It is possible to have expert experience in chemistry and to find MNT preposterous for reasons derived from that experience. In fact, it's a common reaction; not totally universal, but very common. And the second quote from leplen sums up why, quite nicely and accurately. Even if one trusts the calculations in Nanosystems regarding the stability of the various structures on display there, they will still look like complete fantasy to someone used to ordinary methods of chemical synthesis, which really do resemble "shaking a large bin of lego in a particular way while blindfolded"!

Nanosystems itself won't do much to convince someone who thinks that assembly is the main barrier to the existence of such structures. Maybe subsequent papers by Merkle and Freitas would help a little. They argue that you could store HCCH in the interior of nanotubes as a supply of carbons, which can then be extracted, manipulated, and put into place - if you work with great delicacy and precision...

But it is a highly nontrivial assertion, that positional control of small groups of atoms, such as one sees in enzymatic reactions, can be extended so far as to allow the synthesis of diamond through atom-stacking by nanomechanisms. Chemists have a right to be skeptical about that, and if they run across an intellectual community where people blithely talk of an AI ordering a few enzymes in the mail and then quickly bootstrapping its way to possession of a world-eating nanobot army, then they really do have a reason to think that there might be crackpots thereabouts; or, more charitably, people who don't know the difference between science fiction and reality.