Chemistry – Page 52 – David Bradley

Totally tubular peptide rings

The highly unique crystal structure of nanotubes constructed from cyclic peptides is revealed this month by Japanese researchers in the journal Organic Biomolecular Chemistry. The descendents of these novel nanotubes could find a role in future molecular electronic devices, according to the team, who allude to the high macrodipole moment of their materials.

Shunsaku Kimura and colleagues at Kyoto University, have built on the work of ETH’s Dieter Seebach and Wisconsin’s Sam Gellman to use supramolecular chemistry to construct through self-assembly a stacked column of cyclic peptides, themselves made from three ACHC amino acids linked in a ring. ACHC is the trans-2-aminocyclohexylcarboxylic acid. The team used Fourier transform infra-red and nuclear magnetic resonance spectroscopy measurements and computational calculations to demonstrate that this cyclic tri-beta-peptide has C3-symmetry with the amide groups in the trans positions.

To read my full article visit the spectroscopyNOW.com crystallography channel.

Solvent solution

Interest in alternative solvents to replace volatile organic compounds is on the increase, so improved understanding of the properties of these alternatives is needed. One class of solvents researchers are keen to learn more about are the room temperature ionic liquids (RTILs). Researchers have commonly used absorption or fluorescence to study solvation properties. But now scientists in Japan, have carried out a Raman spectroscopic study of a series of RTILs using diphenylcyclopropenone (DPCP) and phenol blue (PB) as probes to reveal information about solvent acceptor numbers. Their results could have implications for the use of these “green” solvents.

Find out more in my latest news write-up on SpectroscopyNOW (Raman channel)

Bubbly extractions

Air-assisted solvent extraction (AASX) process is an important new technique for the extraction of valuable metals such as copper, nickel, cobalt and uranium, as well as wastewater treatment where metal concentrations are typically low.

Now, a Canadian research team has discovered that it is the bubbles that play a critical role in providing a high solvent-specific surface area and ease of phase separation. Now, the team has used layer interferometry (in the UV-vis region) to measure the time-dependent thickness of a film formed by blowing an air bubble in kerosene-based solvents. They used Fourier transform infra-red spectroscopy to determine its chemical composition.

Read more in my news article on the IR channel on spectroscopyNOW.com

Understanding soil pollution

A lack of understanding of how problematic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), pesticides, and herbicides interact with soil organic matter (SOM) is an issue that can hinder remediation of polluted sites, muddy the waters when it comes to determining the ultimate fate of pollutants, and reduce the viability of risk assessment models when considering new uses for brownfield and old industrial sites. Fortunately, Canadian scientists have now suggested that a range of techniques, including NMR and mass spectrometry, could clarify the various underlying mechanisms.

According to Myrna Simpson of the University of Toronto, Canada, a combination of conventional methods, such as equilibrium sorption and isotherm modelling, with NMR characterization of organic matter in soil, could help researchers get to the root of the problem.

Dig in at SpectroscopyNOW.com to read my complete article.

Lighting up the near infra red

A novel class of lanthanide compounds that emit in the near-infra-red could open up new possibilities for the use of NIR in biological imaging as well as leading to materials for optical amplifiers and light-emitting diodes (LEDs) operating at telecommunications frequencies.

According to Jean-Claude BÃ¼nzli of the EPFL, the Federal Polytechnic School in Lausanne, Switzerland, lanthanide compounds are of great interest in a number of fields because they produce narrow and easily recognisable emission lines in the NIR, they also have relatively long excited state lifetimes relative to organic chromophores. It is this latter characteristic of lanthanide coordination polymers that makes them of particular interest as they can be applied to time-resolved spectroscopy in analytical procedures allowing an enhanced signal-to-noise ratio and so much-improved sensitivity for luminescent analyses and imaging.

Follow my full write-up in the IR channel on SpectroscopyNOW.com.

Nanotechnology and medicine

X-ray imaging is a very mature, although not infallible, field of medicine, but it does not lend itself to the detection of small tumours or their metastases. Now, Sangeeta Bhatia in Boston, Massachusetts and colleagues at the Harvard-MIT Division of Health Sciences and Technology hope to remedy that by using iron oxide nanoparticles to allow MRI to visualize areas of tumor invasion.

The key to their novel imaging agent is a tumour-specific protease, which is found, as the name would suggest, primarily in and around tumour cells. Bhatia and her team engineered a method by which iron(III) oxide nanoparticles could form aggregate clusters under physiological conditions.

Find out more about how Bhatia and her colleagues hope to exploit nanotechnology to improve medicine in my current news round-up on SpectroscopyNOW.com

Molecular Weight Search on ChemSpy

Ever wondered whether there might be a way to extract more than the usual information from your chemical data. A query on the sciencebase site wanted to know whether there were a way to convert molecular weight into a formula.

The reverse – calculating molecular weight from a formula, is obviously trivial, just add up the atomic masses of all the elements in the formula. In fact, the likes of ChemDraw, ChemSketch and other chemistry drawing packages have a built in applet to extract the molecular weight from any molecule you can construct or import into them. But, how might one go about converting a molecular weight into a formula?

ChemSketch’s Tony Williams tells me that the visitor was more than likely looking to use monoisotopic mass to derive a molecular formula. In the ChemSketch program: “Use Formulae Generator to generate the possible molecular or fragment ion formulae.”

http://www.nullcdlabs.com/products/spec_lab/exp_spectra/ms/proc_features.html

But, just going back to the ambiguous nature of the query.

