Molecular Manufacturing: Adding Positional Control to Chemical Synthesis

by Ralph C. Merkle, Xerox PARC, 3333 Coyote Hill Road, Palo Alto, CA 94304

Copyright 1993 by Xerox Corporation. All Rights Reserved.

This is a revised version of a paper first published in Chemical Design Automation News, Volume 8, Numbers 9 & 10, September/October 1993, page 1.


Manufactured products are made from atoms. The properties of those products depend on how those atoms are arranged. Viewed from the molecular level today's macroscopic manufacturing methods are crude and imprecise. Casting, milling, welding and all the other traditional manufacturing methods spray atoms about in great statistical herds. Even lithography (which already lets us put millions of transistors on a chip no bigger than your fingernail) is fundamentally statistical and random. Exactly how many dopant atoms are in a single transistor and exactly where each individual dopant atom is located is neither specified nor known: if we have roughly the right number in roughly the right place, we can make a working transistor. For today, that is good enough.

The exception is chemistry. Large high purity crystals can have almost every atom in the right place. So, too, can many long polymers. The structures of proteins with hundreds and even thousands of amino acids can be specified down to the last atom. Most dramatically (and fortunately for us!) DNA strands with many tens of millions of bases can be copied with almost perfect accuracy. And it seems that almost any small molecule (with perhaps several dozens of atoms) can be synthesized, if only we have the skill and patience.

Yet the laws of physics and chemistry in principle permit arranging and rearranging the elements in so many combinations and permutations that all of our manufacturing skills and all of our chemical skills barely suffice to scratch the surface of what is possible.

The Utility of Diamond

Almost any manufactured product could be improved, often by several orders of magnitude, if we could precisely control its structure at the molecular level. We often want our products to be light and strong. Diamond is light and strong: the strength-to-weight ratio of diamond is over 50 times that of steel. Yet we do not today have diamond spars in airplanes nor diamond hulls for rockets. Today we can't economically make diamond. Even if we could, simple diamond crystals can shatter. We'd have to modify the structure to make it tough and shatter proof: perhaps diamond fibers. While easily done in principle, we can't do this in practice today.

Great strength and light weight are not the exclusive province of diamond: graphite can be stronger. And if we consider the many ways in which carbon atoms can be arranged and rearranged, then it's obvious that there are a host of other possibilities. Yet all share a common problem: we can't yet economically make them in the exact shapes that we want.

Great strength is only one property that we prize highly: when we make computers we are more concerned by electrical properties. Here, too, diamond excels. Today's computers are made of semiconductors, and the semiconductor of choice is silicon. This is not because silicon is the ideal semiconductor from which to make computers, but because we know how to make devices from it. The computer industry has strong opinions about what makes a good logic device and what makes a good computer[1, 2], and diamond will let us make better computers than silicon[3]. Diamond has a wider bandgap, hence electrical devices will work at higher temperatures. It has greater thermal conductivity, so devices can be more easily cooled. It has a greater breakdown field, hence devices can be smaller. It has higher electron and hole mobility which, when combined with higher electric fields, will result in higher speed. But again, we see no diamond computers, just as we see no diamond airplanes: we can't economically manufacture them yet. Large pure crystals of silicon can be made relatively easily, but large pure crystals of diamond are scarce. We can etch the silicon surface and add dopants with a precision measured in tenths of microns, while the corresponding steps for diamond are more difficult. Not more difficult in principle: just more difficult today.

Long Range Complex Order

Making computers highlights another problem. It's not enough to make a pure crystal, it must also have an extremely precise and complex pattern of impurities. The exact location of the dopant atoms in the semiconductor lattice controls how devices function and where signals can propagate. Local order is crucial to make each device work, but long range complex order is crucial to make the computer as a whole work. While we can make some things today that are highly precise and have simple long range order (e.g., crystals), it is the requirement for complex long range order that prevents us from making computers of the kind we'd like to make. While it's plausible we could make high density memory from crystals and perhaps some types of cellular automatons, we couldn't make anything that resembled the computers on the market today. Today's high speed semiconductor-based digital computers (like the 80486 or the Pentium) have millions of logic elements wired together in complex and highly idiosyncratic patterns. This is well beyond the capabilities of crystal growth or bio-polymer synthesis. It will require a fundamentally new manufacturing technology: molecular manufacturing.

