Highly Specific Reaction Between Two Compounds example essay topic

... dress of atoms in them are quite feasible. Larger atomically precise structures with complex three-dimensional shapes can be viewed as a connected sequence of small atomically precise structures. While chemists have the ability to precisely sculpt small collections of atoms there is currently no ability to extend this capability in a general way to structures of larger size. An obvious structure of considerable scientific and economic interest is the computer. The ability to manufacture a computer from atomically precise logic elements of molecular size, and to position those logic elements into a three- dimensional volume with a highly precise and intricate interconnection pattern would have revolutionary consequences for the computer industry. A large atomically precise structure, however, can be viewed as simply a collection of small atomically precise objects which are then linked together.

To build a truly broad range of large atomically precise objects requires the ability to create highly specific positionally controlled bonds. A variety of highly flexible synthetic techniques have been considered in. We shall describe two such methods here to give the reader a feeling for the kind of methods that will eventually be feasible. We assume that positional control is available and that all reactions take place in a hard vacuum. The use of a hard vacuum allows highly reactive intermediate structures to be used, e. g., a variety of radicals with one or more dangling bonds. Because the intermediates are in a vacuum, and because their position is controlled (as opposed to solutions, where the position and orientation of a molecule are largely random), such radicals will not react with the wrong thing for the very simple reason that they will not come into contact with the wrong thing.

Normal solution-based chemistry offers a smaller range of controlled synthetic possibilities. For example, highly reactive compounds in solution will promptly react with the solution. In addition, because positional control is not provided, compounds randomly collide with other compounds. Any reactive compound will collide randomly and react randomly with anything available. Solution-based chemistry requires extremely careful selection of compounds that are reactive enough to participate in the desired reaction, but sufficiently non-reactive that they do not accidentally participate in an undesired side reaction.

Synthesis under these conditions is somewhat like placing the parts of a radio into a box, shaking, and pulling out an assembled radio. The ability of chemists to synthesize what they want under these conditions is amazing. Much of current solution-based chemical synthesis is devoted to preventing unwanted reactions. With assembler-based synthesis, such prevention is a virtually free by-product of positional control. To illustrate positional synthesis in vacuum somewhat more concretely, let us suppose we wish to bond two compounds, A and B. As a first step, we could utilize positional control to selectively abstract a specific hydrogen atom from compound A. To do this, we would employ a radical that had two spatially distinct regions: one region would have a high affinity for hydrogen while the other region could be built into a larger 'tip's structure that would be subject to positional control. A simple example would be the 1- radical, which consists of three co-linear carbon atoms and three hydrogen atoms bonded to the sp 3 carbon at the 'base' end.

The radical carbon at the radical end is triply bonded to the middle carbon, which in turn is singly bonded to the base carbon. In a real abstraction tool, the base carbon would be bonded to other carbon atoms in a larger structure which provides positional control, and the tip might be further stabilized by a surrounding 'collar' of un reactive atoms attached near the base that would prevent lateral motions of the reactive tip. The affinity of this structure for hydrogen is quite high. Propane (the same structure but with a hydrogen atom bonded to the 'radical' carbon) has a hydrogen-carbon bond dissociation energy in the vicinity of 132 kilocalories per mole.

As a consequence, a hydrogen atom will prefer being bonded to the 1- hydrogen abstraction tool in preference to being bonded to almost any other structure. By positioning the hydrogen abstraction tool over a specific hydrogen atom on compound A, we can perform a site specific hydrogen abstraction reaction. This requires positional accuracy of roughly a bond length (to prevent abstraction of an adjacent hydrogen). Quantum chemical analysis of this reaction by Musgrave et. al. show that the activation energy for this reaction is low, and that for the abstraction of hydrogen from the hydrogenated diamond (111) surface (modeled by iso butane) the barrier is very likely zero. Having once abstracted a specific hydrogen atom from compound A, we can repeat the process for compound B. We can now join compound A to compound B by positioning the two compounds so that the two dangling bonds are adjacent to each other, and allowing them to bond.

This illustrates a reaction using a single radical. With positional control, we could also use two radicals simultaneously to achieve a specific objective. Suppose, for example, that two atoms A 1 and A 2 which are part of some larger molecule are bonded to each other. If we were to position the two radicals X 1 and X 2 adjacent to A 1 and A 2, respectively, then a bonding structure of much lower free energy would be one in which the A 1-A 2 bond was broken, and two new bonds A 1-X 1 and A 2-X 2 were formed. Because this reaction involves breaking one bond and making two bonds (i. e., the reaction product is not a radical and is chemically stable) the exact nature of the radicals is not critical. Breaking one bond to form two bonds is a favored reaction for a wide range of cases.

Thus, the positional control of two radicals can be used to break any of a wide range of bonds. A range of other reactions involving a variety of reactive intermediate compounds (carbines are among the more interesting ones) are proposed in, along with the results of semi-empirical and ab init io quantum calculations and the available experimental evidence. Another general principle that can be employed with positional synthesis is the controlled use of force. Activation energy, normally provided by thermal energy in conventional chemistry, can also be provided by mechanical means. Pressures of 1.7 mega bars have been achieved experimentally in macroscopic systems.

At the molecular level such pressure corresponds to forces that are a large fraction of the force required to break a chemical bond. A molecular vise made of hard diamond-like material with a cavity designed with the same precision as the reactive site of an enzyme can provide activation energy by the extremely precise application of force, thus causing a highly specific reaction between two compounds. To achieve the low activation energy needed in reactions involving radicals requires little force, allowing a wider range of reactions to be caused by simpler devices (e. g., devices that are able to generate only small force). Further analysis is provided in.

Feynman said: 'The problems of chemistry and biology can be greatly helped if our ability to see what we are doing, and to do things on an atomic level, is ultimately developed - a development which I think cannot be avoided. ' Drexler has provided the substantive analysis required before this objective can be turned into a reality. We are nearing an era when we will be able to build virtually any structure that is specified in atomic detail and which is consistent with the laws of chemistry and physics. This has substantial implications for future medical technologies and capabilities. One consequence of the existence of assemblers is that they are cheap. Because an assembler can be programmed to build almost any structure, it can in particular be programmed to build another assembler.

Thus, self reproducing assemblers should be feasible and in consequence the manufacturing costs of assemblers would be primarily the cost of the raw materials and energy required in their construction. Eventually (after amortization of possibly quite high development costs), the price of assemblers (and of the objects they build) should be no higher than the price of other complex structures made by self-replicating systems. Potatoes - which have a staggering design complexity involving tens of thousands of different genes and different proteins directed by many megabits of genetic information - cost well under a dollar per pound. The three paths of protein design (biotechnology), bio mimetic chemistry, and atomic positioning are parts of a broad bottom up strategy: working at the molecular level to increase our ability to control matter. Traditional miniaturization efforts based on microelectronics technology have reached the sub micron scale; these can be characterized as the top down strategy. The bottom-up strategy, however, seems more promising.