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Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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May 22, 2013

Underappreciated Analytical Techniques

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Posted by Derek

A conversation the other day about 2-D NMR brought this thought to mind. What do you think are the most underused analytical methods in organic chemistry? Maybe I should qualify that, to the most underused (but potentially useful) ones.

I know, for example, that hardly anyone takes IR spectra any more. I've taken maybe one or two in the last ten years, and that was to confirm the presence of things like alkynes or azides, which show up immediately and oddly in the infrared. Otherwise, IR has just been overtaken by other methods for many of its application in organic chemistry, and it's no surprise that it's fallen off so much since its glory days. But I think that carbon-13 NMR is probably underused, as are a lot of 2D NMR techniques. Any other nominations?

Comments (62) + TrackBacks (0) | Category: Analytical Chemistry | Life in the Drug Labs


1. Anonymous on May 22, 2013 10:29 AM writes...

Optical Rotation

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2. Kerry on May 22, 2013 10:44 AM writes...

Melting point

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3. ClutchChemist on May 22, 2013 10:49 AM writes...

This may sound naive for a PhD, but I had no idea until I worked in the industry that quantitative carbon NMR was even possible. You just need a concentrated enough sample and big enough NMR tubes. Had I known this in grad school/post-doc (and had the capabilities), I would have been all over that!

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4. littlegreenpills on May 22, 2013 11:05 AM writes...

In my experience most synthetic chemist use MS, 1H NMR, and 13C NMR. If everything generally agrees with what they wanted then they are finished. But I have seen a number of cases where the product was not correct and 2D NMR could have given them the correct answer.

13C NMR provides a lot of information but there are much more information rich techniques. For example, DEPT gives you the 13C shifts as well as information about multiplicity in about the same amount of time as 13C NMR. HSCQ and HMBC provide 13C shifts along with connectivity in less time than a 13C NMR, but you have to have some protons.

NMR prediction software is also very useful, though I have no idea how much it is used by organic chemists.

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5. Paul on May 22, 2013 11:08 AM writes...

I'd vote for the TOCSY NMR technique; basically NOE for through bond couplings. In 1D mode, it's amazing for deconvoluting spectra with overlapping peaks and I've found it to be easier to interpret than COSY where phantom peaks can be confusing.

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6. Gaspode on May 22, 2013 11:13 AM writes...

compared to IR i wouldn't consider Melting Point a useful technique. Its incredible how much Information an IR-Spectra contains if you are able to "read" it. A lot of structural determination was done with it in "the old days" just like NMR today.

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7. processchemist on May 22, 2013 11:20 AM writes...

Melting point is routinely used in the final characterization of a batch, much more than NMR or LCMS. And it's maybe the fastest way to see if there's something wrong before a deeper investigation.

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8. JC on May 22, 2013 11:42 AM writes...

Combustion Analysis


Mixed Melting point, where you make the compound by two different routes & combine them to check the melting point.

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9. Anonymous on May 22, 2013 11:48 AM writes...

Nitrogen-15 NMR. I have never seen synthetic publications use this to characterize compounds. N15 HMBC and N15 HSQC are easy to do and give valuable information.

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10. Anonymous on May 22, 2013 12:00 PM writes...

Hydrophilic Interaction Liquid Chromatography.

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11. Anon Electrochemist on May 22, 2013 12:11 PM writes...

Anything using electrochemistry, which people tend to innately hate.

Capillary electrophoresis offers ridiculously high resolution. Amperometric detection on LC is extremely sensitive and selective. Then tack on all the traditional wet-cell techniques like pulse voltammetry, etc.

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12. ROGI on May 22, 2013 12:15 PM writes...

Interesting question. Oddly enough, continuous UV spectroscopy (Woodward rules, vs Woodward-Hoffman rules) has helped me enormously on several occasions to elucidate double bond placement and fused ring structures for some complex derivatives/natural products. The empirical rules that RB developed in the 40's in and of itself at the time, would have qualify for the Nobel Prize. I highly doubt that anyone under the age of 60 even knows what they are and how useful they can be to confirm or eliminate structural assignments. One would be very surprised that, with experience in IR interpretation, especially with FT enhancement combined with UV experience (i.e., having shagged enough chemical golf balls),you can nail down structural assignments.down structural assignments.

