Fragrance Chemistry: Another Look

In our previous blog post, we introduced concepts from organic chemistry, such as esters, commercial uses of esters, and the process of diffusion. Before we continue in our discussion about esters and fragrances, it is probably important to learn about how smell actually occurs.

How Smell Occurs (the Chem Way!)

Everything that we smell, whether it is food, smoke, wood, soap or shampoo, emits molecules that reach our nose. The molecules that are emitted are all volatile and relatively light. As we have learned, to be a volatile substance, it must be easily to evaporate. Objects that have no smell, such as NaCl, behave this way because they are non-volatile solids.

Behind the inside of one’s nose lie a set of neurons. Unlike many other sets of neurons in our body, they are regularly exposed to oxygen. Also, these neurons have cilia, or tiny hairs, that are special to the nose. the molecule emitted from our volatile substance  attach to the cilia in our nostrils and trigger a sensation in the neurons of our nose. The neurons send a signal to our brain that translates it into a smell.

But, the inquisitive mind may ask, what molecules are emitted from our volatile objects that enter our nostrils? Many natural objects and plants emit molecules that are present when the object undergoes esterification. A banana, for instance, emits the ester isoamyl acetate (CH3COOC5H11.) Oranges produce Octyl Acetate (CH3COOC8H17) when they undergo the same process.


How Perfume Works

As you may or may not be aware, perfume is very dilute. Someone may think it is because the producer’s of the perfume are trying to minimize their costs, possibly to the detriment of the product, but this is not the case. In mixtures such as perfume, there are a variety of different alcohols in the same liquid. Alcohols all are very strong-scented; they emit many molecules that are received by the cilia in your nostrils. If it were a very concentrated substance, perfume would give off all the smells of the different alcohols within it simultaneously. Although they might be sweet on their own, the smells together would not be nearly as enjoyable, as we can no longer distinguish one from the other.

Perfumes contain different alcohols mostly due to the way they are supposed to work. There are three stages to perfume smells; top notes, heart notes, and base notes. Top note smells occur within 15 minutes of spraying the perfume on your skin. These chemicals are the first to evaporate, and thus the first molecules to be received by your nostrils. These scents are strange or exotic, and are made that way to interest consumers, yet not stay too long to be sick of them. Heart note smells occur 3-4 hours after application. These are generally the floral smells of a perfume. Base note smells occur 5-8 hours after application, and are usually musky or mossy. The relation to kinetics is the rate it takes for each individual scent to be activated. This can be represented using rate laws and reaction coordinate diagrams, to indicate exactly which scents are being activated at what time. The rate for the top notes will be the fastest, followed by the heart notes and base notes.

One must be careful with perfume, as light has enough energy to speed the decay of top note chemicals. Air also corrodes the fragrance through oxidation, and this occurs quicker after application. Also, top notes will evaporate faster on warmer skin that is less oily than on cold and oily skin. It is because of this that one must store their perfume in a dark, room temperature area to maximize its shelf life.

Classifying Perfumes

In the previous section, we mentioned how the duration of perfumes can help in classifying a perfume. Another way for classifying perfumes is by their smell. As we know, esters give the perfume its fragrance. A consultant in the fragrance industry, Michael Edwards, devised a qualitative way of describing fragrances for perfumes. This classification can be seen in the fragrance wheel, as shown in the picture below.

We know that perfumes can have scents, and that esters have the ability to cover up scents. But, how do we actually create a perfume? That question will be answered in the next section.

 How Perfumes Are Made

First, all ingredients necessary for a perfume must be obtained. A perfume can have over 100 different ingredients, so this step is essential. This process may of extracting oils from plants, extracting scents from fatty substances of animals, or using synthetic fragrances developed by chemists. For example, the citrus tree blossom or the myrrh resins can be extracted and used in perfumes.


These ingredients are grouped into 4 categories: primary scents, modifiers, blenders, and fixatives. The primary scents are the most important scents required to give a perfume its scent. The modifiers are often esters, such as having a fruity ester and floral ester to make the scent fruity floral. Modifiers essentially replace one scent with one more geared towards the perfume scent, just like how an ester replaces an odor. The blenders and fixatives add some more scent to the primary scent to make it easier to transition between the three stages (top, heart, and base notes).

