Category Archives: Chemistry

Google McGoogle

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I cannot account for why I never looked previously, but there are web resources that explain how Google does its job and how to make better use of it.  Doh!!  Even if you aren’t involved in marketing and have nothing to sell, it makes sense to have a better knowledge of how this system works.

If you are involved in selling things, eventually you have to turn to the internet and view your ranking on the various search engines.  Google uses some kind of black magic to rank websites.  While the details may be proprietary, many of the general principles are out in the open. One of the criteria is the extent of interconnectedness the site has with other sites.  Sites that are linked to by many other sites will be ranked higher than those with fewer links, all else being the same. Clues to the ranking mechanisms are revealed in the Google patent appln link here. 

Th’ Gaussling is not so bored with life yet that this patent appln is high on the reading list. But digital savants and code monkeys out there may dig reading this stuff.

Markush Claim Reform

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The USPTO is proposing changes in the rules related to the practice of writing “Markush” claims. Markush claims are used heavily in chemical patent applications and allow applicants to claim vast arrays of chemical species by way of composition of matter or by association with a claimed process. The Markush claim makes use of generic formulae that represent the substance of interest as well as a class of equivalent entities.  It is not difficult to specify features of a simple formula that claim many hundreds or thousands of chemical species. 

The PTO admits that it is overwhelmed with the workload associated with these large collections of substances.  I have no doubt that this is true. Patent prosecution requires a search of the prior art for the novelty requirement. A Markush space filled with a large number of compounds slows down the workflow.  

I would hope that the congress and the PTO consider the cost to the public in performing due diligence as well.  I wonder if our cheminformatics friends can find a way to map the space defined by a Markush claim. This would make a due diligence exercise more cost effective and reliable.

Colorado History- Gold and Tuberculosis

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Recently Th’ Gaussling & family spent some time at a mineral spa in Idaho Springs, CO. Having been to a number of mineral springs in the West, I have some sense of what is reasonable and ordinary.  All hot spring operators preach or otherwise encourage the benefits of soaking in a hot mineral bath. Mud treatments and massage are lucrative extras offered by proprietors of mineral springs.  Sadly, by constitution Th’ Gaussling is refractory to the mystical enchantments of this hot saline jive (wisdom or weakness?). I really need to see a mechanism.

Hot springs are egalitarian destinations where the young and old, rail-thin and morbidly obese, tatoo’d and blank skinned can comingle in the hydrothermal aqua from the plutonic realm. 

This particular hot spring was a hotel-pool establishment that had seen better times, but the proprietors were managing growth by adding cabins and a ribs catering operation.  We enjoyed our stay there and will probably return.

My only critical comment is that the water was not particularly loaded with minerals and didn’t favor the bather with even a whiff of sulfur.  A hydrothermal pool without the primordial tang of sulfur is but half of the experience. 

We visited the Phoenix Mine, which is a shoestring gold mining operation a few miles west of Idaho Springs.  If you want to understand Colorado, you have to come to grips with mining. It is one of the two great enthusiasms that lead the settlement wave in Colorado in the mid 1800’s- gold / silver and sanitariums (tuberculosis).  

Much of the activity stemming from the gold rush of 1859 occured along what is now the I-70 mountain corridor.  The discovery of placer deposits of gold and silver quickly lead to hard rock mining activity in the many canyons connecting with Clear Creek.  Placer gold was also found in streams in what is now the Denver Metro area and Cripple Creek.

The recovery of gold from stream sediment (placer gold) is called prospecting.  Hacking it out of hardrock is called mining.  The recovery of placer gold uses somewhat different technology from hardrock mining. Placer gold is isolated by direct settling of the higher density metal from a slurry of gravel and sand. The prospector uses a pan, sluice, rocker, or trommel. The owner of this particular mine has several miles of stream that you can pan from to get the experience of seeing placer gold first hand.  It is hard work and seems to appeal to people who like to gamble.

The tour guide stated that the Phoenix mine operation is centered on a sandstone vein containing 6-15 troy oz of gold per ton (the number varied considerably during the tour so it is hard to tell what it actually is).  But what is interesting is that the vein is a sandstone matrix varying from a few inches to 4 ft thick with a large variety of metals- Au, Ag, Cu, Pb, and Zn.  Glinting xtal faces could be seen as well as green Cu salts in the “Resurrection” vein.  As you walk through the mine it can be seen quite plainly.  The miners just follow the vein where ever it goes.

