Energetics of binding

Structural variations on the Ac2-L-Lys-D-Ala-D-Ala ligand also have a sizeable impact on the energetics of binding with vancomycin thus, replacing the o-Ala terminal with D-lactate [197] or D-Ser [198] reduces the binding affinity by 4.1 and 1.8 kcal/mol, respectively, while changing the terminal amide NH with a methylene (CH2) costs 1.5 kcal/mol [197]. 

In most cases these interactions can be regarded as equilibrium reactions governed by the law of mass action. Association constants provide a measure of the affinity of a ligand molecule to a substrate hence the tendency to form associates can be compared on a thermodynamic level. This provides information on the energetics of binding via the following relationship ... 

There has been some discussion in the literature as to whether a H-bond is stronger than a D-bond. That is, how does the isotopic substitution of a protium nucleus by a twice-as-rnassive deuterium affect the energetics of binding. Since the electronic part of the interaction energy is based upon the Born-Oppenheimer approximation which places the nuclei at rest, AE j is unaffected by any isotopic substitution, including this one. Indeed, the po-... 

From computations with basis sets of the polarized 6-3IG type, at SCF and MP2 levels, the change from formic acid dimer to acetic acid dimer has only a very minor influence upon the energetics of binding . This conclusion is indeed verified by resonant laser photoacoustic spectroscopic measurements i 79,181,182 which find further that trifluoroacetic and propionic acid dimers have a very similar binding enthalpy to formic dimer. One may extrapolate that the formic acid dimer Fl-bond energy is probably applicable for most carboxylic acids with alkyl chains replacing the CH group. 

Table 2.40 Energetics of binding (kcal/mol) in the formic acid dimer. Data corrected for BSSE .

Figure 6.15 Energetics of binding of H3O to various alkylated O bases. The data points were computed explicitly and the solid curve is derived from Equation (6.2). ...

General Computational Approach to Study the Energetics of Binding... 

In our previous studies, the in vitro influence of different concentrations of Al ions, physiological and toxic ones, on pepsin activity was investigated. Kinetic studies were undertaken to determine the nature of the enzyme modulation (type and mechanism) by investigated metal ion. The mechanism of A13+ ions on pepsin activity evaluated from kinetic studies and was classified as a case of non-essential activation with jjartial noncompetitive character (Pavelkic et aL 2008). With the application of theory, DSC method has been used as a tool to estimate binding constants (Pavelkic et al. 2011) as well as to characterize the energetic of binding and imfolding. 

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