Multigraphs in Chemistry

Today we are going to talk about multigraphs and apply them to chemistry.  A multigraph is just a graph in which multiple edges and loops are allowed.  Multiple edges are the name for having more than one edge between two vertices, and loops are edges both of whose ends are at the same vertex.  It turns out we can once again represent Lewis structures like this.  A lone pair is a loop, a double bond is two edges, and a triple bond is three edges.

Above is a multigraph, courtesy of the great Wikipedia:  http://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Multi-pseudograph.svg/220px-Multi-pseudograph.svg.png.

Note that you have the red multiple edges and the blue loops.

So what are the properties of a mutigraph we are concerned with?  Once again we have vertices, edges, and degree.  The vertices are the gray dots in the above diagram, and the edges are the black, red, and blue in the diagram.  Degree is defined to be the number of edges adjacent to a vertex, where loops are counted twice, one for each end.  In this way the sum of all degrees is still twice the number of vertices.

This is nice.  For starters we can represent any Lewis structure much more completely with this convention.  Graph theoretic properties once again have interesting meanings.  Every edge still represents an electron pair.  The degree of a vertex still represents the number of electrons in its valence shell after bonding, where loops are counted twice for a vertex.  Formal charge has an interesting representation now.  It is the difference between the number of electrons present on the individual atom and the degree in the accompanying graph.

Pictures might be an excellent aid, but it’s better to construct lewis structures yourself!  Draw the Lewis dot structure of your favorite compound, say glucose.  Go on now.  Do it on paper.  Start by making a graph with the atoms as vertices.  Now, turn the lone pairs into loops, so for every lone pair, drawn an edge from that lone pair’s atom to itself.  Finally, draw an edge between two atoms with a single bond, draw two between two with a double bond, and draw three between two with a triple bond.  There you go.

Now, once again these multigraphs can be applied to calculate the formula of certain compounds!  Let’s start with hydrocarbons because they are simple.  Say we have an acyclic hydrocarbon with 5 carbons and 8 hydrogens.  What bonds can it have?

Note that this is an alkane so there are no cycles.  There are also no lone pairs because carbon is not very electronegative and instead makes 4 bonds.  The carbons in total have degree 20 because they need to be adjacent to 4 edges (electron pairs).  Since 8 of these are taken up by carbon-carbon sigma bonds (there are 4, because of our tree with 4 edges, but each is counted twice for each of the carbons), and 8 by C-H bonds, C-C pi bonds are counted a total of 4 times, which means that there are 2 of them.  So either there is a triple bond or two double bounds.

Let’s do another example.  What does carbon monoxide look like?  First, we can draw the simple graph for it, which is a carbon connected to an oxygen.  The edges in the simple graph represent the sigma bonds that do not hold lone pairs, and onto them we will draw the extra multiple edges which represent pi bonds.  Clearly 5 edges need to be drawn in some capacity, since we need 10 total valence electrons.  4 are for the carbon, and 6 for the oxygen.  The only way to do this is to make two extra pi bonds between C and O and then give each of C,O a lone pair.  So we have a graph on two vertices connected by a triple edge, each of which has a loop attached to it.

So we have seen that the idea of interpreting Lewis structures as simple graphs can be extended to interpreting them as multiple graphs.  Once again, this allows us to mathematically capture the structure of many compounds and rationalize their structures to some extent using degree arguments.  Once again, there is still nothing about the actual shape of the molecules involved here, but that is covered very nicely in our previous posts on Group Theory.  Stay tuned for next time!

Sonochemistry: Part 2

In our group’s previous blog post, acoustic cavitation was explained and how it affected both homogeneous and heterogeneous solutions. To summarize, acoustic cavitation is when the intermolecular forces cannot withstand the mechanical activation put on them. This process ultimately forms cavitation bubbles, or small bubbles of gas, that expand until they become too big and burst.

