Single Organic Molecules Research Articles

Single-molecule identification via electric current noise.

Label-free and real-time single-molecule detection may aid the development of high-throughput biosensing platforms. Molecular fluctuations are a source of noise that often hinders single-molecule identification by obscuring the fine details of molecular identity. In this study, we report molecular identification through direct observation of quantum-fluctuation-induced inelastic noise in single organic molecules. We investigated current fluctuations flowing through a single molecule that is chemically connected to two electrodes. We found increased current oscillations synchronous to electric field excitations of characteristic molecular vibrational modes that contribute to inelastic electron tunnelling. This finding demonstrates a large contribution of charge interaction with nuclear dynamics on noise properties of single-molecule bridges and suggests a potential use of inelastic noise as a valuable molecular signature for single-molecule identification.

Seeing the spin through

Interfaces can have quite different properties from those of their constituent materials. But it's surprising that the adsorption of a single organic molecule onto a magnetic surface can drastically modify that surface's magnetism.

Spin- and Energy-Dependent Tunneling through a Single Molecule with Intramolecular Spatial Resolution

We investigate the spin- and energy-dependent tunneling through a single organic molecule (CoPc) adsorbed on a ferromagnetic Fe thin film, spatially resolved by low-temperature spin-polarized scanning tunneling microscopy. Interestingly, the metal ion as well as the organic ligand show a significant spin dependence of tunneling current flow. State-of-the-art abinitio calculations including also van der Waals interactions reveal a strong hybridization of molecular orbitals and substrate 3d states. The molecule is anionic due to a transfer of one electron, resulting in a nonmagnetic (S=0) state. Nevertheless, tunneling through the molecule exhibits a pronounced spin dependence due to spin-split molecule-surface hybrid states.

A scanning microcavity for in situ control of single-molecule emission

We report on the fabrication and characterization of a scannable Fabry–Perot microcavity, consisting of a curved micromirror at the end of an optical fiber and a planar distributed Bragg reflector. Furthermore, we demonstrate the coupling of single organic molecules embedded in a thin film to well-defined resonator modes. We discuss the choice of cavity parameters that will allow sufficiently high Purcell factors for enhancing the zero-phonon transition between the vibrational ground levels of the electronic excited and ground states.

Fundamentals of energy transport, energy conversion, and thermal properties in organic–inorganic heterojunctions

Hybrid devices built from organic and inorganic moieties are being actively researched as replacements for inorganic electronics, thermoelectrics, and photovoltaics. However, energy transport and conversion, at the organic–inorganic interface is not well understood. One approach to study this interface is to look at the smallest hybrid building block – the heterojunction of a single organic molecule with inorganic contacts. We present a review of this work, focused on fundamental transport properties of metal–molecule–metal junctions that are related to thermoelectric energy conversion, i.e., electronic conductance, thermopower, and thermal conductance. We describe the motives, strategies, and future directions for considering heterojunctions as building blocks for thermoelectric materials.

Photoluminescent nanodiamonds: Comparison of the photoluminescence saturation properties of the NV color center and a cyanine dye at the single emitter level, and study of the color center concentration under different preparation conditions

Nitrogen-Vacancy (NV) color centers in diamond nanoparticles (NanoDiamonds, NDs) have a great number of applications, in particular in quantum information processing and as cellular fluorescent labels. In this work we compare the photoluminescence properties of a single NV color center embedded in a 30 nm diameter nanodiamond to that of a single organic fluorescent molecule. We also study the photoluminescence properties of NDs prepared under different conditions in order to find the optimal parameters to achieve a high fluorescence yield, which is still an open question in the case of nanocrystals compared to bulk diamond. The results of this study are of interest for the applications of small and bright diamond nanoparticles in nanophotonics and biology.

Molecular Electronics Devices: A Short Review

Molecular electronics has recently attracted a lot of attention due to promising application in nanoscale electronic devices. In this review we highlight recent results in this field, focusing on single organic molecules working as devices and addressing important effects related with electronic transport, such as push–pull molecules, or bridges, Coulomb blockage, negative differential resistance, molecular radicals, temperature dependence, environment sensibility, strong and weak coupling, quantum interference, coherent and incoherent transport, tunneling regime, switches, and a few applications will be addressed.

