Picosecond spectroscopy dynamical structures

The two-pulse TR experiments allow one to readily follow the dynamics and structural changes occurring during a photo-initiated reaction. The spectra obtained in these experiments contain a great deal of information that can be used to clearly identify reactive intermediates and elucidate their structure, properties and chemical reactivity. We shall next describe the typical instrumentation and methods used to obtain TR spectra from the picosecond to the millisecond time-scales. We then subsequently provide a brief introduction on the interpretation of the TR spectra and describe some applications for using TR spectroscopy to study selected types of chemical reactions. 

The major reasons for using intrinsic fluorescence and phosphorescence to study conformation are that these spectroscopies are extremely sensitive, they provide many specific parameters to correlate with physical structure, and they cover a wide time range, from picoseconds to seconds, which allows the study of a variety of different processes. The time scale of tyrosine fluorescence extends from picoseconds to a few nanoseconds, which is a good time window to obtain information about rotational diffusion, intermolecular association reactions, and conformational relaxation in the presence and absence of cofactors and substrates. Moreover, the time dependence of the fluorescence intensity and anisotropy decay can be used to test predictions from molecular dynamics.(167) In using tyrosine to study the dynamics of protein structure, it is particularly important that we begin to understand the basis for the anisotropy decay of tyrosine in terms of the potential motions of the phenol ring.(221) For example, the frequency of flips about the C -C bond of tyrosine appears to cover a time range from milliseconds to nanoseconds.(222)... 

The complexity of the physical properties of liquid water is largely determined by the presence of a three-dimensional hydrogen bond (HB) network [1]. The HB s undergo continuous transformations that occur on ultrafast timescales. The molecular vibrations are especially sensitive to the presence of the HB network. For example, the spectrum of the OH-stretch vibrational mode is substantially broadened and shifted towards lower frequencies if the OH-group is involved in the HB. Therefore, the microscopic structure and the dynamics of water are expected to manifest themselves in the IR vibrational spectrum, and, therefore, can be studied by methods of ultrafast infrared spectroscopy. It has been shown in a number of ultrafast spectroscopic experiments and computer simulations that dephasing dynamics of the OH-stretch vibrations of water molecules in the liquid phase occurs on sub-picosecond timescales [2-14],... 

Transient IR spectroscopy in the range of the amide I band is a direct tool to follow the structural dynamics of the peptide moiety. IR difference spectra on the bicyclic molecule bc-AMPB are plotted in Fig. 5. Shortly after excitation the absorption is dominated by a red shift. Such a red shift is expected for a strong vibrational excitation of the molecule. On the time-scale of a few picosecond this red shift decays to a large extent and is replaced by a dispersive feature of opposite sign at tD = 20 ps. At later delay times this feature changes details of its shape, it sharpens up and some substructure appears around 1680 cm 1. After 1.7 ns the shape is similar, but not completely identical to the difference spectrum recorded with stationary FTIR spectroscopy. This time dependence shows that the dominant structural change responsible for the IR difference spectrum occurs on the 20 ps time-scale and that minor structural changes continue until nanoseconds and even later times. 

Beyond imaging, the combination of CRS microscopy with spectroscopic techniques has been used to obtain the full wealth of the chemical and the physical structure information of submicron-sized samples. In the frequency domain, multiplex CRS microspectroscopy allows the chemical identification of molecules on the basis of their characteristic Raman spectra and the extraction of their physical properties, e.g., their thermodynamic state. In the time domain, time-resolved CRS microscopy allows the recording of the localized Raman free induction decay occurring on the femtosecond and picosecond time scales. CRS correlation spectroscopy can probe three-dimensional diffusion dynamics with chemical selectivity. 

Furthermore, femtosecond diffuse reflectance spectroscopy with a white continuum probe pulse has been applied to detect the dynamics of hole transfer from photoexcited TiC>2 to adsorbed reactant molecules. As shown in Figure 18, at pH < 7 of the TiC>2 aqueous suspension with KSCN, ultrafast hole transfer takes place in less than 1 ps (Furube et al., 2001b). Subsequent structure stabilization of dimer anion radicals, (SCN)2, within a few picoseconds and slow hole transfer with a time constant of a few hundred picoseconds are clearly observed (Furube et al., 2001b). Fast hole transfer is caused by a surface-trapped state interacting strongly with adsorbed molecules. Slow hole transfer observed at pH values >7 is caused by deep trapped states with a Boltzmann distribution... 

The prevalence of structural compared with dynamical information arises from a scarcity of appropriate spectroscopic techniques. For example, the measurement process in NMR spectroscopy takes place on a millisecond timescale. The dominating part of the fluctuation correlation function responsible for dephasing processes, on the other hand, decays on the picosecond timescale, so that spin transitions are strongly in the motional... 

Thus far, the only excited-state structural dynamics of oligonucleotides have come from time-resolved spectroscopy. Very recently, Schreier, et al. [182] have used ultrafast time-resolved infrared (IR) spectroscopy to directly measure the formation of the cyclobutyl photodimer in a (dT)18 oligonucleotide. They found that the formation of the photodimer occurs in 1 picosecond after ultraviolet excitation, consistent with the excited-state structural dynamics derived from the resonance Raman intensities. They conclude that the excited-state reaction is essentially barrierless, but only for those bases with the correct conformational alignment to form the photoproducts. They also conclude that the low quantum yields observed for the photodimer are simply the result of a ground-state population which consists of very few oligonucleotides in the correct alignment to form the photoproducts. 

Another approach of great importance for studies of excited state dynamics is sub-picosecond time resolved spectroscopy. A number of authors have reported femtosecond pump-probe measurements of excited state lifetimes in A, C, T, and G [13-16] and base pair mimics [17]. Schultz et al. have reported time resolved photoelectron spectroscopy and electron-ion coincidence of base pair mimics [18]. these studies can also be compared with similar measurements in solution [19-24], While time resolved measurements provide direct lifetime data, they do have the limitation that the inherent bandwidth reduces the spectral resolution, required for selecting specific electronic states and for selecting single isomers, such as cluster structure and tautomeric form. 

The vibronic spectra of Do — Di — D2 electronic states recoded by da Silva Filho et al. [45] revealed resolved vibrational structures of the Do and D2 electronic states and a broad and structureless band for the Di state. A slow ( 3-20 ps) and fast k, 200 fs) relaxation components are estimated for the Dq D2 transition in a (femto)picosecond transient grating spectroscopy measurements [16]. The fast component is attributed to the Do D2 transition and a nonradiative relaxation time of 212 fs is also estimated from the cavity ringdown (CRD) spectroscopy data [42]. Electronic structure results of Hall et al. [107] suggest that the nonradiative Do D2 relaxation occurs via two consecutive sloped type CIs [66,108]. We developed a global model PESs for the Do — Di— D2 electronic states and devised a vibronic coupling model to study the nuclear dynamics underlying the complex vibronic spectrum and ultrafast excited state decay of N +[20]. 

The approach is capable of achieving a resolution of about 10 ps [43]. Optical/ vibrational spectroscopies can follow events and structural changes on such fast time scales since their characteristic time scales are sub-picosecond, even femtosecond. The methodology is therefore suitable to study the dynamics of en2ymatic catalysis over multiple time scales from picoseconds to minutes [44],... 

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