Excitation Of Single Molecules Research Articles

Driving a Third Generation Molecular Motor with Electrons Across a Surface.

Excitation of single molecules with electrons tunneling between a sharp metallic tip of a scanning tunneling microscope and a metal surface is one way to study and control dynamics of molecules on surfaces. Electron tunneling induced dynamics may lead to hopping, rotation, molecular switching, or chemical reactions. Molecular motors that convert rotation of subgroups into lateral movement on a surface can in principle also be driven by tunneling electrons. For such surface-bound motor molecules the efficiency of motor action with respect to electron dose is still not known. Here, the response of a molecular motor containing two rotor units in the form of overcrowded alkene groups to inelastic electron tunneling has been examined on a Cu(111) surface in ultrahigh vacuum at 5 K. Upon vibrational excitation, switching between different molecular conformations is observed, including conversion of enantiomeric states of chiral conformations. Tunneling at energies in the range of electronic excitations causes activation of motor action and movement across the surface. The expected unidirectional rotation of the two rotor units causes forward movements but with a low degree of translational directionality.

Pulse-shaped broadband multiphoton excitation for single-molecule fluorescence detection in the far field

Multiphoton excitation of fluorescence has many potential advantages over resonant (one-photon) excitation, but the method has not found widespread use for ultrasensitive applications. We recently described an approach to the multiphoton excitation of single molecules that uses a pulse shaper to compress and tailor pulses from an ultrafast broadband laser in order to optimise the brightness and signal-to-background ratio following non-linear excitation. Here we provide a detailed description of the setup and illustrate its use and potential by optimising two-photon fluorescence of a common fluorophore, rhodamine 110, at the single-molecule level. We also show that a DNA oligonucleotide labelled with a fluorescent nucleobase analogue, tC, can be detected using two-photon FCS, whereas one-photon excitation causes rapid photobleaching. The ability to improve the signal-to-background ratio and to reduce the incident power required to attain a given brightness can be applied to the multiphoton excitation of any fluorescent species, from small molecules with low multiphoton cross sections to the brightest nanoparticles.

Accessing a Charged Intermediate State Involved in the Excitation of Single Molecules.

Intermediate states are elusive to many experimental techniques due to their short lifetimes. Here, by performing single-electron alternate charging scanning tunneling microscopy of molecules on insulators, we accessed a charged intermediate state involved in the rapid toggling of individual metal phthalocyanines deposited on NaCl films. By stabilizing the transient species, we reveal how electron injection into the lowest unoccupied molecular orbital leads to a pronounced change in the adsorption geometry, characterized by a different azimuthal orientation. This observation allows clarifying the nature of the toggling process, unveiling the role of transient ionic states involved into fundamental processes occurring at interfaces.

Detuning dependent Rabi oscillations of a single molecule

A single organic dye molecule at cryogenic conditions is resonantly excited in a confocal microscope. Under strong laser illumination it undergoes Rabi oscillations. Mathematically, this was well described and had been experimentally implemented. These oscillations can be measured as side-bands on their resonance fluorescence, e.g. in the Mollow-Triplet. An alternative method is to research this effect by an analysis of the single molecule anti-bunched photon statistics. This has been performed in this work. Here we research on the detuning dependence of this signal—it is experimentally demanding since the utilized laser might drift or single emitters are not necessarily spectrally stable enough, such that the spectrum can be measured indefinitely. We therefore apply a measurement technique in which the photon correlation signal is acquired in detuning dependent steps. This is performed by continuous laser sweeps over the single molecule excitation spectrum. A single recording of the anti-bunched photons takes 20–50 ms. After approx. 1 h of repetitive laser detunings a full anti-bunching curve is reconstructed for each spectral position. An alternative technique with 100 ns laser pulses allows us to acquire a set of comparable data. Our study is derived from a single dibenzanthanthrene molecule with a natural linewidth of 2π×16 MHz. It emits under resonant excitation more than 380.000 photons per second. Under spectral detuning, Rabi-oscillations are observed up to ΩRabi = 2π×160 MHz.

Effects of quantum coherence and interference in atoms near nanoparticles

Optical properties of ensembles of realistic quantum emitters coupled to plasmonic systems are studied by using adequate models that can take into account full atomic geometry. In particular, the coherent effects such as forming ``dark states,'' optical pumping, coherent Raman scattering, and the stimulated Raman adiabatic passage (STIRAP) are revisited in the presence of metallic nanoparticles. It is shown that the dark states are still formed but they have more complicated structure, and the optical pumping and the STIRAP cannot be employed in the vicinity of plasmonic nanostructures. Also, there is a huge difference in the behavior of the local atomic polarization and the atomic polarization averaged over an ensemble of atoms homogeneously spread near nanoparticles. The average polarization is strictly related to the polarization induced by the external field, while the local polarization can be very different from the one induced by the external field. This is important for the excitation of single molecules, e.g., different components of scattering from single molecules can be used for their efficient detection.

