Scholarly Silliness

The American Chemical Society is suing Google to defend its trademark SciFinder Scholar from confusion with Google Scholar. There’s a lot of worthy discussion about the problem on the CHMINF list. ACS is obviously worried about that word "Scholar" being used by Google and that Google’s millions of users might assume there is a connection. But the pundits should get real, I’m pretty sure that outside of chemistry, 99.999% of the world’s population will never have heard of the American Chemical Society let alone, SciFinder Scholar and only a fraction of those billions have even heard of Google, and of those that have, even fewer will have heard of or be even vaguely interested in Google Scholar.

Anyway, isn’t the word “scholar” a generic term relating to education in some way? Surely, it’s analogous to the word quot;cola" which comes in many flavours made by many different companies? If Google had called their academic search engine Google Scifinder, I suppose that would have been very different. The lawyers must be rubbing their hands with glee. (Incidentally, there are 29 hits when one searches PubMed with the author field "Scholar"), I wonder if I could change my name to Dr Searchengine Scholar?

Burning Water

Photo from www.joe-ks.com

Just this minute, I received an email from someone claiming they had discovered how to burn water.

No matter what experimental conditions they set up this is physically impossible – fundamentally standard combustion involves the oxidation of some material into the oxidized form of that material and water. The reaction 2H2 + O2 –> 2H2O puts it at its simplest. Energy is released in this reaction. The reverse process is possible, it can be done by adding a small amount of ionic material to the water to make it a salt solution and passing through it an electric current. That splits the water molecules, releasing hydrogen gas and oxygen in a process known as electrolysis. But, this is not combustion, energy must be fed into the system (electrical in this case) to split the water molecules, the ionic salt particles simply act as carriers of the current.

The notion that somehow you could overcome the bonding between hydrogen and oxygen atoms in H2O might be overcome in a combustible manner rears its ugly head on a frequent basis. But, as you can see it’s just not tenable. If you were stupid enough to connect a car battery’s terminals to a bowl of salt water, you could ignite the resulting hydrogen bubbling from the mixture, but that could be no more describes as “burning water” as baking a cake by mixing and freezing the ingredients in a cake tin.

The idea that burning water might be possible is yet another example of the kind of thinking that repeatedly suggests perpetual motion might be possible, it’s desperate grasping, it’s almost a cry for help: “We have messed up the world, but I can fix it, if you listen to me!!!” That kind of thing!

And, while we’re at it, there’s a College in the UK that offers absolutely no science courses, but does offer dowsing, and advanced dowsing! It’s the Women’s Institute Denman College, apparently.

This post, was originally published in the old Sciencebase blog – SciObs – on December 8, 2004, but I’ve resurrected it and edited it up in the light of events that took place in 2007. You can read about the posts that emerged here:

How not to grab the blogosphere – this one is very closely related to this old post.

Free cure-alls – not just cure-alls for disease but for all the problems that ail the world. Yeah, right!

Chemical Image Problem

It’s not been a hot week for the image of the chemical industry. This week marked the 20th anniversary of the Bhopal tragedy. There were more revelations about problems with pharmaceuticals. Researchers reported that benzene is worse than we thought even at low levels. And, the industry is denying WHO claims that chemicals harm kids.

Couple that with further discussion about the future, or rather lack of, chemistry teaching at British universities and the supposed benefits of downsizing the number of chemistry departments and one begins to wonder whether there will be any chemical industry to speak of in five years time.

Chemophobia has been high on the agenda perhaps since even before Rachel Carson’s Silent Spring. What is to be done about redressing the balance? Industrial visitors to Sciencebase may wish to get in touch with their ideas…

Chemistry of Moores Law

Everyone knows a version of Moore’s Law that states: the number of components on a unit area computer chip will double every 12 months. Empirically, it’s turned out to be every 18 months, but it doesn’t just apply to chip density, but highest hard drive capacity at any given time, CPU speeds, and RAM requirements (the computer hardware and software industries form a self-perpetuating ascending double helix in case you hadn’t noticed). The Chemical Heritage Foundation is marking the fortieth anniversary of Intel co-founder Gordon E Moore’s Law in May next year a celebration of the fact that without an equivalent doubling in chemical savvy none of those advances in computing would have been possible.

