Posted in chemistry

Another layer of onion chemistry has been peeled away

After 150 years, the structure of the enzyme responsible onion’s eye irritation has been found.

It’s common knowledge that cutting onions can make you cry. Upon damage to the plant tissue, onions release a compound called lachrymatory factor (LF) as a chemical defence mechanism, irritating the eyes and causing them to water. What is less well known is the mechanism the onions use in order to generate the chemical. In fact, scientists have been stumped for over 150 years.

Despite the knowledge that LF is produced by a reaction catalysed by the enzyme lachrymatory factor synthase (LFS), analysing the conversion of the initial substrate – usually a sulfenic acid – to LF has been difficult to achieve. Unfortunately, the rapid reactivity of the substrate and the instability of the LF makes them very challenging to observe.

In order to surmount this problem, a team of US researchers determined the crystal structure of LFS. By analysing the crystal structure, they were able to observe the structure of the enzyme both as a whole and as its active site bound to another compound. Using this data in conjunction with known information about similar proteins, they were able to deduce the chemical mechanism used in the enzyme catalysed reaction – a sequential proton transfer accompanied by the formation of a carbocation intermediate (as illustrated in Figure 1).

mechanism

Figure 1

Tabitha Watson

 

The paper, entitled ‘Enzyme that makes you cry – crystal structure of lachrymatory factor synthase from Allium cepa‘ can be found in the journal ACS Chemical Biology [DOI: 10.1021/acschembio.7b00336]

Posted in chemistry, science

The perfume conundrum – why it smells different on different people

I’m sure you’ve noticed that perfume never smells the same on any two people, a fact that can be jolly frustrating when you’re out shopping for a new scent. Something that smells divine in the bottle or when worn by a friend can easily seem cloying and repugnant once applied to your skin. So, why do these variations occur?

Well. As you would expect, it all begins in the nose. Our sense of smell is dependent on a small patch of specialised olfactory sensory neurons located high up in the nasal cavity. This patch is called the olfactory epithelium, and it is covered by a carpet of olfactory receptors. On average, humans tend to have around 450 different types of olfactory receptor, each capable of binding to a wide array of odour molecules. Unlike conventional receptors which only bind to one type of thing, olfactory receptors can be activated by many different molecules (and each molecule can activate many different receptors). Each molecule/receptor combination binds in a slightly different way, and these differences provide us with our nuanced sense of smell. In fact, your sense of smell is probably better than you think – researchers at Rockefeller University have found that humans are capable of detecting over one trillion individual scents.

Due to natural variation, different people have a different number and combination of olfactory receptors. This leads to different experiences of smell. Someone could find the aroma of patchouli in a perfume overpowering, whilst another may not be able to detect the scent at all. Whilst this difference in interpretation is certainly a part of the puzzle, it doesn’t explain why the same perfume smells different on different people. Don’t worry – I’m getting to that bit.

As you may know, each individual has a unique ‘skin chemistry’. This is influenced by a great deal of factors ranging from temperature, humidity and sweat composition to the types of medication you’re taking and the range of aromatic herbs in your diet. In some circumstances, your skin chemistry can alter by the hour. When you apply perfume, the naturally occurring chemicals on your skin mingle with those present in the perfume, creating a subtly different scent. The environment you’re in can also influence your perception of a smell – sampling a perfume in someone’s bedroom will often be an entirely different experience to testing a new brand at your local shop.

Along with the influence of your skin chemistry, the time after application can also have an impact on your perception of a perfume or cologne. Each concoction tends to be made up of three different ‘notes’ – top, middle and base. The top notes are the ones you smell immediately after application (their small and volatile structures evaporate easily and float straight towards the nose). The middle notes are next, emerging after around two hours due to their larger molecular weight. The base notes are the last to appear, a good five hours after initial application. They are the largest molecules, so require prolonged exposure to body heat in order to evaporate.