Many sonochemical reactions are done in an ultrasonic bath because of its experience with cavitation bubbles. Normally, ultrasonic baths help clean contaminated objects by using cavitation bubbles to excite a liquid, which puts force against the contamination. Ultrasonic baths are very easy to use, which is another reason why many chemists use them for many sonochemical reactions. Also, ultrasonic baths can be easily obtained. This is an important advantage for scientists because many types of sonochemical equipment are very expensive and are hard to find. Other advantages include its ability to distribute sound evenly throughout the bath, there is little to no other technology needed to operate the bath, and it works well for high frequency applications. However, there are also quite a few disadvantages.

In ultrasonic baths, it is extremely hard to control the temperature. This is because ultrasonic baths usually warm up when they are in use, resulting in an inconsistent temperature. Many sonochemical reactions need to be at a certain temperature, so this serves as a major disadvantage. Some baths come with cooling jackets, but if a cooling jacket is not available, the person doing the experiment must come up with a new way to regulate the temperature. In addition, the power that goes into the reaction is not very large. This means that in some reactions, there is not enough power to carry out the reaction. The amount of power that goes into the reaction depends on a variety of factors. These factors include the size of the bath, the type of the reaction vessel, and where the reaction vessel is situated. This harsh disadvantage causes scientists to think about purchasing a new ultrasonic bath, which can be aggravating for most. Finally, there are some types of ultrasonic baths that are specifically designed for sonochemistry. These types of baths are usually much more expensive than regular ultrasonic baths. These disadvantages when conducting sonochemical reactions in an ultrasonic bath can lead scientists conduct regular thermodynamical reactions rather than using sonochemistry. 

In general, there still are some beneficial effects that come from sonochemical reactions. Nanoparticles can easily be formed at a steady rate and with similar shapes from sonochemical reactions. Also, ultrasonic cavitation uses forces to turn solids into tiny particles instead.  Conducting sonochemical reactions to liquids can help eliminate gas particles when they are unnecessary in the reaction. Some other major benefits of sonochemical reactions include removing contamination from water and soil, breaking down smoke and other fumes, removing pollutants from organisms, called bioremediation, and many others. When looking at all the disadvantages shown above, sonochemistry does not look like an efficient way to conduct a reaction. However, all of these advantages and benefits from sonochemical reactions shows why many scientists today are using sonochemistry to conduct many reactions that regular thermodynamic reactions cannot.

More Sonochemistry!

As discussed in the previous blog post, the most practical use for sonochemistry in the lab is for reactions involving liquids and solids, because of the acoustic cavitation process.  Again, acoustic cavitation refers to the ultrasound-induced implosive collapse of a gas bubble in a liquid, and it occurs when the alternating regions of high pressure and low pressure in the sound wave cause the bubble to becomes too large for the intermolecular forces to hold it together, as pictured below.

Acoustic cavitation occurs both when a homogeneous liquid solution is exposed to ultrasound and when a heterogeneous solution with solids is exposed to ultrasound. However, the specific effects of this process are significantly different for each of the two phases, so acoustic cavitation in homogeneous liquid solutions must be distinguished from acoustic cavitation in heterogeneous solutions with liquid-solid interfaces.

For acoustic cavitation in homogeneous liquid solutions, the bubble collapse produces extremely large amounts of energy by converting sound energy to kinetic energy of the liquid molecules, and then to heat energy.  The site of the bubble collapse becomes a localized high energy spot in the solution, having temperatures of about 5200 K and pressures of hundreds of atmospheres, according to experiments done by Dr. Kenneth S. Suslick, a chemistry professor at the University of Illinois.  These extreme conditions inside the cavities induce many effects in the rest of the system, one notable effect being chemical reactions.  The heat energy in the cavities can be used to overcome the activation energy barrier, and the unequal distribution of pressure as a result of the high pressure cavities spontaneously mixes the solution, which of course, causes the reaction to occur at a faster rate.  Therefore, sonochemical reactions involving homogeneous liquid solutions occur in the same way as traditional reactions (reactions that are induced simply by directly adding heat) just at faster rates.  Another effect that the localized high energy cavities can have on homogeneous liquid solutions, under certain conditions, is sonoluminescence.  Sonoluminescencerefers to the ultrasound-induced emission of light from imploding bubbles.  The exact mechanism of sonoluminescence is uncertain, but it occurs when various atoms present in the cavity become ionized because of the extremely high temperatures, and then recombine with the removed electrons and release photons.  Here is an image of sonoluminescence reproduced in a lab.


