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Sample records for single-molecule interfacial electron

  1. Single-molecule interfacial electron transfer in donor-bridge-nanoparticle acceptor complexes.

    PubMed

    Jin, Shengye; Snoeberger, Robert C; Issac, Abey; Stockwell, David; Batista, Victor S; Lian, Tianquan

    2010-11-18

    Photoinduced interfacial electron transfer (IET) in sulforhodamine B (SRhB)-aminosilane-Tin oxide (SnO(2)) nanoparticle donor-bridge-acceptor complexes has been studied on a single molecule and ensemble average level. On both SnO(2) and ZrO(2), the sum of single molecule fluorescence decays agree with the ensemble average results, suggesting complete sampling of molecules under single molecule conditions. Shorter fluorescence lifetime on SnO(2) than on ZrO(2) is observed and attributed to IET from SRhB to SnO(2). Single molecule lifetimes fluctuate with time and vary among different molecules, suggesting both static and dynamic IET heterogeneity in this system. Computational modeling of the complexes shows a distribution of molecular conformation, leading to a distribution of electronic coupling strengths and ET rates. It is likely that the conversion between these conformations led to the fluctuation of ET rate and fluorescence lifetime on the single molecule level. PMID:20225886

  2. Simultaneous Spectroscopic and Topographic Imaging of Single-Molecule Interfacial Electron-Transfer Reactivity and Local Nanoscale Environment.

    PubMed

    He, Yufan; Rao, Vishal Govind; Cao, Jin; Lu, H Peter

    2016-06-16

    The fundamental information related to the energy flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure is critical for understanding interfacial electron-transfer (ET) dynamics. The inhomogeneous nanoscale molecule-surface and molecule-molecule interactions are presumably the origins of the complexity in interfacial ET dynamics; thus, identifying the environment of molecules at nanoscale is crucial. We have developed atomic force microscopy (AFM) correlated single-molecule fluorescence intensity/lifetime imaging microscopy (AFM-SMFLIM) capable of identifying and characterizing individual molecules distributed across the heterogeneous surface at the nanometer length scale. Using the novel AFM-SMFLIM imaging, we are able to obtain nanoscale morphology and interfacial ET dynamics at a single-molecule level. Moreover, the observed blinking behavior and lifetime of each molecule in combination with the topography of the environment at nanoscale provide the location of each molecule on the surface (TiO2 vs cover glass) at nanoscale and the coupling strength of each molecule with TiO2 nanoparticles. PMID:27214587

  3. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  4. Chemical principles of single-molecule electronics

    NASA Astrophysics Data System (ADS)

    Su, Timothy A.; Neupane, Madhav; Steigerwald, Michael L.; Venkataraman, Latha; Nuckolls, Colin

    2016-03-01

    The field of single-molecule electronics harnesses expertise from engineering, physics and chemistry to realize circuit elements at the limit of miniaturization; it is a subfield of nanoelectronics in which the electronic components are single molecules. In this Review, we survey the field from a chemical perspective and discuss the structure-property relationships of the three components that form a single-molecule junction: the anchor, the electrode and the molecular bridge. The spatial orientation and electronic coupling between each component profoundly affect the conductance properties and functions of the single-molecule device. We describe the design principles of the anchor group, the influence of the electronic configuration of the electrode and the effect of manipulating the structure of the molecular backbone and of its substituent groups. We discuss single-molecule conductance switches as well as the phenomenon of quantum interference and then trace their fundamental roots back to chemical principles.

  5. Single Molecule Spectroscopy of Electron Transfer

    SciTech Connect

    Michael Holman; Ling Zang; Ruchuan Liu; David M. Adams

    2009-10-20

    The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

  6. Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

    PubMed Central

    Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2012-01-01

    The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

  7. Single-molecule junctions beyond electronic transport

    NASA Astrophysics Data System (ADS)

    Aradhya, Sriharsha V.; Venkataraman, Latha

    2013-06-01

    The idea of using individual molecules as active electronic components provided the impetus to develop a variety of experimental platforms to probe their electronic transport properties. Among these, single-molecule junctions in a metal-molecule-metal motif have contributed significantly to our fundamental understanding of the principles required to realize molecular-scale electronic components from resistive wires to reversible switches. The success of these techniques and the growing interest of other disciplines in single-molecule-level characterization are prompting new approaches to investigate metal-molecule-metal junctions with multiple probes. Going beyond electronic transport characterization, these new studies are highlighting both the fundamental and applied aspects of mechanical, optical and thermoelectric properties at the atomic and molecular scales. Furthermore, experimental demonstrations of quantum interference and manipulation of electronic and nuclear spins in single-molecule circuits are heralding new device concepts with no classical analogues. In this Review, we present the emerging methods being used to interrogate multiple properties in single molecule-based devices, detail how these measurements have advanced our understanding of the structure-function relationships in molecular junctions, and discuss the potential for future research and applications.

  8. Single Molecule Electron Transfer Process of Ruthenium Complexes.

    SciTech Connect

    Hu, Dehong; Lu, H PETER.

    2006-03-01

    Transition metal complexes such as ruthenium complexes, having metal-to-ligand charge transfer states, are extensively used in solar energy conversion and electron transfer in biological systems and at interfaces. The dynamics of metal-to-ligand charge transfer and subsequent intermolecular, intramolecular, and interfacial electron transfer processes can be highly complex and inhomogeneous, especially when molecules are involved in interactions and perturbations from heterogeneous local environments and gated by conformation fluctuations. We have employed the single-molecule spectroscopy, a powerful approach for inhomogeneous systems to study the electron transfer dynamics of ruthenium complexes. We have applied a range of statistical analysis methods to reveal nonclassical photon emission behavior of the single ruthenium complex, i.e., photon antibunching, and photophysical ground-state recovering dynamics on a microsecond time scale. The use of photon antibunching to measure phosphorescence lifetimes and single-molecule electron transfer dynamics at room temperature is demonstrated.

  9. Single molecules as whispering galleries for electrons

    NASA Astrophysics Data System (ADS)

    Reecht, G.; Bulou, H.; Schull, G.; Scheurer, F.

    2016-04-01

    Whispering gallery modes, well-known for acoustic and optical waves, have been shown recently for electrons in molecules on surfaces. The existence of such waves opens new possibilities for nanoelectronic devices. Here we propose a simple analytical textbook model which allows the main characteristic features of such electronic waves to be understood. The model is illustrated by two- and three-dimensional experimental situations.

  10. Single molecules as whispering galleries for electrons.

    PubMed

    Reecht, G; Bulou, H; Schull, G; Scheurer, F

    2016-04-27

    Whispering gallery modes, well-known for acoustic and optical waves, have been shown recently for electrons in molecules on surfaces. The existence of such waves opens new possibilities for nanoelectronic devices. Here we propose a simple analytical textbook model which allows the main characteristic features of such electronic waves to be understood. The model is illustrated by two- and three-dimensional experimental situations. PMID:26987969

  11. Molecular electronics with single molecules in solid-state devices.

    PubMed

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-09-01

    The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong. PMID:19734925

  12. Electron Transport in Short Peptide Single Molecules

    NASA Astrophysics Data System (ADS)

    Cui, Jing; Brisendine, Joseph; Ng, Fay; Nuckolls, Colin; Koder, Ronald; Venkarataman, Latha

    We present a study of the electron transport through a series of short peptides using scanning tunneling microscope-based break junction method. Our work is motivated by the need to gain a better understanding of how various levels of protein structure contribute to the remarkable capacity of proteins to transport charge in biophysical processes such as respiration and photosynthesis. We focus here on short mono, di and tri-peptides, and probe their conductance when bound to gold electrodes in a native buffer environment. We first show that these peptides can bind to gold through amine, carboxyl, thiol and methyl-sulfide termini. We then focus on two systems (glycine and alanine) and show that their conductance decays faster than alkanes terminated by the same linkers. Importantly, our results show that the peptide bond is less conductive than a sigma carbon-carbon bond. This work was supported in part by NSF-DMR 1507440.

  13. Single-Molecule Electronics: Chemical and Analytical Perspectives.

    PubMed

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance. PMID:26048551

  14. Single-Molecule Electronics: Chemical and Analytical Perspectives

    NASA Astrophysics Data System (ADS)

    Nichols, Richard J.; Higgins, Simon J.

    2015-07-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  15. Single-Molecule Electronic Measurements with Metal Electrodes

    ERIC Educational Resources Information Center

    Lindsay, Stuart

    2005-01-01

    A review of concepts like tunneling through a metal-molecule-metal-junction, contrast with electrochemical and optical-charge injection, strong-coupling limit, calculations of tunnel transport, electron transfer through Redox-active molecules is presented. This is followed by a discussion of experimental approaches for single-molecule measurements.

  16. Electronic transport in benzodifuran single-molecule transistors

    NASA Astrophysics Data System (ADS)

    Xiang, An; Li, Hui; Chen, Songjie; Liu, Shi-Xia; Decurtins, Silvio; Bai, Meilin; Hou, Shimin; Liao, Jianhui

    2015-04-01

    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices. Electronic supplementary information (ESI) available: The fabrication procedure for BDF single-molecule

  17. Electron transport in single molecules: from benzene to graphene.

    PubMed

    Chen, F; Tao, N J

    2009-03-17

    Electron movement within and between molecules--that is, electron transfer--is important in many chemical, electrochemical, and biological processes. Recent advances, particularly in scanning electrochemical microscopy (SECM), scanning-tunneling microscopy (STM), and atomic force microscopy (AFM), permit the study of electron movement within single molecules. In this Account, we describe electron transport at the single-molecule level. We begin by examining the distinction between electron transport (from semiconductor physics) and electron transfer (a more general term referring to electron movement between donor and acceptor). The relation between these phenomena allows us to apply our understanding of single-molecule electron transport between electrodes to a broad range of other electron transfer processes. Electron transport is most efficient when the electron transmission probability via a molecule reaches 100%; the corresponding conductance is then 2e(2)/h (e is the charge of the electron and h is the Planck constant). This ideal conduction has been observed in a single metal atom and a string of metal atoms connected between two electrodes. However, the conductance of a molecule connected to two electrodes is often orders of magnitude less than the ideal and strongly depends on both the intrinsic properties of the molecule and its local environment. Molecular length, means of coupling to the electrodes, the presence of conjugated double bonds, and the inclusion of possible redox centers (for example, ferrocene) within the molecular wire have a pronounced effect on the conductance. This complex behavior is responsible for diverse chemical and biological phenomena and is potentially useful for device applications. Polycyclic aromatic hydrocarbons (PAHs) afford unique insight into electron transport in single molecules. The simplest one, benzene, has a conductance much less than 2e(2)/h due to its large LUMO-HOMO gap. At the other end of the spectrum, graphene

  18. Single-Molecule Electronic Monitoring of DNA Polymerase Activity

    NASA Astrophysics Data System (ADS)

    Marushchak, Denys O.; Pugliese, Kaitlin M.; Turvey, Mackenzie W.; Choi, Yongki; Gul, O. Tolga; Olsen, Tivoli J.; Rajapakse, Arith J.; Weiss, Gregory A.; Collins, Philip G.

    Single-molecule techniques can reveal new spatial and kinetic details of the conformational changes occurring during enzymatic catalysis. Here, we investigate the activity of DNA polymerases using an electronic single-molecule technique based on carbon nanotube transistors. Single molecules of the Klenow fragment (KF) of polymerase I were conjugated to the transistors and then monitored via fluctuations in electrical conductance. Continuous, long-term monitoring recorded single KF molecules incorporating up to 10,000 new bases into single-stranded DNA templates. The duration of individual incorporation events was invariant across all analog and native nucleotides, indicating that the precise structure of different base pairs has no impact on the timing of incorporation. Despite similar timings, however, the signal magnitudes generated by certain analogs reveal alternate conformational states that do not occur with native nucleotides. The differences induced by these analogs suggest that the electronic technique is sensing KF's O-helix as it tests the stability of nascent base pairs.

  19. Electronic Single Molecule Measurements with the Scanning Tunneling Microscope

    NASA Astrophysics Data System (ADS)

    Im, Jong One

    Richard Feynman said "There's plenty of room at the bottom". This inspired the techniques to improve the single molecule measurements. Since the first single molecule study was in 1961, it has been developed in various field and evolved into powerful tools to understand chemical and biological property of molecules. This thesis demonstrates electronic single molecule measurement with Scanning Tunneling Microscopy (STM) and two of applications of STM; Break Junction (BJ) and Recognition Tunneling (RT). First, the two series of carotenoid molecules with four different substituents were investigated to show how substituents relate to the conductance and molecular structure. The measured conductance by STM-BJ shows that Nitrogen induces molecular twist of phenyl distal substituents and conductivity increasing rather than Carbon. Also, the conductivity is adjustable by replacing the sort of residues at phenyl substituents. Next, amino acids and peptides were identified through STM-RT. The distribution of the intuitive features (such as amplitude or width) are mostly overlapped and gives only a little bit higher separation probability than random separation. By generating some features in frequency and cepstrum domain, the classification accuracy was dramatically increased. Because of large data size and many features, supporting vector machine (machine learning algorithm for big data) was used to identify the analyte from a data pool of all analytes RT data. The STM-RT opens a possibility of molecular sequencing in single molecule level. Similarly, carbohydrates were studied by STM-RT. Carbohydrates are difficult to read the sequence, due to their huge number of possible isomeric configurations. This study shows that STM-RT can identify not only isomers of mono-saccharides and disaccharides, but also various mono-saccharides from a data pool of eleven analytes. In addition, the binding affinity between recognition molecule and analyte was investigated by comparing with

  20. Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Widawsky, Jonathan R.

    In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine

  1. Vibrationally dependent electron-electron interactions in resonant electron transport through single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Erpenbeck, A.; Härtle, R.; Bockstedte, M.; Thoss, M.

    2016-03-01

    We investigate the role of electronic-vibrational coupling in resonant electron transport through single-molecule junctions, taking into account that the corresponding coupling strengths may depend on the charge and excitation state of the molecular bridge. Within an effective-model Hamiltonian approach for a molecule with multiple electronic states, this requires to extend the commonly used model and include vibrationally dependent electron-electron interaction. We use Born-Markov master equation methods and consider selected models to exemplify the effect of the additional interaction on the transport characteristics of a single-molecule junction. In particular, we show that it has a significant influence on local cooling and heating mechanisms, it may result in negative differential resistance, and it may cause pronounced asymmetries in the conductance map of a single-molecule junction.

  2. Single-molecule resolution of protein structure and interfacial dynamics on biomaterial surfaces

    PubMed Central

    McLoughlin, Sean Yu; Kastantin, Mark; Schwartz, Daniel K.; Kaar, Joel L.

    2013-01-01

    A method was developed to monitor dynamic changes in protein structure and interfacial behavior on surfaces by single-molecule Förster resonance energy transfer. This method entails the incorporation of unnatural amino acids to site-specifically label proteins with single-molecule Förster resonance energy transfer probes for high-throughput dynamic fluorescence tracking microscopy on surfaces. Structural changes in the enzyme organophosphorus hydrolase (OPH) were monitored upon adsorption to fused silica (FS) surfaces in the presence of BSA on a molecule-by-molecule basis. Analysis of >30,000 individual trajectories enabled the observation of heterogeneities in the kinetics of surface-induced OPH unfolding with unprecedented resolution. In particular, two distinct pathways were observed: a majority population (∼ 85%) unfolded with a characteristic time scale of 0.10 s, and the remainder unfolded more slowly with a time scale of 0.7 s. Importantly, even after unfolding, OPH readily desorbed from FS surfaces, challenging the common notion that surface-induced unfolding leads to irreversible protein binding. This suggests that protein fouling of surfaces is a highly dynamic process because of subtle differences in the adsorption/desorption rates of folded and unfolded species. Moreover, such observations imply that surfaces may act as a source of unfolded (i.e., aggregation-prone) protein back into solution. Continuing study of other proteins and surfaces will examine whether these conclusions are general or specific to OPH in contact with FS. Ultimately, this method, which is widely applicable to virtually any protein, provides the framework to develop surfaces and surface modifications with improved biocompatibility. PMID:24235137

  3. Single Molecule Spectroelectrochemistry of Interfacial Charge Transfer Dynamics In Hybrid Organic Solar Cell

    SciTech Connect

    Pan, Shanlin

    2014-11-16

    Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an

  4. Atomic-Scale Control of Electron Transport through Single Molecules

    NASA Astrophysics Data System (ADS)

    Wang, Y. F.; Kröger, J.; Berndt, R.; Vázquez, H.; Brandbyge, M.; Paulsson, M.

    2010-04-01

    Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of the surface electrode. Nonequilibrium Green’s function calculations reproduce the trend of the conductance and visualize the current flow through the junction, which is guided through molecule-electrode chemical bonds.

  5. Basic concepts of quantum interference and electron transport in single-molecule electronics.

    PubMed

    Lambert, C J

    2015-02-21

    This tutorial outlines the basic theoretical concepts and tools which underpin the fundamentals of phase-coherent electron transport through single molecules. The key quantity of interest is the transmission coefficient T(E), which yields the electrical conductance, current-voltage relations, the thermopower S and the thermoelectric figure of merit ZT of single-molecule devices. Since T(E) is strongly affected by quantum interference (QI), three manifestations of QI in single-molecules are discussed, namely Mach-Zehnder interferometry, Breit-Wigner resonances and Fano resonances. A simple MATLAB code is provided, which allows the novice reader to explore QI in multi-branched structures described by a tight-binding (Hückel) Hamiltonian. More generally, the strengths and limitations of materials-specific transport modelling based on density functional theory are discussed. PMID:25255961

  6. Break junction under electrochemical gating: testbed for single-molecule electronics.

    PubMed

    Huang, Cancan; Rudnev, Alexander V; Hong, Wenjing; Wandlowski, Thomas

    2015-02-21

    Molecular electronics aims to construct functional molecular devices at the single-molecule scale. One of the major challenges is to construct a single-molecule junction and to further manipulate the charge transport through the molecular junction. Break junction techniques, including STM break junctions and mechanically controllable break junctions are considered as testbed to investigate and control the charge transport on a single-molecule scale. Moreover, additional electrochemical gating provides a unique opportunity to manipulate the energy alignment and molecular redox processes for a single-molecule junction. In this review, we start from the technical aspects of the break junction technique, then discuss the molecular structure-conductance correlation derived from break junction studies, and, finally, emphasize electrochemical gating as a promising method for the functional molecular devices. PMID:25560965

  7. Molecular tips for scanning tunneling microscopy: intermolecular electron tunneling for single-molecule recognition and electronics.

    PubMed

    Nishino, Tomoaki

    2014-01-01

    This paper reviews the development of molecular tips for scanning tunneling microscopy (STM). Molecular tips offer many advantages: first is their ability to perform chemically selective imaging because of chemical interactions between the sample and the molecular tip, thus improving a major drawback of conventional STM. Rational design of the molecular tip allows sophisticated chemical recognition; e.g., chiral recognition and selective visualization of atomic defects in carbon nanotubes. Another advantage is that they provide a unique method to quantify electron transfer between single molecules. Understanding such electron transfer is mandatory for the realization of molecular electronics. PMID:24420248

  8. Single-molecule electronics: Cooling individual vibrational modes by the tunneling current

    NASA Astrophysics Data System (ADS)

    Lykkebo, Jacob; Romano, Giuseppe; Gagliardi, Alessio; Pecchia, Alessandro; Solomon, Gemma C.

    2016-03-01

    Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.

  9. Single-molecule electronics: Cooling individual vibrational modes by the tunneling current.

    PubMed

    Lykkebo, Jacob; Romano, Giuseppe; Gagliardi, Alessio; Pecchia, Alessandro; Solomon, Gemma C

    2016-03-21

    Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions. PMID:27004879

  10. Two-photon-induced hot-electron transfer to a single molecule in a scanning tunneling microscope

    SciTech Connect

    Wu, S. W.; Ho, W.

    2010-08-15

    The junction of a scanning tunneling microscope (STM) operating in the tunneling regime was irradiated with femtosecond laser pulses. A photoexcited hot electron in the STM tip resonantly tunnels into an excited state of a single molecule on the surface, converting it from the neutral to the anion. The electron-transfer rate depends quadratically on the incident laser power, suggesting a two-photon excitation process. This nonlinear optical process is further confirmed by the polarization measurement. Spatial dependence of the electron-transfer rate exhibits atomic-scale variations. A two-pulse correlation experiment reveals the ultrafast dynamic nature of photoinduced charging process in the STM junction. Results from these experiments are important for understanding photoinduced interfacial charge transfer in many nanoscale inorganic-organic structures.

  11. Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

    SciTech Connect

    Fratalocchi, A.; Ruocco, G.

    2011-03-11

    X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

  12. Photon counting imaging and centroiding with an electron-bombarded CCD using single molecule localisation software

    NASA Astrophysics Data System (ADS)

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-06-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times.

  13. Photon counting imaging and centroiding with an electron-bombarded CCD using single molecule localisation software

    PubMed Central

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-01-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times. PMID:27274604

  14. Role of solvents in the electronic transport properties of single-molecule junctions

    PubMed Central

    Luka-Guth, Katharina; Hambsch, Sebastian; Bloch, Andreas; Ehrenreich, Philipp; Briechle, Bernd Michael; Kilibarda, Filip; Sendler, Torsten; Sysoiev, Dmytro; Huhn, Thomas; Erbe, Artur

    2016-01-01

    Summary We report on an experimental study of the charge transport through tunnel gaps formed by adjustable gold electrodes immersed into different solvents that are commonly used in the field of molecular electronics (ethanol, toluene, mesitylene, 1,2,4-trichlorobenzene, isopropanol, toluene/tetrahydrofuran mixtures) for the study of single-molecule contacts of functional molecules. We present measurements of the conductance as a function of gap width, conductance histograms as well as current–voltage characteristics of narrow gaps and discuss them in terms of the Simmons model, which is the standard model for describing transport via tunnel barriers, and the resonant single-level model, often applied to single-molecule junctions. One of our conclusions is that stable junctions may form from solvents as well and that both conductance–distance traces and current–voltage characteristics have to be studied to distinguish between contacts of solvent molecules and of molecules under study. PMID:27547624

  15. Controlling electronic access to the spin excitations of a single molecule in a tunnel junction

    NASA Astrophysics Data System (ADS)

    Hirjibehedin, Cyrus F.; Warner, Ben; El Hallak, Fadi; Prueser, Henning; Ajibade, Afolabi; Gill, Tobias G.; Fisher, Andrew J.; Persson, Mats

    Spintronic phenomena can be utilized to create new devices with applications in data storage and sensing. Scaling these down to the single molecule level requires controlling the properties of the current-carrying orbitals to enable access to spin states through phenomena such as inelastic electron tunneling. Here we show that the spintronic properties of a tunnel junction containing a single molecule can be controlled by their coupling to the local environment. For tunneling through iron phthalocyanine (FePc) on an insulating copper nitride (Cu2N) monolayer above Cu(001), we find that spin transitions may be strongly excited depending on the binding site of the central Fe atom. Different interactions between the Fe and the underlying Cu or N atoms shift the Fe d-orbitals with respect to the Fermi energy, and control the relative strength of the spin excitations, an effect that can described in a simple co-tunneling model. This work demonstrates the importance of the atomic-scale environment in the development of single molecule spintronic devices.

  16. Research Update: Molecular electronics: The single-molecule switch and transistor

    SciTech Connect

    Sotthewes, Kai; Heimbuch, René Kumar, Avijit; Zandvliet, Harold J. W.; Geskin, Victor

    2014-01-01

    In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

  17. Nonlinear thermoelectric transport in single-molecule junctions: the effect of electron-phonon interactions.

    PubMed

    Zimbovskaya, Natalya A

    2016-07-27

    In this paper, we theoretically analyze steady-state thermoelectric transport through a single-molecule junction with a vibrating bridge. The thermally induced charge current in the system is explored using a nonequilibrium Green function formalism. We study the combined effects of Coulomb interactions between charge carriers on the bridge and electron-phonon interactions on the thermocurrent beyond the linear response regime. It is shown that electron-vibron interactions may significantly affect both the magnitude and the direction of the thermocurrent, and vibrational signatures may appear. PMID:27248442

  18. Single-Molecule Measurements of T4 Lysozyme using Carbon Nanotube Electronic Circuits

    NASA Astrophysics Data System (ADS)

    Sims, Patrick Craig

    Because of their unique electronic and chemical properties, single-walled carbon nanotubes (SWNTs) are attractive candidates for label-free, single-molecule sensing and detection applications. In this work, a field-effect transistor (FET) architecture comprised of an individual SWNT is used to transduce the conformational motion of a single T4 lysozyme protein, conjugated to the SWNT side wall, into a corresponding electrical current signal. The SWNTs are grown using chemical vapor deposition, and metal electrical contacts are formed using electron beam evaporation. Using N-(1-Pyrene)maleimide, the protein is conjugated to the SWNT side wall. After conjugation, the sensing area of the device is submerged in an electrolyte solution, and the source-drain current is measured while applying an electrolyte-gate. Analysis of the signal provided single-molecule resolution of the dynamical activity of lysozyme as it hydrolyzes macromolecular peptidoglycan, a component of bacterial cell walls. This analysis revealed seven different independent time scales that govern the activity of lysozyme, the pH dependence of these time scales, and a lower limit on the number rate-limiting steps in lysozyme's hinge opening and closing motions. Furthermore, the signals elucidated differences in how lysozyme traverses and catalyzes structurally varying peptidoglycan constructs.

