Dinesh Chandra Khara

Fluorescence Quenching of CdS Quantum Dots by 4‐Azetidinyl‐7‐Nitrobenz‐2‐Oxa‐1,3‐Diazole: A Mechanistic Study

Fluorescence quenching of CdS quantum dots (QDs) by 4-azetidinyl-7-nitrobenz-2-oxa-1,3-diazole (NBD), where the two quenching partners satisfy the spectral overlap criterion necessary for Förster resonance energy transfer (FRET), is studied by steady-state and time-resolved fluorescence techniques. The fluorescence quenching of the QDs is accompanied by an enhancement of the acceptor fluorescence and a reduction of the average fluorescence lifetime of the donor. Even though these observations are suggestive of a dynamic energy transfer process, it is shown that the quenching actually proceeds through a static interaction between the quenching partners and is probably mediated by charge-transfer interactions. The bimolecular quenching rate constant estimated from the Stern-Volmer plot of the fluorescence intensities, is found to be exceptionally high and unrealistic for the dynamic quenching process. Hence, a kinetic model is employed for the estimation of actual quencher/QD ratio dependent exciton quenching rate constants of the fluorescence quenching of CdS by NBD. The present results point to the need for a deeper analysis of the experimental quenching data to avoid erroneous conclusions.

Effect of the Alkyl Chain Length on the Rotational Dynamics of Nonpolar and Dipolar Solutes in a Series of N-Alkyl-N-Methylmorpholinium Ionic Liquids

Rotational dynamics of two dipolar solutes, 4-aminophthalimide (AP) and 6-propionyl-2-dimethylaminonaphthalene (PRODAN), and a nonpolar solute, anthracene, have been studied in N-alkyl-N-methylmorpholinium (alkyl = ethyl, butyl, hexyl, and octyl) bis(trifluoromethansulfonyl)imide (Tf2N) ionic liquids as a function of temperature and excitation wavelength to probe the microheterogeneous nature of these ionic liquids, which are recently reported to be more structured than the imidazolium ionic liquids (Khara and Samanta, J. Phys. Chem. B2012, 116, 13430-13438). Analysis of the measured rotational time constants of the solutes in terms of the Stokes-Einstein-Debye (SED) hydrodynamic theory reveals that with increase in the alkyl chain length attached to the cationic component of the ionic liquids, AP shows stick to superstick behavior, PRODAN rotation lies between stick and slip boundary conditions, whereas anthracene exhibits slip to sub slip behavior. The contrasting rotational dynamics of these probe molecules is a reflection of their location in distinct environments of the ionic liquids thus demonstrating the heterogeneity of these ionic liquids. The microheterogeneity of these media, in particular, those with the long alkyl chain, is further evidence from the excitation wavelength dependence study of the rotational diffusion of the dipolar probe molecules.

Fluorescence response of coumarin-153 in N-alkyl-N-methylmorpholinium ionic liquids: are these media more structured than the imidazolium ionic liquids?

The fluorescence behavior of coumarin-153 (C153) has been studied in four N-alkyl-N-methylmorpholinium ionic liquids differing in the alkyl chain length attached to the N-methylmorpholinium cation as a function of the excitation wavelength and temperature to understand some of the physicochemical characteristics of these largely unexplored ionic liquids. While the polarity of the ionic liquid with the smallest alkyl chain length is found comparable to that of the commonly used imidazolium ionic liquids, the probe molecule experiences a less polar environment with increasing chain length of the alkyl group attached to the morpholinium cation. The room temperature steady-state fluorescence spectrum of C153 in these solvents is found to be dependent on the excitation wavelength, and this effect is most pronounced in long chain containing ionic liquids. A bathochromic shift of the fluorescence maximum is observed at higher temperature. The excitation wavelength and temperature dependence of the fluorescence of C153 is explained considering a domain structure of these ionic liquids. The time-resolved fluorescence anisotropy measurements indicate the microviscosity around the probe molecule to be significantly different from the bulk viscosity of the long-chain ionic liquids. The solvent reorganization dynamics, as studied by monitoring the time-dependent fluorescence Stokes shift of C153 in these ionic liquids, is found to be slow and similar to that in imidazolium ionic liquids. The time-resolved measurements under isoviscous conditions seem to provide additional support to the organized domain structure of these ionic liquids.

