Symmetrical Hydrogen Bonds

In one of the first blog posts, we questioned the importance of symmetry in chemistry and gave multiple ways how symmetry is involved in basically every aspect of chemistry. In this blog post, we are going to focus on one of these ways: the symmetrical "hydrogen bond". The symmetrical "hydrogen bond" has the potential to be over forty times stronger than a regular "hydrogen bond", but you are probably wondering why "hydrogen bonds" are so important. After mentioning "hydrogen bonding" multiple times, you have probably noticed that I put it in quotations. This is because hydrogen bonding is not actually bonding, but rather an attraction between molecules.

"Hydrogen Bonding"
The red atoms represent oxygen
The yellow atoms represent hydrogen

What are "hydrogen bonds"? "Hydrogen bonds" are an intermolecular force (a special case of covalent bonding) which are essential to basically all biological systems, and are formed when an atom contains a hydrogen bonded to a fluorine, oxygen, nitrogen, and sometimes chlorine. One can even argue that without "hydrogen bonding", many creatures would cease to exist! "Hydrogen bonding" explains many of the extraordinary properties of water such as its surface tension, ability to act as a universal solvent, cohesion, capillary action, and much more. As seen in the image on the right, the water molecules are sticking together, known as cohesion. The water molecules are polar, as the hydrogen is pseudo-positive and the oxygen is pseudo-negative, and each molecule is attracted to each other (the hydrogen of one is attracted to the oxygen of the other). This causes an incredibly strong "bond" to be formed, illustrated by the dotted line connecting the red (oxygen) and yellow (hydrogen) atoms together, known as "hydrogen bonding".

A property of a hydrogen bond, cohesion, is seen here. The water molecules
are sticking together on top of this penny creating a dome-like shape.

Neon Atom

Boron Atom

"Hydrogen bonds" are also responsible for the stabilization of large macromolecules such as proteins and nucleic acids, key for all living specimens. So as you can tell, "hydrogen bonds" are incredibly important, and an even stronger bond could create an even more versatile molecule! A symmetrical "hydrogen bond", seen below, is exactly what it sounds like: a molecule with symmetry (it can be any kind of symmetry) of hydrogen bonds. In prior posts, we have discussed how molecules which are symmetric are more stable. Stable molecules, contain strong bonds, so they are incredibly difficult to "separate". Just to make this a little more clear, I will give you an example. We can say that neon, a noble gas, has symmetry within its second energy level, while boron, does not. From this information, it would seem that neon should have a higher first ionization energy, the energy required to rip off an electron, because this atom wants to be stable and symmetric. So when we look up in a table and find that neon has a first ionization energy of 2081 kJ/mol and boron has one of 800.6 kJ/mol we are not surprised. Therefore, if a "hydrogen bond" is symmetric, it should require more energy to split it; thus, becoming stronger. 

Symmetrical "Hydrogen Bond"

Just to recap, we went over what a "hydrogen bond" is, and why it is important for virtually all living creatures on earth. We then discussed how symmetry leads to stability and stronger bonds/ attractive forces. This then takes me to the point where I can begin talking about the symmetrical hydrogen bond, but I will leave you pondering the implications of a symmetrical hydrogen bond until a future blog post.

   

Group Theory-- A Brief Introduction

In one of our first posts, we briefly introduced the concept of mathematical group theory and how that relates to chemistry. Specifically, different symmetric molecules with different types of symmetryies are placed in different "groups," which have special mathematical and chemical properties of their own.

Before we begin on our chemathical journey, check out this introductory video! It offers a lot of information and explanations to group theory.

We hope you enjoy! We'll discuss more in depth about this topic in upcoming posts! (:

Symmetry with Black Holes?

           Some interesting news was reported on December 13 2012 in regard to black holes and symmetry. And if you don't feel like clicking the link, I will explain it here. But first I will start with the basics.
          A black hole is created when a sun of great mass, collapse on itself. Once it compresses, the gravity at one point in space is so large that a black hole is created. The black hole's gravity is so strong that not even light can escape it. And naturally since light can't even escape a black hole, it is invisible to the human eye. So that begs the question how does one see them. Well, there are multiple methods of doing that. One has a scientist looking at how things around the black hole are affected, but another uses special telescopes that can sense gamma rays, like the Swift satellite and Fermi Gamma-ray space telescope. These are used to detect the jets or beams that come out of the black hole. But wait a minute, you might be thinking how do these "gamma rays" escape a black hole when even light can't. Well, think of these gamma ray beams or GRBs are an energy release of a black hole.

Astronomers examining the properties of black hole jets compared 54 gamma-ray bursts with 234 active galaxies classified as blazars and quasars. Surprisingly, the power and brightness of the jets share striking similarities despite a wide range of black hole mass, age and environment. Regardless of these differences, the jets produce light by tapping into similar percentages of the kinetic energy of particles moving along the jet, suggesting a common underlying physical cause. (Credit: NASA's Goddard Space Flight Center)

Since matter and energy can not be created or destroyed, everything a black hole absorbs has to go somewhere. And as gamma ray aren't really affected by anything, they have no problem getting away from a black hole. However, as interesting as this may sound, I have not got to the cool part yet. If gamma rays are a result of black holes releasing energy, why then do they almost always share the same characteristics no matter the black hole they come from?  This is what has astronomers stumped. A team of scientists examined 54 different GRBs from many different blazars and quasars and found that no matter what, the release of gamma ray jets are always the same. This is yet another example of natural symmetry.  The article then states that the scientists hope to discover more about this phenomenon and I hope they do. Thanks for reading.

