Paper Citing NAMD - Abstract
Sezer, Deniz; Prandolini, M. J.; Prisner, Thomas F.
Dynamic nuclear polarization coupling factors calculated from molecular dynamics simulations of a nitroxide radical in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:6626-6637, 2009
The magnetic resonance signal obtained from nuclear spins is strongly affected by the presence of nearby electronic spins. This effect finds application in biomedical imaging and structural characterization of large biomolecules. In many of these applications nitroxide free radicals are widely used due to their non-toxicity and versatility as site-specific spin labels. We perform molecular dynamics simulations to study the electron-nucleus interaction of the nitroxide radical TEMPOL and water in atomistic detail. Correlation functions corresponding to the dipolar and scalar spin-spin couplings are computed from the simulations. The dynamic nuclear polarization coupling factors deduced from these correlation functions are in good agreement with experiment over a broad range of magnetic field strengths. The present approach can be applied to study solute-solvent interactions in general, and to characterize solvent dynamics on the surfaces of proteins or other spin-labeled biomolecules in particular.