  19. Single-molecule spectroscopy exposes hidden states in an enzymatic electron relay

    NASA Astrophysics Data System (ADS)

    Grossman, Iris; Yuval Aviram, Haim; Armony, Gad; Horovitz, Amnon; Hofmann, Hagen; Haran, Gilad; Fass, Deborah

    2015-10-01

    The ability to query enzyme molecules individually is transforming our view of catalytic mechanisms. Quiescin sulfhydryl oxidase (QSOX) is a multidomain catalyst of disulfide-bond formation that relays electrons from substrate cysteines through two redox-active sites to molecular oxygen. The chemical steps in electron transfer have been delineated, but the conformational changes accompanying these steps are poorly characterized. Here we use single-molecule Förster resonance energy transfer (smFRET) to probe QSOX conformation in resting and cycling enzyme populations. We report the discovery of unanticipated roles for conformational changes in QSOX beyond mediating electron transfer between redox-active sites. In particular, a state of the enzyme not previously postulated or experimentally detected is shown to gate, via a conformational transition, the entrance into a sub-cycle within an expanded QSOX kinetic scheme. By tightly constraining mechanistic models, smFRET data can reveal the coupling between conformational and chemical transitions in complex enzymatic cycles.

  20. Electron diffraction of CBr4 in superfluid helium droplets: A step towards single molecule diffraction

    NASA Astrophysics Data System (ADS)

    He, Yunteng; Zhang, Jie; Kong, Wei

    2016-07-01

    We demonstrate the practicality of electron diffraction of single molecules inside superfluid helium droplets using CBr4 as a testing case. By reducing the background from pure undoped droplets via multiple doping, with small corrections for dimers and trimers, clearly resolved diffraction rings of CBr4 similar to those of gas phase molecules can be observed. The experimental data from CBr4 doped droplets are in agreement with both theoretical calculations and with experimental results of gaseous species. The abundance of monomers and clusters in the droplet beam also qualitatively agrees with the Poisson statistics. Possible extensions of this approach to macromolecular ions will also be discussed. This result marks the first step in building a molecular goniometer using superfluid helium droplet cooling and field induced orientation. The superior cooling effect of helium droplets is ideal for field induced orientation, but the diffraction background from helium is a concern. This work addresses this background issue and identifies a possible solution. Accumulation of diffraction images only becomes meaningful when all images are produced from molecules oriented in the same direction, and hence a molecular goniometer is a crucial technology for serial diffraction of single molecules.

  1. Electron diffraction of CBr4 in superfluid helium droplets: A step towards single molecule diffraction.

    PubMed

    He, Yunteng; Zhang, Jie; Kong, Wei

    2016-07-21

    We demonstrate the practicality of electron diffraction of single molecules inside superfluid helium droplets using CBr4 as a testing case. By reducing the background from pure undoped droplets via multiple doping, with small corrections for dimers and trimers, clearly resolved diffraction rings of CBr4 similar to those of gas phase molecules can be observed. The experimental data from CBr4 doped droplets are in agreement with both theoretical calculations and with experimental results of gaseous species. The abundance of monomers and clusters in the droplet beam also qualitatively agrees with the Poisson statistics. Possible extensions of this approach to macromolecular ions will also be discussed. This result marks the first step in building a molecular goniometer using superfluid helium droplet cooling and field induced orientation. The superior cooling effect of helium droplets is ideal for field induced orientation, but the diffraction background from helium is a concern. This work addresses this background issue and identifies a possible solution. Accumulation of diffraction images only becomes meaningful when all images are produced from molecules oriented in the same direction, and hence a molecular goniometer is a crucial technology for serial diffraction of single molecules. PMID:27448887

  2. Nanopore integrated with Au clusters formed under electron beam irradiation for single molecule analysis

    NASA Astrophysics Data System (ADS)

    Choi, Seong Soo; Park, Myoung Jin; Han, Chul Hee; Kim, Sung In; Yoo, Jung Ho; Park, Kyung Jin; Park, Nam Kyou; Kim, Yong-Sang

    2016-02-01

    Recently the single molecules such as protein and deoxyribonucleic acid (DNA) have been successfully characterized using a solidstate nanopore with an electrical detection technique. However, the optical plasmonic nanopore has yet to be fabricated. The optical detection technique can be better utilized as next generation ultrafast geneome sequencing devices due to the possible utilization of the current optical technique for genome sequencing. In this report, we have investigated the Au nanopore formation under the electron beam irradiation on an Au aperture. The circular-type nanoopening with ~ 5 nm diameter on the diffused membrane is fabricated by using 2 keV electron beam irradiation by using field emission scanning electron microscopy (FESEM). We found the Au cluster on the periphery of the drilled aperture under a 2 keV electron beam irradiation. Immediately right after electron beam irradiation, no Au cluster and no Au crystal lattice structure on the diffused plane are observed. However, after the sample was kept for ~ 6 months under a room environment, the Au clusters are found on the diffused membrane and the Au crystal lattice structures on the diffused membrane are also found using high resolution transmission electron microscopy. These phenomena can be attributed to Ostwald ripening. In addition, the Au nano-hole on the 40 nm thick Au membrane was also drilled by using 200 keV scanning transmission electron microscopy.

  3. Electron Transport, Energy Transfer, and Optical Response in Single Molecule Junctions

    NASA Astrophysics Data System (ADS)

    White, Alexander James

    The last decade has seen incredible growth in the quality of experiments being done on single molecule junctions. Contemporary experimental measurements have expanded far beyond simple electron transport. Measurement of vibronic eects, quantum interference and decoherence eects, molecular optical response (Raman spectroscopy), and molecular spintronics are just some of the continuing areas of research in single molecule junctions. Experimental advancements demand advanced theoretical treatments, which can be used accurately within appropriate physical regimes, in order to understand measured phenomena and predict interesting directions for future study. In this dissertation we will study systems with strong intra-system interactions using a many-body states based approach. We will be focused on three related processes in molecular junctions: electron transport, electronic energy transfer, and molecular excitation. Inelastic electron transport in the regime of strong and nonlinear electron-vibration coupling within and outside of the Born-Oppenheimer regime will be investigated. To understand their appropriateness, we will compare simple semi-classical approximations in molecular redox junctions and electron-counting devices to fully quantum calculations based on many-body system states. The role of coherence and quantum interference in energy and electron transfer in molecular junctions is explored. Experiments that simultaneously measure surface enhanced Raman scattering and electron conduction have revealed a strong interaction between conducting electrons and molecular excitation. We investigate the role of the molecular response to a classical surface plasmon enhanced electric eld considering the back action of the oscillating molecular dipole. Raman scattering is quantum mechanical by nature and involves strong interaction between surface plasmons in the contacts and the molecular excitation. We develop a scheme for treating strong plasmon-molecular excitation

  4. Single-Molecule Electronic Measurements of the Dynamic Flexibility of Histone Deacetylases

    NASA Astrophysics Data System (ADS)

    Froberg, James; You, Seungyong; Yu, Junru; Haldar, Manas; Sedigh, Abbas; Mallik, Sanku; Srivastava, D. K.; Choi, Yongki

    Due to their involvement in epigenetic regulation, histone deacetylases (HDACs) have gained considerable interest in designing drugs for treatment of a variety of human diseases including cancers. Recently, we applied a label-free, electronic single-molecule nano-circuit technique to gain insight into the contribution of the dynamic flexibility in HDACs structure during the course of substrates/ ligands binding and catalysis. We observed that HDAC8 has two major (dynamically interconvertible) conformational states, ``ground (catalytically unfavorable)'' and ``transition (catalytically favorable)''. In addition, we found that its cognate substrates/ligands reciprocally catalyze the transition of the ground to the transition state conformation of HDAC8. Thus, we propose that both enzymes and their substrates/ligands serve as ``catalysts'' in facilitating the structural changes of each other and promoting the overall chemical transformation reaction. Such new information provides the potential for designing a new class of mechanism-based inhibitors and activators of HDAC8 for treating human diseases.

  5. A study of planar anchor groups for graphene-based single-molecule electronics

    SciTech Connect

    Bailey, Steven; Visontai, David; Lambert, Colin J.; Bryce, Martin R.; Frampton, Harry; Chappell, David

    2014-02-07

    To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for –OH and –CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains.

  6. Effects of electron-vibration coupling in transport through single molecules.

    PubMed

    Franke, Katharina J; Pascual, Jose Ignacio

    2012-10-01

    Using scanning tunneling spectroscopy, we study the transport of electrons through C(60) molecules on different metal surfaces. When electrons tunnel through a molecule, they may excite molecular vibrations. A fingerprint of these processes is a characteristic sub-structure in the differential conductance spectra of the molecular junction reflecting the onset of vibrational excitation. Although the intensity of these processes is generally weak, they become more important as the resonant character of the transport mechanism increases. The detection of single vibrational levels crucially depends on the energy level alignment and lifetimes of excited states. In the limit of large current densities, resonant electron-vibration coupling leads to an energy accumulation in the molecule, which eventually leads to its decomposition. With our experiments on C(60) we are able to depict a molecular scale picture of how electrons interact with the vibrational degrees of freedom of single molecules in different transport regimes. This understanding helps in the development of stable molecular devices, which may also carry a switchable functionality. PMID:22964796

  7. Single-molecule spectroscopy exposes hidden states in an enzymatic electron relay

    PubMed Central

    Grossman, Iris; Yuval Aviram, Haim; Armony, Gad; Horovitz, Amnon; Hofmann, Hagen; Haran, Gilad; Fass, Deborah

    2015-01-01

    The ability to query enzyme molecules individually is transforming our view of catalytic mechanisms. Quiescin sulfhydryl oxidase (QSOX) is a multidomain catalyst of disulfide-bond formation that relays electrons from substrate cysteines through two redox-active sites to molecular oxygen. The chemical steps in electron transfer have been delineated, but the conformational changes accompanying these steps are poorly characterized. Here we use single-molecule Förster resonance energy transfer (smFRET) to probe QSOX conformation in resting and cycling enzyme populations. We report the discovery of unanticipated roles for conformational changes in QSOX beyond mediating electron transfer between redox-active sites. In particular, a state of the enzyme not previously postulated or experimentally detected is shown to gate, via a conformational transition, the entrance into a sub-cycle within an expanded QSOX kinetic scheme. By tightly constraining mechanistic models, smFRET data can reveal the coupling between conformational and chemical transitions in complex enzymatic cycles. PMID:26468675

  8. How to probe transverse magnetic anisotropy of a single-molecule magnet by electronic transport?

    NASA Astrophysics Data System (ADS)

    Misiorny, M.; Burzuri, E.; Gaudenzi, R.; Park, K.; Leijnse, M.; Wegewijs, M.; Paaske, J.; Cornia, A.; van der Zant, H.

    We propose an approach for in-situ determination of the transverse magnetic anisotropy (TMA) of an individual molecule by electronic transport measurements, see Phys. Rev. B 91, 035442 (2015). We study a Fe4 single-molecule magnet (SMM) captured in a gateable junction, a unique tool for addressing the spin in different redox states of a molecule. We show that, due to mixing of the spin eigenstates of the SMM, the TMA significantly manifests itself in transport. We predict and experimentally observe the pronounced intensity modulation of the Coulomb peak amplitude with the magnetic field in the linear-response transport regime, from which the TMA parameter E can be estimated. Importantly, the method proposed here does not rely on the small induced tunnelling effects and, hence, works well at temperatures and electron tunnel broadenings by far exceeding the tunnel splittings and even E itself. We deduce that the TMA for a single Fe4 molecule captured in a junction is substantially larger than the bulk value. Work supported by the Polish Ministry of Science and Education as `Iuventus Plus' project (IP2014 030973) in years 2015-2016.

  9. Electron transport in endohedral metallofullerene Ce@C{sub 82} single-molecule transistors

    SciTech Connect

    Okamura, Naoya; Yoshida, Kenji; Sakata, Shuichi; Hirakawa, Kazuhiko

    2015-01-26

    We have investigated the electron transport in endohedral metallofullerene Ce@C{sub 82} single-molecule transistors (SMTs) together with that in reference C{sub 84} SMTs. The vibrational modes (bending and stretching) of the encapsulated single Ce atom in the C{sub 82} cage appear in Coulomb stability diagrams for the single-electron tunneling through Ce@C{sub 82} molecules, demonstrating the single-atom sensitivity of the transport measurements. When a bias voltage larger than 100 mV is applied across the source/drain electrodes, large hysteretic behavior is observed in the current-voltage (I-V) characteristics. At the same time, the pattern in the Coulomb stability diagram is changed. No such hysteretic behavior is observed in the I-V curves of hollow-cage C{sub 84} SMTs, even when the bias voltage exceeds 500 mV. This hysteretic change in the I-V characteristics is induced by a nanomechanical change in the configuration of the Ce@C{sub 82} molecule in the nanogap electrode due to the electric dipole that exists in Ce@C{sub 82}.

  10. Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

    PubMed Central

    2011-01-01

    Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

  11. Electrical properties and mechanical stability of anchoring groups for single-molecule electronics.

    PubMed

    Frisenda, Riccardo; Tarkuç, Simge; Galán, Elena; Perrin, Mickael L; Eelkema, Rienk; Grozema, Ferdinand C; van der Zant, Herre S J

    2015-01-01

    We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ) technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene) (OPE3), while having different aurophilic anchoring groups: thiol (SAc), methyl sulfide (SMe), pyridyl (Py) and amine (NH2). The focus of this paper is on the combined characterization of the electrical and mechanical properties determined by the anchoring groups. From conductance histograms we find that thiol anchored molecules provide the highest conductance; a single-level model fit to current-voltage characteristics suggests that SAc groups exhibit a higher electronic coupling to the electrodes, together with better level alignment than the other three groups. An analysis of the mechanical stability, recording the lifetime in a self-breaking method, shows that Py and SAc yield the most stable junctions while SMe form short-lived junctions. Density functional theory combined with non-equlibrium Green's function calculations help in elucidating the experimental findings. PMID:26425407

  12. Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

    PubMed Central

    Frisenda, Riccardo; Tarkuç, Simge; Galán, Elena; Perrin, Mickael L; Eelkema, Rienk; Grozema, Ferdinand C

    2015-01-01

    Summary We report on an experimental investigation of transport through single molecules, trapped between two gold nano-electrodes fabricated with the mechanically controlled break junction (MCBJ) technique. The four molecules studied share the same core structure, namely oligo(phenylene ethynylene) (OPE3), while having different aurophilic anchoring groups: thiol (SAc), methyl sulfide (SMe), pyridyl (Py) and amine (NH2). The focus of this paper is on the combined characterization of the electrical and mechanical properties determined by the anchoring groups. From conductance histograms we find that thiol anchored molecules provide the highest conductance; a single-level model fit to current–voltage characteristics suggests that SAc groups exhibit a higher electronic coupling to the electrodes, together with better level alignment than the other three groups. An analysis of the mechanical stability, recording the lifetime in a self-breaking method, shows that Py and SAc yield the most stable junctions while SMe form short-lived junctions. Density functional theory combined with non-equlibrium Green’s function calculations help in elucidating the experimental findings. PMID:26425407

  13. Manipulation and characterization of thin-film interfacial chemistry: Sol-gel deposition and single molecule tracking experiments

    NASA Astrophysics Data System (ADS)

    Barhoum, Moussa

    Single molecule trajectories of 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbo - cyanine perchlorate (DiI) fluorophores diffusing on planar supported 1,2-dimyristoyl-snglycero- 3-phosphocholine (DMPC) lipid bilayers imaged through total internal reflection fluorescence (TIRF) microscopy at different temperatures are investigated. The spatial resolution limit for detecting molecular motion is evaluated by characterizing the apparent motion which arises from the limited signal-to-noise ratio (S/N) of imaged and simulated stationary DiI molecules. Statistical criteria for reliably distinguishing molecular motion from stationary molecules using F-test statistics, including the computation of local signal-to-noise ratios are then established and used for reliably detecting subdiffraction motion of DiI molecules on DMPC. The same single molecule tracking concept is used in investigating the temperature dependence of subdiffraction diffusional confinement of single Rhodamine 6G molecules in polymer brushes of poly (N-isopropylacrylamide), pNIPAAm, above and below its lower critical solution temperature (LCST) of 32°C. Reliably distinguishing subdiffraction molecular motion from stationary events is crucial in validating the application of single molecule tracking experiment in probing nanometersized hydrophobic environments of polymer structure. A versatile and rapid sol-gel technique for the fabrication of high quality one-dimensional photonic bandgap materials was developed. Silica/titania multilayer materials are fabricated by a sol-gel chemistry route combined with dip-coating onto planar or curved substrate. A shock-cooling step immediately following the thin film heat-treatment process is introduced. The versatility of this sol-gel method is demonstrated by the fabrication of various Bragg stack-type materials with fine-tuned optical properties. Measured optical properties show good agreement with theoretical simulations confirming the high quality of these sol

  14. Dependence of magnetic field and electronic transport of Mn4 Single-molecule magnet in a Single-Electron Transistor

    NASA Astrophysics Data System (ADS)

    Rodriguez, Alvar; Singh, Simranjeet; Haque, Firoze; Del Barco, Enrique; Nguyen, Tu; Christou, George

    2012-02-01

    Dependence of magnetic field and electronic transport of Mn4 Single-molecule magnet in a Single-Electron Transistor A. Rodriguez, S. Singh, F. Haque and E. del Barco Department of Physics, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816 USA T. Nguyen and G. Christou Department of Chemistry, University of Florida, Gainesville, Florida 32611 USA Abstract We have performed single-electron transport measurements on a series of Mn-based low-nuclearity single-molecule magnets (SMM) observing Coulomb blockade. SMMs with well isolated and low ground spin states, i.e. S = 9/2 (Mn4) and S = 6 (Mn3) were chosen for these studies, such that the ground spin multiplet does not mix with levels of other excited spin states for the magnetic fields (H = 0-8 T) employed in the experiments. Different functionalization groups were employed to change the mechanical, geometrical and transport characteristics of the molecules when deposited from liquid solution on the transistors. Electromigration-broken three-terminal single-electron transistors were used. Results obtained at temperatures down to 240 mK and in the presence of high magnetic fields will be shown.

  15. LeRoy Apker Award Talk: Electronics at the Nanoscale: Graphene, Carbon Nanotubes, and Single-Molecule Devices

    NASA Astrophysics Data System (ADS)

    Datta, Sujit

    2009-03-01

    Low-dimensional nanostructures are emerging as model systems for fundamental studies of quantum transport, as well as promising candidates for novel post-silicon electronic devices incorporating quantum size effects. Key examples of these include few-layer graphene, carbon nanotubes, polymer nanofibers, and even single molecules. In this talk, I will summarize my work combining experimental and computational tools to study, control, and apply molecular nanomaterials of low dimensionality -- using scanning probe microscopy techniques to study electronic phenomena in few-layer graphene and carbon nanotubes, as well as to elucidate the structure of biochemically-functionalized carbon nanotubes; using computer simulations to investigate key electronic properties of single-molecule transistors; and demonstrating a straightforward chemical technique by which samples of few-layer graphene can be etched along their crystallographic directions, potentially enabling the creation of a variety of new graphene-based nanostructures.

  16. Fine-tuning of single-molecule conductance by tweaking both electronic structure and conformation of side substituents.

    PubMed

    Aragonès, Albert C; Darwish, Nadim; Im, JongOne; Lim, Boram; Choi, Jeongae; Koo, Sangho; Díez-Pérez, Ismael

    2015-05-18

    Herein, we describe a method to fine-tune the conductivity of single-molecule wires by employing a combination of chemical composition and geometrical modifications of multiple phenyl side groups as conductance modulators embedded along the main axis of the electronic pathway. We have measured the single-molecule conductivity of a novel series of phenyl-substituted carotenoid wires whose conductivity can be tuned with high precision over an order of magnitude range by modulating both the electron-donating character of the phenyl substituent and its dihedral angle. It is demonstrated that the electronic communication between the phenyl side groups and the molecular wire is maximized when the phenyl groups are twisted closer to the plane of the conjugated molecular wire. These findings can be refined to a general technique for precisely tuning the conductivity of molecular wires. PMID:25847688

  17. Nature of Asymmetry in the Vibrational Line Shape of Single-Molecule Inelastic Electron Tunneling Spectroscopy with the STM

    NASA Astrophysics Data System (ADS)

    Xu, Chen; Chiang, Chi-lun; Han, Zhumin; Ho, W.

    2016-04-01

    Single molecule vibrational spectroscopy and microscopy was demonstrated in 1998 by inelastic electron tunneling with the scanning tunneling microscope. To date, the discussion of its application has mainly focused on the spatial resolution and the spectral energy and intensity. Here we report on the vibrational line shape for a single carbon monoxide molecule that qualitatively exhibits inversion symmetry when it is transferred from the surface to the tip. The dependence of the line shape on the molecule's asymmetric couplings in the tunnel junction can be understood from theoretical simulation and further validates the mechanisms of inelastic electron tunneling.

  18. Nature of Asymmetry in the Vibrational Line Shape of Single-Molecule Inelastic Electron Tunneling Spectroscopy with the STM.

    PubMed

    Xu, Chen; Chiang, Chi-Lun; Han, Zhumin; Ho, W

    2016-04-22

    Single molecule vibrational spectroscopy and microscopy was demonstrated in 1998 by inelastic electron tunneling with the scanning tunneling microscope. To date, the discussion of its application has mainly focused on the spatial resolution and the spectral energy and intensity. Here we report on the vibrational line shape for a single carbon monoxide molecule that qualitatively exhibits inversion symmetry when it is transferred from the surface to the tip. The dependence of the line shape on the molecule's asymmetric couplings in the tunnel junction can be understood from theoretical simulation and further validates the mechanisms of inelastic electron tunneling. PMID:27152811

  19. Towards single molecule switches.

    PubMed

    Zhang, Jia Lin; Zhong, Jian Qiang; Lin, Jia Dan; Hu, Wen Ping; Wu, Kai; Xu, Guo Qin; Wee, Andrew T S; Chen, Wei

    2015-05-21

    The concept of using single molecules as key building blocks for logic gates, diodes and transistors to perform basic functions of digital electronic devices at the molecular scale has been explored over the past decades. However, in addition to mimicking the basic functions of current silicon devices, molecules often possess unique properties that have no parallel in conventional materials and promise new hybrid devices with novel functions that cannot be achieved with equivalent solid-state devices. The most appealing example is the molecular switch. Over the past decade, molecular switches on surfaces have been intensely investigated. A variety of external stimuli such as light, electric field, temperature, tunneling electrons and even chemical stimulus have been used to activate these molecular switches between bistable or even multiple states by manipulating molecular conformations, dipole orientations, spin states, charge states and even chemical bond formation. The switching event can occur either on surfaces or in break junctions. The aim of this review is to highlight recent advances in molecular switches triggered by various external stimuli, as investigated by low-temperature scanning tunneling microscopy (LT-STM) and the break junction technique. We begin by presenting the molecular switches triggered by various external stimuli that do not provide single molecule selectivity, referred to as non-selective switching. Special focus is then given to selective single molecule switching realized using the LT-STM tip on surfaces. Single molecule switches operated by different mechanisms are reviewed and discussed. Finally, molecular switches embedded in self-assembled monolayers (SAMs) and single molecule junctions are addressed. PMID:25757483

  20. Single-molecule bioelectronics.

    PubMed

    Rosenstein, Jacob K; Lemay, Serge G; Shepard, Kenneth L

    2015-01-01

    Experimental techniques that interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. In this study, we review several technologies that can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  1. Single-Molecule Bioelectronics

    PubMed Central

    Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

    2014-01-01

    Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  2. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array.