A Gap

Today, there is a gap in our synthetic abilities: we can make complex mechanical machinery and electronic devices (including computers, which have millions of transistors), but we can't make such devices with the precision with which the chemist can synthesize a crystal, a bio-polymer, or a relatively small molecule. With chemistry we can make precise molecular structures and compounds, but we haven't been able to scale up that success to molecular computers (and other macroscopic products as precise as molecules).

Molecular manufacturing will, by definition, let us economically manufacture almost any specified structure that is consistent with the laws of chemistry and physics. To simplify the problem somewhat we can narrow our focus to structures that resemble diamond in a broad sense: the diamondoid structures as defined by Drexler[4]. This class includes (among other things) diamond crystals of arbitrary shape but with stably terminated surfaces (e.g., hydrogenated (111) or the like) and with impurities at precise locations in the diamond lattice (e.g., substitutional boron). Our objective is to manufacture particular diamondoid structures once the location and type of every atom has been specified by design.

The Interest of the Computer Industry

The attraction of molecular manufacturing for the computer industry should be clear. It should let us make computers at a manufacturing cost of less than a dollar per pound, operating at frequencies of tens of gigahertz or more, with linear dimensions for a single device of roughly 10 nanometers, high reliability, and energy dissipation (using conventional methods) of roughly 10^-18 joules per logic operation. If we make thermodynamically reversible computers (which the author and others have recently shown can be made from conventional electronic devices, e.g., CMOS)[5,6,7,8] then the energy dissipation per logic operation can be reduced to well below kT at T = 300 Kelvins (well below 10^-21 joules).

The computer industry is spending billions of dollars to make better computers. It is widely acknowledged within the industry that lithography is approaching its limits. Articles like The Future of the Transistor[1], Miniaturization of Electronics and its Limits[9] and Outlook for VLSI: Will the Balloon Burst?[10] quite clearly show that conventional lithography will run out of steam (in perhaps a decade, though there is less agreement about the exact time frame). There is already interest in molecular logic devices[11] and that interest will increase sharply as improvements in conventional manufacturing methods become increasingly difficult. However, any new proposal for manufacturing molecular computers will be weighed against (at least) the criteria mentioned above. If it cannot easily beat conventional methods after they have been pushed to their uttermost limits, then it will be rejected. The computer industry will soon be pouring vast sums into research aimed at molecular computing, but the great bulk of funding will go towards well thought out proposals that offer a realistic possibility of substantially exceeding the performance of the ultimately evolved silicon VLSI technology that we expect to develop over the next decade. If you can't beat tomorrow's mainstream computers, you might as well not try.

The Problem

For this and many other reasons the class of diamondoid structures is a reasonable one to consider. The problem of building a diamondoid electronic computer captures many of the fundamental issues in molecular manufacturing, and poses clearly the issue of building large structures that cannot be made by regular repetition of some substructure (e.g., the unit cell of a crystal or the monomeric unit in a bio-polymer).

This brings us to a core issue in molecular manufacturing: how do we synthesize such things?

How We Make Diamond Today

Today, we can synthesize diamond at low pressure and low temperature by using CVD (Chemical Vapor Deposition) methods[12,13]. Diamond CVD growth involves highly reactive species (radicals, carbenes, etc.) in a gas over the growing diamond surface that bombard and react with that surface at random. Because reaction sites are random, growth of many defect structures occurs (dislocations, etc.) as well as the desired perfect diamond structure.

Two fundamental mechanisms in the growth process include (1) abstraction of hydrogens from the diamond surface leaving behind reactive sites (dangling bonds, radicals) and (2) interaction of carbon species (both reactive (CH2, CH3, etc.) as well as relatively unreactive species (C2H2)) with the surface, thus depositing carbon.

