Chemistry Blog

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

Mitch
Read the rest of this entry »

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.

Sep 17

How many ways can you say something without plagiarizing?


In a recent post by Derek Lowe on a Chinese journal’s finding that 31% of its submitted papers contained plagiarized material, an editor for a scientific journal noted in the comments that he randomly selected a Tetrahedron Letters paper from a developing country and Googled the first sentence. That sentence (“Multicomponent reactions (MCRs) are important for generating high levels of diversity…”) shows up in very similar form in three different papers, all from institutions in Iran and China. In two of the papers, the second sentence of the paper is exactly the same, all 22 words.

Also, compare the two first sentences, the first by Shaterian et al.[1] and the second by Adib et al.[2]  The highlighted words are the same.

Multi-component reactions (MCRs) are important for the achievement of high levels of brevity and diversity. They allow more than two simple and flexible building blocks to be combined in practical, time-saving one-pot operations, giving rise to complex structures by simultaneous formation of two or more bonds, according to the domino principle.”

Multicomponent reactions (MCRs) are important for generating high levels of diversity, as they allow more than two building blocks to be combined in practical, time-saving one-pot operations, giving rise to complex structures by simultaneous formation of two or more bonds.

While cutting and pasting other people’s introductory sentences is certainly embarrassing and almost certainly plagiarism, there is some difficulty in summarizing a set of facts in a different way each time. It certainly can be done — below are three different labs’ introductory sentences for chemistry towards the total synthesis of the azaspiracids, which are marine natural products. Again, the same words are highlighted in red.
Nicolaou et al.[3]: “The azaspiracids are a group of notorious marine neurotoxins whose accumulation in mussels causes serious human poisoning known as azaspiracid poisoning syndrome (AZP) upon their consumption.”
Geisler, Nguyen and Forsyth[4]: “The azaspiracids are remarkable natural products that combine a unique, complex structure with an acute and perhaps chronic human health hazard.”
Evans et al.[5]: “(-)-Azaspiracid-1 is a structurally complex marine neurotoxin that is implicated in seafood poisoning.”
You can see that Nicolaou, Forsyth and Evans all have specific ideas they’re trying to get across: what the compound is, where it comes from and what it does to people. But they’ve all managed to have relatively few words actually overlap.

Is this sort of cutting-and-pasting ‘real’ plagiarism? — it’s just the quotation of a particularly useful string of words, one might assert, not the stealing of ideas. I don’t think this is a very good way of thinking about things, but I can’t quite reason why. In addition, I doubt that any of the authors of the MCR papers were native speakers of English. Clearly, that plays some role in their choice to cut and paste; again, not an excuse, but another contributing factor. I’m trying to see if I can come up with extenuating circumstances, but I just can’t.

My adviser in graduate school held out “the same five words in a row” as a general rule of thumb for how to spot and/or avoid plagiarism — what about the same five ideas in a row? What do you think, reader? How do you avoid cutting and pasting? And what should we do (if we should) to stop this sort of thing? Do we need TurnYourJournalSubmissionIn.Com?

References:
1. Shaterian, H.R.; Yarahmadi, H.; Ghashang, M. Arkivoc. 2007, 16, 298-313.
2. Adib, M.; Mahdavi, M.; Bagherzadeh, S.; Zhu, L.-G.; Rahimi-Nasrabadi, M. Tet. Lett. 2010, 51, 27-29.
3. Nicolaou, K.C.; Frederick, M.O.; Petrovic, G.; Cole, K.P.; Loizidou, E.Z. Angew. Chem. Int. Ed. 2006, 45, 2609-2615.
4. Geisler, L.K.; Nguyen, S.; Forsyth, C.J. Org. Lett., 2004, 6, 4159-4162.
5. Evans, D.A.; Kvaerno, L.; Mulder, J.A.; Raymer, B.; Dunn, T.B.; Beauchemin, A.; Olhava, E.J.; Juli, M.; Kagechika, K. AngewChem. Int. Ed. 2007, 46, 4693-4697.

Sep 14

Why is High Fructose Corn Syrup so bad for you?


Is high fructose good for you or bad for you?

How many of you said bad?  Leads to obesity, right?  Gotta stay away from HFCS, right? That’s what ‘everyone’ says, right?

Consider: The sugar we call ‘table sugar’ is sucrose: a disaccharide: a molecule of glucose and a molecule of fructose (two monosaccharides) covalently bonded to each other.  Sucrose is broken into fructose and glucose by enzymes within living organisms (like humans).  Humans don’t use sucrose for energy, first we break it into glucose and fructose and metabolize the monosaccharides for energy.  So we ingest sucrose, digest it to glucose and fructose, then use the monosaccharides for energy.

One molecule of sucrose becomes 1 molecule of glucose and 1 molecule of fructose.  That means that sucrose is digested to a 50/50 mixture of fructose and glucose.

Consider: High fructose corn syrup is a straight mixture of unbonded glucose and fructose.  There are two common types of HFCS: HFCS 55 and HFCS 42.  HFCS 55 is ~55% fructose and ~42% glucose.  HFCS 42 is ~42% fructose and ~53% glucose.

So what’s the difference?

Sucrose becomes a 50/50 mixture of fructose and glucose.  HFCS 55 is a 55/42 mixture of fructose and glucose.  Chemically, there’s no difference between fructose from sucrose and fructose from HFCS.  Our bodies can’t tell the difference between fructose from sucrose or fructose from HFCS.  We’ve been fretting so much about a 5% difference between the fructose content in the two sweeteners.

If our body can’t tell the difference, and the percent content of fructose is essentially the same, why is HFCS so much worse for us than ‘natural,’ or ‘organic’ sugar?

It’s not.

HFCS is no worse for us, and causes no more obesity than table sugar.  Once ingested, table sugar and HFCS are metabolized by our bodies in exactly the same way.

So what’s the problem?  Well, the problem is sugars (both sucrose and HFCS) are in EVERYTHING.  Too much sugar (again, either from sucrose or from HFCS) IS bad for us, and will lead to higher caloric intake, and eventually weight gain.  So the problem is too much sugar – not too much HFCS, and the solution is to eat less sugars overall – not to ban HFCS from everything.

But that’s not what ‘everyone’ is saying.  And the court of public opinion can be quite harsh.  So harsh, in fact, that the HFCS manufacturers are attempting to rebrand.  No longer will we find HFCS on the ingredient list.  Now, we will see ‘Corn Sugar.’  This means the same thing.  It’s the same 55/43 mixture of fructose to glucose, but they’re rebranding to move away from the negative associations.

What do you think?  Good idea or bad idea?  Should we just ban HFCS/Corn Sugar?  Should we regulate the amount of sweetener that’s allowed to be in a Suggested Serving Size?  Do you agree with the decision by the HFCS manufacturers?



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