    PubMed

    Fuller, Carl W; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J; Kasianowicz, John J; Davis, Randy; Roever, Stefan; Church, George M; Ju, Jingyue

    2016-05-10

    DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

  3. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

    PubMed Central

    Fuller, Carl W.; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P. Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T.; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J.; Kasianowicz, John J.; Davis, Randy; Roever, Stefan; Church, George M.; Ju, Jingyue

    2016-01-01

    DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

  4. Density functional theory based direct comparison of coherent tunneling and electron hopping in redox-active single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Kastlunger, Georg; Stadler, Robert

    2015-03-01

    To define the conductance of single-molecule junctions with a redox functionality in an electrochemical cell, two conceptually different electron transport mechanisms, namely, coherent tunneling and vibrationally induced hopping, compete with each other, where implicit parameters of the setup such as the length of the molecule and the applied gate voltage decide which mechanism is the dominant one. Although coherent tunneling is most efficiently described within Landauer theory and the common theoretical treatment of electron hopping is based on Marcus theory, both theories are adequate for the processes they describe without introducing accuracy-limiting approximations. For a direct comparison, however, it has to be ensured that the crucial quantities obtained from electronic structure calculations, i.e., the transmission function T (E ) in Landauer theory and the transfer integral V , the reorganization energy λ , and the driving force Δ G0 in Marcus theory, are derived from similar grounds, as pointed out by Nitzan and coworkers in a series of publications. In this paper our framework is a single-particle picture, for which we perform density functional theory calculations for the conductance corresponding to both transport mechanisms for junctions with the central molecule containing one, two, or three Ruthenium centers, from which we extrapolate our results in order to define the critical length of the transition point of the two regimes which we identify at 5.76nm for this type of molecular wire. We also discuss trends in the dependence on an electrochemically induced gate potential.

  5. Site-dependent electronic structures of a single molecule on a metal surface studied by scanning tunneling microscopy and spectroscopy

    NASA Astrophysics Data System (ADS)

    Katano, Satoshi; Hori, Masafumi; Kim, Yousoo; Kawai, Maki

    2014-10-01

    Single-molecule observation of the electronic structures of para-cyanobenzoate (pCB) adsorbed on Cu(1 1 0) has been performed using scanning tunneling microscopy (STM) and spectroscopy (STS). We found that pCB has two types of the adsorption site on Cu(1 1 0); i.e., two oxygen atoms of pCB are bridged between adjacent Cu atoms at the short- or long-bridge sites. STS and STS mapping revealed that the pCB adsorbed at the short-bridge site has a resonant peak at 2.0 V above the Fermi level, which is assigned to the lowest unoccupied molecular orbital (LUMO) of pCB. However, the LUMO state is shifted toward lower voltage (1.2 V) when the pCB molecule is adsorbed at the long-bridge site. The energy levels of the LUMO state, depending on the adsorption site of pCB, can thus be ascribed to the degree of the electronic interaction between pCB and the Cu substrate. The site transformation of pCB induced by the injection of tunneling electrons from the STM tip has also been presented.

  6. Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.

    PubMed

    Nakamura, Eiichi

    2013-01-01

    "The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. PMID:23280645

  7. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  8. Electron and heat transport in porphyrin-based single-molecule transistors with electro-burnt graphene electrodes

    PubMed Central

    Sangtarash, Sara

    2015-01-01

    Summary We have studied the charge and thermal transport properties of a porphyrin-based single-molecule transistor with electro-burnt graphene electrodes (EBG) using the nonequilibrium Green’s function method and density functional theory. The porphyrin-based molecule is bound to the EBG electrodes by planar aromatic anchor groups. Due to the efficient π–π overlap between the anchor groups and graphene and the location of frontier orbitals relative to the EBG Fermi energy, we predict HOMO-dominated transport. An on–off ratio as high as 150 is predicted for the device, which could be utilized with small gate voltages in the range of ±0.1 V. A positive thermopower of +280 μV/K is predicted for the device at the theoretical Fermi energy. The sign of the thermopower could be changed by tuning the Fermi energy. By gating the junction and changing the Fermi energy by +10 meV, this can be further enhanced to +475 μV/K. Although the electrodes and molecule are symmetric, the junction itself can be asymmetric due to different binding configurations at the electrodes. This can lead to rectification in the current–voltage characteristic of the junction. PMID:26199845

  9. Electron and heat transport in porphyrin-based single-molecule transistors with electro-burnt graphene electrodes.

    PubMed

    Sadeghi, Hatef; Sangtarash, Sara; Lambert, Colin J

    2015-01-01

    We have studied the charge and thermal transport properties of a porphyrin-based single-molecule transistor with electro-burnt graphene electrodes (EBG) using the nonequilibrium Green's function method and density functional theory. The porphyrin-based molecule is bound to the EBG electrodes by planar aromatic anchor groups. Due to the efficient π-π overlap between the anchor groups and graphene and the location of frontier orbitals relative to the EBG Fermi energy, we predict HOMO-dominated transport. An on-off ratio as high as 150 is predicted for the device, which could be utilized with small gate voltages in the range of ±0.1 V. A positive thermopower of +280 μV/K is predicted for the device at the theoretical Fermi energy. The sign of the thermopower could be changed by tuning the Fermi energy. By gating the junction and changing the Fermi energy by +10 meV, this can be further enhanced to +475 μV/K. Although the electrodes and molecule are symmetric, the junction itself can be asymmetric due to different binding configurations at the electrodes. This can lead to rectification in the current-voltage characteristic of the junction. PMID:26199845

  10. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  11. Single Molecule Transcription Elongation

    PubMed Central

    Galburt, Eric A.; Grill, Stephan W.; Bustamante, Carlos

    2009-01-01

    Single molecule optical trapping assays have now been applied to a great number of macromolecular systems including DNA, RNA, cargo motors, restriction enzymes, DNA helicases, chromosome remodelers, DNA polymerases and both viral and bacterial RNA polymerases. The advantages of the technique are the ability to observe dynamic, unsynchronized molecular processes, to determine the distributions of experimental quantities and to apply force to the system while monitoring the response over time. Here, we describe the application of these powerful techniques to study the dynamics of transcription elongation by RNA polymerase II from Saccharomyces cerevisiae. PMID:19426807

  12. Resolving metal-molecule interfaces at single-molecule junctions

    PubMed Central

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-01-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT. PMID:27221947

  13. Resolving metal-molecule interfaces at single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-05-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT.

  14. Electronic transport, transition-voltage spectroscopy, and the Fano effect in single molecule junctions composed of a biphenyl molecule attached to metallic and semiconducting carbon nanotube electrodes.

    PubMed

    Brito da Silva Júnior, Carlos Alberto; Leal, José Fernando Pereira; Aleixo, Vicente Ferrer Pureza; Pinheiro, Felipe A; Del Nero, Jordan

    2014-09-28

    We have investigated electronic transport in a single-molecule junction composed of a biphenyl molecule attached to a p-doped semiconductor and metallic carbon nanotube leads. We find that the current-voltage characteristics are asymmetric as a result of the different electronic natures of the right and left leads, which are metallic and semiconducting, respectively. We provide an analysis of transition voltage spectroscopy in such a system by means of both Fowler-Nordheim and Lauritsen-Millikan plots; this analysis allows one to identify the positions of resonances and the regions where the negative differential conductance occurs. We show that transmittance curves are well described by the Fano lineshape, for both direct and reverse bias, demonstrating that the frontier molecular orbitals are effectively involved in the transport process. This result gives support to the interpretation of transition voltage spectroscopy based on the coherent transport model. PMID:25109887

  15. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  16. Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality

    SciTech Connect

    Brito Silva, C. A. Jr.; Granhen, E. R.; Silva, S. J. S. da; Leal, J. F. P.; Del Nero, J.; Pinheiro, F. A.

    2010-08-15

    We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

  17. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  18. Theory of plasmon enhanced interfacial electron transfer.

    PubMed

    Wang, Luxia; May, Volkhard

    2015-04-10

    A particular attempt to improve the efficiency of a dye sensitized solar cell is it's decoration with metal nano-particles (MNP). The MNP-plasmon induced enhancement of the local field enlarges the photoexcitation of the dyes and a subsequent improvement of the charge separation efficiency may result. In a recent work (2014 J. Phys. Chem. C 118 2812) we presented a theory of plasmon enhanced interfacial electron transfer for perylene attached to a TiO2 surface and placed in the proximity of a spherical MNP. These earlier studies are generalized here to the coupling of to up to four MNPs and to the use of somewhat altered molecular parameters. If the MNPs are placed close to each other strong hybridization of plasmon excitations appears and a broad resonance to which molecular excitations are coupled is formed. To investigate this situation the whole charge injection dynamics is described in the framework of the density matrix theory. The approach accounts for optical excitation of the dye coupled to the MNPs and considers subsequent electron injection into the rutile TiO2-cluster. Using a tight-binding model for the TiO2-system with about 10(5) atoms the electron motion in the cluster is described. We again consider short optical excitation which causes an intermediate steady state with a time-independent overall probability to have the electron injected into the cluster. This probability is used to introduce an enhancement factor which rates the influence of the MNP. Values larger than 500 are obtained. PMID:25764984

  19. Theory of plasmon enhanced interfacial electron transfer

    NASA Astrophysics Data System (ADS)

    Wang, Luxia; May, Volkhard

    2015-04-01

    A particular attempt to improve the efficiency of a dye sensitized solar cell is it's decoration with metal nano-particles (MNP). The MNP-plasmon induced enhancement of the local field enlarges the photoexcitation of the dyes and a subsequent improvement of the charge separation efficiency may result. In a recent work (2014 J. Phys. Chem. C 118 2812) we presented a theory of plasmon enhanced interfacial electron transfer for perylene attached to a TiO2 surface and placed in the proximity of a spherical MNP. These earlier studies are generalized here to the coupling of to up to four MNPs and to the use of somewhat altered molecular parameters. If the MNPs are placed close to each other strong hybridization of plasmon excitations appears and a broad resonance to which molecular excitations are coupled is formed. To investigate this situation the whole charge injection dynamics is described in the framework of the density matrix theory. The approach accounts for optical excitation of the dye coupled to the MNPs and considers subsequent electron injection into the rutile TiO2-cluster. Using a tight-binding model for the TiO2-system with about 105 atoms the electron motion in the cluster is described. We again consider short optical excitation which causes an intermediate steady state with a time-independent overall probability to have the electron injected into the cluster. This probability is used to introduce an enhancement factor which rates the influence of the MNP. Values larger than 500 are obtained.

  20. Stereoelectronic switching in single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Su, Timothy A.; Li, Haixing; Steigerwald, Michael L.; Venkataraman, Latha; Nuckolls, Colin

    2015-03-01

    A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur-methylene σ bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.

  1. Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies

    PubMed Central

    Cattoni, Diego I.; Thakur, Shreyasi; Godefroy, Cedric; Le Gall, Antoine; Lai-Kee-Him, Josephine; Milhiet, Pierre-Emmanuel; Bron, Patrick; Nöllmann, Marcelo

    2014-01-01

    SpoIIIE/FtsK are a family of ring-shaped, membrane-anchored, ATP-fuelled motors required to segregate DNA across bacterial membranes. This process is directional and requires that SpoIIIE/FtsK recognize highly skewed octameric sequences (SRS/KOPS for SpoIIIE/FtsK) distributed along the chromosome. Two models have been proposed to explain the mechanism by which SpoIIIE/FtsK interact with DNA. The loading model proposes that SpoIIIE/FtsK oligomerize exclusively on SpoIIIE recognition sequence/orienting polar sequences (SRS/KOPS) to accomplish directional DNA translocation, whereas the target search and activation mechanism proposes that pre-assembled SpoIIIE/FtsK hexamers bind to non-specific DNA, reach SRS/KOPS by diffusion/3d hopping and activate at SRS/KOPS. Here, we employ single-molecule total internal reflection imaging, atomic force and electron microscopies and ensemble biochemical methods to test these predictions and obtain further insight into the SpoIIIE–DNA mechanism of interaction. First, we find that SpoIIIE binds DNA as a homo-hexamer with neither ATP binding nor hydrolysis affecting the binding mechanism or affinity. Second, we show that hexameric SpoIIIE directly binds to double-stranded DNA without requiring the presence of SRS or free DNA ends. Finally, we find that SpoIIIE hexamers can show open and closed conformations in solution, with open-ring conformations most likely resembling a state poised to load to non-specific, double-stranded DNA. These results suggest how SpoIIIE and related ring-shaped motors may be split open to bind topologically closed DNA. PMID:24297254

  2. Photon and electron stimulated surface dynamics of single molecules. Final report on D.O.E. No. DE-FG0295ER14563

    SciTech Connect

    Harrison, Ian

    2001-05-01

    The initial goal of this work was to build up an entirely new low-temperature scanning tunneling microscopy (STM) and ultrahigh vacuum system to examine the electron- and photon-induced chemistry of single molecules at low surface temperatures where thermal diffusion would be quenched. The photochemistry of methyl bromide on Pt(111) was first examined at 90 K using liquid nitrogen cooling. Br atoms were quite mobile even at 90 K, and were only visible by STM when coalesced along Pt step edges or in Br islands structures. The 193 nm photofragmentation of methyl bromide efficiently created monovacancies in the substrate at 90 K. It was found that at elevated temperatures there is considerable restructuring and reactive attack of the Pt surface by halogens, but for traditional, lower temperature studies of alkyl radicals prepared by thermal dissociative adsorption of alkyl iodides there is probably no problem with adsorbing I generating monovacancies on the surface. The dynamics of the ho t Br atoms formed by dissociative adsorption of Br{sub 2} was also examined. It was discovered that hot Br atoms from Br{sub 2} dissociative adsorption travel farther than hot O atoms from O{sub 2} dissociative adsorption; hot atom motion from different dissociative adsorption systems had not previously been compared for the same metal substrate. The experimental results strengthened the theoretical case that corrugation of the adsorbate/substrate potential is the key issue in determining hot atom travel. In addition, the data provided strong evidence for the transient existence of a weakly adsorbed and mobile Br{sub 2} precursor to dissociative adsorption. Some experiments imaging individual molecules at 15 K were also conducted.

  3. Combining single-molecule manipulation and single-molecule detection.

    PubMed

    Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

    2014-10-01

    Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. PMID:25255052

  4. Electrical, Mechanical and Thermal Properties of Single Molecules

    SciTech Connect

    Tao, Nongjian

    2014-08-20

    The specific aims of the prior DOE grant are to determine the stability of a single molecule bound to two electrodes, study local heating in single molecule junctions due to electron-phonon and electron-electron interactions, measure electron-phonon interactions in single molecule wires; and explore piezoelectric properties of single molecules. We have completed all the major tasks, and also expanded naturally the scope of the project to address several other critical issues in single molecule properties, developed new experimental capabilities, and observed a number of unexpected phenomena. We summarized here some of the findings that are most relevant to the present renewal proposal. More details can be found in the publications resulted from this grant and annual progress reports.

  5. Nanochannel Based Single Molecule Recycling

    PubMed Central

    Lesoine, John F.; Venkataraman, Prahnesh A.; Maloney, Peter C.; Dumont, Mark

    2012-01-01

    We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering. PMID:22662745

  6. Interfacial electronic effects control the reaction selectivity of platinum catalysts.

    PubMed

    Chen, Guangxu; Xu, Chaofa; Huang, Xiaoqing; Ye, Jinyu; Gu, Lin; Li, Gang; Tang, Zichao; Wu, Binghui; Yang, Huayan; Zhao, Zipeng; Zhou, Zhiyou; Fu, Gang; Zheng, Nanfeng

    2016-05-01

    Tuning the electronic structure of heterogeneous metal catalysts has emerged as an effective strategy to optimize their catalytic activities. By preparing ethylenediamine-coated ultrathin platinum nanowires as a model catalyst, here we demonstrate an interfacial electronic effect induced by simple organic modifications to control the selectivity of metal nanocatalysts during catalytic hydrogenation. This we apply to produce thermodynamically unfavourable but industrially important compounds, with ultrathin platinum nanowires exhibiting an unexpectedly high selectivity for the production of N-hydroxylanilines, through the partial hydrogenation of nitroaromatics. Mechanistic studies reveal that the electron donation from ethylenediamine makes the surface of platinum nanowires highly electron rich. During catalysis, such an interfacial electronic effect makes the catalytic surface favour the adsorption of electron-deficient reactants over electron-rich substrates (that is, N-hydroxylanilines), thus preventing full hydrogenation. More importantly, this interfacial electronic effect, achieved through simple organic modifications, may now be used for the optimization of commercial platinum catalysts. PMID:26808458

  7. Interfacial electronic effects control the reaction selectivity of platinum catalysts

    NASA Astrophysics Data System (ADS)

    Chen, Guangxu; Xu, Chaofa; Huang, Xiaoqing; Ye, Jinyu; Gu, Lin; Li, Gang; Tang, Zichao; Wu, Binghui; Yang, Huayan; Zhao, Zipeng; Zhou, Zhiyou; Fu, Gang; Zheng, Nanfeng

    2016-05-01

    Tuning the electronic structure of heterogeneous metal catalysts has emerged as an effective strategy to optimize their catalytic activities. By preparing ethylenediamine-coated ultrathin platinum nanowires as a model catalyst, here we demonstrate an interfacial electronic effect induced by simple organic modifications to control the selectivity of metal nanocatalysts during catalytic hydrogenation. This we apply to produce thermodynamically unfavourable but industrially important compounds, with ultrathin platinum nanowires exhibiting an unexpectedly high selectivity for the production of N-hydroxylanilines, through the partial hydrogenation of nitroaromatics. Mechanistic studies reveal that the electron donation from ethylenediamine makes the surface of platinum nanowires highly electron rich. During catalysis, such an interfacial electronic effect makes the catalytic surface favour the adsorption of electron-deficient reactants over electron-rich substrates (that is, N-hydroxylanilines), thus preventing full hydrogenation. More importantly, this interfacial electronic effect, achieved through simple organic modifications, may now be used for the optimization of commercial platinum catalysts.

  8. Single-Molecule DNA Analysis

    NASA Astrophysics Data System (ADS)

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

    The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

  9. Nanodevices for Single Molecule Studies

    NASA Astrophysics Data System (ADS)

    Craighead, H. G.; Stavis, S. M.; Samiee, K. T.

    During the last two decades, biotechnology research has resulted in progress in fields as diverse as the life sciences, agriculture and healthcare. While existing technology enables the analysis of a variety of biological systems, new tools are needed for increasing the efficiency of current methods, and for developing new ones altogether. Interest has grown in single molecule analysis for these reasons.

  10. Manipulating transport through a single-molecule junction

    SciTech Connect

    Sotthewes, Kai; Heimbuch, René; Zandvliet, Harold J. W.

    2013-12-07

    Molecular Electronics deals with the realization of elementary electronic devices that rely on a single molecule. For electronic applications, the most important property of a single molecule is its conductance. Here we show how the conductance of a single octanethiol molecule can be measured and manipulated by varying the contact's interspace. This mechanical gating of the single molecule junction leads to a variation of the conductance that can be understood in terms of a tunable image charge effect. The image charge effect increases with a decrease of the contact's interspace due to a reduction of the effective potential barrier height of 1.5 meV/pm.

  11. The symmetry of single-molecule conduction.

    PubMed

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

    2006-11-14

    We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research. PMID:17115774

  12. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  13. Electric field controlled magnetic anisotropy in a single molecule.

    PubMed

    Zyazin, Alexander S; van den Berg, Johan W G; Osorio, Edgar A; van der Zant, Herre S J; Konstantinidis, Nikolaos P; Leijnse, Martin; Wegewijs, Maarten R; May, Falk; Hofstetter, Walter; Danieli, Chiara; Cornia, Andrea

    2010-09-01

    We have measured quantum transport through an individual Fe(4) single-molecule magnet embedded in a three-terminal device geometry. The characteristic zero-field splittings of adjacent charge states and their magnetic field evolution are observed in inelastic tunneling spectroscopy. We demonstrate that the molecule retains its magnetic properties and, moreover, that the magnetic anisotropy is significantly enhanced by reversible electron addition/subtraction controlled with the gate voltage. Single-molecule magnetism can thus be electrically controlled. PMID:20687519

  14. Electric Field Controlled Magnetic Anisotropy in a Single Molecule

    NASA Astrophysics Data System (ADS)

    Zyazin, Alexander S.; van den Berg, Johan W. G.; Osorio, Edgar A.; van der Zant, Herre S. J.; Konstantinidis, Nikolaos P.; Leijnse, Martin; Wegewijs, Maarten R.; May, Falk; Hofstetter, Walter; Danieli, Chiara; Cornia, Andrea

    2010-09-01

    We have measured quantum transport through an individual Fe$_4$ single-molecule magnet embedded in a three-terminal device geometry. The characteristic zero-field splittings of adjacent charge states and their magnetic field evolution are observed in inelastic tunneling spectroscopy. We demonstrate that the molecule retains its magnetic properties, and moreover, that the magnetic anisotropy is significantly enhanced by reversible electron addition / subtraction controlled with the gate voltage. Single-molecule magnetism can thus be electrically controlled.

  15. Mechanical studies on single molecules: general considerations

    NASA Astrophysics Data System (ADS)

    Bensimon, David; Croquette, Vincent

    2015-10-01

    The following sections are included: * Elements of molecular biology * Advantages and drawbacks of single molecule studies * Order of magnitude of the relevant parameters at the single molecule level * Single molecule manipulation techniques * Comparison of the different techniques * DNA mechanical properties * Conclusion * Bibliography

  16. Electrochemical detection of single molecules.

    PubMed

    Fan, F R; Bard, A J

    1995-02-10

    The electrochemical behavior of a single molecule can be observed by trapping a small volume of a dilute solution of the electroactive species between an ultramicroelectrode tip with a diameter of approximately 15 nanometers and a conductive substrate. A scanning electrochemical microscope was used to adjust the tip-substrate distance ( approximately 10 nanometers), and the oxidation of [(trimethylammonio)methyl] ferrocene (Cp(2)FeTMA(+)) to Cp(2)FeTMA(2+) was carried out. The response was stochastic, and anodic current peaks were observed as the molecule moved into and out of the electrode-substrate gap. Similar experiments were performed with a solution containing two redox species, ferrocene carboxylate (Cp(2)FeCOO(-)) and Os(bpy)(3)(2+) (bpy is 2,2'-bipyridyl). PMID:17813918

  17. Cobalt single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Yang, En-Che; Hendrickson, David N.; Wernsdorfer, Wolfgang; Nakano, Motohiro; Zakharov, Lev N.; Sommer, Roger D.; Rheingold, Arnold L.; Ledezma-Gairaud, Marisol; Christou, George

    2002-05-01

    A cobalt molecule that functions as a single-molecule magnet, [Co4(hmp)4(MeOH)4Cl4], where hmp- is the anion of hydroxymethylpyridine, is reported. The core of the molecule consists of four Co(II) cations and four hmp- oxygen atom ions at the corners of a cube. Variable-field and variable-temperature magnetization data have been analyzed to establish that the molecule has a S=6 ground state with considerable negative magnetoanisotropy. Single-ion zero-field interactions (DSz2) at each cobalt ion are the origin of the negative magnetoanisotropy. A single crystal of the compound was studied by means of a micro-superconducting quantum interference device magnetometer in the range of 0.040-1.0 K. Hysteresis was found in the magnetization versus magnetic field response of this single crystal.

  18. Room temperature single molecule microscopes

    SciTech Connect

    Ambrose, W.P.; Goodwin, P.M.; Enderlein, G.; Semin, D.J.; Keller, R.A.

    1997-12-31

    We have developed three capabilities to image the locations of and interrogate immobilized single fluorescent molecules: near-field scanning optical, confocal scanning optical, and wide-field epi-fluorescence microscopy. Each microscopy has its own advantages. Near-field illumination can beat the diffraction limit. Confocal microscopy has high brightness and temporal resolution. Wide-field has the quickest (parallel) imaging capability. With confocal microscopy, we have verified that single fluorescent spots in our images are due to single molecules by observing photon antibunching. Using all three microscopies, we have observed that xanthene molecules dispersed on dry silica curiously exhibit intensity fluctuations on millisecond to minute time scales. We are exploring the connection between the intensity fluctuations and fluctuations in individual photophysical parameters. The fluorescence lifetimes of Rhodamine 6G on silica fluctuate. The complex nature of the intensity and lifetime fluctuations is consistent with a mechanism that perturbs more than one photophysical parameter.

  19. A 3-terminal single molecule nanoscale amperometer

    NASA Astrophysics Data System (ADS)

    Hliwa, M.; Ami, S.; Joachim, C.

    2006-07-01

    A 3-terminal single molecule transducer is presented which is able to measure tunnel current intensities. The conformation of a pyrene-phenyl molecule is changed under an intramolecular inelastic current effect. This conformation change is detected by a third lateral electrode interacting also with the molecule. The full multi-channel electronic scattering matrix of the device is calculated taking into account the chemisorption of the molecule at one end and the details mechanics of the conformation change of this molecule. A semi-classical model is used to describe the intramolecular transduction effect between the electrons transferred through the molecule and its conformation change. It results a linear transduction curve between the input and the detection currents of the device for a range of tunnel current of interest for mono-molecular electronics.

