Single-molecule Spectroscopy Experiments Research Articles

Theoretical investigation of non-Förster exciton transfer mechanisms in perylene diimide donor, phenylene bridge, and terrylene diimide acceptor systems.

The rates of exciton transfer within dyads of perylene diimide and terrylene diimide connected by oligophenylene bridge units have been shown to deviate significantly from those of Förster's resonance energy transfer theory, according to single molecule spectroscopy experiments. The present work provides a detailed computational and theoretical study investigating the source of such a discrepancy. Electronic spectroscopy data are calculated by time-dependent density functional theory and then compared with experimental results. Electronic couplings between the exciton donor and the acceptor are estimated based on both the transition density cube method and transition dipole approximation. These results confirm that the delocalization of the exciton to the bridge parts contributes to significant enhancement of donor-acceptor electronic coupling. Mechanistic details of exciton transfer are examined by estimating the contributions of the bridge electronic states, vibrational modes of the dyads commonly coupled to both donor and acceptor, inelastic resonance energy transfer mechanism, and dark exciton states. These analyses suggest that the contribution of common vibrational modes serves as the main source of deviation from Förster's spectral overlap expression.

Alpha-Carbonic Acid Revisited: Carbonic Acid Monomethyl Ester as a Solid and its Conformational Isomerism in the Gas Phase.

In this work, earlier studies reporting α‐H2CO3 are revised. The cryo‐technique pioneered by Hage, Hallbrucker, and Mayer (HHM) is adapted to supposedly prepare carbonic acid from KHCO3. In methanolic solution, methylation of the salt is found, which upon acidification transforms to the monomethyl ester of carbonic acid (CAME, HO‐CO‐OCH3). Infrared spectroscopy data both of the solid at 210 K and of the evaporated molecules trapped and isolated in argon matrix at 10 K are presented. The interpretation of the observed bands on the basis of carbonic acid [as suggested originally by HHM in their publications from 1993–1997 and taken over by Winkel et al., J. Am. Chem. Soc. 2007 and Bernard et al., Angew. Chem. Int. Ed. 2011] is inferior compared with the interpretation on the basis of CAME. The assignment relies on isotope substitution experiments, including deuteration of the OH‐ and CH3‐ groups as well as 12C and 13C isotope exchange and on variation of the solvents in both preparation steps. The interpretation of the single molecule spectroscopy experiments is aided by a comprehensive calculation of high‐level ab initio frequencies for gas‐phase molecules and clusters in the harmonic approximation. This analysis provides evidence for the existence of not only single CAME molecules but also CAME dimers and water complexes in the argon matrix. Furthermore, different conformational CAME isomers are identified, where conformational isomerism is triggered in experiments through UV irradiation. In contrast to earlier studies, this analysis allows explanation of almost every single band of the complex spectra in the range between 4000 and 600 cm−1.

Robust light harvesting by a noisy antenna.

Photosynthetic light harvesting can be very efficient in solar energy conversion while taking place in a highly disordered and noisy physiological environment. This efficiency is achieved by the ultrafast speed of the primary photosynthetic processes, which is enabled by a delicate interplay of quantum effects, thermodynamics and environmental noise. The primary processes take place in light-harvesting antennas built from pigments bound to a fluctuating protein scaffold. Here, we employ ultrafast single-molecule spectroscopy to follow fluctuations of the femtosecond energy transfer times in individual LH2 antenna complexes of purple bacteria. By combining single molecule results with ensemble spectroscopy through a unified theoretical description of both, we show how the protein fluctuations alter the excitation energy transfer dynamics. We find that from the thirteen orders of magnitude of possible timescales from picoseconds to minutes, the relevant fluctuations occur predominantly on a biological timescale of seconds, i.e. in the domain of slow protein motion. The measured spectra and dynamics can be explained by the protein modulating pigment excitation energies only. Moreover, we find that the small spread of pigment mean energies allows for excitation delocalization between the coupled pigments to survive. These unique features provide fast energy transport even in the presence of disorder. We conclude that this is the mechanism that enables LH2 to operate as a robust light-harvester, in spite of its intrinsically noisy biological environment.

AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations.

