Chemistry – Page 13 – David Bradley

Forensic saliva test within spitting distance

The latest issue of SpectroscopyNOW is online. This week I cover everything from MRI for testicular cancer to egg-shaped carbon balls by way of energy molecules, copper proteins, secret writing, first up a forensic science test for distinguishing saliva deposits from other substances at a crime scene:

Non-destructive spit test – Raman spectroscopy can identify samples of an unknown substance at a crime scene as human saliva during forensic analysis, according to a US study, the technique would preserve DNA evidence. I asked research team leader, Igor Lednev to tell me about his aspirations for the technique.

“The major motivation of this research project, funded by the National Institute of Justice, is to bring our novel method to the forensic lab and a crime scene as soon as possible,” he told me. “The method is at the developmental stage at the moment and several further developments need to be done before moving to the “real” world crime scene.” These include (i) automation of the technique and making it a user-friendly “black-box type” apparatus, (ii) expansion to potential mixtures of body fluids, (iii) protection from possible interference from substrate materials and possible contaminants, and (iv) expansion to possible evidence degradation under various environmental conditions.

To achieve those goals the team is collaborating with “real world” practitioners, CSIs including Barry Duceman, Director of Biological Science, at the NY State Police Forensic Investigation Center and John Hicks, Director of the Northeast Research Forensic Institute. Lednev revealed to me that a first prototype of the device should be in forensic laboratories within two to three years.

Also, in my SpectroscopyNOW column this week:

MRI on the ball – MRI proves to be a good diagnostic tool for testicular cancer and could spare some men unnecessary surgery.

Focus on energy molecule – Organisms use ATP as a universal energy storage molecule, now carbon nanotubes, modified with luciferase, have been used as near-infrared detectors for cellular ATP. The work has potential for studies of ischaemia, Parkinson’s disease, hypoglycaemia and more.

Copper, on the beat with NMR – The first NMR spectroscopy study of the copper site in an important blue metalloprotein, azurin, has been undertaken. Copper mediates many biochemical redox reactions and azurin plays an important role in catalysing electron transfer in cellular reactions.

Sunscreen spies – Sunscreen and boron can work together to make a compound that changes colour when touched under ultraviolet light. The compound changes from blue-green to yellow with the gentlest of rubs and then reverts quickly to blue-green when gently warmed, although the process is reversible at room temperature.

Bucky eggs cracked – Unusual egg-shaped fullerene molecules are rulebreakers because they do what no other fullerenes seem to do – fuse three pentagons of carbon atoms, according to chemists in China. The discovery of these molecules could lead to new insights into fullerene chemistry as well as offering new opportunities for synthesising novel materials.

Forensic saliva test montage by Albany’s Aliaksandra Sikirzhytskaya.

Virkler, K., & Lednev, I. (2010). Forensic body fluid identification: The Raman spectroscopic signature of saliva The Analyst, 135 (3) DOI: 10.1039/b919393f

Correct your chemical spelling mistakes

The current version of the chemical spellcheck is 3.0 now available via the sciencebase download. It sports a massively reduced filesize, adds OpenOffice accessibility and includes lots of new user-suggested words. Check it out…

Chemist Adam Azman contacted me more several years ago to ask if I knew of a free or open source chemistry spellchecker custom dictionary for Word or OpenOffice. Searches had revealed only paid-for dictionaries. We both agreed that a free chemical spellchecker would be very useful to all scientists working with chemicals, so Adam set about creating from scratch an open access chemistry dictionary.

The spellchecker files were originally hosted on my Chemspy.com site but are now available on Sciencebase.com. Adam did a lot of extra work with my good friend Tony Williams of Chemspider to develop the new, improved version 3.0: Chemistry Dictionary for Word/OpenOffice (1MB zip file).

Keywords: Open Access Chemistry Dictionary, Open Source Chemistry Dictionary, Microsoft Word Chemistry Dictionary, OpenOffice Chemical Dictionary. Original post 2008-02-08

Chemistry Passwords – Nerdy passwords, secure and memorable

TL:DR – In 2010, I devised a neat way for chemists to devise a memorable password based on a chemical formula. It was fun, but I do not recommend.

WARNING: Do not simply use the formula of a common chemical without obfuscating it in some way. It could be dictionary cracked very easily if you do. A serious recommendation is to use a strong password generator rather than this technique and to store passwords in a digital safe itself locked with a strong password.

Coming up with a secure password that cannot be bruteforce or dictionary attacked but that is easy to remember is quite troubling. So, here’s the nerdiest approach yet.

Think of a compound, any compound, but preferably one with which you are familiar. If you’re in science, then you could pick a compound associated with your research thesis or perhaps the medication you needed to get through the viva.

