Ultrafast Vibrational Dynamics and Infrared Spectroscopy of Biologically Relevant Hydrogen Bonds

该项目的目标是开发用于处理生物相关系统中氢键的超快非线性光谱的方法。在方法论方面，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。这是通过识别耦合到波动环境的相关系统来实现的。或者，应进行基于一阶稳定性矩阵传播的完全经典模拟。两个应用将被考虑：第一，在溶液中的取代腺嘌呤-尿嘧啶碱基对的氢键NH伸缩振动的动力学。在这里，我们希望找到一个微观解释的振动弛豫增加后氢键。其次，我们将研究环肽短杆菌肽S中氢键的酰胺A型振动。在第一步中，应使用气相中特定NH振动的光谱位置的非谐计算来验证某种构象。随后，模拟的一个和两个颜色的泵探测光谱将使我们能够分配这些氢键也在其不同的松弛途径。

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.