Vibrational relaxation and energy distribution in adenosine monophosphate

Abstract

Vibrational relaxation in a hydrogen-bonded adenosine monophosphate has been studied in classical dynamics procedures. The initial excitation stored in the phosphate OH vibration is shown to mainly redistribute in the ribose moiety through efficient energy pumping by the phosphoester bond. The efficiency is due to the phosphoester bond couples with neighboring bonds and transports the initial excitation to the ribose in a series of small steps. In the ribose unit, energy travels the carbon–carbon pathway and distributes mainly in the C–O–H side chains. Energy distribution in the phosphate unit is minor, but the extent is significantly higher than the amount distributed in the adenine moiety, which shares only about 10% of the initial excitation due to the inefficient energy pumping of the ribose-to-adenine bond. The numerical procedures are repeated to prevent the leakage of zero-point energies by modifying the kinetic energy for each bond.