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13. Flatland on May 22, 2013 12:19 PM writes...

DOSY (Diffusion Ordered Spectroscopy)- 15 minute experiment to tell you if you really only have one compound in your sample, and if not, separates the resonances for each.

TLC- some people are just damn lazy about running them, when they will tell you a lot more than a fancy mass spec will (hint, not everything is volatile). Also, people have forgotten some of fancy stains that you can use.

Taste test (just joking, this is in honor of my old organic professor)

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14. paperclip on May 22, 2013 12:51 PM writes...

NOESY/ROESY. It's not just for biomolecules or for some exotically shaped molecule ("It looks like a horseshoe!") It can be useful for regular organic compounds and can help with stereochemical assignment.

Lol about taste test, but seriously how about one's eyes, and, rarely, one's nose? (Just a whiff!) They certainly aren't reason to throw out the NMR, but many a time the color of a molecule (it's not all white) has been an important, immediate clue for me.

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15. Teddy Z on May 22, 2013 12:55 PM writes...

I like the vote for DOSY. I was involved in a counterfeiting investigation and the standard techniques could figure out what it was. A DOSY identified it as a binary mixture, the HSQC and HMBC identified the components uniquely. Voila. Counterfeiting ring busted!

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16. Curious Wavefunction on May 22, 2013 1:00 PM writes...

ORD and CD

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17. CMCguy on May 22, 2013 1:05 PM writes...

My first reaction was same as number 1 with OR (assuming working on chiral molecules). However #13 comment on taste made me wonder if it could be the Organoleptic use of Senses: Seeing and Smelling do not get critically applied enough in evaluation of compounds (and taste could be added in rare circumstances). One would hope this in ingrained as basic observational responsiveness in scientists although I have run across people who crapped up reactions by not using clues that could be seen or smelled.

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18. MoD on May 22, 2013 1:31 PM writes...

Combustion analysis and TLC. Too many crackerjacks are relying solely on LCMS to follow reactions and decide whether or not the product formed.

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19. Inflammable on May 22, 2013 1:35 PM writes...

Second vote for combustion analysis. I once sat through a talk on how to tell if you had residual PF6 after your HBTU couplings, and they never once thought of getting a simple CHN.

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20. daen on May 22, 2013 1:40 PM writes...

Funnily enough, my last consulting gig was validating software for a FTIR spectrometer used in our customer's QC department.

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21. Hap on May 22, 2013 2:00 PM writes...

Wouldn't 31P NMR be an easier way to detect PF6- in product than combustion analysis? I had always heard that combustion analysis was also expensive, which would explain why it wasn't a first instinct.

This isn't really analytical, but I thought it was interesting, anyway. I know 19F NMR has been used for some things to look at binding events, but until I saw a paper earlier this year, I hadn't realized what 31P and 19F can do for identifying carbons - 31P helped determine the regioisomer of a phosphine in a patent which was unclear from context, and in a separate paper, the aryl carbons and protons in a compound with p-FPh groups could be readily assigned by their coupling constants. I thought that was neat.

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22. Ted on May 22, 2013 2:32 PM writes...


I've always been amazed that so many organic chemists consider an internal temperature probe "optional."

The first professional lab I worked in (as a process chemist) had "It's the Temperature, Stupid!" written on the white board.


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23. curt on May 22, 2013 2:32 PM writes...

X-ray crystallography

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24. Anon on May 22, 2013 2:38 PM writes...


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25. Chemjobber on May 22, 2013 2:39 PM writes...

Agred w/#3. Quantitative NMR is pretty neat stuff, when it works right.

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26. anon on May 22, 2013 2:43 PM writes...