  20. Impact of Anchoring Groups on Ballistic Transport: Single Molecule vs Monolayer Junctions

    PubMed Central

    2015-01-01

    Tuning the transport properties of molecular junctions by chemically modifying the molecular structure is one of the key challenges for advancing the field of molecular electronics. In the present contribution, we investigate current–voltage characteristics of differently linked metal–molecule–metal systems that comprise either a single molecule or a molecular assembly. This is achieved by employing density functional theory in conjunction with a Green’s function approach. We show that the conductance of a molecular system with a specific anchoring group is fundamentally different depending on whether a single molecule or a continuous monolayer forms the junction. This is a consequence of collective electrostatic effects that arise from dipolar elements contained in the monolayer and from interfacial charge rearrangements. As a consequence of these collective effects, the “ideal” choice for an anchoring group is clearly different for monolayer and single molecule devices. A particularly striking effect is observed for pyridine-docked systems. These are subject to Fermi-level pinning at high molecular packing densities, causing an abrupt increase of the junction current already at small voltages. PMID:26401191

  1. Single-molecule imaging by optical absorption

    NASA Astrophysics Data System (ADS)

    Celebrano, Michele; Kukura, Philipp; Renn, Alois; Sandoghdar, Vahid

    2011-02-01

    To date, optical studies of single molecules at room temperature have relied on the use of materials with high fluorescence quantum yield combined with efficient spectral rejection of background light. To extend single-molecule studies to a much larger pallet of substances that absorb but do not fluoresce, scientists have explored the photothermal effect, interferometry, direct attenuation and stimulated emission. Indeed, very recently, three groups have succeeded in achieving single-molecule sensitivity in absorption. Here, we apply modulation-free transmission measurements known from absorption spectrometers to image single molecules under ambient conditions both in the emissive and strongly quenched states. We arrive at quantitative values for the absorption cross-section of single molecules at different wavelengths and thereby set the ground for single-molecule absorption spectroscopy. Our work has important implications for research ranging from absorption and infrared spectroscopy to sensing of unlabelled proteins at the single-molecule level.

  2. Single Molecule Studies of Chromatin

    SciTech Connect

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  3. Electromechanical Properties of Single Molecule Devices

    NASA Astrophysics Data System (ADS)

    Bruot, Christopher

    Understanding the interplay between the electrical and mechanical properties of single molecules is of fundamental importance for molecular electronics. The sensitivity of charge transport to mechanical fluctuations is a key problem in developing long lasting molecular devices. Furthermore, harnessing this response to mechanical perturbation, molecular devices which can be mechanically gated can be developed. This thesis demonstrates three examples of the unique electromechanical properties of single molecules. First, the electromechanical properties of 1,4-benzenedithiol molecular junctions are investigate. Counterintuitively, the conductance of this molecule is found to increase by more than an order of magnitude when stretched. This conductance increase is found to be reversible when the molecular junction is compressed. The current-voltage, conductance-voltage and inelastic electron tunneling spectroscopy characteristics are used to attribute the conductance increase to a strain-induced shift in the frontier molecular orbital relative to the electrode Fermi level, leading to resonant enhancement in the conductance. Next, the effect of stretching-induced structural changes on charge transport in DNA molecules is studied. The conductance of single DNA molecules with lengths varying from 6 to 26 base pairs is measured and found to follow a hopping transport mechanism. The conductance of DNA molecules is highly sensitive to mechanical stretching, showing an abrupt decrease in conductance at surprisingly short stretching distances, with weak dependence on DNA length. This abrupt conductance decrease is attributed to force-induced breaking of hydrogen bonds in the base pairs at the end of the DNA sequence. Finally, the effect of small mechanical modulation of the base separation on DNA conductance is investigated. The sensitivity of conductance to mechanical modulation is studied for molecules of different sequence and length. Sequences with purine-purine stacking

  4. Nanometer Resolution Imaging by SIngle Molecule Switching

    SciTech Connect

    Hu, Dehong; Orr, Galya

    2010-04-02

    The fluorescence intensity of single molecules can change dramatically even under constant laser excitation. The phenomenon is frequently called "blinking" and involves molecules switching between high and low intensity states.[1-3] In additional to spontaneous blinking, the fluorescence of some special fluorophores, such as cyanine dyes and photoactivatable fluorescent proteins, can be switched on and off by choice using a second laser. Recent single-molecule spectroscopy investigations have shed light on mechanisms of single molecule blinking and photoswitching. This ability to controllably switch single molecules led to the invention of a novel fluorescence microscopy with nanometer spatial resolution well beyond the diffraction limit.

  5. Single-Molecule Solvation-Shell Sensing

    NASA Astrophysics Data System (ADS)

    Leary, E.; Höbenreich, H.; Higgins, S. J.; van Zalinge, H.; Haiss, W.; Nichols, R. J.; Finch, C. M.; Grace, I.; Lambert, C. J.; McGrath, R.; Smerdon, J.

    2009-02-01

    We present a new route to single-molecule sensing via solvation shells surrounding a current-carrying backbone molecule. As an example, we show that the presence of a water solvation shell “gates” the conductance of a family of oligothiophene-containing molecular wires, and that the longer the oligothiophene, the larger is the effect. For the longest example studied, the molecular conductance is over 2 orders of magnitude larger in the presence of a shell comprising just 10 water molecules. A first principles theoretical investigation of electron transport through the molecules, using the nonequilibrium Green’s function method, shows that water molecules interact directly with the thiophene rings, significantly shifting transport resonances and greatly increasing the conductance. This reversible effect is confirmed experimentally through conductance measurements performed in the presence of moist air and dry argon.

  6. Spin blockade effect in single-molecule transistors

    NASA Astrophysics Data System (ADS)

    Luo, Guangpu; Park, Kyungwha

    Recently single-molecule transistors consisting of individual single-molecule magnets trapped between electrodes have been experimentally realized and electron transport properties through individual single-molecule magnets have been measured. For a single-molecule magnet the (2S+1)-fold degeneracy of magnetic levels in a given spin multiplet is lifted even in the absence of external magnetic field, due to the magnetic anisotropy induced by spin-orbit coupling. This anisotropic nature of single-molecule magnets allowed one to discover interesting, unexpected transport properties. A recent theoretical study showed that an Eu-based anisotropic magnetic molecule can switch its magnetic anisotropy between magnetic easy plane and easy axis upon varying the charge state of the molecule. Motivated by this report, we investigate how this switch of magnetic anisotropy influences the electron transport through the molecule, by considering sequential electron tunneling. We calculate current-voltage characteristics by solving the master equation based on the model Hamiltonians. We explore this interesting effect in the absence and presence of external magnetic field. Funding from NSF DMR-1206354.

  7. Signatures of molecular magnetism in single-molecule transport spectroscopy.

    PubMed

    Jo, Moon-Ho; Grose, Jacob E; Baheti, Kanhayalal; Deshmukh, Mandar M; Sokol, Jennifer J; Rumberger, Evan M; Hendrickson, David N; Long, Jeffrey R; Park, Hongkun; Ralph, D C

    2006-09-01

    We report single-molecule-transistor measurements on devices incorporating magnetic molecules. By studying the electron-tunneling spectrum as a function of magnetic field, we are able to identify signatures of magnetic states and their associated magnetic anisotropy. A comparison of the data to simulations also suggests that sequential electron tunneling may enhance the magnetic relaxation of the magnetic molecule. PMID:16968018

  8. Quantum Oscillations in an Interfacial 2D Electron Gas.

    SciTech Connect

    Zhang, Bingop; Lu, Ping; Liu, Henan; Lin, Jiao; Ye, Zhenyu; Jaime, Marcelo; Balakirev, Fedor F.; Yuan, Huiqiu; Wu, Huizhen; Pan, Wei; Zhang, Yong

    2016-01-01

    Recently, it has been predicted that topological crystalline insulators (TCIs) may exist in SnTe and Pb1-xSnxTe thin films [1]. To date, most studies on TCIs were carried out either in bulk crystals or thin films, and no research activity has been explored in heterostructures. We present here the results on electronic transport properties of the 2D electron gas (2DEG) realized at the interfaces of PbTe/ CdTe (111) heterostructures. Evidence of topological state in this interfacial 2DEG was observed.

  9. Extracting Models in Single Molecule Experiments

    NASA Astrophysics Data System (ADS)

    Presse, Steve

    2013-03-01

    Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

  10. Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level

    NASA Astrophysics Data System (ADS)

    Keller, Adrian; Kopyra, Janina; Gothelf, Kurt V.; Bald, Ilko

    2013-08-01

    Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)-, (M-O)-, C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 × 10-19 cm2. To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 ± 0.2) × 10-14 cm2 at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.

  11. Temperature dependence of charge transport in conjugated single molecule junctions

    NASA Astrophysics Data System (ADS)

    Huisman, Eek; Kamenetska, Masha; Venkataraman, Latha

    2011-03-01

    Over the last decade, the break junction technique using a scanning tunneling microscope geometry has proven to be an important tool to understand electron transport through single molecule junctions. Here, we use this technique to probe transport through junctions at temperatures ranging from 5K to 300K. We study three amine-terminated (-NH2) conjugated molecules: a benzene, a biphenyl and a terphenyl derivative. We find that amine groups bind selectively to undercoordinate gold atoms gold all the way down to 5K, yielding single molecule junctions with well-defined conductances. Furthermore, we find that the conductance of a single molecule junction increases with temperature and we present a mechanism for this temperature dependent transport result. Funded by a Rubicon Grant from The Netherlands Organisation for Scientific Research (NWO) and the NSEC program of NSF under grant # CHE-0641523.

  12. Low-energy cross-section calculations of single molecules by electron impact: a classical Monte Carlo transport approach with quantum mechanical description

    NASA Astrophysics Data System (ADS)

    Madsen, J. R.; Akabani, G.

    2014-05-01

    The present state of modeling radio-induced effects at the cellular level does not account for the microscopic inhomogeneity of the nucleus from the non-aqueous contents (i.e. proteins, DNA) by approximating the entire cellular nucleus as a homogenous medium of water. Charged particle track-structure calculations utilizing this approximation are therefore neglecting to account for approximately 30% of the molecular variation within the nucleus. To truly understand what happens when biological matter is irradiated, charged particle track-structure calculations need detailed knowledge of the secondary electron cascade, resulting from interactions with not only the primary biological component—water--but also the non-aqueous contents, down to very low energies. This paper presents our work on a generic approach for calculating low-energy interaction cross-sections between incident charged particles and individual molecules. The purpose of our work is to develop a self-consistent computational method for predicting molecule-specific interaction cross-sections, such as the component molecules of DNA and proteins (i.e. nucleotides and amino acids), in the very low-energy regime. These results would then be applied in a track-structure code and thereby reduce the homogenous water approximation. The present methodology—inspired by seeking a combination of the accuracy of quantum mechanics and the scalability, robustness, and flexibility of Monte Carlo methods—begins with the calculation of a solution to the many-body Schrödinger equation and proceeds to use Monte Carlo methods to calculate the perturbations in the internal electron field to determine the interaction processes, such as ionization and excitation. As a test of our model, the approach is applied to a water molecule in the same method as it would be applied to a nucleotide or amino acid and compared with the low-energy cross-sections from the GEANT4-DNA physics package of the Geant4 simulation toolkit

  13. Broadband single-molecule excitation spectroscopy

    PubMed Central

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F.

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy. PMID:26794035

  14. Molecular junctions: Single-molecule contacts exposed

    NASA Astrophysics Data System (ADS)

    Nichols, Richard J.; Higgins, Simon J.

    2015-05-01

    Using a scanning tunnelling microscopy-based method it is now possible to get an atomistic-level description of the most probable binding and contact configuration for single-molecule electrical junctions.

  15. Broadband single-molecule excitation spectroscopy

    NASA Astrophysics Data System (ADS)

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F.

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy.

  16. A single-molecule diode

    PubMed Central

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-01-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

  17. Giant single-molecule anisotropic magnetoresistance at room temperature.

    PubMed

    Li, Ji-Jun; Bai, Mei-Lin; Chen, Zhao-Bin; Zhou, Xiao-Shun; Shi, Zhan; Zhang, Meng; Ding, Song-Yuan; Hou, Shi-Min; Schwarzacher, Walther; Nichols, Richard J; Mao, Bing-Wei

    2015-05-13

    We report an electrochemically assisted jump-to-contact scanning tunneling microscopy (STM) break junction approach to create reproducible and well-defined single-molecule spintronic junctions. The STM break junction is equipped with an external magnetic field either parallel or perpendicular to the electron transport direction. The conductance of Fe-terephthalic acid (TPA)-Fe single-molecule junctions is measured and a giant single-molecule tunneling anisotropic magnetoresistance (T-AMR) up to 53% is observed at room temperature. Theoretical calculations based on first-principles quantum simulations show that the observed AMR of Fe-TPA-Fe junctions originates from electronic coupling at the TPA-Fe interfaces modified by the magnetic orientation of the Fe electrodes with respect to the direction of current flow. The present study highlights new opportunities for obtaining detailed understanding of mechanisms of charge and spin transport in molecular junctions and the role of interfaces in determining the MR of single-molecule junctions. PMID:25894840

  18. Quantitative Aspects of Single Molecule Microscopy

    PubMed Central

    Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

    2015-01-01

    Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

  19. Binding configurations and intramolecular strain in single-molecule devices.

    PubMed

    Rascón-Ramos, Habid; Artés, Juan Manuel; Li, Yuanhui; Hihath, Joshua

    2015-05-01

    The development of molecular-scale electronic devices has made considerable progress over the past decade, and single-molecule transistors, diodes and wires have all been demonstrated. Despite this remarkable progress, the agreement between theoretically predicted conductance values and those measured experimentally remains limited. One of the primary reasons for these discrepancies lies in the difficulty to experimentally determine the contact geometry and binding configuration of a single-molecule junction. In this Article, we apply a small-amplitude, high-frequency, sinusoidal mechanical signal to a series of single-molecule devices during junction formation and breakdown. By measuring the current response at this frequency, it is possible to determine the most probable binding and contact configurations for the molecular junction at room temperature in solution, and to obtain information about how an applied strain is distributed within the molecular junction. These results provide insight into the complex configuration of single-molecule devices, and are in excellent agreement with previous predictions from theoretical models. PMID:25686263

  20. Single-Molecule Studies in Live Cells

    NASA Astrophysics Data System (ADS)

    Yu, Ji

    2016-05-01

    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies.

  1. Sample preparation for single molecule localization microscopy.

    PubMed

    Allen, John R; Ross, Stephen T; Davidson, Michael W

    2013-11-21

    Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations. PMID:24084850

  2. Single-Molecule Studies in Live Cells.

    PubMed

    Yu, Ji

    2016-05-27

    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies. PMID:27070321

  3. Protein folding at single-molecule resolution

    PubMed Central

    Ferreon, Allan Chris M.; Deniz, Ashok A.

    2011-01-01

    The protein folding reaction carries great significance for cellular function and hence continues to be the research focus of a large interdisciplinary protein science community. Single-molecule methods are providing new and powerful tools for dissecting the mechanisms of this complex process by virtue of their ability to provide views of protein structure and dynamics without associated ensemble averaging. This review briefly introduces common FRET and force methods, and then explores several areas of protein folding where single-molecule experiments have yielded insights. These include exciting new information about folding landscapes, dynamics, intermediates, unfolded ensembles, intrinsically disordered proteins, assisted folding and biomechanical unfolding. Emerging and future work is expected to include advances in single-molecule techniques aimed at such investigations, and increasing work on more complex systems from both the physics and biology standpoints, including folding and dynamics of systems of interacting proteins and of proteins in cells and organisms. PMID:21303706

  4. Single molecule nanometry for biological physics

    PubMed Central

    Kim, Hajin; Ha, Taekjip

    2013-01-01

    Precision measurement is a hallmark of physics but the small length scale (~ nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ~ 0.3 nm precision at ~ 1 millisecond time resolution, and how these new tools are providing fundamental insights on how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate movements of multiple components. Finally, we will discuss recent progress in combining angstrom precision optical tweezers with single molecule fluorescent detection, opening new windows for multi-dimensional single molecule nanometry for biological physics. PMID:23249673

  5. Electronic structures of interfacial states formed at polymeric semiconductor heterojunctions

    NASA Astrophysics Data System (ADS)

    Huang, Ya-Shih; Westenhoff, Sebastian; Avilov, Igor; Sreearunothai, Paiboon; Hodgkiss, Justin M.; Deleener, Caroline; Friend, Richard H.; Beljonne, David

    2008-06-01

    Heterojunctions between organic semiconductors are central to the operation of light-emitting and photovoltaic diodes, providing respectively for electron-hole capture and separation. However, relatively little is known about the character of electronic excitations stable at the heterojunction. We have developed molecular models to study such interfacial excited electronic excitations that form at the heterojunction between model polymer donor and polymer acceptor systems: poly(9,9-dioctylfluorene-co-bis-N,N-(4-butylphenyl)-bis-N,N-phenyl-1,4-phenylenediamine) (PFB) with poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT), and poly(9,9-dioctylfluorene-co-N-(4-butylphenyl)diphenylamine) (TFB) with F8BT. We find that for stable ground-state geometries the excited state has a strong charge-transfer character. Furthermore, when partly covalent, modelled radiative lifetimes (~10-7s) and off-chain axis polarization (30∘) match observed `exciplex' emission. Additionally for the PFB:F8BT blend, geometries with fully ionic character are also found, thus accounting for the low electroluminescence efficiency of this system.

  6. COCIS: Markov processes in single molecule fluorescence

    PubMed Central

    Talaga, David S.

    2009-01-01

    This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the FPT distributions out of those states must be describable by a simple exponential law. The observation of non-exponential first-passage time distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system. PMID:19543444

  7. Controlling single-molecule junction conductance by molecular interactions

    PubMed Central

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  8. Controlling single-molecule junction conductance by molecular interactions.

    PubMed

    Kitaguchi, Y; Habuka, S; Okuyama, H; Hatta, S; Aruga, T; Frederiksen, T; Paulsson, M; Ueba, H

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  9. Density Functional Theory with Dissipation: Transport through Single Molecules

    SciTech Connect

    Kieron Burke

    2012-04-30

    A huge amount of fundamental research was performed on this grant. Most of it focussed on fundamental issues of electronic structure calculations of transport through single molecules, using density functional theory. Achievements were: (1) First density functional theory with dissipation; (2) Pseudopotential plane wave calculations with master equation; (3) Weak bias limit; (4) Long-chain conductance; and (5) Self-interaction effects in tunneling.

  10. A gate-tunable single-molecule diode

    NASA Astrophysics Data System (ADS)

    Perrin, Mickael L.; Galán, Elena; Eelkema, Rienk; Thijssen, Joseph M.; Grozema, Ferdinand; van der Zant, Herre S. J.

    2016-04-01

    In the pursuit of down-sizing electronic components, the ultimate limit is the use of single molecules as functional devices. The first theoretical proposal of such a device, predicted more than four decades ago, is the seminal Aviram-Ratner rectifier that exploits the orbital structure of the molecule. The experimental realization of single-molecule rectifiers, however, has proven to be challenging. In this work, we report on the experimental realization of a gate-tunable single-molecule rectifier with rectification ratios as high as 600. The rectification mechanism arises from the molecular structure and relies on the presence of two conjugated sites that are weakly coupled through a saturated linker. The observed gate dependence not only demonstrates tunability of the rectification ratio, it also shows that the proposed rectification mechanism based on the orbital structure is operative in the molecule.In the pursuit of down-sizing electronic components, the ultimate limit is the use of single molecules as functional devices. The first theoretical proposal of such a device, predicted more than four decades ago, is the seminal Aviram-Ratner rectifier that exploits the orbital structure of the molecule. The experimental realization of single-molecule rectifiers, however, has proven to be challenging. In this work, we report on the experimental realization of a gate-tunable single-molecule rectifier with rectification ratios as high as 600. The rectification mechanism arises from the molecular structure and relies on the presence of two conjugated sites that are weakly coupled through a saturated linker. The observed gate dependence not only demonstrates tunability of the rectification ratio, it also shows that the proposed rectification mechanism based on the orbital structure is operative in the molecule. Electronic supplementary information (ESI) available: DFT calculations on the DPE molecule, three-terminal measurements on the DPE molecule, additional analysis

  11. Single Molecule Raman Spectroscopy Under High Pressure

    NASA Astrophysics Data System (ADS)

    Fu, Yuanxi; Dlott, Dana

    2014-06-01

    Pressure effects on surface-enhanced Raman scattering spectra of Rhdoamine 6G adsorbed on silver nanoparticle surfaces was studied using a confocal Raman microscope. Colloidal silver nanoparticles were treated with Rhodamine 6G (R6G) and its isotopically substituted partner, R6G-d4. Mixed isotopomers let us identify single-molecule spectra, since multiple-molecule spectra would show vibrational transitions from both species. The nanoparticles were embedded into a poly vinyl alcohol film, and loaded into a diamond anvil cell for the high-pressure Raman scattering measurement. Argon was the pressure medium. Ambient pressure Raman scattering spectra showed few single-molecule spectra. At moderately high pressure ( 1GPa), a surprising effect was observed. The number of sites with observable spectra decreased dramatically, and most of the spectra that could be observed were due to single molecules. The effects of high pressure suppressed the multiple-molecule Raman sites, leaving only the single-molecule sites to be observed.

  12. Single-molecule methods to quantify adsorptive separations (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Landes, Christy

    2015-08-01

    Interfacial adsorption and transport are the chemical and physical processes that underlie separations. Although separations technology accounts for hundreds of billions of dollars in the global economy, the process is not well-understood at the mechanistic level and instead is almost always optimized empirically. One of the reasons is that access to the underlying molecular phenomena has only been available recently via single-molecule methods. There are still interesting challenges because adsorption, desorption, and transport are all dynamic processes, whereas much of the advances in super-resolution imaging have focused on imaging static materials. Our lab has focused in recent years on developing and optimizing data analysis methods for quantifying the dynamics of adsorption and transport in porous materials at nanometer-resolution spatial scales. Our methods include maximizing information content in dynamic single-molecule data and developing methods to detect change-points in binned data. My talk will outline these methods, and will address how and when they can be applied to extract dynamic details in heterogeneous materials such as porous membranes.

  13. Automated imaging system for single molecules

    DOEpatents

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  14. Artifacts in single-molecule localization microscopy.

    PubMed

    Burgert, Anne; Letschert, Sebastian; Doose, Sören; Sauer, Markus

    2015-08-01

    Single-molecule localization microscopy provides subdiffraction resolution images with virtually molecular resolution. Through the availability of commercial instruments and open-source reconstruction software, achieving super resolution is now public domain. However, despite its conceptual simplicity, localization microscopy remains prone to user errors. Using direct stochastic optical reconstruction microscopy, we investigate the impact of irradiation intensity, label density and photoswitching behavior on the distribution of membrane proteins in reconstructed super-resolution images. We demonstrate that high emitter densities in combination with inappropriate photoswitching rates give rise to the appearance of artificial membrane clusters. Especially, two-dimensional imaging of intrinsically three-dimensional membrane structures like microvilli, filopodia, overlapping membranes and vesicles with high local emitter densities is prone to generate artifacts. To judge the quality and reliability of super-resolution images, the single-molecule movies recorded to reconstruct the images have to be carefully investigated especially when investigating membrane organization and cluster analysis. PMID:26138928

  15. Single-Molecule Analysis of Biomembranes

    NASA Astrophysics Data System (ADS)

    Schmidt, Thomas; Schütz, Gerhard J.

    Biomembranes are more than just a cell's envelope - as the interface to the surrounding of a cell they carry key signalling functions. Consequentially, membranes are highly complex organelles: they host about thousand different types of lipids and about half of the proteome, whose interaction has to be orchestrated appropriately for the various signalling purposes. In particular, knowledge on the nanoscopic organization of the plasma membrane appears critical for understanding the regulation of interactions between membrane proteins. The high localization precision of ˜20 nm combined with a high time resolution of ˜1 ms made single molecule tracking an excellent technology to obtain insights into membrane nanostructures, even in a live cell context. In this chapter, we will highlight concepts to achieve superresolution by single molecule imaging, summarize tools for data analysis, and review applications on artificial and live cell membranes.

  16. Single-molecule Studies of Riboswitch Folding

    PubMed Central

    Savinov, Andrew; Perez, Christian F.; Block, Steven M.

