Friday, July 25, 2008

mechanosynthesis with penta-adamantane

On the left is adamantane with four hydrogen atoms abstracted. Previous simulations gave reason to suspect it would fail in mechanosynthesis due to internal cyclization. However I have misplaced those results. In order to overcome this problem a larger building block was chosen, penta-adamantane, rendered on the right also with four hydrogen atoms abstracted. I chose this because it has a similar shape as adamantane, and my collaborators decided we could run with it.

Here is a HD rendering of the system I built in the NanoHive-1 simulator:

The basic idea is a penta-adamantane block is attached to the tooltip by a single covalent bond. The tooltip drops the block into place where it forms three covalent bonds on the workspace. As the tooptip retracts, these bonds hold the block to the surface as the tooltip bond breaks.

Here is a close up of the system in the NanoHive-1 simulator with lines showing where the bonding is to take place:

I've worked out the bumps that were preventing me from making a full POV-Ray movie of this run. I intend to post one soon. The sim is pretty neat.

Working on this with Brian and Damian was one of coolest things I've been a part of to date.

Tuesday, July 22, 2008

hang on- I lost the results for the adamantane mechanosynthesis run

I guess I didn't back up that run. I (with lots of help from Damian and Brian) did the simulation for the setup in the previous post months ago with NanoHive-1 using the AIREBO forcefield. I thought I would post that picture and then the simulation results the next day, but I don't have the results anymore and obviously didn't check before posting that. If you are dying to know, the adamantane molecules are too small: two of the open carbon atoms bond to each other before they reach the workspace. I understand this is referred to as internal cyclization.

I might try to redo this simulation to show what happens, but I'm still holding out hope that we may get the band back together on this project, so don't want to post too much just yet.

Also I'm having some trouble making POV-Ray movies with NanoHive which are what I will want to post and not just screen captures.

Please stand by.