Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent

Abstract

A systematic molecular dynamics (MD) simulation study of the photoinduced heat transfer from the model peptide N-methylacetamide (NMA) to various solvents is presented, which considers four types of solvent (water, dimethyl sulfoxide, chloroform, and carbon tetrachloride), and in total 24 different force field models for these solvents. To initiate nonstationary energy flow, an initial temperature jump of NMA is assumed and nonequilibrium MD simulations are performed. As expected from simple theoretical models of heat transfer, the cooling process is proportional to the heat capacity C(V) and--to some extent--to the viscosity eta of the solvent. The complex interplay of Coulomb and Lennard-Jones interactions is studied by scaling these interaction energies. The study reveals that realistic changes (< or approximately 10%) of the Lennard-Jones and Coulomb parameters do not change the cooling time considerably. Including polarizibility, on the other hand, appears to enhance the energy dissipation. Moreover, the solvent's internal degrees of freedom may significantly participate in the heat transfer. This is less so for water, which possesses only three high-frequency vibrational modes, but certainly so for the larger solvent molecules dimethyl sulfoxide and chloroform, which possess several low-frequency vibrational modes. For water, the simulated cooling rate is in excellent agreement with experiment, while only qualitative agreement (up to a factor of 2) is found for the other considered solvents. The importance of the force field model and quantum-mechanical effects to correctly describe the cooling process is discussed in some detail.

Vibrational energy flow in the villin headpiece subdomain: Master equation simulations

“…Damping rates for solute modes in water vary widely; [64][65][66][67] we use a 5 ps lifetime as representative for a protein in water, in rough agreement with results of experimental and computational studies of energy flow from peptides and proteins into water. 68,69 We observe in Fig. 6 that energy that flows into a residue in less than 1 ps decays, due to the presence of water, after a few ps, or even earlier, as is the case for residue 4, which begins to decay around 1 ps into the simulation.…”

Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment

“…This value is somewhat larger as the 6 ps cooling time recently found in a nonequilibrium MD study of small peptides in water. 28 A possible reason for the deviation might be that an impulsive excitation was assumed in the latter study, while the decay of the photoswitch energy in Figure 4 still delivers energy to the peptide at later times. As a consequence of the cooling of the photoswitch and the peptide, the kinetic energy of the solvent rises on a 3 ps time scale and reaches a plateau after ≈20 ps.…”

Time-resolved observation of protein allosteric communication

“…A number of studies have discussed possible connections between allostery and vibrational energy transport (21,24,32,62). From various experimental and theoretical studies, it is well established that the dissipation of excess kinetic energy (e.g., due to photoexcitation or a chemical reaction) occurs on a timescale of tens of picoseconds (48,49). As the structural rearrangement underlying allostery was shown to take at least nanoseconds to evolve, it appears obvious that vibrational energy transport and the propagation of structural change are physically different phenomena.…”

“…2A, Inset reveals that the response of d21,76(t) depends on the solvent viscosity only for t 0.1 ns (see below). The elastic phase also features the dissipation of photoinduced excess kinetic energy (i.e., the cooling of PDZ2S to the solvent temperature), which typically occurs on a timescale of tens of picoseconds (48,49).…”