Saturday, 2 June 2007

p-Cresole Vibrations

I destroyed my ankle at a basketball tournament in Berlin. Now I am chained to my desk and lovenox is my only excitement (I don't get why it's ok to call a drug lovenox). So how do you entertain yourself on a friday night when you are not allowed to leave the house? You could calculate the vibrations of p-cresole and find a way to incorporate them into jmol (I could also study for an exam but I don't feel like doing that until the labs are over).

p-Cresole is about the borderline for what you can do ab-initio at your home computer. I drew the structure in Ghemical-GMS and optimised it and calculated the vibrations in GAMESS (US). To get fairly decent results you need much more than a minimal basis for vibrations. I took TZV which is kind of overdoing it maybe. The modes are still 5-10% too high but it did not improve compared to 6-311G. A problem is that the structure wasn't totally optimised even after 20 iterations that took about an hour. And the program tells me that the result is not valid because of that but I think the energy gradient was low enough.

Before you read on you can try to think of the infrared spectrum of the substance.

For 16 atoms there are 42 vibrational modes. I picked a few representative ones. A nice program for looking at them is ChemCraft. But that way I couldn't show them here. So I wrote a Visual Basic script that extracts the information out of the .out file and makes an .XYZ+vib file out of it that jmol can use.

The shown frequencies are proportional to the actual frequencies where 1600/cm corresponds to 1s cycle time.

The highest wavenumber is the OH stretch (4056/cm according to this computation).

Next come the aromatic C-H stretches (this one with 3302/cm).

Aliphatic C-H stretches are a little bit (lower 3138/cm for this one). Normally the borderline should be 3000/cm. So we are a little bit too high here.

Aromatic C-C stretches (1756/cm).

Aromatic C-H out of plane bends (938/cm).

A very low frequency vibration (369/cm).


baoilleach said...

That's pretty cool - I didn't realise that you could get Jmol into a blog.

Typically, even at the HF limit (i.e. infinite basis set), calculated frequencies are too high compared to experiment. This is apparently because the calculations assume that the vibration is harmonic, whereas in reality it is not, but it's a good approximation.

Felix said...

jmol is kind of a pain to use in a blog because you can't have two jmolInitialize commands at the same page. so I can't really use it again for the next 5 posts. but it is just such a nice program

baoilleach said...

Just been lookng at Jmol.js. Why not test the value of _jmol.initialized (see line 35 or so), and if it's already set, don't call jmolInitialize. Alternatively, just remove the 'alert' at line 36 and that will stop the warning popping up (I don't know why they didn't' just write a warning to the Javascript console instead of a popup).

Felix said...

in the .js file I am using the alert is blocked out. the problem is that the browser just crashes without saying why. debugging is no fun if you don't get an error message

Lightnir said...

Yes you can use it in the next 5 posts if you do it the right way ];) Since the new Bloger 2 offers wiggets to arrange the layout of the page just add a new "Page Element" in the template tab and choose "HTML/JavaScript" from the list. Add the jmolInitialize section in it and move your new Page Element before the post section so it will executed only once every time the page is loaded. Tada - it's Jmol time ]:D

PS. Gutte besserung mit den Knöchel

Felix said...

cool, I'll give that a try

danke, der knöchel ist schon ein bisschen besser