Chemistry – Page 3 – David Bradley

The fading scent of violets

TL:DR – The chemical ionone gives violets their scent, but the scent temporarily fades if you keep sniffing the flowers.

Savour the scent of violets for too long and the smell will eventually fade. In fact, you won’t be able to smell anything for a while after until the chemical, ionone, that give violets their scent has dissipated from within your olfactory cavities.

Close up of Violet flowers

The combination of ionones gives violets their sweet but dry and powdery smell. These chemicals (also known as rose ketones) have an interesting effect on your olfactory receptors, inhibiting them after initially stimulating them and this steals away your sense of smell. This was an effect that was once considered magical and immortalised in folklore for generations. But, it’s much more magical than anything supernatural, it’s chemistry!

Still arguing about the periodic table 150 years later

Mendeleev used the periodicity of the chemical elements to organise a chart that we now refer toÂ quite obviously as the Periodic Table of the Chemical Elements. He did it 150 years ago. This anniversary year chemists are celebrating his “invention”. Trouble is lots of them don’t think the classic PT is the way we should display the chemical elements and have been arguing the point for years and years.

Periodic debate in Chemistry Views

And, just to prove the point about how much they want to argue this topic, my article entitled “Periodic Debate” which featured in Chemistry Views magazine back in June 2011 has been read by more than 122000 people!

The arguments made by my interviewees in that piece are all still active as far as I know, they each have a view about how the Periodic Table should be arranged, the exact order of the elements and even whether it really ought to be a three-dimensional spiral array rather than a flat grid.

You can still read the article – Periodic Debate – here.

Weapons grade chilli dressing

UPDATE: I blitzed them in the food processor today and converted the jar of pickled chillis into a lethal cocktail for drizzling into curries and marinades etc. Thought I had better put a hazmat type sign on the bottle.

Turns out these are Scotch Bonnets, up to 400,000 Scoville units in terms of capsaicin concentration. I’ve now chopped, deseeded and blanched half a pound of them to freeze and pickle.

I wore rubber gloves, a facemask and goggles while I did so, but the house is now full of their volatiles and neither Mrs Sciencebase nor myself can stop coughing and sneezing. I just touched my face with a formerly gloved finger that I thought I’d washed thoroughly and the skin there is sizzling gently…why do we use these weapons on mass destruction in food again, remind me?

UPDATE: I was talking chillis in the pub last night with biochemist and brewer friend Mark. He reckons the best thing to do is blend them up with some salt and white wine vinegar or cider vinegar, seeds and all, to make a useful drizzle to add a bit of fire to anything you cook, as and when. He also warned against adding anything fresh and rottable, such as freshly plucked chillis to oil to make a chilli oil, for instance, as there is a significant risk of botulism with such homemade products unless you add the requisite preservatives that defeat Clostridium botulinum.

Apparently, the chilli peppers I have grown are ~~habanero~~ Scotch Bonnet (1000s times hotter than a jalapeno on the Scoville scale). I chopped one without the seeds into scrambled eggs for lunch and almost couldn’t breathe while they were frying…my stomach is still complaining three hours later, my nose is running, and my lips feel like I’ve been chewing wasps. I only ate the tiniest fragment and none of the seeds. Although there is usually very little capsaicin in chilli seeds its highest concentration being found in the pith that attaches them to the interior of the fruit.

My chillis are now destined for homemade chilli pizza oil, I reckon. I daren’t cook with them again. They’re weapons grade.

In case you were wondering: The Scoville scale is a subjective measure of the heat of peppers, or other spicy foods, basically acting as a proxy for capsaicin concentration. Capsaicin is perhaps the most well known of the many related pungent capsaicinoids compounds in chillis. The scale is named for American pharmacist Wilbur Scoville, whose invented an organoleptic test for chilli heat in 1912. It is still discussed but high-performance liquid chromatography (HLPC) provides a more objective way of testing capsaicinoid concentration.

Capsaicin has the chemical name 8-methyl-N-vanillyl-6-nonenamide) it is a serious irritant to all mammals causing a burning sensation in any tissue with which it comes into contact, particularly sensitive parts of the body such as the eyes and nose, any part of the alimentary tract from top to bottom, and for some unfortunate chilli “chefs” who don’t wash their hands thoroughly after handling, any part of the reproductive tract too…hence the phrase – Chilli Willy – familiar to many waiters in restaurants serving spicy food.