After all the scents are gathered, the scents are blended together to create the perfume. After the blending of ingredients, ethyl alcohol and water is added. The amount of alcohol added is based on what strength of the perfume is desired. The concentration of the perfume mixture is often mentioned in units of either volume percent or weight/volume percent. The perfume is then aged in tanks for several weeks and filtered before being put into bottles.

The fragrance industry is a large, growing industry in the world, and new formulas are constantly being developed for new fragrances. It is important to remember that alcohol is added to fragrances to give them scents that come in three notes or phases, the top note, heart note, and base note. Fragrances can be grouped by their qualitative scents by the fragrance wheel as well as by their duration. The process of making fragrances can involve many ingredients of various types, and can be altered to create new fragrances for commercial sale.

We hope you enjoyed reading our series of blog posts! Thank you for your support!

Wallpaper groups and Crystalline groups

Last time, we talked about the various symmetries of simple molecules, and how that can tell us about the electrostatic properties of certain substances. However, symmetry in chemistry doesn’t stop at the level of methane or ammonia, where there’s an easy central atom that we can analyse with respect to. Today, we will learn about the symmetric properties of wallpaper, and how that can help you, the chemist, analyse a salt.

Go to an old fashioned, traditional, reasonably well-off house, maybe your Nan’s place, and look at the wall of the study, or maybe the master bedroom. If we’re lucky, there are patterns in the wallpaper that can be identified, repeated throughout the wall. Looking at the nice (or maybe horrible, for I have no idea how well yours and your grandmum’s tastes match) embroidery, you begin to wonder – How many different patterns can we design a piece of wallpaper?

Before we go further, let’s restrict the constraints of the question that you have asked yourself. First, let’s say that our wallpaper can fill an entire plane – that is, go infinitely far in two cardinal axes. Although we’ve likely destroyed the wallpaper industry, this means we don’t have to worry about the size of the wallpaper, and even better, this means we can consider translations of the wallpaper freely.

Let’s look at the word ‘pattern’. What we really want to know about is the degree of symmetry that the wallpaper has. Regular, nice patterns always conserve the relative position of tiles in some translation, which, as you recall from the second blog post, is the definition of isometry, a more specific version of symmetry. So what we want is a group of isometries that describes the wallpaper.

Also, we want our patterns to ‘fill the space’, so to say. In other words, we don’t want to have any regions in our wallpaper that don’t have any tiles. How we (for now; we’ll see why removing the following will be important later) deal with this is constraining the problem so that we have that our wallpaper must be conserved under two linearly-independent (which just means they can’t be collinear) vector translations. In this way, we have an infinite array of tiles that fill the entire plane.

We also realise that we want there to be some ‘minimal’ tile. We want our wallpaper to be constructible for bounded subsets of the plane. So we say that there is some bounded region that generates the wallpaper by allowing a partition into congruent parts.

So, the question is rephrased as follows:

How many finite groups of isometries of the Euclidean plane are there that contains two linearly-independent translations?

Turns out the answer is rather simple: 17.

wallpapergroups.pngWe can begin by classifying our operations. All the isometric transformations from blog 2 still work here. You can rotate or reflect (point inversion can be described as a reflection and a rotation), and the fact that we’re working on the Euclidean plane means we can translate.

Our constraints mean that there are only certain rotations allowed; specifically, they are order 2, 3, 4, or 6.

We’ll prove that the maximal order is 6; try to show by yourself that order 5 is not possible.

Let O be the centre of rotation of the rotation operator r, for which o(r)=n. Since there is a translation of minimal distance, let A be the image of O under a translation t of minimal distance. The orbit of A over <r> gives a regular n-gon. t^-1 r^-1 t r gives a translation maps A to r(A), as t^-1 maps to O, r^-1 maps to O, t maps to A, and r to r(A).

For n>6, the distance between r(A) and A, which is the length of the side of the regular n-gon, is less than the distance between O and A. This contradicts our assumption that t is the minimal translation vector, which proves our proposition.

Note that this also proves that any rotation has finite order; the orbits rotations of infinite order are dense, which means there is some rotation with an angle of less than 60º.

