Properties Of Single Molecules Research Articles

Nanoscale properties of single atoms and molecules investigated by scanning tunneling microscope light emission spectroscopy

Nanoscale properties of single atoms and molecules investigated by scanning tunneling microscope light emission spectroscopy

A theoretical study of π-stacking tetracene derivatives as promising organic molecular semiconductors

Computational methods are used recently as reliable tools to uncover the properties of novel conjugated organic materials and understand the physico-chemical mechanism that ultimately controls the overall organic-based device efficiency. Since modelling of charge transport across organic layers needs to address simultaneously single molecule properties together with electronic couplings between neighbouring molecules, which truly depends on the molecular packing, we employ dispersion-corrected Density Functional Theory methods to accurately extract key molecular parameters governing this phenomenon at the nanoscale. It is concluded that controlled functionalization (cyanation and/or halogenation) of state-of-the-art molecules (tetracene) is an efficient way to modulate the charge mobilities.

Characterization of nanowires with the low energy electron point source (LEEPS) microscope

AbstractThe low energy electron point source (LEEPS) microscope is an instrument for the characterization of structural, electrical, and mechanical properties of single molecules and nanostructures. In this work, we review our efforts in advancing LEEPS as tool for the characterization of electric properties of nanowires. Individual nanowires of different size and material were examined, including compositions of metallic as well as semiconducting character. The nanowires were characterized by electrical conductance measurements with a metallic tip as movable electrode and the sample support as its counterpart. Beyond these measurements, we developed a scheme to deduce the electrical conductivity of a single nanowire directly from its LEEPS image. This substantially reduces the data acquisition time and widens the applicability of LEEPS microscopy.

A model for structure and thermodynamics of ssDNA and dsDNA near a surface: A coarse grained approach

New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6–8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all-atom simulations. Our average tilt results are also in agreement with all-atom simulations for the case of dense systems.

ChemInform Abstract: The Rheology of n Alkanes: Decane and Eicosane

We examine the rheological behavior of n alkanes, in particular n decane (C10H22) and n eicosane (C20H42). We observe, for the first time in a molecular dynamics simulation, the phenomenon of shear thickening. Over the accessible range of strain rates we see a regime of shear thinning, and then shear thickening in both fluids. The transition from shear thinning to shear thickening is correlated with a qualitative change in the single molecule properties; in particular the distribution of alignment angles and end‐to‐end distances.

Spin and Orbital Magnetic Moment Anisotropies of Monodispersed Bis(Phthalocyaninato)Terbium on a Copper Surface

The magnetic properties of isolated TbPc(2) molecules supported on a Cu(100) surface are investigated by X-ray magnetic circular dichroism at 8 K in magnetic fields up to 5 T. The crystal field and magnetic properties of single molecules are found to be robust upon adsorption on a metal substrate. The Tb magnetic moment has Ising-like magnetization; XMCD spectra combined with multiplet calculations show that the saturation orbital and spin magnetic moment values reach 3 and 6 mu(B), respectively.

First-principles study on quantum-transport properties of single molecule depending on adsorption conditions

We present a first-principles electron-transport simulation within the framework of the density functional theory for a 1,4-benzenedithiol molecule suspended between semi-infinite Au electrodes. The transport properties are demonstrated under the several adsorption conditions. It is found that the conducting electrons have two types of resonant-tunneling transport properties with different responses to changes in adsorption conditions.

The fabrication and characterization of adjustable nanogaps between gold electrodes onchip for electrical measurement of single molecules

This work reports on a new method to fabricate mechanically controllable breakjunctions (MCBJ) with finely adjustable nanogaps between two gold electrodes on solidstate chips for characterizing electron transport properties of single molecules. Thesimple, low cost, robust and reproducible fabrication method combines conventionalphotolithography, chemical etching and electrodeposition to produce suspended electrodesseparated with nanogaps. The MCBJ devices fabricated by the method can undergo manycycles in which the nanogap width can be precisely and repeatedly varied fromzero to several nanometers. The method improves the success rate of the MCBJexperiments. Using these devices the electron transport properties of a typical molecularsystem, commercially available benzene-1,4-dithiol (BDT), have been studied. TheI–V andG–V characteristic curves of BDT and the conductance value for a single BDT moleculeestablished the excellent device suitability for molecular electronics research.

Pulling Apart Molecular Magnetism

Mechanical control can be used to probe and tune the magnetic properties of single molecules.