    2014-01-01

    The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. PMID:24727093

  17. Superresolution Imaging using Single-Molecule Localization

    PubMed Central

    Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

    2013-01-01

    Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680

  18. Multichannel conductance of folded single-molecule wires aided by through-space conjugation.

    PubMed

    Chen, Long; Wang, Ya-Hao; He, Bairong; Nie, Han; Hu, Rongrong; Huang, Fei; Qin, Anjun; Zhou, Xiao-Shun; Zhao, Zujin; Tang, Ben Zhong

    2015-03-27

    Deciphering charge transport through multichannel pathways in single-molecule junctions is of high importance to construct nanoscale electronic devices and deepen insight into biological redox processes. Herein, we report two tailor-made folded single-molecule wires featuring intramolecular π-π stacking interactions. The scanning tunneling microscope (STM) based break-junction technique and theoretical calculations show that through-bond and through-space conjugations are integrated into one single-molecule wire, allowing for two simultaneous conducting channels in a single-molecule junction. These folded molecules with stable π-π stacking interaction offer conceptual advances in single-molecule multichannel conductance, and are perfect models for conductance studies in biological systems, organic thin films, and π-stacked columnar aggregates. PMID:25694026

  19. Single Molecule Dynamics of Branched DNA Polymers

    NASA Astrophysics Data System (ADS)

    Mai, Danielle; Sing, Charles; Schroeder, Charles

    This work focuses on extending the field of single polymer dynamics to topologically complex polymers. Here, we report the direct observation of DNA-based branched polymers. Recently, we recently demonstrated a two-step synthesis method to generate star, H-shaped, and comb polymers for single molecule visualization. Following synthesis, we use single-color or dual-color single molecule fluorescence microscopy to directly visualize branched polymer dynamics in flow, in particular tracking side branches and backbones independently. In this way, our imaging method allows for characterization of molecular properties, including quantification of polymer contour length and branch distributions. Moving beyond characterization, we use molecular rheology and single molecule techniques to study the dynamics of single branched polymers in flow. Here, we utilize precision microfluidics to directly observe branched DNA polymer conformations during transient stretching, steady-state extension, and relaxation from high stretch. We specifically measure backbone end-to-end distance as a function of time. Experiments and Brownian dynamics simulations show that branched polymer relaxation is a strong function of the number of branches and position of branch points along the main chain backbone.

  20. Laser-Assisted Single Molecule Refolding

    NASA Astrophysics Data System (ADS)

    Zhao, Rui; Marshall, Myles; Aleman, Elvin; Lamichhane, Rajan; Rueda, David

    2010-03-01

    In vivo, many RNA molecules can adopt multiple conformations depending on their biological context such as the HIV Dimerization Initiation Sequence (DIS) or the DsrA RNA in bacteria. It is quite common that the initial interaction between the two RNAs takes place via complementary unpaired regions, thus forming a so-called kissing complex. However, the exact kinetic mechanism by which the two RNA molecules reach the dimerized state is still not well understood. To investigate the refolding energy surface of RNA molecules, we have developed new technology based on the combination of single molecule spectroscopy with laser induced temperature jump kinetics, called Laser Assisted Single-molecule Refolding (LASR). LASR enables us to induce folding reactions of otherwise kinetically trapped RNAs at the single molecule level, and to characterize their folding landscape. LASR provides an exciting new approach to study molecular memory effects and kinetically trapped RNAs in general. LASR should be readily applicable to study DNA and protein folding as well.

  1. Trapping and manipulating single molecules of DNA

    NASA Astrophysics Data System (ADS)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  2. Biomedical applications of single molecule detection

    NASA Astrophysics Data System (ADS)

    Kelso, D. M.

    1997-05-01

    The search for increased sensitivity of bio-analytical techniques has recently shifted from signal generation to detection. While enzyme amplifiers and chemiluminescent reporters developed by chemists over the last two decades gradually moved detection limits to the attomol level, it has taken engineers only a few years to reach single- molecule sensitivity with the development of new instrumentation. A number of different approaches have successfully achieved single-molecule fluorescence detection including confocal and near-field scanning optical microscopy, photon-counting cameras, fluorescence- correlation and time-gated spectroscopy. They detect labels immobilized on substrates, diffusing in solution and flowing in electro-osmotic and hydrodynamically focused streams. Biotechnology has created numerous application s for single- molecule detection. In research labs, it can dramatically increase the rate of DNA sequencing, screen libraries for products of directed evolution, and characterize compounds in drug discovery programs. In medical diagnostics, ultra- sensitive detection technologies can be used for genetic screening, detection of infectious diseases, or multi- analyte profiles. It can be applied to immunoassays as well as DNA or RNA hybridization assays.

  3. Single-Molecule Imaging of Cellular Signaling

    NASA Astrophysics Data System (ADS)

    De Keijzer, Sandra; Snaar-Jagalska, B. Ewa; Spaink, Herman P.; Schmidt, Thomas

    Single-molecule microscopy is an emerging technique to understand the function of a protein in the context of its natural environment. In our laboratory this technique has been used to study the dynamics of signal transduction in vivo. A multitude of signal transduction cascades are initiated by interactions between proteins in the plasma membrane. These cascades start by binding a ligand to its receptor, thereby activating downstream signaling pathways which finally result in complex cellular responses. To fully understand these processes it is important to study the initial steps of the signaling cascades. Standard biological assays mostly call for overexpression of the proteins and high concentrations of ligand. This sets severe limits to the interpretation of, for instance, the time-course of the observations, given the large temporal spread caused by the diffusion-limited binding processes. Methods and limitations of single-molecule microscopy for the study of cell signaling are discussed on the example of the chemotactic signaling of the slime-mold Dictyostelium discoideum. Single-molecule studies, as reviewed in this chapter, appear to be one of the essential methodologies for the full spatiotemporal clarification of cellular signaling, one of the ultimate goals in cell biology.

  4. Application of Recognition Tunneling in Single Molecule Identification

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan

    Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.

  5. Interplay between magnetic anisotropy and vibron-assisted tunneling in a single-molecule magnet transistor

    NASA Astrophysics Data System (ADS)

    Park, Kyungwha; McCaskey, Alexander; Yamamoto, Yoh; Warnock, Michael; Burzuri, Enrique; van der Zant, Herre

    2015-03-01

    Molecules trapped in single-molecule devices vibrate with discrete frequencies characteristic to the molecules, and the molecular vibrations can couple to electronic charge and/or spin degrees of freedom. For a significant electron-vibron coupling, electrons may tunnel via the vibrational excitations unique to the molecules. Recently, electron transport via individual anisotropic magnetic molecules (referred to as single-molecule magnets) has been observed in single-molecule transistors. A single-molecule magnet has a large spin moment and a large magnetic anisotropy barrier. So far, studies of electron-vibron coupling effects in single-molecule devices, are mainly for isotropic molecules. Here we investigate how the electron-vibron coupling influences electron transport via a single-molecule magnet Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (arXiv:1411.2677). We show that the magnetic anisotropy of the Fe4 induces new features in vibrational conductance peaks and creates vibrational satellite peaks. The main and satellite peak heights have a strong, unusual dependence on the direction and magnitude of applied magnetic field, because the magnetic anisotropy barrier is comparable to vibrational energies. Funding from NSF DMR-1206354, EU FP7 program project 618082 ACMOL, advanced ERC grant (Mols@Mols). Computer resources from SDSC Trestles under DMR060009N and VT ARC.

  6. Single-molecule magnets: two-electron reduced version of a Mn12 complex and environmental influences on the magnetization relaxation of (PPh4)(2)[Mn(12)O(12)(O(2)CCHCl2)(16)(H2O)4].

    PubMed

    Soler, Monica; Wernsdorfer, Wolfgang; Abboud, Khalil A; Huffman, John C; Davidson, Ernest R; Hendrickson, David N; Christou, George

    2003-03-26

    The complex [Mn(12)O(12)(O(2)CCHCl(2))(16)(H(2)O)(4)] (2) in MeCN exhibits three quasi-reversible one-electron reduction processes at significantly higher potentials than [Mn(12)O(12)(O(2)CMe)(16)(H(2)O)(4)] (1). This has allowed the two-electron reduced version of 2 to be generated and isolated. Reaction of 2 with one and two equivalents of PPh(4)I led to isolation of (PPh(4))[Mn(12)O(12)(O(2)CCHCl(2))(16)(H(2)O)(4)] (3) and (PPh(4))(2)[Mn(12)O(12)(O(2)CCHCl(2))(16)(H(2)O)(4)] (4), respectively. The latter represents a new isolated oxidation level of the Mn(12) family of single-molecule magnets (SMMs). Crystallization from CH(2)Cl(2)/hexanes yields a mixture of two crystal forms, 4.4CH(2)Cl(2).H(2)O (4a) and 4.6CH(2)Cl(2) (4b), both of which have been structurally characterized as triclinic and monoclinic, respectively. The molecular structures are very similar, with the added electrons localized on former Mn(III) ions to give a trapped-valence 2Mn(II), 6Mn(III), 4Mn(IV) oxidation state description. Dried solid analyzed as unsolvated 4. (1)H NMR spectral data in CD(2)Cl(2) confirm that 4 retains its solid-state structure in solution. Bulk DC magnetization data for dried 4 in the 1.80-4.00 K and 10-70 kG ranges were fit to give S = 10, D = -0.275 cm(-1), g = 2.00 and |D|/g = 0.14 cm(-1), where D is the axial zero-field splitting (anisotropy) parameter. Complexes 4a and 4b give resolvable frequency-dependent out-of-phase (chi(M)'') signals in AC susceptibility studies resulting from the magnetization relaxation of SMMs. Relaxation rate vs T data to 1.8 K obtained from the chi(M)'' vs temperature studies were supplemented with rate vs T data measured to lower temperatures via magnetization vs time decay data, and these were fit to the Arrhenius equation to give the effective barrier to relaxation (U(eff)). The U(eff) values are 18.5 and 30.3 K for 4a and 4b, respectively. A similar analysis for dried 4 using AC data gave U(eff) = 32 K. Magnetization vs DC field

  7. Single molecule microscopy and spectroscopy: concluding remarks.

    PubMed

    van Hulst, Niek F

    2015-01-01

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1st floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives. PMID:26606461

  8. Simulated single molecule microscopy with SMeagol

    PubMed Central

    Lindén, Martin; Ćurić, Vladimir; Boucharin, Alexis; Fange, David; Elf, Johan

    2016-01-01

    Summary: SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation and optimization of advanced analysis methods for live cell single molecule microscopy data. Availability and implementation: SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction–diffusion simulations. Documentation, source code and binaries for Mac OS, Windows and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net. Contact: johan.elf@icm.uu.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153711

  9. Single-molecule electrophoresis. Final report

    SciTech Connect

    Castro, A.; Shera, E.B.

    1996-05-22

    A novel method for the detection and identification of single molecules in solution has been devised, computer-simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required by individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed beforehand in order to estimate the experimental feasibility of the method, and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented.

  10. PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

    NASA Astrophysics Data System (ADS)

    Tao, Nongjian

    2012-04-01

    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

  11. Spin coherence in a Mn3 single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Abeywardana, Chathuranga; Mowson, Andrew M.; Christou, George; Takahashi, Susumu

    2016-01-01

    Spin coherence in single crystals of the spin S = 6 single-molecule magnet (SMM) [Mn3O(O2CEt)3(mpko)3]+ (abbreviated Mn3) has been investigated using 230 GHz electron paramagnetic resonance spectroscopy. Coherence in Mn3 was uncovered by significantly suppressing dipolar contribution to the decoherence with complete spin polarization of Mn3 SMMs. The temperature dependence of spin decoherence time (T2) revealed that the dipolar decoherence is the dominant source of decoherence in Mn3 and T2 can be extended up to 267 ns by quenching the dipolar decoherence.

  12. Theoretical investigation on single-molecule chiroptical spectroscopy

    SciTech Connect

    Wakabayashi, M.; Yokojima, S.; Fukaminato, T.; Ogata, K.; Nakamura, S.

    2013-12-10

    Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.

  13. Hybrid photodetector for single-molecule spectroscopy and microscopy

    PubMed Central

    Michalet, X.; Cheng, Adrian; Antelman, Joshua; Suyama, Motohiro; Arisaka, Katsushi; Weiss, Shimon

    2011-01-01

    We report benchmark tests of a new single-photon counting detector based on a GaAsP photocathode and an electron-bombarded avalanche photodiode developed by Hamamatsu Photonics. We compare its performance with those of standard Geiger-mode avalanche photodiodes. We show its advantages for FCS due to the absence of after-pulsing and for fluorescence lifetime measurements due to its excellent time resolution. Its large sensitive area also greatly simplifies setup alignment. Its spectral sensitivity being similar to that of recently introduced CMOS SPADs, this new detector could become a valuable tool for single-molecule fluorescence measurements, as well as for many other applications. PMID:21822361

  14. Spin Manipulation by Creation of Single-Molecule Radical Cations

    NASA Astrophysics Data System (ADS)

    Karan, Sujoy; Li, Na; Zhang, Yajie; He, Yang; Hong, I.-Po; Song, Huanjun; Lü, Jing-Tao; Wang, Yongfeng; Peng, Lianmao; Wu, Kai; Michelitsch, Georg S.; Maurer, Reinhard J.; Diller, Katharina; Reuter, Karsten; Weismann, Alexander; Berndt, Richard

    2016-01-01

    All-trans-retinoic acid (ReA), a closed-shell organic molecule comprising only C, H, and O atoms, is investigated on a Au(111) substrate using scanning tunneling microscopy and spectroscopy. In dense arrays single ReA molecules are switched to a number of states, three of which carry a localized spin as evidenced by conductance spectroscopy in high magnetic fields. The spin of a single molecule may be reversibly switched on and off without affecting its neighbors. We suggest that ReA on Au is readily converted to a radical by the abstraction of an electron.

  15. Electric field breakdown in single molecule junctions.

    PubMed

    Li, Haixing; Su, Timothy A; Zhang, Vivian; Steigerwald, Michael L; Nuckolls, Colin; Venkataraman, Latha

    2015-04-22

    Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S-Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor-acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si-Si and Ge-Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si-Si, Si-C, and Si-O bonds and find that Si-C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level. PMID:25675085

  16. Single-molecule studies of collagen mechanics

    NASA Astrophysics Data System (ADS)

    Forde, Nancy; Rezaei, Naghmeh; Kirkness, Michael

    Collagen is the fundamental structural protein in vertebrates. Its triple helical structure at the molecular level is believed to be strongly related to its mechanical role in connective tissues. However, the mechanics of collagen at the single-molecule level remain contentious. Estimates of its persistence length span an order of magnitude, from 15-180 nm for this biopolymer of 300 nm contour length. How collagen responds to applied force is also controversial, with different single-molecule studies suggesting one of three different responses: extending entropically, overwinding, or unwinding, all at forces below 10 pN. Using atomic force microscopy to image collagens deposited from solution, we find that their flexibility depends strongly on ionic strength and pH. To study force-dependent structural changes, we are performing highly parallelized enzymatic cleavage assays of triple helical collagen in our new compact centrifuge force microscope. Because proteolytic cleavage requires a locally unwound triple helix, these experiments are revealing how local collagen structure changes in response to applied force. Our results can help to resolve long-standing debates about collagen mechanics and structure at the molecular level.

  17. Single molecule dynamics in lipid membranes

    NASA Astrophysics Data System (ADS)

    Skaug, Michael James

    Lipid membranes are self-assembled molecular materials that form the membranes of cells. Because of their biological function, lipid membranes are important from a biomedical and biotechnological standpoint. Because of their complex fluid properties, they also provide a rich testbed for studying the structure and dynamics in self-assembled materials and for developing other bio-mimetic structures. In this work, we studied the dynamics of single lipid molecules using experimental and computational techniques. Using single molecule fluorescence microscopy, we tracked the diffusive motion of lipids in phase separated lipid membranes. With the additional techniques of atomic force microscopy and Monte Carlo simulation, we were able to, for the first time experimentally, directly correlate the observed obstructed diffusion with lipid membrane organization. The single molecule tracking tracking experiments required the addition of impurity fluorescent molecules and the assumption that the impurities do not alter the dynamics of the system. To test this assumption, we performed atomistic molecular dynamics simulations of a fluorescently labeled lipid in a lipid membrane. We showed that the fluorescent impurity could have a significant impact on some membrane properties, such as phase behavior, but that relative changes in diffusive behavior are unaffected.

  18. Single Molecule and Single Cell Epigenomics

    PubMed Central

    Hyun, Byung-Ryool; McElwee, John L.; Soloway, Paul D.

    2014-01-01

    Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells. PMID:25204781

  19. Interfacial defects in thin refractory metal films imaged by low-energy electron microscopy

    NASA Astrophysics Data System (ADS)

    Świȩch, W.; Mundschau, M.; Flynn, C. P.

    1999-05-01

    Low-energy electron microscopy is employed to image defects at buried interfaces through the strains they cause at the front surface. The interfacial defects studied here occur in high quality films of Mo(110) grown by molecular beam epitaxy on Al2O3(112¯0). The defects include steps and inclusions on the original sapphire surface and interfacial dislocations created where epitaxial strain causes slip.

  20. PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

    NASA Astrophysics Data System (ADS)

    Tao, Nongjian

    2012-04-01

    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

  1. Single molecule detection for in vitro diagnostics

    NASA Astrophysics Data System (ADS)

    Kirner, Thomas; Ackermann, Jörg; Mathis, Harald P.; Greiner, Benjamin; Tonn, Thomas; Tschachojan, David; Kukoc-Zivojnov, Natasa; Giehring, Sebastian

    2008-02-01

    In this paper we present a novel highly sensitive detection system for diagnostic applications. The system is designed to meet the needs of medical diagnostics for reliable measurements of pathogens and biomarkers in the low concentration regime. It consists of a confocal detection unit, micro-structured sampling cells, and a "Virtual lab" analysis software. The detection unit works with laser induced fluorescence and is designed to provide accurate and highly sensitive measurement at the single molecule level. Various sampling cells are micro-structured in glass, silicon or polymers to enable measurements under flow and nonflow conditions. Sampling volume is below one microliter. The "Virtual lab" software analyzes the light intensity online according to the patent pending "Accurate Stochastic Fluorescence Spectroscopy" (ASFS) developed by FluIT Biosystems GmbH. Tools for simulation and experiment optimization are included as well. Experimental results for various applications with relevance for in vitro diagnostics will be presented.

  2. Single-Molecule Observations of Ribosome Function

    PubMed Central

    Blanchard, Scott C.

    2009-01-01

    Summary of Recent Advances Single-molecule investigations promise to greatly advance our understanding of basic and regulated ribosome functions during the process of translation. Here, recent progress towards directly imaging the elemental translation elongation steps using fluorescence resonance energy transfer (FRET)-based imaging methods is discussed, which provide striking evidence of the highly dynamic nature of the ribosome. In this view, global rates and fidelities of protein synthesis reactions may be regulated by interactions of the ribosome with mRNA, tRNA, translation factors, and potentially many other cellular ligands, that modify intrinsic conformational equilibria in the translating particle. Future investigations probing this model must aim to visualize translation processes from multiple structural and kinetic perspectives simultaneously, to provide direct correlations between factor binding and conformational events. PMID:19223173

  3. Theory of single molecule emission spectroscopy

    SciTech Connect

    Bel, Golan; Brown, Frank L. H.

    2015-05-07

    A general theory and calculation framework for the prediction of frequency-resolved single molecule photon counting statistics is presented. Expressions for the generating function of photon counts are derived, both for the case of naive “detection” based solely on photon emission from the molecule and also for experimentally realizable detection of emitted photons, and are used to explicitly calculate low-order photon-counting moments. The two cases of naive detection versus physical detection are compared to one another and it is demonstrated that the physical detection scheme resolves certain inconsistencies predicted via the naive detection approach. Applications to two different models for molecular dynamics are considered: a simple two-level system and a two-level absorber subject to spectral diffusion.

  4. Theory of single molecule emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Bel, Golan; Brown, Frank L. H.

    2015-05-01

    A general theory and calculation framework for the prediction of frequency-resolved single molecule photon counting statistics is presented. Expressions for the generating function of photon counts are derived, both for the case of naive "detection" based solely on photon emission from the molecule and also for experimentally realizable detection of emitted photons, and are used to explicitly calculate low-order photon-counting moments. The two cases of naive detection versus physical detection are compared to one another and it is demonstrated that the physical detection scheme resolves certain inconsistencies predicted via the naive detection approach. Applications to two different models for molecular dynamics are considered: a simple two-level system and a two-level absorber subject to spectral diffusion.

  5. Single-molecule spectroscopy using microfluidic platforms.

    PubMed

    Kim, Samuel; Zare, Richard N

    2010-01-01

    Microfluidics serves as a convenient platform for single-molecule experiments by providing manipulation of small amounts of liquids and micron-sized particles. An adapted version of capillary electrophoresis (CE) on a microchip can be utilized to separate chemical species with high resolution based on their ionic mobilities (i.e., charges and sizes), but identification of separated species is not trivial, especially for complex mixtures of sticky biomolecules. We describe here how to use a surfactant mixture system for CE on a poly(dimethylsiloxane) (PDMS) microchip, capture separated peaks within a 50-pl chamber using microvalves, analyze the fluorescence signals with correlation spectroscopy to extract molecular diffusion characteristics, and to identify the biomolecular clusters in a model immunocomplex system. PMID:20580962

  6. Bringing single-molecule spectroscopy to macromolecular protein complexes

    PubMed Central

    Joo, Chirlmin; Fareh, Mohamed; Kim, V. Narry

    2013-01-01

    Single-molecule fluorescence spectroscopy offers real-time, nanometer-resolution information. Over the past two decades, this emerging single-molecule technique has been rapidly adopted to investigate the structural dynamics and biological functions of proteins. Despite this remarkable achievement, single-molecule fluorescence techniques must be extended to macromolecular protein complexes that are physiologically more relevant for functional studies. In this review, we present recent major breakthroughs for investigating protein complexes within cell extracts using single-molecule fluorescence. We outline the challenges, future prospects and potential applications of these new single-molecule fluorescence techniques in biological and clinical research. PMID:23200186

  7. Variable-Temperature Tip-Enhanced Raman Spectroscopy of Single-Molecule Fluctuations and Dynamics.

    PubMed

    Park, Kyoung-Duck; Muller, Eric A; Kravtsov, Vasily; Sass, Paul M; Dreyer, Jens; Atkin, Joanna M; Raschke, Markus B

    2016-01-13

    Structure, dynamics, and coupling involving single-molecules determine function in catalytic, electronic or biological systems. While vibrational spectroscopy provides insight into molecular structure, rapid fluctuations blur the molecular trajectory even in single-molecule spectroscopy, analogous to spatial averaging in measuring large ensembles. To gain insight into intramolecular coupling, substrate coupling, and dynamic processes, we use tip-enhanced Raman spectroscopy (TERS) at variable and cryogenic temperatures, to slow and control the motion of a single molecule. We resolve intrinsic line widths of individual normal modes, allowing detailed and quantitative investigation of the vibrational modes. From temperature dependent line narrowing and splitting, we quantify ultrafast vibrational dephasing, intramolecular coupling, and conformational heterogeneity. Through statistical correlation analysis of fluctuations of individual modes, we observe rotational motion and spectral fluctuations of the molecule. This work demonstrates single-molecule vibrational spectroscopy beyond chemical identification, opening the possibility for a complete picture of molecular motion ranging from femtoseconds to minutes. PMID:26679007

  8. Conduction mechanisms in biphenyl dithiol single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Bürkle, M.; Viljas, J. K.; Vonlanthen, D.; Mishchenko, A.; Schön, G.; Mayor, M.; Wandlowski, T.; Pauly, F.

    2012-02-01

    Based on density-functional theory calculations, we report a detailed study of the single-molecule charge-transport properties for a series of recently synthesized biphenyl-dithiol molecules [D. Vonlanthen , Angew. Chem., Int. Ed.1433-785110.1002/anie.200903946 48, 8886 (2009); A. Mishchenko , Nano Lett.NALEFD1530-698410.1021/nl903084b 10, 156 (2010)]. The torsion angle ϕ between the two phenyl rings, and hence the degree of π conjugation, is controlled by alkyl chains and methyl side groups. We consider three different coordination geometries, namely, top-top, bridge-bridge, and hollow-hollow, with the terminal sulfur atoms bound to one, two, and three gold surface atoms, respectively. Our calculations show that different coordination geometries give rise to conductances that vary by one order of magnitude for the same molecule. Irrespective of the coordination geometries, the charge transport calculations predict a cos2ϕ dependence of the conductance, which is confirmed by our experimental measurements. We demonstrate that the calculated transmission through biphenyl dithiols is typically dominated by a single transmission eigenchannel formed from π electrons. For perpendicular orientation of the rings a residual conductance arises from σ-π couplings. But only for a single molecule with a completely broken conjugation we find a nearly perfect degeneracy of the σ-π eigenchannels for the hollow-hollow-type contact in our theory.