Now, work out, or look up, its chemical formula. BUT DO NOT STOP THERE…Next, think of a simple algorithm to obfuscate the formula (reverse it and chop off each end perhaps, or if it is a long formula extract all the numbers and put them at one end instead of after each element symbol, you get the idea). Of course, if you pick a compound that happens to share the first couple of letters with the name of the site to which you are logging in, then that should make it easier to remember too.

If you suffer from hayfever you might be using flixonase, when you login to flickr, for example. Formula: C25H31F3O5S, password could be CHFOS253135 or 5O3F13H52. No bruteforce hack attack is going to figure those out in a hurry. Specialists in secondary messenger chemistry with a MySpace account could choose myo-inositol (C6H12O6 –> CHO6126), while nutritional chemists could hide their Facebook behind Factor II (vitamin B12) C₆₃H₈₉CoN₁₄O₁₄P –> CHCONOP63891414.

Of course, you will have to think of your own examples, but with CAS and ChemSpider registering tens of millions of structures, that should not be too hard to do.

Of course, being a chemist you also know about InChi and Smiles string, which could provide you with an even more sophisticated password. The InChi string for aspirin, for instance, is <span class=”chem:inchi”>InChI=1/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/f/h11H</span>. You could make your obfuscating algorithm to remove all the zeros and reverse the string. The Smiles string is not quite so long O=C(Oc1ccccc1C(=O)O)C, but what about choosing that and adding the same string reversed to the end of the original?

It could all get very convoluted and seemingly random very quickly. But, isn’t that the aim of a good password? According to the password strength tester, the untouched Smiles string for aspirin is “best”, but apply an algo and it will be even better.

The neat part is that you pick a compound you will remember, you can look up its formula any time and you know the obfuscating algorithm. So you thus have a memorable password that is essentially a pseudo-random alphanumeric.

Originally posted Jun 18, 2007 @14:00

Asian flush, blush, glow

UPDATE: March 9, 2010 – Baclofen, the muscle relaxant and GABA agonist is being touted once more as a treatment for alcoholism. Read my thoughts on sibling science site SciScoop.com.

As with much of medical science, the appearance of a fascinating research paper and an accompanying press release do not usually mean that a new pharmaceutical intervention, a medicine, is ready to be prescribed to patients on the very day that the paper appears. The drug discovery, research, and testing processes are much more long-winded than that.

One example was a recent paper on Alda-1, the simplified name for N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide, a small organic molecule that activates the enzyme ALDH2 (aldehyde dehydrogenase 2). ALDH2 is involved in metabolising the aldehyde byproducts of other substances in the body particularly alcohol.

In September 2008, Alda-1 was touted by the media as a “new drug hope for controlling heart damage”. By activating ALDH2 it was suggested that those people who have an inactive form of that enzyme (some 40% of East Asians and people of East Asian descent) could be treated with the compound to preclude the cardiotoxicity of aldehydes formed when they drink alcohol.

More recently, the same researchers involved in the 2008 study, Thomas Hurley of the University School of Medicine in Indianapolis and Daria Mochly-Rosen, of Stanford University School of Medicine, and colleagues, have published a crystallographic study showing more details of how Alda-1 works to activate ALDH2. You can read my write-up on this work today in the latest issue of the X-ray ezine on SpectroscopyNOW.com.

However, press releases are notoriously hopeful about the actual use to which a piece of biomedical research might be put so I asked Hurley for some additional insight into the likely fortunes of Alda-1.

“Alda-1 is not ready for human trials, nor is it ever likely to be,” he told me. “Its potency is relatively low for an effective in vivo agent, especially when one accounts for its solubility.”

The compound is, as those in pharma research will have realised from the off, simply a lead compound. A compound that researchers will use as the starting point for novel and potentially more efficacious and more soluble compounds, analogues, that would be designed for testing and clinical trials.

“We have much work to do on this before clinical trials can even start to evaluate whether this is an effective strategy in vivo,” conceded Hurley, “I doubt there will anything ready for clinical application for 7-10 years, unless we get really lucky here in the next year with our analogue design and testing,” he adds.

One thing that the original media attention did get right is that Alda-1 might eventually lead to a primary clinical application in the area of cardioprotective effects. This would be rather than it being developed as a drug to allow East Asian drinkers with the ALDH2 mutation to imbibe more alcohol than their flush response, nausea, and palpitations would normally allow them.

“Its use as an activator for alcohol metabolism will, hopefully, be regulated,” Hurley told me, “There are broad ethical issues associated with an application toward reducing alcohol intolerance in the East Asian population or individuals of East Asian descent.”