For acoustic cavitation in heterogeneous solutions with a liquid-solid interface, the bubbles still collapse and create local high energy spots, but one major difference is that the collapses occur in irregular shapes, as opposed to the spherical shapes of the collapses in homogeneous liquid solutions.  The cavities occur in irregular shapes because of the uneven distribution of solid particles around the bubble, which of course restricts the bubbles’ spacial arrangements.  It is partly because of these irregularly shaped cavities that sonoluminescence does not generally occur in heterogeneous solutions with a liquid-solid interface; sonoluminescence is a process that only occurs in homogeneous liquid solutions.  Another major difference is that the extreme conditions of the local high energy cavities have different effects on liquid-solid interfaces than they do on just liquid interfaces.  In liquid interfaces, the extreme conditions really only result in the liquids mixing with each other, but in liquid-solid interfaces, the extreme conditions can generate jets of high speed liquid, as shown in the image below.

 

These jets of high – speed liquid can reach speeds of up to 100 m/s can accelerate the solid particles in the solution, if they come into contact with them, which often results in high velocity collisions between solid particles (see video above starting at 2:05).  These collisions can cause significant damage to the solid particles, including changing the surface morphology and composition.  There are also high-pressure shock waves associated with the high-speed jets, that can have pressures as large as 10^4 atm.  These shockwaves themselves can also cause deformation of the solid particles.  These effects on the solids are significant for the chemical system as a whole, because they can drastically change the mechanisms of the chemical reactions that occur, or even cause completely different reactions to occur, reactions that would never happen if only heat was added to the system.

Breaking Down the Chemistry of Soap

Created by Matthew Tittensor, Nicholas Lang, and Sohum Sanghvi

Introduction

We have examined many aspects of soap and shampoo thus far; Creation, Chemical Composition, interaction with water, and even why soap bubbles. This section will take a closer look into some chemistry aspects involved with soap, as well as as the creation and mass production of soap products on a small and large scale.

A Closer Look at the Soap-Making Process

In our previous blog post, we discussed some basic properties of how soap is made using the saponification reaction. With the help of La Shonda Tyree, owner of Handmade Soap Coach, we were able to understand various thermodynamic and kinetic properties of this reaction.

Thermodynamics

The first part of the saponification reaction is ionization, which takes place when sodium hydroxide is mixed with water. This ionizes, or breaks down the sodium hydroxide into separate sodium ions and hydroxide ions. When this happens, the water temperature increases to as much as 200°, and thus the reaction is exothermic to get rid of this excess heat. Dissolution of NaOH Demo

In the previous blog post, we discussed the formation of triglyceride molecules from fatty acids and glycerol. For the next step of saponification, the triglyceride needs to be broken down into fatty acids and glycerol through a two step process called steam hydrolysis. The steam hydrolysis yields a fatty acid without its salt as well as glycerol. Then, the sodium ions (from the ionization) hook up with the fatty acids to form a fatty acid salt, or a sodium soap. The hydroxide ions attach to the glycerol to form glycerin. Note that because of the high-temperature steam hydrolysis, the overall enthalpy of the saponification reaction isendothermic.Saponification Reaction
The fat/oil can be considered as the triglyceride being treated by the Na+ and OH- ions. Note that heat is required for the reaction to be completed. 