  9. Visualizing electromagnetic fields at the nanoscale by single molecule localization.

    PubMed

    Steuwe, Christian; Erdelyi, Miklos; Szekeres, G; Csete, M; Baumberg, Jeremy J; Mahajan, Sumeet; Kaminski, Clemens F

    2015-05-13

    Coupling of light to the free electrons at metallic surfaces allows the confinement of electric fields to subwavelength dimensions, far below the optical diffraction limit. While this is routinely used to manipulate light at the nanoscale, in electro-optic devices and enhanced spectroscopic techniques, no characterization technique for imaging the underlying nanoscopic electromagnetic fields exists, which does not perturb the field or employ complex electron beam imaging. Here, we demonstrate the direct visualization of electromagnetic fields on patterned metallic substrates at nanometer resolution, exploiting a strong "autonomous" fluorescence-blinking behavior of single molecules within the confined fields allowing their localization. Use of DNA-constructs for precise positioning of fluorescence dyes on the surface induces this distance-dependent autonomous blinking thus completely obviating the need for exogenous agents or switching methods. Mapping such electromagnetic field distributions at nanometer resolution aids the rational design of nanometals for diverse photonic applications. PMID:25915093

  10. Single-molecule magnets ``without'' intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.

    2012-02-01

    Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

  11. Figuration and detection of single molecules

    NASA Astrophysics Data System (ADS)

    Nevels, R.; Welch, G. R.; Cremer, P. S.; Hemmer, P.; Phillips, T.; Scully, S.; Sokolov, A. V.; Svidzinsky, A. A.; Xia, H.; Zheltikov, A.; Scully, M. O.

    2012-08-01

    Recent advances in the description of atoms and molecules based on Dimensional scaling analysis, developed by Dudley Herschbach and co-workers, provided new insights into visualization of molecular structure and chemical bonding. Prof. Herschbach is also a giant in the field of single molecule scattering. We here report on the engineering of molecular detectors. Such systems have a wide range of application from medical diagnostics to the monitoring of chemical, biological and environmental hazards. We discuss ways to identify preselected molecules, in particular, mycotoxin contaminants using coherent laser spectroscopy. Mycotoxin contaminants, e.g. aflatoxin B1 which is present in corn and peanuts, are usually analysed by time-consuming microscopic, chemical and biological assays. We present a new approach that derives from recent experiments in which molecules are prepared by one (or more) femtosecond laser(s) and probed by another set. We call this technique FAST CARS (femto second adaptive spectroscopic technique for coherent anti-Stokes Raman spectroscopy). We propose and analyse ways in which FAST CARS can be used to identify preselected molecules, e.g. aflatoxin, rapidly and economically.

  12. The spontaneous formation of single-molecule junctions via terminal alkynes

    NASA Astrophysics Data System (ADS)

    Pla-Vilanova, Pepita; Aragonès, Albert C.; Ciampi, Simone; Sanz, Fausto; Darwish, Nadim; Diez-Perez, Ismael

    2015-09-01

    Herein, we report the spontaneous formation of single-molecule junctions via terminal alkyne contact groups. Self-assembled monolayers that form spontaneously from diluted solutions of 1, 4-diethynylbenzene (DEB) were used to build single-molecule contacts and assessed using the scanning tunneling microscopy-break junction technique (STM-BJ). The STM-BJ technique in both its dynamic and static approaches was used to characterize the lifetime (stability) and the conductivity of a single-DEB wire. It is demonstrated that single-molecule junctions form spontaneously with terminal alkynes and require no electrochemical control or chemical deprotonation. The alkyne anchoring group was compared against typical contact groups exploited in single-molecule studies, i.e. amine (benzenediamine) and thiol (benzendithiol) contact groups. The alkyne contact showed a conductance magnitude comparable to that observed with amine and thiol groups. The lifetime of the junctions formed from alkynes were only slightly less than that of thiols and greater than that observed for amines. These findings are important as (a) they extend the repertoire of chemical contacts used in single-molecule measurements to 1-alkynes, which are synthetically accessible and stable and (b) alkynes have a remarkable affinity toward silicon surfaces, hence opening the door for the study of single-molecule transport on a semiconducting electronic platform.

  13. The spontaneous formation of single-molecule junctions via terminal alkynes.

    PubMed

    Pla-Vilanova, Pepita; Aragonès, Albert C; Ciampi, Simone; Sanz, Fausto; Darwish, Nadim; Diez-Perez, Ismael

    2015-09-25

    Herein, we report the spontaneous formation of single-molecule junctions via terminal alkyne contact groups. Self-assembled monolayers that form spontaneously from diluted solutions of 1, 4-diethynylbenzene (DEB) were used to build single-molecule contacts and assessed using the scanning tunneling microscopy-break junction technique (STM-BJ). The STM-BJ technique in both its dynamic and static approaches was used to characterize the lifetime (stability) and the conductivity of a single-DEB wire. It is demonstrated that single-molecule junctions form spontaneously with terminal alkynes and require no electrochemical control or chemical deprotonation. The alkyne anchoring group was compared against typical contact groups exploited in single-molecule studies, i.e. amine (benzenediamine) and thiol (benzendithiol) contact groups. The alkyne contact showed a conductance magnitude comparable to that observed with amine and thiol groups. The lifetime of the junctions formed from alkynes were only slightly less than that of thiols and greater than that observed for amines. These findings are important as (a) they extend the repertoire of chemical contacts used in single-molecule measurements to 1-alkynes, which are synthetically accessible and stable and (b) alkynes have a remarkable affinity toward silicon surfaces, hence opening the door for the study of single-molecule transport on a semiconducting electronic platform. PMID:26314486

  14. Single-Molecule Sensors: Challenges and Opportunities for Quantitative Analysis.

    PubMed

    Gooding, J Justin; Gaus, Katharina

    2016-09-12

    Measurement science has been converging to smaller and smaller samples, such that it is now possible to detect single molecules. This Review focuses on the next generation of analytical tools that combine single-molecule detection with the ability to measure many single molecules simultaneously and/or process larger and more complex samples. Such single-molecule sensors constitute a new type of quantitative analytical tool, as they perform analysis by molecular counting and thus potentially capture the heterogeneity of the sample. This Review outlines the advantages and potential of these new, quantitative single-molecule sensors, the measurement challenges in making single-molecule devices suitable for analysis, the inspiration biology provides for overcoming these challenges, and some of the solutions currently being explored. PMID:27444661

  15. Microarray analysis at single molecule resolution

    PubMed Central

    Mureşan, Leila; Jacak, Jarosław; Klement, Erich Peter; Hesse, Jan; Schütz, Gerhard J.

    2010-01-01

    Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

  16. From single molecule to single tubules

    NASA Astrophysics Data System (ADS)

    Guo, Chin-Lin

    2012-02-01

    Biological systems often make decisions upon conformational changes and assembly of single molecules. In vivo, epithelial cells (such as the mammary gland cells) can respond to extracellular matrix (ECM) molecules, type I collagen (COL), and switch their morphology from a lobular lumen (100-200 micron) to a tubular lumen (1mm-1cm). However, how cells make such a morphogenetic decision through interactions with each other and with COL is unclear. Using a temporal control of cell-ECM interaction, we find that epithelial cells, in response to a fine-tuned percentage of type I collagen (COL) in ECM, develop various linear patterns. Remarkably, these patterns allow cells to self-assemble into a tubule of length ˜ 1cm and diameter ˜ 400 micron in the liquid phase (i.e., scaffold-free conditions). In contrast with conventional thought, the linear patterns arise through bi-directional transmission of traction force, but not through diffusible biochemical factors secreted by cells. In turn, the transmission of force evokes a long-range (˜ 600 micron) intercellular mechanical interaction. A feedback effect is encountered when the mechanical interaction modifies cell positioning and COL alignment. Micro-patterning experiments further reveal that such a feedback is a novel cell-number-dependent, rich-get-richer process, which allows cells to integrate mechanical interactions into long-range (> 1mm) linear coordination. Our results suggest a mechanism cells can use to form and coordinate long-range tubular patterns, independent of those controlled by diffusible biochemical factors, and provide a new strategy to engineer/regenerate epithelial organs using scaffold-free self-assembly methods.

  17. 'Single molecule': theory and experiments, an introduction

    PubMed Central

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

  18. Molecular design of light-harvesting photosensitizers: effect of varied linker conjugation on interfacial electron transfer.

    PubMed

    Jiang, Jianbing; Swierk, John R; Hedström, Svante; Matula, Adam J; Crabtree, Robert H; Batista, Victor S; Schmuttenmaer, Charles A; Brudvig, Gary W

    2016-07-28

    Interfacial electron transfer dynamics of a series of photosensitizers bound to TiO2via linkers of varying conjugation strength are explored by spectroscopic and computational techniques. Injection and recombination depend on the extent of conjugation in the linker, where the LUMO delocalization determines the injection dynamics but both the HOMO and HOMO-1 are involved in recombination. PMID:27364769

  19. Nonlinear coherent spectroscopy in the single molecule limit (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Potma, Eric O.

    2015-10-01

    Detecting coherent anti-Stokes Raman scattering (CARS) signals from signal molecules is a longstanding experimental challenge. Driving the vibrational CARS response with surface plasmon fields has proven notoriously difficult due to strong background contributions, unfavorable heat dissipation and the phase dispersion of the plasmon modes in the ensemble. In this work we overcome previous experimental limitations and demonstrate time-resolved, vibrational CARS from molecules in the low copy number limit, down to the single molecule level. Our measurements, which are performed under ambient and non-electronic resonance conditions, establish that the coherent response from vibrational modes of individual molecules can be studied experimentally, opening up a new realm of molecular spectroscopic investigations.

  20. n and p type character of single molecule diodes.

    PubMed

    Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

    2015-01-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface. PMID:25666850

  1. n and p type character of single molecule diodes

    PubMed Central

    Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

    2015-01-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface. PMID:25666850

  2. n and p type character of single molecule diodes

    NASA Astrophysics Data System (ADS)

    Zoldan, Vinícius Claudio; Faccio, Ricardo; Pasa, André Avelino

    2015-02-01

    Looking for single molecule electronic devices, we have investigated the charge transport properties of individual tetra-phenylporphyrin molecules on different substrates by ultrahigh-vacuum scanning tunneling microscopy and spectroscopy and by first-principles calculations. The tetra-phenylporphyrins with a Co atom (Co-TPP) or 2 hydrogens (H2-TPP) in the central macrocycle when deposited on Cu3Au(100) substrates showed a diode-like behavior with p and n type character, respectively. After removing the central hydrogens of H2-TPP molecule with the STM tip an ohmic behavior was measured. The rectifying effect was understood from the theoretical point of view by assuming for Co-TPP HOMO conduction and for H2-TPP LUMO conduction, both selectively elected by the hybridization of states between molecule and substrate surface.

  3. Charge Transport in Azobenzene-Based Single-Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Garcia-Lekue, Aran; Kim, Youngsang; Sysoiev, Dmytro; Frederiksen, Thomas; Groth, Ulrich; Scheer, Elke

    2013-03-01

    The azobenzene class of molecules has become an archetype of molecular photoswitch research, due to their simple structure and the significant difference of the electronic system between their cis and trans isomers. However, a detailed understanding of the charge transport for the two isomers, when embedded in a junction with electrodes is still lacking. In order to clarify this issue, we investigate charge transport properties through single Azobenzene-ThioMethyl (AzoTM) molecules in a mechanically controlled break junction (MCBJ) system at 4.2 K. Single-molecule conductance, I-V characteristics, and IETS spectra of molecular junctions are measured and compared with first-principles transport calculations. Our studies elucidate the origin of a slightly higher conductance of junctions with cis isomer and demonstrate that IETS spectra of cis and trans forms show distinct vibrational fingerprints that can be used for identifying the isomer.

  4. Tunneling spectroscopy of organic monolayers and single molecules.

    PubMed

    Hipps, K W

    2012-01-01

    Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the

  5. Collective effects in Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Subedi, Pradeep

    Single molecule magnets (SMMs), such as Mn12-acetate, are composed of transition metal ions and consists of identical molecules with large ground-state spin (S = 10) and a strong uniaxial anisotropy (65 K). Below about 3 K, Mn12-acetate exhibits magnetic hysteresis with steps at specific values of longitudinal magnetic field due to resonant quantum tunneling between spin up and down projections along the easy axis. The intermolecular exchange interactions between spins on molecules are quite small and spins are considered to be independent and non-interacting. However, the molecules do interact with each other both through magnetic dipolar interactions and through the lattice (e.g. phonons). I have investigated collective effects in SMMs due to these intermolecular interactions. In the thesis I will present experiments that explored magnetic ordering due to magnetic dipole interactions in Mn12-acetate and Mn12-acetate-MeOH. I will also present exper- iments on the onset of magnetic de agration in Mn12-acetate due to a thermal instability. The magnetic ordering studies involved investigating the effect of transverse fields on the susceptibility of single crystals of Mn12-acetate and Mn12-acetate- MeOH. Transverse fields increase quantum spin uctuations that suppress long- range order. However, the suppression of the Curie temperature by transverse fields in Mn12-acetate is far more rapid than predicted by the Transverse-Field Ising Ferromagnetic Model (TFIFM) and instead agrees with the predictions of the Random-Field Ising Ferromagnet Model. It appears that solvent disorder in Mn12-acetate gives rise to a distribution of random-fields that further suppress long-range order. Subsequent studies on Mn12-acetate-MeOH, with the same spin and similar lattice constants but without solvent disorder as Mn12-acetate, agrees with the TFIFM. The magnetic de agration studies involved studying the instability that leads to the ignition of magnetic deflagration in a thermally

  6. Action spectroscopy for single-molecule reactions - Experiments and theory

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Motobayashi, K.; Frederiksen, T.; Ueba, H.; Kawai, M.

    2015-05-01

    We review several representative experimental results of action spectroscopy (AS) of single molecules on metal surfaces using a scanning tunneling microscope (STM) by M. Kawai's group over last decade. The experimental procedures to observe STM-AS are described. A brief description of a low-temperature STM and experimental setup are followed by key experimental techniques of how to determine an onset bias voltage of a reaction and how to measure a current change associated with reactions and finally how to observe AS for single molecule reactions. The experimental results are presented for vibrationally mediated chemical transformation of trans-2-butene to 1.3-butadiene molecule and rotational motion of a single cis-2-butene molecule among four equivalent orientations on Pd(1 1 0). The AS obtained from the motion clearly detects more vibrational modes than inelastic electron tunneling spectroscopy with an STM. AS is demonstrated as a useful and novel single molecule vibrational spectroscopy. The AS for a lateral hopping of water dimer on Pt(1 1 1) is presented as an example of novelty. Several distinct vibrational modes are detected as the thresholds in the AS. The assignment of the vibrational modes determined from the analysis of the AS is made from a view of the adsorption geometry of hydrogen-bond donor or acceptor molecules in water dimer. A generic theory of STM-AS, i.e., a reaction rate or yield as a function of bias voltage, is presented using a single adsorbate resonance model for single molecule reactions induced by the inelastic tunneling current. Formulas for the reaction rate R (V) and Y (V) , i.e., reaction yield per electron Y (V) = eR (V) / I are derived. It provides a versatile framework to analyze any vibrationally mediated reactions of single adsorbates on metal surfaces. Numerical examples are presented to demonstrate generic features of the vibrational generation rate and Y (V) at different levels of approximations and to show how the effective

  7. Single-molecule spectroscopy and dynamics at room temperature

    SciTech Connect

    Xie, X.S.

    1996-12-01

    The spirit of studying single-molecule behaviors dates back to the turn of the century. In addition to Einstein`s well-known work on Brownian motion, there has been a tradition for studying single {open_quotes}macromolecules{close_quotes} or a small number of molecules either by light scattering or by fluorescence using an optical microscope. Modern computers have allowed detailed studies of single-molecule behaviors in condensed media through molecular dynamics simulations. Optical spectroscopy offers a wealth of information on the structure, interaction, and dynamics of molecular species. With the motivation of removing {open_quotes}inhomogeneous broadening{close_quotes}, spectroscopic techniques have evolved from spectral hole burning, fluorescence line narrowing, and photo-echo to the recent pioneering work on single-molecule spectroscopy in solids at cryogenic temperatures. High-resolution spectroscopic work on single molecules relies on zero phonon lines which appear at cryogenic temperatures, and have narrow line widths and large absorption cross sections. Recent advances in near-field and confocal fluorescence have allowed not only fluorescence imaging of single molecules with high spatial resolutions but also single-molecule spectroscopy at room temperature. In this Account, the author provides a physical chemist`s perspective on experimental and theoretical developments on room-temperature single-molecule spectroscopy and dynamics, with the emphasis on the information obtainable from single-molecule experiments. 61 refs., 9 figs.

  8. Single molecule image formation, reconstruction and processing: introduction.

    PubMed

    Ashok, Amit; Piestun, Rafael; Stallinga, Sjoerd

    2016-07-01

    The ability to image at the single molecule scale has revolutionized research in molecular biology. This feature issue presents a collection of articles that provides new insights into the fundamental limits of single molecule imaging and reports novel techniques for image formation and analysis. PMID:27409708

  9. Single-molecule mechanics of protein-labelled DNA handles

    PubMed Central

    Wruck, Florian

    2016-01-01

    Summary DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG)-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp) were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG) beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD) imaging control experiments revealed that quantum dot–streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition

  10. Structure and mechanics of proteins from single molecules to cells

    NASA Astrophysics Data System (ADS)

    Brown, Andre E.

    2009-07-01

    Physical factors drive evolution and play important roles in motility and attachment as well as in differentiation. As animal cells adhere to survive, they generate force and "feel" various mechanical features of their surroundings and respond to externally applied forces. This mechanosensitivity requires a substrate for cells to adhere to and a mechanism for cells to apply force, followed by a cellular response to the mechanical properties of the substrate. We have taken an outside-in approach to characterize several aspects of cellular mechanosensitivity. First, we used single molecule force spectroscopy to measure how fibrinogen, an extracellular matrix protein that forms the scaffold of blood clots, responds to applied force and found that it rapidly unfolds in 23 nm steps at forces around 100 pN. Second, we used tensile testing to measure the force-extension behavior of fibrin gels and found that they behave almost linearly to strains of over 100%, have extensibilities of 170 +/- 15%, and undergo a large volume decrease that corresponds to a large and negative peak in compressibility at low strain, which indicates a structural transition. Using electron microscopy and X-ray scattering we concluded that these properties are likely due to coiled-coil unfolding, as observed at the single molecule level in fibrinogen. Moving inside cells, we used total internal reflection fluorescence and atomic force microscopy to image self-assembled myosin filaments. These filaments of motor proteins that are responsible for cell and muscle contractility were found to be asymmetric, with an average of 32% more force generating heads on one half than the other. This could imply a force imbalance, so that rather than being simply contractile, myosin filaments may also be motile in cells.

  11. Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

    PubMed Central

    Hines, Keegan E.; Bankston, John R.; Aldrich, Richard W.

    2015-01-01

    The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

  12. Gating a single-molecule transistor with individual atoms

    NASA Astrophysics Data System (ADS)

    Martínez-Blanco, Jesús; Nacci, Christophe; Erwin, Steven C.; Kanisawa, Kiyoshi; Locane, Elina; Thomas, Mark; von Oppen, Felix; Brouwer, Piet W.; Fölsch, Stefan

    2015-08-01

    Transistors, regardless of their size, rely on electrical gates to control the conductance between source and drain contacts. In atomic-scale transistors, this conductance is sensitive to single electrons hopping via individual orbitals. Single-electron transport in molecular transistors has been previously studied using top-down approaches to gating, such as lithography and break junctions. But atomically precise control of the gate--which is crucial to transistor action at the smallest size scales--is not possible with these approaches. Here, we used individual charged atoms, manipulated by a scanning tunnelling microscope, to create the electrical gates for a single-molecule transistor. This degree of control allowed us to tune the molecule into the regime of sequential single-electron tunnelling, albeit with a conductance gap more than one order of magnitude larger than observed previously. This unexpected behaviour arises from the existence of two different orientational conformations of the molecule, depending on its charge state. Our results show that strong coupling between these charge and conformational degrees of freedom leads to new behaviour beyond the established picture of single-electron transport in atomic-scale transistors.

  13. Interfacial Electron Transfer and Transient Photoconductivity Studied with Terahertz Spectroscopy

    NASA Astrophysics Data System (ADS)

    Milot, Rebecca Lee

    Terahertz spectroscopy is distinguished from other far infrared and millimeter wave spectroscopies by its inherent phase sensitivity and sub-picosecond time resolution making it a versatile technique to study a wide range of physical phenomena. As THz spectroscopy is still a relatively new field, many aspects of THz generation mechanisms have not been fully examined. Using terahertz emission spectroscopy (TES), THz emission from ZnTe(110) was analyzed and found to be limited by two-photon absorption and free-carrier generation at high excitation fluences. Due to concerns about the continued use of fossil fuels, solar energy has been widely investigated as a promising source of renewable energy. Dye-sensitized solar cells (DSSCs) have been developed as a low-cost alternative to conventional photovoltaic solar cells. To solve the issues of the intermittency and inefficient transport associated with solar energy, researchers are attempting to adapt DSSCs for water oxidation and chemical fuel production. Both device designs incorporate sensitizer molecules covalently bound to metal oxide nanoparticles. The sensitizer, which is comprised of a chromophore and anchoring group, absorbs light and transfers an electron from its excited state to the conduction band of the metal oxide, producing an electric current. Using time-resolved THz spectroscopy (TRTS), an optical pump/THz probe technique, the efficiency and dynamics of electron injection from sensitizers to metal oxides was evaluated as a function of the chromophore, its anchoring group, and the metal oxide identity. Experiments for studying fully functioning DSSCs and water oxidation devices are also described. Bio-inspired pentafluorophenyl porphyrin chromophores have been designed and synthesized for use in photoelectrochemical water oxidation cells. Influences on the efficiency and dynamics of electron injection from the chromophores into TiO2 and SnO2 nanoparticles due to changes in both the central substituent to

  14. Single-molecule spectroscopy and imaging over the decades.

    PubMed

    Moerner, W E; Shechtman, Yoav; Wang, Quan

    2015-01-01

    As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many

  15. Molecular 'OR' and 'AND' logic gates integrated in a single molecule

    NASA Astrophysics Data System (ADS)

    Ami, S.; Hliwa, M.; Joachim, C.

    2003-01-01

    Based on the N electrodes elastic scattering quantum chemistry (NESQC) technique, an intramolecular circuit simulator is presented for the design of electronic logic functions integrated inside a single molecule interconnected to the N electrodes. Using molecular rectifier groups, a molecule-OR and a molecule-AND are designed, their current-voltage characteristics calculated and their logic response presented. Both the OR and AND molecules have approximatively the targeted function. The running current of the OR gate, 10 fA, is quite low and the AND gate works only in an output voltage mode. This forbids the design of larger logic functions inside a single molecule with molecular rectifiers.

  16. Controlled switching of single-molecule junctions by mechanical motion of a phenyl ring.

    PubMed

    Kitaguchi, Yuya; Habuka, Satoru; Okuyama, Hiroshi; Hatta, Shinichiro; Aruga, Tetsuya; Frederiksen, Thomas; Paulsson, Magnus; Ueba, Hiromu

    2015-01-01

    Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch. The switch can be actuated by dual triggers, either by a voltage pulse or by displacement of the electrode, and electronic manipulation of the ring by chemical substitution enables rational control of the on-state conductance. Owing to its simple mechanics, structural robustness, and chemical accessibility, we propose that phenyl rings are promising components in mechanical molecular devices. PMID:26665080

  17. Superconducting molybdenum-rhenium electrodes for single-molecule transport studies

    SciTech Connect

    Gaudenzi, R.; Island, J. O.; Bruijckere, J. de; Burzurí, E.; Zant, H. S. J. van der; Klapwijk, T. M.

    2015-06-01

    We demonstrate that electronic transport through single molecules or molecular ensembles, commonly based on gold (Au) electrodes, can be extended to superconducting electrodes by combining gold with molybdenum-rhenium (MoRe). This combination induces proximity-effect superconductivity in the gold to temperatures of at least 4.6 K and magnetic fields of 6 T, improving on previously reported aluminum based superconducting nanojunctions. As a proof of concept, we show three-terminal superconductive transport measurements through an individual Fe{sub 4} single-molecule magnet.

  18. Controlled switching of single-molecule junctions by mechanical motion of a phenyl ring

    PubMed Central

    Kitaguchi, Yuya; Habuka, Satoru; Hatta, Shinichiro; Aruga, Tetsuya; Paulsson, Magnus; Ueba, Hiromu

    2015-01-01

    Summary Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch. The switch can be actuated by dual triggers, either by a voltage pulse or by displacement of the electrode, and electronic manipulation of the ring by chemical substitution enables rational control of the on-state conductance. Owing to its simple mechanics, structural robustness, and chemical accessibility, we propose that phenyl rings are promising components in mechanical molecular devices. PMID:26665080

  19. Dissecting single-molecule signal transduction in carbon nanotube circuits with protein engineering

    PubMed Central

    Choi, Yongki; Olsen, Tivoli J.; Sims, Patrick C.; Moody, Issa S.; Corso, Brad L.; Dang, Mytrang N.; Weiss, Gregory A.; Collins, Philip G.