Is symmetry discovered?

In direct response to the question that we asked on our very first blog post (whether science is created or discovered), Dr. Sool Cho commented that, 

"Antoine-Laurent de Lavoisier contributed a lot whether it is descovered or created..discovered is closer to answer in my opinion."

To re-cap, we defined in our second post the words "discovery" and "creation" as the following:

Discover: gain sight or knowledge of (something previously unseen or unknown)

Create: to cause to come into being, as something unique that would not naturally evolve or that is not made by ordinary processes.

With regards to symmetry, Dr. Cho's argument makes a lot of sense! After all, our minds are programmed to  try to find and form patterns and symmetries in our lives! So it's no wonder that we have "found" so many symmetric objects and molecules.
Also, when we talked about quasicrystals, for example, we explained how, although we were "sure" that such crystals could not exist at first, the revolutionary crystals were eventually discovered in nature! Such symmetry had existed before we as humans even existed. 

    

(icosahedrite, Al63Cu24Fe13)

However, it can also be argued that Dan Shechtman and his team had first synthesized the molecule, way before a natural example was found! So would that make the concept of quasicrystals a creation?

Similarly, as we discussed a bit before, the formation of 2,3,7,8 TCDD was also a human-made creation! 

(2,3,7,8-tetrachloro-dibenzo-p-dioxin, or 2,3,7,8 TCDD)

The symmetric and toxic chemical was actually a by-product of another synthesis reaction, meaning that we created the beast ourselves...

However, it's just as important to note that this was an accident-- meaning that the creation wasn't intentional! So wouldn't it make sense that this symmetric molecule was rather discovered by chance, than created? Wouldn't that be much more probable?

The fact of the matter is, disappointingly, with only the facts present here, it's not definitive whether symmetry is discovered or created! 

Nonetheless, thank you, Dr. Cho, for your input! We appreciate you reading our blog, and we hope you enjoy and continue reading!

Hexaferrocenylbenzene: Beautiful, unlike its name

A very interesting and uniquely symmetric molecule that we came across is one called "Hexaferrocenylbenzene."

How is it unusual? Well, just look at the picture, and be awed by its symmetry.

Reminds you of a flower, doesn't it? Here's another perspective of it:

Wait! So it's great that it looks really pretty and all...but what exactly is this molecule?

Its chemical formula can be written as C₆[(η⁵-C₅H₄)Fe(η⁵-C₅H₅)]_6. Basically, it's a benzene ring with 6 ferrocene (C10H10Fe) groups attached:

     

(Left: A picture of a benzene ring; Right: A picture of ferrocene.)

Ferrocene is also just two hydrocarbon rings (C5H5) with an iron (represented in purple) atom in the middle. This molecule also has very nice and unique symmetry.)

Just from looking at the picture, you can see just how difficult making such a crowded complicated molecule would be. That's why for decades, scientists thought that synthesizing it would be an impossible task!

Well, that claim was broken in 2006 by chemists in both the US and Denmark. 

A team of Peter Vollhardt, from the University of California at Berkeley, and other colleagues successfully synthesized this miraculous molecule. Scientists who once doubted their existence were in shock.

Vollhardt and his team also explained how it has great potential in being useful in numerous fields, such as electronics, magnetism, optics and catalysis. He also argued that this molecule can be a starting point for creating even more complicated molecules! Crazy, huh?

In addition, the team explained in their paper that the molecule was synthesized "using Negishi coupling of hexaiodidobenzene and diferrocenylzinc, usingtris(dibenzylideneacetone)dipalladium(0) as catalyst, in tetrahydrofuran."

HUH? What does that mean? The picture below explains a lot more clearly:

Essentially, in the process of "Negishi coupling," an "organozinc" molecule (a molecule that includes a carbon-zinc bond), an organic halide, and a nickel/palladium catalyst are used to create new carbon-carbon covalent bonds. And that's exactly what happened in the synthesis of the hexaferrocenylbenzene.

(A clear and brief animation of Negishi coupling)

Yet undoubtedly, the symmetry that it has definitely helped in its formation-- without such a beautifully symmetric form, the molecule would have required a substantially more complicated procedure. 

Nonetheless, with such a complicated process, no wonder so many scientists thought that it would be impossible to make! 