Ironically, capsaicin has been used as a topical painkiller (in shingles for instance) and it has also demonstrated antifungal activity. Indeed, it may well have evolved in the plants for this purpose to protect the seeds, which are dispersed in avian guano (birds don’t feel the burn).

Sugru in space

There are only really two types of important problem out there: the first can be fixed with gaffer tape, the second with WD40. It’s an old engineer’s joke that has circulated on the internet for many a year. It plays on the idea that if something out to be moving and isn’t then a low-viscosity, sprayable petroleum product will be the answer whereas if something is moving that ought not to be then it can be bound in place by a high-adhesive polymer-textile composite tape.

In recent times, I’d add a third solution to the world’s problems, Sugru. It’s marketed as mouldable glue and most readers will no doubt have heard of its ascent and widespread adoption among scientists, hobbyists and makers, plumbers, and amateurs and professionals alike, who need to quickly replace a component, fill a hole, adapt a product for a new use all without the need to invest in a 3D printer.

Sugru came to mind this morning in listening to a report on the radio news that the International Space Station (the ISS) has sprung a leak. Apparently, a tiny chunk of space rock, presumably a millimetre or two across has slammed into the body of the spacecraft and punched a hole clean through. The astronauts on board have repaired the damage with thermo-resistant tape. Sounds like the gaffer tape approach to their problem.

But, it also seems to me that while the tape may hold and NASA has announced that the crew are in no immediate danger, such a problem could have been remedied with a little piece of mouldable flexible more effectively. I suppose the issue would be whether or not the makers of that product produce a thermo-resistant, space grade version.

Original Periodic Table song – Tom Lehrer’s The Elements

TL:DR – American musician and songwriter Thomas Andrew Lehrer wrote a humourous song in which he sings the names of the chemical elements to the tune of the Major-General’s Song from Gilbert and Sullivan’s operetta The Pirates of Penzance.

Periodic Table Song

I’ve been meaning to learn and record a cover of this song, but am yet to get around to it. Meanwhile, here are the original lyrics to The Elements.

The Elements (To be sung to the tune of Gilbert and Sullivan’s A Modern Major General)

by Tom Lehrer

There’s antimony, arsenic, aluminum, selenium,
And hydrogen and oxygen and nitrogen and rhenium
And nickel, neodymium, neptunium, germanium,
And iron, americium, ruthenium, uranium,
Europium, zirconium, lutetium, vanadium
And lanthanum and osmium and astatine and radium
And gold, protactinium and indium and gallium
And iodine and thorium and thulium and thallium.

There’s yttrium, ytterbium, actinium, rubidium
And boron, gadolinium, niobium, iridium
And strontium and silicon and silver and samarium,
And bismuth, bromine, lithium, beryllium and barium.

There’s holmium and helium and hafnium and erbium
And phosphorus and francium and fluorine and terbium
And manganese and mercury, molybdenum, magnesium,
Dysprosium and scandium and cerium and caesium
And lead, praseodymium, and platinum, plutonium,
Palladium, promethium, potassium, polonium, and
Tantalum, technetium, titanium, tellurium,
And cadmium and calcium and chromium and curium.

There’s sulfur, californium and fermium, berkelium
And also mendelevium, einsteinium and nobelium
And argon, krypton, neon, radon, xenon, zinc and rhodium
And chlorine, carbon, cobalt, copper,
Tungsten, tin and sodium.

These are the only ones of which the news has come to Harvard,
And there may be many others but they haven’t been discovered.

You can listen to Lehrer here (3700kb Quicktime Mov file). Search on The Vatican Rag and Masochism Tango for more of Lehrer’s wonderful material

Check out a fantastic animated version of The Elements here. (Someone should do a Peter Kay to this song and get it back in the Top Twenty, that would do wonders for the image of chemistry, I’m sure).

Read about the discoveries of elements 111 and 115, and our historical timeline showing the discovery of the elements. An updated version to cope with the new elements was written and recorded by Helen Arney.

What is diamorphine?

Diamorphine is another name for heroin.

Chemical structure of heroin

(5a,6a)-7,8-didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol diacetate.

