Chemicalize.org could be seen as one way in which chemists might benefit from the semantic web, paste in text, structures, or a web address and it [...]]]> The semantic web is slowly but surely emerging from academia and offering useful ways to handle data, let’s hope they don’t start calling it Web 3.0 though, eh?

Chemicalize.org could be seen as one way in which chemists might benefit from the semantic web, paste in text, structures, or a web address and it will send back the whole gamut of chemical information about the compounds mention in the text. Once I’d started using Chemicalize, I quickly realised that it would be neat to be able to Chemicalize any web page from my browser address bar.

Firefox users will be well aware that their browser has “smart keywords”. Smart keywords are simple way to search specific websites directly from the Firefox address bar. Instead of going to the targeted website, finding the search box, and running a search, you can search the given website from the address bar directly. To set this up you do have to visit the site in question once. You right-click the search box and save the link as a keyword by choosing “Add a keyword for this search”. Then when you type that keyword followed by a space and your search string into your address bar, and hit return, your browser runs the search.

For example, right-click the Google search box in the Reactive Reports sidebar to add the search to your favorites as a keyword, call it RR for instance. Now, type “RR” followed by a space and some text e.g. “carbon” (all without the quotes) and hit return. The browser carries out the search and returns a list of articles that mention “carbon”.

I use this function for a whole range of sites, but figured that it could be used quite neatly to render any web page as a Chemicalized web page. You can manually Chemicalize any page simply by adding the following string before the full URL for the page in question.

So, http://www.reactivereports.com/chemistry-blog/carbon-dioxide-solution.html

Becomes:

http://www.chemicalize.org/?q=http://www.reactivereports.com/chemistry-blog/carbon-dioxide-solution.html

When viewed in a standard browser, that Chemicalized page will reveal structures and information about any chemicals mentioned in the page. Of course, this is a trivial example, but what about a page from JACS or a PubChem page, or perhaps even a ChemSpider results page? The possibilities are much more diverse and useful than my example might suggest.

So, first bookmark the Chemicalizing URL

http://www.chemicalize.org/?q=%s, “%s” will be replaced by the URL of the page you wish to Chemicalize.

Now, give the bookmark the keyword “chem”

Finally, test it out, put “chem http://www.reactivereports.com/chemistry-blog/carbon-dioxide-solution.html” in the address bar, hit return, and let your browser and Chemicalize do the rest.

Zudans provides a link to his MolPort site where you can see for yourself that on the entry for atomic hydrogen (the proton, in other words), Apollo [...]]]> An intriguing twitter post from Imants Zudans tells us: “Apparently 2 companies are selling atomic hydrogen. I wonder what is the packaging and how it is shipped.”

Zudans provides a link to his MolPort site where you can see for yourself that on the entry for atomic hydrogen (the proton, in other words), Apollo Scientific and Sigma Aldrich are both offering this stuff for sale. Sigma offers no price, but Apollo asks visitors to enquire. Very odd, but they’re obviously just covering all bases for customers searching for hydrogen.

But, it wasn’t the fact that atomic hydrogen is being offered for sale that was most curious it was the incredible difference between the SMILES string and the INCHIkey for the hydrogen atom that caught my eye. Those abbreviated forms of chemical formulae notation that both allow three-dimensional or even two-dimensional flat structures to be represented as a one-dimensional text string are incredibly useful, but I’ve never used either for the hydrogen atom. Nevertheless, the difference between the two is rather amusing:

Hydrogen atom in SMILES = [H]

InChI Key = UFHFLCQGNIYNRP-UHFFFAOYAN

Did I say the InChI Key was an abbreviated form at 25 characters and the SMILEs at three, where H by itself would just about do it for most people.

Glucagon is a hormone with the [...]]]> Glucagon for weight loss seems to be a common search phrase hitting my science site, so I thought it was time to write a short summary of what glucagon is and what role it might have to play in weight loss and addressing the growing problem of obesity.

Glucagon is a hormone with the opposite action to insulin. It is made in the pancreas and is involved in carbohydrate metabolism. It is released when blood glucose levels start to fall below a threshold level and triggers the liver to convert stored glycogen into glucose and release it into the bloodstream, raising blood glucose levels and so preventing hypoglycemia.

However, the picture is complicated by the fact that glucagon also stimulates the release of insulin, so that newly available glucose in the bloodstream can be taken up and used by insulin-dependent tissues. The role of glucagon supplements for weight loss is undecided. My personal advice? Eat less and get plenty of cardiovascular and load-bearing exercise.

Researchers at the University of Liverpool point out that this is not necessarily the answer:

“For obese individuals, successful weight loss and maintenance are notoriously difficult. Traditional drug development fails to exploit knowledge of the psychological factors that crucially influence appetite, concentrating instead on restrictive criteria of intake and weight reduction, allied to a mechanistic view of energy regulation,” they say in a recent research paper (see citation below).

