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Author Topic: Feel the Chemistry!
ScholasticSpastic
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Icon 1 posted November 10, 2007 12:36      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
Well, hello, my fellow geeks! You may have been wondering, where is ScholasticSpastic? Does he still love us? Doesn't he miss us at all? Why won't he even stop by and say hi, the insensitive jerk?

Well, there are two answers:
1) I am socially incompetent
2) I've been busy trying to learn enough chemistry to publish a paper.

As my college has acquired new equipment, I now (under a real professor) have two projects in the works involving mass spectrometric analysis of tar-sands and then following up with a photo-acoustic assay of the tar-sands and complexes of EDTA with various cations. So I'm busy, as I haven't even had an analytical chemistry course yet and the learning curve is steep. I'm an embarrassment to the Biology department- we're not supposed to get so excited about the physical sciences. But we're not doing any work in Biology at my campus that promises to net me a poster/paper and those are a big deal.

This is not just a blog parasitizing the Forums, it is also a plea for help:

Do you recall the stupid (and frustrating) YouTube hoax in which the video-author claimed to be able to make Mtn. Dew glow? Well, that led to an obsession with chemo-luminescence in my spare time and I'm working on a private project to synthesize diphenyl oxalate from phenol and oxalic acid. The reaction is a simple Fischer estrification and not difficult to pull off at all.

I was wondering if I might have some independent input regarding the feasability of my proposed process:

In a round-bottomed flask combine one mol-eq. of oxalic acid with three mol-eq. of phenol (=excess phenol- this will be my solvent) in the presence of a few drops of HCl (my acid-catalyst).

Heat mixture at reflux for 1-2 hours. Add sodium salycilate after cooling to room temp. as required to obtain a pH between 8 and 9.

Add a few drops of fluorescent dye, then add excess (>2 mol-eq.) concentrated H2O2 (about 30%).

Make happy noises if the mixture emits light.

For anyone who's wondering what a mol-eq. is, that's my abbreviation for molar equivalent because I'm a lazy sort of guy.

Please understand that I'm a paper-publishing-oriented person at this time and that any information furnished may lead to the publication of a paper. Know in advance that informal assistance will not necessarily be credited in any papers that I publish unless we come to a formal agreement prior to publication. Collaborators are welcome, but I would require a RL correspondence (sans-nicknames) with a written (snail-mail) element protecting both of our rights as collaborators prior to collaboration-level cooperation.

Why am I so cagey? Because we've recently been screwed by another University and I've just realized what a cut-throat endeavor the paper-publishing business can be. That made me angry- until now I was working under the delusion that researchers are more ethical than car-salespeople (no offence intended to any car-selling geeks lurking on the Forum).

Feel free to offer advice or ask questions. Diphenyl oxalate is not my baby- you can feel free to run the synthesis on your own for kicks and I won't pout.

Input regarding possible synthesis pathways for a simple fluorescent dye would be especially appreciated- the more from-scratch the project is, the more satisfying the accomplishment of the synthesis will be.

I'd also appreciate any input regarding unforseen risk in any of the steps of the synthesis such as evolution of toxic fumes or unintended synthesis of particularly explosive or flammable by-products. I am not a real organic chemist and so I am open to the possibility that untold dangers lurk within the wide-open spaces of my ignorance.

And yes, I do miss you guys when I'm not living up to the obsessive science-major stereotype. [crazy]

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Xanthine

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Icon 1 posted November 10, 2007 13:21      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
Organic synthesis isn't something I've thought about in years, I can't offer you much help beyond a "NICE TO SEE YOU BACK!"
Publishing is brutally cut-throat, especially if your topic is at all competitive. I've participated in and been caught in the blowback of some publishing nightmares. I've also heard some awful stories. Interestingly enough, one guy who tried very hard to fsck us is now a collaborator. We wrote an official letter and everything. Apparently, in my little corner of the science world, if you can't beat 'em into the ground, collaborate. Who gets credit for what and why is also a smarmy, nasty business that can ruin friendships quicker than lending money ever will.