Recent advances in single molecule fluorescence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomolecular force fields. Here, we developed, characterized, and implemented AMBER-DYES, a modular fluorescent label force field, for a set of 22 fluorescent dyes and their linkers from the Alexa, Atto, and Cy families, which are in common use for single molecule spectroscopy experiments. The force field is compatible with the AMBER protein force fields and the GROMACS molecular dynamics simulation program. The high electronic polarizability of the delocalized π-electron orbitals, as found in many fluorescent dyes, poses a particular challenge to point charge based force fields such as AMBER. To quantify the charge fluctuations due to the electronic polarizability, we simulated the 22 dyes in explicit solvent and sampled the charge fluctuations using QM/MM simulations at the B3LYP/6-31G*//TIP3P level of theory. The analysis of the simulations enabled us to derive ensemble fitted RESP charges from the solvated charge distributions of multiple trajectories. We observed broad, single peaked charge distributions for the conjugated ring atoms with well-defined mean values. The charge fitting procedure was validated against published charges of the dyelike amino acid tryptophan, which showed good agreement with existing tryptophan parameters from the AMBER, CHARMM, and OPLS force field families. A principal component analysis of the charge fluctuations revealed that a small number of collective coordinates suffices to describe most of the in-plane dye polarizability. The AMBER-DYES force field allows the rapid preparation of all atom molecular dynamics simulations of fluorescent systems for state of the art multi microsecond trajectories.

Bayesian Detection of Intensity Changes in Single Molecule and Molecular Dynamics Trajectories

Single molecule spectroscopy experiments and molecular dynamics simulations have several profound features in common, chief among which is that both follow the dynamics of some degrees of freedom of a single molecule over time. The analysis is essentially the same: one investigates the changes in the degrees of freedom followed. For instance, in a single molecule fluorescence experiment, the degree of freedom is often the number of photons detected in some time period. In this article, we introduce a straightforward Bayesian method for detecting if and when changes occurred. In contrast to methods based upon maximum likelihood estimates, a Bayesian approach allows for a more systematic means not only to change point detection but also to cluster the data into states. Most importantly, the Bayesian method supplies a simpler hypothesis testing framework. Although we focus on Poisson-distributed data, the Bayesian methods outlined here can in principle be applied to data sampled from any distribution.

Open quantum system approach to single-molecule spectroscopy

In this paper, single-molecule spectroscopy experiments based on continuous laser excitation are characterized through an open quantum system approach. The evolution of the fluorophore system follows from an effective Hamiltonian microscopic dynamic where its characteristic parameters, i.e., its electric dipole, transition frequency, and Rabi frequency, as well as the quantization of the background electromagnetic field and their mutual interaction, are defined in an extended Hilbert space associated to the different configurational states of the local nanoenvironment. After tracing out the electromagnetic field and the configurational states, the fluorophore density matrix is written in terms of a Lindblad rate equation. Observables associated to the scattered laser field, such as optical spectrum, intensity-intensity correlation, and photon-counting statistics, are obtained from a quantum-electrodynamic calculation also based on the effective microscopic dynamic. In contrast with stochastic models, this approach allows one to describe in a unified way both the full quantum nature of the scattered laser field as well as the classical nature of the environment fluctuations. By analyzing different processes such as spectral diffusion, lifetime fluctuations, and light assisted processes, we exemplify the power of the present approach.

Metal-Enhanced Fluorescence of Chlorophylls in Single Light-Harvesting Complexes

AbstractWe show that the fluorescence of peridinin-chlorophyll a-protein complexes can be strongly enhanced via coupling with plasmon excitations localized in metal nanostructures. The results of ensemble and single-molecule spectroscopy experiments at room temperature demonstrate six-fold increase of the emission intensity of the light-harvesting complex when it is placed in the vicinity of chemically prepared silver islands. Irrespective of the enhancement, we observe no effect of the metal nanoparticle on the fluorescence emission energy of the complex. This observation implies that plasmon excitations may be applied for controlling the optical properties of complex biomolecules.

Surface-enhanced Raman spectroscopy of dyes: from single molecules to the artists’ canvas

This perspective presents recent surface-enhanced Raman spectroscopy (SERS) studies of dyes, with applications to the fields of single-molecule spectroscopy and art conservation. First we describe the development and outlook of single-molecule SERS (SMSERS). Rather than providing an exhaustive review of the literature, SMSERS experiments that we consider essential for its future development are emphasized. Shifting from single-molecule to ensemble-averaged experiments, we describe recent efforts toward SERS analysis of colorants in precious artworks. Our intention is to illustrate through these examples that the forward development of SERS is dependent upon both fundamental (e.g., SMSERS) and applied (e.g., on-the-specimen SERS of historical art objects) investigations and that the future of SERS is very bright indeed.

