N-甲基乙酰胺分子上的能量耗散途徑

Abstract

為了了解生物相關分子上的能量耗散途徑，我們使用GROMACS 軟體架構出 N-methylacetamide molecules 模型，計算原子的速度與位置組態，由速度組態計算出功率譜，找出譜上特定化學鍵峰值隨時間的變化，以及不同振動模態隨時間的消長，分析能量傳遞路徑和遲豫時間。在幾種不同的操作方式下，我們得到很穩定一致的遲豫時間，約為4.5~5.0 ps，這和最近實驗觀察到的遲豫時間4.9 ps及瞬時正則模數值模擬的總耗散時間11.7 ps 很相近。「時變功率譜」分析成為另一種描述分子內能量耗散的可用工具，有別於anti-Stokes Raman 分析及瞬時正則模分析。

In order to understand the energy transduction path way in biologically relevant molecules, we use GROMACS to construct N-methylacetamide molecule models, calculate their atomic speeds and configurations,convert these information to power spectral density, extract the evolution of the frequency peaks of specific chemical bonds, find out the relations between peak variations, and analyze the paths of energy transfer and relaxation time. Under various protocols, we obtain fairlystable and consistent relaxation time around 5.0ps, which is close to theexperimentally measured relaxation time 4.9ps and the total relaxationtime 11.7ps calculated by the instantaneous normal mode analysis. The time-dependent power spectrum analysis turns out to be another feasible tool for analyzing intra molecular energy relaxations, beyond the anti-Stokes Raman analysis and the instantaneous normal mode analysis.