Run some literature searches. There're probably some answers to your questions out there. SciFinder is probably the search engine to start with. As far as dyes go, well, how does your system work? Is it something akin to FRET, where diphenyl oxalate is emitting photons outside the visible range, thes photons excite the dye, and the dye then spits out light in the visible range? I'm just guessing, so forgive me if these questions are out of line and stupid. But if it is working something like FRET, before you run off buying or making dyes you need to figure out what wavelength diphenyl oxalate emits at and what dyes will be excited by that wavelength. I'm not sure where to come by any of that information. You could probably get an emmission spectra for your ester out of the CRC, but for the dyes I don't know. You might be able to hust google for it, or consult with Sigma-Aldrich.

As for the life vs. physical sciences thing, well, as a crystallographer and biochemist (in today's world, you gotta be both, but I'm way better at the former) I straddle the two sides and get the according flak. I have plenty of company in my awkward position so it's more amusing than lonely.

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And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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ScholasticSpastic
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Icon 1 posted November 10, 2007 13:44      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Xanthine:

Run some literature searches. There're probably some answers to your questions out there. SciFinder is probably the search engine to start with. As far as dyes go, well, how does your system work? Is it something akin to FRET, where diphenyl oxalate is emitting photons outside the visible range, thes photons excite the dye, and the dye then spits out light in the visible range? I'm just guessing, so forgive me if these questions are out of line and stupid. But if it is working something like FRET, before you run off buying or making dyes you need to figure out what wavelength diphenyl oxalate emits at and what dyes will be excited by that wavelength. I'm not sure where to come by any of that information. You could probably get an emmission spectra for your ester out of the CRC, but for the dyes I don't know. You might be able to hust google for it, or consult with Sigma-Aldrich.

Hello, Xanthine! I dinna forget your xray crystallography- that's some coolness. You are correct about needing to research emission frequencies for diphenyl oxalate prior to investing in random dyes. This is unfortunate, because the simpler the experiment can be, the more likely I am to come up with publishable work. I've only recently gained full electronic access to the university library because I'm attending a regional campus and some foreign national did stupid things that ended up restricting off-campus journal access. My Prof. I'm working with has had a vpn connection installed in my cubby/office that I can now use to access papers. It's been a great boone to my edumacation and I pitty the students on my campus who haven't found a professor to follow around.

The only real secret here is the type of publication- I've done a literature search and found nothing in a certain field using synthesis of diphenyl oxalate. There's a journal I have in mind that's low in prestige, but within my reach as an undergraduate student researching independently. Having published anything at all at this point in my edumacation could go a long way toward getting me accepted/financed in a good graduate program. If my evil plan works out, I will end up with a paper with my name first, followed by my Prof. (he's already said that, since this is my idea, I get to be primary author) and that would be an incredible fact to include on my resume. The only down-side is that he's decided to reduce his availability for assistance because he's not overfond of organic synthesis and he's voluntarily reduced the benefit he'll get out of working on the project with me. First-authorship would make me happy enough to giggle like a schoolgirl even more than usual, though, so I'm plowing ahead.

I was hoping to try the synthesis next Monday, but the revelation that all dyes aren't created equal has given me pause. Maybe I'll be able to run the reaction minus the final step and just verify my product yield using FT/IR and NMR. Those are fun machines to play with and at least I'd know I'm on the right track. I'm pretty confident that I'll end up with product and the real questions revolve around getting the mixture to glow, but some results are better than no results.

I truly hope this thing pans out. Pissing in my own corner of the world of publication would be a lot of fun right now.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Xanthine

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Icon 1 posted November 10, 2007 14:13      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
Dude, research doesn't happen overnight.

Do the experiment you set out to do and do it right. If it takes you a little while to figure out which dye to use then that's okay. Unless you're graduating tomorrow, there's no reason to rush.

And yes, getting anywhere on an author list as an undergrad is good application grease for grad school.