Chemical Structure Drawing Software

I made this drawing in less than five minutes, but it took me sixty years to be able to do that

— Pierre-Auguste Renoir (1841-1919)

Sketchbook Chemistry – Chemists think in pictures, structures are all. It comes as no surprise that chemical-drawing packages are among the most popular software components available. Indeed, ACD/Labs own ChemSketch had, at the time of writing, reached its 341,320th download in less than six years since the launch of the freeware version. So, what makes chemical sketching such a valuable tool for chemists and others whose research touches on this underpinning science? David Bradley reports on the views of ChemSketch users.

“I saw a colleague using ChemSketch, and became amazed by its simplicity,” Barbaros Akkurt of the Turkish Chemical Society told us. Carlos Franco PhD of the Department of Chemistry at the National Pedagogical University of Colombia echoes the sentiment, saying that ChemSketch is “an excellent free software package that users can apply either in the classroom or in their chemical research.” Clyde Metz of the Department of Chemistry and Biochemistry at the College of Charleston came across ChemSketch at an American Chemical Society meeting via a demo disc in action. “As new versions were released, I kept up to date.” Metz has an academic site license for the department so that his students can use the structure building features for copying over to lab reports, papers, etc.

It is easy to see why ACD/Labs has such a rapidly growing number of followers for its ChemSketch program. With the freeware version 5.0 of ChemSketch, users can draw molecules freehand, build their structures from a wide range of ready to use templates or import various standard chemical structure formats and modify them to their own needs. For instance, it is possible to import and export ChemDraw, ISIS Sketch, MDL molfile, and SMILES strings. ACD/Labs describes the process as “click and draw molecules” with ions, stereo-bonds, text, polygons, arrows, etc., all readily available. Once a molecule is complete, users can automatically calculate molecular weight and formula, display estimates of density, refractive index, molar volume, and many other useful parameters.

“I’ve encountered no difficulties in getting used to the software,” says Akkurt. He adds that the best feature of the package is its 3D optimization, although the IUPAC naming facility comes a close second. “The IUPAC naming service is very nice,” he adds, “as many other programs cannot recognize a number of special organic radicals.” Akkurt goes on to explain how ChemSketch has helped him greatly in quickly processing elemental analysis data for various organic compounds as well as producing their IUPAC names. “ChemSketch allows me to produce reliable structures quickly,” he says, “I don’t use nor need to run any other program.” Interestingly, while he uses the ChemSketch Draw mode mainly for chemistry-related sketches, he has also found it amenable to creating non-chemistry structures, such as organization trees too.

The freeware version also includes the tautomers module, dozens of templates, the 3D viewer program and one of the most interesting features, the Name Freeware Add-On, which allows users to convert a structure into an IUPAC name for their molecule. For users who opt for the full version, ChemSketch includes the ACD/Dictionary module, which contains more than 125,000 systematic and non-systematic names of structures and so can speed up the structure-drawing process considerably.

There are many specialist users too. “I first saw ChemSketch at a meeting of the American Society for Mass Spectrometry,” says David Powell, Director of Spectroscopic Services in the Department of Chemistry, University of Florida at Gainesville, where a number of groups use ChemSketch. “I found ChemSketch a little easier to learn so the learning curve was faster,” says Powell, “ACD/Labs also gave us the ability to import a structure directly into our sample submission form for mass spectrometry, working with us to set up a macro in ChemSketch to do this.” Powell is also enthusiastic about one of the program’s specialist features which can be purchased as an add-on, “I really like the MS Fragmenter routine,” he told us, “which allows prediction of fragment masses and structures, this is very useful for interpreting unknown mass spectra.”

Another specialist user is forensic toxicologist Chip Walls, Technical Director of the Department of Pathology at the University of Miami. He first saw a favorable review on the Web about chemical drawing programs that did a nice comparison. “I downloaded the free version of ChemSketch and found it much easier to use,” he said. He was so impressed, he bought the full version with the dictionary. “With each revision I grow more attached to the ease of use and the ever expanding dictionary,” he added. The many more import and export features and the dictionary are major advantages over other packages and keep Walls coming back for more. “I use the structures in my procedures and in talks I have to present,” he explained, “I export the drawings in windows metafile format (WMF) and can insert them as a picture in just about any application. You can change color of the structure easily making it a snap to insert into PowerPoint slides with colored backgrounds.” He adds that the WMF is small, fast to load and easy to keep within a presentation. “Of course, you can also insert the ChemSketch file and link to it to keep it up to date with any changes,” he adds.

