Signaling Recognition Events with Fluorescent Sensors and Switches.

When a molecule absorbs a photon of appropriate energy, a chain of photophysical events ensues, such as internal conversion or vibrational relaxation (loss of energy in the absence of light emission), fluorescence, intersystem crossing (from singlet state to a triplet state) and phosphorescence, as shown in the Jablonski diagram for organic molecules (Fig. 1). Each of the processes occurs with a certain probability, characterized by decay rate constants (k). It can be shown that the average length of time τ for the set of molecules to decay from one state to another is reciprocally proportional to the rate of decay: τ = 1/k. This average length of time is called the mean lifetime, or simply lifetime. It can also be shown that the lifetime of a photophysical process is the time required by a population of N electronically excited molecules to be reduced by a factor of e. Correspondingly, the fluorescence lifetime is the time required by a population of excited fluorophores to decrease exponentially to N/e via the loss of energy through fluorescence and other non-radiative processes. The lifetime of photophycal processes vary significantly from tens of femotoseconds for internal conversion1,2 to nanoseconds for fluorescence and microseconds or seconds for phosphorescence.1






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Figure 1


Jablonski diagram and a timescale of photophysical processes for organic molecules.

/pdf/fluorescence-lifetime-measurements-and-biological-imaging-xfalzh4w7e.pdf

Fluorescence Lifetime Measurements and Biological Imaging

This is an overview of some of the important, challenging, and problematic issues in contemporary electron transfer research. After a qualitative discussion of electron transfer, its time and distance scales, energy curves, and basic parabolic energy models are introduced to define the electron transfer process. Application of transition state theory leads to the standard Marcus formulation of electron transfer rate constants. Electron transfer in solution is coupled to solvent polarization effects, and relaxation processes can contribute to and even control electron transfer. The inverted region, in which electron transfer rate constants decrease with increasing exoergicity, is one of the most striking phenomena in electron transfer chemistry. It is predicted by both semiclassical and quantum mechanical models, with the latter appropriate if there are coupled high- or medium-frequency vibrations. The intramolecular reorganizational energy has different contributions from different vibrational modes, whic...

Contemporary Issues in Electron Transfer Research

6.1.2. Aqueous V(III) Chemistry 877 6.1.3. Oxidation State of Vanadium in Tunicates 878 6.1.4. Uptake of Vanadate into Tunicates 879 6.1.5. Vanadium Binding Proteins: Vanabins 879 6.1.6. Model Complexes and Their Chemistry 880 6.1.7. Catechol-Based Model Chemistry 880 6.1.8. Vanadium Sulfate Complexes 881 6.2. Fan Worm Pseudopotamilla occelata 883 7. Vanadium Nitrogenase 883 7.1. Nitrogenases 883 7.2. Biochemistry of Nitrogenase 884 7.3. Clusters in Nitrogenase and Model Systems: Structure and Reactivity 885

/pdf/the-chemistry-and-biochemistry-of-vanadium-and-the-4v5q292kxm.pdf

The chemistry and biochemistry of vanadium and the biological activities exerted by vanadium compounds.

A general approach has been developed to determine the conductivity of individual nanostructures while simultaneously recording their structure. Conventional lithography has been used to contact electrically single ends of nanomaterials, and a force microscope equipped with a conducting probe tip has been used to map simultaneously the structure and resistance of the portion of the material protruding from the macroscopic contact. Studies of individual carbon nanotubes demonstrate that the structurally most perfect nanotubes have resistivities an order of magnitude lower than those found previously and that defects in the nanotube structure cause substantial increases in the resistivity.

https://science.sciencemag.org/content/sci/272/5261/523.full.pdf

Probing Electrical Transport in Nanomaterials: Conductivity of Individual Carbon Nanotubes