This is a type of mining that targets a highly concentrated vein, so the amount of mass that has to be processed is relatively small as these things go. This is in contrast to very large ore bodies that contain highly dilute levels of gold value. Such operations require large scale equipment for beneficiation and produce vast quantities of tailings. The operators of the Phoenix mine limit their beneficiation to milling and frothing. Concentrates are sent to Canada for the final recovery and refining. The guide was reluctant to say it, but my guess is that they ship out drums of liquid concentrate.

The other great enthusiasm for Colorado in the 19th century was for the convalescence of patients afflicted with consumption, later called tuberculosis. The thin dry air and the sunny climate was thought to be beneficial for consumption patients. Throughout history, hot springs have attracted the afflicted and the infirm.  The abundance of hot springs in Colorado attracted spa operators who catered to tourists.  The railroad provided the means of transportation for patients to arrive from distant quarters for their convalescence.  

Colorado Springs was an early destination for consumption patients as was Glennwood Springs. The ill-tempered old west figure Doc Holliday died from a long bout with consumption and is buried somewhere under a subdivision in Glennwood Springs, his marker sits on a hilltop cemetery above town. 

REACH for the Sky. EU Comes Down on Chemicals.

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I suppose there are more than a few out there who are not familiar with REACH.  Those of us in the States are a bit confused about the implications on trade and the possibility that the US EPA will attempt to adopt and promulgate the same sort of regulation. REACH has formally begun, as of June 1, 2007.

From the EU Parliament website-

Parliament adopted the compromise it negotiated with Council on the new regulation for chemicals, REACH, which will oblige producers to register all those chemical substances produced or imported above a total quantity of 1 tonne per year. Registration will affect about 30,000 substances. For more hazardous substances, producers will have to submit a substitution plan to replace them with safer alternatives.

When no alternative exists, producers will have to present a research plan aimed at finding one.

Hold the bus!!  “Where no alternative exists, producers will have to present a research plan aimed at finding one.”  Hopefully, there are provisions for reactive precursors or intermediates.

Reactive chemicals are useful chemicals.  Synthesis chemistry is about the management of reactivity.  Differential reactivity gives selectivity.  Chemical manufacturing is all about selectivity.

What if you need a ton of butyllithium or triphosgene or PCl3? Hopefully there is language that provides for manufacturing non-commodity, specialty chemicals with reagents that are highly reactive.  

It will be interesting to watch the unintended consequences pop out of the ground on this program.  The business of testing may end up being more profitable than specialty chemical manufacturing.  The bedrock of western economics is manufacturing. I hope the EU doesn’t chase away to much of its manufacturing base.

Becoming a Major Player: The Chinese Lanthanide Industry

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It is interesting to note how certain countries dominate particular parts of the periodic table.  South Africa has a large lock on the Platinum Group Metals (PGM’s) and crystalline carbon (diamonds).  According to the South African Department of Minerals and Energy, South Africa has 62 % of the worlds supply of PGM’s.  The ore bodies are located in the Bushveld complex in the northeastern section of the country. 

China finds itself flush with perhaps the largest reserves of rare earths- scandium, yttrium, and the lanthanides.  In my travels I see that a good bit of applied research is being done with rare earths in China, some of which is being reported in publications that I only see from a Google search. OK, I don’t have a matrix of data to prove this.  But it appears that SciFinder hasn’t covered Chinese research as well as I thought.  Not too surprising I suppose, given the language and distance barriers.

It is very clear that China has a thriving, though unruly, rare earth metals industry.  The value of this natural resource is not lost on them. They are not content to export tech grade products so that others can squeeze the value added from refinement. They are busy trying to extract that other natural resource- the value of skillful application. 

Expired Chemical Patents- Corey’s Oxazaborolidine

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While tunneling deep through the compacted patent strata, I happened to notice that E. J. Corey’s oxazaborolidine patent appears to be expired.  US Patent 4,943,635 (July 24, 1990) was assigned to the President and Fellows of Harvard College and listed Professor Elias J. Corey as inventor.  This is a patent with 30 claims, of which 3 are independent claims.  All of the claims are for composition of matter. 

The description teaches methods of preparation of a variety of oxazaborolidines, with a special emphasis on the preferred embodiment based on proline.  The use of the catalyst for asymmetric reductions is taught in the description as well. 

Curiously, Corey is the only inventor on the patent. Hmmm.  Knowing that he was well into his career by 1988 when the application was filed, I can only guess that he must have been very busy running multiple reactions, doing flash columns, and burning NMR spectra. \;-)

The next oxazaborolidine patent to expire will be the Merck US 5,039,802 (Aug. 13, 1991) patent.  This is a process patent claiming a method for the preparation of the diarylproline system using aryl Grignard addition to a pyrrolo[1,2-c]oxazole-1,3-dione.

