Chemistry Blog

Oct 17

Inquiring Minds Need Your Help

My current adviser has successfully managed a research group for more than 30 years. He has produced hundreds of publications and acquired a wealth of chemistry knowledge. Last week, when the group moved into a new lab, we boxed and unboxed the tools that helped build this knowledge: a grand collection of equipment, glassware and chemicals.

It has become abundantly clear that with much knowledge comes much glassware.

And not simply your everyday beakers or Erlenmeyer flasks, but unique glassware created for specific experiments. While this glassware once had high utility, it is now a fossil of long-ago projects gathering dust in the archives (and by archives I mean that drawer full of weird glassware that no one uses).

The graduate student or postdoc who preformed the long-forgotten experiment has moved on and taken with them the explanation of the glassware’s function.

The inquiring minds of my research group would like your help in identifying/explaining the five of the most interesting specimens.

1) The Immersion Condenser
The first item is an immersion condenser or cold finger with an o-ring connector and an inlet/outlet for cold water. The question is why does it have the weird tip at the end?

Since many of you are currently trying your hardest to come up with a funny/witty comment, I will make a preemptive, unclever strike: PENIS! PENIS! PENIS!

2) The Pitch Fork
Each of the glass rods in this image has a small (~1-2 mm) tube inside so it behaves as a four-way junction. Why this specific shape?

3) The Meth Pipe
This item has two openings. The smaller one has a long stem that encircles the larger opening several times until they both meet in a conical chamber. As you can tell from my label, our guesses on this glassware’s purpose were limited.

4) The all-in-one Reflux/Distillation/Addition Funnel Apparatus
The form of this item is relatively straight forward with the exception of the absent Teflon or glass stopcock just above the lowest round bottom flask. What is it for?

5) The Bubbler
This is the piece that I am most curious about. At first glance it appears to be a plain bubbler with a smaller inlet tube that runs to the bottom of the larger chamber which has an outlet near the top. Upon further inspection, we find that there is an additional, independent piece of glass in the inner tube that is free to move vertically (inset). The independent piece of glass is a sealed chamber either filled with a gas or is simply a vacuum. On the top of this piece is a ground-glass ball joint. The counter to this ball joint is a socket with an opening from the top inlet. Our best guess for this piece is that, unlike a normal bubbler, the inlet is reversed and is for liquid to flow directly into the larger chamber. As that chamber fills, the freely moving piece is buoyant and will continue to move upward with the solvent. Once the chamber has filled with enough solvent it will push the ball and socket joint together preventing the further flow of liquid. If this guess is indeed correct, what would you use it for?

Any insight you can offer is greatly appreciated.

Oct 14

ACS Grid View TOC

Anyone who pokes around ACS’ JACS beta site will have noticed they now offer a grid view for TOC abstracts. Screen shot below

At a recent ACS on campus focus group I remarked to a member of the JACS beta team how similar it looks to ChemFeeds (screenshot below). The young marketing graduate said with a big smile, “Yeah, we know.” “We knew about it.”

If you want to play with ACS’ TOC Grid View read the instructions here: Grid View TOC

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Oct 13

Cytotoxic Gold Nanoparticles

In a new AOP from Nature Chemistry, Vincent Rotello’s group report a new way of killing cells. There system uses gold nanoparticles (AuNPs) as the core, and attached to the core is a diaminohexane group. The diaminohexane fragment is sheathed from the cell by cucurbit[7]uril (CB[7]).

Once the AuNPs enter the cell they can be triggered to expose its cytotoxic diaminohexane appendages by introducing 1-adamantylamine (ADA); ADA outcompetes the diaminohexane for CB[7].

The paper shows some very nice chemistry and it does a nice job selling the point that their gold nanoparticles are toxic to cells. However, I am worried when they say they are “exploring this strategy in vivo…” as the current generation of their system seems indiscriminate. But, I always enjoy being proven wrong.

Link to paper: Recognition-mediated activation of therapeutic gold nanoparticles inside living cells
Other recent papers by Vincent Rotello

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Oct 06

A guide for reporters on the 2010 Nobel Prize in Chemistry

(cross-posted with Chemjobber)

Somewhere in the good ol’ US of A, USA (DON’T HAVE TO CREDIT CHEMJOBBER):

3 chemistry professors, Richard Heck (formerly of the University of Delaware), Ei-ichi Negishi (Japanese descent, of Purdue University) and Akira Suzuki (Japanese descent, of Hokkaido University) were awarded the 2010 Nobel Prize in Chemistryfor palladium-catalyzed cross couplings in organic synthesis” by the Royal Swedish Academy of Sciences. These are techniques for bonding (or connecting) smaller carbon-based molecules together to make larger carbon-based molecules.

Creating carbon-carbon bonds can be difficult and can sometimes involve using dangerous, impractical or environmentally unfriendly reaction chemistry; the techniques pioneered by Suzuki, Heck, and Negishi make these reactions simple enough for novice chemists to perform and practical enough that they can be run on multi-ton scale. Since their introduction in the late 1970′s, palladium-catalyzed chemical reactions have touched every part of the field of chemistry, including life-saving drugs, plastics and organic LEDs. The modern pharmaceutical industry would not be able to produce many of their products without palladium-catalyzed reactions.

The prize has been long-awaited by many chemists. “It’s about damn time”, said Chemjobber, a very junior synthetic organic chemist. “I don’t know what it took to get those Swedes to finally get their thumb out.” It is believed that part of the reason is the rules of the Nobel Prize: there can be no more than 3 awardees at one time, and they all must be living. Many chemists contributed to the field of palladium-catalyzed reactions. Professors Sonogashira, Tsuji, and Kumada could have all been part of this award, and the chemistry Nobel committee is notoriously controversy-shy.

