Calculating Thermodynamic Properties Using a Force Field

17 Calculating Thermodynamic Properties Using a Force Field 

Molecular mechanics can be used to calculate heats of formation. To do so requires the energy to form the bonds in the molecule to be added to the steric energy. These bond energies are typically obtained by fitting to experimentally determined heats of formation and are stored as empirical parameters within the force field. The accuracy with which heats of formation can be predicted with molecular mechanics is, in appropriate cases, comparable with experiment. Thus, the steric energy of a given structure may vary considerably from one force field to another, but its heat of formation should be much closer (if the force fields have been properly parametrised). 

The sources of strain are often quantified by examining the different components (bonds, angles, etc.) of the force field. Such analyses can provide useful information, especially for cases such as highly strained rings. However, in many molecules the strain is distributed 

46 The DNA base pairs guanine (G), cytosine (C), adenine (A) and thymine (T) The uraciI-2,6-dkminopyridine pair can also form three hydrogen bonds but has a much lower association constant than G-C 

The association constant of the G-C base pair in chloroform is between 10 and 10 whereas the association between the A-T base pair is significantly weaker, at 40-130 M . One obvious reason for this difference is that there are three hydrogen bonds in the G-C base pair and only two in the A-T base pair. However, a simple hydrogen-bond count 

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