Nucleophilic attack on phosphate diesters: A density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

Article Abstract:

A density functional study of the hydrolysis reaction of phosphodiesters with a series of attacking nucleophiles in the gas phase and in solution is described. The study of in-line reactivity in dianionic, monoanionic and neutral systems shows that solvent stabilization has a deep impact on the relative barrier heights for dianionic, monoanionic and neutral reactions.

Usage, Density functionals, Density functional theory, Hydrolysis, Chemical properties, Nucleophiles

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Dissecting the vibrational entropy change on protein/ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor

Article Abstract:

The vibrational entropy change on the burial of a crystallographically well-ordered water molecule in bovine pancreatic trypsin inhibitor (BPTI) using normal-mode analysis is dissected. A detailed analysis is performed of how the translational and rotational degrees of freedom of the isolated water molecule are transformed into vibrational modes in the complex.

Analysis, Ligand binding (Biochemistry), Spectra, Entropy (Physics), Entropy (Thermodynamics), Atomic properties, Trypsin inhibitors

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Protein/Ligand binding free energies calculated with quantum mechanics/molecular mechanics

Article Abstract:

The Poisson-Boltzman/surface area PB/SA combined with a quantum mechanical description of the ligand in protein/ligand binding affinity calculation is investigated. The result reveals quantum mechanics/molecular mechanics QM/MM is promising new avenue for automated docking and scoring of flexible ligands.

Quantum theory, Quantum mechanics, Ligands, Ligands (Chemistry), Gibbs' free energy

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