Temperature is an important aspect of the reaction. When combining the triglyceride and sodium hydroxide solution, having a temperature of less than 120° is ideal, since a higher temperature will speed up the reaction too much. The addition of scent ingredients, such as honey, milk, cinnamon, and clove can affect the reaction’s heat by increasing the temperature of the raw soap. These ingredients should be handled properly, since having too many ingredients will cause the heat to increase too much and cause the soap to separate during the hottest phase of saponification (called the gel phase) during which the soap is in a mold. If the ingredients are properly added to the soap, the soap will harden without falling apart in the cooling and hardening phase.

Kinetics:

As mentioned before, the use of heat definitely impacts the rate of the saponification reaction. If the reaction takes place at a temperature higher than 120°, the raw soap will saponify too quickly and become thick. Additionally, the crafter would not have enough time add scent, color, and herbs to the raw soap. Having a thick raw soap may make it difficult to pour into molds.

The reaction rates for saponification are based on the method that is used to create the soap. The two common methods for producing soap are the cold process and the hot process. The cold process for making soap takes 18 to 24 hours to complete the saponification process. The hot process requires only two hours for the saponification reaction because it is reheated by a double boiler. The soap from the cold process requires at least 2 weeks to “cure” in which the soap loses water to eventually become hard. The hot process usually requires only one week to harden. Cold process soap tends to be of higher quality, and the remaining glycerin from the saponification reaction is usually added to the soap as a natural skin softener. The cold process soap also tends to have more designs since it is not heated in extremely high temperatures.

The Difference Between Liquid and Solid Soap:

While soaps come in many varieties, the most easily distinguishable types are hard and soft soaps.  Soap is made during the process in which a base reacts with a fat, either a vegetable oil or an animal fat.  This base ultimately determines the final state of the soap.  A sodium hydroxide base results in a harder soap unlike the soap produced by potassium hydroxide. Another factor is what kind of fat is used.  A soft oil will make liquid soap easier to form more purely and with a more clear complexion.   The difference of physical states between the two caustic bases is practical because it allows for different functions.  For instance KOH is used often in making shaving cream as it is very soluble in water.  Other reasons for having both varieties of soap include catering to a wider market of people; many people have a distinct preference in soap and having variety allows for many people to be reached.  makes a liquid soap as opposed to 

Mass Production of Soap:

    In large amounts, soap is created in factories for commercial purposes, but through a variety of different ways. One such fashion, as described by the Alabu Soap Company, begins with over an ounce of goat milk, coconut oil, food-grade oils, and soybean oil. After the oils are melted, olive oil is added. In some specific soaps, exotic oils are added as well, such as Squalane and Shea Butter. The mixture is mixed with lye and poured into molds, to set for 12 hours. After this period, it is put through a conveyor belt with high-tension strings on the end to be cut into individual bars, as the mold created a solid about 5 feet long. After 4 weeks, the soap is ready to be packaged and sent away.

Another way of creating soaps is called the hot process.In contrast to cold processes of making soap, hot processed soap saponifies during or immediately after the mixture is handled by people/machines, whereas the cold process takes a while longer to saponify. In hot processes, the hydroxide and lipids are mixed just below the boiling point of the solution, allowing them to saponify faster. The advantage of doing so is that one does not need to know the exact amount of Hydroxide in the mixture.

Performing the cold processing method of soap-making requires more careful consideration and planning. The exact amount of oils and fats must be known. Also, the saponification values of the oils and fats must be consulted in the corresponding saponification chart. Too much lye, for instance, can make soap irritable to the skin.

During this process, lye is dissolved in water, and the oils are made into a warm liquid state,either by heating a liquid or melting a solid. They are mixed until two stages are fully emulsified.

Bonus Video: The How It’s Made series has a video on the production of soap bars. This further explains the commercial production of soap.

We would like to give special thanks to Ms. La Shonda Tyree of Soap Coach for her input for our blog post.

