CO MOs

I talked about the nitrogen MO scheme a while ago. Let's see what happens if you take a proton from one of the nuclei and give it to the other one.

The molecular orbitals were calculated from a minimal basis with AM1 parametrisation in Arguslab. They are pretty close to the ones of nitrogen. The difference is that lower energy MOs are rather O-centered and higher energy MOs rather C-centered. This makes sense because of the fact that the atomic orbitals of oxygen are lower in energy. It can be seen that the HOMO and the LUMO [1] are centered on the carbon. This causes the strong σ-donor and π-acceptor characteristics of CO.

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The table has the LCAO coefficients for the different orbitals. The color coding shows if orbitals have a bonding or antibonding interaction [2]. It can be seen the the lowest energy AO (O-2s) has the strongest impact on the lowest energy MO, and that the highest energy AO (C-2p) has the strongest impact on the highest energy MO.

C-2s	C-2pσ	C-2pπ	O-2s	O-2pσ	O-2pπ
0.29	0.721		-0.234	0.585
		-0.865			0.502
		0.865			-0.502
0.583	-0.619		0.105	0.515
		-0.502			-0.865
		0.502			0.865
-0.634	-0.036		0.523	0.568
-0.416	-0.31		-0.813	0.264

CO is usually drawn with a formal positive charge on the oxygen and a negative charge on the carbon.
Formal charge and polar bonds work in opposite ways. This results in a very small dipole moment of .1 Debye. Its direction was argued over for a while. Now theoristical chemists are pretty sure that at equilibrium distance the carbon atom is the negative end.

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[1] Theorists always seem to be kind of careful when talking about unoccupied MOs. In order to sound serious I have to do that, too: One has to remember the fact that unoccupied MOs are even less real than occupied ones. For some reason they are pretty good if you use a minimal base. But as soon as you move from plain LCAO to using more basis functions you will just get a lot of "virtual" MOs close together in energy with no physical significance.

[2] For σ-MOs the color corresponds to the sign that the wave function has in between the nuclei, for π-MOs it corresponds to the sign in the positive x-direction of the atom.

MTBE

Thanks to modern imaging techniques you just have to look at this guy's face to know that tetraethyl-lead is bad to the bone. It's not because it's inorganic. Inorganic chemistry is nice once in a while. Actually I don't even know the difference. It think it's that inorganic chemists grease their joints?


Well, actually I wasn't going to make jokes here. What I wanted to do, is talk about anti-knocking agents, something that caught my interest studying for organic technology.

"Knocking" means that the gasoline air mixture inside the cylinder explodes before the ignition when the piston is at the wrong position. This wastes energy and damages the engine. As I understand it, knocking is caused by the formation of instable radicals when n-alkanes break apart. The octane rating is a measure for the autoignition resistance of gasoline.

Tetraethyl lead produces ethyl radicals that recombine with other radicals. Therefore it inhibits knocking and raises the octance number. By modern standards you can't imagine having things drive around that spread lead all over the country-side. Anyway, that's what it used to be like until about 20-30 years ago. The soil next to roads is still recovering. A problem with lead in modern cars is that it would poison the catalytic converter.

The modern solution is methyl-t-butyl-ether. I guess it has to do with the fact that a tertiary radical is formed when a radical attacks the oxygen. The tertiary radical may be stable until the ignition. A reason for taking MTBE is that it is cheap. It is formed after adding methanol and acid to the C₄ fraction of steamcracking. Only isobutene will react and form MTBE. It is a step for separating the C₄ fraction which contains the 7 possible alkanes and alka(di)enes. This is difficult to do through destillation.


I thought that MTBE was an interesting substance. But if I wouldn't have posted this I'd probably forget and then I would wonder what it was, next time I think about it. I will post more theoretical things soon. But probably not before the 25th.

Why kcal?

Careful readers may have noticed that I am slightly drawn toward theoretical chemistry. But before actually becoming a theorist I have to use my chance to complain about them.

Initially the unit of heat was defined using the specific heat of water. A calorie was the energy needed to heat up 1 gram of water by 1°C. Eventually people found out that energy and work are basically the same. The new heat unit J was equal to the work unit Nm. Many scientists accepted the new SI unit because it is easier to transform it into different units. The kcal remained only the unit of food energy.

Only the unit of food energy? No, the unit of theoretical chemistry, too. Where everyone else thinks of lunch, a theorist thinks of reactions.

I guess all a theorists really cares about is Hartrees. He transforms those into some other arbitrary unit thinking that people would like that. But isn't everybody used to kJ/mol? How much is a barrier of 8 kcal/mol? Does that mean 1 mol of my substance has to eat 2 grams of sugar to be able to react? What is the ideal gas constant in kcal/(mol K)?

On German Wikipedia I read that with 2010 it will be forbidden to use the kcal on food packaging in the EU. I sure hope that theoretical chemists will adjust faster than that.

Maybe I got it all wrong, maybe other fields are just as bad or maybe many theorists use kJ. But if not, then this had to be said.

