Photophysical Molecular Probes

Abstract Conjugated polymers have many unique photophysical properties that make them useful for a variety of applications within the fields of chemistry, molecular biology, and medicine, specifically their ability to produce a conformation-dependant spectral signature reflective of changes in their local environment. This physical property makes conjugated polymers an indispensible tool in the toolbox of fluorescent reporters, and within this chapter, their utilization as molecular probes for studying protein structure and conformation is emphasized. 

Our motivation for offering a further consideration of excimer fluorescence is that it is a significant feature of the luminescence behavior of virtually all aryl vinyl polymers. Although early research was almost entirely devoted to understanding the intrinsic properties of the excimer complex, more recent efforts have been directed at application of the phenomenon to solution of problems in polymer physics and chemistry. Thus, it seems an appropriate time to evaluate existing information about the photophysical processes and structural considerations which may influence excimer formation and stability. This should help clarify both the power and limitations of the excimer as a molecular probe of polymer structure and dynamics. 

Photoluminescence (PL) is widely applied to investigate surfaces and surface chemical phenomena with a high degree of sensitivity. The technique provides extremely rich information when applied to the study of photoluminescence sites on bulk oxides with a large surface to volume ratio on sites located on the surface of a support, for example oxide-supported catalysts on sites that can be modified by thermal treatments (calcination, reduction, etc.) and when the local environment of the emitting sites is altered by the adsorption of molecular probes. By way of introduction, basic photophysical aspects essential for the rationalization of PL data will be summarized. 

Multiphoton Microscope and Photophysical Technologies Probing Molecular Dynamics of Life... 

In the previous sections, it has been shown how powerful the time-resolved fluorescence techniques are in real time probing of photoinduced processes and in allowing the determination of reaction rates from fluorescence lifetimes. The present section is devoted to the method of UV/vis transient absorption spectroscopy, which is a key method in probing non emissive species and is thus crucial to detect photoreaction products or intermediates following optical excitation of molecules in their electronic excited states. When carried out on short time scales, i.e. with femtosecond to subnanosecond excitation sources, fluorescent species can also be detected by their stimulated emission. Combining time-resolved fluorometry and transient absorption spectroscopy is ideal for the study of photochemical and photophysical molecular processes. 

An improved approach to the noncovalent detection of bends and kinks would be to use a photophysical probe that approximates the size of the feature to be probed (Fig. 4.22). For example, one could imagine using a large organic bis-intercalator dye, such as TOTO or YOYO (commercially available from Molecular Probes Fig. 4.23), instead of a mono-intercalator, to interact with oli-... 

CE Bunker, TL Bowen, Y-P Sun. A photophysical study of molecular probe 6-propionyl-2-(lV,lV-dimethylamino)-naphthalene (PRODAN) in aqueous and non-aqueous solutions. Photochem Photobiol 58 499, 1993. 

Abstract Fluorescent molecules have been widely used as biomolecular labels, enzyme substrates, environmental indicators, and cellular stains and thus constitute indispensable tools in chemistry, physics, biology, and medicinal sciences. The large variation in the photophysics of the available fluorophores connected with chemical alterations give fluorescent probe techniques an almost unlimited scope for the detection of specific molecules and the investigation of intermolecular interactions on a molecular scale. 

Dendrimers have precise compositional and constitutional aspects, but they can exhibit many possible conformations. Thus, they lack long-range order in the condensed phase, which makes it inappropriate to characterize the molecular-level structure of dendrimers by X-ray diffraction analysis. However, there have been many studies performed using indirect spectroscopic methods to characterize dendrimer structures, such as studies using photophysical and photochemical probes by UV-Vis and fluorescence spectroscopy, as well as studies using spin probes by EPR spectroscopy. 

Scheme 1 summarizes four different approaches used to characterize dendrimer structures by photophysical and photochemical probes 1. Non-covalent, inter-molecularly bound interior probes - to study the internal cavities and the encapsulation abilities of dendrimers. 2. Non-covalent, intermolecularly bound surface probes - to study surface characteristics of dendrimers. 3. Covalently linked probes on dendrimer surfaces - to study the molecular dynamics of dendrimers. 4. Covalently linked probes at the dendrimer central core - to study the site isolation of the core moiety and define the hydrodynamic volume of dendrimers by the concentric dendrimer shells. Critical literature in these four categories will be described using representative examples. 

An overview of the synthesis, structure, photophysical properties, and applications of squaraine rotaxanes as fluorescent imaging probes and chemosensors is provided in a recent review [67]. Although a variety of squaraine dyes form rotaxanes with the molecular cage 25 or with a tetralactam macrocyclic system introduced by Leigh and co-workers [16, 17], there is no evidence in the literature that conventional cyanine dyes can be embedded in these macrocycles. 

The results reported here and in earlier publications in this series suggest that cavity size and limitations to molecular motion play a dominant role in the photochemistry and photophysics of alkyl aryl ketones included in zeolites. In the case of Silicalite the size and polarity of various substituted 8-phenylpropiophenones seem to determine the efficiency of inclusion and ultimately of luminescence. The same factors, relating to size and mobility can be expected to play an important role in the use of zeolites as catalysts for other reactions, whether these are photochemical or thermal processes. In this sense studies with 8-phenylpropiophenones may lead to considerable information on adsorption sites and on the freedom (or lack of it) of molecular motion as well as on the accessibility of these sites to other reactants. Recent work from Turro s laboratory has shown that pyrene aldehyde can be used to probe the nature of inclusion sites in various zeolites (27) dibenzyl-ketones were also used as probes on porous silica (28). 

Recent rapid developments in ultrashort pulse laser [1-5] make it possible to probe not only the dynamics of population of the system but also the coherence (or phase) of the system. To treat these problems, the density matrix method is an ideal approach. The main purpose of this paper is to briefly describe the application of the density matrix method in molecular terms and show how to apply it to study the photochemistry and photophysics [6-9]. Ultrafast radiationless transactions taking place in bacterial photosynthetic reaction centers (RCs) are very important examples to which the proposed theoretical approach can be applied. 

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