Organic Technology Lab

There are two things I learned in my organic technology lab. The first one is that formic acid is corrosive. The second one is that a superslurper can take 600 times its weight in water.

Who would have thought that vinegar's little cousin is so nasty to your skin? It has the same R and S statements as acetic acid. How would I have known it's so bad? I guess I could have known because ants wouldn't use it if it weren't bad (but how do they handle it?). Anyway, it was only a small bit of my skin.

A less dangerous procedure is synthesising the essential part of a diaper. A super slurper is starch copolymerised with acrylnitrile and 2-acrylamido-2-methyl-1-propanesulfonic acid. The nitrile groups are partially hydrolysed, then it looks like this.

You start out with a few crumbs ...

... add water ...

... and you get huge amounts of jelly.

It took about 100 times its weight in water. This apparently goes up to 600.

HF-SCF bases

I found some time to try out GAMESS a little bit more. What I was interested in is how a geometry optimisation changes with different bases.

I tried out most of the standard bases that GAMESS offers without any extra functions. The input looks like this (enter the base instead of ***). After evaluation I extracted the information with Visual Basic.

! Ethane staggered
!
 $CONTRL SCFTYP=RHF RUNTYP=Optimize $END
 $SYSTEM TIMLIM=30 $END
 $BASIS *** $END
 $GUESS GUESS=HUCKEL $END
 $DATA
Ethane...staggered...***
S2n 3

C           6.0   0.0000000000   0.0000000000  -0.7688320347
H           1.0  -1.0157199281   0.0000000000  -1.1532895468
 $END

This is the result. You see the C-C and C-H bond lengths (in Angstrom) and the C-C-H angle. The table is arranged according to the complexity of the base (information). In the first line are the literature values [1], in the other lines relative deviations.

Basis	C-C	C-H	C-C-H
Experimental	1.5351	1.0940	111.17°
MNDO	-0.0143	0.0152	0.0221°
AM1	-0.0348	0.0231	-0.4514°
PM3	-0.0306	0.0038	0.4605°
STO-2G	0.0029	-0.0020	-0.0537°
STO-3G	0.0026	-0.0080	-0.4380°
STO-4G	0.0002	-0.0116	-0.4738°
STO-5G	-0.0001	-0.0128	-0.4628°
STO-6G	-0.0004	-0.0125	-0.4612°
3-21G	0.0072	-0.0099	-0.3732°
6-21G	0.0064	-0.0099	-0.3084°
4-31G	-0.0062	-0.0106	-0.0081°
5-31G	-0.0054	-0.0098	0.0183°
6-31G	-0.0052	-0.0096	0.0236°
6-311G	-0.0070	-0.0113	0.0494°
DZV	0.0024	-0.0102	-0.1002°
TZV	-0.0047	-0.0109	-0.0096°

The first three are semiemperical methods. They show the worst results (as it is supposed to be).

It's more difficult to say things about the ab-initio calculations. It can be seen that bond lengths never differ much more than 0.01 (which is nice). Another interesting fact is that with a better basis, bond lengths tend to be shorter [2]. At the HF-SCF limit (self-consistent eigenfunctions of the Fock operator) bond lengths are usually too short (which is not nice). This is just shows a limitation of the method. Sometimes medium sized bases give better results than large bases. To overcome the problem, you need correlated calculations.

[1]Lide DR. Handbook of Chemistry and Physics 86^th Ed. 2005-2006. CRC
[2]Kutzelnigg W. Pure appl. Chem. 49, 981 (1977)

Inorganic technology lab

Inorganic technology has been over for a while so it's about time I show off all the cool things I got from there.

This is my glas cutter. Its central piece is an Al₂O₃ ceramic piece that was used for a 4-point bending strength experiment.

Its hardness is way above glass. That's why you can easily use it for scratching.

If you want more strength and you don't need quite as much hardness you move from ceramics to hardmetals.

This is a used indexable insert made of WC in a Co matrix. It's covered in TiN to give it a nice golden look (and maybe surface properties).

It can be used for steel machining. And to produce mystery swarfs.

Why is it purple? It's plain steel but it's covered in a thin oxide layer that developed in the process of turning. The color is because of interference (like in an oil puddle).

Are there any hardmetals in everyday life? Yes, a ball point pen ball is typically made of a hardmetal. This is the only way to get the right porosity.

Messing up the environment

If you haven't watched Al Gore's "Inconvenient Truth", go check it out. Not only because you'll find the coolest ideas for preparing your next slideshow. It made me wonder what the US and the world would have been like if the votes had not been recounted that day in Florida. But I guess not much different because the only inconvenient truth for a high ranking polititian is how difficult it is to satisfy all the companies that sponsored the campaign.

