Time-resolved Stokes shifts

The method is based on the ability of the excited state of suitable chromophores to both drive and respond to motions in their immediate environment. For example, coumarin excited states have a large dipole moment that causes nearby charged groups to move to stabilize the dipole. As these groups move and reduce the energy of the excited state, the fluorescence shifts toward the red. In simple solutions, this time-resolved Stokes shift (TRSS) experiment measures the time-dependent polarity of the solvent surrounding the coumarin [9]. 

Figure 1. The absolute time-resolved Stokes shift for normal DNA (circles) is linear on a logarithmic time axis with a slope of Aq = 218 cm 1 per decade. The Stokes shift of coumarin in a typical polar liquid [12] (ethanol, solid curve) is shown as a reference. The absolute Stokes shift is expected to reach zero near 0.1 ps, Extrapolation (dashed line) of the DNA fit does not reach this point, suggesting that a substantial change in the relaxation form occurs at early times.

Figure 2a compares the time-resolved Stokes shift of the normal sequence and the abasic sequence. For ease of comparison, the data is shifted to overlap the sequences at early times. In the first nanosecond, the Stokes shifts from both sequences overlap almost perfectly. This results suggests that there is not a large scale collapse of the normal DNA structure at the abasic site. However after 1 ns, the abasic sequence has additional dynamics beyond those of the normal sequence. The fit of the abasic sequence has the same logarithmic component of the normal sequence fit, but with an additional exponential term for the fast rise in the Stokes shift after 1 ns S(t) = S0 + A0 logl0(t/t0) + 4,(l-exp(-f/r)), with an exponential time constant r of 25 ns. 

Time-resolved Stokes shift have proven to be an effective means of measuring the dynamics of DNA on nanosecond and picosecond time scales. They have revealed a number of unusual features in the dynamics that are unique to DNA. The current results show that this method can also see variation in dynamics due to changes in DNA structure, including changes that mimic biologically relevant lesions. 

In this study we use the dye Coumarin 343 (C343) adsorbed on the surfaces of ZrC>2 nano particles in aqueous solution to study the solvation dynamics close to these surfaces. Zr02 is, in many respects, very similar to Ti02 and serves as a suitable model substance since, due to its higher band gap energy, electron injection from adsorbed dyes does not occur. To measure the time resolved Stokes shift, we used femtosecond frequency-resolved upconversion. 

M. Maroncelli, V. P. Kumar and A. Papazyan, A simple interpretation of polar solvation dynamics, J. Phys. Chem., 97 (1993) 13-17 E. W. Castner, Jr. and M. Maroncelli, Solvent dynamics derived from optical Kerr effect, dielectric dispersion, and time-resolved Stokes shift measurements an empirical comparison, J. Mol. Liq., 77 (1998) 1-36. 

L. E. Fried and S. Mukamel, Solvation structure and the time-resolved Stokes shift in non-Debye solvents, J. Chem. Phys., 93 (1990) 932 16. 

Figure 43. Solvation dynamics from MD simulations for isomer 2. (a) The linear-response calculated time-resolved Stokes shifts for indole-protein, indole-water, and their sum. (b) Direct nonequilibrium simulations of the time-resolved Stokes shifts for indole-water, indole-protein, and their sum. Note the lack of slow component in indole-water relaxation in both (a) and (b), which is opposite to isomer 1 in Fig. 42. Also shown is the indole-water (within 5 A of indole) with coupled long-time negative solvation, (c) Relaxation between indole-lys79 and indole-glu4. The interaction energy changes from these two residues nearly cancel each other, (d) The distance changes between the indole and two charged residues, but both residues move away from the indole ring.

Castner Jr. EW, Maroncelli M. Solvent dynamics derived from optical Kerr effect, dielectric dispersion, and time-resolved Stokes shift measurements an empirical comparison. J Mol Liq 1998 77 1-36. 