Symmetry In the Smallest Organic Measure

            Symmetry is a very important feature in our lives allowing people to function normally. Without some sense of balance, a regular human would not be able to function normally; maybe not function at all. And this tends to be true for most complex animals, whether they are mammals, fish, or birds. However, does this hold true for microscopic organisms? Well, if one were to simply look at the amoeba, then you would say no, not everything requires symmetry to work. But what if we were to go even smaller? What if we were to look at things like viruses?
            Viruses are very interesting beings, considering the fact that most people do not even consider them to be alive. They only display common features of living things, such as reproduction when they are within a host cell. But that is a story for another day. The thing that will be focused on here will be their outer protein shell, the things that contains their genetic material. The problem is that a regular virus has such a  little amount of genetic material, it can not possibly have the coding for many different types of proteins. 2 scientists named James Watson (1928-) and Francis Crick (1916-) came up with 2 proposals for how a virus might solve this problem. The first proposal is that, "The only reasonable way to build a protein shell with small viral nucleic acids is to use the same type of molecule over and ever again, hence their theory of identical subunits". Then that proposal leads into  the second one which is, "The subunits must be packed so as to provide each with an identical environment in the protein shell or capsid; only possible on cubic(icosahedral) or helical symmetry".   And here is symmetric part of the virus. A body with a cubic symmetry has a number of axes which     when rotated will always yield an identical appearance. And the reason that many viruses display   this type of symmetry is because it is the most efficient form. It is because icosahedral symmetry allows for the lowest-energy configuration of particles interacting isotropically on the surface of a sphere. In layman's terms, the energy-per particle is the smallest possible amount in that form. An icosahedron is composed of 20 facets, each an equilateral triangle, and with 12 vertices. That leads a to a symmetry with 5:3:2 symmetry. All this together leads to 60 identical subunits being required in order to create the shell of a virus. But here is where the problem starts. When microscopes advanced to the point where they could give high resolution photos of a virus, there seemed to be a structural paradox. The number of units seen were never 60 or some multiple of 60, but a number over 60 was often seen. This broke the original idea created by Crick and Watson. What is the solution then? Asymmetrical subunits. By using asymmetrical subunits, a virus could make a shell that still followed the 5:3:2 rule. This was discovered in 1962, when Donald Caspar and Aaron Klug created 2 ideas accounting for the structure properties of icosahedral things with more than 60 subunits. The first was that each asymmetrical subunit occupies a quasi-equivalent position  Which is to say that the bonding properties of subunits in different structural environments are similar but not identical. The second was the idea of triangulation, the description of a triangular face of a large icosahedral structure in terms of its subdivision into smaller triangles termed facets. This process is described by the Triangulation number T, which gives the number of structural units per face. The iscoshedron itself has 20 equilateral triangular facets and therefore 20 T structures given by the rule : T=P*F(SQR) where P can by any number in the series 1,3,7,13,19,21, 31 and F is any integer.

        So what does this all mean. Basically symmetry is everywhere and you can escape that fact as easily as you can escape viruses. Thanks for reading.


     

Relating the Body's Symmetry to Molecular Symmetry

Dr. Michael J. Flannery, a chiropractor, told our blog that, "Having good symmetry in the lower limbs will make the upper symmetry more functional." Lets dive into this topic.

Leonardo da Vinci's
Virtuvian Man

The human body is made up of several different components, and oddly, it is rather symmetric. Leonardo da Vinci was the first man to find this out when he painted the Virtuvian Man at about 1487. In the diagram to the right, da Vinci determined that humans demonstrate symmetry along the y-axis, assuming that the center of the head is in the middle of the y- axis. According to da Vinci, it is no coincidence that humans have two arms of the same length, two legs of the same length, two ears of the same length, and two eyes of the same length which are all the same distance from the center of the body.

But what would happen if a human's symmetry is altered? If a man or woman lost his/ her "symmetry" by losing a leg, due to a random disease such as symmetrical peripheral gangrene (you might not want to click on this if you are squeamish), he would be unstable. That is, he/ she would fall over when trying to get out of bed, or he/ she would fall down when trying to walk. Unless this patient was able to get a prosthetic limb, we can claim that he/ she will not be able to function effectively. After realizing that this person cannot live the rest of his/ her live without a prosthetic, he/ she would eventually go out and buy one. Surprisingly, this is actually quite different for symmetric compounds (of course the compound will not go out to the nearest element store and buy the necessary atom, but you get my gist).

We all know that the more symmetric a compound is, the more stable it is. However, symmetry is not synonymous with effectiveness. Symmetry in protein structures leads to an increased stability, but compounds that are perfectly symmetrical actually can become more functional as they shy away from this flawless symmetry (this is all relative to the desired activity of the compound). This concept is quite different from human beings as a man with one arm will definitely be much more functional if he were to have his arm back... or will he be? It is all relative to the desired function of the person. Is there any activity that YOU think a person who has lost his symmetry will be more effective at?

  

Moving Symmetry?

We found a very interesting paper and corresponding video by researchers at the University of Regensburg that suggests that symmetry may even affect how molecules move in their surroundings.

Huh? How??

This video shows a copper complex that was used in the experiment. They found that,

The symmetry of the molecule determines where on the surface the compound absorbs, in which direction it moves, and whether and how much it rotates.

It's almost scary how much of an effect symmetry plays on materials. Not only does it have both physical and chemical implications regarding numerous characteristics of the material, but it can significantly affect how each individual molecule moves!

This highlights why studying symmetry is so important-- maybe symmetry can be the key to solving the world's mysteries...How poetic!

Can Symmetry be Dangerous?

Before, one of our friends' blogs wrote about the dangers of Agent Orange. Basically, the toxic molecule in question is named "2,3,7,8-tetrachloro-dibenzo-p-dioxin," or 2,3,7,8 TCDD" for short. It is formed as a by-product from the production of herbicides and pesticides, and was used excessively during the Vietnam War. It was especially emphasized in their blog that, "It is actually the most potent synthetic carcinogen ever tested in a laboratory."

But what does Agent Orange have to do with symmetric molecules?

(A 2,3,7,8-TCDD molecule diagram)

Well, you can see from the molecular structure shown above that, in fact, this molecule is almost perfectly symmetric! (For those of you who are group-theory-nuts out there, this molecule possesses D2h symmetry! More to come on that later on in the blog.)

