Chemistry – Page 47 – David Bradley

Generate molecular formula

A rather common search on the sciencebase site seems to ask how to generate a molecular formula. Well, the method I use is to go straight to ChemSketch and fire up ACD/Dictionary, type in the name of the compound I want to produce and paste it into the ChemSketch window. That gives you the everyday 2D structure. A quick click of the “3D Viewer” button does what it promises to do and opens the molecule as a 3D view. At this point, it’s still flat and has to be optimised, so the “3D optimization” button is next. That renders the molecule as a three-dimensional molecular structure. Now, save as a mol file and as a ChemSketch structure.

Now, I follow one of several paths at this point depending on what use I am to put the molecular formula. If it’s to illustrate a scientific piece I’d often be simply using the 2D version. But, if I want something a bit flashier I’ll usually use the 3D view and tweak the settings to change background colour, add or remove hydrogen atoms, or re-render it as a space-filling or ball and stick molecule, depending on which format will best get across the chemical message.

Alternatively, I may shut ChemSketch altogether and re-open the mol file in Diamond from Crystal Impact, which can produce wonderful pseudo photographic quality molecular structures. And, if these aren’t good enough, the next step is to do a full 3D rendering in Pov-Ray, which provides scenic backgrounds, quasi-shadowing, and other wonderful effects to produce a beautifully metallic textured molecule hovering in space, for instance.

Next stop, Chemistry Central

A new open access site for chemists – Chemistry Central – launches today as part of the newly announced Open Access Central group of sites from the makers of BioMedCentral.

CC collates peer-reviewed research from a range of open-access journals and makes available the original research articles as soon as they are published.

Deputy Publisher and former chemist Bryan Vickery explains the motivation, “We have seen increasing interest from chemists in the open access publishing model and, having launched two chemistry-specific titles in the last 18 months, the time seemed right for BioMed Central to create an open access publishing website to meet the needs of chemists,” he says.

On the CC roster are OA articles from Geochemical Transactions, the Beilstein Journal of Organic Chemistry, and chemistry-related articles from BMC Pharmacology, BMC Biochemistry, and BMC Chemical Biology.

As well as viewing the latest research highlights and content from featured journals, the Chemistry Central site provides a forum for the discussion of articles, and users can subscribe to email alerts.

“The BioMed Central team has created an open access publishing website to meet the needs of chemists,” Vickery told Sciencebase, he adds that, “The initial launch phase of Chemistry Central has three main thrusts. Firstly, to raise awareness among chemists that a credible open access alternative to traditional scholarly publications exists, that will disseminate their work more widely and increase readership and use. Secondly, it showcases the chemistry research which BioMed Central’s journals are already publishing, proving their technical suitability for chemistry research. Thirdly, by launching Chemistry Central we are offering our open access publishing services to those who wish to launch new open access journals in chemistry, or to transfer existing journals to this model.”

For a totally unrelated discussion forum check out this link where you can share your thoughts on almost anything, it seems, from news and sport to photos and music.

Plan B contraceptive

On Friday, August 18, Barr Laboratories asked the US Food and Drugs Administration to reconsider its application to make its Plan B contraceptive available over the counter. According to FierceBiotech’s John Carroll, “Given the FDA’s sudden willingness to work out a marketing plan for the contraceptive, Barr has a good shot at finally obtaining an approval that should have come through in 2004.” Carroll reckons that the FDA now has the opportunity to show the US that science and not ideology controls how therapeutics are reviewed. “Given the Bush administration’s clear preference for ideology,” Carroll says, “the FDA may have more difficulties ahead. But for now, there’s reason for hope.”

Plan B is an “emergency” contraceptive, backup birth control, in other words, a form of contraception often referred to as a morning after pill. It comes in the form of two levonorgestrel pills, which are taken orally after unprotected sex. Plan B reduces the risk of pregnancy. Those who oppose it on ideological grounds posit that it is tantamount to an abortion despite the fact that the timescale within which it must be used can be shorter than the time within which conception generally occurs.

More on Plan B from the FDA here. The FDA announced at the end of July that, “It is proceeding to work with [Barr] to resolve the remaining policy issues associated with the marketing of Plan B as an over-the-counter option.”

Will keep you posted on this or you can subscribe for free to FierceBiotech to get the low down.

The Loh down on corrosion

Once more, a news story from the Sciencebase global offices features in Sandra Tsing Loh’s science news podcast out of Caltech. Click the little speaker icon, top left of this post to hear her voice.

“…there’s a new way to stop corrosion: Put it to SLEEP.

The secret, say Dmitry Shchukin of the Max Planck Institute in Germany and colleagues? A gel-like material embedded with nanoparticles .. tiny bits, billionths of a meter across, which house a chemical additive called benzotriazole.”

An elephant task

The ivory trade was banned by CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) in 1989. However, illegal trade continues and as such researchers in India suggest that there is a continued need to characterize Asian elephant ivory and to be able to compare it with African ivory so that national and international laws can be implemented more effectively.

