Friday, July 17, 2015

Blog contest: This machine goes "hiss!" and "ping!"



The other day, some folks on Twitter were trying to explain NMR:
@sciencenotscary: There's, um, some precessing and relaxation times and...uhhhh...
@chemprofcramer: rotating frame! rotating frame!
@chemjobber: There's a radio pulse, and a spinning thing and it goes ding! 
So, for amusement, I am offering a fine prize to the person who can offer the funniest, yet most accurate explanation of a chemical spectroscopic technique. Nominees to be decided by commenter acclaim, winner to be decided by a panel to be determined. Deadline for entry in the comments or by e-mail by midnight (Eastern time), July 24, 2015.

The fine prize: A 1 pound bag of hard candies, a certificate fit for framing, 50 of the finest Chemjobber business cards, a handwritten thank you note (by me) and a $10 Starbucks gift card.

(A serious note to grad students, especially fellow organickers: understanding the fundamentals and the details of spectroscopic techniques is important. Asking questions about them during oral exams is perfectly cromulent, in my opinion.) 

39 comments:

  1. Stick your molecules in a tube, then stick the tube in a magnet so the dipoles in the atoms in the molecules line up. Turn on a radio, and the atoms sway to one side while dancing with each other. Turn off the radio and watch as the dipoles in the atoms dance back. Repeat until you can draw it yourself.

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  2. NMR is the chemical equivalent of StoryCorps. Tune into the right frequency and you'll learn something about a specific situation that can also teach you something broad and fundamental about the environment in which it occurs.

    NMR is like radio-frequency-based molecular Twitter. Hit your sample with one short, pointed "statement" on a given frequency and then sit back listen to all the related nuclear opinions that come back at you. Fair warning: lot of it will just be noise.

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  3. Sum frequency generation, where a surface becomes a Thunderdome: two frequencies enter, one leaves.

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  4. Dr. Evil: Alright, here's the plan. Here's the plan. Back in the 60's, I had a mass spectrometry machine that used, in essence, a sophisticated laser beam which we called an "Ninja Assassin." Using these "Assassins," we superheat the sample of interest "Bound" to a base coating of aromatic compounds, which we scientists call "The Matrix." "Animating the Matrix" creates a superheated plume of gas containing every ion in the sample, a "Cloud Atlas" if you will. By timing the "Speed" at which ions "Race" to the detector we can determine their mass with incredible precision. "Reloading the Matrix" with new analyte allows the same detecting plate to be used multiple times, lading to massive profits and a "Matrix Revolutions" in mass spectrometry.

    Scott: Why did you pluralize the word revolution and use so many air quotes?

    Dr. Evil: It's a V, for Vendetta, not an air quote, Scott. Okay?

    Scott: Huh?

    Dr. Evil: Any ways, the key to this plan is controlling the rising gas. Like "Jupiter Ascending' it can quickly overload detector without proper safeguards. Because overall futuristic flair, and the polish source of "The Matrix", we shall call the device the Wachowski Starship.

    Number Two: [pause] That also already been created. It's called MALDI-TOF.

    Dr. Evil: Right, people you have to tell me these things, okay? I've been frozen for thirty years, okay? Throw me a frickin' bone here! I'm the boss! Need the info.

    ReplyDelete
    Replies
    1. ...I should have edited that better.

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    2. Well, I'm impressed. "Laser" in this context should always have "quotes." Also Wachowski Starship should be in quotes - it seems to me that for multiple-word phrases Dr. Evil uses quotes for each word, (e.g. "ozone" "layer" - watch that finger action!) hence "Wachowski" "Starship." But perhaps this is being overly pedantic.

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    3. The dialogue could also be made 'politically relevant' by adding in the following snippet:

      Dr. Evil: "Oh well, let's just do what we normally do, harass and ostracize a promising faculty member until he develops personal problems."

      Delete
  5. NMR- play BBC radio 3 at your sample, and record the screams.

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  6. The Iron ChemistJuly 17, 2015 at 2:31 PM

    EPR is like NMR but with electrons.

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  7. IR is like a TV remote control. You shine an IR source (spectrometer or remote control) at your sample (chemical or TV), and the signal that you get in return doesn't usually tell you anything useful that you don't already know.

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  8. FT spectroscopy is like listening to a grand piano crashing to the ground from a 10 story drop in order to determine which notes were out of tune.

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  9. GC/MS - Gas Chromatography/Mass Spectrometry
    A mixture of compounds and internal standards is injected into the gas chromatograph . The carrier gas sweeps the mixture over hot metal surfaces, where the compounds of interest degrade or rearrange, into a column where they are separated. Molecules that exit the column (i.e., those not pyrolyzed in the injection port) and enter the ion source of the MS, where they are bombarded by electrons and ionized to form one or more positive ions. These ions are separated by a mass filter (typically a quadrupole or quadruple after spell-check) and the relative intensities of each ion with a particular mass/charge ratio is determined by the data system. (Senior citizens will say computerized data system.)

    The retention times of compounds may change as the stationary phase changes due to deposition of residues from dirty samples and reaction with oxygen from leaks. For compounds with similar mass spectra (e.g., xylenes) errors in identification may occur. This usually only happens when data are to be published or the sample is a PT sample.

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  10. @ CJ,

    Thanks for using "cromulent". I had to look it up and I've embiggened by my knowledge. You really demonstrated your brilliantness.

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    Replies
    1. A perfectly cromulent comment, IMHO, which embiggens the whole blogosphere.