Other characteristics of its symmetry include the following:

• All atoms in the molecule have completely full octets-- in other words, there are no electrons missing from their valence shells.
• There are no net dipole moments, which can be easily seen from the symmetric nature of the molecule.
• No formal charge differences exist among the atoms.
• No angles between atoms are "strained": all bonds are in their ideal angles.

So we can see just how beautifully symmetric this molecule really is.

But what does its symmetry have to do with its side-effects? 

If you think that the molecule's symmetry is just a coincidence, and that the dangerous side-effects of this molecule stem from other properties, you are not fully correct; its symmetry does affect its level of danger! 
Because of the symmetry discussed above, the molecule is VERY stable, which only adds to the damage. This stability gives 2,3,7,8-TCDD a half-life of 7-12 years, which means that the toxin will last for a very long time. So not only are the side-effects of TCDD-exposure devastating, but the risks of being exposed long after its introduction are also very high.

Also, because this dioxin shares structural similarities between it and aromatic hydrocarbons (or molecules made up of carbons and hydrogens and containing at least one benzene ring), the TCDD molecule can fight for the receptor site of aromatic hydrocarbon proteins. This allows the toxin to be absorbed into the body more easily. 

(Examples of aromatic hydrocarbons: Each big circle and hexagon in the diagram represents a benzene ring, which is an actual "ring" composed of 6 carbon atoms and 6 hydrogen atoms.)

So overall Agent Orange shows that despite their beautiful appearance and stability, symmetric molecules can be just as dangerous as any other molecules-- and in this case, even more dangerous.

Lastly, we now have to ask ourselves-- is it really worth pursuing the formation of new chemical products or other symmetric molecules? After all, although 2,3,7,8-TCDD was a by-product, it was still human-made-- we essentially brought this upon ourselves! So is it worth playing around with such molecules, with the giant health risks on our backs? We leave this question open to the reader.

Symmetry with that Glass of Emulsion: Yummy

Now, we have seen the symmetry of the aforementioned quasicrystals and we see the beauty. But we need to understand symmetry and its impact at home, at the breakfast table. You sit down (not that hungry, people are not usually very hungry when they wake up in the morning) at the breakfast table to do just that, to break your fast. You sit down to have a nice glass of emulsion with a pancake that has some of that sweet solid emulsion sitting right on top. Sounds pretty friggen disgusting? Strange how this is so intricately involved with the stark beauty of symmetry.

These are colloidal properties. Colloids are not quite heterogeneous and not quite homogenous. In terms of size, colloids meets the two types of mixtures in the middle at 1.0 x 10^-6. "Suspension of colloidal particles have been widely employed as model systems to study" phase changes. Now when measuring and studying this, spherical pictures of atoms and molecules are always used. Other shapes likes rods have been used as models but for very specific research purposes. It is well known that spheres do not account for the vast array of molecule shape and size. What people need to do is synthesize some of these micro particles. This has been done to some degree. Great minds at Yale University, Jin-Gyu Park,Jason D. Forster, and Eric R. Dufresne, have synthesized colloidal water. These are polymer particles with the same imitated symmetry as water molecules for the purposes of the study and research of condensed matter. 

Figure 1

Figure 2

Multistep polymerization is used. Take a quick peep above this text (Figure 1) and you will get the picture. The spherical micrometer sized colloids are swelled with a monomer solution. It is heated and this drives separation of the monomers (the solvent). Seeded polymerization is what is used. The results were seen under a scanning electron microscope (Figure 2). This is a genuine synthesis of chemical symmetry, all utilizing the lexicon of solutions. A symmetrical molecule, water, has been created using colloidal micro-molecules. This can be expanded beyond the domain of simple molecules like water, for sure. These colloidal properties, using seeded polymerization as the medium, can yield results, results that show that symmetry can be created, artificially, in the solutions market place.  

Are the Foundations of Science as Secure as We Think?

A few posts earlier we had mentioned how Dan Shechtman and his team had once been ridiculed for their theories and discoveries of quasicrystals. For years since the team's first discovery, they were even pressured by other scientists to give up and move to another field. Yet now we know that quasicrystals were actually only early for the time, and that now they are crucial substances that hold many practical and academic applications, especially in the world of crystallography. They have even been shown to exist naturally!

This, however, brings up a troubling question: if such an "established" theory as the Crystallographic Restriction Theorem, which, by the way, was proven not just scientifically but also mathematically, how do we know that other "established" theories that we "know" of are also flawed? How do we know that this is the only case in which our scientific community was incorrect?

The truth is, we don't know. We must remember that science cannot prove anything, since it merely uses observational data. Compelled by the logic of induction, science can at best strongly predict what happens. If we look a bit to the past, for example, we remember how at one point people believed in the geocentric-- rather than the heliocentric-- model. At the time, the former model of the universe was labeled correct, and other projections of the universe were quickly shot down.

But now we see that isn't the case, and that those who opposed the scientific community of the time were right all along-- scientists like Galileo and Copernicus.

So what does this all imply? That we must be cautious of the things we hold for granted. Hypotheses, theories, and even laws that we hold onto dearly today might just be history tomorrow, as was the case in the field of crystallography.

That's probably why such landmark discoveries are labeled as "revolutionary."

Quasicrystals "In Space!"

