二维红外光谱是蛋白质和小分子等体系的结构动力学研究领域中的一种新兴探测手段。二维红外光谱系统的仪器组成复杂、采集数据量大，峰形提取和分析过程受容易受噪音信号影响，实验精度容易受环境和仪器状态因素干扰，数据分析流程不成熟。为此，我们针对实验室现有的脉冲整形二维中红外光谱实验系统，在日常调试和测试过程中针对相关仪器参数和实验条件重新编写了瞬态二维红外光谱数据处理程序，从中提取峰位、峰强，基于谱峰中心线提取峰形参数，提取频频相关函数等信息，并优化了中心线搜索和数据筛选算法，引入了新的峰形参数，实现了从实验数据筛选到寻峰拟合的一套图形界面操作程序，自动生成测试报告。在此基础上，我们借助叠氮基团探针对二甲基巯基丙酸内盐（DMSP）依赖性裂解酶DddK的活性位点封闭水分子以及高压液态水中的水分子氢键动力学的二维红外光谱数据进行了分析研究。

本文主要包括下列研究内容：
  二维红外光谱数据分析程序；
  DddK酶活性位点水分子动力学的二维红外数据分析研究；
  水分子氢键动力学与结构相变的二维红外数据分析研究。

本文的研究表明，从二维红外谱峰的中心线中提取的斜率以及中心点二阶导数、红蓝区斜率差、对称分量积分等反映弯曲程度的参数及其动力学寿命对所测吸收模式的频率轨迹的演化特性敏感，适用于探测振动模式的化学环境的细微转变，这一特性为蛋白质活性位点以及高压水体系中的水分子氢键动力学研究提供了条件。
 

Two-dimensional infrared spectroscopy (2D-IR) is an emerging probe in studies concerning the structural dynamics of systems such as proteins and small molecules.
Due to the complexity of its optical system and large dimension of data acquired during experiments, the pocessing of which is hindered by various sources of noise signal that can detriment the result of peak shape extraction and analysis, the experimental accuracy of 2D-IR spectroscopy is easily disturbed by environmental as well as instrumental factors, as a result of which the data analysis protocol in our laborotory was not well-established. In this regard, we have rewritten the transient 2D infrared spectroscopy data processing program for the existing pulse-shaping 2D mid-infrared spectroscopy system in the laboratory during its commissioning and sample testing processes when various instrumental parameters and experimental conditions can occur, so as to extract spectral informations including peak positions and peak intensities, as well as peak shape parameters computed from the centre lines of spectral peaks, from which frequency-frequency correlation functions and other information can be retrieved. The author then revamped the traditional centre line searching approaches and data filtering algorithms, on the basis of which new peak shape parameters are defined. A graphical user interface is provided by the author in order to automate/standardize the spectrogram processing procedure from data screening and peak searching down to fitting extracted spectral parameters to yield a comprehensive report of a series of transient 2D-IR experiments. On this basis, we have analysed the two-dimensional infrared spectra of the hydrogen bonding dynamics around the water molecule confined in the active site of the Dimethylsulfoniopropionate (DMSP) -dependent lyase DddK as well as water molecules in high-pressure liquid water with the aid of azide group probes.

The paper consists of the following studies:
  Two-dimensional infrared spectroscopy data analysis program;
  Data analysis of a study on water molecule dynamics at the active site of the enzyme DddK;
  Data analysis of a study on hydrogen bonding dynamics and structural phase transitions of water molecules.

The studies in this paper show that the slope extracted from the centre line of the two-dimensional infrared spectral peak, as well as parameters reflecting the degree of its bending such as the second-order derivative at the centre point, the slope difference in the red and blue regions, and the integral of symmetric component, whose magnetude and dynamic lifetimes are sensitive to the evolutionary properties of the frequency trajectories of the measured absorption modes and are suitable for detecting subtle transitions in the chemical environments of such vibrational modes. With such properties 2D-IR analysis provides a useful tool for studying protein active sites as well as water molecules in high-pressure water systems.