The Molecular Mechanics Model

One great advantage of the molecular mechanics model is that it can be applied to large molecules on your average PC. Apart from single molecular structure... 

We close this section with one more note on careful nomenclature. A code renders a model into a set of instructions that can be understood by a digital computer. Thus, if one applies a particular model, let us say the molecular mechanics model called MM3 (which will be described in the next chapter) to a particular problem, say the energy of chair cyclohexane, the results should be completely independent of which code one employs to carry out the calculation. If two pieces of software (let s call them MyProg and YourProg) differ by more than the numerical noise that can arise because of different round-off conventions with different computer chips (or having set different tolerances for what constitutes a converged calculation) then one (or both ) of those pieces of software is incorrect. In colloquial tenns, there is a bug in the incorrect code(s). 

From the discussion above it emerges that the total strain energies, which are often equated with enthalpy terms, are dependent on the molecular mechanics model used and its associated parameter set. For this reason strain energies are generally taken to have significance only relative to one another. Even with the same model and force field, strain energies are generally of little value in terms of absolute potential en-... 

If molecular mechanics is to be a valid modeling tool for the design of new compound and the interpretation of experimental results, the compounds under consideration must belong to a class for which the molecular mechanics model is well defined. In other words, the accuracy of the results obtained depends critically on the parameterization of the force field and how this has been obtained (Fig. 5.1). 

Rotation about the central bond costs energy and there are two components to this one arises from the repulsion between the first and fourth atoms in the sequence and the other is intrinsic to the bond. The former component is included in the nonbonded interactions of the molecular mechanics model but the other component must be explicitly included by means of a torsion angle potential energy function. 

Thus, we generate a single point of attachment of the olefin to the metal, but we do not interrupt the C-C connectivity. A similar approach has been used for the molecular mechanics modeling of cyclopentadienyl ligands (25-28). 

In this section, we shall work through a few different approaches to the molecular mechanics modeling of Ziegler-Natta catalysis. Other approaches used to model this system are listed in Tables 1 and 2. 

Accordingly, in all scientific papers where an ab initio calculation could be performed that fits the experimentally observed structure of a molecule, the result is taken to theoretically explain this observation. But what does this mean for the overwhelming number of molecules that are intractable within the ab initio approach Do we have to assume that their structure is, and must remain, unexplained Most chemists would deny this. A look in classical textbooks of chemistry, especially organic chemistry, shows that the most common explanatory principle in the context of the everyday molecular structures does not refer to the Schrodinger equation at all. ft is rather a principle that lies at the heart of the molecular mechanics model the principle of steric strain. 

The molecular mechanics model is extremely popular among chemists and there is an overwhelming number of articles reporting the application of this method. Their broad application also is considered to raise our understanding and our capability to explain the structural features of the treated molecules.5 But still, as the last example shows, there exist upper limits concerning the size of the molecules for which a proper prediction of structure can be made. Especially in the case of proteins, such predictions can have tremendous practical importance. The last model, I discuss is a method used to predict the secondary structure of a protein, i.e., its folding mode, starting with only information on its primary structure, i.e., its amino acid sequence. 

The Molecular Mechanics Model illustrates how chemists proceed when they try to explain molecular structures. It turns out that explanation remains an issue here and that mere prediction, as in the case of the neural network approach, is not, eo ipso, explanatorily relevant. On the other hand it is remarkable that not a single, but rather two conceptually quite different models were both praised for their explanatory... 

This case seems to be more promising. Let s consider the DN-model first. As described above, the molecular mechanics model is based on a number of force-field potentials that refer to proper scientific laws. Given the molecular graph the different types of atoms contained in a molecule and their connections and a set of force-field parameters the total strain energy of the molecule can be deduced for every possible atomic arrangement. Is this a DN-explanation The answer is no, and... 

Iam deliberately sticking to the Molecular Mechanics model here. As we all know, from a quantum physical perspective, the process of a molecule absorbing and exchanging energy is in fact irreducibly discrete. The fact that quantum physics poses some severe problems for the process account of causality, however, is readily admitted by Salmon. 

The interpretation of molecular orbital calculations on conformational isomers is not as straightforward as for molecular mechanics methods. Because MO calculations treat all of the bonding forces of the molecule, the difference between two conformations represents only a small part of the total energy. Furthermore, unlike the molecular mechanics model in which energies are assigned to specific interatomic interactions, the energy of a specific molecular orbital may encompass contributions from a number of intermolecular interactions. Thus, the identification of the structural features responsible for the energy difference between two conformers may be very difficult. 

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