Key steps of the cis-platin-DNA interaction: density functional theory-based molecular dynamics simulations

Article Abstract:

It has been possible to make parameter-free simulations of the first, rate-limiting, step of the hydrolysis reaction and a partial investigation of the final step of the binding process to DNA. This work should be relevant to the study of square planar complexes in water in general.

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Formamide hydrolysis investigated by multiple-steering ab initio molecular dynamics

Article Abstract:

An ab initio Car-Parrinello molecular dynamics (CPMD)(super 35) investigation of the initial step of the uncatalyzed and the base-catalyzed reactions of formamide in liquid water is presented. In conclusion, the MSMD methodology appears to be a fast and reliable technique to study chemical processes though, a special care has to be paid when dealing with transformations that require other rearrangements of the system, characterized by short relaxation times.

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Calculation of redox properties: Understanding short- and long-range effects in rubredoxin

Article Abstract:

A combination of density functional theory (DFT) and classical molecular dynamics is used to quantitatively estimate the key redox properties of two variants of rubredoxin, a small and comparatively simple iron-sulfur protein. The results have confirmed that in the case of rubredoxin the redox potential modulation is obtained by the short-range contribution, while the reorganization free energy is dominated by long-range effects.

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