© 1999 Robert A. Freitas Jr. All Rights Reserved.

Robert A. Freitas Jr., Nanomedicine, Volume I: Basic Capabilities, Landes Bioscience, Georgetown, TX, 1999

2.3.2 Molecular and Supramolecular Chemistry

A second broad category of enabling technology for molecular manufacturing includes molecular chemistry -- the conscious design of completely artificial, nonbiological chemical structures that could potentially serve as molecular "parts" or which have specific devicelike functionality.^10,322 For example, catalysts may very loosely "be thought of as rudimentary assemblers that are slightly programmable through changes in the reaction milieu (i.e., changes in pH, temperature, etc.)".²⁶⁰³ The number of natural molecular "parts" is immense -- perhaps a few hundred thousand bioorganic compounds have been separated, purified and identified -- but by 15 February 1999 chemists had already registered 19,245,458 well-characterized artificial molecules or other "substances" in the CAS Registry.²⁸⁶³ Synthesis of natural molecules containing ~100 atoms (e.g., a ~1 nm³ molecular "part"), using methods of classical organic synthesis often requiring ~1 synthesis step per atom with ~90% yield per step,²⁵⁵³ was state-of-the-art in 1998.

"What is exciting about modern nanotechnology," says Nobel chemist Roald Hoffmann,³¹⁷⁴ "is (a) the marriage of chemical synthetic talent with a direction provided by 'device-driven' ingenuity coming from engineering, and (b) a certain kind of courage provided by those incentives, to make arrays of atoms and molecules that ordinary, no, extraordinary chemists just wouldn't have thought of trying. Now they're pushed to do so. And of course they will. They can do anything."

Molecular chemists study how small numbers of atoms combine covalently with each other to produce molecules with a wide variety of different properties. Supramolecular chemists are primarily concerned with the much weaker noncovalent forces that can arise between molecules -- such as hydrogen bonds and van der Waals interactions -- that can be sufficient to bind collections of molecules tightly enough to form functional nanometer-sized structures. Supramolecular chemistry^{765,2445,2446} studies "chemistry beyond the molecule"⁷⁶⁵ or "the chemistry of the noncovalent bond".²⁵²³ Its subject matter includes atomically precise supermolecules (well-defined discrete oligomolecular species resulting from the intermolecular association of a few components, such as a receptor and its substrate) and polymerlike supramolecular assemblies (polymolecular entities that result from the spontaneous association of a large undefined number of components).

Self-assembly is a key concept in supramolecular chemistry^{2433,2455,2456,2491,2527} as it is in nature,²⁹⁶⁸ allowing the manufacture of large numbers of compound objects simultaneously and in parallel, rather than sequentially. Molecular self-assembly is a strategy for nanofabrication that involves designing molecules and supra-molecular entities so that complementarity causes them to aggregate into desired structures. Self-assembly of atomically precise supermolecules thus demands well-defined adhesion between selected molecules, which may require steric (shape and size) complementarity, interactional complementarity, large contact areas, multiple interaction sites, and strong overall binding.⁷⁶⁵

G.M. Whitesides²⁴³³ explains that self-assembly has a number of advantages as a strategy. First, it carries out many of the most difficult steps in nanofabrication -- those involving the smallest atomic-level modifications of structure -- using the very highly developed techniques of synthetic chemistry. Second, it draws from the enormous wealth of examples in biology for inspiration; self-assembly is one of the most important strategies used in biology for the development of complex, functional structures, such as the well-studied examples of complex biomachine self-assembly of whole bacteriophage virions^{1179,1180,2434,2435} and flagellar rotor motors^216,581,1397 from their smaller molecular "parts". Third, self-assembly can incorporate biological structures directly as components in the final systems. Fourth, self-assembly requires target structures to be among the most thermodynamically stable available to the system, thus tends to produce structures that are relatively defect-free and self-healing. As Lehn⁷⁶⁵ points out: "By increasing the size of its entities, nanochemistry works its way upward towards microlithography and microphysical engineering, which, by further and further miniaturization, strive to produce ever smaller elements". Hierarchical self-assembly of many billions of micron-scale spherical components into a periodic honeycomb-structured photonic crystal optical device ~30 microns thick and ~1 cm² in area was demonstrated in 1998.²⁴⁶¹

There is a wide range of different molecular systems that can self-assemble, including those which form ordered monomolecular structures by the coordination of molecules to surfaces,²⁶⁰⁹ called self-assembled monolayers (SAMs),^{2433,2455,2565} self-assembling thin films^2455,2564 and Langmuir-Blodgett films,²⁶⁰⁸ and self-organizing nanostructures.^123,2563 In these systems, a single layer of molecules affixed to a surface allows both thickness and composition in the vertical axis to be adjusted to 0.1 nm by controlling the structure of the molecules comprising the monolayer, although control of in-plane dimensions to <100 nm is very difficult. Fluidic self-assembly of microscale parts¹¹⁵⁰ and the dynamics of Brownian self-assembly²⁸⁸⁹ have also been described, and the theory of designable self-assembling molecular machine structures is beginning to be addressed.²⁹⁵⁶