Photon-by-Photon Hidden Markov Model Analysis for Microsecond Single-Molecule FRET Kinetics

The function of biological macromolecules involves large-scale conformational dynamics spanning multiple time scales, from microseconds to seconds. Such conformational motions, which may involve whole domains or subunits of a protein, play a key role in allosteric regulation. There is an urgent need for experimental methods to probe the fastest of these motions. Single-molecule fluorescence experiments can in principle be used for observing such dynamics, but there is a lack of analysis methods that can extract the maximum amount of information from the data, down to the microsecond time scale. To address this issue, we introduce H2MM, a maximum likelihood estimation algorithm for photon-by-photon analysis of single-molecule fluorescence resonance energy transfer (FRET) experiments. H2MM is based on analytical estimators for model parameters, derived using the Baum-Welch algorithm. An efficient and effective method for the calculation of these estimators is introduced. H2MM is shown to accurately retrieve the reaction times from ∼1 s to ∼10 μs and even faster when applied to simulations of freely diffusing molecules. We further apply this algorithm to single-molecule FRET data collected from Holliday junction molecules and show that at low magnesium concentrations their kinetics are as fast as ∼104 s-1. The new algorithm is particularly suitable for experiments on freely diffusing individual molecules and is readily incorporated into existing analysis packages. It paves the way for the broad application of single-molecule fluorescence to study ultrafast functional dynamics of biomolecules.

Temporal behavior of the singlet molecular oxygen emission in imidazolium and morpholinium ionic liquids and its implications.

The solvent effect of ionic liquids on the lifetime of singlet molecular oxygen, O2((1)Δg), was investigated by means of time-resolved near-IR emission spectroscopy. O2((1)Δg) was generated by photosensitization of methylene blue in morpholinium and imidazolium ionic liquids, both comprising various alkyl chains of different lengths. The measured time profiles of O2((1)Δg) luminescence for the (1)Δg → (3)Σg(-) transition were represented by a single-exponential decay function. The phosphorescence lifetime was found to be correlated with the alkyl chain length of the morpholinium ionic liquids. This observation was interpreted by considering efficient quenching of O2((1)Δg) through energy transfer to the high-frequency C-H stretching modes of the N-alkyl chain in the morpholinium cation. Interestingly, we found that O2((1)Δg) quenching by the C-H stretching modes of the ring of the cations was remarkably depressed. The kinetics of the O2((1)Δg) emission decay process was discussed on the basis of the heterogeneous structure of ionic liquids consisting of polar and nonpolar domains.

Does excited-state proton-transfer reaction contribute to the emission behaviour of 4-aminophthalimide in aqueous media?

4-Aminophthalimide (AP) is an extensively used molecule both for fundamental studies and applications primarily due to its highly solvent-sensitive fluorescence properties. The fluorescence spectrum of AP in aqueous media was recently shown to be dependent on the excitation wavelength. A time-dependent blue shift of its emission spectrum is also reported. On the basis of these findings, the excited-state solvent-mediated proton-transfer reaction of the molecule, which was proposed once but discarded at a later stage, is reintroduced. We report on the fluorescence behaviour of AP and its imide-H protected derivative, N-BuAP, to prove that a solvent-assisted excited-state keto-enol transformation does not contribute to the steady-state and time-resolved emission behaviour of AP in aqueous media. Our results also reveal that the fluorescence of AP in aqueous media arises from two distinct hydrogen-bonded species. The deuterium isotope effect on the fluorescence quantum yield and lifetime of AP, which was thought to be a reflection of the excited-state proton-transfer reaction in the system, is explained by considering the difference in the influence of H(2)O and D(2)O on the nonradiative rates and ground-state exchange of the proton with the solvent.

DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size

Abstract We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.

Fluorescence, Phosphorescence, and Delayed Fluorescence of Benzil in Imidazolium Ionic Liquids

Temperature dependence of the emission behaviour of benzil has been studied in three imidazolium ionic liquids differing in their polarity and viscosity. Room temperature absorption and steady-state emission spectra suggest that the ground and excited state conformers of benzil in ionic liquids are similar to those in conventional organic solvents. The non-degassed solutions of benzil in ionic liquids show phosphorescence at room temperature in contrast to conventional solvents where phosphorescence is commonly observed in degassed conditions. This study reveals that a thermally activated reverse intersystem crossing (T1↝S1) process is responsible for the drastic change in phosphorescence intensity with temperature in ionic liquids. The rate constant () of this process is found to be dependent on the polarity of the media and is 5 times higher in most polar ionic liquids. The evidence of the presence of multiple conformers of benzil in frozen conditions is obtained from the excitation wavelength dependence of the phosphorescence spectra.