Quantum molecular probes

Schwartz, B. J. and Rossky, P. J. Pump-probe spectroscopy of the hydrated electron a quantum molecular dynamics simulation, J. Chem.Phys., 101 (1994), 6917-6926... 

In the literature, fluorescence spectroscopy in OFD has been limited to the use of ultraviolet (UV) or visible dyes as molecular probes.(1) The most common fluorescent dye used in OFD is fluorescein and its derivatives/21 23) Fluorescein possesses a good fluorescence quantum yield and is commercially available with an isothiocyanate functionality for linking to the polymeric support/24-26 Additionally, selective laser excitation can be performed because the absorbance maximum of fluorescein coincides with the 499-nm laser line emitted from an argon laser. Unfortunately, argon lasers are costly and bulky, thus limiting the practicality of their use. Similar difficulties exist with other popular commercial dyes. 

In order to prepare successful NIR molecular probe dyes, NIR dyes must meet the following criteria adequate response to analytes, high lipophilicity and/or reactive functional groups, absorbance maxima compatible with available laser diodes, high fluorescence quantum yield, molar absorptivity, and high photostability. 

Texas Red hydrazide is a derivative of Texas Red sulfonyl chloride made by reaction with hydrazine (Molecular Probes, Pierce). The result is a sulfonyl hydrazine group on the No. 5 carbon position of the lower ring structure of sulforhodamine 101. The intense Texas Red fluorophore has a quantum yield that is inherently higher than either the tetramethylrhodamine or the Lissamine rhodamine B derivatives of the basic rhodamine molecule. Texas Red s luminescence is shifted maximally into the red region of the spectrum, and its emission peak only minimally overlaps with that of fluorescein. This makes derivatives of this fluorescent probe among the best choices of labels for use in double staining techniques. 

Rajan SS, Liu HY, Vu TQ (2008) Ligand-bound quantum dot probes for studying the molecular scale dynamics of receptor endocytic trafficking in live cells. ACS Nano 2 1153— 1166... 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

Recently, Pcs organized on surface have been used as molecular probes for the determination of quantum confined effects [207], CoPc molecules form ordered self-assembled monolayers (SAM) on the top of Pb(lll) thin films grown on a Si( 111) substrate with the Pc units lying flat on the surface, as revealed by atomically resolved STM. A close analysis of the STM data revealed that the Pc molecules adsorb and self-assemble on the surface following a thickness-dependent adsorption pattern, which is ultimately related to the quantum size effects of the metal surface. 

One has to emphasize that Eqs. (82) and (83) do not involve the Born-Oppenheimer approximation although the nuclear motion is treated classically. This is an important advantage over the quantum molecular dynamics approach [47-54] where the nuclear Newton equations (82) are solved simultaneously with a set of ground-state KS equations at the instantaneous nuclear positions. In spite of the obvious numerical advantages one has to keep in mind that the classical treatment of nuclear motion is justified only if the probability densities (R, t) remain narrow distributions during the whole process considered. The splitting of the nuclear wave packet found, e.g., in pump-probe experiments [55-58] cannot be properly accounted for by treating the nuclear motion classically. In this case, one has to face the complete system (67-72) of coupled TDKS equations for electrons and nuclei. 

If the intrinsic fluorescence of the extract is a serious problem limiting sensitivity, one can either extract the fluorescent compounds prior to analysis (see above) or use one of the other fluorogenic substrates synthesized by Molecular Probes, Inc. In particular, resorufin glucuronide yields resorufin, which has an extraordinarily high extinction coefficient and quantum efficiency, and its excitation (570 nm) and emission (590 nm) are conveniently in a range where plant tissue does not heavily absorb or fluoresce. In addition, it fluoresces maximally at neutral pH, making it unnecessary to stop the reaction. Because of the tendency of resorufin to be reduced to a non-fluorescent form, omit DTT or beta-mercaptoethanol from the reaction mix. 

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