Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations.
We present a combined theoretical approach based on analyzing molecular dynamics trajectories (at the nanosecond scale) generated by use of classical polarizable force fields and on quantum calculations to compute averaged hyperfine coupling constants. That method is used to estimate the constant of a prototypical nitroxide: the dimethylnitroxide. The molecule is embedded during the simulations in a cubic box containing about 500 water molecules and the molecular dynamics is generated using periodic conditions. Once the trajectories are achieved, the nitroxide and its first hydration shell molecules are extracted, and the coupling constants are computed by considering the latter aggregates by means of quantum computations. However, all the water molecules of the bulk are also accounted for during those computations by means of the electrostatic potential fitted method. Our results exhibit that in order to predict accurate and reliable coupling constants, one needs to describe carefully the out-of-plane motion of the nitroxide nitrogen and to sample trajectories with a time interval of 400 fs at least to generate an uncorrelated large set of nitroxide structures. Compared to Car-Parrinello molecular dynamics techniques, our approach can be used readily to compute hyperfine coupling constants of large systems, such as nitroxides of great size interacting with macromolecules such as proteins or polymers.
Houriez
Céline
C
UMR 6264 Laboratoire Chimie Provence, Equipe Chimie Theorique, Faculte des Sciences de Saint-Jerôme Case 521, Avenue Escadrille Normandie-Niemen, 13397 Marseille Cedex 20, France.
Ferré
Nicolas
N
Masella
Michel
M
Siri
Didier
D
D003198:Computer Simulation; D015394:Molecular Structure; D009038:Motion; D009589:Nitrogen Oxides / Q000737:chemistry*; D011108:Polymers; D011506:Proteins; D011789:Quantum Theory; D012996:Solutions; D014867:Water / Q000737:chemistry
D009589:Nitrogen Oxides; D011108:Polymers; D011506:Proteins; D012996:Solutions; D014867:Water