Simultaneous Measurement of the Three-Dimensional Orientation of Excitation and Emission Dipoles

The emission properties of most fluorescent emitters, such as dye molecules or solid-state color centers, can be well described by the model of an oscillating electric dipole. However, the orientations of their excitation and emission dipoles are, in most cases, not parallel. Although single molecule excitation and emission dipole orientation measurements have been performed in the past, no experimental method has so far looked at the three-dimensional excitation and emission dipole geometry of individual emitters simultaneously. We present the first experimental study, using defocused imaging in conjunction with radially polarized excitation scanning, to measure both the excitation as well as emission dipole orientations of single molecules, which allows us to sample the distribution of their mutual orientation. We find an unexpectedly broad distribution of the angle between both dipoles which we attribute to the interaction between the observed molecules and the substrate they are immobilized on.

Shaped and Feedback-Controlled Excitation of Single Molecules in the Weak-Field Limit.

Coherent control uses tailored femtosecond pulse shapes to influence quantum pathways and drive a light-induced process toward a specific outcome. There has been a long-standing debate whether the absorption properties or the probability for population to remain in an excited state of a molecule can be influenced by the pulse shape, even if only a single photon is absorbed. Most such experiments are performed on many molecules simultaneously, so that ensemble averaging reduces the access to quantum effects. Here, we demonstrate systematic coherent control experiments on the fluorescence intensity of a single molecule in the weak-field limit. We demonstrate that a delay scan of interfering pulses reproduces the excitation spectrum of the molecule upon Fourier transformation, but that the spectral phase of a pulse sequence does not affect the transition probability. We generalize this result to arbitrary pulse shapes by performing the first closed-loop coherent control experiments on a single molecule.

Multicolour single molecule emission and excitation spectroscopy reveals extensive spectral shifts.

We explore the distribution and shape of single molecule spectra at room temperature, when embedded in a polymer host. Multicolour excitation and emission spectroscopy is implemented to capture the full inhomogeneous distribution. We observe dramatic spectral changes in a distribution of single quaterrylene diimide (QDI) molecules isolated in a PMMA matrix. The molecules are strongly blue shifted with respect to the ensemble absorption maximum and spread over a staggering 200 nm range. Despite these strong shifts, the shape of the emission spectra does not differ much between individual molecules. We demonstrate that a considerable number of molecules may be invisible in single molecule experiments, as they typically rely on only a single excitation wavelength, which predetermines which subensemble is probed in the experiment. Lastly, we make a first step towards single molecule excitation spectroscopy under ambient conditions, which allows us to determine the spectral range at which individual molecules absorb light most efficiently. We show how single molecule emission and excitation spectroscopies can complement each other and a combination of both techniques can help in understanding the origin of underlaying spectral properties of individual molecules.

Engineering bright sub-10-nm upconverting nanocrystals for single-molecule imaging

Imaging at the single-molecule level reveals heterogeneities that are lost in ensemble imaging experiments, but an ongoing challenge is the development of luminescent probes with the photostability, brightness and continuous emission necessary for single-molecule microscopy. Lanthanide-doped upconverting nanoparticles overcome problems of photostability and continuous emission and their upconverted emission can be excited with near-infrared light at powers orders of magnitude lower than those required for conventional multiphoton probes. However, the brightness of upconverting nanoparticles has been limited by open questions about energy transfer and relaxation within individual nanocrystals and unavoidable tradeoffs between brightness and size. Here, we develop upconverting nanoparticles under 10 nm in diameter that are over an order of magnitude brighter under single-particle imaging conditions than existing compositions, allowing us to visualize single upconverting nanoparticles as small (d = 4.8 nm) as fluorescent proteins. We use advanced single-particle characterization and theoretical modelling to find that surface effects become critical at diameters under 20 nm and that the fluences used in single-molecule imaging change the dominant determinants of nanocrystal brightness. These results demonstrate that factors known to increase brightness in bulk experiments lose importance at higher excitation powers and that, paradoxically, the brightest probes under single-molecule excitation are barely luminescent at the ensemble level.

Radio-frequency excitation of single molecules by scanning tunnelling microscopy

We have upgraded a low-temperature scanning tunnelling microscope (STM) with a radio-frequency (RF) modulation system to extend STM spectroscopy to the range of low energy excitations (<1 meV). We studied single molecules of a stable hydrocarbon π-radical weakly physisorbed on Au(111). At 5 K thermal excitation of the adsorbed molecules is inhibited due to the lack of short-wavelength phonons of the substrate. We demonstrate resonant excitation of mechanical modes of single molecules by RF tunnelling at 115 MHz, which induces structural changes in the molecule ranging from controlled diffusion and modification of bond angles to bond breaking as the ultimate climax (resonance catastrophe). Our results pave the way towards RF-STM-based spectroscopy and controlled manipulation of molecular nanostructures on a surface.