Some users do not take to ChemSketch immediately, Tamas Gunda of the University of Debrecen in Hungary, for instance, gave the program a quick try after finding it on the Internet. It was only later when he did a probing review of chemical drawing applications that he began to see its advantages over other packages. “The freeware version contains more features than other free chemical drawing applications,” he says, and although every application has its strong and weak sides, one of the big pros of ChemSketch is in making poster-sized drawings. Gunda adds, “In my experience, ChemSketch is best for joining chemistry and other pictures together for direct printing or transferring to a general drawing package in Windows Meta Format.”

Metz adds that the free 3D viewer is also a rather attractive feature, “I realize that this is the front-end for other programs which we don’t have, but it is for student use and works fine,” he explains. Indeed, ChemSketch has become an integral part of the curriculum for the College’s NCSI/CCCE workshops to show and let people work with it. “For what is in the free version of ChemSketch/3D Viewer, it is done well,” adds Metz, “and for someone with no funding, it is a way to introduce a little molecular modeling and visualization into an undergraduate course.”

Funding levels are an important consideration for many users. Franco admitted that finances are a main driver in choosing software in a country where resources are limited: “The primary advantage over other similar packages is that the free version of ChemSketch is fully functional in all its options.” That said, Franco points out that all users can view models in 3D dimensions, with animation or from different perspectives. “The ChemSketch drawing tool is an easy way to make presentations, make templates and export images to a word processor, for instance.”

“As a teacher of 16-18 years olds,” adds British educator Steve Lewis, “I was looking for a quick means of producing simple structures. The initial attraction of ChemSketch was the freeware version!”

While some users rely on the more advanced features, others, including Lewis, have relatively unsophisticated needs for their chemical-drawing software. ChemSketch, he says, meets these well, “ChemSketch itself is not unsophisticated, rather, it’s designed well enough that I can use it to my advantage without being overwhelmed by too much functionality intended for more advanced purposes.” Having said that, he adds that he is “very impressed by the 3D viewer facilities,” which he uses for school ‘open’ event displays.

ChemSketch is downloaded from the ACD/Labs website at a rate of about 300 copies every day and every single country in the world has downloaded it at least once! At the time of writing, the Top 5 countries by number of downloads were USA (>67,000), Germany (>23,000), Canada (>15,000), United Kingdom (>14,000), and China (>11,000). There have even been almost 200 downloads from users in the Vatican City State domain! There are thousands of others in many different countries from the Philippines to Puerto Rico via Antarctica showing just how chemistry brings nations together.

ChemSketch users also have the ability to interact with the software itself through the freeware Programming Language for the Freeware ChemSketch (http://www.acdlabs.com/products/chem_dsn_lab/chembasic/). More than 15,000 users have downloaded the language, which forms the basis of the popular ACD/Goodies. ACD/Labs updates these user contributions to the program store regularly. (http://www.acdlabs.com/products/chem_dsn_lab/goodies.html).

ACD/Labs remains at the cutting edge of structure drawing and visualization including the first structure drawing applet (freeware version at http://www.acdlabs.com/download/sda.html) and recent PDA-based tools (http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/chempalm/). Site licenses of the commercial version of ACD/ChemSketch v5.0 are currently being donated to any interested academic institution (http://www.acdlabs.com/educators/chsk_licenses.html).

This article was originally commissioned as a promotional feature article by ACD/Labs, creators of ChemSketch and Reactive Reports. – ChemSketch – Elemental Discoveries – 08/04

Elemental Discoveries – The history of the chemical elements

The history of the chemical elements – An elemental chronology compiled by David Bradley back in 2004

Ancient Times – gold, silver copper iron lead tin mercury sulfur carbon
Time of the Alchemists – arsenic, antimony
13th Century India – zinc
1669 phosphorus
1737 cobalt (~1735)
1741 platinum (1735)
1751 nickel
1753 bismuth
1755 magnesium (1775)
1766 hydrogen
1772 nitrogen
1774 oxygen, chlorine, manganese
1778 molybdenum
1782 tellurium
1783 tungsten
1789 uranium (1841)
1789 zirconium
1793 strontium (1808)
1794 yttrium
1797 titanium (1791)
1797 chromium
1798 beryllium