Another approach using solid-phase peptide synthesis and a massively convergent self-assembly process was employed by M.R. Ghadiri and colleagues,^2436-2440 who designed and synthesized a number of self-assembling peptide-based nanotubes using cyclic peptides with an even number of alternating D- and L-amino acids for the building blocks of the nanotubes. The alternating stereo-chemistry of the cyclic peptides allowed all the side chains of the amino acids to be pointing outwards which would not be possible in an ordinary all L-cyclic peptide. In this conformation, the amide backbone can H-bond in a direction perpendicular to the plane of the cyclic peptide. The stacking of two cyclic peptides forms an H-bonding network resembling an antiparallel beta-sheet²⁴⁴¹ as is commonly found in natural proteins. The H-bonding lattice quickly propagates perpendicular to the plane of the cyclic peptide, forming a tubular microcrystalline structure with 0.75-nm pores, or, in another experiment, 1.3-nm pores.²⁴⁴² Another group of nanotubes was designed with a highly hydrophobic outer surface and a hydrophilic inner pore. These nanotubes were easily inserted into a lipid bilayer and have been shown to be highly efficient ion channels;^1177,2440 nanotubes with slightly larger pores transport small molecules such as glucose as well.²⁴⁴³ Stable flat nanodisks with diameters continuously (chemically) adjustable from 30-3000 nm have been self-assembled in surfactant solutions.²⁹³⁴

Self-assembled crystalline solids such as zeolites^{2447,2468,2469} incompletely fill space, leaving substantial voids that may be occupied by solvent molecules or other guest molecules, producing solid-state host-guest complexes known as clathrates (from the Latin clathratus, meaning "enclosed by the bars of a grating"). MacNicol and coworkers²⁴⁵³ reported the first rationally designed clathrate host in 1978, but the first true de novo design of an organic clathrate was in 1991²⁴⁵⁴ and involved the formation of an extensive three-dimensional diamondlike porous lattice built from a single Tinkertoy-type subunit containing four tetrahedrally arrayed pyridone groups that acted as connectors to assemble the units together in a well-defined geometry. However, the crystal was held together only by weak hydrogen bonds and the links had a rotational degree of freedom, rendering the exact crystal molecular arrangement unpredictable.²⁸⁵⁰ Engineered nanoporous molecular crystals can provide molecular-scale voids with controlled sizes, shapes, and embedded chemical environments at resolutions of 0.3-4.0 nm.^{430,431,695,1522,2447-2449} Other self-assembling crystal structures have been described^2494,2561 including the crystal engineering of diamondoid networks,²⁶⁷⁸ template-directed colloidal crystallization or colloidal epitaxy,²⁸³⁷ organic templating to form crystalline zeolite-type structures with ordering lengths <3 nm,²⁸⁹² 3-D polymer channels with chemically functionalizable channel linings,²⁹²¹ and micromolding combined with templating and cooperative assembly of block copolymers (Section 3.5.7.1) to produce hierarchical ordering over discrete and tunable characteristic length scales of ~10 nm, ~100 nm, and ~1000 nm in a single body.²⁸⁹³

Dendrimers,^{2470,2531,2580-2591} also known as arborols or fractal polymers, are a well-known set of self-assembling structures²⁶¹⁰ that possibly could be used as tools to assist in the assembly of early nanomachines. Dendrimers are large regularly-branching macro-molecules resembling fractal patterns, made by an iterative process in which small linear molecules are allowed to bind to each other at a certain number of sites along their length, building up branches upon branches with each iteration working outward from a core molecule having at least two chemically reactive arms, somewhat mimicking tree growth (e.g., Fig. 2.20C). Different core molecules or building-block chains produce macromolecules with different shapes, and the outer surface can be terminated with chemical groups of specific functionality, producing hundreds of differently-surfaced branched molecules²⁴⁷¹ that have already found use in medical research.²⁶⁷¹ Growth is regulated, so size can be accurately controlled -- dendrimers are typically a few nanometers wide but have been constructed with masses exceeding a million protons (~10⁵ atoms) and with diameters larger than 30 nm. In 1999, convergent assembly of specified 6-mer dendrimers, via trimerization of precursor dimer "parts," was demonstrated.³²⁷⁵

Autocatalysis or self-replication (Section 2.4.2 and Chapter 14) is yet another approach to the chemical self-assembly of subunits. In 1989, J. Rebek^{131,2450-2452} reported the synthesis of super-molecules that could generate copies of themselves when placed in a sea of simpler molecular parts, with each component part consisting of up to a few dozen atoms. Molecular self-replication has continued to be studied by others.^{2524-2526,2602} Ghadiri²⁴⁵⁷ reported a self-replicating peptide in 1996, and by 1998 his laboratory had moved on to studies of more complex autocatalytic cycle networks.^2458-2460 It is unknown how complex such assembly cycles may be made, but Ghadiri was investigating a self-replicating 256-component molecular ecosystem incorporating ~32,000 possible binary interactions,²⁶⁰¹ in 1998.