Single-molecule detection and radiation control in solutions at high concentrations via a heterogeneous optical slot antenna

We designed a heterogeneous optical slot antenna (OSA) that is capable of detecting single molecules in solutions at high concentrations, where most biological processes occur. A heterogeneous OSA consists of a rectangular nanoslot fabricated on heterogeneous metallic films formed by sequential deposition of gold and aluminum on a glass substrate. The rectangular nanoslot gives rise to large field and fluorescence enhancement for single molecules. The near-field intensity inside a heterogeneous OSA is 170 times larger than that inside an aluminum zero-mode waveguide (ZMW), and the fluorescence emission rate of a molecule inside the heterogeneous OSA is about 70 times higher than that of the molecule in free space. Our proposed heterogeneous optical antenna enables excellent balance between performance and cost. The design takes into account the practical experimental conditions so that the parameters chosen in the simulation are well within the reach of current nano-fabrication technologies. Our results can be used as a direct guidance for designing high-performance, low-cost plasmonic nanodevices for the study of bio-molecule and enzyme dynamics at the single-molecule level.

Crystal structure and luminescence properties of 4-(4-benzoyloxy-2-hydroxyphenyl)-2,2-difluoro-6-phenyl-1,3,2-dioxaborine

The crystal structure of 4-(4-benzoyloxy-2-hydroxyphenyl)-2,2-difluoro-6-phenyl-1,3,2-dioxaborine (1) was determined by X-ray diffraction analysis. π-π-Stacking interaction between the molecules results in joining the molecules into a three-dimensional layered framework. Luminescence of the aggregates is observed in concentrated solutions of compound 1. Two routes of excimer formation in crystal were revealed by steady-state and time-resolved luminescence spectroscopy: via excitation of single molecules and via excitation of aggregates.

Chromophore-Controlled Self-Assembly of Highly Ordered Polymer Nanostructures

Single-molecule excitation polarization anisotropy and molecular dynamics simulations reveal that the folding of polymers composed of conjugated phenylene vinylene (PPV) oligomers joined by flexible linkers can be influenced by the length of the conjugated segments. By varying the number of PPV repeat units from three to five to seven, both the structure and the spectral properties of the polymer can be controlled at the synthetic level. The stronger interactions between longer conjugated units of the polymers lead to more ordered conformations. The mean modulation depth of a septamer containing PPV (M = 0.75) was found to be even higher than that of the traditional homopolymer MEH-PPV (M = 0.66), which suggests that these new polymers provide access to highly aligned nanostructures not typically found in homopolymer systems.

Single molecule electrical excitation

AbstractOptical studies of individual molecules offer the unique possibility of investigating the local environment of single quantum objects on nanometre length scales and of employing molecular systems as non‐classical light sources at room temperature. Usually, single molecule excitation is based on optical stimulation by laser radiation. In this feature article, we present an alternative approach by utilizing charge injection in combination with molecular electron–hole recombination to electrically excite single fluorescent dyes. The successful implementation of this strategy promotes the realization of electrically driven single photon sources on demand operating at room temperature and being feasible on a vast number of molecules emitting at e.g. telecommunication wavelengths. Moreover, these probes render probing the charge carrier transport and recombination on molecular length scales. In this article, we will first discuss the interaction of single charge carriers with optically excited molecules characterized by a decrease of photoluminescence intensity with increasing current density. As it is demonstrated, this effect originates from strong electrical pumping of triplet state populations upon charge carrier recombination. Secondly, the prospect of using phosphorescent emitters as electrically driven single photon sources at room temperature will be discussed. Finally, we will highlight that photoluminescence quenching of single fluorescent dyes provides a sensitive tool to quantify local current densities and recombination dynamics in operational organic light emitting diode devices with molecular spatial resolution.

Nanoscale Probing of Dielectric Interfaces with Single-Molecule Excitation Patterns and Radially Polarized Illumination

We present new results on the theoretical and experimental study of the excitation patterns acquired upon scanning a single molecule through the focal region of a radially polarized laser beam when the emitter is located at a glass–air interface and in bulk glass. Our calculations show that the presence of a dielectric interface, which coincides with the focal plane of a radially polarized laser beam, strongly changes the field intensity distribution within the focus, which results in the modification of the single molecule excitation pattern obtained upon scanning a molecule through the focal region. By changing the dielectric properties of the surrounding media in situ we show experimentally that the same individual molecule possessing the same orientation with respect to the laser beam axis exhibits different shapes of excitation patterns, depending on whether it is located on the dielectric interface or in medium with constant refractive index.