If we are to synthesize diamondoid structures it is plausible that we begin our search for the basic reaction steps involved in this synthesis by looking at existing reactions that occur in the CVD growth of diamond. The use of a reactive gas in the synthesis process, however, would seem to defeat any hope of making precisely patterned diamondoid structures, for the gas will interact with the growing surface at random.

Positional Control is Fundamental

Here, we introduce the fundamental concept of molecular manufacturing: positional control over the site of reactions. To take a specific example we consider site specific hydrogen abstraction from the diamond (111) surface. The ability to remove specific hydrogen atoms from the surface of the diamondoid work piece under construction is likely to be a fundamental unit operation in any attempt to make atomically precise diamondoid structures.

Hydrogen abstraction during CVD diamond growth typically involves a radical reaction between atomic H from the gas with H bonded to carbon on the surface producing H2. It is unclear how to make this process site specific. However, there are other structures with a high affinity for hydrogen which offer greater possibilities for positional control. In particular, the propynyl radical C3H3 (figure 1) has a great affinity for hydrogen. Further, this radical has the very useful property that it has two ends: one end is a highly reactive radical while the other end is a stable sp3 carbon. Thus, we could synthesize a larger molecule with the propynyl radical at its end. The larger molecule would be held at the tip of a positional device. The positional device would provide control over the orientation and position of this hydrogen abstraction tool (e.g., a six degrees of freedom manipulator) and thus control the site of abstraction by controlling the position of the tool.

Figure 1. A site specific hydrogen abstraction tool.

Ab initio quantum chemical analysis of the abstraction of hydrogen from isobutane using an ethynyl abstraction tool supports the idea that the barrier to this reaction is zero[14]. The reaction will proceed rapidly and, because of the large exothermicity, irreversibly. Calculated barriers for abstraction from several other molecules were also small, suggesting that this hydrogen abstraction tool could be used to abstract hydrogen from a wide range of different molecules. Molecular dynamics simulations[14b] provide evidence that the abstraction reaction will select the correct hydrogen atom in the face of thermal noise at room temperature, as well as providing further support for the basic mechanism.

The site specific abstraction of hydrogen illustrates the core concept in molecular manufacturing: selecting the reaction site by controlling the position and orientation of the reactants. The (relatively stiff) diamondoid workpiece is held in place, while a tool (in our example, a hydrogen abstraction tool) is positioned using a rather conventional (if also rather small) robotic arm[15]. The ideas of using tools, controlling the position of those tools with a general purpose manipulator, and building complex structures by putting together components using those positionally controlled tools are rather common and even mundane at the macroscopic level. At the molecular level, they are new and almost shocking: yet it is simply mapping onto the molecular world the concepts and ideas that have proven so useful and powerful in macroscopic manufacturing. By adding positional control we should be able to develop a method of molecular manufacturing which combines the best features of both conventional macroscopic manufacturing and chemical synthesis.

Other Molecular Tools

If we are to grow diamond, we must also have carbon deposition tools. Drexler has suggested the use of positionally controlled carbenes (figure 2) and alkynes (figure 3) and proposed reaction pathways and surface structures where these tools would apply[4]. In both cases, the tools are positioned at a precise point on the growing diamondoid structure and are used to deposit one or more carbon atoms at a desired location. These deposition reactions parallel proposals in the CVD literature except for the addition of positional control (e.g., at least one portion of the moiety must be part of an extended "handle" which can be held by a positional device). These are only two examples from the wide range of tools that are capable of depositing carbon on a surface.

Figure 2. A positionally controlled carbene

Figure 3. A positional controlled strained cycloalkyne

The broad range of possible tools coupled with the great power of ab initio computational chemistry should let us define and verify a complete set of molecular tools capable of synthesizing essentially any diamondoid structure. The work by Musgrave et. al.[14] and Sinnott et. al. [14b] are first steps toward this objective. Modern ab initio methods can produce results that are sufficiently accurate for this type of analysis[16, 17]. Further research in this area is feasible and should be pursued.

