Comment on "from subtle to substantial: Role of metal ions on pi-pi interactions"

Article Abstract:

The statistical analysis performed on a number of biomolecules taken from the Cambridge Structural Database and Brookhaven Protein Data Bank (PDB) is addressed by providing an extended statistical analysis on the biomolecules found in the PDB. It is shown that M-pi-pi motifs (where M = [Ca.sup.2+], [Mg.sup.2+], [Na.sup.+], [K.sup.+] and [Li.sup.+] and pi = benzene, indole, phenol and imidazole) in which the pi electronic cloud of the arene ring directly interacts with the cation are rare in the PDB.

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Self-healing umbrella sampling: A non-equilibrium for quantitative free energy calculations

Article Abstract:

A new approach for the umbrella sampling method in molecular dynamics simulations of complex systems is proposed. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system.

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Energetic fitness of histidine protonation states in PDB structures

Article Abstract:

The energetic fitness of histidine in its three protonation states is investigated. Molecular mechanics calculations are used for this purpose.

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