Showing posts with label IR. Show all posts
Showing posts with label IR. Show all posts

Sunday, July 17, 2016

Undergrad Tech: Remember When?

Recently, I sat with a friend sipping coffee, watching passers-by hurriedly moving from one tall building to another. Remarks drifted back towards research - as they're wont to do when chatting with chemists - and she said: "Remember how hard it was just to order things?"

I knew exactly what she meant. Lab tech changes quickly, and you may not even notice until you take a step away from the bench. I'm not part of the generation who spent hours sketching molecules by hand from a rubber template pre-ChemDraw, but nor am I a grad student in the era of tablet computers that can access PDB or Aldrich from a free wireless connection in any lecture hall.

Maybe I'll take a quick stroll down memory lane to see how different things really were when I first started undergraduate research...

Planning: Then, as now, most projects kicked off using pen-and-paper or chalkboard sessions; whiteboards were in about 30% of classrooms and gaining ground, but my first experiences with drawing molecules for my coworkers covered my fingers in tacky powder. I can still smell lab chalk: musty, earthy, sometimes tinged with a faint amine odor if stored too near the reagents cabinet.

Courtesy of Dr. Freddy, at Synthetic Remarks, who seems to recall
chalkboards much more fondly than I.

Once you'd had the discussion, you transcribed it into a lab notebook - usually bound with black vinyl, perhaps featuring brown or maroon faux-leather accents and a bookmark string - and signed the page. Then it was time to dive into the literature. First, you staked out some territory at one of the few hulking beige monitors attached to your shared lab computers. Plan for coffee, since reboots and blue-screen crashes could usually be expected to last 10 minutes, with accompanying Windows jingles or goofy Mac cursor wheels.

(Why were operating systems always a generation behind on shared computers?)

Your 10-minute excuse to go grab a coffee.

Beilstein and SciFinder both offered installed systems with single-user seats. This meant you walked down your lab hallway, shouting "Does anyone need anything on SciFinder?" before logging in. The user interfaces were very Internet 1.0 - muted grey windows, inscrutable black text, fuzzy structures. Mostly, you would up transcribing the reference into your notebook alongside the idea. To get the paper, you usually brought a stack of dimes down to the reference library, and spent the next 20 minutes finding and then copying (don't forget to rotate every other page!) the journal article. The still-warm, toner-scented stapled copies were lugged back to your wooden desk to be pored over until evening. My fingers would often be tinged with more than one color of highlighter or colored pen after a night of intense study.

SciFinder Scholar, 1999. Source: ISTL.org

Synthesis: OK, you know what you want to make, so you need some reagents. Maybe first you glanced through the 2,000-row Excel file your lab has as its de facto "inventory" system. I remember some groups also had a dog-eared, yellowing notebook dangling from a rope of masking tape that listed all the chemicals no one needed any longer - hope you enjoy distillation! Failing these approaches, the trusty catalogs are all lined up against the single lab window, effectively blocking out 20% of the available visual real estate. Names of vendors I remember included Fisher, VWR, Aldrich, Sigma, TCI, and Columbia. Each one had different account reps, pricing, and delivery specs; you'd better believe your boss would ask if you looked up pricey, boutique reagents in more than one source. Someone had the lab job of calling these vendors every few days, providing the lab P.O. number or group credit card, and then taking delivery later that week. Collections of cardboard boxes large and small would be piled near the front door, and every week was Christmas (even if it was just your reagent-grade TEA).




The first and last physical Aldrich catalogs I remember ordering from.
Source: Alfred Bader, Sigma-Aldrich
At some point, you'd have everything needed to run your experiment. Hours passed, TLCs ran, and you scribbled long-hand in that same lined lab notebook. I'm fairly certain I spent thousands of hours hunched over, detailing exactly how the workup went, or scrawling single-line corrections (with initials!) for changes and errors.

Analysis: Instruments fell largely into two camps - things you ran and printed out to later affix into 3-ring binders, or numbers on an LED screen you hastily scribbled onto a Post-it note. UV-Vis and optical rotation fell into this latter camp; I still smile whenever I see a forgotten, tucked-away bookmark reading "+8.75 deg."

