Binding energies conformer stabilization

Kurnig et al. reexamined the relative stabilities of the linear and cyclic trimers, motivated by experimental indications that two conformers coexist . They included correlation via the ACPF method which they consider equivalent in this case to CPF, along with a basis set of [321/31] quality. Their results in Table 5.6 show that the linear trimer is more stable than the cyclic by 2 kcal/mol, with respect to binding energy at the SCF level, but this difference is reduced to 0.7 with correlation included. Including zero-point vibrations and other corrections yields the AH° data in the last row which nearly mirror the trends in AE. Given the errors which remain at this level of calculation, the calculated preference for the linear trimer by 0.5 kcal/mol in AH° was not considered by the authors as definitive, and the smallness of this quantity accounted for the presence of both geometries in the experiments. 

Enzymes adopt conformations that are structurally and chemically complementary to the transition states of the reactions that they catalyze. Sets of interacting amino acid residues make up sites with the special structural and chemical properties necessary to stabilize the transition state. Enzymes use five basic strategies to form and stabilize the transition state (1) the use of binding energy, (2) covalent catalysis, (3) general acid-base catalysis, (4) metal ion catalysis, and (5) catalysis by approximation. Of the enzymes examined in this chapter, three groups of enzymes catalyze the addition of water to their substrates but have different requirements for catalytic speed and specificity, and a fourth group of enzymes must prevent reaction with water. 

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