Mid-infrared sensing of organic pollutants in aqueous environments.

The development of chemical sensors for monitoring the levels of organic pollutants in the aquatic environment has received a great deal of attention in recent decades. In particular, the mid-infrared (MIR) sensor based on attenuated total reflectance (ATR) is a promising analytical tool that has been used to detect a variety of hydrocarbon compounds (i.e., aromatics, alkyl halides, phenols, etc.) dissolved in water. It has been shown that under certain conditions the MIR-ATR sensor is capable of achieving detection limits in the 10–100 ppb concentration range. Since the infrared spectral features of every single organic molecule are unique, the sensor is highly selective, making it possible to distinguish between many different analytes simultaneously. This review paper discusses some of the parameters (i.e., membrane type, film thickness, conditioning) that dictate MIR-ATR sensor response. The performance of various chemoselective membranes which are used in the fabrication of the sensor will be evaluated. Some of the challenges associated with long-term environmental monitoring are also discussed.

Supramolecular Chemistry at Interfaces: Molecular Recognition on Nanopatterned Porous Surfaces

Through the illustration of key examples that have recently appeared in the literature, the intention of this review is to provide a perspective of current advances on the molecular recognition at the interfaces aimed at the engineering of multifunctional organic-based materials. The great interest in such systems has been motivated by the need to fabricate smaller and smaller components in order to improve, for example, the information storage capabilities of classical silicon-based devices. Although great progress has been achieved on the exploitation of "top-down" approaches, strong hope is now put on the development of hybrid devices in which the elementary components are replaced with single organic molecules. Nevertheless, the drive towards such devices is restricted by both their stability and difficulties to precisely control and manipulate the structural organisation at the molecular level. To overcome these restrictions, the use of nanotemplated surfaces featuring porous domains in which responsive functional molecules can be precisely accommodated at the single-molecule level is one of the most promising approaches. In the first part of this manuscript, we therefore illustrate the main engineering strategies [1) through non-covalent interactions, 2) surface-confined covalent reactions and 3) assembly of pre-organised cavities such as synthetic macrocycles] currently in use to create two-dimensional (2D) patterned surfaces displaying porous structures at the nanoscale level. Such networks, featuring periodic hollow domains (controllable both in shape and size), are of particular significance as their cavities can be used as receptors for the recognition of remotely controllable functional molecules. In the second part, the confinement of molecular guests within the cavities is discussed, emphasising the selectivity and dynamics of key assemblies, with a particular focus on the biomolecular recognition and post-assembly covalent functionalisation, which could provide the opportunity to fabricate devices currently beyond our reach on an unprecedented precision and efficiency. All the examples will be discussed in terms of structural organisation as studied by scanning tunnelling microscopy (STM) techniques.

Manifestation of single macromolecule quantum dynamics in photon distribution function of blinking fluorescence

Distribution function w(N)(T) for photons created by three-level nanoparticle in time interval T under cw laser excitation is calculated for various methods of photon counting. It is found that each exponential process exp(-lambda(i)t) in quantum dynamics of three-level nanoparticle manifests itself via Poissonian function P(N)(lambda(i)t)=(lambda(i)t)(N) exp(-lambda(i)t)/N! in the photon distribution function w(N)(T). The distribution function w(N)(T) is expressed via two or three integrals of two or three Poissonian functions P(N)(lambda(i)t). The simple mathematical expression for w(N)(T) enables one to calculate photon distribution in blinking fluorescence with on and off intervals. A scaling between photon distribution function w(N)(T) and photoelectric pulse distribution function w(n)(T) is found. Comparison of the theoretical distribution w(n)(T) and the distribution measured in blinking fluorescence of single polymer molecule dPPV-PPyV and complex organic molecule 1,1(')-didodecyl-3,3,3('),3(')-tetramethylindocarbocyanine perchlorate (DiI) is carried out. The theoretical distributions are able to describe those found in an experiment.

