By exploiting symmetries in the MBBs and in the construction process, it is possible to mutually cancel irregular angles introduced by the particular chemistries of the links.
A very important question concerns the exact number of links that have to be established to integrate a MBB into a growing structure, and in what sequence these links should be made. The first thing that comes to mind is that this number should be as low as possible. The lower the number, the fewer are the necessary chemical reactions and the higher is the yield of the final product (or maybe rather: the higher is the chance of getting a functional product at all, in the case of machinery). In addition, the difficulties of steric hindrance are somewhat relaxed if fewer links have to be established after the first one connects the newly added MBB with the structure. Maybe one could call this phenomenon a reduction of "link-density per volume" ?
In a very nice analysis of 3D-networks [Wel77] it is argued in chapt.4, that in order to form a regular 3D-lattice, a repeat-unit of this lattice has to have six free links for hooking up with neighbors, arranged in three pairs of diametrically opposed links, these link pairs being parallel to three non-coplanar axes, respectively. Unfortunately, it is very difficult to conceive of an organic molecule which would be able to undergo six link-forming reactions. Such a MBB would have to be an object with a cube-like geometry, and it is non-trivial to find an appropriate skeleton structure that would provide the required attachment geometries for the links.
But the argument in [Wel77] runs a step further: the repeat-units themselves can be built up from smaller parts, for example by joining two MBBs capable of forming four links each (leading to the diamond lattice in the case of tetrahedral geometry). Most currently investigated molecular aggregates, named "designer solids" in [Ama93], do not yet seem to have employed these lattice building concepts in a conscious design strategy. A good exception though can be found in [See82].
One could even use MBBs with only three links,
and then four of them would be needed to construct a repeat-unit. This
possibility is illustrated symbolically in figure 1.
FIGURE 1: A repeat-unit in a 3D lattice, composed of four smaller MBBs. The
chemistry of the links indicated should just be taken symbolically.
FIGURE 1: A repeat-unit in a 3D lattice, composed of four smaller MBBs. The chemistry of the links indicated should just be taken symbolically.
A macromolecular structure would be assembled not by adding these rather large and elongated, inconveniently shaped repeat-units, but by adding the smaller constituent MBBs one at a time. On the average, one thus would have to form 1.5 links per block added, so one would alternate between forming one and two links per block. In this way, one has to go into the trouble of making two links at the same time only with half of all the MBBs used.
Here an important trade-off issue arises: the obviously beneficial desire to use MBBs with as few links as possible leads to more open and loose lattices which are less densely interknitted (lower link-density per volume) which also very favorably facilitates the access to individual bonds during construction. But because of the lesser crowding one will have to make sure that MBBs at the construction site, which are tied into the growing structure by so far only one completed link, do not obtain too many degrees of rotational freedom and twist away so that they still can be easily aligned for subsequent reactions. One way of solving this problem is to use link-chemistries which do not generate bonds that allow torsional freedom.
Also, the looser structures tend to show less mechanical rigidity, and the fairly large cavities in the interior of such lattices will be filled with solvent molecules instead of something that could contribute more to the stiffness of the structure. So it would be desirable to fill the empty spaces with some stuffing material which could increase the stiffness through non-covalent, van der Waals-type (vdW) interactions. This could be achieved by additional side chains that are attached to the MBBs and that pack in a definable way (see the further discussion on the CavityStuffer program below).