--------------------
And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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ScholasticSpastic
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Icon 1 posted November 10, 2007 14:17      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
Oh, hey, for those who are curious, the process by which diphenyl oxalate is involved in chemoluminescence is commonly known enough to have its own Wiki article.
Wiki article

So, yep, short-wavelength light comes out, excites fluorophores, and the fluorophores then emit visible-wavelength light. The secret of glowsticks. Wiki is even kind enough to provide a list of dyes for me to try out. I'll be looking into availability through my college's favorite vendors next week to see which dyes are cheapest and I may decide to be trusting enough to try a cheap enough dye without checking my emission/absorption facts. The important factors are affordability and availability because, ultimately, what I'm doing is looking for a fifty-dollar process to come up with a 25-cent product. It'll make more sense when I've finished my work and published (if I publish) so I can tell you what my angle is.

Ultimately, as an undergraduate researcher, my best bet is to look for understood processes and then find sneaky little novel applications for them. Groundbreaking work needs to wait until I'm a graduate-level student or a post-Doc. And then it'll be work in the fields of bioremediation or limnology rather than chemistry.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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ScholasticSpastic
Highlie
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Icon 1 posted November 10, 2007 14:39      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Xanthine:
Dude, research doesn't happen overnight.

Do the experiment you set out to do and do it right. If it takes you a little while to figure out which dye to use then that's okay. Unless you're graduating tomorrow, there's no reason to rush.

And yes, getting anywhere on an author list as an undergrad is good application grease for grad school.

You are correct. If this weren't already a well-understood subject I would do well to keep to strict protocols. Fortunately for my giggly-impulsive self, the process is my goal rather than the results. I'm coming up with a recipe rather than any quantitative output.

Of course, it would be preferable if I also had a means of purifying the mixture containing the diphenyl oxalate prior to reacting it to make pretty colors. Quantitative steps are always a good and being able to include a percent-yield calculation would be ideal.

My primary problem is not one of fluorophores, but one of separation of the diphenyl oxalate from the phenol solvent after the reaction. Qualitative results should be possible while leaving the product in the solvent (assuming that my dye and the salicylate are at least sparingly soluble in phenol), but a separation step will be necessary for any quantitative results.

I'm leaning toward fractional distillation, possibly repeated distillation steps, because the boiling points of phenol and diphenyl oxalate are about 100C apart. Then I could use EtOH for my new solvent for increased safety and the fact that ethanol is a more versatile solvent than phenol or water. Ideally, though, I want to end up with a process that has minimal steps and can be completed in less than four hours.

If I could tell you what my real goal was, I'd be better able to 'splain what I'm on about. I don't like being cagey- it goes against my nature. I'd much rather tell you what I'm doing and be open about the whole thing.

On the bright side, at least I have, in the Geek Culture Forums, a place to be geeky. I may be the only undergraduate student at my campus who enjoys talking about sciencey things in their spare time. I look forward to making my way to a real campus so I may enjoy some real peer interaction.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Xanthine

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Icon 1 posted November 10, 2007 17:08      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
Is there any reason why you can't just try to purify your product by recrystallizing it? Small molecule preps aren't my bag, so that may have been a really fscking stupid question, but I remember doing that in organic chemistry class.

ETA: if you really want to tell me your plan, you can PM me. There is absolutely no way in hell I'd ever steal your work. I'm not sure I'm even offering helpful advice. But as far as ethical shadiness goes, first, I don't do that shit. Second, I don't have the time. Thirdly, while I proved to myself as an undergrad that I can do organic synthesis, I also proved to myself that it's really not for me. I react poorly with most solvents and I'm clumsy enough that I was risking an ER trip every time I picked up a round bottom flask. I very much prefer my happy biological molecules, which hang out in water and react very nicely at 37 degrees C. You can keep your dicholoromethane, your boiling acid catalysts, your phenol, your diethyl ether, and god knows what else all to yourself. [Razz]

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And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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ScholasticSpastic
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Icon 1 posted November 10, 2007 17:29      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
Phenol and diphenyl oxalate are both liquids at room temperature (and far enough below room temperature that it's not feasible to try to crash things out in my modest little lab). I've thought about halogenating the ring on the phenol prior to estrification to produce 2,4,6-Trichlorodiphenyl oxalate, which would be a solid at room temperature, but I'd have to add another step for that to work and it would be ideal to go from precursors to products in as few steps as possible.