Single Molecule Charging by Atomic Force Microscopy

AFM/KPM charging and charge mapping of polyamine charge carriers in a PMMA matrix is reported. Selective charging of the designed charge carrier is demonstrated at concentrations down to a single molecule. This works constitutes electrochemical charging and detection of single redox-active organic molecules in low dielectric matrices by probe microscopy.

Ab initio modeling of noncontact atomic force microscopy imaging of benzene on Cu(110) surface

AbstractThe imaging of the detailed atomic structure of single organic molecules adsorbed on a surface is still a challenge for noncontact atomic force microscopy (NC‐AFM). To investigate such a NC‐AFM imaging process, we performed ab initio calculations to simulate the interaction of clean silicon tips with a benzene molecule adsorbed on a Cu(110) surface. The apex structure of the AFM tip was modeled by Si4H3 and Si4H9 clusters. These two nanotips were approached on top of three different molecular sites. The forces acting on the Si4H3 nanotip are always repulsive and lead to a displacement of the benzene molecule on the Cu(110) surface. On the contrary, the forces acting on the Si4H9 nanotip can be attractive or repulsive depending on the approaching molecular site. In this case, the benzene molecule can bind to the tip and is retracted from the surface. The different behavior of the two nanotips considered in our study is analyzed in the framework of the frontier orbital theory. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Towards the detection of single polychlorotriphenylmethyl radical derivatives by means of Electron Spin Noise STM

The Electron Spin Noise Scanning Tunnelling Microscopy (ESN-STM) technique is one of the most promising techniques detecting one single spin, combining the spatial resolution of the STM with the ability of spectral resolution and spin manipulation of Electron Spin Resonance. After its first observation, the effectiveness of this technique has been tested by different groups to study the properties of small aggregates or single organic radical molecules. We report on the ongoing ESN-STM study on nano-aggregates of tris(2,4,6-thrichlorophenyl)methyl radical (TTM) derivatives, whose possibility to be used as wires, switches and memory devices has already been investigated in bulk. After deposition on Au(111), TTM radicals preserved their magnetism. To treat the collected noise data we followed a statistical approach; some peculiar characteristics of this analysis will be addressed.

Fluorescence of Single Molecules in Polymer Films: Sensitivity of Blinking to Local Environment

The single-molecule fluorescence blinking behavior of the organic dye Atto647N in various polymer matrixes such as Zeonex, PVK, and PVA as well as aqueous media was investigated. Fluorescence blinking with off-times in the millisecond to second time range is assigned to dye radical ions formed by photoinduced electron transfer reactions from or to the environment. In Zeonex and PVK, the measured off-time distributions show power law dependence, whereas, in PVA, no such dependence is observed. Rather, in this polymer, off-time distributions can be best fitted to monoexponential or stretched exponential functions. Furthermore, treatment of PVA samples to mild heating and low pressure greatly reduces the frequency of blinking events. We tentatively ascribe this to the removal of water pockets within the polymer film itself. Measurements of the dye immobilized in water in the presence of methylviologen, a strongly oxidizing agent, reveal simple exponential on- and off-time distributions. Thus, our data suggest that the blinking behavior of single organic molecules is sensitive to their immediate environment and, moreover, that fluorescence blinking on- and off-time distributions do not inherently and uniquely obey a power law.

Analytical Currents: Detection of cocaine by an aptamer-based machine | Watching single organic molecules move | Analyzing DNA by multinanopore force spectroscopy | CMOS-compatible nanowires as detectors| Dynamically changing concentrations in droplets | Large-scale phosphoproteomics studies with ETD |Cantilevers measure solution-phase thermodynamics | Dual-wavelength SERRS for multiplex DNA detection

Analytical Currents: Detection of cocaine by an aptamer-based machine | Watching single organic molecules move | Analyzing DNA by multinanopore force spectroscopy | CMOS-compatible nanowires as detectors| Dynamically changing concentrations in droplets | Large-scale phosphoproteomics studies with ETD |Cantilevers measure solution-phase thermodynamics | Dual-wavelength SERRS for multiplex DNA detection

Imaging of Single Organic Molecules in Motion

High-resolution transmission electron microscopy revealed nearly atomically precise images of stepping conformational change and translational motion of single hydrocarbon molecules confined in carbon nanotubes. One or two C12 or C22 alkyl chains were tethered to a carborane end group and then embedded in the nanotubes. Images of the hydrocarbon chains interacting with each other and with a graphitic surface provide information on three-dimensional structures and dynamic molecular interactions that cannot be obtained by other analytical methods.

