Dealing with excess hydrogen or carbon

As butadiyne provides both carbon and hydrogen in a fixed ratio, it is possible that either (a) there will be an excess of carbon or (b) there will be an excess of hydrogen.

If there is an excess of carbon, then we could build carbon-rich structures. The obvious candidate is graphite. As the present paper is focused on the synthesis of the molecular tools and assumes that it is possible to make diamondoid structures (including graphite) from them, we will not investigate the reactions needed for the synthesis of graphite here.

If we deal with an excess of carbon by building carbon-rich structures and keeping them within the assembler, then we need not design mechanisms for ejecting waste from the assembler. This "zero residue" design is attractive because of its simplicity.

The second possibility is that we have too much hydrogen. In this case, we could build hydrogen-rich structures. Such structures would need to have a higher ratio of hydrogen to carbon than our feedstock molecule, C₄H₂. Even a 1:1 ratio would suffice, as in hydrogenated graphite. A more attractive structure is polyethylene, which has a ratio of two hydrogens for every carbon. As our feedstock has four carbons for every two hydrogens, one of the four carbons would have to be used in polyethylene to absorb the waste hydrogen (if we assume that no hydrogen at all was used in the actual structures being built). If our assembler was pure carbon (with no hydrogen at all) we would still be able to use three out of every four carbon atoms. As this seems unlikely, we should be able to use more than 75% of the carbon from the feedstock molecule if waste hydrogen is converted to polyethylene.

Strictly speaking, the use of polyethylene violates our stiffness constraint: polyethylene is floppy. The use of hydrogenated graphite does not violate this constraint and still provides a 1:1 ratio of hydrogen to carbon, which is sufficient. It seems likely, however, that many floppy structures can be synthesized with the tools proposed here, and that in many instances this will be convenient. The use of stiff diamondoid "jigs" to constrain the motion of otherwise floppy structures is one approach to their synthesis. Bonding to structures to constrain their motion is another approach. The end of a growing polymer chain could be held in a fixed position with respect to the next monomer to be added, as is done by the ribosome. As polymers are routinely synthesized today, it seems likely that methods for synthesizing them in an assembler are feasible. While convenient, such an ability is not necessary in an appropriately designed assembler, nor in a wide range of useful products that such an assembler could make.

Again, we assume that the synthesis of hydrogen-rich structures is feasible but do not analyze methods for synthesizing specific structures in this paper.

Another approach -- more efficient when large amounts of excess hydrogen are present -- would be to make large bucky balls and store the excess hydrogen inside them as H₂ gas. Especially for large spherical bags the ratio of hydrogen stored to carbon used would be very high, as the amount of stored hydrogen would increase as the cube of the size of the bag, while the surface area (and hence the amount of carbon) would increase only as the square. This would eventually be limited by the strength of graphite (a sufficiently large bucky ball made of a single layer of graphite would eventually burst from the pressure) but bucky balls able to contain hydrogen at a pressure of perhaps 10⁸ Pascals (~1,000 atmospheres) with a radius of some hundreds of nm should be feasible.

A third approach would be to generate hydrogen gas and pump it out of the assembler. This seems less desirable, as the hydrogen might reenter through the binding sites designed to bring larger molecules into the assembler. This would require more complex systems (such as the multi-stage cascade proposed by (Drexler, 1992)) to ensure that the interior of the assembler was not contaminated with any H₂.

As the production of hydrogen gas inside the assembler cannot be allowed (for example, it would react with the hydrogen abstraction tool and other reactive structures that assume an inert environment) its production would have to be isolated in some fashion from the rest of the assembler. The production of hydrogen gas, although it has advantages, makes the system design more complex. The incorporation of hydrogen into hydrogen-rich structures seems like a simpler approach.