Ultrafast Vibrational Dynamics and Infrared Spectroscopy of Biologically Relevant Hydrogen Bonds

本项目的目标是开发处理生物相关系统中氢键的超快非线性光谱的方法。在方法方面，这涉及非线性响应函数的混合量子力学/分子力学轨迹模拟。这是通过识别与波动环境相耦合的相关系统来实现的。或者，应根据一阶稳定性矩阵的传播进行完全经典的模拟。两个应用将被考虑：第一，氢键NH拉伸振动的取代腺嘌呤-尿嘧啶碱基对在溶液中的动力学。在这里，我们想找到氢键时振动弛豫增加的微观解释。其次，我们将研究环肽gramicidin s中氢键的酰胺A型振动。在第一步，对气相应使用中特定nh振动的光谱位置进行非调和计算，以验证某种构象。随后，对单色和双色泵浦探测光谱的模拟将使我们能够根据它们不同的弛豫路径来分配这些氢键。

The goal of this project is to develop methods for treating the ultrafast nonlinear spectroscopy of hydrogen bonds in biologically relevant systems. On the methodological side this involves hybrid quantum mechanics/molecular mechanics trajectory simulations of nonlinear response functions. This is achieved by identifying a relevant system coupled to the fluctuating environment. Alternatively, fully classical simulations shall be performed which are based on the propagation of the first order stability matrix. Two applications will be considered: First, the dynamics of the hydrogen-bonded NH stretching vibration of a substituted adenine-uracil base pair in solution. Here, we want to find a microscopic explanation for the increase of vibrational relaxation upon hydrogen bonding. Second, we will investigate the amide A type vibrations of the hydrogen bonds in the cyclic peptide gramicidin S. In a first step anharmonic calculations of the spectral positions of specific NH-vibrations in the gas phase shall be used to validate a certain conformation. Subsequently, the simulation of one- and two-color pump-probe spectra shall enable us to assign these hydrogen bonds also in terms of their distinct relaxation pathways.