As there are only 4 rotational generators, this gives us a bound on the number of distinct groups of symmetry.

Why do we care about wallpaper groups? Because we can generalise wallpaper groups to three dimensions, as crystallographic groups. In crystallographic (or point) groups, there are three linearly-independent translations, and we consider isometries of the Euclidean 3-space.

The lattices that we studied in chemistry illustrated the Bravais lattices, but real crystals have further structure. For example, NaCl, table salt, has a face-centred cubic unit cell. In the case of NaCl, the crystal group can be generated by the three translations, three reflections along the x-y, x-z, y-z planes, and the two rotations. However, gas hydrates, which are solids where molecules are trapped by cages of hydrogen-bonded water molecules, like that of methane at low temperatures, have more exotic crystal structures, called the Weaire-Phelan structure.

Lastly, let’s revisit the point of translations. What would happen if we remove the constraint that we need to be conserved under translations, and say the whole space is simply divided into bounded subregions? Turns out, there are non-trivial groups of this sort. Going back to 2-d analogues, these are called Penrose tilings.

Many of these retain reflectional and rotational symmetries, as the one above, but do not have translational symmetry. Also note how this is of order 5 rotational symmetry. Generalised to three dimensions, the theory of quasicrystals is an ongoing field of research – maybe one that you can delve into!

A Look Into Physical Chemistry

As one of the last blog posts for today, we will be discussing the field of chemistry where quantum mechanics and essentially quantum theory has been derived from: physical chemistry. One of the first ideas that was proposed that started quantum theory was proposed by Planck which was the idea that energy was discontinuous. This idea originated from the observation of blackbody radiation. The definition of the blackbody is an object that has the property that no form of radiation is reflected over the body i.e. the blackbody is able to absorb all of the radiation. Logically, this type of object that can perfectly absorb all radiation can also perfectly emit all radiation. As a result, this type of object will be able to radiate the maximum amount of energy possible at a given temperature. Additionally, this type of object would be able to emit this type of energy infinitely. However, based on variety of observations and experiments, researchers saw that this blackbody object was not able to emit energy for an infinite amount of time. The reason for this explanation is the basis of quantum theory.

What happens in quantum mechanics is that energy is limited to a specific set of values. Each of these values is not continuous but the differences in these energy levels is small tiny jumps which are known as quantums. These quantums are equivalent to small energy packets, hence the small difference in energy in different energy levels. Because of this revelation and the assumption that any atom that exist on the surface of a heated solid vibrates at the given frequency, Planck created his most famous equation known as Planck’s equation:

Planck's equationwhere E is the energy, v is frequency, and h is planck’s constant which is equal to 6.62607*10^-34 J*s. However, when this was initially created, it was highly skeptical because his hypothesis could not be applied to anything other than blackbody radiation.

However, another phenomenon in chemistry came to light that fully supported Planck’s hypothesis about the existence of quantums. This phenomenon was known as the photoelectric effect which states that when light is shined on a substance, electrons are ejected from that substance. Through experiments, it has been shown that the frequency of light which is proportional to how much energy the light actually contains, must be above a certain limiter value in order to allow electrons to be fully emitted. In order to explain this effect, which contradicted normal classical chemistry because under the classical world, electrons would be ejected at any frequency as long as the light had enough intensity but this was proven completely false due to experimentation, Einstein proposed that any radiation also had particle like qualities. These particles of light were known as photons. Each of these photons has an energy level that is equal to quantum of energy and it is this value of energy that must be reached in order for an electron to leave a metallic surface. The quantum of energy is described by the following equation:

 E = hv = 1/2*(m)*(u^2) + w

where the first part of the RHS is the kinetic energy while w = work.

Photoelectric EffectThe reason why this effect is so significant is because the relationship between radiation and a particle of matter allowed scientists to understand the wave theory of radiation wasn’t going to be enough to explain the majority of phenomena in the world. This led to the discovery of wave-particle duality, which states that light is both a particle and a wave. This was later shown through G.P. Thomson’s famous double slit experiment which showed the interference patterns that occurs when light enters 2 different slits. This can only occur if light is indeed a wave. All in all, quantum theory has started to allow us to describe many of the phenomena within the world of chemistry and hopefully one day, we can fully explain and understand every phenomena in chemistry through the world of quantum mechanics.