Monitoring fluorescence of individual chromophores in peridinin–chlorophyll–protein complex using single molecule spectroscopy

Single molecule spectroscopy experiments are reported for native peridinin–chlorophyll a–protein (PCP) complexes, and three reconstituted light-harvesting systems, where an N-terminal construct of native PCP from Amphidinium carterae has been reconstituted with chlorophyll (Chl) mixtures: with Chl a, with Chl b and with both Chl a and Chl b. Using laser excitation into peridinin (Per) absorption band we take advantage of sub-picosecond energy transfer from Per to Chl that is order of magnitude faster than the Förster energy transfer between the Chl molecules to independently populate each Chl in the complex. The results indicate that reconstituted PCP complexes contain only two Chl molecules, so that they are spectroscopically equivalent to monomers of native-trimeric-PCP and do not aggregate further. Through removal of ensemble averaging we are able to observe for single reconstituted PCP complexes two clear steps in fluorescence intensity timetraces attributed to subsequent bleaching of the two Chl molecules. Importantly, the bleaching of the first Chl affects neither the energy nor the intensity of the emission of the second one. Since in strongly interacting systems Chl is a very efficient quencher of the fluorescence, this behavior implies that the two fluorescing Chls within a PCP monomer interact very weakly with each other which makes it possible to independently monitor the fluorescence of each individual chromophore in the complex. We apply this property, which distinguishes PCP from other light-harvesting systems, to measure the distribution of the energy splitting between two chemically identical Chl a molecules contained in the PCP monomer that reaches 280 cm − 1 . In agreement with this interpretation, stepwise bleaching of fluorescence is also observed for native PCP complexes, which contain six Chls. Most PCP complexes reconstituted with both Chl a and Chl b show two emission lines, whose wavelengths correspond to the fluorescence of Chl a and Chl b. This is a clear proof that these two different chromophores are present in a single PCP monomer. Single molecule fluorescence studies of PCP complexes, both native and artificially reconstituted with chlorophyll mixtures, provide new and detailed information necessary to fully understand the energy transfer in this unique light-harvesting system.

Theoretical study on single-molecule spectroscopy

The photon-by-photon approach for single molecule spectroscopy experiments utilizes the information carried by each detected photon and allows the measurements of conformational fluctuation with time resolution on a vast range of time scales, where each photon represents a data point. Here, we theoretically simulate the photon emission dynamics of a single molecule spectroscopy using the kinetic Monte Carlo algorithm to understand the underlying complex photon dynamic process of a single molecule. In addition, by following the molecular process in real time, the mechanism of complex biochemical reactions can be revealed. We hope that this theoretical study will serve as an introduction and a guideline into this exciting new field.

Mori−Zwanzig Memory Analysis in Single-Molecule Spectroscopy

We study the dynamical behavior of the Rhodospirillum molischianum LH2 complex based on intensity time series obtained from single-molecule spectroscopy experiments. This is achieved by reconstructing the memory function describing the time-dependent fluctuations of the excited states. We conclude that the apparent stochastic evolution of the dynamics is controlled by at least two different non-Markovian main processes.

Single molecule spectroscopy of disordered circular aggregates: A perturbation analysis

Analytical expressions for various spectroscopic observables are derived for statically disordered circular aggregates using first order perturbation theory. Quantities relevant to single molecule spectroscopy experiments on circular aggregates such as the distribution of energy splittings between levels that are degenerate in the absence of disorder, and the distribution of intensity of levels that are forbidden in the absence of disorder are derived. For simplicity only diagonal disorder is considered here. The approach, however, can be extended to include other types of disorder. Expressions are written in terms of standard deviations of Gaussian disorder, the symmetry number of the aggregate, and in some cases intermolecular couplings. The approach is compared to numerical simulations and shows excellent agreement over a large range of parameters. The expressions, however, provide a more direct framework to examine and understand the effects of disorder on spectroscopy of aggregates than do the simulations. The potential utility of the expressions for quantifying disorder and intermolecular couplings from single molecule experiments is also demonstrated.