There are no stupid questions, and recrystallization is an excellent (far better than distillation) method for purification and separation of mixture components when we can get it to work.

I've considered trying to extract product using a separatory funnel and taking advantage of the differential solubilities of the product and phenol in aqueous solution. That might be worth a try, but phenol is very miscible in water, so it could just end up being a waste of time. Fortunately, I needn't bother with the kind of precision that's usually required for publication.

Success will be measured, not by precission or by percent yield, but by coming up with an easily reproduced procedure. That means I can justify mucking around in the lab and trying things out- which is a lot of fun because I've always thought that a nice, big collection of glassware and bubbling liquids looks pretty cool.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Xanthine

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Icon 1 posted November 10, 2007 18:48      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
Is phenol all that soluble in water? Our lab stores the phenol stock under a neutral buffer and it forms a pretty distinct separation layer . But, then again, the buffer also smells like phenol so I guess some fraction stays in there.

Phenol definitely mixes better with chloroform than it does with water. You could try extracting with that, except your product might also decide it likes chloroform too (given the great big greasy aromatic rings you've got, this is not unlikely). Hmmm.

Having seen your PM, it comes down to this: is it less labor intensive to halogenate and recrystallize or purify the straight up diphenyl oxalate?

--------------------
And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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ScholasticSpastic
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Icon 1 posted November 10, 2007 19:11      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
I've been thinking, and most of my experience with phenol involves ethanol as well. So it might be less watersoluble than I recall due to the unique properties of a water-ethanol solution (meaning I may have made an assertion with confidence that turns out to be incorrect). It's entirely likely that the phenol, with its single oxygen on a ring, might be significantly less water-soluble than diphenyl oxalate, which has twice as many oxygens per ring. I've been having some trouble finding information about the solubilities of diphenyl oxalate in various solvents. So some hope remains for the separatory funnel idea. Unless it's a relatively simple separation, though, the distillation might be easier.

Halogenation opens some possibilities while closing off others. Oxalyl chloride reacts dangerously with water to produce HCl gas, so I'd do well to avoid any reaction that might result in the production of oxalyl chloride.

I'm also not familiar with the reactivity of diphenyl oxalate with water- whether it will remain stable in an aqueous solution or if there will be degradation of the sample. Another reason I'm looking at ethanol more than water as a phenol alternative. Dry techniques using aprotic solvents would be preferable to wetter methods. Aprotic solvents also tend to lend themselves more readily to analysis with NMR and GC-MS, which may be useful for verifying that I'm getting the reaction I'm shooting for.

I'd definitely go for the halogenation step if not for safety considerations further down the chain of events.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Ashitaka

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Icon 1 posted November 11, 2007 02:48      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
Well organic systhesis is also not my specialty,i'm into analytics, which may help with your purification. Have you considered prep. LC for purification? It is a really uncomlicated procedure, in my eyes, compared to re-crystallization . The problem is how much solvent one needs to purify (depending on how good you caan make your method) and not everyone has a prep LC and prep LC columns lying around.

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"If they're not gonna make a distinction between Muslims and violent extremists, then why should I take the time to distinguish between decent, fearful white people and racists?"

-Assif Mandvi

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ScholasticSpastic
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Icon 1 posted November 11, 2007 14:05      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
Ashitaka, yes, prep LC looks good, but no, I don't have the columns laying around. We are currently in the market for an HPLC to use for sample preparation prior to feeding complex samples through our GC-MS, but funding is iffy right now and I don't know if I can rely upon equipment acquisition prior to my graduation. Best to assume that I'm limited to techniques that can be accomplished using simple glassware and wet-chemistry methods.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Ashitaka

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Icon 1 posted November 12, 2007 10:57      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
The wikipedia link gives the reaction as the estrification of Phenol and oxalic acid. The source at the botom of the page links to an article that is the reaction of dimethyl oxalate with phenol. A quick lit. search gives this as the stardard procedure. Does oxalic acid and phenol first form dimethyl oxalate and then diphenyl oxalate? The literature give the reaction for dimethyl oxalate as the carbonylation of methanol. The lit. search basically gave this process over and over again with different catalysts.