      Delete
    2. There it is AGAIN! Damn it!

      Delete
  11. I like: http://www.jkwchui.com/2011/12/interpreting-proton-nmr-overview/

    More about reading a spectrum, but still useful.

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  12. Sit down by the fire, kids, and let ol' See Arr Oh tell you about the spectral technique every O-chemist loves: Proton-decoupled carbon-13 NMR. You see, back in the 1950s, gents in well-tailored suits with big glasses posed next to giant, room-filling machines capable of only a fraction of today's tablet computers' power. These men - and they were always men, then - would place thin glass tubes of their molecule into relatively misshaped magnetic fields and send in specific radio waves, hoping out the other side to see their recorder pens transcribe a forest of little inky peaks.

    Now, this worked fine if you wanted ALL the information about each and every proton in the molecule, but what if all you wanted to do was count carbons? Sending in radio waves tuned to carbon sent back little patterns of 2, 3, 4 (or more) peaks, depending on how many Hs were bound to each C. Too much info!

    Instead, if you blast all the protons with one high-powered radio pulse, their coupling to C falls apart, and you can sneak in a carbon-only pulse just afterwards. Et voila! Simple, single peaks shifted to match the chemical environment of where you found 'em in the molecule. Carbons next to things that tug on their electrons are on your left. "Saturated" carbons with lots of protons or buried deep with other carbons are on your right. Easy as pie.

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  13. The difference between CW and FT NMR Spectroscopy
    Disclaimer: I cannot claim originality on this. I heard it in an NMR course taught by Horst Schirra.

    Imagine you're playing a piano to someone (the sample). In the olden days (I.e when I learnt NMR) you had to start from one end of the keyboard playing each note in turn, and writing down which notes they responds to. This was called sweeping the field.
    Now imagine instead that your audience has been replaced by a cyborg. Now bend your arms at 90 degrees and bring them down violently on the keyboard playing all the notes at once. Crash! Sounds horrible but your cyborg friend does some maths in its head to convert the slowly decaying signals into their respective notes and says "I like the D flat"

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  14. Unstable IsotopeJuly 18, 2015 at 9:31 AM

    You put your precious sample in a complicated machine and out come lines of great meaning. (This applies to multiple spectroscopy techniques.)

    Who is judging this contest anyway?

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    Replies
    1. It will probably be:

      Renee Webster
      an unnamed NMR spectroscopist friend of mine
      (someone who has not agreed yet)
      (or someone else)

      I think I'm not going to judge (at least, I hope not to.)

      Delete
  15. Time of flight mass spectrometry is akin to a foot race between skinny kids and heavier kids. They all start approximately at the same starting line. The gun goes off and the race starts. The lighter kids travel faster and the heavier kids are slower through the race course. The skinnier kids get to the finish line first while the heavier kids finish later.

    I can say all of this because I'm a fat kid.

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  16. Radiocarbon AMS dating:

    You take an irreplaceable archaeological artifact, smash it, pour acid on it, burn it, then catapult any remains as fast as current technology will allow.

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  17. In NMR there is shimming and that...

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  18. NMR spectroscopy is like making love to a beautiful woman.
    You start vertical, but then get excited and end up horizontal. Then you roll around a few times...and relax.

    For any non-British readers, who wish to appreciate the origin of this: https://en.wikipedia.org/wiki/Swiss_Toni

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    Replies
    1. For the curious:

      https://youtu.be/iBw-aEixWuo

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    2. This one made me laugh both before and after looking up Swiss Toni. That's an imaginitive way to describe a 90-degree pulse, standrews!

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    3. Swiss Toni explaining NMR? Brilliant.

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  19. So imagine you're a circus performer in a room, standing by the doorway. Your act consists of you holding a fairly large butterfly net, ready to catch what ever miniature clowns run through that doorway. But the mini clowns don't actually run in, they are actually being shot out of a cannon. Through the door. Into your net. But your cannon is kinda crappy so if the clown is too big, it just kinda plops out of the cannon and doesn't make it very far... Probably won't even make it through the doorway. But if the clowns are small, they get launched from the cannon with impressive speed... Probably too much speed so that when you try to catch them, they rip the net right out of your hands and keep going on their trajectory straight into the audience, perhaps into that section of nuns. It turns out, for the trick to work allowing the audience to see your daring clown capture, you need clowns of just the right size. Since you don't have a scale, the only way to find clowns of the right size is trial and error.

    This is essentially how a magnetic sector mass spec instrument works.

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  20. Poison Ivy LeagueJuly 21, 2015 at 2:42 PM

    1Hokey-31Pokey

    You make your sample up
    You book your sample in
    You let your sample down and you spin it all around
    You send in some RF waves and let the atoms have a shout
    That’s what it’s all about

    ReplyDelete
    Replies
    1. My current favorite - for simplicity and the variation on the original rhyme scheme, if nothing else.

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  21. My understanding of Raman is like the states it measures: virtual, but somehow good enough for publication.

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  22. Elemental Analyfish IIJuly 21, 2015 at 3:58 PM

    Elemental Analysis is like weighing out your sample
    except the sample is on fire
    and you're on fire
    because passing CHN is Hell.

    ReplyDelete
    Replies
    1. [Applause]

      (Are you the original Analyfish?!?!? Huge fan of your work, if so.)

      Delete
    2. Elemental Analyfish IIJuly 21, 2015 at 4:10 PM

      No, but fish do not live so long, right? Department's solution is to buy replacement goldfish and nobody remembers...

      Delete