Stretching method item

Co(NH3)6]3+ and /e/3-[Co(en)3]3+ refine with over long bonds (1.98 A instead of 1.96 A each, see Table 17.10.1). The obvious thing to do now is to decrease r0. You can do that as before, in the Force Field Editor. However, a more efficient method is to directly edit the Parameter Array. To do that, you have to be sure that the correct Interaction Array has been stored. This array can be built in the menu item Build Interactions under Tools. You can then edit the force field parameters in the Parameter Array field of Edit/View. Click the corresponding parameter (STR C03 NT, i. e., the stretching interaction between cobalt(III) and aliphatic amine donors) and enter the new values in the Change Values line Assign the parameter set and Save them. 

Delocalized electronic systems present special problems in molecular mechanics. From what has been described previously, one clearly needs to know properties on a bond basis in order to carry out molecular mechanics calculations. That is, for each bond one must know the stretching force constant, the value for 1q, and other items. If we talk about an x-y bond, for example, these numbers are usually constants and present no particular problem, as long as their values are known. However, in delocalized system, there are a whole spectrum of bonds which vary in length, and in force constant and other properties, between X and Y. Consider naphthalene as an example. The bonds are somewhat benzenoid, but not exactly. Some are longer, some are shorter. How do we describe this with molecular mechanics There is the brute force method, where one simply gives the different atoms in naphthalene, for example, different atom type numbers, and then gives different bond properties to the different bonds. This would be OK for this molecule, but if one wants to consider a whole series of molecules, where bond lengths vary incrementally... 

---