Previously, Erich Raubenheimer and colleagues in the Department of Oral Pathology, Medical University of Southern Africa, established an ivory database that would allow law enforcers to trace the source of illegal ivory and so identify poorly managed game parks, particularly in Africa. However, the ivory of Asian elephants, of which half are found in India, is more prized than African ivory. It is only the males of the Asian elephant that has tusks and they are much smaller than those of its African counterpart. Despite the illegal price differential between continents, the ivory of African and Asian elephants is indistinguishable in superficial appearance, particularly once processed, so it is almost impossible to trace the origin of tusks or a piece of work.

Read the elephant’s tale on spectroscopynow.com

Chemistry jobs

There are lots of opportunities out there in the job market for chemists, so check out our newly updated chemistry jobs newsfeed powered by ScienceJobs.net. You will find the latest opportunities in all areas of the chemical sciences: Lectureships, research jobs, MBAs, tenure track positions, fellowships, university programs, lectureships, post-doctoral positions, research experience opportunities, research assistant jobs, and faculty positions from all the big players.

Technical tasks include Pfizer looking to fill Molecular & Cell Biology Pathways R4-R6 2 positions and Cell Biologist / Assay Development R3-R5. On the admin side of science, Memorial Sloan-Kettering Cancer Center is looking for an Assistant to Chairman.

Clinilabs has several jobs to fill in New York: Clinical Research Associate, Clinical Research Coordinator, Director of Business Development, Quality Assurance and Compliance Manager, and several others.

For more science jobs, check out the Careers section here.

Brazilians wax lyrical on food testing

Brazilian researchers have developed a method to analyse the metal ion content of food products by combining X-ray spectroscopy (XRS) with a partial least-squares (PLS) data treatment. Their approach promises to be faster, more widely applicable to a range of food and agricultural products, and less expensive than other methods.

Food quality control is critical to consumer safety and satisfaction. Knowing levels of inorganic analytes, such as the toxic elements arsenic, cadmium, chromium, and lead, is important, as is information on macro-nutrients like calcium, potassium, magnesium, sodium, phosphorus, and sulfur and micronutrients (copper, iron, manganese, and zinc).

Read the complete story in the latest science news round-up from David Bradley in Spectroscopynow.com

Watching the stars closely

NASA’s Hubble Space Telescope continues to surprise astronomers, this time by identifying the parent star of a distant planet through the observational technique of gravitational microlensing. By elucidating detailed information about the star associated with an exoplanet, astronomers should now be able to unearth the properties of the planet itself and so improve our understanding of planet formation and evolution.

Read the full story in the latest issue of Spotlight from David Bradley and Intute.

Also in this month’s Spotlight – Cornell physicist J.C. SÃ©amus Davis and colleagues at Tokyo University and AIST Labs, Tsukuba, Japan, have been watching superconductors ever so closely, atom by atom in fact. Now, his shocking observations could turn up the heat on this area of research as he has found that high-temperature superconductors may be much more like low-temperature superconductors than scientists previously thought. The discovery has implications for making new superconducting materials. Read on…

And…

The radioactive decay of the rust-coloured mineral monazite can help scientists synchronise their geological clocks thanks to work carried out at New York’s Vanderbilt University. Microscopic crystals of the material act as tiny clocks allowing a date to be stamped on rich ore deposits in rock formations altered by high-temperature fluids. More…

20 year model relieves stress

No…not that kind of model!

“The formation and evolution of dislocation cell structures (patterning) is one of the most important aspects of the deformation process in ductile metals,” according to Lyle Levine and colleagues at the National Institute of Standards and Technology (NIST), Oak Ridge National Laboratory (ORNL), and the University of Southern California. Metallurgists already know that this patterning process arises as clusters of dislocations interact with each other while recent diffraction-resolved studies have shown that the process is initiated by crystal lattice breakup. However, predicting exactly how a metal will behave under stress remains an unresolved problem. Now, Levine and his colleagues have turned to a twenty-year old model to help them out.

Read on…

Brain protein unlocked

A key protein linked to neurodegenerative diseases, such as Huntington’s and Alzheimer’s diseases, has been characterised using NMR by US researchers.

John Cavanagh, Douglas Kojetin, David Kordys, and Richele Thompson of North Carolina State University teamed with colleagues Ronald Venters of Duke University and Rajiv Kumar of the Mayo Clinic and Foundation have obtained a structure for the protein, calbindin-D28K. This protein modulates calcium levels by sequestering calcium from areas that have too much or serves as an on/off switch for further chemical reactions. It is found in the kidneys, pancreas, ocular nerve and large amounts are present in the brain. It is its role in the brain as a “bodyguard” against the action of the enzyme caspase-3 that links it to neurodegenerative diseases. By binding to and inhibiting caspase-3, calbindin D28K prevents the formation of damaging plaque and tangle formation in the brain, which are hallmarks of neurodegenerative disease. The structure of this key protein has remained elusive, until now.

Read on…