Figure 6 - uploaded by Hao Ren
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The frequency-frequency correlation functions for the ÅÅ-ÅÅ* excitation energy of PYP for (a) pG and (b) pR. The raw data is represented by the black dots and the exponential fit to equation 9 is represented by the blue line.
Source publication
We present simulations of one and two-dimensional infrared (2DIR) and stimulated resonance Raman (SRR) spectra of the dark state (pG) and early red-shifted intermediate (pR) of photoactive yellow protein (PYP). Shifts in the amide I and Glu46 COOH stretching bands distinguish between pG and pR in the IR absorption and 2DIR spectra. The one-dimensio...
Citations
... However, T1DIR spectroscopy only probes changes in the frequencies and absorption intensities of molecular vibrations, and these properties are related to the conformation only in an indirect manner. Transient twodimensional infrared (T2DIR) spectroscopy is a much more direct probe of structural changes at the molecular level [12][13][14][15][16][17] . The two-dimensional infrared (2DIR) spectrum of a molecule reveals the couplings between its vibrational modes 18,19 . ...
Synthetic molecular machines are promising building blocks for future nanoscopic devices. However, the details of their mechanical behaviour are in many cases still largely unknown. A deeper understanding of mechanics at the molecular level is essential for the design and construction of complex nanodevices. Here, we show that transient two-dimensional infrared (T2DIR) spectroscopy makes it possible to monitor the conformational changes of a translational molecular machine during its operation. Translation of a macrocyclic ring from one station to another on a molecular thread is initiated by a UV pulse. The arrival of the shuttling macrocycle at the final station is visible from a newly appearing cross peak between these two moieties. To eliminate spectral congestion in the T2DIR spectra, we use a subtraction method applicable to many other complex molecular systems. The T2DIR spectra indicate that the macrocycle adopts a boat-like conformation at the final station, which contrasts with the chair-like conformation at the initial station.
In recent years visible pump/mid-IR probe spectroscopy has established itself as a key technology to unravel structure-function relationships underlying the photo-dynamics of complex molecular systems. In this contribution we review the most important applications of mid-infrared absorption difference spectroscopy with sub-picosecond time-resolution to photosynthetic complexes. Considering several examples, such as energy transfer in photosynthetic antennas and electron transfer in reaction centers and even more intact structures, we show that the acquisition of ultrafast time resolved mid-IR spectra has led to new insights into the photo-dynamics of the considered systems and allows establishing a direct link between dynamics and structure, further strengthened by the possibility of investigating the protein response signal to the energy or electron transfer processes. This article is part of a Special Issue entitled: Vibrational Spectroscopies in Molecular Bioenergetics.