Rapid photoinduced electron transfer is demonstrated over a distance of greater than 40 angstroms between metallointercalators that are tethered to the 5' termini of a 15-base pair DNA duplex. An oligomeric assembly was synthesized in which the donor is Ru(phen)2dppz2+ (phen, phenanthroline, and dppz, dipyridophenazine) and the acceptor is Rh(phi)2phen3+ (phi, phenanthrenequinone diimine). These metal complexes are intercalated either one or two base steps in from the helix termini. Although the ruthenium-modified oligonucleotide hybridized to an unmodified complement luminesces intensely, the ruthenium-modified oligomer hybridized to the rhodium-modified oligomer shows no detectable luminescence. Time-resolved studies point to a lower limit of 10(9) per second for the quenching rate. No quenching was observed upon metallation of two complementary octamers by Ru(phen)3(2+) and Rh(phen)3(3+) under conditions where the phen complexes do not intercalate. The stacked aromatic heterocycles of the DNA duplex therefore serve as an efficient medium for coupling electron donors and acceptors over very long distances.

https://science.sciencemag.org/content/sci/262/5136/1025.full.pdf

Long-range photoinduced electron transfer through a DNA helix

We report evidence for fast photoinduced electron transfer mediated by the DNA helix that requires metal complexes that are avid intercalators of DNA. Here the donor bis(phenanthroline)(dipyridophenazine)ruthenium(II) [Ru(phen)2dppz2+] and acceptor bis(9,10-phenanthrenequinone diimine)(phenanthroline)rhodium(III) [Rh(phi)2phen3+] intercalate into DNA with Kb > 10(6) M-1. Luminescence quenching experiments in the presence of two different lengths of DNA yield upward-curving Stern-Volmer plots and the loss of luminescence intensity far exceeds the change in emission lifetimes. In the presence of a nonintercalative electron acceptor, Ru(NH3)3+(6), Ru(phen)2dppz2+ luminescence is quenched much less efficiently compared to that found for the intercalative Rh(phi)2phen3+ quencher and follows linear Stern-Volmer kinetics; steady-state and time-resolved Stern-Volmer plots are comparable in scale. These experiments are consistent with a model involving fast long-range electron transfer between intercalators through the DNA helix.

https://www.pnas.org/content/pnas/91/12/5315.full.pdf

Fast photoinduced electron transfer through DNA intercalation

Stimulated nuclear polarization (SNP) and time resolved electron spin resonance (TR ESR) spectra were recorded during the laser flash photolysis of [sup 13]C carbonyl labeled [alpha]-methyldeoxybenzoin solubilized in a series of alkyl sulfate micelles of different sizes. While the SNP spectra show a decrease in the splitting of the two hyperfine lines with decreasing micelle size, this decrease in hyperfine splitting is not seen in the experimental TR ESR spectra The qualitatively different variations between the SNP and TR ESR spectra, as a function of micelle size were interpreted in terms of the stochastic Liouville equation as applied to the model of the microreactor. 28 refs., 6 figs., 2 tabs.

Examination of the Exchange Interaction through Micellar Size. 3. Stimulated Nuclear Polarization and Time Resolved Electron Spin Resonance Spectra from the Photolysis of Methyldeoxybenzoin in Alkyl Sulfate Micelles of Different Sizes

The probability of recombination (P r ) of the primary geminate radical pairs derived from optically active methyldeoxybenzoin (MDB) and from diastereomerically pure 2,4-diphenylpentan-3-one (DPP) have been determined in alkyl sulfate micelles of different sizes. These probabilities have been measured by monitoring the extent of isomerization in the recovered ketone as a function of conversion. The P r values for these two ketones, as a function of micelle size, display disparate behavior: P r for MDB increases as the micelle size increases, while P r for DPP decreases as the micelle size increases

Naresh D. Ghatlia

Papers

Long-range photoinduced electron transfer through a DNA helix

Fast photoinduced electron transfer through DNA intercalation

Examination of the Exchange Interaction through Micellar Size. 3. Stimulated Nuclear Polarization and Time Resolved Electron Spin Resonance Spectra from the Photolysis of Methyldeoxybenzoin in Alkyl Sulfate Micelles of Different Sizes

Probing the exchange interaction through micelle size. 1. Probability of recombination of triplet geminate radical pairs

Regioselective photodimerization of enones in zeolites