I worked in lab right at the death knell of chart-recorders - little red pens in threaded holders that traced a curve based on numeric readouts from an IR or GC. NMR, graciously, always emerged on an ink-jet printer in the corner of a sub-level lab. I was a Bruker shim-jockey for quite a while, bragging that I could shim, acquire, FT, pick, and integrate an 8-scan 1H in under 2 minutes. Of course, many academic labs now have robotic cherry-pickers and automatic data transfer, which must save tons of time (unless you're a biophysicist or monitor kinetics; we might as well chain you to the 600MHz).

Source: Cal State LA / Bruker Instruments

Presentation: My first lab group still owned an overhead transparency viewer, and we were encouraged to print or sketch acetate slides each week for discussion. As these smudged easily when warm or done hastily, there were many grumblings and thrown elbows at the photocopier from fellow labmates on group meeting day. PowerPoint was reserved for "big" talks - oral exams, defense seminars, or preparing a poster for ACS meetings. Once saved and laid out the way you wanted, these were burned onto a CD-R or stored on a 100MB USB flash drive your boss might loan you. The walk to FedEx felt tense, because you didn't want to lose this uncomfortable piece of plastic, which contained the only copy of your slides.
Just don't write on the glass itself, or the PI will get really angry. Trust me.
Source: Amazon

I'm sure that I'm missing more fun events from lab life and technology from the late 20th century. Readers, if you have a special memory from back in the day, please feel free to share it in the comments. I'll update the post if I've missed something vital.

Monday, May 21, 2012

Calimari Calligraphy: Same Ink, 160 Million Years Later

Old news: Geologists, digging up ancient British sea bed, unearth a fossilized cephalopod.


Big news: Its pigment sacs contain the same ink squid still use today!


Fossilized Ink Sac
Source: British Geological Soc. | Nat Geo
This archaeology, with a dash of chemistry for good measure, went to press in PNAS earlier today. As Nat Geo, Discovery News, and msnbc tell it, a stroke of luck brought the multi-national (Japan, India, USA, UK) team a fully intact ink sac, which still contained eumelanin, the ubiquitous black pigment found in skin, hair, and feathers throughout the biological world (for more on the structure and function of melanins, click here).  


Quoth the lead author, John D. Simon (UVA-Charlottesville), to Discovery: 
"Out of all of the organic pigments in living systems, melanin has the highest odds of being found in the fossil record" 
In other words, this collection of highly-oxidized tyrosine and indoleacetic acid residues, chained into polymeric pigments, stays preserved - and structurally sound - for 160 Million Years. Could we say that about most of the materials we make today? Moreover, by comparison of various spectral techniques, the authors wager that the ancient melanin composition looks nearly identical to what squid use today to scare off predators.


IR Data, "flipped"
Source: PNAS Supp Info
Well, I'd like to see some data, wouldn't you? Digging through the Supporting Info, I see loads of evidence: degradation studies, EPR, IR, Mass Spec, CHN analysis, Carbon-13 NMR, UV, pyrrolysis TIC, and X-Ray photoelectron spectroscopy (Whew!). 


Let's examine two of these a little closer. For the IR data, I've switched the view around 180 degrees, to present the peaks the way you'd normally see 'em in the lab. Note the top 2, calcium carbonate and hydroxyapatite, with their nice, sharp C=O and P=O stretching bands. When the researchers looked in the partially-fossilized sediment, they found mostly these two...but look at the dye! Even after all those millennia, the absorbances for the fossil dye line up almost perfectly with the modern-day sample.


Total Ion Chromatogram, Current (top) vs. Fossil (bottom)
Source: PNAS Supp Info
How about a little heat? If you cook the ink at 600 Celsius, then pass it quickly through a mass spec, plotting ion current vs. time, you get the next spectrum, the TIC. It shows the same breakdown products, a variety of small heterocycles and fatty acids, and something I wasn't familiar with: diagenetic products. These products, formed from reactions that occur during fossilization, show up here as sulfur heteorcycles. Since the samples have had quite a bit of time underground, they show much more diagenetic decomposition.