Anyway, the reason I went into science is that I don't want to deal with those things too much. Let's take a look at the chemistry behind the greenhouse effect. Why can CO₂, methane, N₂O, and SF₆ absorb but N₂ and O₂ can't? Yes, it's because they have IR-active modes. The more they have the worse it gets, it seems. That's why burning methane is better than letting methane into the atmosphere. It works in chemical plants but I don't think they've found a way to convince cows to light a match before belching (yes, I am impressed that they can live on cellulose but can't they keep an oxidative environment in their stomachs?).

Game theory is why I sometimes think that biology is cool. As I know after reading Dawknins' "Selfish Gene" pretty much all of life comes down to prisoner's dilemmas. Prisoner's dilemmas can be overcome if the two individuums meet each other often enough. The problem with environmental policies is that so many people are involved that the solution is more difficult.

Let's look at the following situation: a town with 1000 inhabitants. The question is if they choose to drive their car to work. Driving a car is nice, let's say every inhabitant that drives their car gets 100 happiness points. On the other hand cars are bad for the community (they are noisy and smelly, they clog up the streets, they endanger pedestrians, ...). Let's say every car costs 1 happiness point to every member of the community. Will a rational citizen (according to these rules) take their car? Of course: It's a net increase of 99 happiness points. If everyone drives their car, he gets 100 happiness points out of that but he loses a 1000 happiness points because of all the people driving cars. The net effect is -900 happiness points.

Now a courageous Austrian ex-actor becomes the mayor of the town (after retiring from California). Car driving becomes against the law. First everyone is angry because they lose 100 happiness points. But then they find out that they can open their window without constant noise, that they can ride their bike without being stuck in traffic jams, that they don't have to be scared crossing streets anymore, ... Everyone is 900 happiness points better off than before.

The problem is that it is better for the individual to do a bad thing but it would be better for the whole if he doesn't. That's why environmental laws are so important (unless people are nice by themselves). US and Australian readers may feel bad now because they are out of the only developed countries that did not ratify the Kyoto protocol. I can assure you, it's alright: we Austrians (without "al") are just as bad. It's ratified but we have no idea how we could reach the goals. So it's also our fault that the world will be a horrible desolate place in 50 years.

Alright, that was my political, improving the world post but I have to say that I like writing about basis sets and drawing funny pictures better. By the way, there is a pretty cool post on carbon capture technologies.

Free cake

You may have come here for the cake. I am afraid it's all gone already.

GAMESS

For serious ab initio calculations there is GAMESS. It's not as easy to use as ArgusLab but you can do many more cool things with it. I just figured out how to use it. So I'll write about that a little bit. I use the windows version but things are probably similar with other operating systems.

For properly using GAMESS you need two more programs. One to create the input and one for looking at the output file. Ghemical-GMS works as a front end program. But you can also type the input file into a text editor. That's what I did because extracting the .zip did not work. I downloaded Chemcraft for looking at the results. MacMolPlt is probably also a good program but I haven't tried it out.

For my first example I optimised the geometry of iron-pentacarbonyl. The input file looks like this (spaces before $ are important):

! Geometry optimisation for iron-pentacarbonyl.
!
$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE $END
$SYSTEM TIMLIM=30 $END
$BASIS GBASIS=N21 NGAUSS=3 $END
$GUESS GUESS=HUCKEL $END
$DATA
iron-pentacarbonyl...3-21G
Dnh 3

Fe  26
C   6       1.5
O   8       2.5
C   6       0 0 1.5
O   8       0 0 2.5
$END

After a short comment comes the $CONTRL group. In there I am saying that I want restricted hartree fock which works for closed shell molecules and that I want to optimize the geometry. Next I set the time limit to 30 minutes. Next I am saying that I want to use Pople's 3-21G basis set (because that sounded nice, information may be found here). Then I am saying that I want the program to guess the initial orbitals of the SCF run according to the extended Hückel theory.

The actual molecule is in $DATA. First an arbitrary name. Next the symmetry group D_3h. Then comes the molecule data. I only have to put symmetry unique atoms here. Iron with nuclear charge 26 at the origin (I could write 0 0 0 here). Then an equatorial C and O along the x-axes 1.5 and 2.5 angstroms away from the center. Two more CO sets are added because of the symmetry group. Then I add the axial C and O along the z-axis (by default the main axis of rotation). The other one is added automatically.

Next I create the jobs.bat file in batmaker.exe. If I click this file, the job is executed. The result can be visualised in ChemCraft.

This is what the geometry optimisation looked like. Every second step is shown. The optimisation was fast even though the molecule is rather big because of symmetry. There are only 4 parameters that can be changed, the equatorial and axial Fe-C and C-O distances.


With GAMESS and ChemCraft you can produce nice looking MO graphics. I chose most of the totally symmetrical A'1 MOs.