Single Organic Molecules Research Articles

Atomically Wired Molecular Junctions: Connecting a Single Organic Molecule by Chains of Metal Atoms

Using a break junction technique, we find a clear signature for the formation of conducting hybrid junctions composed of a single organic molecule (benzene, naphthalene, or anthracene) connected to chains of platinum atoms. The hybrid junctions exhibit metallic-like conductance (~0.1-1G0), which is rather insensitive to further elongation by additional atoms. At low bias voltage the hybrid junctions can be elongated significantly beyond the length of the bare atomic chains. Ab initio calculations reveal that benzene based hybrid junctions have a significant binding energy and high structural flexibility that may contribute to the survival of the hybrid junction during the elongation process. The fabrication of hybrid junctions opens the way for combining the different properties of atomic chains and organic molecules to realize a new class of atomic scale interfaces.

Differential anodic oxidation of single organic linkage molecules enabling orthogonal bio-immobilization

We report a novel method for preparing electrode surfaces that present thiol-containing or thiol-reactive groups using a single organic silane linkage terminated with 1,3-dithiane via differential anodic oxidation of 1,3-dithiane. We found that the surface groups resulting from the anodic oxidation reaction differed according to the concentration of H2O in the electrolyte solution during the oxidation reaction. The differential anodic oxidation was used successfully for the orthogonal immobilization of two different proteins. We demonstrated also the preparation of an immunoassay platform via orthogonal immobilization, which was then used to detect multiple target antigens based on a sandwich immunoassay.

Two-color laser manipulation of single organic molecules based on nonlinear optical response

We theoretically propose two-color laser manipulation with greatly improved efficiency to mechanically manipulate single organic molecules. The present method is based on the nonlinear resonant laser manipulation proposed in a recent study. In the first part, we describe a method to trap single organic molecules that can be more effective than ever before utilizing two-color beams. In the second part, we demonstrate the possibility to selectively “pull” single organic molecules with a particular type of electronic-level scheme by using single-side illumination of traveling light.

単一ナノ分子・磁気抵抗素子

Giant magnetoresistance (GMR) through a single phthalocyanine molecule (H2Pc) was studied by means of a spin-polarized scanning tunneling microscopy (STM) technique. Single molecular magnetic junction was fabricated by contacting a ferromagnetic STM tip to a single molecule on nano magnets. We obtained GMR of +60% and −50% through [Co/H2Pc/Co(111)] and [Fe/H2Pc/Mn(001)] junctions, respectively, in ultra-high vacuum at 4.6 K. Single organic molecules can be a new material for spintronics.

Resonance optical manipulation of nano-objects based on nonlinear optical response

Optical manipulation is a technique to control the mechanical motion of small objects by using electromagnetic radiation force. Optical tweezers are the most popular tool to trap and move microparticles suspended in a medium. Recent interest has been shifting to manipulating nano-objects considerably smaller than the wavelength of light. Since the radiation force exerted on nano-objects is extremely small, an innovative method is necessary to make this concept feasible. Utilizing the resonant optical response of the objects to electronic transitions is one of the promising ways to approach nanoscale optical manipulation, and several advances in this direction have been made recently. Despite experimental studies on resonance optical tweezers showing favorable results, conventional theories have been unable to explain the results though demonstrations of resonant manipulations for traveling and standing waves have shown favorable results. In the present article, we provide a perspective view of resonance optical manipulation based on nonlinear optical response that we have recently proposed. This idea coherently elucidates recently reported puzzling phenomena appearing in studies concerning resonance optical tweezers that contradict the conventional understanding of resonance optical trapping. Further, this concept opens up the possibility to develop potentially powerful manipulation techniques because the nonlinear optical response involves processes with considerably greater degrees of freedom than those of the linear optical response. As examples, we propose a method for trapping single organic molecules that is more effective than ever before, selectively pulling the molecules with a particular transition energy, and our proposed method allows for high-spatial-resolution optical manipulation beyond the diffraction limit.

Bond Order Via Microscopy

a scanning-probe microscopy method can reveal subtle bond order differences between individual bonds in single organic molecules, according to a study led by researchers at IBM and published in Sci...

A simple model of molecular imaging with noncontact atomic force microscopy

Using functionalized tips, the atomic resolution of a single organic molecule can be achieved by noncontact atomic force microscopy (nc-AFM) operating in the regime of short-ranged repulsive Pauli forces. To theoretically describe the atomic contrast in such AFM images, we propose a simple model in which the Pauli repulsion is assumed to follow a power law as a function of the probed charge density. As the exponent in this power law is found to be largely independent of the sample molecule, our model provides a general method for simulating atomically resolved AFM images of organic molecules. For a single perylene-tetracarboxylic-dianhydride (PTCDA) molecule imaged with a CO-terminated tip, we find excellent agreement with the experimental data. Our model eliminates the need to take into account the full tip and sample system and therefore reduces computational cost by three orders of magnitude.