Professor Heck has retired and currently lives with his wife in the Philippines. Professor Negishi is still teaching and research at Purdue University in West Lafayette, Indiana. Professor Suzuki is still teaching and researching at Hokkaido University in Sapporo, Japan.

(CJ here: Man, this is harder than you would think.)

Oct 02

Maker Faire NYC 2010 was Awesome!

The Maker Faire is a “World Science Fair” event conceived and organized by those who produce Make magazine, which is described as “a do-it-yourself technology magazine written by makers.”  It was held in three cities this year – NYC, Detroit, and the Bay Area.  The Faire happened in NYC at the New York Hall of Science in Queens last weekend and was a fantastic, energetic composite of things going on.  Well worth the trek to get out that far into Queens!

The event embodied the “do-it-yourself technology” theme, featuring exhibits with a heavy focus on science, cool demonstrations, and lots of do-it-yourself booths where “makers” hosted hands-on activities for children and adults alike.   Naturally, something like this was irresistible to me, and I was able to attend for free since I was volunteering at a booth (unrelated to science or technology – I was with a group of a different kind of maker).  I didn’t get too much of a chance to spend time at many of the huge number of booths and exhibits, unfortunately, which was a huge bummer.

The schedule was overwhelmingly packed – definitely intended for people to spend an entire day there.  There was a demonstration stage, multiple craft tents, a huge food area, a beer tent tucked in there (which seemed to result in me getting security to throw out one guy who was harassing one of the women I was working with), and a large handmade craft sale section hosted by BUST magazine called BUST Craftacular.

Activities included “Cardboard Music,” where instruments were made from cardboard and found objects, a live presentation called “Thinking Like a Scientist” (some demonstrations of which are 200 years old) given by Wizard IV (Steve Jacobs), who also happens to be the science consultant for MythBusters.   MakerBot Industries was there – they create 3D printers that you assemble and then can then function as a little factory to make things for you (see the company website for more awesomeness).  One of the biggest pulls for visitors was the “Reverse Geocache (TM) Puzzle” – unlike using GPS to locate boxes around the country/world, you are given the box, but it won’t open unless you are at particular coordinates that’ve been programmed into it, and you have a limited number of clues to find that exact location.   Add this fun kind of intellectually stimulating product, activities and ideas, to children’s rides, music shows, tasty paella, and handmade crafts, and you’ve got one heck of a good sciencey time.

Check out images of the event on their own website, as well as those on CNET, guaranteed to be focused on the super techie stuff.

Sep 19

$cience is Important

Last week Kei Koizumi, Assistant Director for Federal Research & Development for the White House Office of Science and Technology Policy, paid a visit to the University of North Carolina-Chapel Hill (my new home as of mid-June). The visit included a tour of several laboratories where everyone did their very best to convince him that our funding (e.g. my salary) is worthwhile as well as a presentation by Mr. Koizumi that outlined the Presidents plans/goals/vision for scientific funding.

On many occasions, President Obama has voiced his strong support of the sciences. In an address to the National Academy of Sciences on April 27, 2009 he emphasized the importance of science by stating “Science is more essential for our prosperity, our security, our health, our environment, and our quality of life than it has ever been before.” In addition to this type of powerful dialogue we have seen significant action.  Perhaps the most obvious example of this is the scientific funding boost that came through with the American Recovery and Reinvestment Act (ARRA, purple block in the graph below). In addition to this quick funding boost there is a continuing effort by the administration to double the 2006 budget for the Department of Energy, the National Institute of Standards and Technology and the National Science Foundation by the year 2017. The approved 2011 budget continues with this upward funding trend as outline in the graph below.

So what does the future hold? Every year a memorandum is sent from the Office of Management and Budget to the major funding agencies requesting their budget proposals for the upcoming year. In this memorandum the current administration outlines how they intend to direct their funding. In the 2012 memorandum, the Obama administration emphasized the following six areas of focus:

  • Promoting sustainable economic growth and job creation.
  • Defeating the most dangerous diseases and achieving better health outcomes for all while reducing health care costs.
  • Moving toward a clean energy future to reduce dependence on energy imports while curbing greenhouse gas emissions.
  • Understanding, adapting to, and mitigating the impacts of global climate change.
  • Managing the competing demands on land, fresh water, and the oceans for the production of food, fiber, biofuels, and ecosystem services based on sustainability and biodiversity.
  • Developing the technologies to protect our troops, citizens, and national interests.

The proposal writing process is no doubt an exercise in balancing wishful thinking and self control. Along these lines it is not unusual for an agency to submit several versions of their budget (above, below and the same as the previous year). However, due to the recent economic issues, the administration was particular in asking all agencies to submit a funding request that is reduced by 5 percent relative to the previous year. As of Monday, September 13th the new budget proposals for the 2012 fiscal year were due. Over the next several months negotiations between the Office of Management and Budget and the Office of Science Technology Policy will determine the 2012 funding situation.  The 2012 budget will then be announced in the first week of February 2011. Although it is unlikely that every agencies budget will be reduced by 5% , 2012 is likely to be a tough year for many researchers.

tl;dr: All you have to do to guarantee funding in 2012 is submit a solid proposal for a commercially viable, bulletproof, CO2 detecting solar energy converter that cures diseases while still maintaining the ecosystem.

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