The Chemistry of Harmonicas, Accordions, and Theremins

Mechanics of the harmonica“Music is an art and a passion. It is something that can be enjoyed by almost everyone, and created by almost everyone. It affects our thoughts and affects emotions, but how does it work? What chemistry lies behind the beauty: behind the strings of a guitar and the head of a drum; behind the bell of a trumpet and the reed of a saxophone; behind the bow, gracefully gliding across the strings of a violin?” While the last few blog posts about music and chemistry have focused on the guitar, the drums, and the cymbals, this blog post will briefly describe the chemistry behind accordions, harmonicas, and theremins; each being a unique instrument with very variant sounds.


The harmonica is the number one instrument for travelers. Its rich sound is also adored by many blues musicians. Harmonica is a free reed wind instrument. What that means is the reeds of the harmonica is attached only at one end, and is put to vibration by blowing into the instrument.Basic assembly of a harmonica

The reeds of a harmonica are usually made of brass, stainless steel or bronze. The shape and weight of those reeds determine the pitch of the instrument. If the reed is heavy and flexible, it produces a low-pitched sound. On the other hand, if the reed is light and stiff, it produces a high-pitched sound. This is because the comb of the harmonica has an opening which the reed covers, and the vibration of the reeds causes them to undulate in and out of the gaps of the comb, blocking and letting in air through the comb as the result. This is how the harmonica is able to create the sound. Since heavy and flexible reeds vibrate at a slower rate than light and stiff ones, the frequency of the vibration is lower, hence a lower pitch, and vice versa. This site goes into more detail about how the harmonica produces sounds, whereas this site shows the manufacturing materials and process for producing harmonicas.

Here is a video of Billy Joel performing Piano Man. Take note of the interesting sound that he can create using a harmonica.


An accordionThe accordion is also a reed instrument that has a keyboard. When the keys are pressed, the metal reeds vibrate, which create sound. These free-standing reeds produce sound in a method similar to the harmonica, illustrated above. The length and thickness of the reed determines the pitch of the note it produces. Long reeds produce lower notes than shorter reeds. The frame and most other parts of an accordion are made of poplar wood. This kind of wood is useful because it is sturdy and lightweight.

The mechanics of an accordion

If you want to hear the sound of an accordion, view this following video, which shows a couple of French songs being played by an accordion. You might want to turn down the volume (Not because it sounds bad, but because it’s loud). If you want to read more into the history of accordions, check this out. This link shows the amount of work and precision that goes into producing an accordion.


The theremin was by far the most interesting musical instrument for it’s time; running only using electrical energy, instead of using mechanical energy, it was the first electronic instrument created. The concept was discovered by Léon Theremin, who had been tinkering with an oscillating circuit. He found that moving his hand in and out of the electric field generated by said radio frequency oscillator changed the frequency it produced. This was due to the human body having a natural capacitance (the amount of electric charge it can hold), which interfered with the electric field. This is more on the physics side of things, but if you are interested in electric fields and potential, this is a great place to start. Theremin, being a cellist, instantly went to work on creating an instrument using this knowledge.

 Watch the video above to see the magic in action; it seems almost unreal, doesn’t it? However, while it seems like magic, there is a thorough explanation to why this eerie instrument works, and the best person to explain would have to be the maker himself!

“By using an alternating current of suitable frequency, tones of varying pitch are easily obtainable. A small vertical rod is used as the antenna. When the instrument is in operation, electromagnetic waves of very weak energy are generated around this rod. These waves are of a definite length and frequency. The approach of a hand, which is an electrical conductor, alters the conditions in the electromagnetic field surrounding the antenna, changes its capacity and thus affects the frequency of the alternating current generated by the apparatus. In this manner, a kind of invisible touch is produced in the space surrounding the antenna, and, as in a cello, a finger pressing on a string produces a higher pitch as it approaches the bridge, in this case also, the pitch increases as the finger is brought nearer the antenna.