Will It Go ‘Round in Circles: PAHs

What are PAHs?

PAHs, short for Polycyclic Aromatic Hydrocarbons, are groups of naturally occurring or man-made chemicals that result from the incomplete burning of many fuels such as coal, oil and even gas. When drawn, they look like multiple rings of benzene bonded together to form chains or sheets or… other odd shapes. You’re probably thinking, “How are rings going to hurt me?” Yet they do. They have been linked to cancer and can even hinder reproductive health. Clearly, in our current age and society the abundance of PAHs is potentially much higher than any previous generation. It is also necessary to notice that substances which produce the most PAHs are the compounds with the most moles of Carbon. Other than messing around, PAHs have two primary uses: research and dyes. They are also used to make plastics and pesticides. 

That’s Great, but what do we actually see?

PAHs in their base forms, because they are made of only carbon and hydrogen, are organic molecules and are thus nonpolar. Thus, they barely dissolve in water if at all, but they love to dissolve in fats, oils, and other organic solvents. PAHs are all solids, but their form depends on which method is used to crystallize them–some end up forming needles or plates. Their colors vary: for instance, anthracene is colorless in its purest state, benzo(a)pyrene is pale yellow, and pyrene can be either depending on the method it is crystallized.

 

I Thought Rings Were for Marriage

You’re probably thinking, “Oh, it’s an organic molecule, right? It can’t possibly be bad for me…” Apparently, the only type of rings the body tolerates come in the form of engagement and marriage. The body really doesn’t want PAHs inside. For starters, 200 of them are found in cigarette smoke, and many of these have the ability to hinder reproduction. Then they have the ability to indirectly cause cancer.

Benzo[a]pyrene is one of the worst PAHs there are; its effects have been well documented. Chimney sweeps often found themselves getting scrotal cancer due to this compound–in the mid 19th century. In today’s world, benzo[a]pyrene has been found in cigarette smoke, being one of the molecules that could potentially cause lung cancer, among others, by binding to DNA. In doing so, they may end up interfering with DNA replication. The mechanisms by which the DNA is metabolized are far too complex to be understood here (at least at the high school level for someone who hasn’t done any research), but know this: the body metabolizes it to form its toxic forms. Not only that, but it hampers your immune system. Overall, the body metabolizes benzo[a]pyrene and many other PAHS through microsomal enzymes, forming compounds that bind to DNA and introduce mutations.

And You Might Be Wearing Them Now

Most PAHS lack practical everyday uses, barring that some of them are toxic. Most of them that are used are used for research purposes only. Yet, as previously mentioned, some could be on you right now in your clothing. They were used in the process of making the color. The PAHs that have dyeing abilities include but are not limited to anthracene, carbazole, and pyrene. Anthracene is used to make red dyes, carbazole for violet, and pyrene for fluorescence. This technology has been used for quite a while; the patent for anthracene and its process was filed in 1925. Also, while its status as a PAH is debatable, naphthalene has been found in mothballs, a critical component of clothing storage, though it has been phased out because it has a tendency to catch on fire. But in the more practical sense, PAHs show up in many things derived from coal tars, including asphalt (the stuff cars drive on) and even cosmetics (things you put on your face).

 

And in a way that could actually benefit humanity, some PAHs are implemented into dye-sensitized solar cells. Dyes are used to boost output in otherwise unfavorable conditions while also diminishing costs by eliminating some of the expensive materials used in it. These dyes are often coated on the titanium dioxide found in the solar panel. The dyes can be based off of PAHs, for they give them superb photoconducting skills. For instance, carbazole is made electron-rich due to its nitrogen atom, making it useful for the  electron transfer necessary to induce current. And a dye known as TC501, bridged by anthracene, improved the open-circuit photovoltages and short-circuit photocurrent densities of a dye-sensitized solar cell, so much so that the solar conversion efficiency jumped to 7.03%, which is a relatively remarkable number. Many of the mechanisms by which PAHs assist in photoelectric conversions are specific to that PAH, and some of them are not yet fully understood. And speaking of extraterrestrial energy…