          As you may or may not know quasicrystals were discovered by scientists only in the last 40 or so years. And before that most scientists refused to believe that they even existed because of how crazy the concept of quasicrystals were. So imagine the surprise when two people by the name of Paul J Steinhardt and Luca Bindi discovered a meteorite containing quasicrystals in eastern Russia within the Koryak Mountains around the 1980s. Before this discovery, only one natrual quasicrystal had been documented. The sample in question, currently located in the Museum of Natural Florence, Italy, was found to have the symmetry of a soccerball; with six axes of five-fold symmetry forbidden to ordinary crystals. And what makes this all more interested was the type of meteorite that the quasicrystals were discovered in. This meteorite was a CV3 carbonaceous chondrite. And for the 3 of you people that don't understand meteor terminology, it means that this rock was formed around 4.5 billion years ago; around the time that the solar system first began. 

Meteor striking Earth's atmosphere. Scientists reveal that new, naturally occurring quasicrystal samples have been found in an environment that does not have the extreme terrestrial conditions needed to produce them, therefore strengthening the case that they were brought to Earth by a meteorite. (Credit: © JRB / Fotolia)

        This is a huge discovery. It means that something that's existence has been acknowledged within the last 40 years or so has been in production by the universe since the beginning of the universe or at least our own solar system. This creates several questions that have to be solved, and according to Paul J. Steinhardt, those questions are: "What does nature know that we don't?", How did the quasicrystal form so perfectly inside a complex meteorite when we normally have to work hard in the laboratory to get anything as perfect?", What other new phases can we find in this meteorite and what can they tell us about the early solar system?". While these questions are very good, I feel the need to add one more, call it some food for thought. What other things are there that modern science has already dismissed that are in fact legitimate? Thanks for reading.

Symmetry on a Larger Scale

We previously discussed how vital symmetry is on a small scale, but is symmetry important on a large scale? Just to refresh everyone's memory, symmetry is significant as it contributes to the boiling point of a compound, can assist in determining the compounds structure, or can effect the bond strength (a symmetrical "hydrogen bond" is stronger than a regular "hydrogen bond"). Quasicrystalls, incredibly symmetrical crystals, are versatile and can be used in various situations, but they are only about 150 micrometers in size! So does symmetry only effect small particles or molecules? Well, this depends because last year, the discovery channel claimed that the Milky Way galaxy is symmetric. Yes, we have just claimed that a 150 micrometer crystal is symmetric and the a 100,000-120,000 light year galaxy is symmetric. Just to put that into perspective: 1 light year is equal to 9.46*10^21 micrometers.

Milky Way galaxy

Quasicrystal under a scanning electron microscope

If symmetry applied to smaller molecules is applied to the Milky Way, many questions rise. As stated before, when molecules are symmetric and stacked on top of each other, they are incredibly difficult to separate. Since galaxies move, what if another galaxy, symmetric like the Milky Way, stacks atop the Milky Way. There are though to be at least 500 billion galaxies in the universe, so there has to be at least 1 that is symmetric like the Milky Way. Will there be attractive forces so strong that these galaxies will turn into one galaxy? As previously stated, scientists are able to determine a compound structure, so will the symmetry of our universe allow us to discover our universe's "structure"? Will knowing that our universe is symmetric cut out half of the work for astronomers?

Image depicting galaxies moving moving close to each other

Now, how can the Milky Way galaxy be symmetric? Simply put, half of the Milky Way galaxy is virtually the exact mirror image of the other half. This is incredibly similar to many molecules who's right side is just a mirror image of its left side. So if our galaxy is symmetric, does this mean that another planet exactly the same as earth must be on the opposite side of the galaxy? How many other galaxies are symmetric and what will be the deleterious effects of symmetry? Is our universe symmetric? Only time will tell.

Usage of Quasicrystals in Tools

           Quasicrystals have many different characteristics that allow them to used in many different scenarios. The first quasicrystals were metastable, meaning that if the crystals were exposed to heat or reheated at some point in time, it might vanish. This heavily limited there use  But within a few years stable quasicrystals were found in several different materials systems, including aluminum–copper–iron and aluminum–palladium–manganese.
                                    