1801 vanadium, niobium
1802 tantalum
1803 cerium, rhodium, palladium, osmium, iridium
1807 potassium, sodium
1808 calcium, barium
1811 iodine
1817 lithium, cadmium, selenium
1823 silicon (1824)
1825 aluminum/aluminium (1827)
1826 bromine
1828 thorium
beryllium
1839 lanthanum
1843 terbium, erbium
1844 ruthenium
1860 caesium/cesium (rubidium)
1861 rubidium, thallium
1863 indium
1868 helium, boron
1875 gallium
1878 ytterbium
1879 thulium, scandium (1878), holmium (1878), samarium
1880 gadolinium
1885 praseodymium, neodymium
1886 germanium, fluorine (1866), dysprosium
1894 argon
1898 neon, krypton, xenon, radon, polonium,
1899 actinium

1901 europium (1890)
1907 lutetium
1917 protactinium (1913)
1923 hafnium
1925 rhenium
1937 technetium
1939 francium
1940 astatine, neptunium (plutonium)
1941 plutonium (1940)
1944 curium
1945 americium (1944), promethium
1949 berkelium
1950 californium
1952 einsteinium
1953 fermium (1952)
1955 mendelevium
1958 nobelium
1961 lawrencium
1964 rutherfordium
1970 dubnium (1967)
1974 seaborgium
1976 bohrium (1975)
1982 meitnerium
1984 hassium
1994 darmstadtium, unununium
1996 ununbium
1999 ununquadium

2004 ununtrium, ununpentium – read about the discoveries of the most recent chemical elements.

For a list complete with details of the discoveries try the Wikipedia entry or the About site, there are discrepancies between the two, however (see bracketed entries above) and I’d say the only definitive elemental data online is provided by Mark Winter’s WebElements.

Poisonous Zebra Mussels

poisonous zebra mussel

Inland lakes in Michigan that have been invaded by zebra mussels, an exotic species that has plagued bodies of water in several states since the 1980s, have higher levels of algae that produce a toxin that can be harmful to humans and animals, according to a Michigan State University researcher.

In a paper published in the recent issue of Limnology and Oceanography, Orlando ‘Ace’ Sarnelle, an associate professor in MSU’s Department of Fisheries and Wildlife, and colleagues report that lakes that are home to zebra mussels have, on average, three times higher levels of a species of blue-green algae known as Microcystis.

Those same lakes also have about two times higher levels of microcystins, a toxin produced by the algae.

‘If these blooms of blue-green algae are a common side effect of zebra mussel invasion, then hard-fought gains in the restoration of water quality may be undone,’ Sarnelle said. ‘Right now, it appears that the numbers of blooms in Michigan have been increasing and appear to be correlated with the spread of zebra mussels.’

Initially, water samples were taken from nearly 100 inland lakes in Michigan’s Lower Peninsula, ranging from Benzie County in the northwest to Oakland County in the southeast, that had established zebra mussel populations.

Follow-up experiments by Sarnelle and colleagues in west Michigan’s Gull Lake showed that zebra mussels are indeed the cause of the increase in toxic algae.

There have been documented cases in which animals, including cattle and dogs, died after drinking water with high levels of microcystins. The toxin is also believed to be responsible for liver damage in humans.

Surprisingly, zebra mussels seem to have no effect on the amount of blue-green algae in lakes with high levels of phosphorus, a nutrient that builds up in lakes and other bodies of water as a result of erosion, farm run-off and human waste.

In contrast, zebra mussels cause an increase in toxic Microcystis in lakes with low to moderate levels of phosphorus, anywhere between 10 and 25 micrograms per liter. Such lakes are not normally expected to have very many blue-green algae, Sarnelle said.

‘Our data suggest that zebra mussels promote Microcystis at low to medium phosphorus levels — not at very low or very high phosphorus levels,’ he said. ‘However, we’re still not sure why this happens.’

Zebra mussels have been causing problems in the Great Lakes since the late 1980s. For example, in Lake Erie, Sarnelle said, increased incidence of blue-green algae blooms have been reported since the establishment of zebra mussels.