By 1998, chemists had already synthesized a vast variety of simple molecular parts of which only a tiny sampling can be mentioned here. For instance, carbon rings have been linked edge-on or by corners to create propeller-shaped molecules called propellanes²⁴⁹⁷ (Fig. 2.4) or rotanes (Fig. 2.5), or stacked with short hydrocarbon links to make gear-looking molecules such as cyclophane²⁴⁹³ and superphane (Fig. 2.6). Hydrocarbon molecular polyhedra in the shape of triangular (e.g., triangulane²⁵⁷¹), cubic (e.g., cubane, first made by P. Eaton in 1964²⁵⁷⁰), pentagonal and hexagonal prisms, collectively known as prismanes, have been created (Fig. 2.7), along with more unusual geometrical forms such as paddlane, housane, basketane, churchane, pagodane, and bivalvane³⁸² (Fig. 2.8; one carbon atom at each vertex). Cryptands,²⁴⁷⁹ spherands,²⁴⁹² cryptaspherands and carcerands,⁴¹⁰ corannulene baskets,²⁶³⁹ and calixarenes⁴¹¹ are bowl-shaped molecules whose benzene ring walls hold their cavities rigid. The bowl rim of a calixarene (Fig. 2.9) can be lined with chemical groups to determine which guests it will accept, or two bowls can be bonded together,²⁵⁴⁷ making a hollow nanoscale reaction vessel, and various molecular cages and capsules with precise sizes and characteristics have been assembled.^{1262,2549-2551} A variety of nonchiral and chiral square molecules have been synthesized,^2473,2543 as well as molecular "bottlebrushes";²⁴⁷⁵ DNA-polymer constant-force springs;^2476,2477 the ferric wheel (Fig. 2.10);²⁵⁵² molecular barrels²⁵⁵⁸ and molecular tennis balls;²⁵⁵¹various helical,^{2554-2556,2569,2605,2638} boxlike,²⁵⁵⁹ and other hollow organic²⁵⁷² structures; molecular "turnstiles"²⁵⁷³ and "molecular tweezers";²⁶⁷⁷ simple and complex trefoil knot molecules;²⁵⁶² and stable carbyne* molecular rods with chain lengths up to ~300 carbon atoms having alternating single and triple covalent bonds.³¹⁷ Chemists are justifiably awed by the creation of structures like the ferric wheel; "for me," observed Nobel chemist Roald Hoffmann,¹²⁵ "this molecule provides a spiritual high....The molecule is beautiful because its symmetry reaches directly into the soul, [playing] a note on a Platonic ideal."

* In chemical nomenclature, hydrocarbons with single carbon-carbon bonds are "-anes," double bonds make "-enes," and triple bonds make "-ynes."

Molecular gear systems first became a popular object of chemical study during the 1980s. For example, G. Yamamoto¹⁶⁴ described "compounds that exist in conformations which are regarded as static meshed gears with two-toothed and three-toothed wheels and some of them behave as dynamic gears." H. Iwamura¹⁶³ prepared one system that formed a chain of beveled molecular gears with ~GHz rotation rates, and another "doubly connected bevel gear system...[Transfer] of information from one end of the molecular system to the other end could take place in large molecules via cooperativity of the torsional motions of the chain." Kurt Mislow²⁴⁷² gave numerous examples of molecular gear systems that he had synthesized using the methods of traditional solution chemistry, which "resemble to an astonishing degree the coupled rotations of macroscopic mechanical gears." He added: "It is possible to imagine a role for these and similar mechanical devices, molecules with tiny gears, motors, levers, etc., in the nanotechnology of the future."

In 1998, Gimzewski and coworkers²⁴⁷⁴ synthesized and observed a 1.5-nm diameter gearlike single molecule (hexatertbutyl decacyclene) rotating within a supramolecular bearing (a void in a 2-D lattice) at room temperature on the surface of a Cu{100} lattice. The authors suggest that added nonthermal noise (e.g., temperature differences produced by tunnel current heating of the rotor) could be rectified by asymmetries in the rotor/neighbor potential energy curve, allowing the rotor to turn unidirectionally. Says Gimzewski: "Our wheel is frictionless in the conventional sense of the word, and it doesn't wear out." Gimzewski's experimental work confirms Drexler's calculations¹⁰ that van der Waals bearings can operate in molecular systems, that multiatomic bearing surfaces with higher load capacities than sigma bond bearings can be built, that these bearings can run with no lubricants, and that such bearings have sufficiently low energy barriers to allow turning by thermal vibrations alone.

By 1998, limited control of the mechanical action of molecular parts had been demonstrated. For example, in 1994 T. Ross Kelly's group created a "paddlewheel" molecule (a spinning propeller-shaped wheel) with a built-in chemically-controlled brake. In solution, the wheel spins freely, but when Hg⁺⁺ ions are added, a blocking ligand physically rotates into a new position (tripping the brake) and stopping the rotation; removal of the mercury causes the wheel to spinning.¹⁷ In 1997, Kelly's group used similar techniques to synthesize the first molecular ratchet,²⁵⁴⁶ a propeller with three benzene ring "blades" that serve as gear teeth. A row of four rings (the pawl) sits between two of the blades, such that the propeller cannot turn without pushing it aside; because of a twist in the pawl, it is easier to turn clockwise than counterclockwise under thermal agitation, providing mechanical rectification without net motion or energy extraction.²⁶¹¹ Shinkai and colleagues^382,2478 fabricated a pair of molecular tongs for grasping metal ions that uses two crown ether rings as the jaws, linked by two benzene rings joined through two double-bonded nitrogen atoms (Fig. 2.11). Irradiation with ultraviolet light induces photoisomerization of the double bond between the nitrogen atoms, closing the jaws; heat reverses the process, opening the jaws. In related systems, collectively called "butterfly molecules," irradiation with visible light or pH changes can also induce opening. Seeman's chemically-operated mechanical DNA system²⁴⁰⁹ provides similar control of molecular mechanical movement (Section 2.3.1). Numerous controllable molecular electronics devices and possible nanocomputer components are reviewed in Section 10.2.