The Context of Tool Use

For such tools to be usable in a system context we must satisfy certain constraints. First and foremost, we must have a device capable of positioning the tool to within something like an atomic diameter. On the diamond (111) surface, the distance between adjacent hydrogens is about 2.5 Angstroms. Thus, positional accuracy of 1 to 2 angstroms for the hydrogen abstraction tool is required to prevent abstraction of the wrong hydrogen. Second, because the tools can be highly reactive, we require an inert environment. A simple inert environment is vacuum. Compressed helium or some other inert gas would also work. Third, because it is the relative tool-workpiece position that must be controlled, the workpiece under construction must be relatively rigid (e.g., not subject to vibrational motions that would exceed about an angstrom). Fourth and last, we must have some way of generating the sometimes highly reactive tools (e.g., we need to define a precursor to the hydrogen abstraction tool, as well as precursors to the other tools).

In some sense, the analysis that we will now pursue is similar in type to retrosynthetic analysis[18]. We start with the final product that we wish to build (a macroscopic diamondoid computer, for example), and then consider the possible predecessor structures which would yield the final product in one step. Then we consider the predecessor structures to those structures, and so on. We extend retrosynthetic analysis beyond its traditional bounds, but the general concept remains the same: given the finished product we deduce the possible ways in which it could have been constructed. This approach has been called "backwards chaining" by Drexler[4].

Positional Devices and Molecular "Arms"

Work with SPMs (Scanning Probe Microscopes)[19] clearly show that it is possible to achieve positional accuracies of a small fraction of an angstrom. Small (~0.1 microns) diamondoid "arms" or positional devices with similar positional accuracy are in principle quite feasible. The field of robotics provides a broad range of designs for positional devices[15] which are largely scale independent. Shrinking these designs to submicron size is conceptually straightforwards. A factor of crucial importance in the design of molecular-scale positional devices is the accuracy with which the tip can be positioned, particularly in the face of thermal noise. While atomically precise bearings and joints will not suffer from chatter, backlash, wear, tooth-to-tooth errors and other sources of inaccuracy caused by imprecise manufacturing[4, 20], they will still suffer from positional errors caused by thermal noise. To control this source of error, it is essential that the robotic arm be very stiff, and so the use of stiff materials is desirable. The Young's modulus for diamond is about 10^12 Pascals (very stiff), and back-of-the-envelope calculations show that a hollow cylinder of such material that is perhaps 100 nanometers long and 30 nanometers in diameter should have a positional accuracy at the tip, in the face of thermal noise at room temperature, of a small fraction of an atomic diameter. A more detailed design and analysis of a jointed tubular robotic arm taking into account the bending and rocking motions of joints in the arm further supports this conclusion[4].

Alternatives to the simple robotic arm are available which might be more attractive.

Other Requirements for Tool Use

Creating an inert environment also presents no fundamental problems: high quality vacuums are common in laboratories today. If our objective is to have a very small very high quality vacuum, then a relatively thin wall of diamondoid material could be used as a barrier to keep a volume which was a modest fraction of a cubic micron free of any contaminants. If the volume were initially constructed free of contaminants then such a barrier would keep the inside free of any contaminants with high probability.

Because we are building diamondoid structures, they will be very stiff. As a consequence, it is relatively easy to meet the requirement that the objects that are being manufactured must themselves be stiff.

Finally, generation of "activated" tools from relatively stable precursors can be done by a variety of methods. Because we are assuming an environment in which we have positional control we can use particularly simple precursors. We illustrate this by considering a precursor to the hydrogen abstraction tool (see figure 4). This precursor has two handles, and X is chosen so that the X-C bond is weaker than the C-C bond. X might be Si or Ge. If we pull on the two handles with sufficient force, something will break. Because the X-C bond was deliberately selected to be weaker than the other bonds in the structure, it will break. This gives us the activated hydrogen abstraction tool.

Figure 4. A possible precursor to the hydrogen abstraction tool of figure 1.

A related question is: how can we get the hydrogen off the tip of the abstraction tool? A simple answer is: don't. Throw the tool away after one use. In a system design using this approach, it would be necessary to provide a continuous stream of precursors. These would be activated, used once, and then discarded. A more elegant approach would be to remove the hydrogen from the tip and recycle the tool, as discussed by Drexler[4] and Musgrave et. al.[14].

