Nanomedicine, Volume I: Basic Capabilities

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

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

Four issues are considered briefly here. First, can diamond or sapphire be chemically solvated? Second, does any microbe likely exist which is capable of attacking a diamond or sapphire surface? Third, could such a microbe evolve naturally? Fourth, could such a microbe be artificially engineered? (The author thanks R. Bradbury, M. Krummenacker, R. Merkle, and J. Soreff for helpful discussions and important contributions to this Section.)

I. Can diamond or sapphire be chemically solvated? Although carbon is soluble in molten Fe (e.g., >1808 K at 1 atm),763 Co, Mn, Ni, and Cr, there is no known room temperature solvent that dissolves pure crystalline diamond. Intact diamond and fullerene surfaces are extremely inert. For example, after facet-cutting, gem diamonds are boiled in concentrated sulfuric acid for cleaning, leaving the gem surface unaffected. The outer faces of natural hydrophobic diamond may be terminated partly by hydrogen and partly by bridging oxygen, with a significant proportion of carbonyl groups and a small number of -OH and carboxyl (-COOH) groups as well.1596

Diamond is almost completely resistant to attack by room-temperature ground-state molecular oxygen (see Eqn. 9.55), although oxidative erosion by atomic oxygen has been shown at rates of ~0.04 nm/min1599 and ozone or various radicals might also be effective. Molecular fluorine only fluorinates the surface,1598 producing a "Teflon" coat (stable up to ~1120 K)1596 while not disturbing the underlying C-C bonds because F makes only single bonds; chlorine is also taken up by diamond surfaces.1600 Molten sodium nitrate attacks diamond at >~700 K.1597 At high temperature or pressure, carbon from diamond can migrate and form a metal carbide phase in carbide-forming metals including W, Ta, Ti, and Zr,1597 and metal oxides of Cu, Fe, Co, and Ni are reduced to the metal (a redox reaction with the carbon escaping as oxide) upon heating in vacuo.1596

Non-intact diamondoid surfaces may be more susceptible to chemical attack. For instance, open-ended single-walled fullerene nanotubes are consumed by a 3:1 mixture of sulfuric (98%) and nitric (70%) acids at 343 K at a rate of ~130 nm/hour even in the absence of sonication;1525 the same mixture intercalates and exfoliates graphite.1524 A 4:1 mixture of sulfuric acid (98%) and hydrogen peroxide (30%) at 343 K also etches the exposed ends of open nanotubes at ~200 nm/hour, "much like the burning of a fuse."1525 Etch rate may vary with the chiral indices (n, m) of the nanotubes.1525 COCl-derivatized single-walled carbon nanotubes will solvate in organic solvents,2164 and high-strain sites such as the outer fold of a kinked nanotube are subject to attack by nitric acid.2954

Sapphire is primarily corundum or a-Al2O3, the oxide ions forming a hexagonally close-packed array and the Al ions distributed symmetrically among the octahedral interstices.691 The solubility of a-Al2O3 in ~neutral water at room temperature is given variously as 10-7 - 10-5 M (~60-6000 atoms/micron3) at equilibrium,1602,1603 but solubility rises sharply below pH 4 and above pH 9 in an almost U-shaped curve.1603 (Human blood pH normally ranges from 7.35-7.45).1604 Aluminum oxide is amphoteric, forming hydrated Al+++ ions in acidic solutions (pH < 4) and Al(OH)4- ions in alkaline solutions (pH > 9).1603 Corundum dissolves slowly in boiling nitric acid and in orthophosphoric acid to 570 K, and dissolves well in potassium bisulfate at 670-870 K, or in borax or sodium fluoaluminate (cryolite) at 1070-1270 K.1602

Air-exposed Al metal is protected by a thin1601 (~5 nm) adherent oxide layer having a defect rock-salt structure691 easily compromised by amalgamation or halogens, or by alkali hydroxides (e.g., NaOH) with the generation of hydrogen in seconds at room temperature. Complex-forming reagents such as Cu++ + Cl- also react with oxide-coated aluminum metal in less than 1 minute.

II. Does any existing microbe possess the natural ability to attack a diamond or sapphire surface? Extensive tests have not yet been performed, and negatives cannot be proven, but the prospects are poor. Most organisms develop the means for attacking materials in their environment because these materials are abundant and provide essential molecules or elements that are needed for energy production or important biochemical functions.

For diamondophagy to evolve naturally, a microbe probably must occupy a niche in which diamond is more abundant than competing carbon sources. This is unlikely except many kilometers below the natural oil/coal deposits in the Earth's crust, though the possibility cannot be definitely ruled out because deep-crustal-dwelling bacteria and other archaic biota have been found in rocks at depths of at least 2.7 kilometers, a field of study now known as geomicrobiology.1592,3096 However, far more abundant nonpolymeric carbon sources are usually available. Highly polymeric molecules including long-chain hydrocarbons, cellulose, and starches tend to be fairly resistant to enzymatic degradation -- nature has found it relatively difficult to devise an attack strategy for cellulose (e.g., wood) and chitin (e.g., crab and insect shells). With their crystalline arrays, diamond and sapphire would seem to fall into this category as well.