Noncovalent self-assembly of molecular parts has also been demonstrated. For example, Fraser Stoddart and colleagues^{1805,2482-2484} have extensively investigated the rotaxanes,²⁴⁸¹ molecules in which one part is threaded through a hole or loop in another, and kept from unthreading by end-groups, like a ring trapped on a barbell. In one system (Fig. 10.8), a ring-shaped molecule slides freely along a shaft-like chain molecule, moving back and forth between stations at either end with a frequency of ~500 Hz, making an oscillating "molecular shuttle".²⁴⁸³ This shuttling behavior can be controlled by a series of different chemical, electrochemical, or photochemical external stimuli.^2484,3541 Using a different approach, G. Wenz²⁴⁸⁷ threaded ~120 molecular beads onto a single, long, poly-iminooligomethylene polymer chain, making a "molecular necklace." Other groups are pursuing related research^{2522,2529,2530} regarding [n]rotaxanes^2538,2539 and pseudorotaxanes (mechanically-threaded molecules),^2541,2542 while still others are using the necklace technique as a means, for example, of self-assembling ~2 nm wide cyclodextrin nanotubes.²⁴⁸⁸

Another interesting molecular system that can be made entirely by self-assembly is the catenanes,²⁴⁸¹ which have two or more closed rings joined like the links of a chain. The rings are mechanically linked -- there are no covalent bonds between separate links. The first [2]catenane (2 linked rings) was constructed by Edel Wasserman of AT&T Bell Laboratories in 1960, using simple hydrocarbon rings; the first [3]catenane was synthesized in 1977. In 1994, Fraser Stoddart and David Amabilino constructed the first [5]catenane,²⁴⁸⁵ having ~372 atoms, dubbed "olympiadane" because of its resemblance to the Olympic rings, and in 1997 the same group announced the first deterministically-ordered 7-ring heptacatenane;²⁵³⁵ another group later reported the spontaneous self-assembly of a 10-component catenane.³²⁸⁵ By 1998, much research on larger polymeric chains of linked rings (e.g., oligocatenanes²⁵³²), supramolecular "daisy chains",^2533,2534 fullerene-containing catenanes,²⁵³⁶ and supramolecular weaving²⁵³⁷ was in progress. The smallest [2]catenane constructed to date has dimensions 0.4 nm x 0.6 nm.²⁵²⁸ Self-assembled mechanically-interlocked 2-dimensional^2595-2597 and 3-dimensional^2598,2599 "infinite" arrays of single molecular ring-like species are known. Interestingly, in 1998 it was discovered that many viral coats (which also self-assemble) appear to be a 2-dimensional "chain-mail" weave of mechanically-interlocked protein rings -- for instance, the spherical bacteriophage HK97 capsid shell consists of exactly 72 interlinked protein rings, specifically 60 hexamers and 12 pentamers.²⁴⁸⁶

Complex molecular parts also can be built up from simpler molecular parts by covalent bonding as low-symmetry shape-invariant molecular object polymers,²⁶⁹² or via processes variously known as modular chemistry,^2498,2499 heterosupramolecular chemistry,³²²⁰ chemical assembly,³⁵⁴¹ or structure-directed synthesis^2489,2490 -- including the well-known Diels-Alder reactions²⁵⁵⁷ (e.g., see Fig. 2.20F) which may be employed repetitively to fabricate a series of atomically-precise molecular rods, rings, and nanocages (e.g., "beltenes" and "collarenes"²⁴⁸⁹) composed of polyacenequinone units with nanometer-scale dimensions. Such efforts have been described as steps toward "molecular LEGO",²⁴⁸⁹ "molecular Meccano",²⁴⁸⁰ "molecular Tinkertoys",^{2509-2516,2842} or "molecular building blocks".²⁸⁵⁰ Some structure-directed assembly has been achieved with simple DNA forms.¹⁹¹⁶ Other simple techniques for synthesizing nanowires,⁶⁴³ nanorods,^2672,2710 nanotubes,^{1411,2673,2674,2862} and nanocages,^{2640,2675,2862} or for selecting polymers for length,²⁶⁸⁶ are well-known.

For instance, Jean-Marie Lehn²⁶⁷⁹ has created rectangular grid complexes by mixing rodlike ligands that make use of different numbers of binding sites -- one example is a 4 x 5 array consisting of nine ligands and 20 metal ions, nanoscale grids which he claims might one day find use "as components within a futuristic information storage and processing nanotechnology". C.M. Drain^2680,2681 has described a 21-component (5 nm)² square array of nine porphyrins tethered together by 12 palladium ions shaped like a four-pane window. The structure is built from three different kinds of porphyrins -- (1) an X-shaped unit that coordinates to four metal ions, forming the center of the array, (2) a T-shaped unit that coordinates to three metals and forms each side of the array, and (3) an L-shaped unit that coordinates to only two metals and forms each corner of the array. When these components are placed in solution in the correct ratio, they form the square array within a half hour at room temperature with about 90% yield. The same porphyrin units can be combined in different ratios and induced to form wires or tapes. The properties of such arrays can be fine-tuned by choosing the appropriate metal ion linker and functionalized porphyrin unit.²⁶⁷⁹