Right now I am interested in making clear glass christmas ornaments filled with red and green glowing Diphenyl oxalate. I think thoughit will be easier if I will just buy red and green glow sticks and break them open. I can easily aquire some phenol, oxalic acid and even diethyl oxalate, but I can't get the dyes.

My godmother's ex-husband was a manager at a factory in Indiana that made these glow sticks. I don't suppose she would want, or know how to , get me in contact with him.

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"If they're not gonna make a distinction between Muslims and violent extremists, then why should I take the time to distinguish between decent, fearful white people and racists?"

-Assif Mandvi

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TheMoMan
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Icon 1 posted November 12, 2007 17:53      Profile for TheMoMan         Edit/Delete Post   Reply With Quote 
Okay you three ___________________ Now the TheMoMan has a question, and good to see you back ScholasticSpastic. I was in a discount retailer today and they were selling off Halloween goodies, yeah I turned away from the candy but, some luminissant toys did catch my eye. I bought a couple and plan on keeping them in the car, truck and motorcycle as emergency tail lights. The question is they caution against high temps. What about freezing?

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Those who would give up essential liberty to purchase a little temporary safety deserve neither liberty nor safety.


Benjamin Franklin,

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Xanthine

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Icon 1 posted November 12, 2007 19:15      Profile for Xanthine     Send New Private Message       Edit/Delete Post   Reply With Quote 
Freezing makes glowsticks last longer, so as long it doesn't get so cold your housing cracks, it should be fine. It might not glow at freezing temps though...IIRC, you have to thaw the glowstick.

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And it's one, two, three / On the wrong side of the lee / What were you meant for? / What were you meant for?
- The Decemberists

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ScholasticSpastic
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Icon 1 posted November 12, 2007 22:41      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Ashitaka:
The wikipedia link gives the reaction as the estrification of Phenol and oxalic acid. The source at the botom of the page links to an article that is the reaction of dimethyl oxalate with phenol. A quick lit. search gives this as the stardard procedure. Does oxalic acid and phenol first form dimethyl oxalate and then diphenyl oxalate? The literature give the reaction for dimethyl oxalate as the carbonylation of methanol. The lit. search basically gave this process over and over again with different catalysts.

I found lots of methods with dimethyl oxalate reacting with phenol to yield diphenyl oxalate, too. I think that the idea is that there's an intermediate formed in which the phenol and the methyl group share the oxalate and then methanol serves as a stable leaving group. I'm not sure, though, and it's not the reaction I want to do. I've also found a few chemoluminescence lab abstracts (which were wonderful leads for dyes) that use diphenyl oxalate. Looks like rubrene would be the brightest dye and so that's one I'll have to price tomorrow. It would be interesting to see if chlorophyll will work.

quote:
Right now I am interested in making clear glass christmas ornaments filled with red and green glowing Diphenyl oxalate. I think thoughit will be easier if I will just buy red and green glow sticks and break them open. I can easily aquire some phenol, oxalic acid and even diethyl oxalate, but I can't get the dyes.

Unless you're interested in the synthesis for the sake of doing the synthesis, purchasing the glowsticks would be cheaper and more time-efficient. You might look into doing the synthesis if you plan to give them away as gifts because hand-made means more than purchased and I would imagine that the degree of hand-madeness effects the degree of increased meaningness (but I'm not sure about that). The stuff you'd get in glowsticks isn't exactly diphenyl oxalate, but it's very close and it'll actually react more vigorously. The red glowsticks often have the dye embedded in the plastic rather than in the liquid in order to produce more light. You may have to do green and yellow, instead.

--------------------
"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Ashitaka

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Icon 1 posted November 13, 2007 06:14      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
Ok, this is why I should stay out of discussions of organic synthesis. Dimethyl oxalate is oxalic acid. Same stuff.