Quasicrystals are extremely poor electrical and thermal conductors. In fact the thermal conductivity of quasicrystals containing more than 70 atomic percent aluminum is two orders ofmagnitude below that of aluminum and roughly equivalent to that of zirconia, which is used as a refractory material. Quasicrystals are
also exceptionally hard, and their surfaces have very low coefficients of friction, good wear resistance, and good oxidation and corrosion resistance. Also, depending on how they are prepared, quasicrystals can have coefficients of friction so low they are comparable to the coefficient of a diamond gliding over a diamond film.At first, there was an apparent obstacle to exploiting these properties: Bulk quasicrystalline materials are brittle at temperatures below a few hundred degrees Celsius. The solution to this problem was that quasicrystals made into coatings by the standard techniques of metallurgy, such as atomization and plasma spraying, retain the desirable properties, but not the brittleness, of the bulk material. So with these features, what can quasicrystals be used for? The first use lies in medicine, specifically medical tools. Put simply, there quasicrystals easily made into very strong and durable tools. Continuing on, titanium-based quasicrystals  particularly titanium–zirconium–nickel, would be very useful for hydrogen storage. The reason being that hydrogen likes to sit in tetrahedral sites in transition metals. Quasicrystals because of their shape have huge amounts of tetrahedral sites. In addition, hydrogen is very specific about its bonding partners. It doesn’t work well with aluminum, but it works beautifully with titanium, zirconium, and the rare earths. So the titanium quasicrystals have the combination of a favorable chemistry and a favorable structural unit. Ken Kelton of Washington University in St. Louis found that titanium–zirconium–nickel quasicrystals can absorb nearly two hydrogen atoms per metal atom which is more hydrogen than is absorbed by related crystalline and amorphous materials. Moreover, it is more hydrogen than is absorbed by the hydrogen-storage materials currently in use, such as the lanthanum–nickel compounds in renewable batteries in laptop computers. “We can store almost double the weight percent of hydrogen that can be stored in lanthanum–nickel-5,” Kelton said. Some problems with is though is that Titanium–zirconium–nickel tends to form a surface oxide that can delay hydrogen loading. “This is not uncommon,” Kelton commented, “and we can get around it by gently milling the quasicrystal ribbons or by electrolytic loading.” He also noted that titanium-zirconium–nickel has so far been produced only by melt-spinning. Although the quasicrystal is stable, the reactivity of titanium has prevented it from being produced by the more versatile techniques used to make aluminum-based quasicrystals. The final potential use would be in the field of solar power. While quasicrystals lack exotic optical properties, their resistance to corrosion and abrasion might yield solar panels that do not require the "round the clock" maintenance needed by regular solar panels. The ideal solar-absorber material shows large absorption in the solar spectrum and is highly reflective at longer wavelengths. These characteristics basically give the effect of a window in a closed car. Sunlight comes in and is absorbed by the seats, but  energy re-emitted as infrared radiation is trapped in the car by the windows. Thus, the car’s interior, becomes much hotter than its exterior. By similar means, solar-selective absorbers can reach temperatures as high as 500°C. Using quasicrystals, the closed-car effect can be achieved using a thin-film stack made up of a layer of quasicrystalline aluminum–copper–iron between two layers of the dielectric alumina deposited on a reflective metal had a solar absorptance of 90%.
          While all these uses of the quasicrystal remain mostly untested, many different companies and people are cautiously optimistic of this technology. And for good reason, as these crystals have the to potential to change many things in the world of humans.

Quasicrystals-- A Revolution in Crystallography

For centuries, the field of crystallography-- the science of how atoms and solids are arranged-- has followed a fundamental mathematical theorem called the Crystallographic Restriction Theorem (CRT). It states that periodic crystals, which are ordered on a microscopic level, can only contain 2-fold, 3-fold, 4-fold and 6-fold rotational symmetries.

(A regular snowflake is shown to have 6-fold rotational symmetry.)

This makes sense when you use pictures: for instance, try to cover an entire area with pentagons attached to each other, and you will indeed fail:

However, this theorem-- as well as the basis of crystallography itself-- has been corrected in 1984 with the revolutionary works of Dan Shechtman and his synthesis of aluminum-manganese alloys with icosahedral symmetry.

(A icosahedron has twenty equilateral triangles as its faces.)

This figure is especially troubling to believers of the original CRT, as it has numerous 5-fold symmetric axes. One such axis is shown below:

These crystals, due to their unusual symmetries, have been called quasiperiodical crystals, or in short quasicrystals. Because of their unusual characteristics--especially that of rotational symmetry-- its existence has been doubted by many scientists.

So how can such molecules be made, with the proven CRT still standing? Well, if we look at the second picture of this blog (the one with pentagons), we see that the gaps between the pentagons become the problem; however, in quasicrystals the gaps are filled with differently shaped atoms, while rotational symmetry is still maintained.

As Marjorie Senechal, a specialist in mathematical crystallography, describes it, such symmetries are forbidden. And such criticisms are what Mr. Shechtman and his team faced initially, when they published their highly-controversial results.

(image of Al6Mn)

Even after such criticisms were resolved, numerous scientists refused to believe in the entire concept; they continued to argue that these crystals, nonetheless, could only be formed synthetically (i.e. it cannot be naturally found). This belief was again proven false with the discovery of icosahedrite (Al63Cu24Fe13), the first natural quasicrystal found. This solid also has an icosahedral symmetry.

With the naked eye, it does not appear to be so special:

Yet on a microscopic level, this quasicrystal exhibits 5-fold symmetries-- a fact which surprises scientists even to this day. Its diffraction patterns, or patterns created when beams of X-rays strike a solid and spread into directions provided by the solid's edges, are shown below:

(Pattern (a) shows a 5-fold rotational symmetry, while (b) shows a 3-fold symmetry.)

Thus, since its appearance in the field of crystallography three decades ago, these quasicrystals have been studied vigorously by scientists around the globe. Hundreds of other quasicrystals, with 5-fold, 8-fold, 10-fold, 12-fold and 15-fold symmetries, have also been created.

(One such example is the aluminum-palladium-manganese quasicrystal; its atomic model is shown here. It exhibits 5-fold rotational symmetries but no translational symmetry.)

Paul Steinhardt, professor of physics at Princeton University, summarizes the effect of the emergence of quasicrystals as following:

The 30-year history of quasicrystals is one in which, time after time, the conventional scientific view about what is possible has been proven wrong.

This new subject is undoubtedly revolutionizing the field of crystallography. Thomas Kuhn, a prominent physicist and philosopher of science, would have gladly called it the bringer of a paradigm shift.