Controlling Electronic States and Transport Properties at the Level of Single Molecules

Since molecular electronics has been rapidly growing as a promising alternative to conventional electronics towards the ultimate miniaturization of electronic devices through the bottom-up strategy, it has become a long-term desire to understand and control the transport properties at the level of single molecules. In this Research News article it is shown that one may modify the electronic states of single molecules and thus control their transport properties through designing and fabrication of functional molecules or manipulating molecules with scanning tunneling microscopy. The rectifying effect of single molecules can be realized by designing a donor-barrier-acceptor architecture of Pyridine-sigma-C(60) molecules to achieve the Aviram-Ratner rectifier and by modifying electronic states through azafullerene C(59)N molecules. The effect of the negative differential resistances can be realized by appropriately matching the molecular orbital symmetries between a cobalt phthalocyanine (CoPc) molecule and a Ni electrode. The electronic states and transport properties of single molecules, such as CoPc and melamine molecules, can be altered through manipulation or modifying molecular structures, leading to functionalized molecular devices.

Metal Dilution Effects on Entropy and Light-Induced Valence Tautomeric Interconversion in a 1:1 Cobalt−Dioxolene Complex

The entropy and the light-induced valence tautomeric interconversions of solid solutions of the [Co(Me(2)tpa)(diox)](PF(6)).C(6)H(5)CH(3) complex [Me(2)tpa = bis(6-methyl-(2-pyridylmethyl))(2-pyridylmethyl)amine and diox = catecholato (DBCat) or semiquinonato (DBSQ) forms of 3,5-ditert-butylquinone] in the electronically innocent [Zn(Me(2)tpa)(DBSQ)](PF(6)).C(6)H(5)CH(3) host, in four different molar ratios, have been investigated. It has been found that the entropy driven transition is strongly affected by the Co:Zn molar ratio, whereas the relaxation rates of the optically induced high-spin Co(II)-DBSQ metastable state at cryogenic temperatures are nearly independent of the degree of solid dilution. These results are discussed in the framework of the Jortner theory for adiabatic radiationless multiphonon relaxation processes. It is suggested that the optical bistability in these systems is related to the single molecule properties rather than to the cooperative effects active in the lattice.

Ghost transmission: How large basis sets can make electron transport calculations worse

The Landauer approach has proven to be an invaluable tool for calculating the electron transport properties of single molecules, especially when combined with a nonequilibrium Green's function approach and Kohn-Sham density functional theory. However, when using large nonorthogonal atom-centered basis sets, such as those common in quantum chemistry, one can find erroneous results if the Landauer approach is applied blindly. In fact, basis sets of triple-zeta quality or higher sometimes result in an artificially high transmission and possibly even qualitatively wrong conclusions regarding chemical trends. In these cases, transport persists when molecular atoms are replaced by basis functions alone ("ghost atoms"). The occurrence of such ghost transmission is correlated with low-energy virtual molecular orbitals of the central subsystem and may be interpreted as a biased and thus inaccurate description of vacuum transmission. An approximate practical correction scheme is to calculate the ghost transmission and subtract it from the full transmission. As a further consequence of this study, it is recommended that sensitive molecules be used for parameter studies, in particular those whose transmission functions show antiresonance features such as benzene-based systems connected to the electrodes in meta positions and other low-conducting systems such as alkanes and silanes.

Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach

In the last two decades, new technologies have allowed us to measure properties of single DNA molecules in very accurate ways. At the same time, a number of theoretical models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. To gain insight into this situation we modeled DNA as a discretized worm-like chain; each link is considered a sphere of 6 base pairs in length for dsDNA and 1.5 bases for ssDNA. The chain is tethered to a surface by a fixed length, non-interactive 1 nm linker. Configurational sampling was achieved via Monte-Carlo sampling. Results on the average tilt are in agreement with all atom simulations. New insights into polyelectrolytes near surfaces are shown.

The experimental determination of the conductance of single molecules

The measurement of the electrical properties of molecules, down to the single molecule level, has become an experimental reality in recent years. A number of methods are now available for experimentally achieving this feat. The common aim of these methods is to entrap a single or small numbers of molecules between a pair of metallic contacts. This topical review focuses on describing and comparing experimental methods for entrapping and measuring the electrical properties of single molecules in metallic contact gaps. After describing the methods, reasons are tendered for apparent discrepancies in the literature between measured single molecule conductance values, with a focus on the most widely studied alkanedithiol system. Illustrative examples are then presented of the determination of the electrical properties of a range of single molecular systems, in order to highlight the progress which has been made in recent years.

