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Sample records for single-molecule vibrational spectroscopy

  1. Communication: Atomic force detection of single-molecule nonlinear optical vibrational spectroscopy

    SciTech Connect

    Saurabh, Prasoon Mukamel, Shaul

    2014-04-28

    Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (χ{sup (3)}) and sum or difference frequency generation (χ{sup (2)})

  2. Communication: atomic force detection of single-molecule nonlinear optical vibrational spectroscopy.

    PubMed

    Saurabh, Prasoon; Mukamel, Shaul

    2014-04-28

    Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (χ((3))) and sum or difference frequency generation (χ((2))).

  3. Effect of impurity molecules on the low-temperature vibrational dynamics of polyisobutylene: Investigation by single-molecule spectroscopy

    NASA Astrophysics Data System (ADS)

    Eremchev, I. Yu.; Naumov, A. V.; Vainer, Yu. G.; Kador, L.

    2009-05-01

    The influence of impurity chromophore molecules—tetra-tert-butylterrylene (TBT) and dibenzo-anthanthrene (DBATT)—on the vibrational dynamics of the amorphous polymer polyisobutylene (PIB) has been studied via single-molecule spectroscopy. The measurements were performed in the temperature region of 7-30 K, where the interaction of the chromophores with quasilocalized low-frequency vibrational modes (LFMs) determines the observed spectral line broadening. The analysis of the individual temperature dependences of the linewidths for a large number of single probe molecules yielded effective frequency values of those LFMs which are located near the respective chromophores. In this way the distributions of the LFM frequencies were measured for the two systems, and they were found to be similar. Moreover, they are in good agreement with the vibrational density of states as measured in pure PIB by inelastic neutron scattering. This allows us to conclude that, at least in the case of PIB, doping with low concentrations of the nonpolar and neutral molecules TBT and DBATT does not affect the vibrational dynamics of the matrix markedly.

  4. 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

  5. Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy.

    PubMed

    Skandary, Sepideh; Hussels, Martin; Konrad, Alexander; Renger, Thomas; Müh, Frank; Bommer, Martin; Zouni, Athina; Meixner, Alfred J; Brecht, Marc

    2015-03-19

    The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system.

  6. FCS and Single Molecule Spectroscopy

    NASA Astrophysics Data System (ADS)

    Rigler, Rudolf

    The idea to develop Fluorescence Fluctuation spectroscopy started when working in Manfred Eigens' Laboratory in G¨ottingen in the Max Planck Institute for Physical Chemistry as a postdoctoral fellow. I had just finished the construction and testing of a fluorescence T-jump machine [1] when Jean Pierre Changeux from Institut Pasteur arrived in G¨ottingen with a bag of freshly isolated nicotinic acetyl choline receptor to use the new fluorescence T-jump apparatus for relaxation kinetic studies of the receptor. Due to the high concentration of detergents present in the preparation and limited conductivity of the solvent leading to strong cavitation in the T-jump cell we could not perform the temperature relaxation experiments. However, this experience raised the question whether the analysis of equilibrium fluctuations by observing changes in the quantum yield of fluorescence would not be an alternative way to follow kinetic processes. In this way all problems related to the instantaneous temperature change could be avoided.

  7. Near-field single molecule spectroscopy

    SciTech Connect

    Xie, X.S.; Dunn, R.C.

    1995-02-01

    The high spatial resolution and sensitivity of near-field fluorescence microscopy allows one to study spectroscopic and dynamical properties of individual molecules at room temperature. Time-resolved experiments which probe the dynamical behavior of single molecules are discussed. Ground rules for applying near-field spectroscopy and the effect of the aluminum coated near-field probe on spectroscopic measurements are presented.

  8. Local vibrations in disordered solids studied via single-molecule spectroscopy: Comparison with neutron, nuclear, Raman scattering, and photon echo data

    NASA Astrophysics Data System (ADS)

    Vainer, Yu. G.; Naumov, A. V.; Kador, L.