There’s Plenty of Space for This Poison Elsewhere

Naturally, we are able to observe things specifically on the planet Earth, otherwise we need either telescopes or overactive imaginations (we recommend some of both). Using this, science can now tell us that certain molecules also occur outside in the cold, not-empty void of interstellar space. The spectra of PAHs have been found in conjunction with large molecular and dust clouds; it is speculated that they form by photoionisation, which is also what causes hydrogen clouds to form in these places. Photoionisation, as the name may suggest, involves light providing the energy to ionise molecules and cause them to form into compounds. Sounds like a great way to cook

.

For those who have an inexplicable fear of deep space, there’s something for you as well. PAHs have also been found in the atmosphere of Titan. Titan, as you should probably be required to know, is Saturn’s largest moon. It’s unique because it is the only moon to maintain a substantive atmosphere. To the average flying robot, it is an orange ball. Titan is a lot closer than all interstellar space, so we can accurately detect what is in the ball of Orange. It turns out that, besides a load of nitrogen (boring), there are PAHs as well. Those that the European Space Agency found are a bit more complex than the ones our beleaguered lungs are most familiar with, but they are still the same sort of molecules. It may be worth adding here that Titan also seems to have surface lakes of hydrocarbons, which may be of similar origin. Seti, or the Search for ExtraTerrestrial Intelligence, has found indications that these molecules, besides being distributed in gas clouds, are also found in interstellar dust and locked up in water ice. These are the basic ingredients in planet formation and by extension that of more complex organic forms.

Good Poison?

You learned earlier that PAHs often result from the burning of organic or fossil-derived materials. The existence of such complex  molecules in both interstellar clouds and the atmosphere of a moon suggest that maybe the molecules related to life are not so rare as we might’ve thought, and it certainly opens some new eyes and avenues for which to explore. Scientists have been forever intrigued by the presumably unique condition of life on the planet Earth. With the discovery of new worlds beyond our solar system, and the recent insights into the conditions on some places a bit closer, perhaps we will discover that, just maybe, we are not alone.

Graph Theory and Hydrocarbons

In this post, we will see to an even greater extent than before how (simple) graph theory can be applied to the theory of alkanes and other hydrocarbons.  We will discuss bipartite graphs, and see their application to chemistry.

Say there is some group of boys and girls that go to some dance.  We can draw a graph responding to this group, pairing two people of opposite genders if they dance with one another.  The resulting graph has an interesting property.  We say it is bipartite.  This means we can divide the vertices into two groups, the red vertices (girls) and the blue vertices (boys), such that no two vertices of the same color (gender) have an edge between them.

Now, we saw in the last post that any hydrocarbon with only single bonds can be represented as a graph all of whose degrees are at most 4.  It turns out in chemistry there is a particular kind of hydrocarbon called an alternant hydrocarbon.  The quickest definition is that it is a hydrocarbon whose carbon skeleton is a bipartite graph.  We can see then that a class of chemical compounds can be described mathematically.  All acyclic hydrocarbons are alternant hydrocarbons, because all trees are bipartite (seehttps://docs.google.com/document/d/1m2gRfmlF1MAVmbwc7NDGosU7bMThYuwaCqAfPi6EXq0/edit).  The ones with an even number of atoms (vertices) even alternant and those with an odd number are old alternant.  It turns out that these alternant carbons have several neat properties. These links: (http://www.bama.ua.edu/~blacksto/CH435_CH531/handouts/alternant%20pi%20systems.pdf

) and http://chemistry.umeche.maine.edu/CHY556/Alternant.html

describe many of them, and of course to be bipartite is to be “starrable.”  The pi electrons and molecular orbitals (those not involved in the single bonds, but rather in additional bonds) are evenly distributed, and the electron densities are the same everywhere.  This even distribution means there are no partial positive charges anywhere.  Therefore, there is no charge difference anywhere; it is not merely that just different dipoles cancel out.

