Energetics and Dynamics in MbCN: CN--Vibrational Relaxation from Molecular Dynamics Simulations
journal contributionposted on 11.01.2007, 00:00 authored by Jonas Danielsson, Markus Meuwly
The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide−heme complex is calculated. Two deep minima with a stabilization energy of ≈ 50 kcal/mol corresponding to two different binding orientations (Fe−CN and Fe−NC) of the ligand are found. The Fe−CN conformation is favored over Fe−NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe−CN unit is developed that captures polarization and ligand−metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe−CN conformation with ε-protonation of Hisε64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.
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cyanide anionstabilization energytime scalerelaxation pathwaysnonequilibrium MD simulationsStability argumentsbond lengthenergy surface2 Dbinding orientationatomistic simulationsfrequency shiftscharge modelligandbinding orientationsMolecular Dynamics SimulationsThe dynamicsrelaxation time scalevibrational relaxationFeCNground state25 cmbond strength