Category: Science

The Sciencebase science category, updates on scientific happenings from around the world. Check out the Sciencebase Twitter and Facebook pages for even more.

Ranitidine and other molecules

Occasionally, I get queries from students asking me where they can find the structure of this or that compound, usually it’s something like sildenafil (Viagra), ranitidine (Zantac), or rofecoxib (Vioxx) and is pertinent to their current chemistry homework assignment.

There are lots of databases on the web that contain great swathes of molecular structures including some that I wrote about for Nature recently, such as PubChem. But, another place to start your search might be Molecular Heaven or ChemSpider.com

But, what I don’t understand is why students cannot use the search engines, surely the easiest option would be to type in “molecular model” or structure and the name of the compound. When I tried molecular model ranitidine, the first hit had a molecular structure and loads of other information on the anti-ulcer drug. Of course, with ChemSpider you will likely get more curated data together with more detailed information, so perhaps I’ve answered my own question in that regard.

POST UPDATED: ChemSpider information added September 16, 2008

Oak Aged Mythology

Oak aged mythology – According to recent research at the Public University of Navarre, wine makers get no benefit to their product from leaving wines to mature in oak casks for more than a year. In fact, chemical analysis showed that levels of aromatics in the wine from the oak casks begin to decrease if the wine is left to mature for too long. Legislation insists that Gran Reserva wines be kept for 18 months, but science shows that this isn’t based on sound chemical principles.

Michael Dino

Michael Dino got in touch to tell me about his gallery of space shuttle main engine photos at Dino’s Gallery (You’ll need to login to Photobucket to view the gallery). Apparently, the Shuttle’s solid rocket boosters (SRBs) burn two million pounds of fuel in about 2 minutes, which is about as long as it takes to heat your food in a microwave oven…think about how many pizzas that much fuel could defrost (in an instant)!

Congenital Arthur Miller

According to many of the media reports of the death of Arthur Miller he apparently died of congenital heart failure. Wouldn’t “congenital” imply he had heart failure at birth? Presumably, they meant to say “congestive”, he may have had a congenital heart problem of course that led to heart failure in later life. Meanwhile, one of my chums on the NASW discussion lists explained that in the US, “congestive heart failure” is not an acceptable cause of death for entry on a death certificate. Maybe they should have just said he died of a “dodgy ticker”, makes more sense than congenital.

Rational Drug Design

Science Writer David Bradley is currently working on an RSS newsfeed for Simulated Biomolecular Systems, better known as SimBioSys Inc, a Canadian company that specialises in chemistry software with a difference.

UPDATE: Keen-eyed readers will probably have noticed that Sciencebase is no longer working on this project with the chemistry software company. However, I can point you to some exciting developmental work between my co-workers at Chemspider.com and Symbiosis.

Symbiosis is working with ChemSpider on the LASSO project with ChemSpider. Indeed, LASSO descriptor is now available for almost all 18+ million structures in the Chemspider structure database. They have also added the virtual screening results for all ligands against 40 target families, from the DUD database of decoys.

Chemspider recently revealed the preliminary results of this very large cross screening work and the two businesses are now working together to clean up the interface and more powerful search capabilities.

Images Reveal Titan’s Secrets

Images reveal Titan’s secrets: “Spacecraft is 8.9 feet in diameter and 703 pounds (317 kg).”

Those significant figures fascinate me! Why do news agencies insist on giving us such levels of alleged precision. 8.9 feet! That’s 106.8 inches as opposed to 108 inches. Who cares about that 1.2 when you’ve travelled 2 billion miles from home? And, where did they get that 703 pounds, 317kg? Presumably, thes figures have been converted back and forth as I reckon the craft was more than likely given as 700 pounds and someone turned that into kg somewhere and then turned it back again using different conversion factors…but, who cares. 700 lbs, 300 kg, it’s not like anyone is going back to Titan to check.

Jonathan Goodman

Jonathan Goodman tells me that “Most highly strained molecules have small rings, and most explosive molecules have nitrogen and oxygen atoms close to carbon and each other so they can rearrange easily.” However, when he asks chemists if they can think of a molecule which would spontaneously fall apart, even though it contains only carbon and hydrogen, there are four bonds to every carbon and one to each hydrogen, there are only single bonds, and there are no rings, the usual response is that all such molecules should be stable. His paper shows that this is incorrect, even for rather simple molecules.” Check out his paper on this in J. Chem. Inf. Model. 2005, 45, 81-87 (DOI: 10.1021/ci0497657) You can access the paper by pasting the DOI into the sciencebase DOI lookup tool

Artemisinin Could Kill Selectively

Artemisinin could selectively kill cancer cells while leaving normal cells unharmed. Many moons ago I wrote about pioneering medicinal chemistry into this ancient Chinese fever remedy that was showing promise in fighting malaria. Now, in the spirit of modern drug-multitasking it turns out the twisted little tricyclic can also kill cancer cells!

Half Baked

Half Baked. Interesting comment from Sebastian at Onfolio about scientists not being up to speed with syndicated news content. It occurred to me that one area in which it might be incredibly powerful for active scientists is in the preprint arena. They could release their up-coming papers and posters using a newsfeed and by providing comments space on the paper’s web page get instantaneous feedback to help them fine-tune their paper before submission to their favourite scientific journal.