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27. Anonymous on May 22, 2013 6:10 PM writes...

Electron pushing mechanism

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28. B on May 22, 2013 6:28 PM writes...

@27: What do you think I am? An Orgo 2 student?!

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29. BrokenChemist on May 22, 2013 7:01 PM writes...

Straight UV-Vis spectroscopy (not coupled to an LC). It's not always useful for all reactions, but for some of them (especially reductions of aryl nitro groups to anilines) it can give you a quick and easy determination on whether your reaction's still going. In addition, if you have something like the NanoDrop spectrophotometers, you won't be using any more of you reaction mixture than if you were to run an LCMS and the measurement is much faster.

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30. Can on May 22, 2013 8:06 PM writes...

Raman spectroscopy, IR's unloved brother.

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31. prf on May 22, 2013 8:16 PM writes...

mixed mp and tosylhydrazone mp

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32. Secondaire on May 22, 2013 9:25 PM writes...

I also vote for IR. Supremely useful for converting chlorides to azides, cyanides, telling carbonates from carbamates, and so forth.

Also, the smell test, as already mentioned. Certainly not condoning sticking one's nose into every reaction (and there are things you should never stick your nose into) but it's certainly useful, for example, when converting a low-MW alcohol into the aldehyde or acid (e.g., phenylethanols to phenylacetaldehydes), as SM and product smell vastly different...

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33. ag on May 22, 2013 10:24 PM writes...

IR was the quickest for me to confirm that I had formed the diazoacetamide I needed without isomerizing...

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34. Orion on May 22, 2013 11:44 PM writes...

2D TLC. Sometimes used it as a last-ditch option when I couldn't figure something out, and was always amazed how much useful information it could give.

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35. Just Another Post Doc on May 23, 2013 12:24 AM writes...

I agree with 34. Too many people have never even heard about a 2D TLC. If your crude NMR is surprisingly cleaner than your TLC, it would have been a dead give away. I still hardly ever run them.

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36. BioBritSd on May 23, 2013 12:47 AM writes...

I liked the nomination on DOSY. I did some of those during in my PhD to measure binding coefficients - the affinity of a small ligand to a large substrate leads to a significant change in relaxation that can be used to calculate the affinity.

I'm or sure if this was ever used in a life science setting, this was always artificial receptors. But, assuming you could get about receptor, perhaps yes ?

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37. Slurpy on May 23, 2013 2:00 AM writes...

2D TLC? I'll have to look into that. I didn't realize quantitative C13 NMR was a thing, either.

If I can ever find a local job as a chemist (and not just a lab tech!), I'll definitely have to find an excuse to give them a try!

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38. London Chemist on May 23, 2013 3:00 AM writes...

#13 Got to agree about tlc--I still have a 1000 page (yes, thousand!) book on tlc (by Egon Stahl) on my shelf. Haven't used many of the stains, but it shows you what you can do: even get functional group info out of some of them (even differentiating between amino acids). A few things I've liked: Iodine dip to show up amines (and can tell aliphatic from imidazoles). Vanillin (the smell!) esp. good for non-aromatics (cpds with the benzyloxy group show up deep, deep blue). Once worked next to a guy who only used UV with KMnO4 on his tlcs--he once couldn't get a reaction to work (by tlc). When he used vanillin he saw that his product and SM co-ran, but with the dip he got two different colours...

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39. sepisp on May 23, 2013 3:01 AM writes...

There are two things that were used regularly in the old days, but are not regularly done today: determination of properties and wet chemistry or color reagents. Of properties, old publications always report properties such as melting point, density, refractive index and elemental composition (by combustion). These are sensitive or very sensitive to impurities.

Wet chemistry "old style" may be laborious, but coupled with modern analytics you can go farther than with either alone. Silylation to GC heavy hydroxyl compounds is common, but you can do for instance phosphitylation and 31P NMR. I worked for a project related to pulp, and found that pulp engineers still use a lot of good old 19th or early 20th century analytical chemistry. For instance, bleachability is still determined by adding KMnO4, then converting the excess to I2 with KI and titrating it with thiosulfate. I modified it this by determining excess MnO4- by UV-vis, simplifying the method. The method is still inaccurate, though, since it attacks all oxidizable materials. They still do stupid things like measuring the molar mass by solution viscosity, which should be abandoned for good, in favor of gel permeating chromatography.