Nature: Awed and Humbled

In the words of President Obama these past few days "We are awed and humbled by nature's destructive power," in light of Hurricane Sandy. As a resident on the northeast, let me first offer my sympathies and say I stand in solidarity with all the people involved.

This brought me to this thought process. Forces in nature can cause up to 50 billion dollars in damages and can create beautifully formed, virtually symmetrical compounds. We must respect nature; that is a given. But can we respect it by imitating it, by synthesizing it in the lab? That is a good question, a question I shall attempt to answer now, with all of you, my friends.

If we can, should we? Just because we can doesn't necessarily mean we should. Kudos to Michael Crichton, whose books centered on these issues. Is it moral to create something found in nature? I must say no, I will not make any effort to disguise my opinions. I think that given our abilities, we should use them to the fullest extent and to our benefit, provided that they do not conflict with basic human rights. We are going to talk about the ethics and morals involved and I do not think we can do that without invoking God. Growing up Catholic, I was taught that we are all made in the image and likeness of God and that only God can create a human being. That is why the Roman Catholic Church does not condone cloning. But this same principle can be applied here. If only nature can create a super symmetrical compounds, is it moral for humans to do it?

This is my take. People were put here to do with their resources as they wish. I respect the Church's position on this issue. And perhaps cloning is one extreme; it is a replication, creation (however you would like to term it) of another life form and we can all agree that a compound, quasi-crystal, or anything like that is nothing like an actual animal. But the broader picture is the same. Do people have the right to replicate nature to their benefit? I say if God put us here, he did it so that we can do those very things. 

You know, for all you trekkies out there, and I'm not talking to you hooligans who just jumped on board since the J.J. Abrams movie came out (it was a fantastic movie, don't get me wrong), I hope you remember the scene in Kirk's room in Star Trek II: The Wrath of Khan where Spock, Dr, McCoy, and Kirk are discussing the Genesis project. The Genesis project was a plan to take a lifeless, dead planet and rejuvenate it with life to deal with the problems of over population and food supply. McCoy says "According to myth, the Earth was created in six days, now watch out, here comes Genesis. We'll do it for you in six minutes." Spock quips by saying he was not trying to analyze its moral implications. Eventually, the two scuffled as they usually do, with Spock admonishing Dr. McCoy. He says to him, "You must learn to govern your passions, they will be your undoing. Logic suggests..." wherein Dr. McCoy interjects to talk about the faulty of logic in this situation. Why did I just outline all this? Because I love Star Trek (hell of a thing when Spock died). But also because the same principle and same arguments are presented here. Logic suggests that we follow the path of scientific innovation, without the single glance at the ethical constraints. Dr. McCoy is the voice of a feeling human (not a stoical Vulcan) who has greater respect for such devices. Do we have enough respect for creation as to allow us to create super symmetrical compounds and great technologies for the fulfillment of our intentions (yes, initially good ones). I have to agree with Spock on this one. Those passions are the things that we can feel (and even be proud of) but we should not allow them to get in the way. One of my core beliefs is that I shall not impose my religious or moral beliefs on other people. For example, I believe abortion is morally wrong yet I am adamantly pro-choice. Again, the same principle applies here. I think it is human to go forward with these innovative feelings. "Out of all the souls I have encountered in my travels, his was the most....human." That line out of Spock's eulogy only makes sense to me from this perspective and interpretation.  

There are other schools of thought from which to see this argument and moral dilemma from. Does life hold inherent meaning? Do things have innate meaning or do they only have it when we grant this meaning onto them? Do things have ethical values at all? All depends on the mindset. If you are a fan of Seinfeld, then you are familiar with the absurdist, nihilistic view of life it takes. If you are a religious person, you find deep meaning in your faith.

This applies to super-symmetrical compounds in ways one could not have fathomed. Do we have the right to voraciously create without relishing and appreciating what has allowed us to do that? I implore you to think about these questions. Ponder them. You will come to many conflicting answers. Is this discovery or creation? I define discovery as something that has implications that are conducive to revolutions in science (like the discovery of gravity which is not recognized as a "discovery" by many). When we create these compounds, are we discovering them? Or is that terminology reserved for nature? 

These are the questions that haunt me...and I hope they haunt you too, Constant Reader. 

Artificial Symmetry in Chemistry, the Melting Pot of the Sciences

Chemistry is the melting pot of sciences simply because it coalesces biology and physics unlike any other discipline can. So it only makes sense to, for the sake of these other branches, explain the concept of molecular symmetry in both horizontal and vertical aspects. The chemist Roald Hoffman (pictured here) himself an educator, advocated for a horizontal teaching method, wherein a concept should only be explained in terms of that particular science. For example, symmetry could only be explained using the apropos nomenclature found in chemistry. That will be done in this blog. Having said that, it is also deemed important for people of other scientific disciples to come together and realize the importance of molecular symmetry in their own fields. 

Another Nobel Prize winner Michael Polanyi said at his banquet that "science begins when a body of phenomena is available which shows some coherence and regularities, that science consists  assimilating these regularities in a natural way." Lets use our good ole' common sense for a second here  and recognize that symmetry is nothing more but a manifestation of these regularities. Symmetry is one way in which we can recognize rules patterns. Things like molecular motions are dependent on the rules for symmetry. 

