Molecular mechanics bonding energies

Since molecular mechanics "strain energy" calculations (43, 44) have become a valuable tool in interpretation of molecular structure results from crystallographic studies, certain computing techniques used there will be mentioned. The method is simple in principle the strain energy of a particular conformation of a molecule is expressed as the sum of terms of several types, each related to certain structural parameters for example, bond length, non-bonded contacts, torsion angle. 

A molecular-mechanics steric energy can be combined with empirical bond-energy parameters to calculate gas-phase heats of formation as discussed later... 

Chakraborty A, Zhao Y, Lin H, Tiuhlm DG (2006) Combined valence bond-molecular mechanics potential-energy surface tmd direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction. J Chem Phys 124 044315... 

Electronic properties of chlorophylls and related systems are of fundamental interest to understand the molecular mechanisms of energy and charge transfer in complex antenna and photosynthetic reaction centers [104]. Several studies were dedicated to investigate the electronic absorption spectra of photosynthetic chromophores (see Konig and Neugebauer [105] for a recent review). Most of the available experimental information on the electronic properties of chlorophylls is determined in solution. This feature fostered theoretical studies on the electronic properties of photosynthetic chromophores in solution, [106-114] or in interaction with hydrogen bonding species, [113, 115-122] or with the protein environment [123, 124]. 

VALIDATE" " is a hybrid strategy where the ligand interaction energy (steric, electrostatic and induction) is computed via molecular mechanics. These energy terms were combined with a range of descriptors (rotatable bonds, calculated log P, steric fit, measures of complementary/uncomplementary contact between lipophilic/hydrophilic surfaces), and via partial... 

Figure 7-8. Bonded (upper row) and non-bonded (lower row) contributions to a typioal molecular mechanics force field potential energy function. The latter two types of Interactions can also occur within the same molecule.

We will use the term energy surface to refer not only to systems in which the bonding remains unchanged, as in these two examples, but also where bonds are broken and/or formed. Our discussion will be appropriate to both quantum mechanics and molecular mechanics, except where otherwise stated. 

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