Also, some of the more brutal methods have their value. For instance, TGA.

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40. boglet on May 23, 2013 6:41 AM writes...

In my experience, 13C NMR is somewhat over-used. There seems to be touching faith in counting the carbons. In terms of cost-effectiveness it is quite wasteful in instrument time when proton-detected experiments are often far more informative and quicker (e.g. HSQC and HMBC). This is not to say that there aren't situations where 1D 13C isn't appropriate (e.g. identifying carbons a long way from any protons).

I feel that IR is under-utilised. It often offers structural information that is not visible in NMR spectra (functional groups). I would also vote for 15N HMBC as an excellent addition to the toolbox.

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41. Curt F. on May 23, 2013 7:32 AM writes...

Its a very "young" technique but I nominate HPLC-microcrystallography. That paper was awesome!

On a more serious note, I'm curious if folks here think the answers would be different on the biological side of chemical analysis. What's underutilized for tracking say enzyme reaction progress in live cells or crude lysates? Stable isotope labeling techniques? Some of the newer papers from the Xie lab on video-speed label-free Raman microscopy are amazing.

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42. Scientistbymistake on May 23, 2013 8:15 AM writes...

IR, if only because I used to love making my own KBr disks... :-)

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43. CanChem on May 23, 2013 8:51 AM writes...

As a pharmaceutical analytical chemist, I get to spend my life playing with almost all of the techniques just listed; DSC, TGA, NMR, FTIR, etc... I vote for IR as well; with the "new" ATR probes and rather rudimentary chemometric software reaction progress can be monitored real-time with surprising ease and accuracy. Mettler Toledo's ReactIR is one example. We're currently working on switching some of our in-process control methods to IR because of the ease of analysis.

Being part of a group working towards real-time release for drug product manufacturing, I can't stress enough how useful NIR and Raman are as well. The amount of information you can obtain in a very short time is tremendously powerful.

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44. Harry on May 23, 2013 10:14 AM writes...

TLC, Melt Point, Mixed Melt point.

All nice and quick and dirty, and give you a nice jumping off place for deeper looks. Heck, you can always scrape the TLC spots off and analyze them.

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45. simpl on May 23, 2013 11:25 AM writes...

When I signed on, we regularly used TLC scrapings for assay and degradation product testing. In the previous generation there were some wizards at TLC before HPLC became king.
And I'd still like an IR app on my mobile phone, with an IR laser instead of a second camera.

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46. Screener on May 23, 2013 11:29 AM writes...

@41 I'll vote for enzymology. It's amazing how many projects I've come across where no one has any idea of the MoA or on/off rates of any of their lead series.

Or even any idea of which MoA they want to target (what’s the most abundant form of the protein, if we kept it inactive would that avoid feedback loops, is going after the free form of the enzyme a good idea when most of it in the cell will be bound with co-factor etc).

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47. pete on May 23, 2013 11:34 AM writes...

re: melting point
A final Chem 1 lab we were given a limited amount of unknown inorganic salt and had to determine what it was. Brilliant that I was, I ran to the stockroom and checked out a melting point apparatus. As I'm looking in the scope watching the crystals & rising temperature the TA comes by and snorts through his nose, "Good luck with that !" -- I guess that's why I became a biologist.

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48. DDTea on May 23, 2013 12:38 PM writes...

SECSY (Spin-Echo Correlation Spectroscopy), because it has a funny name that I'd like to read in more papers.

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49. Anonymous on May 23, 2013 5:38 PM writes...

Magnetic Susceptibility.

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50. Paul B on May 24, 2013 3:34 AM writes...

