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!