Molecule fluorescence

Once the excited molecule reaches the S state it can decay by emitting fluorescence or it can undergo a fiirtlier radiationless transition to a triplet state. A radiationless transition between states of different multiplicity is called intersystem crossing. This is a spin-forbidden process. It is not as fast as internal conversion and often has a rate comparable to the radiative rate, so some S molecules fluoresce and otliers produce triplet states. There may also be fiirther internal conversion from to the ground state, though it is not easy to detemiine the extent to which that occurs. Photochemical reactions or energy transfer may also occur from S. ... 

The vast majority of single-molecule optical experiments employ one-photon excited spontaneous fluorescence as the spectroscopic observable because of its relative simplicity and inlierently high sensitivity. Many molecules fluoresce with quantum yields near unity, and spontaneous fluorescence lifetimes for chromophores with large oscillator strengths are a few nanoseconds, implying that with a sufficiently intense excitation source a single... 

The polarization properties of single-molecule fluorescence excitation spectra have been explored and utilized to detennine botli tlie molecular transition dipole moment orientation and tlie deptli of single pentacene molecules in a /7-teriDhenyl crystal, taking into account tlie rotation of tlie polarization of tlie excitation light by tlie birefringent... 

Ambrose W P, Goodwin P M, Martin J C and Keller R A 1994 Alterations of single-molecule fluorescence lifetimes in near-field optical microscopy Science 265 364-7... 

Zumbusch A, Fleury L, Brown R, Bernard J and Orrit M 1993 Probing individual two-level systems in a polymer by correlation of single molecule fluorescence Phys. Rev. Lett. 70 3584-7... 

Reilly P D and Skinner J L 1993 Spectral diffusion of single molecule fluorescence a probe of low-frequency localized excitations in disordered crystals Phys. Rev. Lett. 71 4257-60... 

Brunei C, Lounis B, Tamarat P and Orrit M 1999 Triggered source of single photons based on controlled single molecule fluorescence Phys. Rev. Lett. 83 2722-5... 

Ha T, Ting A Y, Liang J, Caldwell W B, Deniz A A, Chemla D S, Schultz P G and Weiss S 1999 Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism Proc. Natl Acad. Sc/. USA 96 893-8... 

Factors such as dissociation, association, or solvation, which result in deviation from the Beer-Lambert law, can be expected to have a similar effect in fluorescence. Any material that causes the intensity of fluorescence to be less than the expected value given by equation (2) is known as a quencher, and the effect is termed quenching it is normally caused by the presence of foreign ions or molecules. Fluorescence is affected by the pH of the solution, by the nature of the solvent, the concentration of the reagent which is added in the determination of inorganic ions, and, in some cases, by temperature. The time taken to reach the maximum intensity of fluorescence varies considerably with the reaction. 

Figure 1.6 Concept of single molecule fluorescence observation using STM.

Kuhn, S., Hakanson, U., Rogobete, L. and Sandoghdar, V. (2006) Enhancement of single-molecule fluorescence using... 

Weston, K D., Dyck, M., Tinnefeld, P., Muller, C., Herten, D. P. and Sauer, M. (2002) Measuring the number of independent emitters in single-molecule fluorescence images and trajectories using coincident photons. Anal. Chem., 74, 5342-5347. 

A question that becomes obvious at this point is what happens to the molecules that have similar structures to the natural bases but have different photophysical properties, i.e. they fluoresce. These molecules have similar main structure to the bases, similar ring systems and double bonds, and so, according to the previous discussion, similar conical intersections should be expected. If that is true, and conical intersections facilitate efficient radiationless decay, why do these molecules fluoresce instead of decaying nonadiabatically That is a question that has occupied a number of scientists and some answers and insights are given in the following section. 

The importance of water molecules for the structural dynamics and the functioning of ribozymes was investigated by Rhodes and co-workers. They studied non-coded RNA using a combination of explicit solvent molecular dynamics and single molecule fluorescence spectroscopy approaches (Rhodes et al 2006). 

Transfer between identical molecules Fluorescence anisotropy... 

Ha, T. (2001). Single-molecule fluorescence methods for the study of nucleic acids. Curr. Opin. Struct. Biol. 11, 287-92. 

Kalinin, S., Felekyan, S., Antonik, M. and Seidel, C. A. (2007). Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transfer. J. Phys. Chem. B 111, 10253-62. 

The background problem can be further overcome when using a surface-confined fluorescence excitation and detection scheme at a certain angle of incident light, total internal reflection (TIR) occurs at the interface of a dense (e.g. quartz) and less dense (e.g. water) medium. An evanescent wave is generated which penetrates into the less dense medium and decays exponentially. Optical detection of the binding event is restricted to the penetration depth of the evanescent field and thus to the surface-bound molecules. Fluorescence from unbound molecules in the bulk solution is not detected. In contrast to standard fluorescence scanners, which detect the fluorescence after hybridization, evanescent wave technology allows the measurement of real-time kinetics (www.zeptosens.com, www.affinity-sensors.com). 

Fig. 18.9 Single molecule fluorescence detection in LC ARROW chip, (a) Top view of experi mental beam geometry of dye molecule in sub picoliter excitation volume (dotted ellipse) (2exc excitation beam, dF fluorescence signal) (b) fluorescence signal as function of molecules in excitation volume symbols, different experimental runs, dashed line linear fit...

Yin, D. Lunt, E. J. Barman, A. Hawkins, A. R. Schmidt, H., Microphotonic control of single molecule fluorescence correlation spectroscopy using planar optofluidics, Opt. Express 2007, 15, 7290 7295... 

The phenomenon of organic EL was first demonstrated using a small-molecule fluorescent emitter in a vapor-deposited OLED device. The Kodak group first used metal oxinoid materials such as the octahedral complex aluminum tris-8-hydroxyquinoline (Alq3) (discussed above as an ETM) as the fluorescent green emitter in their pioneering work on OLED architectures [167],... 

FIGURE 10.7 Power consumption simulation for a 2.2-in. full-color OLED display using Universal Display s phosphorescent OLEDs, small-molecule fluorescent devices, and polymer OLEDs along with a comparison of the power consumed by an active-matrix liquid crystal display backlight. R G B= 3 6 1, 50% polarizer efficiency, and 30% of pixels lit. (From Mahon, J.K., Adv. Imaging, June, 28, 2003. With permission.)... 

Fu Y, Lakowicz JR (2009) Modification of single molecule fluorescence near metallic nanostructures. Laser Photon Rev 3 221-232... 

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