Likewise, the intensity of the tone can also easily be changed by a simple movement of the hand in space. For this purpose the instrument is equipped with another, in this case circular, antenna around which electromagnetic waves are similarly formed. The approach of a hand toward this antenna causes a change in the degree of the intensity of the alternating current which produces the tone. Thus by raising the hand over the ring-shaped antenna the note sounded grows louder and by lowering the hand it grows softer, until it dies out in the softest pianissimo.” – Leon Theremin

If you want to see Leon Theremin play his own instrument, check out the video below.If you’re interested in theremins, you can build one for yourself at home! In fact, check out this website, which shows projects people have made with theremins.

Conclusive Remarks

We’ve covered a lot of material in the past few blog posts. Hopefully we’ve sparked your interest in chemistry, especially in music. Music brings the human world together, and chemistry is the language through which everything happens. Whether it be through the corrosion of guitar strings, the drum head materials, the alloys in a cymbal, the effects of different frequencies on the brain, the way humans produce vocal sounds, or how accordions, harmonicas, and theremins work, chemistry is everywhere. If you enjoyed reading these, we recommend you check out all the others written by other authors. Have fun!

Finishing Off the Spider’s Web


Figure 1. Representation of silk devices to repair bones

Hello, once again! Where did we leave off last time? Oh, right. We talked about the applications of spider silk and spider venom in real life! Where could we really go from this point, you may ask. Well, since we didn’t want to cut off this great trend of information relating to spiders so abruptly, we figured we would end this series with a closing blog post with some cool new information that you have not heard before, and some interesting links for those even more involved in the learning experience.

First off, we would like to detail some information that we received from an expert in this field! David Kaplan, a Professor and Chair in the Department of Biomedical Engineering at Tufts University, gave us a lot of information about spider silk specifically. He did research on spider silkalong with other scientists, and they found out that spider silk could be used to replace damaged tissue, like discussed in our previous blog post. Let’s get down to some of the information that he sent us in this experiment (“The use of silk-based devices for fracture fixation”).

David Kaplan and his colleagues gave a detailed description of the use of spider silk for health and medicine. “The silk-based devices compare favorably with current poly-lactic-co-glycolic acid fixation systems, however, silk-based devices offer numerous advantages including ease of implantation, conformal fit to the repair site, sterilization by autoclaving and minimal inflammatory response.” Woah. That is a lot of information to take in, so let’s break it down. No pun intended (breaking bones joke).

Figure 1 (top right) shows some uses for silk to repair damaged bones, through the use of binding to the areas that need attention, and fitting to that mold. Like David Kaplan and the other scientists said in their introduction to the experiments, silk-based devices are great because they have a “conformal fit to the repair site.” This is interesting because it opens up a wide range of opportunities with spiders. To think that all of this silk that spiders produce could be used to actually aid people with their recovery processes is truly a miracle in science and chemistry. Wait, there’s that word again, chemistry. Don’t think we forgot about sticking to the chemistry behind this!

Though we’re going to be repeating most of the ideas that we have already mentioned before here, we want to solidify the ideas of why spider silk has these properties of strength and possibility to fit into a bone structure. Spider silk contains the great property of having many polar molecules within it, along with strong covalent bonds between the chains of amino acids. All of these terms should be coming together now, since they have been mentioned in all of the other blog posts. These intermolecular and intramolecular forces all combine with the helical curvature of spider silk to form this extremely strong material. This ability to conform to the space that the spider silk is in also has a chemistry background to it. Spider silk actually has a crystalline, yet amorphous structure. The proteins found in spider silk have both crystalline and amorphous regions, and these amorphous regions are what gives spider elasticity and the ability to conform to space. Several people have went as far as to classify spider silk as a very viscous liquid, but this amorphous portion of spider silk can not be confused as being a liquid. It’s almost like the spider silk is similar to glass, in the way that glass had long been thought of as a liquid, but just takes a very long time to flow.

Figure 2. Demonstrates molecules in amorphous solids vs crystalline

Figure 3. A tropical wandering spider biting on its prey

Wait what? Okay, maybe we’re getting a little carried away here, but it’s true! Many chemists regard glass as a very viscous liquid because the molecules within are still flowing and many would notice that glass in church buildings, being there for a long time, has a thickness at the bottom because many of the molecules have sunken down to that level! However, this myth was altered quite recently when glass was classified officially as an amorphous solid, which are noncrystalline solids which lack a definite lattice pattern (note: a lattice pattern deals with the actual arrangement of the molecules in a substance at a molecular level). Moral of the story: do not confuse amorphousness as being a liquid.

