A density functional theory based analysis of photoinduced electron transfer in a triazacryptand based K+ sensor

The electronic structure and photoinduced electron transfer processes in a K+ fluorescent sensor that comprises a 4-amino-naphthalimide derived fluorophore with a triazacryptand lig- and is investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) in order to rationalise the function of the sensor. The absorption and emission energies of the intense electronic excitation localised on the fluorophore are accurately described using a ∆SCF Kohn-Sham DFT approach, which gives excitation energies closer to experiment than TDDFT. Analysis of the molecular orbital diagram arising from DFT calculations for the isolated molecule or with implicit solvent cannot account for the function of the sensor and it is necessary to consider the relative energies of the electronic states formed from the local excitation on the fluorophore and the lowest fluorophore→chelator charge transfer state. The inclusion of solvent in these calculations is critical since the strong interaction of the charge transfer state with the solvent lowers it energy below the local fluorophore excited state making a reductive photoinduced electron transfer possible in the absence of K+, while no such process is possible when the sensor is bound to K+. The rate of electron transfer is quantified using Marcus theory, which gives a rate of electron transfer of k_ET=5.98 x 10^6 s−1

RPBS: a web resource for structural bioinformatics

RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling. The RPBS server can be accessed at and the specific services at

Practical Time-Resolved Fluorescence Spectroscopy: Avoiding Artifacts and Using Lifetime Standards

In this chapter we describe how artifacts can be avoided in the two most commonly used time-resolved fluorometries, namely the single-photon timing and the multifrequency phase-modulation techniques. The most frequently encountered artifacts (inner filter effect, autofluorescence, polarization effects, color effect, photobleaching, deoxygenation, pulse pile-up, and linearity of the time response in the time-to-amplitude converter) are described in detail and remedies are presented to avoid these pitfalls. An extensive list of fluorescence lifetime standards is presented, which allows the spectroscopist to calibrate and test time-resolved instruments for systematic errors

Pitfalls and their remedies in time-resolved fluorescence spectroscopy and microscopy

Time-resolved fluorescence spectroscopy and microscopy in both time and frequency domains provide very useful and accurate information on dynamic processes. Good quality data are essential in obtaining reliable parameter estimates. Distortions of the fluorescence response due to artifacts may have disastrous consequences. We provide here a concise overview of potential difficulties encountered under daily laboratory circumstances in the use of time- and frequency-domain equipment as well as practical remedies against common error conditions, elucidated with several graphs to aid the researcher in visual inspection and quality-control of collected data. A range of artifacts due to sample preparation or to optical and electronic pitfalls are discussed, as are remedies against them. Also recommended data analysis strategies are described

KINETICS AND IDENTIFIABILITY OF INTRAMOLECULAR 2-STATE EXCITED-STATE PROCESSES WITH ADDED QUENCHER - GLOBAL COMPARTMENTAL ANALYSIS OF THE FLUORESCENCE DECAY SURFACE

The fluorescence decay analysis of intramolecular two-state excited-state processes with added quencher is discussed in terms of compartments. The kinetics specifying the two excited-state species concentrations are derived. The fluorescence decay surface is expressed in terms of the system parameters, namely the rate constants and the spectroscopic parameters b1 and c1. b1 and c1 are respectively the relative absorbance and the normalized spectral emission weighting factor of species 1. The report investigates the prerequisites for obtaining the unique set of system parameters. The results of this identifiability study indicate that the following conditions have to be satisfied in order to make an intramolecular two-state excited-state system with added quencher identifiable. First, the fluorescence decay surface must include at least one set of decay traces measured for a minimum of three different quencher concentrations at the same excitation/emission wavelength setting. One of the quencher concentrations used may be equal to zero. Second, the rate constants of quenching of the two excited species must be different. Third, at least one system parameter, which is not a rate constant of quenching, must be known. Under these conditions, four sets of system parameters are mathematically possible. If the known system parameter is a rate constant, decay traces of a suitable model compound measured at a minimum of two quencher concentrations must be included in the analysis in order to obtain the unique set of values for the rate constants. The unique set of (b1,c1) values can be recovered by including decay curves at a minimum of two quencher concentrations and at an additional excitation wavelength with a different b1, or at another emission wavelength with a different c1. If the known system parameter is a b1 value different from zero and unity, the fluorescence decay surface must include at least nine decay traces measured at four emission wavelengths with different c1 (corresponding to at least three quencher concentrations at the first emission wavelength and at least two quencher concentrations at the other three emission wavelengths), to uniquely determine the set of system parameters. If the known system parameter is a c1 value different from zero and one, at least four excitation wavelengths with different b1 are necessary to obtain the unique set of system parameters. The conclusions of the identifiability study are confirmed by the results from the global compartmental analysis of computer-generated fluorescence decay traces