Towards an Accurate Semi-Empirical Molecular Orbital Treatment of Covalent and Non-Covalent Biological Interactions

  • Jonathan P. Mcnamara
  • Ian H. Hillier
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 7)


Recent developments are described which have allowed computationally rapid semi-empirical molecular orbital methods to make significant advances in modelling biological interactions. Efficient strategies for obtaining the best parameters for use in models such as PM3 and AM1 are discussed. Examples of the use of such parameterised methods to understand phosphoryl transfer reactions, the conformational energetics of carbohydrates and hydrogen tunnelling in enzyme catalysed reactions are described. Recent advances in the development of suitable parameters for transition metals, particularly iron, are described, with associated applications to iron containing proteins such as rubredoxin. The recent development and use of a parameterised PM3 model which includes an empirical correction for dispersive interactions (PM3-D) which is designed to study protein structure-function relationships, is described


Semi-empirical MO PM3 QM/MM. parameters phosphoryl transfer carbohydrate enzyme catalysis hydrogen tunnelling iron-sulfur proteins non-covalent interactions biomolecules PM3-D 


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Jonathan P. Mcnamara
    • 1
  • Ian H. Hillier
    • 1
  1. 1.School of ChemistryUniversity of ManchesterManchesterUK

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