A microbe naturally evolved to attack sapphire would probably be seeking to extract the aluminum (sapphirophagy), since oxygen is plentiful elsewhere. However, Al is generally considered toxic,752,3278-3281 and reports of microbes that feed on Al-rich minerals are extremely infrequent and remain unconfirmed, though microbial aluminum tolerance is well-known.3282,3283 Organisms use +1/+2/+3 metal ions (mostly Cu, Fe, Mn, and more rarely Mo and Co) in enzymes to catalyze specific difficult reactions. Yet in seawater, Al is ~10-1000 times more abundant than Cu, ~50-500 times more abundant than Fe, ~100-1000 times more abundant than Mn, ~500-3000 times more abundant than Mo, and ~10,000 times more abundant than Co,763 suggesting that Nature has gone to great lengths to avoid the use of aluminum in biological systems. Natural sapphire also contains ~0.1% iron atoms (Fe++ and Fe+++), and natural ruby has traces of chromium (Cr+++), biologically useful atoms more conveniently available from alternative sources.

III. Could a microbe capable of attacking diamond or sapphire evolve naturally? There are >1023 bacteria living inside Earth's human population alone. While most of these microbes (>99%) are harmless or beneficial, up to ~1021 may be undesirable pathogens possibly subject to attack by medical nanorobots. Could this large "natural laboratory" population of bacteria evolve diamondophagy or sapphirophagy as a defense against artificial nanomachines?

In the case of sapphire, most biological metal absorption is initiated by secretion of acids strong enough to dissolve the metal-containing material. Evolving an acid production capacity isn't difficult because most bacteria use H+ ion gradients as power sources. Common bacteria normally create a mildly acidic environment. Typical energy sources (e.g., glucose) are oxidized to increase the external H+ ion concentration. The flow of the H+ ions back into the cell through the ATPase enzyme generates ATP (as in mitochondria). Blocking or minimizing ATP production and limiting external H+ diffusion could produce fairly high local H+ concentrations. Bacteria such as Thiobacillus ferrodoxians, found in environments where better energy sources are lacking, oxidize metal sulfides to generate energy.3559,3560 These result in the generation of sulfuric acid and environmental pH values of 2-3. Extremozymes that can work at a pH below 1.0 have been isolated from the cell wall and underlying cell membrane of some acidophilic bacteria;1591 some acids (e.g., HF) that dissolve oxides (e.g., SiO2) may be safely stored in purely organic vessels (e.g., wax or plastic). As noted earlier, sapphire is also attacked by strong alkali (but see below).

Natural evolution of a diamondophagic capability is even more arduous. Acids such as HF, HCl and H2SO4 will not harm either H-terminated diamondoid surfaces or cellular lipid membranes which generally also have hydrogenated surfaces. While high H+ concentrations should remove oxygens from SiO2 or, with more difficulty, from Al2O3, a more efficient attack strategy for H-terminated diamondoid might be an extremely alkaline environment, although the most alkaliphilic bacteria (such as the Natranobacterium gregoryi normally found in soda lakes and high-carbonate soils)3561 only reach a pH of 10-11. High OH- environments can destroy lipid bilayers, RNA, and standard proteases and lipases.1591 Also, the biochemistries of acidophiles and alkaliphiles are so tuned to their natural environments3562 that the predominantly neutral pH found in the human body might prove toxic for these microbes.

Most human-pathogenic bacteria likely to be attacked by medical nanodevices are not extremophiles. Consequently, as R. Bradbury observes, Nature's design challenge is for non-extremophiles to evolve systems of creating very high local H+ concentrations,3563 having the energy resources available to drive this pathway and to minimize ATP production which utilizes the H+ ions. Such evolution seems unlikely. Only if medical nanodevices were constructed of an essential material that is in short supply, such as iron, or could provide a better energy source than the surrounding plasma or cytosol, could bacteria be selected which have the potential of attacking nanomachinery. Whether extremophiles might subsequently repopulate the vacated microecological niches currently occupied by natural pathogenic bacterial species is an open issue worthy of future study.

IV. Could a microbe capable of attacking diamond or sapphire be artificially engineered? Almost certainly the answer is yes. In the simplest case using conventional biotechnology, a bacterium would be designed to produce and secrete an appropriate acid or alkali, creating a highly corrosive environment local to the target material by binding to the surface and secreting the acid (or ions) into sequestered adherent pockets.

J. Soreff suggests other approaches that may employ locally far-from-equilibrium states which are harder to get (at least with fast kinetics) in normal chemistry. One strategy is to engineer artificial enzymelike structures that can bind to the target surface at one end while catalyzing the local production of molecules in excited states (e.g., by crude analogy to luciferase in bioluminescence)3564 at the other end. Enzymes like catalase and superoxide dismutase already handle locally powerful oxidants, and in the presence of light and oxygen, C60 can pass its superfluous excitation energy onto nearby O2 molecules, creating singlet oxygen. An enzyme might be designed to catalyze HOCl + H2O2 ---> HCl + H2O + O2* (singlet state oxygen)3565,3566, other singlets,3567,3568 triplets,3569-3572 quartets,3573 or other electronically-excited oxidizers.3574 However, survival of such an enzyme over multiple cycles is problematical. Another strategy is to design novel mechanochemical tools into the bacterium. Proteins can convert ATP hydrolysis into mechanical motion. Such motion, perhaps combined with a "snap-action" elastic energy storage mechanism to allow tool release speeds comparable to vibrational times, could be used to mechanically hammer an oxidant into a diamond surface, thus reducing the chemical energy required to be released at the point of action.


Last updated on 21 February 2003