Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.
Keywords: Antineoplastic Agents/chemistry ; Electrochemistry ; Electron Transport ; Enzymes/chemistry ; Ligands ; Metalloproteins/chemistry ; Models ; Biological ; Models ; Molecular ; Oxidation-Reduction ; Platinum Compounds/chemistry ; *Systems Biology ; *Thermodynamics
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
Record created on 2008-04-28, modified on 2016-08-08