Saturday, September 20, 2008

more with HyperChem adamantane and nucleic acids

I figured I better post more right away or else my signature MTF could suffer a credibility hit. Here is a POV-Ray trace of an adamantane molecule bonded to the 3' end of a short piece of ssDNA. I have been wondering about the wet chemistry necessary to pull something like this off, connecting to the oxygen (as shown) or to the phosphorous atom. I'm waiting to hear Guy's views on the subject, but if anyone else has some ideas, I would like to hear about them too.

(click for larger pic)


modeling adamantane in Hyperchem

I actually meant to post this a while ago, but you know how things go...

Anyway, armed with my copy of Molecular Modeling for Beginners ( you probably think I should have bought that a long time ago, like before I started getting interested in molecular modeling, but I always jump first and ask questions later) I started getting into some programs used at my school, like HyperChem. The first thing I modeled was formaldehyde and then jumped to adamantane. Here's the short version:

Starting small by laying down six carbon atoms for what I like to call the bottom.

connecting them together...

working my way up...

almost there...

added the hydrogen atoms by selecting Add Hydrogens. Oh man. Did I do something wrong here? I once had the bottom of a box of spaghetti give out and the result looked a lot like this. I figured I had nothing to lose, so I optimized the geometry using RHF and the 6-31G* basis set.

Ta-Da! What were you worried about?