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By the way: drawing protein pictures was pretty fun. If someone liked them, I am sorry, but I am switching my topic. My biochemistry exam is over. I may get back to it eventually because there are a few mechanisms that sound really interesting. For now I'll catch up with more "pure" theoretical chemistry I wanted to talk about. Before that a little bit of organic technology, my next exam. Not really a special interest of mine. Some things are nice, though. And finally I know where chemicals come from.

Chymotrypsin (2)

This is the mechanism of peptide cleavage by chymotrpysin. It features the three amino acids shown in the last post. This time I went back to the standard approach for the visualisation. The main feature is that a proton can be passed back and forth between serine and aspartate with histidine in between. This way you always have a proton at hand without the need of a low pH. Chymotrypsin is not something strange that somehow works. It is an amazing nano machine.

I tried to model the steps of the mechanism at first but I do not really know how to do it. Including the whole protein wouldn't work on my laptop. I tried using only the side chains of these three amino acids with fixed C_α positions. It worked out to pass a proton from protonated serine to aspartate. That was pretty nice. But it did not work out well to do more.

Chymotrypsin

Not only is Chymotrypsin a pretty looking enzyme, it also has an elegant reaction mechanism that should satifsy any organic chemist's need.

Chymotrpysin is a protease, an enzyme used to digest proteins into amino acids. To do that it has to cleave peptide bonds. This reaction is thermodynamically favourable in aqueous solution but it has a high activation energy.

According to the XRD-structure chymotrypsin is a homodimer. Its two units can be seen to the left and right. They can be transformed into each other by a 180° rotation (the corresponding axes points away from the screen).

This is one unit. At the bottom a ball and stick model of the active site is included.

The active site consists of serine, histidine and asparte in close proximity. With that system peptide cleavage can be performed at very moderate conditions (pH 8 and body temperature). The mechanism is close to a typical nucleophilic acyl substituition (or Sn_2t as my professor calls it, but I don't think that's an official term). The difference is that you don't have random solvent molecules accepting and donating protons.

I am not going to say any more about the mechanism so you can think about it yourself. I'll post it if I find a good way to draw or model it.

Rhodanase

In contrast to CO, which bonds to Fe²⁺, CN^- has a stronger affinity to Fe³⁺. This can be understood with typical complex chemistry. The main reasons may be that negatve cyanide will be attracted to the stronger positively charged Fe³⁺ and that it is a weaker π-acceptor. The consequence is that cyanide doesn't bind to hemoglobin but just to cytochrom c oxidase the fourth and last protein complex of the respiratory chain inside the mitochondrion. There it inhibits any oxidative degradation of nutrients. Someone poisended by cyanide will appear red since the oxygen stays on the hemoglobin instead of being used up by the respiratory chain.

The clean way for detoxification is the use of hydroxycobalamin (B₁₂). It binds to CN^- in a stable complex. If this expensive substance is not at hand, detoxification can be done with nitrite. It oxidates hemoglobin to methemoglobin. And cyanide is bonded to its Fe³⁺. The danger of this procedure is that methemoglobin doesn't carry oxygen. So nitrite has to be carefully dosed.

Since cyanide is found in nature (almonds, seeds) it makes sense for the body to have its own detoxification system. The enzyme rhodanase makes thiocyanate out of cyanide. You can see a few helices, random coils and two sets of parallel β-sheets. The active Cys-247 residue is shown left of the center.

The active group is Cys-247, changed to a disulfide. It gives a sulfur atom to cyanide, producing thiocyanate. The disulfide is regenerated with thiosulfate.

In fact the protein is not a pretty thing like shown above but just a bunch of atoms crowded together.
The active cystein residue can be seen as a yellow spot above the center. It is remarkable that it is visible in a spacefill model even though it is right inside of the protein. This of course makes sense because the group has to be accessible in order to be catalytically active.



Here is the jmol applet. I haven't figured out how to change the settings in javascript. So you'll have to do that if you want a different view. You may want to change the style to cartoon to get a better look at it.

The structure was taken from RSCB Protein Data Bank. The images were drawn in PyMOL.

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I made one more picture which I think looks kind of cool. This is the enzyme inside a transparent surface.

Magnets and mushrooms

It does not seem like my alcohol dehydrogenase[1] is well expressed or I may have felt better today. Anyway, I feel like blogging now. I read this great article in symmetry (the Fermilab/SLAC magazine). If you have a few minutes time, check it out. It talks about Fermi's favourite toy, a big magnet. I love the quotes. With his magnet Fermi could produce so many particles that "if [he] could remember the names of all these particles, [he]'d be a botanist."

Let's switch fields. I had this amazing lecture in preparation for a biochemistry lab and it totally changed my view of molds. I just love it if a lecturer is really taken by the topic (even if it's not a special interest of mine). It was cool because she just kept on talking and talking and it did not even stop her when she ran out of powerpoint slides. I guess this could be boring but I just thought it was cool.

Next time I notice a green spot on my bathroom wall I will just be amazed by the fact that this little guy is able to live off nothing but paint and wall. And I will always pity biologists for having to deal with the fact that Hypocrea jecorina and Trichoderma reesei are just two appearances of the same species. So instead of just saying Hypocrea jecorina or just saying Trichoderma reesei, they always have to say Hypocrea jecorina / Trichoderma reesei.

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[1] This seems to be the correct term. But I can't imagine how you would pronounce that in English.