Monday, September 8, 2008

Binding and bonding to butadiyne

A bucky tube, such as the (9,0) bucky tube illustrated at the right, could serve as a binding site for a simple linear molecule like butadiyne (Merkle, 1997a). Such a binding site would serve to bind the butadiyne from the external feedstock solution, and would allow the transfer of the bound butadiyne to the interior of the assembler.

Free molecules inside the assembler must be avoided, as their uncontrolled collisions would produce undesired and unpredictable reactions. It is therefore most convenient to bond to butadiyne so that we can control its position and prevent it from uncontrolled encounters with, e.g., the reactive tools discussed here. As there are initially no bonds to the butadiyne it must be held in place by intermolecular forces (predominantly van der Waals and overlap repulsion forces) during the first bonding operation. This paper does not consider in any detail the structure of the site which both positions the butadiyne and makes it accessible to the appropriate molecular tools for the initial bonding operation. We do, however, point out that it is possible to completely surround the butadiyne with a custom-made structure specifically designed to position it during this operation. We also point out that this site will in general be very different from the binding site used to initially bind butadiyne from the feedstock solution.

As there are several tools, there are several candidates for the initial reaction. A carbene could be inserted into any of the bonds. As there are six atoms and five bonds, the carbene could potentially be inserted into any of five positions. There are three positions that are fundamentally distinct: one of the H-C bonds, one of the C#C triple bonds, or the central C-C single bond. Perhaps the most attractive possibility would be to insert a carbene into the H-C bond exposed when the butadiyne first enters the internal environment from its binding site. If the binding site is a bucky tube, then as the butadiyne first exits the bucky tube it could be met with a carbene. A detailed examination of such geometries is necessary to ensure that (1) the carbene will insert into the H-C bond, (2) the carbene will not insert into the adjacent C#C triple bond (despite the attractive electron density provided by the pi bonds) and (3) the butadiyne won't "slip by" and permit bonding in some other (undesired) location or fail to bond at all.

The use of radical additions might be a more attractive approach. As addition of a single radical would (a) permit the butadiyne considerable freedom (it could rotate around the newly formed bond) and (b) result in an open shelled (radical) structure, it would seem preferable to add to the butadiyne with two radicals and form two bonds to it. As we have several radicals to choose from and four carbons and two hydrogens as potential targets, there are many possible specific choices. One choice that seems particularly useful is two silicon radicals adding at the 1 and 4 positions. Following these additions the butadiyne moiety would be well controlled positionally, and we could remove the two hydrogens by applying two hydrogen abstraction tools. These reactions are illustrated below:

Reactions 1 and 2

If both radicals have the same spin then the obvious closed-shell electronic structure for the product requires an intersystem crossing. To ensure that this takes place rapidly and reliably, Drexler proposed that a "heavy" atom should be in the vicinity of the reaction.

Calculations at the 6-311+G(2d,p) Becke3LYP // 6-31G* Becke3LYP level show a barrier height for the addition of a single silicon radical (SiH3) to a terminal carbon of the C4H2 of 14 × 10-21 J (~ 2 kcal/mol). The geometry was optimized at the lower level of theory while a single point calculation at the optimized geometry was computed using the higher level of theory. Calculations were done using the Gaussian B3LYP keyword without zero-point vibrational correction. Details are available on the web at http://www.zyvex.com/nanotech/comp/. The "transition state" was not actually a stationary point on the potential energy surface as rotations of the SiH3 moiety were blocked. (It is possible that the barrier to addition might be an artifact of this constraint). As the SiH3 is supposed to be the tip of a larger tool (which would hinder any rotations), this better models the expected application.

The computed barrier is about three times thermal noise at room temperature, suggesting that the actual barrier for this radical addition is in any event small, and therefore that this reaction will be satisfactory in the present application (especially as activation energy could if necessary be provided by the use of mechanical force).

The use of silicon radicals in this first step permits us to use hydrocarbon structures to confine the butadiyne with less concern that surface hydrogens will be abstracted: the silicon-hydrogen bond is weaker than the carbon-silicon bond. As the radical will have to approach the butadiyne quite closely during the radical addition, and as the hydrocarbon structure confining the butadiyne will also have to be in close proximity to the butadiyne, allowing close proximity between the silicon radical and the confining structure relaxes a significant design constraint.

Another attractive possibility would be the use of two radicals but with different targets: one would attack a terminal hydrogen and the other would attack the adjacent carbon. If both radicals are appropriately positioned then this reaction could take place as the butadiyne emerged from a bucky tube. The result would be to transfer the hydrogen to one radical and the C4H to the other radical.

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