Organic Crystals with Tunable Emission Colors Based on a Single Organic Molecule and Different Molecular Packing Structures

Organic Crystals with Tunable Emission Colors Based on a Single Organic Molecule and Different Molecular Packing Structures

Contact-structure dependence of transport properties of a single organic molecule between Au electrodes

The contact-structure dependence of the transport properties are studied for the junction systems of a benzene dithiolate (BDT) molecule sandwiched between Au(111) atomic electrodes using the nonequilibrium Green's function method based on the density functional theory. The transport properties for the hollow, bridge, and on-top contact structures are calculated. We show clearly that molecular orbitals of the isolated BDT molecule are responsible for the transmission peaks near the Fermi level. The contribution of these molecular orbitals, observed as broadened and shifted peaks in the projected density of states, is determined by the strength of their interaction with the Au electrodes, and the strength of the molecule-electrode interaction is clearly dependent on the contact structures. In the case of hollow contact, which has the strongest molecule-electrode interaction, we observe a linear potential drop across the junction for the various bias voltages. In the on-top contact structure that has the weakest interaction, on the other hand, the nonlinear potential drop and a weak negative differential conductance are observed. We obtain the largest current for the bridge contact structure, which has a moderate interaction. In this way, the transport properties strongly depend on the strength of the molecule-electrode interaction caused by a change of the contact structure and the unusual behavior is obtained for the contact structure that has the weakest interaction.

A Signal Analysis Approach Applied to the Study of Sequence, Structure and Function of the Proteins

Computational chemistry is largely based on the use of quantitative descriptors of organic molecules, allowing for the analysis of large molecular data sets and for building models that link the chemico-physical and structural descriptions of molecules to their biological activity or chemical reactivity. In the case of the proteins, this approach is severely hampered by the need to take into consideration in a meaningful way the actual sequence of the aminoacid residues. From a purely mathematical perspective, the protein sequences can be viewed as a time series, where the role of time is played by the order of the aminoacid residues along the sequences. In turn, each individual residue can be considered as a single organic molecule that can be represented by the classical molecular descriptors. Thus, in principle the generation of order- dependent synthetic descriptors through the application of time series analysis can be used for building QSAR-like models of proteins. As a matter of fact, Recurrence Quantification Analysis (RQA) of hydrophobicity-coded sequences of proteins has already been demonstrated to be useful in protein science. In this paper, we show merits and pitfalls of RQA in different case studies, ranging from the global description of a large set of diverse proteins, to the study of the effect of mutations in the human cytochrome P450 system.

Thermal gating of the single molecule conductance of alkanedithiols

The temperature dependence of the single molecule conductance (SMC) of alpha,omega-alkanedithiols has been investigated using a scanning tunnelling microscopy (STM) method. This is based on trapping molecules between a gold STM tip and a gold substrate and measuring directly the current across the molecule under different applied potentials. A pronounced temperature dependence of the conductance, which scales logarithmically with T(1), is observed in the temperature range between 293 and 353 K. It is proposed the origin of this dependence is the change in distribution between molecular conformers rather than changes in either the conduction mechanism or the electronic structure of molecule. For alkanedithiols the time averaged conformer distribution shifts to less elongated conformers at higher temperatures thus giving rise to higher conductance across the molecular bridges. This is analysed by first calculating energy differences between different conformers and then calculating their partition distribution. A simple tunnelling model is then used to calculate the temperature dependent conductance based on the conformer distribution. These findings demonstrate that charge transport through single organic molecules at ambient temperatures is a subtle and highly dynamic process that cannot be described by analysing only one molecular conformation corresponding to the lowest energy geometry of the molecule.