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1.2.2. A chemical perspective on molecular manufacturing

Chemistry today (and chemical synthesis in particular) focuses chiefly on the behavior of molecules diffusing and colliding in solution. Reaction rates in solution-phase chemistry are determined by multiple influences, including concentration-dependent collision frequencies, and steric and electronic effects local to the reacting molecules.

Although based on the same principles of physics, mechanosynthesis performed by molecular machinery in vacuum differs greatly from conventional chemistry. Concepts developed to describe diffusing molecules in a gas or liquid (or immobile molecules in a solid) often must be modified in describing systems characterized by nondiffusive mobility. The concept of "concentration,'' for example, in the familiar sense of "number of molecules of a particular type per unit of macroscopic volume'' becomes inapplicable to calculations of reaction rates. Local steric and electronic effects remain important, but the decisive influence on reaction rates becomes mechanical positioning aided by applied force.

a. Machine-phase systems. To emphasize differences from solid-, liquid-, and gas-phase systems, it can be useful to speak of machine-phase systems and chemistry:

  • A machine-phase system is one in which all atoms follow controlled trajectories (within a range determined in part by thermal excitation).

  • Machine-phase chemistry describes the chemical behavior of machine-phase systems, in which all potentially reactive moieties follow controlled trajectories.

The useful distinction between liquid phase and gas is blurred by the existence of supercritical fluids; the useful distinction between solid and liquid is blurred by the existence of glasses, liquid crystals, and gels. Where machine-phase chemistry is concerned, the definitional ambiguities are chiefly associated with the words all and controlled. In a conventional chemical reaction or an enzymatic active site, a moderate number of atoms in a small region can be said to follow somewhat-controlled trajectories, but these examples fall outside the intended bounds of the definition. In a good example of a machine-phase system, large numbers of atoms follow paths that seldom deviate from a nominal trajectory by more than an atomic diameter while executing complex motions in an extended region from which freely-diffusing molecules are rigorously excluded. Machine-phase conditions can be termed °eutactic ("well arranged,'' from the Greek eus, "good,'' and taktikos, "of order or arrangement''). Eutactic conditions are quite unlike those of solution-phase chemistry.*

Mechanosynthesis of the sort discussed in Chapters 8 and 13 is a machine-phase process (Part III discusses mechanosynthesis in a solvent environment). Eutactic mechanosynthesis offers novel chemical capabilities, such as position-based discrimination among chemically equivalent sites, strong suppression of side reactions, and new sources of °activation energy.

Chemistry in the machine phase shares characteristics of gas-, solution-, and solid-phase chemistry, and yet displays unique characteristics; these similarities and differences are discussed further in Sections 6.4.2 and 8.3. Since experience shows that habits of thought developed in the study of liquid- and gas-phase systems can yield misleading conclusions if hastily applied to machine-phase systems, frequent recourse to fundamental principles is necessary. The Index of this volume includes an entry (Chemistry: contrasts between machine and solution phase) that cites discussions of this issue. Table 1.2 provides a compact summary.

1.2.3. Exposition vs. implementation sequence

The implementation sequence for molecular manufacturing might proceed as follows: The ability to make complex molecular objects in solution is extended to objects of greater size and complexity. These molecular objects are used as components in molecular machines capable of directing the mechanosynthesis of yet larger and more complex machines. Through a series of steps, solution-based mechanosynthetic methods are replaced by methods that require an inert environment, then polymeric building materials are replaced by diamondoid materials. Further increases in scale and capability yield advanced molecular manufacturing systems under computer control. (Each of these steps is discussed in Chapter 16.)

Table 1.2. Contrasts between solution-phase and [machine-phase] mechanosynthetic chemistry (a more detailed comparison appears in Table 8.1).
Characteristic Solution-phase chemistry Mechanosynthetic chemistry
Reagent transport Diffusion Mechanical conveyance
Reaction site selectivity Structural influences Direct positional control
Reaction environment Solution Mechanisms in vacuum
Control of
reaction environment
Relatively little Relatively great
Strictly controlled
Unwanted reactions Inter- and intramolecular Chiefly intramolecular
Sensitivity to
energy differences
10 maJ is large 10 maJ is (often) small
Typical product size 10 to 100 atoms >1010 atom

The expository sequence of this volume is quite different. It begins by describing fundamental principles of broad applicability (Part I), then applies them to the design and analysis of advanced systems (Part II). Finally, having described principles and objectives, it turns to implementation pathways (Part III). Thus, the means considered are guided by the objectives pursued.

* D. Cram has introduced the concept of an inner phase to describe the interior of container molecules in which (for example) single, isolated molecules of cyclobutadiene are stable at room temperature because the container walls block intermolecular collisions (Cram et al., 1991). Inner-phase systems prevent collisions; machine-phase systems control them.


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