others to see if it can be done in a large scale or modified to fit their needs. I find it somewhat rude and ignorant to claim some of the most fundimental scientific research (the results of which you use daily in the lab) to be a waste of time.

[Edited on 20-1-2013 by kavu]
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[*] posted on 20-1-2013 at 05:18


Quote: Originally posted by kristofvagyok  
But when they calculate e.g.: the n+1-th metastable state of ice what could only exisist on X pressure and Z temperature and will probably never ever exist in real life... I think that's just waste of time.


You are very wrong. The very same example you mention plays a great role in astrophysics and planetary geology, which translates to greater understanding of evolution of solar systems, which is helpful to a myriad of other sciences.

It's like saying all those obscure and complicated mathematical (ok, math is not a natural science, but for the sake of an argument let's pretend it is) problems that have been solved have no purpose and are a waste of time. Some of them gain purpose after more than half of century.
Nothing in science is a waste of time if done properly. Even failures, if you know it's a failure.

Even if it doesn't find a real world application as soon as it's discovered, it's valuable cause it's knowledge.
If we did only the stuff that has immediate real life application, I guarantee you we wouldn't be typing this right now on a computer because there'd be no digital computers. Perhaps we'd be stuck in some weird 18th century world with cogwheels and brass, ornamented, primitive scientific equipment.

Imagining weird things and trying to find whether they work or not is what pushes humans forward.




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[*] posted on 20-1-2013 at 17:21


Quote: Originally posted by kristofvagyok  
I am not an engineer, but I think that if something is not scaleable, not reproduceable and just good for gathering some impact factor than it is useless.
You must be trolling.

[Edited on 7/12/13 by bfesser]




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[*] posted on 21-1-2013 at 16:19
Size really (might) matter


I didn't see it mentioned that if certain reactions only work on a tiny scale then they may have great utility at that small size. Think analytical lab on a chip, micro-reactors, in addition to the possibility of screening an array of many samples at once as scoping tests. The results could be useful for additional related work at the small scale.

If the complaint is that the experiment is not reproducible, well, that's obviously pretty worthless no matter what the scale used.




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[*] posted on 21-1-2013 at 16:31


Forgot to add - I sympathize with someone's individual idea of what good/fun chemistry is, each to his own. But while some may feel more satisfaction with producing large batches of a product, it seems there could be an important set of skills on the small scale worth developing, especially for the home chemist. Imagine if you could miniaturize your own home "lab" and it fit it into a shoebox. You could fit it under your bed, in a drawer, alot of places. Heck at that size that set of experiments would be portable, say for a field kit for testing samples in places away from the lab. Seems like there could be a set of useful techniques worth honing there.

Having said that I have to admit when I bought a chemistry set for my kid a few years back I was quite dissapointed that the entire set was super miniature. They expected a child to get just as excited when half a drop of liquid turned green as if it was half a jar full. I think if there is an emotional reason, like the excitement of learning, then there is some real value in having a bit larger scale than a couple drops for the visual display. It all depends on what is trying to be achieved.




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[*] posted on 22-1-2013 at 01:18


Quote: Originally posted by kristofvagyok  
[...]
But when they calculate e.g.: the n+1-th metastable state of ice what could only exisist on X pressure and Z temperature and will probably never ever exist in real life... I think that's just waste of time.
Quote: Originally posted by bfesser  
You sound like you belong in engineering...
I am not an engineer, but I think that if something is not scaleable, not reproduceable and just good for gathering some impact factor than it is useless.

Sometimes indeed you need to be practical. I am a software engineer and in many applications time and limited resources are a fact of life and then one has to work straight towards the goal and one has to build something, which is useful and is such as the customer has asked for. This is engineering and has nothing to do with science. Just use proven technology so that there are no strange (costly) surprises while developing the system.

But... if all people always were thinking like that and if there was no real science, then we would not have been where we are now.
A very nice example is the (for most people rather obscure) field of number theory, a branch of mathematics which deals with the structure of numbers and special sets of numbers. Much of this mathematics is from around 1900 and at that time it was only theory, a lot of theory. Nowadays not a single electronic bank transfer and not a single https-session would be possible if that kind of mathematics did not exist. Now we use RSA, DSA, elliptic curves and so on for nearly every form of secure electronic communication and all of these things are based heavily on the structures of numbers, discovered a century or so ago. The mathematicians of 100 years ago never could have imagined how their work would be used in real-life practical application one century in the future. Those people have been struggling and doing painstakingly long and intense computations, all by hand and they just did these things because they liked to do it. What if all of those people just considered this a waste of time?




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[*] posted on 29-1-2013 at 22:34


Quote:
main part of the reactions are on mmol scale and only a few of these are reproducible. Why do they publish these things?


It's all about money. People in the academic establishment are paid for publishing stuff. So they publish stuff that looks 'very learned'...

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[*] posted on 29-1-2013 at 22:39


Quote:
Nowadays not a single electronic bank transfer and not a single https-session would be possible if that kind of mathematics did not exist. Now we use RSA, DSA, elliptic curves and so on for nearly every form of secure electronic communication and all of these things are based heavily on the structures of numbers


Did the guy who invented the enigma machine (an engineer...) rely on number theory at all?

[Edited on 30-1-2013 by learningChem]
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[*] posted on 30-1-2013 at 14:54


I think it's simply less wasteful and more meaningful to use small amounts when studying a reaction, or a set of reactions.

I remember not too long ago, I competed in the ACS Chemistry Olympiad on the state level. Of course, it consisted of a test involving fundamental chemistry and physical concepts.

The "experiments" that we were required to conduct were rather lame. The key however, was to be able to conduct as many tests as possible to support or refute a hypothesis. In many cases, the strength of data can lie in repeatability on a small scale, rather than synthesis on a large scale. From a large set of data, you can do statistical analysis. Naturally I would be skeptical of a paper that mentions a small scale synthesis that is not also repeated numerous times. If a reaction is not tested in a real environment, it's as good as bullshit. After all, a computer or a piece of paper is not able to make proteins or synthesise heterocycles.

I think amateur chemistry is often similar to chemical engineering (in that it often focuses on scaling up reactions), but with a hint of fundamental chemistry. Amateur chemistry is (as I see it) "the pursuit of a better way" through personal ingenuity and perseverance. The pressures in a home lab are different from those in a commercial lab. My best guess about the limitations of a commercial lab is that time, purpose, and success are probably the largest pressures, while an amateur lab has different constraints, most notably financial constraints, limits on accessible scientific literature, and limits on physical capital like analytical equipment.




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[*] posted on 31-1-2013 at 00:27


I am of the opinion that one should work on as large a scale as possible especially during the initial steps of a natural product synthesis. One runs out of material pretty quickly after 15 or more steps due to non-quantitative yields. The microscale chemistry is useful for scouting reactions or during advanced stage work with precious compounds that took months to synthesize. I personally own vial scale glassware, 14/20, and 24/40 up to 12 L. I like running NMR on concentrated samples, less scans, less time and with a CW spectrometer, better resolution.



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[*] posted on 31-1-2013 at 01:12


Quote: Originally posted by learningChem  
Did the guy who invented the enigma machine (an engineer...) rely on number theory at all?
[Edited on 30-1-2013 by learningChem]

I am not sure about the Enigma machine and don't know the details of it, but at that time I think that application of number theoretic algorithms for cryptographic purposes was not feasible. You need a lot of computational power to make these things working. E.g. a 1024 bit RSA operation for encryption takes two 512 bit modular exponentiation steps, which means computing A^B (mod C), with A, B and C being numbers of 512 bits. This is well beyond the 1940's hardware capabilities.




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