Month: May 2006

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)

Human to human bird flu

The World Health Organization has expressed concern that a recent cluster of deaths associated with the H5N1 virus in Indonesia may not have originated with an animal host, suggesting the possibility of human to human transmission of the virus. However, it also cautions that the analytical evidence suggests that the virus has not mutated into a human transmissable form, which means we are not just yet on the verge of a global bird flu pandemic after all.

The news media inevitably picked up on this warning and ran with it, but thankfully the BBC saw the double-edged nature of the WHO announcement points out with some degree of rational response that many people in Indonesia, as in other southeast Asian countries, live in such close proximity to their animals and not necessarily in the most hygienic of circumstances that the likelihood of catching bird flu is much higher in such an environment.

It is the lack of a mutated form of H5N1 among these victims that means we are not yet doomed to see the feathers fly globally.

Uncrackable windows and unbreakable glass

In the same Digg discussion I read of a novel glass replacement called Kwarx that is meant to be unbreakable and so could save all that sweeping up after your next drunken cocktail party and a purported announcement from Bill Gates that the next version of the Windows operating system, Vista, will be unhackable! Is this just a coincidence or is Gates hoping to exploit the sparkling character and shatter-proof nature of Kwarx to keep his Windows nice and clean?

Upgrade Redux

Microsoft, having given Longhorn a far more marketing-exec friendly name in the form of Vista, has now revealed just how powerful computer needs to be to run this all-new version of the Windows operating system. Surprisingly, the spec is actually far lower than the system inside my Dell laptop which died unceremoniously just last week (out of warranty, of course, but only 26 months old).

Would you be surprised if this new spec were not up to actually running Vista though? Of course, not. Throw a CAD program, a tabbed browser, and maybe some DVD burning and the kind of spec MS suggests as a minimum is going to grind to a halt regardless. So, inevitably users will find themselves having to ditch perfectly serviceable and adequate computer equipment and replacing it once again with the next great chip and googol’s of RAM just to get their software to run.

Anyway, this is the spec:
Minimum processor clock speed: 800MHz (recommended 1GHz 32 or 64 bit), System memory (RAM) 512MB min with 1GB, Graphics card needs to be DirectX 9 capable to run all the new 3D icons in the Windows Aero interface and have at least 128MB. You will need 15GB of free space on your hard drive.

Doctors take an alternative view

A group of leading physicians and scientists in the UK has petitioned the National Health Service, because it is concerned about how unproven or disproved treatments are being encouraged within the system. In a letter reproduced in The Times, they ask that practices be reviewed and that the various concerns about such treatments, which generally sit under the umbrella of complementary or alternative medicine, be raised with the governmental Department of Health.

The bottom line, in other words, is that the authors of the letter, “want patients to benefit from the best treatments available” and don’t think NHS money should wasted on including the likes of highly implausible treatments such as homeopathy on the treatment roster.

The authors express the opinion that, “We are sensitive to the needs of patients for complementary care to enhance well-being and for spiritual support to deal with the fear of death at a time of critical illness, all of which can be supported through services already available within the NHS without resorting to false claims.”

Homeopathy is certainly one of the most inflammatory of the CAM therapies. From the scientific standpoint there is absolutely no serious explanation as to how it might work in terms of the chemical components of the treatments. On the other hand, Toby Murcott’s excellent book on the subject of alternative medicine (reviewed briefly here) emphasises that science is yet to explain fully the placebo effect, or more intriguingly the anticipatory effect of treatments wherein the thought of being healed can have some benefit for many patients even before they are given the therapy.

Modern medicine has “eradicated” so many of the old diseases, that countless health centres and organisations across the globe now must heavily promote their various panaceas as the diseases of longevity begin to stack up for which there are no cures as quick and easy as a course of tablets.

As we live longer, so we expect to live healthily for longer. With that in mind it is inevitable that people will turn to CAM to help give achieve this. However, in this letter, Professor Michael Baum and colleagues essentially point out that the hopes of many patients are being pandered to through the irresponsible embracing of alternative therapies for which there is no evidence of efficacy.

Physics of Football

In the run up to the Football World Cup, it was inevitable that press releases would starting dribbling in from the media relations departments of companies, research establishments, and learned societies, each tackling difficult subjects and presenting them as a game of two halves with some vague footy. The ultimate goal as ever to get their name in the press…

Well, the Institute of Physics is no exception to the rule, obviously, basically, at the end of the day, they just kicked off with their first soccer related release, hoping to get a pre-emptive strike at that goal and hoping to avoid a penalty playoff:

Apparently, Nick Linthorne has discovered how players like Gary Neville can achieve the perfect long throw-in. Writing in Physics World’s June issue Linthorne puts a new spin on throwing showing how the physics of projectiles can be used to calculate the optimum angle at which a ball needs to be released to achieve the longest possible throw-in. The article describes how the optimum angle is much less than physicists previously believed.

I am now just waiting for the Royal Society of Chemistry to come racing up the wings with a press release on how novel polymers used in soccer-ball manufacture will allow footballers…blah…blah…blah….

Someone is bound to cry foul before it’s all over.

Oh, by the way, I’m talking about football here, not the padded-up version of rugby played by Americans, that we know as American Football. If you’re interested in the physics of throwing a football, then check out this Youtube clip:

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.

A380 Touchdown

UPDATE: 4 November 2010

A380 crashlanding news

  • “Qantas grounds A380s after incident on Sydney-bound flight” and related posts
  • Qantas mid-air emergency: A380 factfile
  • Factbox: Airbus A380, the world’s biggest passenger jet
  • Qantas Grounds Airbus A380 Fleet After Emergency Landing
  • Qantas Jet Forced To Make Emergency Landing
  • Qantas Suspends All A380 Flights
  • Engine Explodes Aboard Australian Plane, All Of Airline’s Airbus A380s Grounded (RR)
  • Qantas says crashed plane an Airbus A380

THE damage suffered by Qantas flight 32 en route to Sydney has been described by leading aircraft engineers as potentially life-threatening and extremely rare, says Sydney Morning Herald.

The Airbus A380 is a double-deck, wide-body, four-engine airliner manufactured by the European corporation Airbus. The largest passenger airliner in the world, the A380 made its maiden flight on 27 April 2005 from Toulouse, France, and made its first commercial flight on 25 October 2007 from Singapore to Sydney with Singapore Airlines. Also known as the Superjumbo.

ORIGINAL 18 May 2006: At a time when the UK government has stated that nuclear power is effectively the only option to cut down on pollution and help the UK meet its emissions targets under the Kyoto Protocol, is it really something to celebrate that the world’s biggest passenger jet, the Airbus A380, has today touched down at London’s Heathrow Airport for the first time? Just a thought.

Is Resistance Futile?

Structure of platensimycin

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