Whoa, wait a second.  Aren’t there never any charge differences in a hydrocarbon, though?  Aren’t the C-H bonds nonpolar?  Well, any acyclic hydrocarbon, and quite a few cyclic ones such as benzene, are alternating and thus nonpolar, so hydrocarbons people deal with daily tend to be nonpolar.  But it is possible for a molecule to have only C-H bonds and for it to be polar!  So why is this?  And why is it alternant hydrocarbons not have a dipole moment?

Molecular model of Azulene

Consider Azulene.

There are two cycles of carbon with an odd length- the cycle on the left with 7 vertices and the one on the right with 5 vertices.  So it is not bipartite.  And in fact it is polar.  Whoa!  What’s going on there?  It turns out, if you look at all possible resonance structures, some of the carbon atoms get double bonds more than other ones- it’s not like the alternant hydrocarbon benzene.

To fully explain this, we need to talk about dual graphs.  For any graph, we can construct its dual graph whose edges correspond to vertices of the old graph, and whose vertices correspond to edges of the new graph.  We connected two vertices in the new graph if the edges they represented in the old graph shared a vertex.  Note that a cycle on N vertices in a graph will correspond exactly to a cycle on N vertices in its dual graph (the roles of the vertices and edges switch).  So a graph is bipartite if and only if its dual graph is bipartite.  Now, in an alternant hydrocarbon (say benzene), we can therefore color the bonds (edges of the graph, vertical of the dual graph) red and blue so that no two are adjacent.  Then in one resonance (say in benzene), all of the red bonds will be double and the blue single, whereas in the other all the reds will be single and the blues double.  So you have this nice symmetry.  With azulene, however, there is no such symmetry.  So there ends up being a net dipole.

Who knew that hydrocarbons could be polar?  The fact that they are not is dependent on this notion of bipartiteness or alternateness, which we so often take for granted but not every hydrocarbon has.

Cool, huh?  Next time, we will talk about multigraphs.

Spiders: Chemistry of Silk and Venom

Hello everyone. Welcome to our next blog post, where we will go in depth into the chemistry behind spiders, like their webs and their venom. In our previous blog post, you may have noticed we started with talking about spider webs; if you are still not so sure about the basics of spider silk, visit our first post so some of this makes sense! Anyway, let’s get right to it. We mentioned previously that spider silk contains chains of proteins linked together partially with intermolecular forces. Now, we will introduce the idea that spider silk is a “natural polypeptide”, polymeric protein. A polypeptide is a continuous peptide chain, or a long chain of proteins, like we stated earlier but are now just giving it an official name. A polymer is a chain of repeatable links, that are called monomers. These are usually terms that go along with biological compounds. So, since spider silk is a polymer, you should probably understand how polymers are created from monomers. This usually involves a continuous chain of covalent bonds. Covalent bonds are the sharing of a pair of electrons between two atoms in a molecule, and these bonds are what holds the proteins together to form polypeptides. These proteins are what provide the structure for the silk.

The aforementioned proteins are called fibroins. Fibroin is formed from a combination of two proteins, spidroin 1 and 2. Hm, wonder where they got that name from! Anyway, continuing on the chemical structure of spider silk, proteins are made up of long chains of amino acids that determine the properties of that protein. The major amino acids in the protein fibroin are glycine and alanine (as shown below); others include glutamine, serine, leucine, valine, proline, tyrosine, and arginine (you may remember this name from before).

