Mechanosynthesis of chain molecules
The issue with chain molecules
Chain molecules lack stiffness. Therefore when a chain molecule remains mostly unconstrained (e.g. just bond to a surface with one end) thermal motion makes it move much farther around than the sizes of the atoms that are involved in the molecule.
Compared to thermal speeds the nanorobotic machinery for diamondoid mechanosynthesis moves at glacial speeds. So as long the chain molecule remains unconstrained trying to target a single atom on the chain with a mechanosynthesis tip remains utterly impossible. (except maybe very very near 0K temperature - if quantum zero point energy is low enough - not relevant for practical considerations).
Albeit not explicitly mentioned there in the tooltip paper (it's referenced on the mechanosynthesis page) it is demonstrated that chain molecules can indeed be manipulated provided they are properly constrained that is spanned between two tips.
This is necessary even in the synthesis of diamond. While diamond is a stiff policyclic material every cycle starts out as a short appended hydrocarbon chain. That is half rings of several carbon atoms are added. Those half rings behave like floppy chain molecules. Also in the paper longer chains are stretched between two tips.
To synthesize the floppy chain molecules one may be able to employ the following trick: First one starts out with at two opposing tooltips that we'll call the tensioning tooltips. With further tooltips one starts to extends the length of the chain-molecule between the two tensioning tooltips. While increasing the length of the chain-molecule the tensioning tooltips must keep the chain-molecule in tension. Extension of the chainmolecule must always happen near the tensioning tooltips where the thermal fluctuations of the chain are smallest. It may be possible to include branches into the molecule into a double ended tree topology. Every branch will need a separate tensioning tooltip. This will probably require a lot more design effort in comparison to simple mechanosynthesis of diamond and graphitic structures especially if there are many branches which are very close together since the tooltiops start to block there freedom of movement mutually. The classical fat finger challenge. Floppy loops out of various elements are another issue.
Synthesis of diamond can be done at room temperature with acceptable error rates. For the synthesis of these more floppy molecules cooling may be necessary.
Energy turnover & efficiency of mechanosynthesis
In natural systems (that is plants and animals) nourishment molecules are usually synthesized from larger pre-built molecule fragments (obviously there are some exceptions). In an artificial system where smaller groups of atoms are put together more bonds need to be formed. Therefore there is a lot more energy involved. There is more energy turnover. To operate efficiently mechanosynthetic energy recuperation is necessary. It may be possible to have way lower losses at the same production speed or the same losses at way higher production speed.
Mechanosynthesis of chain molecules can be the first step in the future artificial synthesis of food. After synthesis the molecules need to be put in some spacial arrangement. Microscale paste printing suffers from high friction. Maybe an ice matrix could be mechanosynthesized. It seems difficult to drop in mechanosynthesized floppy chain molecules in a controlled way. This leads to the impractical idea of the perfectly replicated food.
Molecule classes that are of interest are e.g.: sugars, starch, fatty acids, lipids, vitamins, amino acids, nucleotides and many many more It probably won't bee too hard too fool our sense of taste, that is this synthesized food may taste damn good but ....
As functional part:
Chain molecules may be useful in entropomechanical converters, sensors (e.g. olfactory sensors) and more. Note that the integration of chain molecules in a diamondoid system may increase vulnerability to radiation and temperature. Narrowing down the overall systems operation parameter regime. See: Consistent design for external limiting factors.