Time-resolved emission spectroscopy (TRES), also referred to as time-resolved Stokes shift spectroscopy, enables one to derive information about the dynamics of biopolymer-solvent interactions on the femtosecond to nanosecond time scales, provided that suitable solvatochromic fluorescent probes have been identified. Such probes should exhibit significant Stokes shifts that change with solvent polarity and should have fluorescent lifetimes on the order of the dynamic solvent exchange process or longer. TRES detects solvent dynamics that influences the energy difference between the excited and the ground states of the fluorophore and is insensitive to dynamic processes that are significantly slower than the fluorescence lifetime. 

Here, we ve a brief review of a method presented in the eailier pqier to descrihe the scdvatkm dynamics associated with the photo ocdtation of a imdecule in polar liquids, which can be probed by the time resolved Stokes shifts. The quantity which ndates the dynamics theory widi the experiment is the solvation timecorrdation function (STCF) defined by,... 

F. Steady-state and time-resolved Stokes shifts... 

F. Steady-State and Time-Resolved Stokes Shifts... 

The time-resolved technique is popular for measuring, on very fast time scales (nanosecond to subpicosecond), solvent molecule reorientation about an excited fluorophore [228-230]. Both steady-state and time-resolved Stokes shifts measurements of a probe molecule in DNA have been reported [231-233] and are discussed in more detail below. The principle of the Stokes shift measurement is illustrated in Figure 4.18. 

However, time-resolved optical spectroscopy is perhaps the premier method for learning about the dynamics of a complex system, especially on nanosecond or picosecond time scales. Some DNA dynamics data from NMR spectroscopy are presented in Table 4.3. Time-resolved emission decays, time-resolved fluorescence anisotropy, and time-resolved Stokes shifts measurements of probe molecules in DNA have been described (and see below) and fast components in the time decays assigned to various DNA motions. The dynamics as a function of sequence are incompletely mapped and provide an exciting area for future investigations. 

Time-resolved Stokes shift experiments of a coumarin derivative (Fig. 4.35) in an oligonucleotide have been reported [232]. Coumarins have long been used to probe solvent dynamics because they have large steady-state Stokes shifts in different solvents that correlate with solvent polarity and thus report on dielectric reorganization of their immediate environment. Coleman s coumarin derivative... 

In the time-resolved Stokes shift experiment, the fluorescence intensity decays were monitored at multiple wavelengths. At the blue edge of the steady-state emission spectrum, at short times there was an additional fast decay overlaid on the fluorescence decay at the red edge of the steady-state spectrum, there was an additional rise at short times (Fig. 4.38). The difference in the decays at the two wavelengths was caused by a dynamic Stokes shift, induced by DNA motion. From the data taken at 10 wavelengths, the emission spectra could be reconstructed to show a red shift in time (Fig. 4.39), and from this information the response function of the DNA was evaluated (Fig. 4.40). It was estimated that 80% of the Stokes shift was happening faster than the time resolution of the experimental setup (100 ps), and the two components that were observable had time constants of 300 ps and 13 ns [232]. 

Several other experimental studies have revealed, surprisingly, the existence of much slower timescale of the order of a few 100 ps to 1 Os of ns. Here time-resolved Stokes shifts in a dye-containing ohgonucleotide have been observed over the entire time range from 40 fs to 40 ns [6]. The dynamics could be fit to a power law with a small exponent of 0.15 (Figure 10.2). The origin of such a slow component in SD has not been understood yet, but it may be due to the correlated motion of the ions and water present in the solution. Simulation studies fail to find such slow dynamics in either water molecules or ions. It is also not clear whether stmctural relaxation of a small DNA polymer can give rise to such slow power law decay. 

Fig. 11 Time-resolved Stokes shift, C(t), of patman in PS-PEO micelles curve 1) and PS-PVP micelles curve 2). inset Time-dependent halfwidth of the time-resolved emission spectra of patman in PS-PEO micelles curve 1 ) and in PS-PVP micelles curve 2 )...

Sen, S., Andreatta, D., Ponomarev, S. Y., Beveridge, D. L., 8c Berg, M. A. (2009). Dynamics of water and ions near DNA Comparison of simulation to time-resolved stokes-shift experiments. Journal of the American Chemical Society, 131,1724. 

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