Anyway, let’s get back on track here. Yes, spider silk has this sort of ability to mold to materials, and its due to this idea that components of it that resemble liquids. In fact, most of David Kaplan’s article details the viscosity, or the state of being thick or a semifluid, of silk and silk solutions. Now, we think that’s enough about spider silk, we’ve pretty much told everything that’s new and interesting about it without freaking you guys out with too much chemistry! It’s probably best to talk about spider venom for a short period of time now just to close off all of this discussion.

Many people might think that spider fangs are just teeth that are no more complex than human teeth. However, spider fangs are actually complex systems in order to optimize the process of injecting venom into the victim. Spider fangs are actually composed of extremely fine layers of chitin fibres. Chitin fibres are actually the same materials used in shells of arthropods, such as arachnids, insects, and crustaceans. Although flies, grasshoppers, and other insects that spiders prey on are shielded by chitin, this same material can be used to paralyze or even kill them by spider fangs.

Figure 3 (top right) actually shows a tropical wandering spider biting an insect shielded by chitin with its chitin layered fangs. How ironic! In fact, these layers of chitin fibres are actually crucial influences of the mechanical properties of spider fangs.

Figure 4. Metal ions found in spider fangs

So you may be wondering how these layers of chitin fibre add functionality to spider fangs, so we will delve right into that. The layers of chitin fibre are actually parallel to the surface of the fang because the parallelism offers a lot of mechanical resistance, causing the fang to be more stiff and more forceful when biting its victim. The chitin fibres are actually what allows the spiders to bite into its victims without breaking its fangs and giving it enough time to inject its venom into the prey to paralyze it. There are also other components to the stiffness of spider fangs. Scientists have actually discovered metal ions of calcium and zinc (figure 4) in the protein matrix of the spider fang. These metal ions are found most concentrated on the tip of the fang, making the tip stiff and sharper. The metals also serve another useful purpose of stabilizing the protein matrix of the fang, and this stable protein matrix effectively sense the stress that arises during the penetration of the victim’s shell. Hm, so that’s why venomous spiders manage to keep a healthy pair of fangs for a long time!

Well, it looks like this wraps up our series on spider silk and venom. All of you have learned about polarity, intermolecular forces, intramolecular forces, covalent bonds, amino acid chains, basic nomenclature, viscosity, solubility, and even some organic chemistryWe hope you guys haven’t gotten lost in the midst of all of this learning. A great thing about knowing the details of spider silk and venom is that it seems like an up-and-coming idea in science to use this spider silk for health and medicine, as aforementioned. Who knows, these blogs may have even sparked an interest in spiders for you! At any rate, now all of you reading these blogs should definitely be able to impress your friends at a party with your knowledge of the inner workings of a spider’s web. This is of course before they find the information too tedious…er, overwhelming with knowledge!  Thanks for following this series on the chemistry of spiders.

What Does Aspirin Actually Do?

The relief or avoidance of pain drives nearly all medical research. By studying how pain is relieved and how the sensation can be avoided, it becomes quite obvious why medical students must spend many hours studying in an organic chemistry classroom. Understanding fundamental chemistry is a key component in determining how to formulate treatments and medicines to alleviate pain. Pain is a sensation that is caused by the release of a chemical called prostaglandin. Prostaglandin stimulates nerve endings in the area of the body experiencing pain, sending an electrical signal to the brain to warn it that the body is in harms way. Some medicines and treatments work to heal or protect the part of the body that is being hurt and injured. Other medicines such as acetylsalicylic acid (C9H8O4), more commonly known as aspirin, alleviate the sensation of pain by inhibiting the formation of prostaglandin. By inhibiting prostaglandin production, aspirin reduces pain, rather than treats it. This action can be understood by looking at the specific shapes of the molecules involved.