More generally the activation of relatively stable precursors can be done by using any of several forms of energy: mechanical, optical, chemical or other. While the use of mechanical means to provide the activation energy for chemical reactions is relatively novel, in an environment where positional control is already available it is quite natural.

Selective Transport Across a Barrier

Having introduced a diamondoid barrier to keep unwanted contaminants out (much as the bacterial wall allows bacteria to maintain an appropriate internal environment in the face of a fluctuating external environment) we must now solve the problem of getting desired raw materials through the barrier. We might, for example, wish to transport the hydrogen abstraction tool precursor across the diamondoid barrier. After use we will also need to eject the spent tool. Several ways to solve this problem are feasible. A proposal by Drexler is to use a rotor embedded in the diamondoid wall which moves binding sites from the outside of the wall to the inside of the wall (figure 5 [4, page 378]). By modulating the affinity of the binding site so that it will have high affinity for the desired molecule outside the barrier and low affinity inside the barrier, efficient transport across the barrier can be achieved. The desired molecule will bind to the binding site when it is outside the barrier, the binding site will be rotated to the inside of the barrier and the binding affinity reduced (in the illustrated proposal by mechanically pushing a rod into the binding site, thus physically precluding occupancy), and the molecule will be released on the inside of the barrier. The result is to increase the concentration of the desired molecule. A few stages of such a filtration system can achieve extremely high purities. The final stage, rather than ejecting the molecule into a liquid, would deliver the molecule into the inert internal environment in a well defined orientation where it could be further processed. One simple method of further processing would be for the oriented molecule to be directly transferred to the tip of the positional device.

Figure 5. Selective transport of desired molecules across a diamondoid barrier. (From Nanosystems: molecular machinery, manufacturing and computation)


Control Signals

Finally, we will need a source of control signals for our molecular arm. One general approach would be to use a molecular computer. We will not consider a particular design for a molecular computer here, it is sufficient to note that many proposals for molecular computation have been considered in the literature and it is generally expected that some type of very small computational device will be feasible in a few decades[4, 11].


This completes our (all too brief) outline of a small device able to manufacture a broad class of diamondoid materials. Basically, the design is driven by the desire to provide the environment needed to synthesize diamond and diamondoid materials using the kinds of reactions that occur naturally during CVD growth of diamond. The device is itself made from diamondoid materials, which means that one such device can manufacture a second such device. This ability to self replicate is crucial in achieving low manufacturing costs. As the reader might appreciate, the design and construction of one such general purpose device might well prove to be a time consuming and expensive undertaking. This cost cannot be justified unless the resulting device has great value. If the device can self replicate then the successful design and development of one such device can be used to build an entirely new manufacturing technology. The manufacturing costs for the second, third, fourth, .... 10^10.... etc. devices will consist largely of the raw materials and energy costs. Thus, a very large R&D cost can (if necessary) be justified.

A number of technical issues involved in self replicating systems are discussed in Self Replicating Systems and Molecular Manufacturing [21] while some of the obvious safety issues are discussed in The Risks of Nanotechnology[22].

Bricks Without Vacuum

The major driving force in the previous design was the desire to approach fundamental limits (strength, stiffness, thermal conductivity, electrical characteristics, etc.) in the manufactured products. This in turn implied the use of diamondoid materials, which, when coupled with the known chemistry of CVD diamond synthesis resulted in a high vacuum system with highly reactive intermediates.

Relaxing the materials requirements gives us a much wider range of possible structures. In particular, we can consider what is sometimes called "brick" or "building block" based nanotechnology. In this approach we first design a set of molecular building blocks, and then assemble the building blocks by the use of positional control. The ribosome can be viewed as the prototype for this approach. The building blocks are amino acids, and they are linked together by the ribosome to form proteins. Our approach differs in two principle respects: first, we add positional and orientational control over the building blocks in three dimensions, while the ribosome can only build structures that are fundamentally one dimensional (relying on linear structures that spontaneously fold into a particular shape to achieve a degree of control in three dimensions). Second, rather than using relatively floppy polymers, we prefer relatively rigid bricks that can be bonded to each other in a stiff three-dimensional framework.