Jeffrey Moore has investigated a three-dimensional nanoscaffolding comprised of a molecular lattice that could serve as a framework for catalysts, photosynthetic molecules, or more complex molecular devices. Moore's original objective was to synthesize modular building blocks with physical and chemical properties that would dictate a "programmed assembly" protocol for "nanoarchitectures".^2574-2579 The characteristics of each modular unit shaped the weak intermolecular attractions -- electrostatic, van der Waals, and hydrogen-bonding forces -- between it and its neighbors so that units would array themselves in a larger structure with the desired spacing and geometry. Moore's group first linked phenylacetylene subunits into oligomers of various lengths which bend and twist like wire sculptures until their ends meet to form closed polyhedral molecules -- the basic scaffold components (of which there were at least half a dozen shapes). These building blocks then self-assembled or folded²⁵⁵⁵ into geometries at least partly controlled by designed hydrogen-bonding interactions. The molecular polyhedra each possessed several phenylene groups, "chemical handles" upon which other molecular groups could be hung. Moore then focused on ~10-nm dendrimeric forms^2580-2585 and later began attaching photosensitive antenna molecules to these structures.^2586-2591 By 1997, Moore had begun investigating norbornadiene on Si{100} in an effort to develop ways to covalently attach molecules onto surfaces with subnanometer spatial precision,^2592,2593 and had suggested a packing model for interpenetrated diamondoid structures.²⁵⁹⁴ Robson's group²⁸⁴⁶ has also investigated possible scaffolding molecules.

Josef Michl is attempting to build a molecular construction kit using molecular rods and connectors, pursuing an explicit vision of "molecular Tinkertoys"^2509-2516 by working with simple molecular structures that form stiff, flexible rods. Michl has assembled rods from a mixture of carbon-boron molecules (e.g., 10-vertex or 12-vertex carboranes²⁴⁹⁵) and carbon-hydrogen molecules, providing fine control over the total rod length. The rods are built up from more primitive molecular parts, such as propellane (a strained form of C₅H₆) and cubane (a strained form of C₈H₈), to make "staffanes"^2500-2510 which are a series of cage units in a linear series (Fig. 2.12). (Strained molecules are constructed with bonds that are forced out of their normal angles, as for example 90° in the case of cubane, compared with carbon's normal orientation of 109.5°.) Michl has fabricated rods whose lengths vary from 0.5 nm to 2.5 nm, in precise 0.1-nm steps. There are other ways of making rodlike molecules, but Michl's are highly inert, do not absorb visible or UV light, are stable up to at least 200°C, and do not react with the oxygen in air even at high temperatures.²⁴⁹⁶

Related work is underway in Michl's laboratory on connectors to join the rods together.²⁴⁹⁶ Metal atoms would be the simplest solution, offering the useful quality of strong joints that can be easily disassembled. Different metals give different binding geometries -- square, octahedral, and so on. Many of the connectors are metal-containing species; some are symmetrically trisubstituted or hexasubstituted benzenes or tetrasubstituted cyclobutadiene complexes. Michl must build the right chemical groups onto the rod termini to make them adhere to the connectors as desired. In one example,²⁴⁹⁶ tiny crosses were built by attaching carboxylate groups to one end of the staffanes, allowing them to bind to a connector made of two rhodium atoms. The groups at the other end of the rods were converted to an ester group, which doesn't bind to rhodium, and so the crosses self-assembled correctly. Michl has also fabricated "star connectors" in which the rods are built into the molecules as covalently bonded arms of a star. For instance, one 3-arm star connector uses three large carboranes coupled to a central benzene ring, allowing a pedestal to be attached vertically to the benzene ring via a ruthenium "sandwich" bond.²⁴⁹⁶ Additional devices could be installed on this molecular scaffolding, such as optically active molecules or even molecular mechanical "windmills".²⁵¹⁶ Nanoscale square^2517-2519 and hexagonal^2520,2521 planar grids have been fabricated. Extensive ab initio quantum mechanical calculations accompany the experimental work and aid in the interpretation of the results. Michl's ultimate goal is "the production of thin layers of solids of completely controlled aperiodic structure consisting of an inert covalent scaffolding carrying selected active groups."

G. Leach and colleagues²⁷⁰⁵ used computers to simulate various diamond and graphite nanostruts using molecular dynamics calculations, analyzing solid rectangular struts with varying aspect ratios, cross-sections, terminating atoms (for diamond), potential energy functions, and temperatures. The most dramatic differences were seen between struts with 100:1 aspect ratios and struts with lower (10:1 or 1:1) aspect ratios -- the diamond strut with a 100:1 aspect ratio and a unit cell (~0.4 nm)² cross-section begins to curl (with end-to-end distance decreasing 1.2 nm after 20 picosec) due to thermal vibration (both at 150 K and 300 K), while a unit strut with an aspect ratio of 10:1 or a 100:1 strut with a (1 nm)² cross-section showed end-to-end length fluctuations of only ~0.1 nm. The authors concluded that support struts with a cross-section of at least (1 nm)² would be sufficient to keep both end-to-end distance and transverse fluctuations below ~0.1 nm in struts with 10:1 aspect ratios. Other work by the same group²⁶⁶⁴ claims that many nanomachine designs may actually perform better than molecular dynamics results might suggest, or may require fewer atoms for the same positional stability.²⁷⁰⁵ The elastic and wear characteristics of diamond are being studied computationally by others.^{2764,2900,2901}