He points out that pescribing a drug descended from Alda-1 to activate mutant ALDH2 would be like curing a lifestyle issue (alcohol intolerance) and replacing it with an increased risk for a devastating disease – alcoholism. “Currently, there is relatively low risk of alcohol abuse or alcoholism in those individuals who are intolerant to ethanol consumption, so ‘curing’ the intolerance is very likely to lead to an increase in the prevalence of these devastating diseases in these low risk populations,” Hurley added.

Once a drug is developed for the cardioprotective benefits emerges on to the market, however, you can bet your last Yen that a blackmarket will quickly emerge where there are large populations of East Asians, for a pill that would allow otherwise lightweight drinkers to put themselves under the table without the flushing, nausea and palpitations. Of course, it won’t ever preclude the need to consider the health risks of excessive drinking and to seek alcohol treatment if one’s drinking becomes a serious problem.

Perez-Miller, S., Younus, H., Vanam, R., Chen, C., Mochly-Rosen, D., & Hurley, T. (2010). Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant Nature Structural & Molecular Biology DOI: 10.1038/nsmb.1737

Classic musical science and Stradivarnish

It won’t necessarily be music to the classical purist’s ear, but chemists have been instrumental in revealing the secret beneath the varnish on a Stradivari violins, and the secret is: there is no secret.

Antonio Stradivari is perhaps the most famous instrument maker of all time. He is especially celebrated for his violins, which he made in Cremona circa 1665 till his death in 1737. The “legendary” varnish on his instruments has fascinated musicians, violin makers, historians, and others ever since and has led to repeated speculation that there was a secret ingredient that endowed a Stradivari violin with its unique and beautiful tone.

Now, European researchers have taken minute samples from carefully selected parts of five violins and subjected them to microscopic and spectroscopic analysis. Although the different instruments were made over a period of three decades it turns out that their varnishes are all very similar. It is only the red pigments that seem to vary through Stradivari’s career and, for those listening in black and white, the colour of a violin has no aural impact.

I asked the creative director at ClassicFM, Tim Lihoreau, what he thought about the discovery. I almost expected an angry, or at least resistant, response along the lines of, “how could the scientists shatter the illusion,” but he was actually rather encouraged by the analytical chemistry:

“At first, I was surprised by this news,” Lihoreau told me, “I’d always heard that it was something in the varnish that made Strads so special – the vintage Rollers of the fiddle world, as it were. Having said that, in many ways it only adds to the mystique of the Cremonese creator – that, in some ‘weird science’ way, it’s his magic art that is the key: a blend of all his crafts, coming together to make such legendary instruments.”

Anyway, more on that story and others in my latest SpectroscopyNOW column.

Absolute chemical headlines

copper-alchemist A wide range of stories again in this week’s Alchemist column on ChemWeb.com

Absolute configurations reveal themselves through NMR spectroscopy using residual dipolar couplings in small molecules, according to an international team who have put it to work on an anticancer compound. Discussed also in more detail on SpectroscopyNOW.com

A failed antidepressant could be marketed as a novel treatment for female sexual dysfunction. Also covered on Reactive Reports.

In the world of inorganic materials, researchers have discovered a new class of composites in which dihydrogen layers trap atoms of the noble gas xenon to form a stable solid under extreme pressures.

A new approach to carbon nanotubes provides chemists with an insider view of these unique materials, while an award for $2.8 million looks set to lead the way to truly room temperature superconductors.

Finally, controversial claims about the state of the environment suggest that total economic collapse or the building of at least one nuclear power station each day (or its non-carbon energy equivalent) is the only way rising carbon emissions will be stopped and catastrophic climate change abated.

Latest science headlines

Time to bring you up to date on the latest science headlines I’ve put together for other sites this last couple of weeks, so here’s a quick round-up:

On the SpectroscopyNOW site, this issue, I covered natural chemicals that can help sunflowers soak up toxic cadmium from the soil (another example of the phytoremediation process I discussed in more detail on Sciencebase.com recently). I also describe a new approach to spectroscopy that could help chemists work out the absolute structure of natural products with medicinal potential.

In the same issue, under the X-ray banner, I explain how US researchers have for the first time homed in on the role of the trace element selenium in male infertility. Their work offers some new clues as to what leads to malformed sperm in some cases.

I also report on yet another “omics”, in which conservators take a leaf out of the biologists’ handbook to find a way to judge a book not by its cover, but by its odour.

Over, on the Intute physical sciences blog, formerly my monthly Spotlight column, I reported on proton spin, magnetic wind, and the latest catalysis research with implications for industry.

