Dynamic quenching

Quenched dynamics is a combination of high temperature molecular dynamics and energy minimization. This process determines the energy distribution of con formational families produced during molecular dynamics trajectories. To provide a better estimate of conformations, you should combine quenched dynamics with simulated annealing. 

High temperature searches of conformational space (see Quenched Dynamics" on page 78), can produce unwanted conformational changes, such as cis-tmnx peptide flips, ring inversions, and other changes that you cannot reverse easily by geometry optimization. You can use restraints to prevent these changes. 

Quenched dynamics can trap structures in local minima. To prevent this problem, you can cool the system slowly to room temperature or some appropriate lower temperature. Then run room temperature molecular dynamics simulations to search for conformations that have lower energies, closer to the starting structure. Cooling a structure slowly is called simulated annealing. 

The temperature of a simulation depends on your objectives. You might use high temperatures to search for additional conformations of a molecule (see Quenched Dynamics on page 78). Room temperature simulations generally provide dynamic properties of molecules such as proteins, peptides, and small drug molecules. Low temperatures (<250 K) often promote a molecule to a lower energy conformation than you could obtain by geometry optimization alone. 

F. Tanaka and N. Mataga, Fluorescence quenching dynamics of tryptophan in proteins. Effect of internal rotation under potential barrier, Biophys. J. 51, 487-495 (1987). 

Using conformational searching/quench dynamics and 7) relaxation measurements, each back-folded isomer was determined to be smaller than its extended counterpart. Thus, the effective distance of electron transfer was not reflected in the hydrodynamic radius of the molecule. Rather, the back-folded isomers were argued to be less mobile with the iron-sulfur core buried more deeply within them. The extended isomers were more mobile with the iron-sulfur core more able to come closer to the molecular surface. By this reasoning, the back-folded isomers had a larger effective electron transfer distance than the extended isomers. 

Influence of solute-solvent interactions on the quenching dynamics of perylene derivatives in an electron donating solvent... 

We present here our investigation of the influence of solute-solvent interactions on the quenching dynamics of perylene (Pe) and derivatives in an electron donating solvent, N,N-dimethylaniline (DMA) [4]. The electron acceptors and the donor solvent are shown in Fig. 1. 

In this chapter, we review important concepts regarding vibrational spectroscopy with the STM. First, the basis of the technique will be introduced, together with some of the most relevant results produced up to date. It will be followed by a short description of experimental issues. The third section introduces theoretical approaches employed to simulate the vibrational excitation and detection processes. The theory provides a molecular-scale view of excitation processes, and can foresee the role of various parameters such as molecular symmetry, adsorption properties, or electronic structure of the adsorbate. Finally, we will describe current approaches to understand quenching dynamics via internal molecular pathways, leading to several kinds of molecular evolution. This has been named single-molecule chemistry. 

Ultrafast fluorescence quenching dynamics were studied by the fluorescence-up-conversion method with femtosecond mode-locked laser systems. For the studies of oxazine dyes, a synchronously pumped hybrid mode-locked dye laser with group velocity... 

Eq. 2. r = fluorescence lifetime of the probe without quencher, ksv = rate constant for quenching (dynamic process), K = equilibrium constant between probe and quencher, I = integral of the quenched fluorescence, /o = integral of the fluorescence without quencher. 

A comparison of the results obtained with the various minimization algorithms described in this section, as well as with quenched dynamics, is given in Ref. 65 where applications to a small peptide and a protein are presented. 

The fluorescence quenching dynamics of excited state electron donors by various pyrimidine and 5,6-dihydropyrimidine substrates have been examined and found to obey the Rehm-Weller relationship." In addition, an unexpected difference was observed between the reduction potentials for the trans-syn and cis-syn diastereoisomers of dimethylthymine cyclobutane dimers, and this has been ascribed to a stereoelectronic effect in the cis-syn dimer anion radical resulting from an unfavourable charge-dipole interaction between the added electron and the O carbonyl group of the pyrimidine ring... 

Quenched dynamics can trap structures in a local minimum. The molecular systan is heated to elevated temperatures to overcome potential energy barriers and then cooled slowly to room temperature. If each structure occurs many times during the search, one is assured that the potential energy surface of that region has been adequately sought. 

Medhage, B., and Alingrei, M., 1992, Diihiaon-influenced fluorescence quenching Dynamics in one to dvee dimensions, J. Fluoresc. 2 7-21. 

---