No discussion of molecular "parts" could be complete without mention of the fullerenes,* first discovered in 1985^2612,2613 and vigorously investigated ever since.^{522,523,1308,1821,2619,2636,2637,2702} Fullerenes are one of the three known allotropic forms of carbon. In graphite, the most common allotrope, carbon atoms are arranged in hexagonal rings and strongly bonded into parallel planar sheets, with much weaker bonding between the sheets, giving graphite its excellent lubricating properties. In diamond, the second allotropic form, carbon atoms are arranged in a symmetric, tetrahedral structure, giving immense strength. Exposed to air, both diamond surfaces and graphite edges are quickly coated or "passivated" with hydrogen or other atoms that tie up the dangling bonds. In fullerenes, the third allotropic form, carbon atoms form large and hollow cage-like structures, often roughly spherical or tubular, made up of closed curved one-atom-thick sheets of carbon atoms arranged in a number of five-, six-, and higher-membered rings. Interestingly, the fullerenes need no passivating hydrogens or other atoms to satisfy their chemical bonding requirements at the surface -- in this sense, "fullerenes are the first and only stable forms of pure, finite carbon".⁵²²

* The first fullerene to be discovered, the spherical C₆₀ molecule, was originally named "buckminsterfullerene" by its discoverers, due to the molecule's similarity to the geodesic domes designed by the famous American architect and engineer, Buckminster Fuller (1895-1983). The name has since been shortened by common usage to "fullerenes," although spherical or tubular fullerenes are sometimes informally called "buckyballs" and "buckytubes," again reflecting the original provenance.

A new journal, Fullerene Science and Technology, appeared in 1993, and by the mid-1990s ~3000 papers on fullerenes and their properties had been published and 149 fullerene-related patents had been issued in the U.S. alone (through 1996). By 1998, an incredible variety of fullerenes of many shapes and sizes had been synthesized.

The original fullerene, C₆₀, consists of exactly 60 carbon atoms arranged in a soccerball structure (Fig. 2.13; lone carbon atom at each vertex) with 20 hexagons and 12 pentagons (with each pentagon entirely surrounded by hexagons). In theory, small molecules such as H₂ or CO, and probably CH₄, would fit inside C₆₀.²⁶²⁸ A slightly larger variant, C₇₀, is the same except that an extra belt of carbon atoms has been inserted around the equator. Smaller (Fig. 2.14) and larger (Fig. 2.15) variants have been observed; as cages get bigger, the corners (where the 12 pentagons needed for closure reside) get sharper. The topologically smallest possible fullerene is a dodecahedron consisting of 12 pentagons and 20 carbon atoms, but the ring isomer of C₂₀ (a hoop of single carbons) is apparently energetically favored over the bowl or spherical (fullerene) isomers; in 1998, C₂₈ was the smallest fullerene that had been observed experimentally,²⁶¹⁴ and C₃₆ could be made in significant quantities by arc-discharge.²⁹¹⁰ The approximate diameter (measured to atomic centers) of a spheroidal fullerene of formula C_n is D_ball ~ 1.1 (n/60)^1/2 nanometers.²⁶¹⁵ In 1998, purified C₆₀ cost $27.50/gm (99.5% pure) or $60/gm (99.9%), C₇₀ $250/gm (98%), and C₈₄ $3,750/gm (90%) from Dynamic Enterprises Ltd. of London.

Insertion of many additional equatorial belts of carbon atoms (incorporated as hexagons) into a spheroidal fullerene results in a long cylinder with graphite-like ("graphene") walls and spherical endcaps, making a class of fullerenes known as the capsular fullerenes or single-walled carbon nanotubes (SWNT) that come in many sizes and chiral forms (Fig. 2.16).^{2626,2651,2652,2857} The molecular form of carbon nanotubes has been likened to rolled chicken wire. SWNTs may be synthesized by vaporizing graphite spiked with 1% catalyst from the nickel, cobalt and iron group above 3000°C, then allowing the vapor to slowly condense. Tubes form because the metal atoms interact with dangling bonds at the end of a tube, favoring tube extension over hemispherical capping by newly arriving carbon vapor atoms. (For any given mass number, ball-shaped fullerenes are energetically favored over tube-shaped fullerenes during high-temperature synthesis in the absence of catalyst.²⁶¹⁵) SWNTs typically self-assemble in 1.1 nm wide tubes, although smaller single-walled nanotubes and larger single-walled and multi-walled nested nanotubes²⁶²⁶ exist. SWNT carbon atoms are bonded in virtually flawless hexagonal arrays. Simulations show that isolated flaws migrate to the ends of the tube and are eliminated, a phenomenon known as "self-healing".¹⁷⁴⁶ Single-molecule nanotubes of C_1,000,000 or larger, with lengths >100,000 times longer than their widths (e.g., ~1 mm long), had been synthesized by 1998. While graphite is a very brittle material, the graphene walls of a carbon nanotube are quite resilient. Computer simulations and experiments confirm that nanotubes kink when bent (Fig. 2.17), then snap back when released.²⁶⁶¹ Nanotube diameter is D_tube = 0.078 (n² + nm + m²)^1/2 nanometers, where (n, m) is the "rollup vector" defined by the number of steps required for a repeat pattern along two crystallographic cylinder wall axes. The cohesive energy per atom required to curve a flat graphene sheet into a cylinder¹³⁰⁸ is E_rollup = (13 zJ-nm² / D_tube²). (1 zeptojoule (zJ) = 10²¹ joules.) As an example, a (10,10) nanotube has D_tube = 1.36 nm and E_rollup = 7 zJ/atom. Young's modulus for individual SWNTs, assuming a hollow (open-ring) cross-section, has been estimated as high as ~5.5 x 10¹² N/m²;²⁶⁵⁹ elastic bending modulus (measured as 1 x 10¹² to 0.1 x 10¹² N/m²) decreases sharply with increasing diameter (from 8-40 nm).³⁰²³ In 1998, purified carbon singlewalled nanotubes were available via the Internet for $1400/gm from Tubes@Rice, or for $200/gm at lesser purity from CarboLex.