Incidentally, I did witness a famous professor actually doing bench chemistry.  A friend and I were wandering around the chemistry building at her alma mater, (The) Ohio State University, in March of 1993 when we happened past the lab of Mel Newman.

There he was, in his 90’s, intently shaking a 2-liter separatory funnel of some dark hellbroth. He was isolating a polyaromatic hydrocarbon that he made.  Newman graciously stopped to talk about his work. Having freshly graduated from a stereochemistry group and a stereochemistry post-doc, I nearly fainted when I met him. It was like meeting Elvis.  Newman passed away a few weeks later. 

Pitstops along the bloggenbahn

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In the mood for PC board snack? The folks at Evil Mad Scientist Laboratories can provide a component by component guide to constructing a confectionary circuit board.  Heavens, they’re tasty.

Can’t get enough of Leonard Nimoy?  Well, here ya go. Knock yerself out.

Some excellent posts on the mortgage industry and Live Earth can be found on Clusterf**k Nation. 

I’m convinced that all chemists are pyro’s at heart.  I didn’t say anarchists or criminals, I meant Pyro in the technical sense of the word.   By 10 years into their careers, most synthesis or process chemists have experienced the awesome spectacle of the Mighty Exotherm at least once.  Significantly, 4th of July demonstrations never recreate celebrated lab explosions or hood fires.

A good BLEVE is a real crowd pleaser and a sight to behold. However, professional pyros choose the more cosmetic displays, ignoring the really elegant deflagrating ether ketyl still or the fabulous ozonide conflagration. I guess we chemists will have to keep those delights for our own enjoyment.

National Treasure: H.R. 3043 and Scientific Publications

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On page 14 of the July 30, 2007, issue of C&EN, an article entitled “Bill Mandates Public Access” by David Hanson describes a section of a bill recently passed from the House to the Senate. The relevent text from the bill is as follows-

SEC. 217. The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law. 

Hanson’s article states that the Professional and Scholarly Publishing (PSP) Division of the Association of American Publishers has asked members of Congress to reconsider this bill, or at least the mandatory submission to PubMed. Hanson reports that the PSP claims that-

“This language could serve to undermine the existing system of peer review and scholarly publication which disseminates high-quality research findings throughout the scientific community,” … 

Further down, Hanson gets to the real issue-

Brian D. Crawford, chair of the PSP committee and senior vice president of the Journals Publishing Group at the American Chemical Society (which publishes C&EN), says the House language violates fundamental copyright principles. The bill “would essentially force authors and publishers to, in essence, forfeit their copyrights” without compensation for their investments and would have many negative impacts on private-sector publishers, he says. [Italics by Gaussling]

What is telling is the quote by Brian D. Crawford, who suggests that the publishers stand to lose their copyright on the copy submitted by the NIH funded researchers.  If you are a publisher, should you be worried about this?  Probably.  The gravy train may be leaving the station.

Yes, the publishers have invested large sums in building publishing and distribution systems for the profitable dissemination of information.  But I would add that they have built these publishing engines on a system that hands voluminous copy to them for free.  Unlike other publishers who have to pay their authors for content, academic publishers do not pay contributors who, I might add, provide some incredibly valuable content. Academic publishers have built publishing businesses using content paid for by government granting agencies, and by extension, the public.

It’s easy to fault publishers for taking advantage of a system that hands them publishable content for free. But, on the other hand, circulation numbers for most publications is quite modest.  Even if advertising is used, the typical low circulation of any given specialized scientific journal is so low that only very modest advertising rates could be obtained. Many journals survive on subscription fees alone.  Examples of journals that have come to terms with advertising are J. Chem. Ed., Nature, and Science. 

The scientific publishing system is a sort of a deal with the Devil- the scientist gets the grant, does the work, and then what?  After dinner talks at the Elks Club? Of course not. A manuscript is prepared and in exchange for free printing and distribution, the publisher obtains the copyright. The copyright is the key.  It is a cash cow in the same way that the copyright to the Beatles songs are a cash cow, only with smaller numbers.

I think that Sec. 217 of H.R. 3043 is the right idea. The public has already paid for the research. Why should it be intercepted at no cost by printers who then have an everlasting copyright and control of what is rightly national treasure? The citizens have to pay taxes for the research and then turn around and pay commercial interests for the right to read it.  That is wrong.

If commercial interests want to make a profit on scientific publishing, then they need to find a better model.  The public shouldn’t be barred from access to what they have already paid for. Advertising may be the way to do it.  Perhaps the funding agency should have the copyright and publishers pay a fee to print and distribute it?  Comments?