Aspirin as a Compound, Not a Pill

The chemical compound of aspirin, C9H8O4, is not very complex. Demonstrated in this image provided by Chemspider acetylsalicylic acid can be shown in a way that can be easily understood. The ring seen in the image is a benzene ring. The carbons form a benzene ring, consisting of 6 carbons with delocalized double bonds. Hydrogen is connected to each of these carbons. However, two of the six carbons in C9H8O4 are not single bonded to hydrogen, but rather to two different functional groups, a carboxylic acid group (seen on the left side), and an ether group (seen on the right). This reference can be used to gain a better understanding of basic functional group purposes and structures. To understand aspirin better as a compound, reference this Pubchem article.


Functional Groups at Work

While carboxylic acid simply comes from a carboxyl group (a combination of a carbonyl and hydroxyl group), it is the ether group that is important to look at. An ether group can be considered a combination of an alcohol (phenol group) and a carboxylic acid. When two compounds of these natures combine, they form ether and water as products. Similarly, the hydrolysis of ether produces alcohol and carboxylic acid. The reaction works in both directions, which is crucial to the usage of aspirin. In the case of aspirin, the ether group is a combination of a simple phenol group (OH) and acetic acid (C2H4O2). When the ether group in aspirin is hydrolyzed, acetic acid is formed, and the aspirin molecule becomes salicylic acid. Uses and the importance of these acids will be discussed later in the blog post. The reaction seen in this image can be further explored through the resources provided by Open University. Interestingly, salicylic acid is one of the earliest natural remedies for pain relief and skin treatment, dating back to 400 BC when the physician Hippocrates unknowingly extracted it from a tree to help relieve pain during childbirth. WebMD provides more information on this compound.

Enzymes and the Importance of Shape

Now that all of that elementary chemistry is taken care of, it is time to cut to the chase. An entire blog post could potentially be written about the formation of the chemical prostaglandin (chemical that causes pain), but for the purpose of this post, it is better to just understand the basics. Prostaglandin is formed from arachidonic acid. This reaction is catalyzed by the enzyme cyclooxygenase (COX). For a basic understanding of how enzymes work, reference this animation from McGraw Hill. In the case of this enzyme-catalyzed reaction, arachidonic acid is the substrate catalyzed in the active site of cyclooxygenase to speed the reaction that forms prostaglandin. The process is shown in the image to the left.

Now it is time to tie all of the ideas together. When aspirin is present, the water present inside of the body hydrolyzes it. This causes the ether group to break up. The result of this process is that the acetal group that once belonged to the aspirin combines with an –OH group (phenol group) present in the enzyme COX. This process is described at acetylating the COX cavity. The outcome of this reaction is quite simply the cavity, or the opening of the active site becoming smaller. As shape is very important to enzymes, this change of shape of the cavity is the magic of aspirin. The enzyme is no longer able to catalyze the formation of prostaglandin, therefore relieving the sensation of pain that should be present. The image to the right shows this idea. The Aspirin Foundation provides a nice summary of all of these ideas, as well as a simple animation to show the timeline of this process.

            With a basic understanding of how aspirin prevents the formation of prostaglandin, it is also important to know exactly what would happen if aspirin was not present. Prostaglandins constitute a class of unsaturated fatty acids produced by cells in many parts of the body. They have a variety of physiological effects. For the purpose of this investigation it is most important to note that they are responsible for the activation of the inflammatory response and production of pain and fevers, as they are produced when white blood cells flood damaged tissue areas. More information regarding prostaglandins was compiled here by Elmhurst College. Research on the relationship between prostaglandins and inflammation has been done as well; an example can be found here.

            An idea to close this post with is the usage of aspirin as a prevention of heart disease, heart attacks, and even strokes. These ideas all relate back to the inhibition of prostaglandin production. When aspirin is fighting pain, it is simultaneously fighting inflammation associated with heart disease. Prostaglandins not only cause pain, but cause blood clots as well. By inhibiting their synthesis, aspirin prevent blood clots and clogged arteries. WebMD devotes an article on the subject of aspirin therapy and its relationship with the heart for those more interested in the biology of the topic.


For a more in-depth and interactive lesson on the topic of aspirin starting from a beginner’s level of knowledge and working forward, use this source. For a more complex and detailed description of the process, does an excellent job in providing the information.