First-principles quantum transport modeling of thermoelectricity in single-molecule nanojunctions with graphene nanoribbon electrodes

We overview the nonequilibrium Green function combined with density functional theory (NEGF-DFT) approach to modeling of independent electronic and phononic quantum transport in nanoscale thermoelectrics with examples focused on a new class of devices where a single organic molecule is attached to two metallic zigzag graphene nanoribbons (ZGNRs) via highly transparent contacts. Such contacts make possible injection of evanescent wavefunctions from the ZGNR electrodes, so that their overlap within the molecular region generates a peak in the electronic transmission around the Fermi energy of the device. Additionally, the spatial symmetry properties of the transverse propagating states in the semi-infinite ZGNR electrodes suppress hole-like contributions to the thermopower. Thus optimized thermopower, together with diminished phonon thermal conductance in a ZGNR|molecule|ZGNR inhomogeneous heterojunctions, yields the thermoelectric figure of merit ZT≃0.4 at room temperature with maximum ZT≃3 reached at very low temperatures T≃10 K (so that the latter feature could be exploited for thermoelectric cooling of, e.g., infrared sensors). The reliance on evanescent mode transport and symmetry of propagating states in the electrodes makes the electronic-transport-determined power factor in this class of devices largely insensitive to the type of sufficiently short organic molecule, which we demonstrate by showing that both 18-annulene and C10 molecule sandwiched by the two ZGNR electrodes yield similar thermopower. Thus, one can search for molecules that will further reduce the phonon thermal conductance (in the denominator of ZT) while keeping the electronic power factor (in the nominator of ZT) optimized. We also show how the often employed Brenner empirical interatomic potential for hydrocarbon systems fails to describe phonon transport in our single-molecule nanojunctions when contrasted with first-principles results obtained via NEGF-DFT methodology.

Atomic‐ and molecular‐scale devices and systems for single‐molecule electronics

AbstractPresent‐day electronic technology, based to a large extent on silicon fabricated devices, is surely approaching size limitations arising from quantum effects. The effort to achieve rapid development of electronic devices requires implementation of entirely new ideas that will allow existing technological constraints to be overcome. Among a wide range of concepts, utilization of single organic molecules, acting as active blocks performing logic operations, appears as one of the most appealing and is based on the state‐of‐the‐art use of modern nanotechnology. In this short review, we offer a selection of recent experiments addressing milestones of single‐molecule computing devices technology. Along with discussion of the latest achievements in atomic‐ and molecular‐scale technologies, we discuss their future perspectives, challenges, and still unsolved issues standing in the way of practical implementation of single‐molecule devices. magnified imageConcept of a single‐molecule electronic device. The molecule is equipped with various functional groups responsible for logic operations and bonding to an underlying surface and metallic nanoelectrodes. The monomolecular nanodevice is deposited on a thin buffer layer assuring the decoupling from a (semi‐)conducting substrate.

Highly Efficient FRET from a Single Nitrogen-Vacancy Center in Nanodiamonds to a Single Organic Molecule

We show highly efficient fluorescence resonance energy transfer (FRET) between negatively charged nitrogen-vacancy (NV) centers in diamond as donor and dye molecules as acceptor, respectively. The energy transfer efficiency is 86% with particles of 20 nm in size. Calculated and experimentally measured energy transfer efficiencies are in excellent agreement. Owing to the small size of the nanocrystals and careful surface preparation, energy transfer between a single nitrogen-vacancy center and a single quencher was identified by the stepwise change of energy transfer efficiencies due to bleaching of single acceptor molecules. Our studies pave the way toward FRET-based scanning probe techniques using single NV donors.

Visualizing quantum mechanics

New STM experiments resolve the nodal structure of individual orbitals of single organic molecules.

Controlling the Phase of a Light Beam with a Single Molecule

We employ heterodyne interferometry to investigate the effect of a single organic molecule on the phase of a propagating laser beam. We report on the first phase-contrast images of individual molecules and demonstrate a single-molecule electro-optical phase switch by applying a voltage to the microelectrodes embedded in the sample. Our results may find applications in single-molecule holography, fast optical coherent signal processing, and single-emitter quantum operations.