My vote is for CHN, its the one technique where its difficult to 'hide'. 20 years ago it was compulsory for all final compounds, today I suspect very few would pass. Comments such as we used TFA in prep and 'we didn't see salts in my previous company' - translate to 'we only checked the proton NMR and MS' and ignored any blind spots!

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51. Bromine on May 24, 2013 7:37 AM writes...

Karl-Fischer moisture titration. People are too lazy to do it, and then wonder why their n-BuLi reactions fail.

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52. Helical_Investor on May 24, 2013 7:57 AM writes...

With macromolecules and oligomers (nucleic acid or peptide), ion exchange chromatography IEC to ID and quantify counterions. Too many 'assume' ion exchanges are effective and stoiciometric, then muck up bioassays (or tox) with TFA, or amine salts.

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53. GladToMoveToProcess on May 24, 2013 8:59 AM writes...

DSC, mentioned several times already. Can give info about polymorphs, and really useful with rather unstable things that you're thinking of scaling up.

Also, tlc with long wave UV examination. Even tiny amounts of fluorescent impurities show up, and it can be very useful in following some reactions where a fluorescent functional group is created or changed.

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54. a. nonymaus on May 24, 2013 11:21 AM writes...

I'd say that 14C-tracer experiments are very underutilized in mechanistic organic chemistry in this century. Do the reaction, degrade the products, identify which degradation product contains the radioactivity. On the other hand, the not-crazy way to do the same thing these days would be 13C labelling and NMR.

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55. Kevin on May 24, 2013 12:19 PM writes...

Interesting to read this as I work not in pharma but polymers and IR, DSC, TGA, and DMA for example are common daily tools. IR and DSC are still extensively used in food chemistry too. Hyphenated TGA with FTIR is a growing technique.

And DSC remains vital with lyophilized materials for both Tg and collapse point.

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56. Henry on May 24, 2013 2:59 PM writes...


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57. Chemcat on May 25, 2013 2:39 PM writes...

Melting point determination, for sure

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58. NatProdChem on May 25, 2013 4:27 PM writes...

Another vote for Circular Dichroism !

Old chiroptic technique largely under-used because of the difficult interpretation of the spectra.
Last years progress in computational chemistry helped a lot with this part.

What a powerfull technique !

Do you know any other way to determine the absolute configuration of a totally unknown natural product (no reference) that won't cristallize ... and from 5 microgram of product (not destroyed) ?

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59. Anon on June 9, 2013 2:16 AM writes...

Not too long ago I attended a seminar (at my university) where the speaker referred to us (grad students) as being from the "NMR generation", and taking for granted the humble technology of IR... which he used to solve what was a characterization issue that had his student perplexed. Indeed, IR was of pertinence to structural elucidation once upon a time, and is now bordering on redundancy. Although we (and I assume many others who publish) foster a culture of taking any novel compound's IR spectra, I don't remember the last time I genuinely accessed the Perkin Elmer to find out what kind of compound I am dealing with (most the time, it's the last thing I do once I've confirmed the structure by IR and MS). But its very nature as a bench-top spectrometer that has no queue or downtime has always been tantalizing, and I do wish I could put it to more use.

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60. Anon on June 9, 2013 2:21 AM writes...

^That should read:

(most the time, it's the last thing I do once I've confirmed the structure by NMR and MS)

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61. Marty on June 12, 2013 8:09 AM writes...

I'm something of a lapsed chemist, with no PhD and having gone to the dark side of Sales, but I was always really impressed with the potential of Raman spectro... it never seems to have gone anywhere. (Except maybe for Hazmat / NBC detection?)

I also used to enjoy faffing about with XPS (mainly because of the ultra-hard vacuum; so many negative exponents).

For a natural products or QC chemist in pharma nothing beats a TLC. 2D is just awesome... and as someone pointed out, it's possible to get semi-quant or quant data out of a good TLC if you have a chromaphore, a camera and a software program - or scrape the spot.

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62. Anonymous on June 15, 2013 1:15 AM writes...


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