So, here we are. After a bit of discussion, it seems like the differences in perfume experience are due to a wide range of factors. Not only does your individual nose play a part, but so does the garlic bread you had for lunch and the weather that day. Pretty pot-luck, eh?

Tabitha Watson

Image Credit: [http://mac.h-cdn.co/assets/15/51/980×490/landscape-1450470504-best-perfume.jpg]

 

Posted in chemistry, physics, science

How do things glow in the dark?

It is relatively common nowadays to see a plethora of glow-in-the-dark products across a vast spectrum of items. Although most regularly found in toys and watches, there seems to be no end to the types of item that can be modified to glow. So, how does this phenomenon occur?

Firstly, it is important to pin-point what is meant by the term ‘glow-in-the-dark’. In this instance, it is used to describe luminescence. Luminescence is the emission of light from a source that has not been heated; due to the lack of heat, it is a form of spontaneous emission. If heat is involved, then the phenomena is labelled incandescence and is not considered spontaneous. There are several different ways in which luminescence can occur, including through chemical reactions, electric currents and the compression of certain types of crystal.

The type of luminescence encountered most commonly in day-to-day products is phosphorescence. Phosphorescence is a specific type of photoluminescence that involves molecules called phosphors. Usually transition metals or rare earth elements, phosphors absorb energy from electromagnetic radiation and emit it as visible light over timescales between nanoseconds and hours. Funnily enough, phosphorus is not defined as a phosphor – it is chemiluminescent as opposed to photoluminescent.

Underpinning the ability for photoluminescent materials to emit light is quantum mechanics. When a photon collides with the phosphor and is absorbed, it excites an electron to a higher transition state. When the electron drops back down to its usual state, it releases a photon whose energy exactly corresponds to the size of the gap between the levels. This is what we perceive as the emitted ‘glow’. In the majority of photoluminescent events, this excitation and relaxation of electrons occurs over extremely short timescales, often in the region of nanoseconds. This is known as fluorescence. However, when phosphors (such as zinc sulphide and strontium aluminate) are involved, phosphorescence can emit light over much longer periods of time. This is the key difference between fluorescence and phosphorescence – the time taken to re-emit the energy.

So, why is it that phosphorescence can occur over such long timescales? Again, it’s all based on quantum mechanics. As you may know, ‘allowed transition states’ and ‘forbidden transition states’ are key within quantum mechanics. These, along with a rather expansive set of rules, govern the movement of electrons in their respective shells. In normal circumstances, when a ground state electron is excited to a higher energy level, it will transition into an exited singlet state. This means that it has paired up with another electron with an opposite spin (i.e. obeying the Pauli Exclusion Principle). The Pauli Exclusion Principle states that no two particles with a half integer spin (such as electrons) can occupy the same orbital at the same time (think of people on a bus – ideally, people aim to sit on an unoccupied pair of seats before going to sit next to a stranger).

However, in some cases (as in phosphorescence), the excited electron will transition into an excited triplet state. This is where things get a little complicated. In an excited triplet state, the excited electron is spinning parallel to the ground state. This is called intersystem crossing. As having the same spin is considered ‘forbidden’ within quantum mechanics (again, due to our friend Pauli), it means that the excited triplet state electron is in a bit of a pickle. The ‘forbidden’ transitions are less kinetically favourable than the ‘allowed’ transitions, meaning that it is more difficult for the electron to relax back to its normal ground state. This prolongs the relaxation progress, ensuring that the glow of released photons lasts for longer.

So, there it is. Objects glow in the dark due to the phenomena of phosphorescence – the process by which electrons are excited to ‘forbidden’ quantum spin states. As the electrons are allowed to relax, they emit a photon of light corresponding to the distance between the energy levels, producing the subtle glow which is now associated with watch hands and plastic stars. In conclusion, the entire glow-in-the-dark industry is reliant upon a small group of rebellious electrons not doing what they should. Pretty neat, huh?

Tabitha Watson