And, ever present, the ubiquitous and omnipresent Alchemist. First to fall under The Alchemist’s crystalline gaze is Korean work into coating yeast particles with a protective silica shell to stabilize the organism for new lines of research. Geochemistry billions of years old reveals a sulfidic past and answers questions about how the Earth got its oxygen-rich atmosphere. In biophysical chemistry, US scientists have found a way to extend the redox range of copper-containing proteins and in computational chemistry Dutch scientists explain precisely how hydrogen interacts with copper surfaces. Good news for those fearful of mercury dental fillings, as a new composite material emerges from polymer and nanochemistry research. Finally, a cash injection from US recovery funds could see the establishment of yet another “Facebook for scientists”, only this time it’s aimed squarely at American institutions.

Alchemical Anomalies

copper-alchemist In the current issue of The Alchemist we learn how to stick methane molecules to metals without breaking carbon-hydrogen bonds and how to make impossible carbene catalysts without the usual prerequisite of an attendant metal centre.

Another seeming impossibility comes to light: a new microscopy technique for visualizing non-fluorescing biomolecules using the kind of stimulated emission suggested by Einstein almost a century ago.

An exchange program leads to a new way to make nanoscopic tools from tiny wires of cadmium sulfide, we hear, while an extract of grape skin shows promise as a novel therapy for sickle cell anaemia.

Finally, a young medicinal chemist receives a prestigious American Chemical Society fellowship in organic chemistry.

All the write-ups and links in the current issue of the ChemWeb chemistry zine.

Food Chemistry News

On the menu today, why red wine is a no-no when it comes to fishy cuisine, how chemists can help you improve your gravy, and a whole platter of food chemistry to tempt your taste buds:

“Red wine with red meat, white wine with fish.” But, have you ever wondered why? Japanese chemists have discovered that the iron in red wine simply makes fish taste too…well…fishy…giving your mouth an unpleasant, fishy aftertaste, according to a report in the Journal of Agricultural and Food Chemistry.

Gravy training – The British probably have as many different recipes for making gravy as they have gravy boats from which to pour it over their roast beef. But, a spot of chemistry can improve not only the flavor, texture, and color, but give gravy a healthy boost. Here’s the definitive chemical guide to making gravy.

Pink pepper is actually the dried berry of the Brazilian weed Schinus terebinthifolius and contains an irritating phenol-type compound known as cardanol. Pink pepper causes a range of toxic reactions including rashes, oral and respiratory irritation, chest pains and tightness, headaches, swollen eyelids, stomach upset, diarrhoea and haemorrhoids. Nice… But, despite that it’s a trendy ingredient among trendy chefs. The Guardian provides the skinny on pink pepper.

Apparently, American gourmets are latching on to the Japanese concept of umami, or “deliciousness”, which is considered the fifth taste after salt, sweet, sour, and bitter. The word roughly translates as “tasty”, although “brothy”, “meaty”, or “savory” could do just as well. It’s difficult to translate a whole concept literally. Recently, scientists homed in on a specific tongue receptor linked to natural “glutamate”; as in the amino acid part of monosodium glutamate, the sodium there to make it soluble in water. Glutamate, of course, is the archetypal umami ingredient, so the link grows stronger.

Now, a couple of stories for those parts of the world now entering the barbecue season. Chemists have figured out how to make meats more succulent and tasty on the grill, while others have figured out that it’s the sour receptors on your tongue that respond to the bubbles in soda pop.

Finally, although British scientists came up with an explanation a decade ago, apparently the French have turned their attention to that Great British passtime – tea drinking – and have found a possible way to solve the perennial problem of the dribbling teapot. They report details in a physics preprint just uploaded to the arXiv servers.

Well, after all this talk of food, I’m now feeling a little peckish, so off to do a little cordon blue in the kitchen…or maybe I’ll just break into the snack cupboard instead…

Sniffer, E coli Clues, Graphene

The second batch of physical science and biomedical research news in the SpectroscopyNOW ezines are live:

Optical sniffer detects poison gas – US researchers have developed an optoelectronic nose that can sniff out toxic gases. The sensor is fast and inexpensive and could be used to detect high exposure risk to hazardous industrial chemicals.

E coli clues – New clues as to the virulence of the potentially lethal bacterium Escherichia coli O157:H7 has emerged from structural and functional relationship studies of its autotransport and proteolytic EspP proteins. A comparison with X-ray diffraction results reveals important clues about these proteins.

Imaging a semiconductor sandwich – A technological mash-up between graphene and the semiconductor gallium arsenide as characterised by optical microscopy and Raman spectroscopy and other techniques could pave the way to hybrid electronics devices that bridge the gap between current silicon circuitry and future molecular electronics