Following molecular structure and dynamics in real time using femtosecond stimulated Raman spectroscopy

要了解功能，就要研究结构。弗朗西斯·克里克（Francis Crick）对DNA结构的阐释不仅在科学界而且在整个社会都掀起了革命，之后他发表了这一声明。虽然它是在微观世界中提出的，但它同样适用于我们日常的宏观世界。如果给我们一个汽车引擎，让我们研究它是如何工作的，我们可能会做两件事：首先，我们把它拆开，找出它是由什么组成的，它是如何构造的，哪些部件在运动。其次，我们可能会改变燃料，玩弄电子设备，连接和断开我们可能发现的任何电缆，以深入了解哪些部件是必不可少的，它们的功能是什么。在很多方面，蛋白质，我们身体的驮马，是一个微观的汽车引擎的等效物，除了它们通常更复杂，更重要的是，它们的工作效率更高。为了理解它们的功能，我们使用上面概述的相同方法。我们试图尽可能多地了解它们的结构，使用各种光谱技术，改变蛋白质的不同部分，它的环境和燃料，以确定它是如何工作的。我们通常唯一不能做的就是实时观察他们的工作。这是多么重要，最好的证明是手表的内部工作原理。观察一块死表的内部会让人很难理解它是如何工作的，但观察所有部件的运动就容易多了。这些概念同样适用于蛋白质的功能，也适用于与一般化学有关的结构变化。观察原子在（生物）化学过程中如何重新排列的基本问题是，它们的运动速度非常快，通常以飞秒为时间尺度。（换个角度来看：1飞秒相当于5分钟，就像5分钟相当于宇宙的存在一样。）因此，有必要制造一台相机，在化学变化进行时捕捉反应物质的结构快照。分子由由电子键连接在一起的原子组成。这些原子的运动通常用分子振动来描述。由于这些键的强度与分子的三维结构密切相关，因此可以通过记录分子振动的能量作为时间的函数来跟踪结构的任何变化。传统上，这种技术的速度太慢，无法直接观察分子变化。为了实现这一目标，我想建立基于振动光谱的新型光谱技术，使用飞秒激光脉冲，可以实时观察分子结构。这些技术将基于最近的结果，这些结果表明，可以绕过不确定原理建立的限制，以达到必要的时间和能量灵敏度。这种能力应该使我能够解决许多与生物学相关的凝聚态的基本问题，例如：能量是如何在分子中重新分配的？溶剂在引导光化学过程中的作用是什么？酶-底物复合物是如何形成的，它们的结构和时间动态是什么？与上面的比较类似：我希望把生物化学反应的运动活塞形象化。

To understand function, study structure . Francis Crick made this statement after his elucidation of the structure of DNA revolutionized not only the scientific community but also society as a whole. While it was made with the microscopic world in mind, it is equally true in our day-to-day macroscopic world. If we were presented with a car engine and asked to investigate how it functions we would probably do two things: Firstly, we take it apart to find out what it consists of, how it is constructed and which parts are moving. Secondly, we might change the fuel, play with the electronics and connect and disconnect any cables we may find to gain insight into which parts are essential and what their function is. In many ways, proteins, the work horses of our body, are a microscopic equivalent of that car engine, except that they usually are much more complex and more importantly, much more efficient at what they do. To understand their function, we use the same approach outlined above. We try to learn as much as possible about their structure using various spectroscopic techniques and change various parts of the protein, its environment and fuel to determine how it works. The only thing we usually cannot do is to watch them do their work in real time. How important this is, is best demonstrated by the inner workings of a watch. Looking inside a dead watch makes it difficult to understand how it works, but watching all the parts move makes it much easier. These concepts are equally true for protein function as for the structural changes associated with chemistry in general.The fundamental problem in observing how atoms rearrange during a (bio)chemical process is that they move incredibly fast, usually on the time scale of femtoseconds. (To put this in perspective: one femtosecond compares to five minutes as five minutes to the existence of the universe.) It is thus necessary to create a camera to capture structural snapshots of the reacting species as the chemical change proceeds. Molecules consist of atoms that are held together by electronic bonds. The motions of these atoms are usually described by molecular vibrations. Since the strength of these bonds is closely connected to the three-dimensional structure of the molecule, it is possible to follow any changes in structure by recording the energy of molecular vibrations as a function of time. Traditionally, such techniques have been orders of magnitude too slow to directly observe molecular change. To achieve this goal I would like to establish novel spectroscopic techniques based on vibrational spectroscopy using femtosecond laser pulses that enable the observation of molecular structure in real time. These techniques will be based on recent results suggesting that the limits established by the uncertainty principle can be circumvented to achieve the necessary temporal and energy sensitivity.This ability should enable me to address many fundamental questions in the, biologically relevant, condensed phase such as: how is energy redistributed throughout a molecule? what is the role of the solvent in guiding a photochemical process? how are enzyme-substrate complexes formed and what are their structural and temporal dynamics? In analogy with the above comparison: I hope to visualize the moving pistons of biochemical and chemical reactions.