From spatial geometry, it is known that hexagonal tiling produces flat sections (like cylinder walls), and inserting pentagons into an hexagonal array produces positive curvature (like spheres), making endcaps. But 7-sided heptagons can also be inserted into hexagonal arrays to induce negative curvature,^1308,2651 thus permitting concave surface deformations such as saddle-shaped fullerenes¹³⁰⁸ (Fig. 2.18) or possibly helical tubular structures.²⁶³⁵ Indeed, note Colbert and Smalley, "the use of hexagonal, pentagonal, and heptagonal substructures are sufficient to produce caged carbon structures of any topology".²⁶⁴³ Nature makes use of this same geometrical principle in the radiolarians,⁵²⁰ tiny protozoans with fullerene-like siliceous skeletons, and in the conical nucleoprotein core particle of the HIV-1 virus²⁶⁸⁴ (Fig. 2.19).* R. Smalley observes that a graphene sheet has the highest tensile strength of any known 2-dimensional network, and the packing density of atoms in the sheet (e.g., atoms/m²) is higher than any other network made of any atoms in the periodic table and higher than the packing density in any 2-dimensional slice through any 3-dimensional object -- even diamond which has the highest known 3-D packing density. Hence the graphene sheet is effectively impermeable under normal chemical conditions.

* Interestingly, conical hexagonal lattices with narrow endcaps that are closed using P pentagons are required by Euler's theorem to have a quantized cone angle q defined by sin(q/2) = 1 - (P/6) for P = 0, 1, ... , 6; minimum cone angle is 19.2^o at P = 5.²⁶⁸⁴

Carbon nanotubes have also been observed with a variety of endcap shapes²⁶⁵⁰ and with tubes that reduced²⁶⁵¹ or increased²⁶⁵⁸ their diameter for some distance before terminating. Toroidal fullerenes can be produced experimentally;^{2632,2657,3206} conelike,^{2652,2653,2684,2688} spindlelike,²⁶⁵⁴ and helical^2655-2657 fullerene objects have also been examined. By 1998, the mechanical properties of fullerenes and carbon nanotubes were being extensively investigated^{2277,2629,2659-2661,2715-2719,2903-2905} and there were experimental demonstrations of:

1. a limited ability to cut fullerene nanotubes to specific desired lengths;^{1525,2685,2855}

2. dissolving derivatized SWNTs in common organic solvents;²¹⁶⁴

3. the synthesis of self-oriented nanotube arrays;²⁶⁹¹ and

4. the trapping of individual C₆₀ molecules in a perforated Langmuir-Blodgett film "workpiece holder"²⁶³⁰ (though an even simpler means for producing 2-nm hole arrays with 78 nm hole spacings was later reported²⁶³¹).

Nanotubes were also being investigated as nanoscale sensor components.^{2908,2909,3023}

Given an ability to synthesize a wide variety of fullerene shapes and sizes, the next task is to find ways to join them together in specific desired molecular architectures. Two hydrogens were readily added to fullerene carbon atoms, making specific isomers of C₆₀H₂ and C₇₀H₂,^2616,2617 and in the 1990s fullerene chemistry began to be explored.^{2618,2619,2649,2906} A little more than a decade after the discovery of C₆₀, gram quantities of buckyballs became widely available²⁶²⁷ for chemical experimentation. Progress in covalent fullerene chemistry exploded.²⁶²⁴ By the late 1990s, fullerene surfaces could be regioselectively functionalized in many interesting ways, including (Fig. 2.20 A B C D E F G):

A. a fullerene dimer,²⁶²⁵

B. a fullerene-polyester polymer,²⁶²¹

C. a fullerene dendrimer,²⁶²⁰

D. a fullerene-rotaxane²⁶²² and catenane,²⁵³⁶

E. a fullerene-nucleotide DNA cleaving agent,²⁶²³

F. a Diels-Alder fullerene adduct that is very stable against cycloreversion,²⁶²⁴ and

G. 3-dimensional extended polymeric multifullerene forms such as acetylenic macrorings²⁶²⁴ and DNA/fullerene hybrid materials.³⁰²⁴

Theory²⁶⁶⁵ and experiment²⁶⁶⁶ suggest that SWNTs may be joined at 30° angles to create complex structures, including helices and three-way nanotube junctions^1308,2614 as suggested by Figure 2.18.