In general, molecular structures built of bricks will be (a) larger (b) weaker (c) less stiff (d) have poorer thermal conductivity (e) have poorer electrical properties (f) etc. etc. etc. The sacrifice made in materials properties is significant. On the other hand, many bricks can be assembled in more conventional environments (solution), and so we can eliminate the need for vacuum. This greatly simplifies the system. Indeed, with brick-based nanotechnology one can relatively easily envision the synthesis of a set of bricks that can, with the addition of positional control, be assembled into a wide range of structures with the stiffness of (say) wood.

Molecular Manipulators

A conceptually simple and relatively near-term way to achieve some degree of positional control would be to use conventional SPMs. The tips used in current SPM's are usually quite crude, and even when it is possible to make a very fine tip the range of possible structures is very limited (tungsten or some other simple material is generally all that's available). The design of tips for the SPM that incorporate individual molecules specifically synthesized for the purpose is a likely next step, and one that seems essential if we are to make progress in using SPM's to guide chemical reactions in a selective way.

Such a "molecular manipulator" should be within reach of today's experimental technology. While the Young's modulus of the things it could make would be substantially inferior to that of diamond, this can be compensated by making them bigger. Scaling laws are such that increasing the size of an object by a factor of 10 also increases its stiffness by a factor of 10, and so reduces the positional inaccuracy from thermal vibration by a factor of 10. If we wish to build a molecular "arm" out of bricks, then to achieve the same positional accuracy as with a diamondoid arm we will have to make the arm bigger -- perhaps several tenths of a micron or more -- but the basic design concepts that were discussed previously for use with a diamondoid arm still hold. We can still position the individual bricks accurately both in position and orientation, we can still build larger structures by putting together many bricks, we can still control the synthesis process by positional means, we can still make a positional device from bricks, etc.

Why pursue such an approach when it can only make relatively inferior materials? There are three primary reasons: (1) it's easier to do (2) it could still make many things that are very valuable by today's standards and (3) such systems could be used to make better systems (e.g., diamondoid systems).

As the reader will appreciate, there are many possible candidates for bricks. Many researchers are already considering the design of molecular building blocks[23], although in most cases they do not consider positional control. Krummenacker discusses several of the issues surrounding the design of molecular bricks intended for assembly via positional control[24]. Adding positional control makes the synthesis of a broad range of molecular structures feasible, but at the same time requires the design and synthesis of a mechanism able to provide such control. The obvious first step is to provide positional control using relatively modest extensions to today's SPMs. The most significant addition is the inclusion of a molecular tip, for today's SPMs typically have a limited range of possible tip structures and are often imprecise at the molecular scale.


The long term goal of molecular manufacturing is to build exactly what we want at low cost. Many if not most of the things that we'll want to build are complex (like a molecular Cray computer), and seem difficult if not impossible to synthesize with currently available methods. Adding programmed positional control to the existing methods used in synthesis should let us make a truly broad range of macroscopic molecular structures. To add this kind of positional control, however, requires that we design and build what amount to very small robotic manipulators. If we are to make anything of any significant size with this approach, we'll need mole quantities of these manipulators. Fortunately, any truly general purpose manufacturing device should be able to manufacture another general purpose manufacturing device, which lets us build large numbers of such devices at low cost. This general approach, used by trees for a very long time, should let us develop a low cost general purpose molecular manufacturing technology.

While we have focused in this article on diamondoid structures and molecular computers based on semiconductors such as diamond, it will probably be easier to first make systems that rely on materials that are simpler to synthesize but whose material properties are not as good as diamond. The general concept of positional control, however, still applies. A future article will discuss in greater detail the design of such simpler systems, and how they can form a stepping stone to mature molecular manufacturing.

Many challenges must be met and it will be many years before we develop molecular manufacturing; but the goal is worthwhile, achievable, and offers great rewards both financial and scientific.


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