‘Similarly, data from the Bay of Quinte in Lake Ontario show a dramatic increase in the biomass of Microcystis after zebra mussel establishment,’ he said. ‘In addition, toxic algal blooms in Saginaw Bay and Lake Erie are disturbing because they come after many years of expensive reductions in nutrient loading to improve water quality.’

Zebra mussels, which are native to the Caspian Sea region of Asia, were first discovered in Lake St. Clair in 1988. It’s believed they were transported to the Great Lakes via ballast water from a transoceanic vessel.

Since then, they have spread to all of the Great Lakes, as well as many other U.S. and Canadian inland lakes and rivers.

Nanoparticles keep buses moving

The 7000-strong Stagecoach UK bus fleet is now using nanoparticles of the Envirox oxidation catalyst as a fuel additive.


Envirox is based on a well-established oxidation catalyst but has now been formulated for use in diesel fuel at just five parts per billion without any need to modify the engine. The result is a cleaner and more complete combustion, which the company claims produces an up to 12% fuel saving as well as reducing carbon deposits in the engine and lowering emissions.

The fuel-borne catalyst is composed of particles of cerium oxide 10 nm across, a material commonly used in conventional catalytic converters to clean up vehicle exhausts. Cerium oxide catalyses the conversion of carbon monoxide and hydrocarbon gases to carbon dioxide and water. It also reduces nitrogen oxides.

Researchers have attempted to formulate the compound as a fuel additive before but have generally failed to improve on fuel efficiency or cut emissions. Cerulean believe they have circumvented the problems with their nanoscale approach because at this size, the catalyst remains evenly suspended in the liquid fuel.

Stagecoach intends to try the product in up to 1000 of its buses across the UK. According to Chief Executive Brian Souter, “We believe this new product has huge potential and we are delighted to once again be leading the way in the UK bus industry in developing new ideas.”

Cerulean International Ltd is a subsidiary of Oxonica Ltd an Oxford University spin-out company. Oxonica’s Christopher Harris recently patented an improvement to the Envirox system that uses an organic solvent system to comminute, or coat the nanoparticles with an organic anhydride or acid, an ester, or a Lewis base. This coating is intended to help the particles disperse still more evenly in diesel fuel.

The permutations for nanoparticles additives are not to merely coating cerium oxide. In the initial nanoparticle patent, Gareth Wakefield describes how the particles might also be doped with a divalent or trivalent metal or metalloid. Doping might improve the properties further, although Stagecoach will be trialling only the undoped version.

The original version of this article by David Bradley originally appeared in The Alchemist in October 2003.

Mutant Venus Flytraps Catch TNT

Computation could allow new high-affinity and specific protein receptors and sensors to be designed for any number of small molecules of interest, thanks to researchers in the US. Such artificial receptors could ultimately find a role to play in medical diagnostics, drug design, and sensors.
According to biochemist Homme Hellinga and colleagues at the Duke University Medical Center, Durham, North Carolina, the formation of complexes between proteins and ligands is a fundamental interaction in molecular biology that lies at the heart of countless biological process.

Hellinga points out that manipulating the molecular recognition between ligands and their associated proteins is crucial to basic biological studies. From a technological standpoint though, improved understanding could also allow us to create bespoke enzymes, tailor-made biosensors, genetic circuits, and to carry out chiral separations very effectively. With such rewards in the offing it is not surprising that the systematic manipulation of binding sites is still “a major challenge”, Hellinga emphasises.

The team has taken a novel approach to improving our understanding of protein-ligand interactions. They have devised a structure-based computational method that can be used to redesign protein ligand-binding specificities, which can then be engineered into a microbial genome for fermentation-like protein manufacture. In a commentary on Hellinga’s research, William DeGrado of the University of Pennsylvania School of Medicine, Philadelphia, explains how organisms use many different small molecules that bind to proteins. Receptors, enzymes, and antibodies for instance all interact with small molecules to control cell communication, signalling, and protection against pathogens. Exploitation of these interactions has so far been limited, but diagnostics and new disease therapies could emerge from greater understanding of them.

