A method for analyzing the vibrational energy flow in biomolecules in solution

Abstract

A method is proposed to analyze the intra- and intermolecular vibrational energy flow occurring in biomolecules in solution during relaxation processes. It is based on the assumption that the total energy exchanged between the vibrational modes is minimal and the global process is essentially statistical. This statistical minimum flow method is shown to provide very useful information about the amount and the rate at which energy is transferred between the individual vibrations of the molecule. To demonstrate the performance of the method, an application is made to the relaxation of the amide I mode of N-methylacetamide-d in aqueous D(2)O solution which yields a detailed quantitative description of the process.

Vibrational energy redistribution during donor–acceptor electronic energy transfer: criteria to identify subsets of active normal modes

“…As it is expected, while the energy is spread among the several active ENMs(S 1 ), the energy transfer is funneled mainly through the 265 ENM(S 2 ). In order to further explore the vibrational energy redistribution during donor-acceptor electronic energy transfer, the SMF method 86 , previously described in Section IID, has been applied. Figure 8 shows the accumulated flux for active modes arranged as bundles of I, E, and L active modes, previously classified in Figure 6.…”

“…The vibrational energy redistribution pathways during donor-acceptor electronic energy transfer can be identified by using the previously developed Statistitical Minimum Flow (SMF) 86 , originally developed to analyze the vibrational energy flow in polyatomic molecules using Instantaneous Normal Modes(INM). Herein, we applied it in terms of ENM(S α ) and we briefly outline its basic equations below.…”

Photoinduced non-adiabatic energy transfer pathways in dendrimer building blocks

“…Different energy transfer pathways can be identified using the statistical minimum flow (SMF) method. 45,46 The antisymmetric flow matrix f XY carries all the information related with the TD transfer between different chromophore units of the molecule. At each time interval ∆t during dynamics simulations, we classify the units according to whether their ⟨ρX⟩ increase or decrease.…”

“…Energy transfer is then monitored by following the changes in the spatial localization of the electronic transition density (TD). The energy flow between the individual chromophores is studied by means of the Statistical Minimum Flow (SMF), 45 developed originally for the analysis of the vibrational energy flow in polyatomic molecules, and recently adapted for the TD flux analysis. 46 By combining these techniques, we were able to obtain further insights into the role of the spatial organization of the building blocks of the nanostar and the energy transfer and the non-radiative relaxation pathways.…”

Electronic Energy Relaxation in a Photoexcited Fully Fused Edge-Sharing Carbon Nanobelt

“…The flux of δ X α ( t ), subsequent to the initial photoexcitation of the nanobelt, is monitored by applying the transition density flux analysis, originally developed to analyze the vibrational energy flow in polyatomic molecules . Herein, we briefly summarize the method.…”