Molecular structure of alanine

 

Molecular structure of glycine

There is a repetition of alanine and glycine in spider silk, called the beta sheet, which accounts for the crystalline fraction of spider webs. Here’s an interesting representation of what the chains and beta sheets look like on a microscopic level:

Basically, what you are seeing here is the proposed model for spider dragline silk, as you may recall as one of the specific types of silk. The Alanine are the red lines in this diagram, while the glycine are the blue lines. The important thing that we want you to notice from this diagram is mostly the fact that alanine and glycine are so closely intertwined in spider silk, as well as the geometry of the  molecular structures here, and how a lot of it eventually turns into a sort of helical structure, which is very stable, as demonstrated by spider silk’s strength.

But, who am I kidding, this isn’t nearly as much chemistry as you want to hear! Let’s get to the good stuff. According to an in-depth study of spider silk, there are hydrogen bonds between carbonyl and amide groups, and Van der Waal interactions in the short chain amino acids found between the molecules. Hm….I don’t think we’ve heard this term yet. Van der Waal interactions are forces that occur between molecules, and are basically a fancy way for saying intermolecular forces, or IMF. Though a large reason for spider silk’s strength is its beta sheet, or 180 degree turns to form helices, those intermolecular forces that we discussed previously seem to keep coming back.  If you’re further interested in the sizes and construction of the spider silk that give it more of its tensile properties, this link gives a good explanation as to why intermolecular/intramolecular forces as well as construction of the spider silk all contribute to its strength and tensile properties.

How about we mix it up a bit now, let’s go into more detail on spider venom. Just as a refresher, we have established so far that general venom corrodes tissue by the process of hydrolysis, or the breakdown of molecules or structures with the use of water. This also combines with enzymes, which make the reaction occur faster. But, it is appropriate to examine more information on this topic now. Though we have mentioned cytotoxic venom before, we will now discuss mostly neurotoxic venom, because it is proven that this is the most common venom that spiders possess. In general, this venom contains consists of three compounds: polyaminespolypeptides, and proteins. Wow, spiders must really be lazy, because their venom is made up of the same compounds that their silk is made out of! Since we don’t really want to quench your chemistry thirst completely yet, we’re just going to explain the structure of these three things in this blog (don’t worry, we’ll discuss functionalities again in our next blog post).

Polyamines consist of a hydrophobic, or resistant to water, carboxylic acid region and a hydrophilic, or attractive to water, amide chain. Polypeptides are similar in structure, but much heavier in molecular mass. What’s molecular mass, you say? Well, molecular mass is basically the mass of a molecule, which is determined by what elements and atoms are in it.A single polypeptide molecule folds up to form a beta sheet, the same one discussed previously. The last compounds are the neurotoxic proteins, highly toxic to invertebrates.  Here are pictures of all three compounds, in order of discussion:

General structure of a spider polyamine

Molecular structure of a spider polyamine

Molecular structure example of a polypeptide

General Structure of a Protein

NOTE: The R’s are side chains of carbons; peptide bonds are covalent bonds between carboxyl groups and amino groups of other molecules.

Now, let’s take some time to go over some of the key points we just mentioned. First, we went over the basics of spider silk, including its structure and composition. We learned that spider silk is a “natural polypeptide”, which ends up being many links and chains of polymers held together by covalent bonds. We also learned a little bit of the biology relating to spider silk (but who wants to be reminded of specific biological terms?), and within this biology, we found that the structure of spider silk is simply a repetition of simple chemical structures forming beta sheets. The last point we went over is the intermolecular forces (specifically hydrogen bonding) that give spider silk its adhesive properties, something that we have already mentioned in our first blog post.

Our second main topic of this post was the neurotoxic venomthat most spiders posses. We went over the three compounds that venom consists of, which are polyamines, polypeptides, and proteins; we also went over each compound’s purpose in the functioning of venom. If you really want to skip ahead and know more about venom, check out this link. Anyway, stay tuned for our next blog post for more in-depth breakdowns of the functionalities of all the parts of spider venom, as well as the tensile properties of spider silk and why it is resistant to solvents and enzymes. We’ll end this with a cinematic picture of a spider web (No worries, there are no scary spiders on it)! Until next time!

File:Spider web with dew drops03.jpg