Abstract Ultrafast X-ray crystallography of the photoactive yellow protein with femtosecond delays using an X-ray free electron laser has successfully probed the dynamics of an early Franck-Condon species. The femtosecond pump-probe application of protein crystallography represents a new experimental regime that provides an X-ray structural probe for coherent processes that were previously accessible primarily using ultrafast spectroscopy. We address how the optical regime of the visible pump, that is necessary to successfully resolve ultrafast structural differences, affects the motions that are measured using the technique. The sub-picosecond photochemical dynamics in PYP involves evolution of a mixture of electronic ground and excited state populations. Additional to photoisomerisation that is considered to proceed through activated barrier crossing, within the dephasing time structural motion include vibrational coherence arising from excited states, the ground state and a ground state intermediate under experimental conditions used for ultrafast crystallography. Intense optical pulses are required to convert population levels in PYP crystals that allow detection by X-ray crystallography, but the compromise currently needed for the optical bandwidth and power has consequences with regard to the contributions to the motions that are experimentally measured with femtosecond delays. We briefly review the ultrafast spectroscopy literature of the primary photoreactions of PYP and discuss relevant physical models taken from coherent control and femtosecond coherence spectroscopy literature that address both the population transfer as well as the vibrational coherences. We apply linear response theory, with the additional use of a high power approximation, of on-resonance impulsive vibrational coherence in the ground state and the non-impulsive coherence in the excited state and discuss experimental approaches to manipulate the coherence contributions. The results are generalised and extended to discuss the future capabilities of high repetition rate X-ray free electron laser instruments providing enhanced sensitivity to perform the crystallographic equivalent of an impulsive Raman measurement of vibrational coherence.

中文翻译：

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飞秒时间分辨光活性黄色蛋白的 X 射线晶体学的种群和相干性

摘要 使用 X 射线自由电子激光器对具有飞秒延迟的光敏黄色蛋白质进行超快 X 射线晶体学研究，成功探测了早期 Franck-Condon 物种的动力学。蛋白质晶体学的飞秒泵浦探针应用代表了一种新的实验方案，它为以前主要使用超快光谱学的相干过程提供了 X 射线结构探针。我们解决了成功解决超快结构差异所必需的可见泵的光学状态如何影响使用该技术测量的运动。PYP 中的亚皮秒光化学动力学涉及电子基态和激发态群的混合物的演化。除了被认为是通过激活的势垒交叉进行的光异构化之外，在移相时间内，结构运动还包括在用于超快晶体学的实验条件下由激发态、基态和基态中间体引起的振动相干性。需要强烈的光脉冲来转换 PYP 晶体中的粒子数水平，以便通过 X 射线晶体学进行检测，但目前需要对光学带宽和功率进行折衷对运动的贡献有影响，这些运动是用飞秒延迟进行实验测量的。我们简要回顾了 PYP 主要光反应的超快光谱文献，并讨论了从相干控制和飞秒相干光谱文献中获取的相关物理模型，这些模型既解决了种群转移问题，也解决了振动相干问题。我们应用线性响应理论，并额外使用高功率近似，基态的共振脉冲振动相干和激发态的非脉冲相干，并讨论操纵相干贡献的实验方法。结果被概括和扩展，以讨论高重复率 X 射线自由电子激光仪器的未来能力，提供更高的灵敏度，以执行振动相干的脉冲拉曼测量的晶体学等效。