Statistical Properties of Single Molecule under Stochastic Gating

We discuss the blinking statistical behaviors of dynamics of single molecule system, using the recently developed generating function method. We make a thor- ough study for the fluorescence blinking behaviors and get the statistical properties of the jumping events respectively onto ON state or OFF state, including the waiting time and waiting time distribution for every directional jumping event, the cumulants of jumping events, the cross correlation, the joint probabilities between two directional jumping events and the probabilities.

Fluorescence Dynamics of Chlorophyll Trefoils in the Solid State Studied by Single-Molecule Fluorescence Spectroscopy

We have comparatively investigated the single-molecule photophysical properties of two chlorophyll trefoils that feature distinctive electronic couplings induced by differences in linkage: one is an ethynyl-linked chlorophyll trefoil (1) in which relatively short and rigid linkage between the chromophores promotes effective electronic coupling, and the other is a phenyl−ethynyl-linked chlorophyll trefoil (2) in which the phenyl addition induces an orthogonal geometry impeding π-conjugation and provides a longer interchlorophyll distance reducing through-space interaction. By recording single-molecule fluorescence intensity trajectories and their corresponding lifetimes, we observed one-step photobleaching behaviors, less frequent on−off behaviors, a narrower fluorescence lifetime distribution, and higher photostability in 1 as compared with 2. These results indicate that the performance of molecular photosynthetic systems in the solid state is strongly associated with electronic couplings and, thus, give ...

Role of molecular orientation in vibration, hopping, and electronic properties of single pyridine molecules adsorbed on Ag(110) surface: A combined STM and DFT study

Abstract A combination of low-temperature scanning tunneling microscopy and density functional theory calculations was used to determine the adsorption characteristics of single pyridine molecules on Ag(1 1 0) surfaces. Pyridine was chemisorbed onto Ag(1 1 0) surfaces at 13 K in either the stand-up or flat-lying configuration. The fractional ratio of the two configurations depended on the molecular coverage: at very low coverage, the flat-lying pyridine predominated on the surface; however, the molecules stood up with increasing surface coverage until the stand-up configuration was favored. The adsorption configurations were characterized by distinct C–H stretching vibrational energies, hopping barriers, and binding characteristics: (i) The C–H stretching energy for the flat-lying configuration was lower than that of the stand-up configuration. (ii) The hopping barrier for the stand-up configuration along the [1 1 ¯ 0] direction was the lowest. (iii) The electrostatic interaction was the dominant contribution to the binding of pyridine on Ag surfaces in both configurations, although the interaction was especially strong for the flat-lying configuration.

Optical Signal Comparison of Single Fluorescent Molecules and Raman Active Gold Nanostars

The relevant photophysical properties of single fluorescent molecules and single SERS active surface-coated gold nanostars tagged with the Raman reporter molecule 4-mercaptopyridine are compared for imaging purposes. Mean count rate distributions are built from the single molecule/single probe level. The individually observed variance and count rates of both systems are compared as well as the behavior over multiple image acquisitions.

Direct measurements of kinesin torsional properties reveal flexible domains and occasional stalk reversals during stepping

Kinesin is a homodimeric motor with two catalytic heads joined to a stalk via short neck linkers (NLs). We measured the torsional properties of single recombinant molecules by tracking the thermal angular motions of fluorescently labeled beads bound to the C terminus of the stalk. When kinesin heads were immobilized on microtubules (MTs) under varied nucleotide conditions, we observed bounded or unbounded angular diffusion, depending on whether one or both heads were attached to the MT. Free rotation implies that NLs act as swivels. From data on constrained diffusion, we conclude that the coiled-coil stalk domains are approximately 30-fold stiffer than its flexible "hinge" regions. Surprisingly, while tracking processive kinesin motion at low ATP concentrations, we observed occasional abrupt reversals in the directional orientations of the stalk. Our results impose constraints on kinesin walking models and suggest a role for rotational freedom in cargo transport.

Design and control of electron transport properties of single molecules

We demonstrate in this joint experimental and theoretical study how one can alter electron transport behavior of a single melamine molecule adsorbed on a Cu (100) surface by performing a sequence of elegantly devised and well-controlled single molecular chemical processes. It is found that with a dehydrogenation reaction, the melamine molecule becomes firmly bonded onto the Cu surface and acts as a normal conductor controlled by elastic electron tunneling. A current-induced hydrogen tautomerization process results in an asymmetric melamine tautomer, which in turn leads to a significant rectifying effect. Furthermore, by switching on inelastic multielectron scattering processes, mechanical oscillations of an N-H bond between two configurations of the asymmetric tautomer can be triggered with tuneable frequency. Collectively, this designed molecule exhibits rectifying and switching functions simultaneously over a wide range of external voltage.