    2013-01-01

    Single molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, non-fluorescent single molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems. PMID:23323846

  20. Measurement and understanding of single-molecule break junction rectification caused by asymmetric contacts

    SciTech Connect

    Wang, Kun; Zhou, Jianfeng; Hamill, Joseph M.; Xu, Bingqian

    2014-08-07

    The contact effects of single-molecule break junctions on rectification behaviors were experimentally explored by a systematic control of anchoring groups of 1,4-disubstituted benzene molecular junctions. Single-molecule conductance and I-V characteristic measurements reveal a strong correlation between rectifying effects and the asymmetry in contacts. Analysis using energy band models and I-V calculations suggested that the rectification behavior is mainly caused by asymmetric coupling strengths at the two contact interfaces. Fitting of the rectification ratio by a modified Simmons model we developed suggests asymmetry in potential drop across the asymmetric anchoring groups as the mechanism of rectifying I-V behavior. This study provides direct experimental evidence and sheds light on the mechanisms of rectification behavior induced simply by contact asymmetry, which serves as an aid to interpret future single-molecule electronic behavior involved with asymmetric contact conformation.

  1. Single-molecule redox blinking of perylene diimide derivatives in water.

    PubMed

    Cordes, Thorben; Vogelsang, Jan; Anaya, Milena; Spagnuolo, Carla; Gietl, Andreas; Summerer, Wolfram; Herrmann, Andreas; Müllen, Klaus; Tinnefeld, Philip

    2010-02-24

    Dynamic developments in ultrasensitive and superresolution fluorescence microscopy call for improved fluorescence markers with increased photostability and new functionalities. We used single-molecule spectroscopy to study water-soluble perylene dicarboximide fluorophores (PDI), which were immobilized in aqueous buffer by attaching the fluorophore to DNA. Under these conditions bright fluorescence, comparable to that of single-molecule compatible organic fluorophores, is observed with homogeneous spectral and fluorescence decay time distributions. We additionally show how the fluorescence of the PDI can be controlled through photoinduced electron-transfer reactions by using different concentrations of reductants and oxidants, yielding either blinking or stable emission. We explain these properties by the redox potentials of PDI and the recently introduced ROXS (reducing and oxidizing system) concept. Finally, we evaluate how this fluorescence control of PDIs can be used for superresolution "Blink-Microscopy" in aqueous or organic media and more generally for single-molecule spectroscopy. PMID:20121094

  2. Real-time single-molecule observations of proteins at the solid-liquid interface

    NASA Astrophysics Data System (ADS)

    Langdon, Blake Brianna

    Non-specific protein adsorption to solid surfaces is pervasive and observed across a broad spectrum of applications including biomaterials, separations, pharmaceuticals, and biosensing. Despite great interest in and considerable literature dedicated to the phenomena, a mechanistic understanding of this complex phenomena is lacking and remains controversial, partially due to the limits of ensemble-averaging techniques used to study it. Single-molecule tracking (SMT) methods allow us to study distinct protein dynamics (e.g. adsorption, desorption, diffusion, and intermolecular associations) on a molecule-by-molecule basis revealing the protein population and spatial heterogeneity inherent in protein interfacial behavior. By employing single-molecule total internal reflection fluorescence microscopy (SM-TIRFM), we have developed SMT methods to directly observe protein interfacial dynamics at the solid-liquid interface to build a better mechanistic understanding of protein adsorption. First, we examined the effects of surface chemistry (e.g. hydrophobicity, hydrogen-bonding capacity), temperature, and electrostatics on isolated protein desorption and interfacial diffusion for fibrinogen (Fg) and bovine serum albumin (BSA). Next, we directly and indirectly probed the effects of protein-protein interactions on interfacial desorption, diffusion, aggregation, and surface spatial heterogeneity on model and polymeric thin films. These studies provided many useful insights into interfacial protein dynamics including the following observations. First, protein adsorption was reversible, with the majority of proteins desorbing from all surface chemistries within seconds. Isolated protein-surface interactions were relatively weak on both hydrophobic and hydrophilic surfaces (apparent desorption activation energies of only a few kBT). However, proteins could dynamically and reversibly associate at the interface, and these interfacial associations led to proteins remaining on the

  3. Probing interfacial electronic structures in atomic layer LaMnO{sub3} and SrTiO{sub 3} superlattices.

    SciTech Connect

    Shah, A. B.; Ramasse, Q. M.; Zhai, X.; Wen, J. G.; May, S. J.; Petrov, I.; Bhattacharya, A.; Abbamonte, P.; Eckstein, J. N.; Zuo, J.-M.; Univ. of Illinois; LBNL

    2010-01-01

    The interfacial electronic structure characterization of a m x (LaMnO{sub 3})/n x (SrTiO{sub 3}) superlattice based on scanning transmission electron microscopy and electron energy loss spectroscopy. Evidence of interfacial band alignment and electron transfer are presented based on the observation of O K edge of individual transition metal and oxygen atomic columns. Electron probe aberration correction was essential for the high spatial resolution mapping of interfacial electronic states.

  4. Graphene-porphyrin single-molecule transistors

    NASA Astrophysics Data System (ADS)

    Mol, Jan A.; Lau, Chit Siong; Lewis, Wilfred J. M.; Sadeghi, Hatef; Roche, Cecile; Cnossen, Arjen; Warner, Jamie H.; Lambert, Colin J.; Anderson, Harry L.; Briggs, G. Andrew D.

    2015-07-01

    We demonstrate a robust graphene-molecule-graphene transistor architecture. We observe remarkably reproducible single electron charging, which we attribute to insensitivity of the molecular junction to the atomic configuration of the graphene electrodes. The stability of the graphene electrodes allow for high-bias transport spectroscopy and the observation of multiple redox states at room-temperature.We demonstrate a robust graphene-molecule-graphene transistor architecture. We observe remarkably reproducible single electron charging, which we attribute to insensitivity of the molecular junction to the atomic configuration of the graphene electrodes. The stability of the graphene electrodes allow for high-bias transport spectroscopy and the observation of multiple redox states at room-temperature. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR03294F

  5. Microscopy beyond the diffraction limit using actively controlled single molecules

    PubMed Central

    MOERNER, W.E.

    2013-01-01

    Summary In this short review, the general principles are described for obtaining microscopic images with resolution beyond the optical diffraction limit with single molecules. Although it has been known for several decades that single-molecule emitters can blink or turn on and off, in recent work the addition of on/off control of molecular emission to maintain concentrations at very low levels in each imaging frame combined with sequential imaging of sparse subsets has enabled the reconstruction of images with resolution far below the optical diffraction limit. Single-molecule active control microscopy provides a powerful window into information about nanoscale structures that was previously unavailable. PMID:22582796

  6. Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules

    SciTech Connect

    Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; Petkiewicz, Shayne; Smith, Jessica M.; Ferry, Vivian E.; Correia, Ana Luisa; Alivisatos, A. Paul; Bissell, Mina J.

    2015-06-03

    Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Lastly, such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.

  7. Single-molecule detection: applications to ultrasensitive biochemical analysis

    NASA Astrophysics Data System (ADS)

    Castro, Alonso; Shera, E. Brooks

    1995-06-01

    Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

  8. Single Molecule Detection and Imaging in Single Living Cells

    NASA Astrophysics Data System (ADS)

    Nie, Shuming

    2002-03-01

    Direct observation of single molecules and single molecular events inside living cells could dramatically improve our understanding of basic cellular processes (e.g., signal transduction and gene transcription) as well as improving our knowledge on the intracellular transport and fate of therapeutic agents (e.g., antisense RNA and gene therapy vectors). This talk will focus on using single-molecule fluorescence and luminescent quantum dots to examine the dynamics and spatial distribution of RNA and proteins inside living cells and on the surface membrane surface. These single-molecule studies yield a detailed description of molecular events and cellular structures under physiological conditions.

  9. Single-molecule imaging at high hydrostatic pressure

    NASA Astrophysics Data System (ADS)

    Vass, Hugh; Lucas Black, S.; Flors, Cristina; Lloyd, Diarmuid; Bruce Ward, F.; Allen, Rosalind J.

    2013-04-01

    Direct microscopic fluorescence imaging of single molecules can provide a wealth of mechanistic information, but up to now, it has not been possible under high pressure conditions, due to limitations in microscope pressure cell design. We describe a pressure cell window design that makes it possible to image directly single molecules at high hydrostatic pressure. We demonstrate our design by imaging single molecules of Alexa Fluor 647 dye bound to DNA, at 120 and 210 bar, and following their fluorescence photodynamics. We further show that the failure pressure of this type of pressure cell window can be in excess of 1 kbar.

  10. Reversible Tuning of Interfacial and Intramolecular Charge Transfer in Individual MnPc Molecules.

    PubMed

    Zhong, Jian-Qiang; Wang, Zhunzhun; Zhang, Jia Lin; Wright, Christopher A; Yuan, Kaidi; Gu, Chengding; Tadich, Anton; Qi, Dongchen; Li, He Xing; Lai, Min; Wu, Kai; Xu, Guo Qin; Hu, Wenping; Li, Zhenyu; Chen, Wei

    2015-12-01

    The reversible selective hydrogenation and dehydrogenation of individual manganese phthalocyanine (MnPc) molecules has been investigated using photoelectron spectroscopy (PES), low-temperature scanning tunneling microscopy (LT-STM), synchrotron-based near edge X-ray absorption fine structure (NEXAFS) measurements, and supported by density functional theory (DFT) calculations. It is shown conclusively that interfacial and intramolecular charge transfer arises during the hydrogenation process. The electronic energetics upon hydrogenation is identified, enabling a greater understanding of interfacial and intramolecular charge transportation in the field of single-molecule electronics. PMID:26528623

  11. Negative differential conductance and super-Poissonian shot noise in single-molecule magnet junctions

    PubMed Central

    Xue, Hai-Bin; Liang, Jiu-Qing; Liu, Wu-Ming

    2015-01-01

    Molecular spintroinic device based on a single-molecule magnet is one of the ultimate goals of semiconductor nanofabrication technologies. It is thus necessary to understand the electron transport properties of a single-molecule magnet junction. Here we study the negative differential conductance and super-Poissonian shot noise properties of electron transport through a single-molecule magnet weakly coupled to two electrodes with either one or both of them being ferromagnetic. We predict that the negative differential conductance and super-Poissonian shot noise, which can be tuned by a gate voltage, depend sensitively on the spin polarization of the source and drain electrodes. In particular, the shot noise in the negative differential conductance region can be enhanced or decreased originating from the different formation mechanisms of negative differential conductance. The effective competition between fast and slow transport channels is responsible for the observed negative differential conductance and super-Poissonian shot noise. In addition, we further discuss the skewness and kurtosis properties of transport current in the super-Poissonian shot noise regions. Our findings suggest a tunable negative differential conductance molecular device, and the predicted properties of high-order current cumulants are very interesting for a better understanding of electron transport through single-molecule magnet junctions. PMID:25736094

  12. Large Conductance Switching in a Single-Molecule Device through Room Temperature Spin-Dependent Transport.

    PubMed

    Aragonès, Albert C; Aravena, Daniel; Cerdá, Jorge I; Acís-Castillo, Zulema; Li, Haipeng; Real, José Antonio; Sanz, Fausto; Hihath, Josh; Ruiz, Eliseo; Díez-Pérez, Ismael

    2016-01-13

    Controlling the spin of electrons in nanoscale electronic devices is one of the most promising topics aiming at developing devices with rapid and high density information storage capabilities. The interface magnetism or spinterface resulting from the interaction between a magnetic molecule and a metal surface, or vice versa, has become a key ingredient in creating nanoscale molecular devices with novel functionalities. Here, we present a single-molecule wire that displays large (>10000%) conductance switching by controlling the spin-dependent transport under ambient conditions (room temperature in a liquid cell). The molecular wire is built by trapping individual spin crossover Fe(II) complexes between one Au electrode and one ferromagnetic Ni electrode in an organic liquid medium. Large changes in the single-molecule conductance (>100-fold) are measured when the electrons flow from the Au electrode to either an α-up or a β-down spin-polarized Ni electrode. Our calculations show that the current flowing through such an interface appears to be strongly spin-polarized, thus resulting in the observed switching of the single-molecule wire conductance. The observation of such a high spin-dependent conductance switching in a single-molecule wire opens up a new door for the design and control of spin-polarized transport in nanoscale molecular devices at room temperature. PMID:26675052

  13. Integrating logic functions inside a single molecule

    NASA Astrophysics Data System (ADS)

    Stadler, R.; Ami, S.; Joachim, C.; Forshaw, M.

    2004-04-01

    In Stadler et al (2003 Nanotechnology 14 138), a scheme for a molecular memory was presented. It was based on the influence of the positions of chemical side-groups attached to aromatic molecules on the paths for electrons propagating through these molecules in the ballistic and tunnelling transport regimes. Here we extend this concept in the following ways. (i) A graphical method is derived from an electron scattering formalism based on a topological Hückel description, which allows us to estimate whether the electron transport between two electrodes attached to specific atomic sites in an arbitrary molecule is finite or zero at the Fermi level. (ii) The same scheme that was used for the implementation of the molecular memory is extended to logic functions, in particular a half-adder. (iii) A more realistic description of the chemical nature of the proposed intra-molecular circuits is achieved by using the elastic scattering quantum chemistry (ESQC) technique in an extended Hückel implementation and by specifying the side-groups as nitro-groups, which are rotated in order to feed the signal inputs into the computational circuit.

  14. Combined optical and electrochemical methods for studying electrochemistry at the single molecule and single particle level: recent progress and perspectives.

    PubMed

    Hill, Caleb M; Clayton, Daniel A; Pan, Shanlin

    2013-12-28

    We present a review of recent efforts aimed at understanding interfacial charge transfer at the single molecule and single nanoparticle level using the combined methods of traditional electrochemistry and optical spectroscopy with high spatial, spectral, and temporal resolution. Elastic light scattering, surface enhanced Raman scattering (SERS), fluorescence, and electrogenerated chemiluminescence (ECL) techniques have been demonstrated to be powerful tools for the study of interfacial charge transfer events involving a single molecule or nanoparticle and for the characterization of nanostructured electrodes. It is shown that these optical methods enable the exploration of electrochemical events with improved temporal and spatial resolution which are usually obstructed by the ensemble averaging inherent in conventional electrochemical methods. In this report, the current status of the field is reviewed and challenges for future work are discussed. PMID:24196825

  15. Multiparameter single-molecule fluorescence measurements of DNA intercalating fluorophores

    NASA Astrophysics Data System (ADS)

    Bowen, Benjamin P.; Enderlein, Jorg; Woodbury, Neal W. T.

    2003-06-01

    Experiments using single-molecules of TOTO-1 intercalated into dsDNA were performed to investigate the DNA sequence dependence on the fluorescence detectable with single-molecule fluorescence spectroscopy. Previous work has shown that there is a difference in the fluorescence lifetime when TOTO-1 is intercalated in poly-AT DNA or in poly-GC DNA. The fluorescence detected from single-molecules in this work for poly-GC and poly-AT DNA showed fluorescence lifetimes of 2.1 and 1.8 nsec, respectively. Analysis of the fluorescence intensity detected from single-molecules of TOTO-1 was performed by fluorescence cross-correlation spectroscopy. TOTO-1 is shown to spend large amounts of time in dark states. These dark states reduce the detectable fluorescence intensity to approximately 10 photons per millisecond on average.

  16. Single-molecule localization software applied to photon counting imaging.

    PubMed

    Hirvonen, Liisa M; Kilfeather, Tiffany; Suhling, Klaus

    2015-06-01

    Centroiding in photon counting imaging has traditionally been accomplished by a single-step, noniterative algorithm, often implemented in hardware. Single-molecule localization techniques in superresolution fluorescence microscopy are conceptually similar, but use more sophisticated iterative software-based fitting algorithms to localize the fluorophore. Here, we discuss common features and differences between single-molecule localization and photon counting imaging and investigate the suitability of single-molecule localization software for photon event localization. We find that single-molecule localization software packages designed for superresolution microscopy-QuickPALM, rapidSTORM, and ThunderSTORM-can work well when applied to photon counting imaging with a microchannel-plate-based intensified camera system: photon event recognition can be excellent, fixed pattern noise can be low, and the microchannel plate pores can easily be resolved. PMID:26192667

  17. Computer systems for annotation of single molecule fragments

    DOEpatents

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  18. Understanding Enzyme Activity Using Single Molecule Tracking (Poster)

    SciTech Connect

    Liu, Y.-S.; Zeng, Y.; Luo, Y.; Xu, Q.; Himmel, M.; Smith S.; Wei, H.; Ding, S.-Y.

    2009-06-01

    This poster describes single-molecule tracking and total internal reflection fluorescence microscopy. It discusses whether the carbohydrate-binding module (CBM) moves on cellulose, how the CBM binds to cellulose, and the mechanism of cellulosome assembly.

  19. Kinetic pathway for interfacial electron transfer from a semiconductor to a molecule.

    PubMed

    Hu, Ke; Blair, Amber D; Piechota, Eric J; Schauer, Phil A; Sampaio, Renato N; Parlane, Fraser G L; Meyer, Gerald J; Berlinguette, Curtis P

    2016-09-01

    Molecular approaches to solar-energy conversion require a kinetic optimization of light-induced electron-transfer reactions. At molecular-semiconductor interfaces, this optimization has previously been accomplished through control of the distance between the semiconductor donor and the molecular acceptor and/or the free energy that accompanies electron transfer. Here we show that a kinetic pathway for electron transfer from a semiconductor to a molecular acceptor also exists and provides an alternative method for the control of interfacial kinetics. The pathway was identified by the rational design of molecules in which the distance and the driving force were held near parity and only the geometric torsion about a xylyl- or phenylthiophene bridge was varied. Electronic coupling through the phenyl bridge was a factor of ten greater than that through the xylyl bridge. Comparative studies revealed a significant bridge dependence for electron transfer that could not be rationalized by a change in distance or driving force. Instead, the data indicate an interfacial electron-transfer pathway that utilizes the aromatic bridge orbitals. PMID:27554412

  20. An Improved Surface Passivation Method for Single-Molecule Studies

    PubMed Central

    Hua, Boyang; Young Han, Kyu; Zhou, Ruobo; Kim, Hajin; Shi, Xinghua; Abeysirigunawardena, Sanjaya C.; Jain, Ankur; Singh, Digvijay; Aggarwal, Vasudha; Woodson, Sarah A.; Ha, Taekjip

    2014-01-01

    We herein report a surface passivation method for in vitro single-molecule studies, which more efficiently prevents non-specific binding of biomolecules as compared to the polyethylene glycol surface. The new surface does not perturb the behavior and activities of tethered biomolecules. It can also be used for single-molecule imaging in the presence of high concentrations of labeled species in solution. Reduction in preparation time and cost is another major advantage. PMID:25306544

  1. Probing interfacial electron dynamics with time-resolved X-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Neppl, Stefan

    2015-05-01

    Time-resolved core-level spectroscopy techniques using laser pulses to initiate and short X-ray pulses to probe photo-induced processes have the potential to provide electronic state- and atomic site-specific insight into fundamental electron dynamics at complex interfaces. We describe the implementation of femto- and picosecond time-resolved photoelectron spectroscopy at the Linac Coherent Light Source (LCLS) and at the Advanced Light Source (ALS) in order to follow light-driven electron dynamics at dye-semiconductor interfaces on femto- to nanosecond timescales, and from the perspective of individual atomic sites. A distinct transient binding-energy shift of the Ru3d photoemission lines originating from the metal centers of N3 dye-molecules adsorbed on nanoporous ZnO is observed 500 fs after resonant HOMO-LUMO excitation with a visible laser pulse. This dynamical chemical shift is accompanied by a characteristic surface photo-voltage response of the semiconductor substrate. The two phenomena and their correlation will be discussed in the context of electronic bottlenecks for efficient interfacial charge-transfer and possible charge recombination and relaxation pathways leading to the neutralization of the transiently oxidized dye following ultrafast electron injection. First steps towards in operando time-resolved X-ray absorption spectroscopy techniques to monitor interfacial chemical dynamics will be presented.

  2. Reliable anchoring groups for single-molecule junctions

    NASA Astrophysics Data System (ADS)

    González, M. Teresa; Leary, Edmund; Evangeli, Charalambos; Arroyo, Carlos; Rubio-Bollinger, Gabino; Agraïit, Nicolás

    2012-02-01

    In the field of molecular electronics, thiols have been extensively used as the most common anchoring groups to bind molecules to gold electrodes. However, other anchoring groups as amines can provide interesting advantages. Recently, C-60 has been also proposed as a possible very efficient binding group. In this talk, I will present our studies on molecular junctions formed by thiol-, amine-, and C-60-terminated molecules. We use a STM (scanning tunneling microscope) break-junction technique to create and characterized single-molecule junctions both in ambient and liquid environment. We compare thiols and amines on the alkane family and an oligo(phenylene ethynylene). Our study of the molecular-junction stretching length allows us to conclude that thiols affect atomic rearrangement at the electrodes significantly more than amines. Using C-60-terminated molecules, we have recently introduced a new technique for controllably wiring one molecule at a time. We first get STM images to located isolated molecules on a gold substrate, which are then specifically targeted and contacted using a STM gold tip. This technique offers a significant improvement over other techniques, as it guaranties that one and only one molecule is contacted at a time between the electrodes.

  3. Gold plasmonic effects on charge transport through single molecule junctions

    NASA Astrophysics Data System (ADS)

    Adak, Olgun; Venkataraman, Latha

    2014-03-01

    We study the impact of surface plasmon polaritons, the coupling of electromagnetic waves to collective electron oscillations on metal surfaces, on the conductance of single-molecule junctions. We use a scanning-tunneling microscope based break junction setup that is built into an optical microscope to form molecular junctions. Coherent 685nm light is used to illuminate the molecular junctions formed with 4,4'-bipyridine with diffraction limited focusing performance. We employ a lock-in type technique to measure currents induced by light. Furthermore, the thermal expansion due to laser heating is mimicked by mechanically modulating inter-electrode separation. For each junction studied, we measure current, and use AC techniques to determine molecular junction resonance levels and coupling strengths. We use a cross correlations analysis technique to analyze and compare the effect of light to that of the mechanical modulation. Our results show that junction transmission characteristics are not altered under illumination, within the resolution of our instrument. We argue that photo-currents measured with lock-in techniques in these kinds of structures are due to thermal effects. This work was funded by the Center for Re-Defining Photovoltaic Efficiency through Molecule Scale Control, an EFRC funded by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DESC0001085.

  4. Mapping the Transmission Functions of Single-Molecule Junctions.

    PubMed

    Capozzi, Brian; Low, Jonathan Z; Xia, Jianlong; Liu, Zhen-Fei; Neaton, Jeffrey B; Campos, Luis M; Venkataraman, Latha

    2016-06-01

    Charge transport phenomena in single-molecule junctions are often dominated by tunneling, with a transmission function dictating the probability that electrons or holes tunnel through the junction. Here, we present a new and simple technique for measuring the transmission functions of molecular junctions in the coherent tunneling limit, over an energy range of 1.5 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different exposed areas, which results in the formation of electric double layers of dissimilar density on the two electrodes. This allows us to electrostatically shift the molecular resonance relative to the junction Fermi levels in a manner that depends on the sign of the applied bias, enabling us to map out the junction's transmission function and determine the dominant orbital for charge transport in the molecular junction. We demonstrate this technique using two groups of molecules: one group having molecular resonance energies relatively far from EF and one group having molecular resonance energies within the accessible bias window. Our results compare well with previous electrochemical gating data and with transmission functions computed from first principles. Furthermore, with the second group of molecules, we are able to examine the behavior of a molecular junction as a resonance shifts into the bias window. This work provides a new, experimentally simple route for exploring the fundamentals of charge transport at the nanoscale. PMID:27186894

  5. Quantum dots for quantitative imaging: from single molecules to tissue.

    PubMed

    Vu, Tania Q; Lam, Wai Yan; Hatch, Ellen W; Lidke, Diane S

    2015-04-01

    Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive, technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes. PMID:25620410

  6. Developing Single-Molecule Technique with Microsecond Resolution

    NASA Astrophysics Data System (ADS)

    Akhterov, Maxim V.

    Molecular machines like proteins are responsible for many regulatory and catalytic functions. Specifically, molecular motions of proteins and their flexibility determine conformational states required for enzyme catalysis, signal transduction, and protein-protein interactions. However, the mechanisms for protein transitions between conformational states are often poorly understood, especially in the milli- to microsecond ranges where conventional optical techniques and computational modeling are most limited. This work describes development of an electronic single-molecule technique for monitoring microsecond motions of biological molecules. Dynamic changes of conductance through a transistor made of a single-walled carbon nanotube (SWNT-FET) report conformational changes of a protein molecule tethered to the SWNT sidewall. In principle, the high operating speed of SWNT-FETs could allow this technique to resolve molecular events with nanosecond resolution. This project focused on improving the technique to a 200 kHz effective bandwidth in order to resolve microsecond-scale dynamics. The improvement was achieved with a home-built electrochemical flow cell. By minimizing parasitic capacitance due to liquid coupling to electrodes and eliminating noise pickup, the flow cell enabled low-noise, high bandwidth measurement of molecular events as short as 2 mus. The apparatus was used to observe closing and opening motions of lysozyme. Preliminary results suggest that lysozyme has a distribution of possible velocities with the most probable speed approaching our experimental resolution of 2 mus.