The researchers have demonstrated how the approach works by constructing new soluble receptors for the explosive TNT (trinitrotoluene), the sugar L-lactate and the medically important hormone serotonin (5-HT). The new receptors have high selectivity and affinity for their ligands and could be used as the sensing component of a detector. Intriguingly, the team has also incorporated their new proteins into a synthetic bacterial signal transduction pathway, which means they can be used to regulate the switching on and off of various genes in response to the presence of TNT or L-lactate in a bacterial culture. “The aim is to create synthetic signal transduction pathways that may allow bacteria to function as biological sentinels to chemical threats and pollutants in the environment by switching on a reporter gene,” Hellinga told us.

They started with a series of bacterial periplasmic binding proteins (PBPs) from Escherichia coli, which DeGrado describes as “Venus-flytrap-like receptors”. These PBPs are composed of two protein domains that snap shut on their ligand, just as the fly-catching plant’s specialist leaves grab their prey. When the ligand binds, a signal is transmitted. “In vivo the signal is binding of the closed form of the protein to a transmembrane receptor that triggers a cytoplasmic phosphorylation cascade that ultimately results in transcriptional activation of a reporter gene,” explains Hellinga. The natural function is the control of chemotaxis or outer membrane protein expression, depending on the system, and the natural ligands include sugars and amino acids. The researchers wanted to redesign the PBP’s trap so that it would bind a range of other small molecules in order to engineer “biological sentinels”. They chose L-lactate, serotonin (5-HT), and TNT as their targets as these compounds demonstrate great molecular diversity structurally and chemically diverse, both from one another and the natural PBP ligands.

A computer model of the PBPs was then investigated by placing a “virtual” version of TNT, 5-HT or lactate in the trap. Their powerful algorithms then mutated the binding site amino acids one at a time and scanned for new protein sequences that had a surface into which the ligand would fit. The results are astounding, with just 12 to 18 amino acids being changed, 10^23 possible sequences are generated, many more than achievable with conventional methods. Moreover, if ligand approach is also considered the combinatorial possibilities rocket to between 10^53 and 10^76.
To screen such a vast array of virtual proteins, Hellinga’s team then used another algorithm – an enhanced version of “dead-end elimination”. The original algorithm was developed by Frank DeSmet of the Catholic University of Leuven, Belgium, but was then enhanced substantially by Hellinga’s team. Further work then allowed them to handle the design of ligand-binding sites needed for their research. The algorithm queries an entry in the library on the basis of hydrogen bonds, van der Waals interactions, electrostatic interactions and atomic solvation. However, rather than scanning each individual entry those library members lower down the diversity tree are pruned off if they don’t fit. The rationale for this being that if a lower member does not fit, then any twiglets further along its branch won’t either. In this way, only the mutant Venus fly traps with a global energy minimum are retained for further investigation. The result – from billions and billions of possibilities, the researchers have pruned down to a top seventeen.

The researchers synthesised these seventeen potential receptors and tested them in vitro against their target small molecules. Fluorescence measurements shed great light on each, revealing them to be highly specific and selective for their respective ligands.

Until now, explains De Grado, the proteins in question have been “developed” either through the generation of large libraries of proteins for testing and improved through evolutionary type methods. However, this is time wasteful and energy consuming. As De Grado points out the Hellinga team has now accomplished the task of creating such a library and screening it by a very rapid computational means.

References

Nature 2003, 423, 185; Loren L. Looger, Mary A. Dwyer, James J. Smith & Homme W. Hellinga
Nature 2003, 423, 132; William F DeGrado.

The old ones are the best

An apocryphal story was doing the rounds of the chemistry discussion groups on the internet a while ago. You can substitute your own alma mater and personal weekend hobby for greater comic effect when relating the tale.

Two undergraduate chemists at Newcastle University did very well in their mid-term exams, their practical results were squeaky clean – both were headed for a first. In fact, the two friends were so certain of their chances they spent the weekend before the crucial final fell walking and partying at a hill-top youth hostel.

Either suffering from all the fresh air or one or two more beers than they should have had on the Sunday night they didn’t make it back to Newcastle until early Monday morning. Rather than taking the crucial final they spoke to Professor Bunsen after the exam and explained that their car got a flat tyre on the way back to University and the spare was dud.

flat-tyre

Bunsen was a lenient chap and agreed they could take the exam the following day. The friends were so relieved and studied hard that night. For the exam they were put in separate rooms and given the question booklet. Question One was a simple test of chemical reactions (5 points) and each thought the exam was going to be easy. They were unprepared, however, for what they saw on the next page. It said: “Which tyre? (95 points)”.