In 1998, the idea of using fullerenes as "Tinkertoys" for molecular construction was just starting to be considered.²⁶⁴³ For example, given the synthesis of C₆₀ exohedral monoadducts and multiple adducts described above, it may be possible to fabricate simple gears by bonding rigid ligands onto the external surfaces of carbon nanotubes in the manner of gear teeth,^2644-2646 although the chemical synthesis of nanotubes with precisely positioned teeth will not be easy.²⁶⁶⁷ Given the success in 1996 of IBM scientists²⁶⁴⁷ in positioning individual organic molecules (each having a total of 173 atoms and a 1.5-nm diameter) at room temperature by purely mechanical means, it might also be possible to align and maintain these molecular gear teeth in atomically precise meshed positions. If this could be done, would such devices actually work in the manner of macroscale gears?

J. Han and colleagues at NASA/Ames²⁶⁴⁸ performed a detailed 2000-atom molecular dynamics simulation to investigate the properties of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C₆₀. Computationally, one gear is powered by forcing the atoms near the end of the nanotube to rotate (Fig. 2.21), and a second gear is allowed to rotate by keeping the atoms near the end of its nanotube constrained to a cylinder (i.e., the ends of the shaft were constrained to not elongate but were allowed to move within a plane transverse to the tube symmetry axis). The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. Each gear is made of a 1.1-nm diameter (14, 0) nanotube with seven benzyne teeth. The spacing between two nanotubes is 1.8 nm and the smallest distance between a tooth atom and a tube atom is ~0.4 nm. The results show that the gears can operate up to 70 GHz in vacuo at room temperature without overheating or slipping. As rotational speed rises above 150 GHz, the gears overheat and begin to slip with tooth tilting up to 20°, but no bond or tooth breaking occurs up to at least 3000 K and slipping gears can always be returned to proper operation by lowering the temperature or the rotation rate. A related nanotube gear system (58 sprockets, 290-464 atoms) simulated by Robertson and colleagues²⁶⁷⁰ at the Naval Research Laboratory (NRL) showed similar overheating at 500 GHz but was stable when accelerated to only 20 GHz.

The NASA group also simulated several other types of nanotube-based gear systems. For instance, a rack and pinion system (Fig. 2.22) was designed using a gear made from a (14, 0) nanotube with teeth separated by two hexagon rings and a shaft made from a (9, 9) tube with teeth separated by three rings. Gear and shaft are 1.94 nm apart, with tooth face normal to the radial direction of nanotube (14, 0) for the gear, but in the axis direction of nanotube (9, 9) for the shaft. The gear could receive power, driving the shaft, or vice versa, and worked well for shaft translational velocities up to ~100 m/sec. (Most devices described in Drexler¹⁰ typically move at 1 m/sec.) Since shaft mass is almost twice gear mass, it takes more power for the gear to drive the shaft. In another simulation involving a large 1.4-nm gear coupled to a smaller 0.8-nm gear (Fig. 2.23), the large gear drives the smaller gear smoothly, but if power is instead applied to the smaller gear at a sufficiently large acceleration, then the smaller gear does not drive the larger one but instead "bounces back and forth several times, like elastic collisions of a small ball between two boards."

Another research group at Oak Ridge National Laboratory (ORNL) used classical molecular dynamics to investigate the properties of molecular bearings consisting of an inner and an outer carbon nanotube.^2662,2663 The graphite bearings ranged in size from inner shafts between 0.4-1.6 nm in diameter up to 12 nm long, and outer cylinders between 1.0-2.3 nm in diameter up to 4 nm long. The original simulations²⁶⁶² found excessive vibrational motion, but subsequent work using a more complete quantum approach^2663,2664 found that under certain conditions the nanobearing is "frictionless" and undergoes superrotation, a classical dynamical behavior reminiscent of superfluidity. The regime of superrotary motion is somewhat restricted when the nanobearing is under load, which suggests that a very careful design is required to ensure optimum performance.

The ORNL group simulated a fullerene motor²⁶⁶⁸ consisting of two concentric graphite cylinders (shaft and sleeve) with one positive and one negative electric charge attached to the shaft. Rotational motion of the shaft was induced by applying one, or sometimes two, oscillating laser fields. The shaft cycled between periods of undesirable rotational pendulum-like behavior and good unidirectional motor-like behavior. The NASA/Ames group simulated a pulsed-laser-powered carbon nanotube gear-motor system which rotated consistently in one direction, although that direction could be either clockwise or counterclockwise.²⁶⁶⁷

G. Leach and colleagues²⁷⁰⁵ also simulated various carbon nanotubes treated as nanostruts using molecular dynamics calculations, as described earlier for diamondoid block struts. The conclusions were similar though less severe. Nanotubes with 100:1 aspect ratio and 0.8-nm diameter at 300 K experienced periodic oscillations in length of ~0.4 nm at ~122 GHz, although multiple modes clearly were being excited; nanotubes of lesser aspect varied by at most ~0.04 nm.

Last updated on 16 April 2004