Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography

Abstract

One contribution of 15 to a theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

The measurement of ultrafast electronic and structural dynamics with X-rays

“…The brightness is high enough to capture structural changes in an ensemble of gas phase small molecules [30] and these measurements have revealed photochemical structural changes that occur over a few 100s of femtoseconds, as is described in the article by Ware et al [31]. Structural changes of much larger photoactive protein molecules, in a nanocrystalline form, have also been studied [32], and this is addressed in the article by Hutchison et al [33]. Optical and terahertz fields can be used to induce non-equilibrium phases in strongly correlated quantum condensed phase materials with new emergent properties and the accompanying structural change has been captured by time-resolved X-ray diffraction [34]; this topic is described in the article by Buzzi et al [35].…”

Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics

“…The inescapable conclusion, supported by the results from decades of time domain Raman spectroscopy research, is that for current applications of femtosecond time resolved pump-probe X-ray crystallography, both ground state and excited state vibrational coherences are generated with significant amplitudes 41,62 . From impulsive Raman spectroscopy, it is known that with under intense femtosecond optical excitation with a moderate laser bandwidth, approximately half of the motion that occurs within the vibrational dephasing time is due to ground state coherence, which is unrelated to the reaction coordinate that is usually of biological interest 41,62 . Realistic experimental bandwidths reported are on the order of ∼3 THz, 1,2 and vibrational dephasing times in proteins are on the order of 1–2 ps 72–76 .…”

“…An as yet unexploited opportunity for analysis of pump-induced differences, which is achievable with current experimental capabilities at XFEL stations, is to analyze the orientation dependence of optical pumping 41 . Stationary laser excitation of a molecular crystal generally results in significant photoselection.…”

“…The crystal morphology variations and resulting refraction will add uncertainty to the polarization retrieval which is performed for propagation inside the crystal medium, but in principle, the analysis is possible by obtaining the crystal orientation from inversion of the indexing matrix 41 . Following the polarization calculation, a conventional calculation of linear and nonlinear conversion can be performed, 41 equivalent to the isotropic analysis of power titration analysis of transient absorption 33,61 . In this approach, the retrieval of linear and nonlinear cross sections obtained from the power density variation results in modeling of photochemical populations.…”

“…The connection between crystal orientation, X-ray diffraction, and phototransformation is shown in Fig. 4 41 . Practically, a pump-probe TR-SFX experiment would need to collect many more stationary diffraction images in order to add orientational analysis.…”