Bloem Robbert, Dijkstra Arend G, Jansen Thomas la Cour, Knoester Jasper
Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
J Chem Phys. 2008 Aug 7;129(5):055101. doi: 10.1063/1.2961020.
Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block N-methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorption spectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrodinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of N-methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in N-methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.
振动本征态之间的粒子转移对于化学中的许多现象都很重要。在溶液中，这种转移是由分子构象以及周围溶剂的波动引起的。我们开发了一种联合静电密度泛函理论图谱，它使我们能够关联肽结构单元N - 甲基乙酰胺的酰胺I和酰胺II模式之间的混合，进而关联它们之间的弛豫。该图谱使我们能够从分子动力学轨迹中提取一个波动的振动哈密顿量。然后通过薛定谔方程的数值积分从这个哈密顿量得到线性吸收光谱、粒子转移和二维红外光谱。我们表明，二维红外光谱中的酰胺I/酰胺II交叉峰原则上允许人们追踪这两种模式之间的振动粒子转移。我们在重水中对N - 甲基乙酰胺的模拟预测，这两种模式之间的弛豫效率很高，时间尺度为790飞秒。这解释了肽中酰胺I带的大部分弛豫，在N - 甲基乙酰胺中观察到其发生时间尺度为450飞秒。因此我们得出结论，在多肽中，向酰胺II模式的能量转移为酰胺I振动提供了主要的弛豫通道。