  7. Magnetic anisotropy and high-spin effects in single-molecule transistors

    NASA Astrophysics Data System (ADS)

    Zyazin, Alexander; van den Berg, Johan; Osorio, Edgar; Konstantinidis, Nikos; Leijnse, Martin; May, Falk; Hofstetter, Walter; Danieli, Chiara; Cornia, Andrea; Wegewijs, Maarten; van der Zant, Herre

    2011-03-01

    Fabrication of single-molecule transistors where electron transport occurs through an individual molecule has become possible due to the recent progress in molecular electronics. Three-terminal configuration allows charging molecules and performing transport spectroscopy in multiple redox states. Single-molecule magnets combining large spin with uniaxial anisotropy are of special interest as appealing candidates for high density memory applications and quantum information processing. We study single-molecule magnets Fe 4 . Three-terminal junctions are fabricated using electromigration of gold nanowires followed by a self-breaking. High-spin Kondo effect and inelastic cotunneling excitations show up in transport measurements. Several excitations feature the energy close to the energy of zero-field splitting (ZFS) of a ground spin multiplet in bulk. This splitting is caused by the anisotropy and is a hallmark of single-molecule magnets. We observe nonlinear Zeeman effect due to a misalignment of an anisotropy axis and a magnetic field direction. The ZFS energy is increased in oxidized and reduced states of the molecule indicating enhancement of the anisotropy in these states.

  8. Single-Molecule Conductance of Viologen-Cucurbit[8]uril Host-Guest Complexes.

    PubMed

    Zhang, Wei; Gan, Shiyu; Vezzoli, Andrea; Davidson, Ross J; Milan, David C; Luzyanin, Konstantin V; Higgins, Simon J; Nichols, Richard J; Beeby, Andrew; Low, Paul J; Li, Buyi; Niu, Li

    2016-05-24

    The local molecular environment is a critical factor which should be taken into account when measuring single-molecule electrical properties in condensed media or in the design of future molecular electronic or single molecule sensing devices. Supramolecular interactions can be used to control the local environment in molecular assemblies and have been used to create microenvironments, for instance, for chemical reactions. Here, we use supramolecular interactions to create microenvironments which influence the electrical conductance of single molecule wires. Cucurbit[8]uril (CB[8]) with a large hydrophobic cavity was used to host the viologen (bipyridinium) molecular wires forming a 1:1 supramolecular complex. Significant increases in the viologen wire single molecule conductances are observed when it is threaded into CB[8] due to large changes of the molecular microenvironment. The results were interpreted within the framework of a Marcus-type model for electron transfer as arising from a reduction in outer-sphere reorganization energy when the viologen is confined within the hydrophobic CB[8] cavity. PMID:27055002

  9. Single molecule dissociation by tunneling electrons in NO-Co-Porphyrin complex on Au(111): A novel mechanics revealed by scanning tunneling spectroscopy and first-principles thermodynamic simulation

    NASA Astrophysics Data System (ADS)

    Chang, Yunhee; Kim, Howon; Lee, Eui-Sup; Jang, Won-Jun; Kim, Yong-Hyun; Kahng, Se-Jong

    2015-03-01

    To microscopically understand the mechanisms of electron-induced NO dissociations, we performed first-principles density-functional theory (DFT) calculations for NO-CoTPP on Au(111). We explain the scanning tunneling microscopy (STM) results that the dissociations of NO were induced by both positive and negative voltage pulses with threshold voltages, +0.68 V and 0.74 V, respectively, at 0.1 nA tunneling current, showing power law relations between tunneling current and dissociation yield. To evaluate first-principles thermodynamics of the NO dissociation, we considered not only adsorption-desorption energetics, zero-point energy, and vibrational free energy at experiment temperature from first-principles, but also the chemical potential of NO gas at the cryogenic ultra-high vacuum condition. Using first-principles thermodynamics for the NO dissociation, we argue that the dissociations are induced with inelastic electron tunneling through molecular orbital resonances.

  10. Interfacial electron transfer dynamics of ru(II)-polypy6ridine sensitized TiO2

    SciTech Connect

    Jakubikova, Elena; Martin, Richard L; Batista, Enrique R; Snoeberger, Robert C; Batista, Victor S

    2009-01-01

    Quantum dynamics simulations combined with density functional theory calculations are applied to study interfacial electron transfer (IET) from pyridine-4-phosphonic acid, [Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 2+} and [Ru(tpy)(bpy)(H{sub 2}O)-Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 4+} into the (101) surface of anatase TiO{sub 2}. IET rate from pyridine-4-phosphonic acid attached to the nanoparticle in bidentate mode ({tau} {approx} 100 fs) is an order of magnitude faster than the IET rate of the adsorbate attached in the monodentate mode ({tau} {approx} 1 ps). Upon excitation with visible light, [Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 2+} attached to TiO{sub 2} in bidentate binding mode will undergo IET with the rate of {approx} 1-10 ps, which is competitive with the excited state decay into the ground state. The probability of electron injection from [Ru(tpy)(bpy)(H{sub 2}O)-Ru(tpy)(tpy(PO{sub 3}H{sub 2}))]{sup 4+} is rather low, as the excitation with visible light localizes the excited electron in the tpy-tpy bridge, which does not have favorable coupling with the TiO{sub 2} nanoparticle. The results are relevant to better understanding of the adsorbate features important for promoting efficient interfacial electron transfer into the semiconductor.

  11. Interfacial valence electron localization and the corrosion resistance of Al-SiC nanocomposite

    NASA Astrophysics Data System (ADS)

    Mosleh-Shirazi, Sareh; Hua, Guomin; Akhlaghi, Farshad; Yan, Xianguo; Li, Dongyang

    2015-12-01

    Microstructural inhomogeneity generally deteriorates the corrosion resistance of materials due to the galvanic effect and interfacial issues. However, the situation may change for nanostructured materials. This article reports our studies on the corrosion behavior of SiC nanoparticle-reinforced Al6061 matrix composite. It was observed that the corrosion resistance of Al6061 increased when SiC nanoparticles were added. Overall electron work function (EWF) of the Al-SiC nanocomposite increased, along with an increase in the corrosion potential. The electron localization function of the Al-SiC nanocomposite was calculated and the results revealed that valence electrons were localized in the region of SiC-Al interface, resulting in an increase in the overall work function and thus building a higher barrier to hinder electrons in the nano-composite to participate in corrosion reactions.

  12. Interfacial valence electron localization and the corrosion resistance of Al-SiC nanocomposite

    PubMed Central

    Mosleh-Shirazi, Sareh; Hua, Guomin; Akhlaghi, Farshad; Yan, Xianguo; Li, Dongyang

    2015-01-01

    Microstructural inhomogeneity generally deteriorates the corrosion resistance of materials due to the galvanic effect and interfacial issues. However, the situation may change for nanostructured materials. This article reports our studies on the corrosion behavior of SiC nanoparticle-reinforced Al6061 matrix composite. It was observed that the corrosion resistance of Al6061 increased when SiC nanoparticles were added. Overall electron work function (EWF) of the Al-SiC nanocomposite increased, along with an increase in the corrosion potential. The electron localization function of the Al-SiC nanocomposite was calculated and the results revealed that valence electrons were localized in the region of SiC-Al interface, resulting in an increase in the overall work function and thus building a higher barrier to hinder electrons in the nano-composite to participate in corrosion reactions. PMID:26667968

  13. Observing single molecule chemical reactions on metal nanoparticles.

    SciTech Connect

    Emory, S. R.; Ambrose, W. Patrick; Goodwin, P. M.; Keller, Richard A.

    2001-01-01

    We report the study of the photodecomposition of single Rhodamine 6G (R6G) dye molecules adsorbed on silver nanoparticles. The nanoparticles were immobilized and spatially isolated on polylysine-derivatized glass coverslips, and confocal laser microspectroscopy was used to obtain surface-enhanced Raman scattering (SERS) spectra from individual R6G molecules. The photodecomposition of these molecules was observed with 150-ms temporal resolution. The photoproduct was identified as graphitic carbon based on the appearance of broad SERS vibrational bands at 1592 cm{sup -1} and 1340 cm{sup -1} observed in both bulk and averaged single-molecule photoproduct spectra. In contrast, when observed at the single-molecule level, the photoproduct yielded sharp SERS spectra. The inhomogeneous broadening of the bulk SERS spectra is due to a variety of photoproducts in different surface orientations and is a characteristic of ensemble-averaged measurements of disordered systems. These single-molecule studies indicate a photodecomposition pathway by which the R6G molecule desorbs from the metal surface, an excited-state photoreaction occurs, and the R6G photoproduct(s) readsorbs to the surface. A SERS spectrum is obtained when either the intact R6G or the R6G photoproduct(s) are adsorbed on a SERS-active site. This work further illustrates the power of single-molecule spectroscopy (SMS) to reveal unique behaviors of single molecules that are not discernable with bulk measurements.

  14. Sizing up single-molecule enzymatic conformational dynamics.

    PubMed

    Lu, H Peter

    2014-02-21

    Enzymatic reactions and related protein conformational dynamics are complex and inhomogeneous, playing crucial roles in biological functions. The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. It is extremely difficult to characterize and analyze such complex dynamics in an ensemble-averaged measurement, especially when the enzymes are associated with multiple-step, multiple-conformation complex chemical interactions and transformations. Beyond the conventional ensemble-averaged studies, real-time single-molecule approaches have been demonstrated to be powerful in dissecting the complex enzymatic reaction dynamics and related conformational dynamics. Single-molecule enzymology has come a long way since the early demonstrations of the single-molecule spectroscopy studies of enzymatic dynamics about two decades ago. The rapid development of this fundamental protein dynamics field is hand-in-hand with the new development of single-molecule imaging and spectroscopic technology and methodology, theoretical model analyses, and correlations with biological preparation and characterization of the enzyme protein systems. The complex enzymatic reactions can now be studied one molecule at a time under physiological conditions. Most exciting developments include active manipulation of enzymatic conformational changes and energy landscape to regulate and manipulate the enzymatic reactivity and associated conformational dynamics, and the new advancements have established a new stage for studying complex protein dynamics beyond by simply observing but by actively manipulating and observing the enzymatic dynamics at the single-molecule sensitivity temporally and spatially. PMID:24306450

  15. Inelastic transport and low-bias rectification in a single-molecule diode.

    PubMed

    Hihath, Joshua; Bruot, Christopher; Nakamura, Hisao; Asai, Yoshihiro; Díez-Pérez, Ismael; Lee, Youngu; Yu, Luping; Tao, Nongjian

    2011-10-25

    Designing, controlling, and understanding rectification behavior in molecular-scale devices has been a goal of the molecular electronics community for many years. Here we study the transport behavior of a single molecule diode, and its nonrectifying, symmetric counterpart at low temperatures, and at both low and high biases to help elucidate the electron-phonon interactions and transport mechanisms in the rectifying system. We find that the onset of current rectification occurs at low biases, indicating a significant change in the elastic transport pathway. However, the peaks in the inelastic electron tunneling (IET) spectrum are antisymmetric about zero bias and show no significant changes in energy or intensity in the forward or reverse bias directions, indicating that despite the change in the elastic transmission probability there is little impact on the inelastic pathway. These results agree with first principles calculations performed to evaluate the IETS, which also allow us to identify which modes are active in the single molecule junction. PMID:21932824

  16. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling.

    PubMed

    Osorio, Henrry M; Catarelli, Samantha; Cea, Pilar; Gluyas, Josef B G; Hartl, František; Higgins, Simon J; Leary, Edmund; Low, Paul J; Martín, Santiago; Nichols, Richard J; Tory, Joanne; Ulstrup, Jens; Vezzoli, Andrea; Milan, David C; Zeng, Qiang

    2015-11-18

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids. These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter of 0.2 for the equivalent aqueous gating system. This study shows that ionic liquids are far more effective media for gating the conductance of single molecules than either solid-state three-terminal platforms created using nanolithography, or aqueous media. PMID:26488257

  17. Single-Molecule Experiments in Vitro and in Silico

    NASA Astrophysics Data System (ADS)

    Sotomayor, Marcos; Schulten, Klaus

    2007-05-01

    Single-molecule force experiments in vitro enable the characterization of the mechanical response of biological matter at the nanometer scale. However, they do not reveal the molecular mechanisms underlying mechanical function. These can only be readily studied through molecular dynamics simulations of atomic structural models: “in silico” (by computer analysis) single-molecule experiments. Steered molecular dynamics simulations, in which external forces are used to explore the response and function of macromolecules, have become a powerful tool complementing and guiding in vitro single-molecule experiments. The insights provided by in silico experiments are illustrated here through a review of recent research in three areas of protein mechanics: elasticity of the muscle protein titin and the extracellular matrix protein fibronectin; linker-mediated elasticity of the cytoskeleton protein spectrin; and elasticity of ankyrin repeats, a protein module found ubiquitously in cells but with an as-yet unclear function.

  18. Single-Molecule Total Internal Reflection Fluorescence Microscopy.

    PubMed

    Kudalkar, Emily M; Davis, Trisha N; Asbury, Charles L

    2016-01-01

    The advent of total internal reflection fluorescence (TIRF) microscopy has permitted visualization of biological events on an unprecedented scale: the single-molecule level. Using TIRF, it is now possible to view complex biological interactions such as cargo transport by a single molecular motor or DNA replication in real time. TIRF allows for visualization of single molecules by eliminating out-of-focus fluorescence and enhancing the signal-to-noise ratio. TIRF has been instrumental for studying in vitro interactions and has also been successfully implemented in live-cell imaging. Visualization of cytoskeletal structures and dynamics at the plasma membrane, such as endocytosis, exocytosis, and adhesion, has become much clearer using TIRF microscopy. Thanks to recent advances in optics and commercial availability, TIRF microscopy is becoming an increasingly popular and user-friendly technique. In this introduction, we describe the fundamental properties of TIRF microscopy and the advantages of using TIRF for single-molecule investigation. PMID:27140922

  19. Open-frame system for single-molecule microscopy.

    PubMed

    Arsenault, Adriel; Leith, Jason S; Henkin, Gil; McFaul, Christopher M J; Tarling, Matthew; Talbot, Richard; Berard, Daniel; Michaud, Francois; Scott, Shane; Leslie, Sabrina R

    2015-03-01

    We present the design and construction of a versatile, open frame inverted microscope system for wide-field fluorescence and single molecule imaging. The microscope chassis and modular design allow for customization, expansion, and experimental flexibility. We present two components which are included with the microscope which extend its basic capabilities and together create a powerful microscopy system: A Convex Lens-induced Confinement device provides the system with single-molecule imaging capabilities, and a two-color imaging system provides the option of imaging multiple molecular species simultaneously. The flexibility of the open-framed chassis combined with accessible single-molecule, multi-species imaging technology supports a wide range of new measurements in the health, nanotechnology, and materials science research sectors. PMID:25832232

  20. Single molecule detection using charge-coupled device array technology

    SciTech Connect

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  1. Single-molecule decoding of combinatorially modified nucleosomes.

    PubMed

    Shema, Efrat; Jones, Daniel; Shoresh, Noam; Donohue, Laura; Ram, Oren; Bernstein, Bradley E

    2016-05-01

    Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation. PMID:27151869

  2. Simultaneous time and frequency resolved fluorescence microscopy of single molecules.

    SciTech Connect

    Hayden, Carl C.; Gradinaru, Claudiu C.; Chandler, David W.; Luong, A. Khai

    2005-01-01

    Single molecule fluorophores were studied for the first time with a new confocal fluorescence microscope that allows the wavelength and emission time to be simultaneously measured with single molecule sensitivity. In this apparatus, the photons collected from the sample are imaged through a dispersive optical system onto a time and position sensitive detector. This detector records the wavelength and emission time of each detected photon relative to an excitation laser pulse. A histogram of many events for any selected spatial region or time interval can generate a full fluorescence spectrum and correlated decay plot for the given selection. At the single molecule level, this approach makes entirely new types of temporal and spectral correlation spectroscopy of possible. This report presents the results of simultaneous time- and frequency-resolved fluorescence measurements of single rhodamine 6G (R6G), tetramethylrhodamine (TMR), and Cy3 embedded in thin films of polymethylmethacrylate (PMMA).

  3. Extending Single-Molecule Microscopy Using Optical Fourier Processing

    PubMed Central

    2015-01-01

    This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules. PMID:24745862

  4. Detectors for single-molecule fluorescence imaging and spectroscopy

    PubMed Central

    MICHALET, X.; SIEGMUND, O.H.W.; VALLERGA, J.V.; JELINSKY, P.; MILLAUD, J.E.; WEISS, S.

    2010-01-01

    Single-molecule observation, characterization and manipulation techniques have recently come to the forefront of several research domains spanning chemistry, biology and physics. Due to the exquisite sensitivity, specificity, and unmasking of ensemble averaging, single-molecule fluorescence imaging and spectroscopy have become, in a short period of time, important tools in cell biology, biochemistry and biophysics. These methods led to new ways of thinking about biological processes such as viral infection, receptor diffusion and oligomerization, cellular signaling, protein-protein or protein-nucleic acid interactions, and molecular machines. Such achievements require a combination of several factors to be met, among which detector sensitivity and bandwidth are crucial. We examine here the needed performance of photodetectors used in these types of experiments, the current state of the art for different categories of detectors, and actual and future developments of single-photon counting detectors for single-molecule imaging and spectroscopy. PMID:20157633

  5. Stochasticity in single-molecule nanoelectrochemistry: origins, consequences, and solutions.

    PubMed

    Singh, Pradyumna S; Kätelhön, Enno; Mathwig, Klaus; Wolfrum, Bernhard; Lemay, Serge G

    2012-11-27

    Electrochemical detection of single molecules is being actively pursued as an enabler of new fundamental experiments and sensitive analytical capabilities. Most attempts to date have relied on redox cycling in a nanogap, which consists of two parallel electrodes separated by a nanoscale distance. While these initial experiments have demonstrated single-molecule detection at the proof-of-concept level, several fundamental obstacles need to be overcome to transform the technique into a realistic detection tool suitable for use in more complex settings (e.g., studying enzyme dynamics at single catalytic event level, probing neuronal exocytosis, etc.). In particular, it has become clearer that stochasticity--the hallmark of most single-molecule measurements--can become the key limiting factor on the quality of the information that can be obtained from single-molecule electrochemical assays. Here we employ random-walk simulations to show that this stochasticity is a universal feature of all single-molecule experiments in the diffusively coupled regime and emerges due to the inherent properties of brownian motion. We further investigate the intrinsic coupling between stochasticity and detection capability, paying particular attention to the role of the geometry of the detection device and the finite time resolution of measurement systems. We suggest concrete, realizable experimental modifications and approaches to mitigate these limitations. Overall, our theoretical analyses offer a roadmap for optimizing single-molecule electrochemical experiments, which is not only desirable but also indispensable for their wider employment as experimental tools for electrochemical research and as realistic sensing or detection systems. PMID:23106647

  6. Fluorinated copper phthalocyanine nanowires for enhancing interfacial electron transport in organic solar cells.

    PubMed

    Yoon, Seok Min; Lou, Sylvia J; Loser, Stephen; Smith, Jeremy; Chen, Lin X; Facchetti, Antonio; Marks, Tobin J; Marks, Tobin

    2012-12-12

    Zinc oxide is a promising candidate as an interfacial layer (IFL) in inverted organic photovoltaic (OPV) cells due to the n-type semiconducting properties as well as chemical and environmental stability. Such ZnO layers collect electrons at the transparent electrode, typically indium tin oxide (ITO). However, the significant resistivity of ZnO IFLs and an energetic mismatch between the ZnO and the ITO layers hinder optimum charge collection. Here we report that inserting nanoscopic copper hexadecafluorophthalocyanine (F(16)CuPc) layers, as thin films or nanowires, between the ITO anode and the ZnO IFL increases OPV performance by enhancing interfacial electron transport. In inverted P3HT:PC(61)BM cells, insertion of F(16)CuPc nanowires increases the short circuit current density (J(sc)) versus cells with only ZnO layers, yielding an enhanced power conversion efficiency (PCE) of ∼3.6% vs ∼3.0% for a control without the nanowire layer. Similar effects are observed for inverted PTB7:PC(71)BM cells where the PCE is increased from 8.1% to 8.6%. X-ray scattering, optical, and electrical measurements indicate that the performance enhancement is ascribable to both favorable alignment of the nanowire π-π stacking axes parallel to the photocurrent flow and to the increased interfacial layer-active layer contact area. These findings identify a promising strategy to enhance inverted OPV performance by inserting anisotropic nanostructures with π-π stacking aligned in the photocurrent flow direction. PMID:23181741

  7. Sorting single molecules: application to diagnostics and evolutionary biotechnology.

    PubMed Central

    Eigen, M; Rigler, R

    1994-01-01

    A method is described that provides for detection and identification of single molecules in solution. The method is based on fluorescence correlation spectroscopy, which records spatio-temporal correlations among fluctuating light signals, coupled with devices for trapping single molecules in an electric field. This technique is applied to studies of molecular evolution, where it allows fast screening of large mutant spectra in which targets are labeled by specific fluorescent ligands. The method expands the horizon in molecular diagnostics by making it possible to monitor concentrations down to (less than) 10(-15) M without any need for amplification. Images PMID:7517036

  8. Single molecule techniques for the study of membrane proteins.

    PubMed

    García-Sáez, Ana J; Schwille, Petra

    2007-08-01

    Single molecule techniques promise novel information about the properties and behavior of individual particles, thus enabling access to molecular heterogeneities in biological systems. Their recent developments to accommodate membrane studies have significantly deepened the understanding of membrane proteins. In this short review, we will describe the basics of the three most common single-molecule techniques used on membrane proteins: fluorescence correlation spectroscopy, single particle tracking, and atomic force microscopy. We will discuss the most relevant findings made during the recent years and their contribution to the membrane protein field. PMID:17497147

  9. Rate of Interfacial Electron Transfer through the 1,2,3-Triazole Linkage

    PubMed Central

    Devaraj, Neal K.; Decreau, Richard A.; Ebina, Wataru; Collman, James P.; Chidsey, Christopher E. D.

    2012-01-01

    The rate of electron transfer is measured to two ferrocene and one iron tetraphenylporphyrin redox species coupled through terminal acetylenes to azide-terminated thiol monolayers by the Cu(I)-catalyzed azide–alkyne cycloaddition (a Sharpless “click” reaction) to form the 1,2,3-triazole linkage. The high yield, chemoselectivity, convenience, and broad applicability of this triazole formation reaction make such a modular assembly strategy very attractive. Electron-transfer rate constants from greater than 60,000 to 1 s−1 are obtained by varying the length and conjugation of the electron-transfer bridge and by varying the surrounding diluent thiols in the monolayer. Triazole and the triazole carbonyl linkages provide similar electronic coupling for electron transfer as esters. The ability to vary the rate of electron transfer to many different redox species over many orders of magnitude by using modular coupling chemistry provides a convenient way to study and control the delivery of electrons to multielectron redox catalysts and similar interfacial systems that require controlled delivery of electrons. PMID:16898751

  10. Magnetic behaviour of TbPc2 single-molecule magnets chemically grafted on silicon surface

    PubMed Central

    Mannini, Matteo; Bertani, Federico; Tudisco, Cristina; Malavolti, Luigi; Poggini, Lorenzo; Misztal, Kasjan; Menozzi, Daniela; Motta, Alessandro; Otero, Edwige; Ohresser, Philippe; Sainctavit, Philippe; Condorelli, Guglielmo G.; Dalcanale, Enrico; Sessoli, Roberta

    2014-01-01

    Single-molecule magnets (SMMs) are among the most promising molecular systems for the development of novel molecular electronics based on the spin transport. Going beyond the investigations focused on physisorbed SMMs, in this work the robust grafting of Terbium(III) bis(phthalocyaninato) complexes to silicon surface from a diluted solution is achieved by rational chemical design yielding the formation of a partially oriented monolayer on the conducting substrate. Here, by exploiting the surface sensitivity of X-ray circular magnetic dichroism we evidence an enhancement of the magnetic bistability of this single-molecule magnet, in contrast to the dramatic reduction of the magnetic hysteresis that characterises monolayer deposits evaporated on noble and ferromagnetic metals. Photoelectron spectroscopy investigations and density functional theory analysis suggest a non-innocent role played by the silicon substrate, evidencing the potentiality of this approach for robust integration of bistable magnetic molecules in electronic devices. PMID:25109254