Take a molecule with molecular weight “2” as an example. That’s fairly easy. Only one answer possible – dihydrogen, H₂. But, what about “28”? It might be carbon monoxide, CO, but then again it could be a compound of hydrogen, boron, and oxygen, HBO, perhaps? Obviously, a bit of chemical nous would lead to a more likely answer, but what if you wanted to automate the process? More to the point, if you had a molecular weight of say, 346, there’s absolutely no way of extracting a unique chemical formula from that. Now, if you know the molecular mass with more precision, two decimal places say then that would narrow the search somewhat, it would almost be like solving sudoku hunting and pecking until the elements fit.

There is another tool that can do the search the Magnus program from Cambridge U’s Jonathan Goodman and colleagues, which is now included in Chemspy with Dr Goodman’s permission under the banner of Molecular Formula Search (you’ll need a java enabled browser to make it work). This tool runs essentially a reverse lookup for high resolution mass spectrometry (HRMS) molecular weights:

Of course, knowing other basic information, such as percent elemental analysis, physical properties, and reactivity, could lead you to the formula quicker still.

(This posting originally appeared on 2006-05-06 but since we’ve now added the tool to ChemSpy.com felt it was worth another mention, especially as Jonathan offered us some additional insights into reverse engineering HRMS molecular weights)

Cutting your Grass Greener

If you’ve been thinking of going green with your gasoline-powered lawnmower by switching to an ethanol based product, then Thomas Eddie Allen of Huntsville, Alabama, reminded me of a little problem that old-timers might face.

Allen read the Ap Weekly Features on “Go Green In The Grass” this weekend and emailed to say that while he is all for ethanol-based gas but there is a problem that is not mentioned in the article.

Older lawn equipment, mowers, weed-eaters, blowers, and chain-saws use plastic gas tanks that were made before ethanol was a factor. It attacks the tank, hoses, filter, and any carburetor gaskets and o-rings that have not been upgraded from rubber to synthetic material. The resulting leaks are a fire hazard, says Allen. Readers should be warned to check with the owner’s manual to be sure their equipment is set up for ethanol before using this “green” fuel.

Just think of all that CO2 that will be released if you set yourself on fire!

I asked civil engineer Tadeusz Patzek of the University of California, Berkeley, about the problem. “Ethanol dissolves sediments in the fuel systems, making them into electrolytes. Once you have an electrolyte, corrosion accelerates. Alcohol
and its own impurities, especially furan, will dissolve with time any elastomeric seal.,” he explained.

So, be warned.

More information available in pdf.

Is Resistance Futile?

The authors of a paper published in this week’s Nature claim to have srtuck a blow against the rising tide of antibiotic resistance. Jun Wang and colleagues at Merck’s Research Laboratories, in Rahway, New Jersey, have found a potent antibiotic from a microbial fungus, which they demonstrate kills many Gram-positive bacteria, including the current media darlings methicillin-[or multiple]-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE).

The new antibiotic, platensimycin, was just one of 250,000 natural product extracts they screened from a strain of the South African soil microbe Streptomyces platensis.

What makes platensimycin so interesting is its mode of action, which is completely different from any other antibiotic. This compound kills bacteria by blocking the enzymes involved in the synthesis of fatty acids, the building blocks of lipids. No existing antibiotics target fatty-acid synthesis in this way. The antibiotic clears Staph infection without any apparent side effects and it or an analog is now very likely to be pursued by the pharmaceutical industry.

Only two new classes of antibiotics have been found since the mid-1960s, the linezolid type (oxazolidinones) and daptomycin (lipopeptide), most of the others we use were found in the 1940s and 1950s and target specific bacterial biochemical processes, such as cell wall construction, their DNA and proteins. This limited arsenal allowed bacteria to evolve resistance to pretty much every antibiotic, which is why a new class is so keenly sought.

According to Eric Brown of McMaster University, in Hamilton, Ontario, “The report reads like a textbook of modern antibacterial drug discovery, beginning with a screen of 250,000 extracts from drug-producing microorganisms. What follows is a series of elegant studies, spanning bacterial genetics, biochemistry, pharmacology and structural biology, and leading to the discovery of a small molecule.”

Ever the cynic I cannot help worry that regardless of how novel this compound is at this point in its clinical history, as with all of its predecessors, bacteria are likely to evolve just as effective defences as their cousins once we begin to use platensimycin in medicine. That was the lesson we should have learned the very first time the prototypical antibiotic penicillin was used! Today’s wonder drug quickly becomes tomorrows acronym, give it a few years and the headlines will be screaming about PRSA, you can bet on it.

Nature, 2006, 441, 358

Chemunpub Forum Redux

Just got wind, by way of old friend Michael Engel, of a rather intriguing forum for chemists called chemunpub.

The Chemistry Unpublished Papers forum, looks like a great place to find out what’s going on underneath the public face of research chemistry, with posters asking what they should do with their ‘green’ ionic liquids once they’ve finished with them and info about papers that shouldn’t have been published at all!

This from the forum FAQ itself:

Section: Unpublished results – Post procedures, experiments etc that any experienced chemist can think will work, judging on experience, similarity among substrates, known reactions, literature, etc. but they actually work only partially or don’t work at all.

Section: X-Files – Unexpected reactions: post here weird and bizzare chemistry behaviour…

Section: Fake Chemistry – in ten years of research, sometimes we encountered papers claiming wonderful yields and easy procedures that turned out to be absolutely irreproducible. In those case, our conclusion is that latitude is a key reaction parameter…

Section: General Chemistry Discussion – anything chemistry related that you (or moderators) think is not appropriate for the other sections, requests, suggestions, meeting announcements, research proposals, trends in chemistry etc.

I think anyone with an interest in the dark side of chemical research should keep a close eye on this forum over the coming months.

This item was originally published on Tuesday, but I’ve brought it back to the front to highlight interesting comments I received today from both Engel and the ChemUnPub webmaster