<homer> Doh.

[blush]

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"If they're not gonna make a distinction between Muslims and violent extremists, then why should I take the time to distinguish between decent, fearful white people and racists?"

-Assif Mandvi

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Metasquares
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Icon 1 posted November 13, 2007 07:19      Profile for Metasquares   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Xanthine:
Organic synthesis isn't something I've thought about in years, I can't offer you much help beyond a "NICE TO SEE YOU BACK!"
Publishing is brutally cut-throat, especially if your topic is at all competitive. I've participated in and been caught in the blowback of some publishing nightmares. I've also heard some awful stories. Interestingly enough, one guy who tried very hard to fsck us is now a collaborator. We wrote an official letter and everything. Apparently, in my little corner of the science world, if you can't beat 'em into the ground, collaborate. Who gets credit for what and why is also a smarmy, nasty business that can ruin friendships quicker than lending money ever will.

Same sort of thing in Computer Science. It is really a pretty screwed up system.
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ScholasticSpastic
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Icon 1 posted November 13, 2007 08:47      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Originally posted by Ashitaka:
Ok, this is why I should stay out of discussions of organic synthesis. Dimethyl oxalate is oxalic acid. Same stuff.

<homer> Doh.

[blush]

It is???!!! [Eek!] That's just stupid! Why bother adding the word dimethyl (meaning two methyl groups stuck on) if it's just oxalate? I hope you're wrong about this- or I've just found another reason not to do organic chemistry professionally.

Alright, I just checked, and dimethyl oxalate is not the same thing as oxalic acid. Taking deep breaths.... feeling more Zen... On the bright side, in the midst of my frustration-fueled search, I stumbled upon a site backing my suspicion that diphenyl oxalate would decompose in an aqueous environment (but not in an alchohol solvent). So, thanks, Ashitaka, for challenging my complacency and making me go learn something. [Applause]

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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Ashitaka

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Icon 1 posted November 13, 2007 11:46      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
well that is what I get for using wikipedia as a source. If you search for dimethyl oxalate, wikipedia automatically takes you to the oxalic acid page. and since the production of diphenyl oxalate from oxalic acid and from dimethyl oxalate was teh same, I thought they were the same compound.

See, I told you I shouldn't discuss organic chem.

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Icon 1 posted November 13, 2007 15:17      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
Wiki is actually a very good starter source for chemistry because anyone who's geeky enough to contribute about chemistry is usually geeky enough to get it right. The issue appears to be one of refferencing, not necessarily one of information refferenced.

I am officially supported as an undergraduate researcher now. The school will buy some rubrene for me once I've demonstrated to their satisfaction that I'm actually making diphenyl oxalate. I'll be running through the synthesis and distillation steps this Friday. Product will be evaluated using IR and NMR. I was a little concerned because phenol is very flammable, but its autoignition point is 700+C and I'm only going to reflux up to 180C, so things should be fine. There's a very good chance that I'll be generating fumes beyond saturation for flammability- I'd be drowning any potential fire in its own fuel. (Yup, I'm using a closed reflux apparatus to trap vapors in order to increase safely.)

The distillation apparatus can be run as an extension of the reflux apparatus, so when I'm ready to pull off the solvent I'll just rearrange some tubes and keep on cooking. My Dr.-boss has confirmed that fractional distillation is probably the prefferable purification method for this kind of mixture. I'll know better when I've seen the behavior of the mixture under laboratory conditions.

I accidentally learned how to cook meth while reading up on titration methods to check for oxalate residue in my product. That's frighteningly simple. Methods for purification of cocain use similar methods... Chemistry is spooky sometimes. By the time I graduate I'll have all the information required to drug people, blow people up, or pretty much do whatever I want. From now on I'm treating chemists with respect. (I also learned some simple explosives related to the titration of oxalates/oxalic acids- probably the same thing that blows up meth-houses.) Got a new idea for a demonstration, though, and that'll be fun.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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littlefish
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Icon 1 posted November 14, 2007 02:51      Profile for littlefish   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
Wiki is actually a very good starter source for chemistry because anyone who's geeky enough to contribute about chemistry is usually geeky enough to get it right. The issue appears to be one of refferencing, not necessarily one of information refferenced.
Don't you believe it. A little knowledge is a dangerous thing. I have only contributed to wikipedia once, and that was because I was looking something up as a quick reference, instead of pulling a book of the shelf.

