Hydrogen bonds semiempirical molecular orbital

Energy Parameters in Polypeptides. III. Semiempirical Molecular Orbital Calculations for Hydrogen-Bonded Model Peptides. 

Most semiempirical molecular orbital methods are known to be inadequate to describe intermolecular interactions, especially on hydrogen bonding interactions because molecular polarizabilities are systematically underestimated in comparison with experiments. Recently, we introduced a polarized molecular orbital (PMO) method which is based on the formalism with... 

The AMI (8) approximation to molecular orbital theory has been used for these studies. This method overcomes the problems that previous semiempirical methods (notably, MNDO) (9) have in describing hydrogen-bonds. It has been used with success in several hydrogen-bonding studies. (10-12) Ab initio studies of H-bonding systems are very sensitive to basis set and correction for electron-... 

Mulholland and Richards [344-346] have carried out ab initio (MP2/6-31-i-G(d) and RHF/6-31+G(d)) and semiempirical (AMI, PM3 and MNDO) molecular orbital calculations focussing on the enzyme citrate synthase. Their calculations were performed on the first stage of the citrate synthase reaction [344], on the substrate oxaloacetate [345] and on a simple model of the condensation reaction [346]. Their aim was to model the nucleophilic intermediate produced by the rate-limiting step, to examine which form of acetyl-CoA is the likely intermediate and how it is stabilised by the enzyme. They have found that the enolate is the likely nucleophilic intermediate in citrate synthase being stabilised by hydrogen bonds. 

Huckel (properly, Huckel) molecular orbital theory is the simplest of the semiempirical methods and it entails the most severe approximations. In Huckel theory, we take the core to be frozen so that in the Huckel treatment of ethene, only the two unbound electrons in the pz orbitals of the carbon atoms are considered. These are the electrons that will collaborate to form a n bond. The three remaining valence electrons on each carbon are already engaged in bonding to the other carbon and to two hydrogens. Most of the molecule, which consists of nuclei, nonvalence electrons on the carbons and electrons participating in the cr... 

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