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Molecular building blocks and development strategies for molecular nanotechnology

Ralph C. Merkle*

Xerox PARC,
3333 Coyote Hill Road, Palo Alto, CA 94304

This is an abstract for a presentation given at the
Seventh Foresight Conference on Molecular Nanotechnology.
The full article is available at

(Most of this work was done while the author was on leave at Zyvex)


Making a self replicating diamondoid assembler able to manufacture a wide range of products is likely to require several major stages, as its direct manufacture using existing technology seems quite difficult. For example, existing proposals call for the use of highly reactive tools in a vacuum or noble gas environment (see A proposed "metabolism" for a hydrocarbon assembler). This requires an extremely clean environment and very precise and reliable positional control of the reactive tools. While these should be readily available in the future, they are not available today.

A more attractive approach as a target for near term experimental efforts is the use of molecular building blocks (MBBs) (see Steps towards Molecular Manufacturing by Markus Krummenacker). Such building blocks would be made from dozens to hundreds of atoms (and perhaps more). Such relatively large building blocks would reduce the positional accuracy required for their assembly. Linking groups less promiscuous than the radicals proposed for the synthesis of diamond would also reduce the rate of incorrect side reactions in the presence of contaminants.

The proposal to use molecular building blocks raises the obvious question: what do they look like?

A few building blocks in common use in biological systems include amino acids, DNA, and RNA. Each such building block has two linking groups, which lets them form polymers. Polymers provide only indirect control of three dimensional structure, and so we require building blocks with more than two linking groups.

Three linking groups readily form planar structures because three points define a plane. Four linking groups not in a common plane are convenient for building three dimensional structures (much as the four bonds in a tetrahedral sp3 carbon atom allow it to form a three-dimensional diamond lattice). More linking groups are feasible, but tend to produce more complex building blocks.

Another desirable quality in a building block is stiffness. Many molecules have many different conformations, making their assembly into large, stiff structures more difficult. This is true of proteins in general, which tend to be much less stiff than diamond even when a specific protein is very limited in the conformations it can adopt.

A stiff tetrahedral molecule which can be readily functionalized is adamantane. Composed of 10 carbon atoms, the Beilstein database lists over 20,000 variants of adamantane, supporting the idea that this family of molecular structures is large, contains many readily synthesized members, and provides enough "design space" to provide solutions able to satisfy the multiple constraints imposed on a "good" molecular building block.

Adamantane is basically a small piece of diamond. This should not come as a great surprise. The requirement for high stiffness puts a premium on polycyclic compounds, while the desire for ease of synthesis makes unstrained compounds preferable. Diamond is a stiff, polycyclic unstrained structure, so small pieces of diamond readily satisfy our basic objectives. Other molecules which resemble small bits of diamond (or hexagonal diamond) also seem attractive as a basis for molecular building blocks.

*Corresponding Address:
Ralph C. Merkle
Xerox PARC
3333 Coyote Hill Road, Palo Alto, CA 94304
Phone: 650-812-4422; Fax: 408-730-5219
E-mail:; Web;


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