A classic introduction to molecular mechanics is Molecular Mechanics, by Ulrich Burkert and Norman L. Allinger, ACS Monograph 177, American Chemical Society, 1982. While out of print, it can often be found in campus libraries.
Nanosystems introduces the basic concepts of molecular mechanics in chapter 3. A great advantage of Drexler's treatment is the adoption of consistent SI units. A slow and careful reading of this chapter is worth the effort.
Many other introductions to molecular mechanics are available. Software packages implementing specific approaches to molecular mechanics are available, and can be very useful in learning the concepts.
sigma2 = kT / ks
This is equation 5.4 introduced in chapter 5 of Nanosystems. This equation should be memorized and basic applications understood. To use it, it is essential to determine the stiffness ks. The stiffness of a structure can be determined from its geometry and material properties. The basic concepts are introduced by Feynman in chapters 38 and 39 of The Feynman Lectures on Physics, by R.P. Feynman, R.B. Leighton, and M. Sands, M. Addison-Wesley (1964). Buying the Feynman Lectures is recommended. Read and understand chapters 38 and 39.
Application of these equations to some robotic devices (including the Stewart platform which, because of its great stiffness, is very attractive for molecular robotic applications) is illustrated in A New Family of Six Degree of Freedom Positional Devices. Applications are also discussed in Chapter 5 of Nanosystems and in section 13.4 which discusses a robotic arm.
A second central idea in nanotechnology is that of self replication. The student should read the web page introducing self replication and select some of the references therein for further reading. The recursion theorem is basic to self replicating systems. This theorem should be understood. Exercise: write a program which prints out an exact copy of itself. Read Kinematic Self-Replicating Machines, it is an excellent survey of the literature.
Before molecular machines can build other molecular machines, we must have a set of molecular tools able to build a similar set of molecular tools. Read A Minimal Toolset for Positional Diamond mechanosynthesis.
For an easy-to-understand introductory video, see Ralph Merkle's 2009 Introduction to Molecular Nanotechnology, available on the web on YouTube.
For a technical introduction to mechanosynthesis, read and understand A Minimal Toolset for Positional Diamond Mechanosynthesis.
After reading this, read Smalley's "Of Chemistry, Love and Nanobots". Then read "Thatís impossible! How good scientists reach bad conclusions" and "The Incredible Shrinking Man" by Ed Regis. What factor's might have influenced Smalley's public statements? Was the decision by Congress to remove funding for molecular nanotechnology from the National Nanotechnology Initiative one which advanced the public good? Was it based on a sound understanding of the relevant scientific issues?
Exercise: how would you fund scientific research if you wanted to benefit humanity? Is it possible for Congress to fund research that the public might fear? What alternatives to direct Congressional funding exist? Would Congress allow any institution it controlled to fund research that might alarm or disturb voters? Wouldn't any organized group that sought public funding have to behave in a similar fashion? Should research into new areas that might be of great value but also might hold unknown risks be blocked? What would the caveman committee assigned to "fire" have concluded?
If the "scientific community" had access to "politically unbiased" funds, would it be able to direct its own funding effectively? Hint: committee based peer review is effective at blocking new and innovative research. Propose an alternative method for allocating research funds. You might wish to review the literature on prediction markets. Does your funding mechanism take into account the tendency for all new ideas to be attacked and dismissed? Does it dismiss most of the new ideas that in fact deserve to be dismissed?
There are, of course, a great many other subjects relevant to the development of nanotechnology. It seemed more useful to provide a short and focused list of critical subject areas that could be mastered with a reasonable effort than a longer and more unwieldy list which included everything of importance. The student can rest assured that there is no shortage of material to study relevant to this new field of research.