Other synonyms diacetylmorphine, morphine diacetate, street names: H, smack, junk, horse, and brown.

Diamorphine is made by the chemical acetylation of morphine, which is derived from natural opium sources. The word morphine was coined by German apothecary Friedrich SertÃ¼rner around 1816 alluding to Morpheus Ovid’s name for the god of dreams (origin Greek “morphe” meaning form, shape, beauty. The word heroin was also coined in Germany, in 1898, as trademark for the morphine substitute invented by Friedrich Bayer & Co.

Understanding red mud pollution: causes, impacts, and mitigation strategies

TL:DR – Red mud pollution is the toxic waste left behind after aluminium oxide is extracted from the bauxite or in aluminium production

Red mud pollution, is bauxite residue. It is a toxic byproduct left over when alumina (aluminium oxide) is extracted from its ore, bauxite, in order to produce aluminium metal in the energy-intensive electrolytic Bayer process. For every ton of alumina produced from bauxite, approximately 1 to 1.5 tons of red mud pollution are released, amounting to almost 200 million tons each year. Red mud pollution is also sometimes known as bauxite tailings, red sludge, or alumina refinery residues.

Red mud is a highly alkaline waste product as well as containing toxic arsenic and mercury, which can cause serious harm if it enters the environment, having spilled from containment areas at bauxite works. This occurred in Ajka in Hungary in 2010 at an alumina plant, with devastating consequences.

Managing red mud pollution is a significant challenge given our reliance on aluminium across so many aspects of industry and the modern world. Scientists have worked on several methods to ameliorate its environmental impact by treating it with mineral acids, coating it with coal dust, or mixing it with silicate materials to reduce its harmful effects. Some of the above was adapted from Stanford University.

The Ajka red mud pollution incident was a major environmental disaster. A containment pond that was holding millions of cubic meters of red mud burst open and released the material into the surrounding towns. Ten people died and more than 100 were injured. The toxic sludge left homes uninhabitable and rendered farmland useless as well as damaging waterways. The cleanup took several years and cost billions of dollars.

The Ajka red mud pollution incident is yet another tragic reminder of the dangers associated with industrial waste and the importance of proper waste management and containment practices.

See also hexavalent chromium, commonly known as “chromium 6”.

Cutting noise from photos

UPDATE: March 2023 – I am currently using DxO PureRaw instead of the full PhotoLab. It does the same with denoising and lens/camera corrections. I then adjust curves and levels with PaintShopPro as I had been doing prior to trying PhotoLab.

UPDATE: January 2023 – I wrote this article back in 2018, since then various programs have come on to the market that offer AI approaches to denoising photographs many of which are much easier to use and work really well. For example, the Topaz AI Denoise tool reduces noise and blur and can even reduce motion blur, as I demonstrated in an article with a photograph of a Peregrine Falcon flying overhead. DxO Photolab is my current denoise software of choice though, its DeepPrime system effectively lowers the ISO of any noisy photograph by the equivalent of about three stops (like shooting at 400 rather than 3200 but with the same shutter speed and aperture). It lens/camera corrections built-in too as well as allowing you to adjust levels, curves, saturation etc etc.

Noise can be nice…look at that lovely grain in those classic monochrome prints, for instance. But, noise can be nasty, those purple speckles in that low-light holiday snap in that flashy bar with the expensive cocktails, for example. If only there were a way to get rid of the noise without losing any of the detail in the photo.

Now, I remember noise in spectroscopy at university, you could reduce it by cutting out any signal that was below a threshold. Unfortunately, as with photos that filtering cuts out detail and clarity. So, a solution was to run multiple spectra of the same sample, like taking the same photo, you could then stack them together so that the parts that are of interest add together. You then apply the filter to cull the dim parts, the noise. The bits that are the same in each shot (or spectrum will be added together, but the random noise will generally not overlap and so will not get stronger with the adding. The low-level filtering then applied will remove the noise and not cut the image. No more ambiguous spectral lines and no more purple speckles. That is in theory, at least. Your mileage in the laboratory or with your photos may vary.

De-noising by stacking together repeat frames of the same shot comes into its own when doing astrophotography where light levels are intrinsically low. Stack together a dozen photos of the Milky Way say, the stars and nebulae add together, then you can apply a cut to anything that isn’t as bright as the dimmest and you can reduce the noise significantly. Stack together a few hundred and your chances are even better, although you will have to use a system to move the camera as time goes on to avoid star trails.