They add that drugs currently being developed that may produce beneficial changes in appetite expression in the obese include glucagon like peptide-1 analogs such as liraglutide, an amylin analog davalintide, the 5-HT(2C) receptor agonist lorcaserin, the monoamine re-uptake inhibitor tesofensine, and a number of combination therapies such as pramlintide and metreleptin, bupropion and naltrexone, phentermine and topiramate, and bupropion and zonisamide.

That said, they also point out that “obesity is typically a consequence of over-consumption driven by an individual’s natural sensitivity to food stimuli and the pleasure derived from eating.” Addressing that issue is as important as ever if we are to circumvent an obesity epidemic of even greater proportions than we currently see in the developed world.

Halford JC, Boyland EJ, Blundell JE, Kirkham TC, & Harrold JA (2010). Pharmacological management of appetite expression in obesity. Nature reviews. Endocrinology PMID: 20234354

He worked out how nature’s catalysts, proteins known as [...]]]> The late, great Linus Pauling, twice Nobel laureate (chemistry and peace) and advocate of mega doses of vitamin C for beating disease and extending life (he died at the ripe old age of 93) was one of the most influential scientists of the 20th century.

He worked out how nature’s catalysts, proteins known as enzymes, speed up biochemical reactions. They bind to the transition states of a substrate molecule and so lower the energy of the highest energy point on a reaction pathway, which means that the reaction can proceed at much greater speed, often millions of times faster than the uncatalyzed reaction in fact.

Chemists have borrowed this in the design of organic catalysts and in making artificial enzymes, for their non-biological reactions. It is not a
complete description of catalytic behavior of enzymes of course, for that you might turn to Nanda and Koder in Nature Chemistry.

However, in a new paper from Simón and Goodman, they reveal a simple system which is common in both enzymic catalysis and organocatalysis, that does not conform to this simple idea of transition state binding. The reaction of carbonyls with a nucleophile to form an oxyanion can be catalyzed by hydrogen bonding, they explain, and there are many examples of this type of process using enzymes and using organocatalysts. The enzymes, however, do not use the arrangement of hydrogen bonds that binds the transition state best.

Instead, the hydrogen bonds are twisted around the carbonyl axis by about ninety degrees. This is less effective for transition state binding, but much less effective for ground state binding. The energy barrier for the reaction is lowered most effectively by arranging the hydrogen bonds to minimize the energy difference between the bound ground state and the bound transition state, and not by maximizing transition state binding.

Enzymes do not bind to transition states; they bind to minimize the energy difference between the ground state and the transition state.

“This has implications for the design of both artificial enzymes and
organocatalysts,” says Goodman.

Simo?n, L., & Goodman, J. (2009). Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes The Journal of Organic Chemistry DOI: 10.1021/jo901503d

This post adapted from materials provided by Dr Goodman.

Three current supposedly “green” initiatives highlight the problem, Pike says.

First, Brits are being [...]]]> Solid science has to underpin any environmental initiatives, both governmental and corporate, that claim to address energy, emissions, and climate change issues, RSC boss Richard Pike says, and we must teach teenagers how to spot the climate clangers now.

Three current supposedly “green” initiatives highlight the problem, Pike says.

First, Brits are being encouraged to drive five miles less each week. But a back of an envelope calculation shows that this will reduce the UK’s carbon footprint by just 0.3% not the significant amount the government claims.

“Each car travels around 10,000 miles a year, or 200 miles each week, so that the reduction in fuel is about 2.5%. However, passenger cars represent only around one-eighth of the country’s carbon footprint, which accounts for the very small overall saving,” Pike explains.

A second example is the manufacture of gas-to-liquid (GTL) kerosene from natural gas for air transport. This will reduce sulfur and particulate emissions, but the process is incredibly energy-intensive.

“Typically, for every tonne of carbon dioxide emitted by a plane, another 0.7 tonnes rises over the Middle East where the GTL fuel is made, so that the total global effect is over one and a half times the emissions of conventional jet fuel,” points out Pike.

Thirdly, average tailpipe emissions of carbon dioxide from new vehicles are to be capped at 130 grams per kilometre (g/km) from 2012. But, for manufacturers to plan their models and production lines, electric cars will be deemed to have zero emissions, even if (as in the UK) most of the electricity used will have been generated from fossil fuels.

Claims for the green credentials of all three examples of green initiatives, and there are many others are often folly. Initiatives must be assessed across the whole life cycle and across all energy and resource inputs and outputs. Pike adds that political decisions made with inadequate scientific or behavioral evidence will inevitably lead to unintended consequences. The same perspective should be applied to the talks in Copenhagen. Let’s just hope they’ve got a team of scientific advisers willing to stand up to the political shenanigans.

Ironically, as plans to maintain Silverstone as the home of the British motor racing Formula 1 Grand Prix and a major guzzler of gas talk of a seventeen-year deal, might we expect the politicians in Denmark to take such a long view?

“Without the right direction and regulatory framework, backed by an understanding of the science and non-science issues, vested interests will continue to provide solutions, unchallenged, over the forthcoming decades that seem persuasive but are actually unsustainable or have little impact.

More discussion at the RSC’s blog – http://www.rsc.org/blog

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