The Neurochemistry of Music

Vegetables and classical music. What could these two unrelated things possibly have in common? Well, current day society has implanted a vague sense in our minds that both of them are good for us. We probably all know why vegetables are good for us, but if you don’t, ask the woman who probably told you to eat your vegetables every day as a child. She will probably have an answer somewhere along the lines of a cleaner digestive system and a healthier body. However, if you ask her why classical music is good for us, she’ll most likely just shake her head and ignore the question. Many people do not exactly know why classical music is good for the brain, even though a lot of them play it to their newborns in order to achieve the benefits of the “Mozart Effect”.

Based on a study from 1993, the “Mozart Effect” is the main connection that people think about when the words brain and music come together. Many people know that music from Mozart has been proven to make focusing much easier, but not many know about the true reasons for why this happens. This ignorance sparked the idea for the series of blog posts to come. People should know what is actually occurring in the brain when they hear music.

Reward, Motivation, and Pleasure -how dopamine and opioids affect the brain.

Music is universal. It is commonly recognized that a specific pitch is heard the same way in China as it is in America. If so, then what makes a certain grouping of pitches sound melancholy while another grouping of pitches sound happy? In the field of Neurochemistry, or the study of specific chemicals that play roles in brain activity, the effects of music can be divided up into how human beings respond to different types of music, mainly the four listed in figure 1 with their correspond neurochemical systems.


In order to efficiently discuss the connections of reward, motivation, and pleasure, it is essential to take into consideration what dopamine actually is. Dopamine is an organic chemical that is synthesized by neurons in the brain but are released all throughout the body in small and large dosages. Dopamine is often referred as one of the most influential neurochemicals in the human body as it regulates our thoughts, movements, attention spans, motivation, and learning. An example of a small release of dopamine from the brain would be the enjoyment of eating a peanut while an example of a large release of dopamine from the brain would be the rush of a large man with a big sword running towards you. Now, I invite you to listen to the attached audio file to this blog in order to feel for yourself what the release of dopamine feels like. Do you feel the dopamine neurons in your brain releasing dopamine in small individual packages? That’s right, you probably don’t because this is actually what is happening in your brain:

Figure 2.

As shown by Figure 2, the process of releasing dopamine into cells throughout your body looks a lot like a pepper grinder sprinkling pepper on the outer layer of cells, and essentially it is just that. Tyrosine, a type of amino acid used to make proteins, is what your brain derives from actions such as eating a slice of pizza or driving a motorcycle. These tyrosines form protein-like neurochemicals called L-dihydroxyphenylalanine or L-DOPA, which are precursors of dopamine. Then, just like the small granules of pepper in your pepper grinder, dopamine go through a synapse, or transfer, stage where dopamine is entered into the cell through dopamine receptors, which are basically guarded doorways that only allow dopamine into the cell.


Opioids are chemicals that are used for pain and stress relief by binding to opioid receptors in both the brain and the nervous system. Opioids exert their salutary effects through a process of activating three opioid receptors in the brain. This activation of the opioid receptors is what causes the opioid system to function and allow the brain to emit feelings of pain or pleasure. For example, if you punch a wall after failing a chemistry test, your body senses pain, so it produces opioid to travel to the receptors in the brain and evoke pleasure, alleviating pain felt in your hand. So, failing chemistry tests actually initiate neurochemical reactions of producing opioids to alleviate pain. However, the body does not produce enough opioid naturally to mitigate pain felt from more severe or chronic injuries or diseases. Figure 3 shows the process of mitigating pain through the process of opioids travelling to their respective receptors in the back of the brain to relieve this pain.


Although opioids are produced naturally in the body, music has been shown to stimulate the production of opioids in the brain and therefore enhance the emotions evoked from listening to music, giving the listener a sense of pleasure.

Conclusion: Music is an art form that human civilization has worked on for over a millennium, but only now are neurologists starting to realize that there is a whole new side of music that many people have overlooked.  Being able to specifically state the impact of music on the brain removes a huge uncertainty of whether or not music actually induce a change in emotions. The discovery that music emits dopamine and opioid directly show the correlation between music and neurological processes. This just might explain why that sweet jazz you listen to every morning may be something more important to your brain than you think.