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: 7723840
• 负责人: ROBIN Main HOCHSTRASSER
• 金额: $ 10.33万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-01 至 2009-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723840
• 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; Range; Rate; Reaction; Research; Research Personnel; Resolution; Resources; Shapes; Solvents; Source; Spectrum Analysis; Standards of Weights and Measures; 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.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 生物学中许多问题的答案需要了解在时间尺度上在状态之间发生变化的结构，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。动力学光谱学方法告诉我们种群交换的速度，从而了解机制。然而，平衡构型的范围和各种中间态的结构并不总是由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及其分布的结构方面，无论它们是多么短暂。预计这种测量将为其他技术无法提供的有关结构片段演变的问题提供答案。这就是这项工作的意义所在。 振动光谱为研究复杂体系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OH或OD伸缩振动模的动力学，分子和原子水离子的振动，以及NH和C=O伸缩振动模，包括多肽或蛋白质在水中的伸缩振动模，对氢键的结构和动力学性质非常敏感并与之相关。原则上，常规红外吸收光谱的形状提供了氢键体系平衡动力学的信息。然而，在许多情况下，谱线形状是由布居寿命和光谱扩散过程决定的，这些过程往往不能简化为描述耦合溶剂核运动的频率和幅度所需的独特参数集。借助于红外光谱中的多维非线性光谱技术，有可能探索这些氢键动力学，并以高时间分辨率提取更多关于结构和动力学的细节。用振动寿命、能量转移、氢键断裂和重整速率以及光谱扩散随时间变化的形式，获得了分子间氢键体系的OH、OD和NH伸缩模式的动力学信息。多肽中氢键的运动在生物过程中是重要的。酰胺羰基经常参与与水或与N-H基团或与两者的动态氢键。在广泛的环境中，关于这些氢键的动力学，仍有许多关于振动布居和相干的实验需要了解。这些化学交换可以通过二维红外实验直接研究，对研究这种超快动力学具有广泛的适用性。此外，为了全面解释2D IR，这种动力学知识是必要的。 这一核心项目的主要目标是： -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2D IR表征方法。 -开发适用于蛋白质折叠反应下坡等连续结构进化的2D IR温度跳跃实验方法。 -光泵-IR和2D IR探测光谱的方法，以研究经历展开转变的蛋白质的反应中间产物的结构。 -氢键交换、2D IR方法和2D IR线形的解释，包括振动不同的分子基团之间的交换。 -开发2D IR方法，结合分子动力学模拟、从头计算和结构/频率图，测量多酰胺单元多肽的频率相关函数。 -双频动力学方法和测定C-H、N-H、酰胺-II和酰胺-I模式的联合相关函数。 -开发通过双频2D IR实验来揭示溶剂化的直接实验方法，该实验激发多肽主干模式并探索响应的溶剂运动。 -产生可靠的方法来测量和解释沿着多肽骨架的振动能量传输。