Unambiguous One-Molecule Conductance Measurements under Ambient Conditions

One of the challenging goals of molecular electronics is to wire exactly one molecule between two electrodes. This is generally nontrivial under ambient conditions. We describe a new and straightforward protocol for unambiguously isolating a single organic molecule on a metal surface and wiring it inside a nanojunction under ambient conditions. Our strategy employs C(60) terminal groups which act as molecular beacons allowing molecules to be visualized and individually targeted on a gold surface using an scanning tunneling microscope. After isolating one molecule, we then use the C(60) groups as alligator clips to wire it between the tip and surface. Once wired, we can monitor how the conductance of a purely one molecule junction evolves with time, stretch the molecule in the junction, observing characteristic current plateaus upon elongation, and also perform direct I-V spectroscopy. By characterizing and controlling the junction, we can draw stronger conclusions about the observed variation in molecular conductance than was previously possible.

Dye-Conjugated Dendrimers as Bright and Photostable Fluorescent Labels for Single Molecule Microscopy

In this work, we report a new class of bright and photostable fluorescent labels for single molecule fluorescence microscopy based on chemically functionalized dendrimers. We synthesized polymeric dendrimers containing multiple fluorophores and versatile functional groups, thereby enabling facile fluorescent labeling of biomolecules (proteins, DNA, RNA) via specific chemical conjugation. We characterized the photophysical properties of single dye-conjugated dendrimer molecules immobilized to chemically modified surfaces using total internal reflection fluorescence microscopy (TIRF-M). Fluorescence photobleaching lifetimes of dye-conjugated dendrimers were observed to far exceed the lifetimes of single conventional organic dye molecules, both in the presence or absence of oxygen scavengers. In addition, single dendrimer molecules are significantly brighter than single conventional organic dye molecules. Furthermore, we determined the precision of centroid position determination for single molecule localization by fitting the fluorescence emission from single dendrimers to a 2-dimensional Gaussian function. Dye-conjugated dendrimers exhibit several advantages as polymeric fluorophores for labeling biological molecules. First, single dendrimer molecules exhibit a relatively small size which is comparable to common GFP-family fluorescent proteins and smaller than inorganic quantum dots. Second, fluorescently-labeled dendrimers are synthesized to contain multiple fluorophores, thereby overcoming blinking in single dyes and short fluorescence “on” times before photobleaching, which are common limitations of single organic dyes for applications in single molecule microscopy. Third, a wide variety of commonly used fluorophores can be conjugated to polymeric dendrimers, thereby increasing their utility for labeling. Overall, we anticipate that dye-conjugated dendritic polymers will be a versatile tool for single molecule microscopy applications, including fine-scale characterization of protein structural dynamics and super-resolution microscopy.

Femtosecond coherence and quantum control of single molecules at room temperature

Quantum mechanical phenomena, such as electronic coherence and entanglement, play a key role in achieving the unrivalled efficiencies of light-energy conversion in natural photosynthetic light-harvesting complexes, and triggered the growing interest in the possibility of organic quantum computing. Since biological systems are intrinsically heterogeneous, clear relations between structural and quantum-mechanical properties can only be obtained by investigating individual assemblies. However, single-molecule techniques to access ultrafast coherences at physiological conditions were not available so far. Here we show by employing femtosecond pulse-shaping techniques that quantum coherences in single organic molecules can be created, probed, and manipulated at ambient conditions even in highly disordered solid environments. We find broadly distributed coherence decay times for different individual molecules giving direct insight into the structural heterogeneity of the local surroundings. Most importantly, we induce Rabi-oscillations and control the coherent superposition state in a single molecule, thus performing a basic femtosecond single-qubit operation at room temperature.

The Shear Flow Processing of Controlled DNA Tethering and Stretching for Organic Molecular Electronics

DNA has been recently explored as a powerful tool for developing molecular scaffolds for making reproducible and reliable metal contacts to single organic semiconducting molecules. A critical step in the process of exploiting DNA-organic molecule-DNA (DOD) array structures is the controlled tethering and stretching of DNA molecules. Here we report the development of reproducible surface chemistry for tethering DNA molecules at tunable density and demonstrate shear flow processing as a rationally controlled approach for stretching/aligning DNA molecules of various lengths. Through enzymatic cleavage of λ-phage DNA to yield a series of DNA chains of various lengths from 17.3 μm down to 4.2 μm, we have investigated the flow/extension behavior of these tethered DNA molecules under different flow strengths in the flow-gradient plane. We compared Brownian dynamic simulations for the flow dynamics of tethered λ-DNA in shear, and found our flow-gradient plane experimental results matched well with our bead-spring simulations. The shear flow processing demonstrated in our studies represents a controllable approach for tethering and stretching DNA molecules of various lengths. Together with further metallization of DNA chains within DOD structures, this bottom-up approach can potentially enable efficient and reliable fabrication of large-scale nanoelectronic devices based on single organic molecules, therefore opening opportunities in both fundamental understanding of charge transport at the single molecular level and many exciting applications for ever-shrinking molecular circuits.

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.