Rate-Determining Factors in the Chain Polymerization of Molecules Initiated by Local Single-Molecule Excitation

Spontaneous chain polymerization of molecules initiated by a scanning tunneling microscope tip is studied with a focus on its rate-determining factors. Such chain polymerization that happens in self-assembled monolayers (SAM) of diacetylene compound molecules, which results in a π-conjugated linear polydiacetylene nanowire, varies in its rate P depending on domains in the SAM and substrate materials. While the arrangement of diacetylene molecules is identical in every domain on a graphite substrate, it varies in different domains on a MoS(2) substrate. This structural variation enables us to investigate how P is affected by molecular geometry. An important determining factor of P is the distance between two carbon atoms which are to be bound by polymerization reaction, R; as R decreases by 0.1 nm, P increases ∼2 times. P for a MoS(2) substrate is ∼4 times higher (with the same value of R) than that for a graphite substrate because of higher mobility of molecules. The exciting correlation of the chain polymerization rate to the geometrical structure of the diacetylene molecules brings a deeper understanding of the mechanism of chain polymerization kinetics. In addition, the fabrication of one-dimensional conjugated polymer nanowires on a semiconducting MoS(2) substrate as demonstrated here may be of immense importance in the realization of future molecular devices.

Electronic coherences and vibrational wave-packets in single molecules studied with femtosecond phase-controlled spectroscopy

Employing femtosecond pulse-shaping techniques we investigate ultrafast, coherent and incoherent dynamics in single molecules at room temperature. In first experiments single molecules are excited into their purely electronic 0-0 transition by phase-locked double-pulse sequences with pulse durations of 75 fs and 20 nm spectral band width. Their femtosecond kinetics can then be understood in terms of a 2-level system and modelled with the optical Bloch equations. We find that we observe the coherence decay in single molecules, and the purely electronic dephasing times can be retrieved directly in the time domain. In addition, the Rabi-frequencies and thus the transition dipole moments of single molecules are determined from these data. Upon excitation of single molecules into a vibrational level of the electronically excited state also incoherent intra-molecular vibrational relaxation is recorded. Increasing the spectral band width of the excitation pulses to up to 120 nm (resulting in a transform-limited pulse width of 15 fs) coherent superpositions of excited state vibrational modes, i.e. vibrational wave packets, are excited. The wave-packet oscillations in the excited state potential energy surface are followed in time by a phase-controlled pump-probe scheme, which permits to record wave packet interference, and to determine the energies of vibrational modes and their coupling strengths to the electronic transition.

Light Dose is a Limiting Factor to Maintain Cell Viability in Fluorescence Microscopy and Single Molecule Detection

A test system for cell viability based on colony formation has been established and applied to high resolution fluorescence microscopy and single molecule detection. Living cells were irradiated either by epi-illumination or by total internal reflection (TIR) of a laser beam, and light doses where at least 90% of irradiated cells survived were determined. These light doses were in the range of a few J/cm2 up to about 200 J/cm2 depending on the wavelength of illumination as well as on the presence or absence of a fluorescent dye (e.g., the membrane marker laurdan). In general, cells were less sensitive to TIR than to epi-illumination. However, comparably high light doses needed for repetitive excitation of single molecules limit the application of super-resolution microscopy to living cells.

A light-induced photochromic nanoswitch capable of non-destructive readout via fluorescence emission: cluster vs. single-molecule excitation of dihydroindolizines

We have synthesized a prototype of a photochromic styrylquinolyl-dihydroindolizine (DHI), which forms a highly coloured and fluorescent betaine upon irradiation with lambda<400 nm. Embedding this photochromic DHI in a thin polymethyl methacrylate (PMMA) film permits the non-destructive readout via fluorescence at low temperature (77 K). Thus, either a non-destructive photoswitch or an information recording system becomes available. Both possibilities have been explored: image recording and read-out, as well as information storage (at 77 K) have been demonstrated. Cluster- and single molecule-fluorescence upon laser excitation (lambda=355 nm) of the styrylquinolyl-dihydroindolizine in a PMMA matrix, and the effect of fluorescence blinking has been observed.

Electronic Excitation Energy Transfer in Multichromophoric Assemblies: A Single Molecule Insight

AbstractIn recent years, single molecule spectroscopy has provided novel insights into the fundamentals of electronic excitation energy transfer in molecular aggregates. In order of increasing structural complexity, we have studied simple molecular dimers and multichromophoric dendrimers. It will be shown that the combination of frequency‐selective single molecule spectroscopy and confocal fluorescence microscopy at 1.4 K is a unique tool to study energy transfer processes in these systems. In particular, from the line widths of single molecule excitation spectra, rate constants of energy transfer can be deduced directly. A detailed analysis shows that, for several cases, the mechanism of energy transfer cannot be described by the simple Förster model (dipole–dipole coupling). Furthermore, novel experiments with dual color pulsed excitation are discussed which allow for controlling the excitation energy flow in individual molecular dimers.