STUDY OF EQUILIBRIUM AND NON-EQUILIBRIUM DYNAMICS BY 2D IR

用二维红外研究平衡和非平衡动力学

• 批准号: 8169537
• 负责人: ROBIN Main HOCHSTRASSER
• 金额: $ 16.62万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-06-01 至 2011-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8169537
• 关键词: Alcohols; Amides; Biological Process; Biology; Chemicals; Complex; Computer Retrieval of Information on Scientific Projects Database; Coupled; Dependence; Development; Diffusion; Energy Transfer; Environment; Equilibrium; Evolution; Frequencies; Funding; Generations; Grant; Hydrogen Bonding; Institution; Ions; Joints; Kinetics; Knowledge; Learning; Maps; Measurement; Measures; Methods; Microscopic; Molecular; Motion; Nuclear; Optical Methods; Peptides; Population; Process; Property; Proteins; Pump; Reaction; Research; Research Personnel; Resolution; Resources; Shapes; Solvents; Source; Spectrum Analysis; Stretching; Structure; System; Techniques; Time; United States National Institutes of Health; Variant; Vertebral column; Water; Work; absorption; aqueous; carbonyl group; method development; molecular dynamics; protein folding; research study; structural biology; temperature jump; vibration

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The answers to many questions in biology require knowledge of structures that are undergoing changes between states on time scales not accessible by the powerful structural biology methods of x-ray diffraction and NMR. Kinetic spectroscopy approaches tell us about the rates at which populations interchange and hence about mechanisms. However the range of equilibrium configurations and the structures of the various intermediate states cannot always be determined by these standard methods. In our work we propose new methods to determine structural aspects of these populations and their distributions regardless of how fleeting they are. Such measurements are expected to provide answers to questions regarding the evolution of segments of structures that are not available from other techniques. This is the significance of this work. Vibrational spectroscopy has provided important experimental access to the microscopic aspects of hydrogen bond dynamics in complex systems. The dynamics of OH or OD stretching vibrational modes in water or alcohol oligomers, the vibrations of molecular and atomic aqueous ions, and the NH and C=O stretching modes including those in peptides or proteins in water are very sensitive to and correlated with the structural and dynamical properties of hydrogen bonds. In principle, the shape of the conventional IR absorption spectrum provides information on the equilibrium dynamics of a hydrogen bonded system. However, in many cases the line shapes are determined by population lifetimes and spectral diffusion processes that often cannot be reduced to the unique set of parameters needed to describe the frequencies and amplititudes of coupled solvent nuclear motions. With the help of multidimensional nonlinear spectroscopic techniques in the IR, it has become possible to probe these hydrogen bond dynamics and extract more details on the structures and dynamics with high time resolution. Dynamical information on the OH, OD, and NH stretching modes of intermolecular hydrogen bonded systems has been obtained in the form of vibrational lifetimes, energy transfer, hydrogen bond breaking and reforming rates, and the time dependence of spectral diffusion. The motions of hydrogen bonds in peptides are of importance in biological processes. The amide carbonyl group is very often involved in dynamic hydrogen bonding either to water or to N-H groups or to both. Much remains to be learned from experiments on the vibrational populations and coherences about the dynamics of these hydrogen bonds for a wide range of environments. These chemical exchanges can be directly studied by 2D IR experiments that have wide applicability for the study of such ultrafast dynamics. Furthermore, for a full interpretation of 2D IR this knowledge of the dynamics is necessary. Major objectives of this core project are: - Methods of characterization by 2D IR of the equilibrium and nonequilibrium dynamics and the spatial variations of solvent structure and dynamics. - Development of methods of 2D IR temperature jump experiments applied to continuous structure evolution such as occurs in downhill protein folding reaction. - Methods of optical pump - IR and 2D IR probe spectroscopy to investigate the structures of reaction intermediates of proteins undergoing unfolding transitions. - Hydrogen bond exchange 2D IR methods and the interpretation of 2D IR line shapes including exchanges between vibrationally distinct groups of molecules. - Development of 2D IR methods to measure the frequency correlation functions of multi-amide unit peptides combined with molecular dynamics simulations, ab initio computations and structure/frequency maps. - Methods of dual frequency dynamics and determination of joint correlation functions of C-H, N-H, amide-II and amide-I modes. - Development of direct experimental approaches to expose solvation by dual frequency 2D IR experiments that excite the peptide backbone modes and probe the solvent motions that respond. - Generation of reliable approaches to the measurement and interpretation of vibrational energy transport along peptide backbones.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 生物学中许多问题的答案需要了解在时间尺度上正在经历状态之间变化的结构知识，而 X 射线衍射和核磁共振等强大的结构生物学方法无法获得这些知识。动力学光谱方法告诉我们种群交换的速率以及机制。然而，平衡构型的范围和各种中间态的结构并不总是可以通过这些标准方法来确定。在我们的工作中，我们提出了新的方法来确定这些种群的结构方面及其分布，无论它们有多短暂。这些测量有望为其他技术无法提供的有关结构片段演化的问题提供答案。这就是这部作品的意义所在。 振动光谱为复杂系统中氢键动力学的微观方面提供了重要的实验途径。水或醇低聚物中 O H 或 O D 伸缩振动模式的动力学、分子和原子水离子的振动以及 N H 和 C=O 伸缩模式（包括水中肽或蛋白质中的伸缩模式）非常敏感与氢键的结构和动力学性质相关。原则上，传统红外吸收光谱的形状提供了有关氢键系统平衡动力学的信息。然而，在许多情况下，线形状是由布居寿命和光谱扩散过程决定的，这些过程通常不能简化为描述耦合溶剂核运动的频率和振幅所需的唯一参数集。借助红外多维非线性光谱技术，可以探测这些氢键动力学并以高时间分辨率提取有关结构和动力学的更多细节。以振动寿命、能量转移、氢键断裂和重整速率以及光谱扩散的时间依赖性的形式获得了分子间氢键系统的 O H、O D 和 N H 拉伸模式的动态信息。肽中氢键的运动在生物过程中非常重要。酰胺羰基经常参与与水或 N-H 基团或两者的动态氢键结合。从关于各种环境下这些氢键动力学的振动群体和相干性的实验中，还有很多东西有待了解。这些化学交换可以通过二维红外实验直接研究，对于此类超快动力学的研究具有广泛的适用性。此外，为了全面解释 2D IR，动态知识是必要的。 该核心项目的主要目标是： - 通过 2D IR 表征平衡和非平衡动力学以及溶剂结构和动力学的空间变化的方法。 - 开发二维红外温度跳跃实验方法，应用于连续结构演化，例如在蛋白质折叠反应中发生的情况。 - 光泵方法 - 红外和二维红外探针光谱法，用于研究经历去折叠转变的蛋白质反应中间体的结构。 - 氢键交换二维红外方法和二维红外线形状的解释，包括振动不同的分子基团之间的交换。 - 开发二维红外方法，结合分子动力学模拟、从头计算和结构/频率图来测量多酰胺单元肽的频率相关函数。 - 双频动力学方法以及 C-H、N-H、酰胺-II 和酰胺-I 模式联合相关函数的确定。 - 开发直接实验方法，通过双频 2D IR 实验暴露溶剂化，激发肽骨架模式并探测响应的溶剂运动。 - 产生可靠的方法来测量和解释沿着肽主链的振动能量传输。