Then it’s down to the software to work its tricks. One such tool called ImageMagick has been around for years and has a potentially daunting command-line interface for Windows, Mac, and Unix machines, but with its “evaluate-sequence” function it can nevertheless quickly process a whole stack of photos and reduce the noise in the output shot.

As a quick test, given it’s the middle of the afternoon here, I went to my office cupboard which is fairly dark even at midday, and searched out some dusty copies of an old book by the name of Deceived Wisdom, you may have heard of it. I piled up a few copies and with my camera on a tripod and the ISO turned as high as it will go to cut through the gloom, I snapped half a dozen close-ups of the spines of the books. The first photo shows one of the untouched photos, with a zoom in on a particularly noisy bit.

Next I downloaded the snaps, which all look essentially identical, but each having a slightly different random spray of noise. I then ran the following command in ImageMagick (there are other apps that will be more straightforward to work with having a GUI rather than relying on a command prompt. Nevertheless, within a minute or so the software has worked its magic(k).

magick convert *.jpg -evaluate-sequence median book-stack.jpg

And, so here’s the result, well the zoomed in area of the composite output photo, the average of the six essentially identical original frames with the noise filtered to a degree from the combined image. There is far less random colour fringing around the letters and overall it’s crisper. The next step would be to apply unsharp masking etc to work it up to a useful image.

It’s not perfect, but there is far less noise than in any of the originals as you can hopefully see. The software you use can have fine adjustments, but perhaps the most important factor is taking more photos of the same thing. That’s probably not going to work at that holiday cocktail bar, but with patience should work nicely for astro shots. Of course, if I wanted a decent noise-free photo of my book, I could have taken them out of the cupboard piled them on my desk, lit them properly, used a flash and diffuser and what have you and got a really nice photo with a single frame. But, then what would you learn from me doing that other than that I still have copies of my old book?

Chemical turn on and off

My latest news article in Chemistry World is about a light switch, not a lightswitch, that can control chemical reactivity. The PR team at the research centre involved have put together a nice video showing the experiments involved, watch for the lasers and dry ice, I’m pretty sure, #RealTime doesn’t involve Pink Floyd stage effects…but, it does look dramatic nevertheless.

Does hotter water freeze faster than cold?

UPDATE: Whether this proves to be right or wrong, my feature was the most well read article on Chemistry Views in 2017.

It sounds like #deceivedwisdom, but there are lots of reputable scientists who believe the Mpemba effect wherein hot water freezes faster than cold water is real. Youtube was replete with videos of people fling pans of boiling water into Canada’s freezing winter air to make clouds of “snow” and their friends with cold water attempting the same and simply getting a puddle in the snow. That effect is probably more to do with rapid evaporation and crystallisation than the Mpemba effect, but it makes for a great show nevertheless.

A couple of years ago, I believe The Royal Society of Chemistry (RSC) ran a competition to find an explanation for the actual Mpemba effect in which a container of warmer water placed in a freezer seems to become ice faster than a container of cold water. There have been very few validated, reproducible experiments on this surprisingly. And, in a recent Chemistry World, of which I only just got wind, a Cambridge team claims to have shown that there is no effect, it is deceived wisdom.

But…

I was sent a research paper that used calculations and vibrational spectroscopy to show that there are some sixteen different types of hydrogen bond present in water and that the distribution of types changes with temperature. Essentially, there being much tighter H-bonds (despite thermal agitation) in hotter water than cold. It is this distribution that means hotter water can nucleate more rapidly on cooling and form microscopic ice crystals that seed the liquid and allow it to freeze faster. You can read more details in my recent Chemistry Views article on this topic.

Incidentally, the snow-making videos are something of a distraction, this isn’t what Cremer and his team are talking about really, and they probably show rapid evaporation and crystallisation rather than the difference in ice formation caused by temperature difference.

What do you think? Is the Mpemba effect deceived wisdom or can different populations of hydrogen bonds persist and override the simple thermal effects and heat loss processes in water?

UPDATE: Dana Roth at Caltech just pointed to another paper that seems to support the existence of the effect and has a similar explanation re H bonds and nucleation.