Hybrid ab-initio/empirical molecular dynamics: combining the ONIOM scheme with the atom-centered density matrix propagating (ADMP) approach

Article Abstract:

A new methodology to perform hybrid empirical/ab-initio molecular dynamics is presented. The method combines the well established hybrid ONIOM scheme with the recently developed ADMP approach, where the one electron density matrix is expanded in an atom-centered Gaussian basis set is propagated as electronic variables along with the classical nuclear degreed of freedom via an extended Laprangian procedure.

Electron microscopy, Molecular dynamics

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Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A

Article Abstract:

QM/MM calculations are used to investigate the irreversible inactivation of carboxypeptidase A (CPA) by 2-benzyl-3-iodopropanoate. The QM/MM calculations using the real inhibitor and the fully solvated enzyme revealed a barrierless reaction path for inactivation of CPA by 2-benzyl-3-iodopropanoate once the pre-reactive complex between the protein and ligand was formed.

Proteases, Quantum theory, Quantum mechanics, Zinc compounds

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The hydrated proton at the water liquid/vapor interface

Article Abstract:

An attempt is made to study the hydrated proton at the water liquid/vapor interface using the multistate empirical valence bond methodology. The findings indicate that the excess proton can effectively behave as an amphiphile, displaying both hydrophobic and hydrophilic character.

Water, Chemistry, Physical and theoretical, Physical chemistry, Hydrophobic effect

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