 A symmetry operation is one where there is a "permutation" of atoms so that the molecules the atoms compose or the crystal lattice structures transforms into something that is for all intents and purposes the same as the starting state. No physical property or wave function was damaged in the making of this operation. The nuclear arrangement and other things are static when there is a symmetry operation. However, there exists dynamic properties such as electronic structure and molecular vibration. In the case of molecular vibration, it is impossible to say that a molecule has perfect symmetry in any case. Bond lengths and bond angles perpetually change when this molecule in question is not at zero Kelvin.   There is a plethora of ways vibrations can affect larger molecules (the ones synthesized in the lab, wink, wink) but let us look at H20 as an example. Here the bonds can be elongated equally, bent symmetrically, or elongated asymmetrically. One can know the symmetry of a molecule from a method called vibrational spectroscopy. 

"The sculpture is already there in the raw stone; the task of a good sculptor is merely to eliminate the unnecessary parts of the stone." I think Michelangelo was on to something. Elimination of the unnecessary to form a symmetrical figure, (a human being in the case of the artist or the molecule in the case of the chemist) is something that is seen in chemistry when it comes to bonding and intra-molecular forces. Concerning electronic structure, which is really what dictates who bonds with whom, is directly correlated with symmetry. Molecular Orbitals, which are based on Atomic Orbitals, are linear combinations of those atomic orbitals. 
There is a large number of possibilities but because many do not meet the criteria that symmetry puts forth, many are not considered to be bonding possibilities. 

Symmetry is essential in materials science. Symmetry is considered in crystals (one unit cell structures) and pseudo-crstals (more than one unit cell). After its discovery in 1982 in an electron-diffraction experiment, pseudo-crystals demonstrated ten fold symmetry which was something that was a true revolution in crystallography. Discovery and creation of  new compounds is born at this moment. Symmetry considerations now can be used to assist research in synthesis and discovery. And this is where our trek begins. The synthesis of symmetrical compounds and their implications, moral, scientific, and practical.

Why is Symmetry Important in Chemistry?

     Asking why symmetry is important to chemistry is analogous to asking why red blood cells are essential to a human being. While many people are unaware of the microscopic cells constantly flowing through their veins and capillaries, people are aware that there life would be incredibly different without these petite cells. This is akin to symmetry and its integral role in chemistry. Symmetry is involved in virtually everything ranging from a substance's boiling point to the types of bonds it contains, but never receives the credit that it deserves. When put into perspective, symmetry is involved in everything and is located everywhere.

     In organic chemistry, symmetry is incredibly important in determining a substance's boiling point. In one article, the author relates each compound to a piece in the game Tetris™. As illustrated below, the molecule which is most symmetric (labelled easy) has the capability to stack and form multiple layers, leaving few, if any, space between each layer. The piece labelled "hard", on the other hand, is able to stack with itself; however, there will be large gaps left between each layer which will result in a lower melting point than its symmetric counterpart.

     The following two diagrams further emphasize how important symmetry is when stacking molecules. Perfectly symmetric molecules can also be described as Legos™ because they fit perfectly together when stacked.

     Simply put, less gaps will occur when a symmetric molecule is stacked with itself, hence, resulting in a greater melting point.

     Another area of chemistry where symmetry comes into play is in hydrogen bonding. One specific type of hydrogen bond is named the symmetrical hydrogen bond. Just as its name implies, this variety of hydrogen bond is unique because the hydrogen atom is equidistant from two interchangeable atoms, illustrated in the diagram to the left. In the prior paragraph, it was stated that symmetry increases the intermolecular forces between molecules, and similarly, the symmetric hydrogen bonds are much stronger than a regular hydrogen bond. The strength of a symmetric hydrogen bond is comparable to that of a covalent bond. This could mean that a symmetric hydrogen bond has the potential to have almost forty times the bond energy of that of a regular hydrogen bond!

Bonds displayed in hexabenzocoronene

     Another element of symmetry that was stated previously is its role in determining differences in bonds. In an experiment conducted by Leo Gross of IBM research in Switzerland, he discovered that the bonds in a buckyball, made of 60 carbon atoms, had different strengths. Achieved for the first time in 2009, Gross used a technique that was capable of measuring individual bonds. The bonds appeared in different colors which assisted Gross and his colleagues in determining the strengths of the bond, but symmetry also came into play. The symmetry of the atom allowed the researchers to differentiate the background effects which may have been produced by the new imaging technique from the actual bonds themselves. This is seen with the image on the right (http://www.newscientist.com/article/dn22269-first-images-of-chemical-bond-differences-captured.html) . With out the scientists familiarity with the compound symmetric structure, this experiment would have been a waste!

Vitruvian Man

     Symmetry has been valued by humans ever since Leonardo da Vinci created the Vitruvian Man in 1487, a drawing that focuses on the proportions and symmetrical nature of human beings. However currently, there are many other implications of symmetry. Defined by dictionary.com as "the correspondence in size, form, and arrangement of parts on opposite sides of a plane, line, or point; regularity of form or arrangement in terms of like, reciprocal, or corresponding parts", this word has a plethora of value which its definition does not imply. Symmetry is key in determining a compounds boiling point and melting point. Scientists are attempting to create drugs with symmetrical properties in order to cure disease. Symmetry is also giving scientists a better understanding of cancer and it provides incite onto how stem cells function. Symmetry may just be another word, but it is found everywhere and its value in chemistry, and life, is indescribable.