I was so offended by the wrongness of what was written on the page on infrared spectroscopy, I had to go in and edit it myself. It was a horrible experience, as the page is just a huge badly written mire of suck. It should be torn down, and re-written from scratch. However, I have better things to do, and don't want to put loads of effort in to something that can be revoked by anyone one a whim. Instead, the page languishes now with all the obvious falsehoods corrected (AFAIK), but with totally the wrong emphasis, and poorly arranged. Writing by committee is not a good thing to do.

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Icon 1 posted November 14, 2007 07:09      Profile for Ashitaka     Send New Private Message       Edit/Delete Post   Reply With Quote 
SS_________Do you have any friends in flow cytometry? I just found out that our flow cytometry lab has both rhodamine b and rhodamine g6 in their labs. The stuff isnt't that expensive. ask around, maybe someone might share some. Even if you have funding for one dye, maybe you can find some others in the labs.

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Icon 1 posted November 14, 2007 09:47      Profile for ScholasticSpastic     Send New Private Message       Edit/Delete Post   Reply With Quote 
littlefish, I undertand that wikipedia should not be considered a credible source. That's why I referred to it as a good starting point for exploration and not a place to find answers. Sometimes there is just enough information there to get people asking better questions and sometimes that's all we need. My words "a very good starter source." Otherwise, yes, there can often be a lot of bogus information or poorly formatted articles. By contributing the way you did, though, you helped the site realize its ultimate goal: you were offended by incorrect information and corrected it. That's the pattern that was intended by the creators of wiki.

Ashitaka, I didn't know about flow cytometry until just now. I certainly does appear to be a research method that would use a wealth of fluorescent dyes. I am located at a regional campus in the middle of the Eastern Utah desert for the duration of my undergraduate career. The location is certainly not prestigious- I'm here for the numerous scholarships provided by the extraction industries as a result of the current energy boom. It's a difficult line for a hippy like me to walk: taking money from the industries I intend to work to render obsolete by whatever means are available. Needless to say, there are not a lot of biology labs around out here. Our lab (there is just the one, for the whole campus, not a building, but a room) is equipped with some biological equipment, including a PCR device and DNA sequencer, which can be fun to play with, but we lack significant investment in research materials. I do look forward to emerging into the real world as a graduate student and taking advantage of the shiny toys available on a larger campus.

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"As in repeating a well-known song, so in instincts, one action follows another by a sort of rhythm; if a person be interrupted in a song, or in repeating anything by rote, he is generally forced to go back to recover the habitual train of thought..." (Darwin, The Origin of Species)

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littlefish
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Icon 1 posted November 14, 2007 11:21      Profile for littlefish   Author's Homepage     Send New Private Message       Edit/Delete Post   Reply With Quote 
quote:
littlefish, I undertand that wikipedia should not be considered a credible source. That's why I referred to it as a good starting point for exploration and not a place to find answers. Sometimes there is just enough information there to get people asking better questions and sometimes that's all we need. My words "a very good starter source."
Yeah, on the whole I'm a fan of wikipedia, but it does have fatal flaws, and in my opinion, it is one of the worst places to start if you know nothing of the field. While it can get you asking the right questions, it can also give you the basics wrong. Building on shaky foundations is not a great way to go.

If you do have foundations already though, and a good bullshit detector, wikipedia is good at filling in the middle level of knowledge. The advanced stuff however, isn't generally there.

Re-reading those paragraphs makes me sound unduly negative. Most people have some grounding, and the high level stuff isn't of too much interest to most, so it's great for many things. However, I'm finding (more commonly these days) that if I need to look it up, I already know more than what is on wikipedia. On a couple of occasions, I've done the research for myself and thought about writing it up, but I've just been too lazy/busy.

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