    2008-06-01

    The energy spectrum of low-frequency vibrational modes (LFMs) in three disordered organic solids—amorphous polyisobutylene (PIB), toluene and deuterated toluene glasses, weakly doped with fluorescent chromophore molecules of tetra-tert-butylterrylene (TBT) has been measured via single-molecule (SM) spectroscopy. Analysis of the individual temperature dependences of linewidths of single TBT molecules allowed us to determine the values of the vibrational mode frequencies and the SM-LFM coupling constants for vibrations in the local environment of the molecules. The measured LFM spectra were compared with the “Boson peak” as measured in pure PIB by inelastic neutron scattering, in pure toluene glass by low-frequency Raman scattering, in doped toluene glass by nuclear inelastic scattering, and with photon echo data. The comparative analysis revealed close agreement between the spectra of the local vibrations as measured in the present study and the literature data of the Boson peak in PIB and toluene. The analysis has also the important result that weak doping of the disordered matrices with nonpolar probe molecules whose chemical composition is similar to that of the matrix molecules does not influence the observed vibrational dynamics markedly. The experimental data displaying temporal stability on the time scale of a few hours of vibrational excitation parameters in local surroundings was obtained for the first time both for polymer and molecular glass.

  9. 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.

  10. Single-molecule fluorescence spectroscopy in (bio)catalysis.

    PubMed

    Roeffaers, Maarten B J; De Cremer, Gert; Uji-i, Hiroshi; Muls, Benîot; Sels, Bert F; Jacobs, Pierre A; De Schryver, Frans C; De Vos, Dirk E; Hofkens, Johan

    2007-07-31

    The ever-improving time and space resolution and molecular detection sensitivity of fluorescence microscopy offer unique opportunities to deepen our insights into the function of chemical and biological catalysts. Because single-molecule microscopy allows for counting the turnover events one by one, one can map the distribution of the catalytic activities of different sites in solid heterogeneous catalysts, or one can study time-dependent activity fluctuations of individual sites in enzymes or chemical catalysts. By experimentally monitoring individuals rather than populations, the origin of complex behavior, e.g., in kinetics or in deactivation processes, can be successfully elucidated. Recent progress of temporal and spatial resolution in single-molecule fluorescence microscopy is discussed in light of its impact on catalytic assays. Key concepts are illustrated regarding the use of fluorescent reporters in catalytic reactions. Future challenges comprising the integration of other techniques, such as diffraction, scanning probe, or vibrational methods in single-molecule fluorescence spectroscopy are suggested.

  11. Current status of single-molecule spectroscopy: Theoretical aspects

    NASA Astrophysics Data System (ADS)

    Jung, YounJoon; Barkai, Eli; Silbey, Robert J.

    2002-12-01

    We survey the current status of single-molecule spectroscopy in the view point of theoretical aspects. After an explanation of basic concepts in single-molecule spectroscopy, we focus on the following topics: (1) line shape phenomena in disordered media, (2) photon counting statistics for time-dependent fluctuations in single-molecule spectroscopy, (3) fluorescence intensity fluctuations for nonergodic systems, (4) time-resolved single-molecule fluorescence for conformational dynamics of single biomolecules, (5) single-molecule reaction dynamics at room temperature, and (6) quantum jump method of single quantum system. We conclude this paper with some open questions and perspectives of single-molecule spectroscopy.

  12. 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.

  13. Single molecule force spectroscopy of asphaltene aggregates.

    PubMed

    Long, Jun; Xu, Zhenghe; Masliyah, Jacob H

    2007-05-22

    Asphaltene aggregation and deposition cause severe problems in nearly all phases of petroleum processing. To resolve those problems, understanding the aggregation mechanisms is a prerequisite and has attracted the interest of a great number of investigators. However, to date, the nature and extent of asphaltene aggregation remain widely debated. In the present study, we attempt to investigate asphaltene aggregation from a completely new perspective. The technique of single molecule force spectroscopy (SMFS) was used to investigate the response of single asphaltene aggregates under an external pulling force. Force curves representing the stretching of single asphaltene aggregates were obtained in simple electrolyte solutions (KCl and calcium) and organic solvents (toluene and heptane). These force curves were well-fitted by the modified worm-like chain model, indicating that those asphaltene aggregates acted like long-chain polymers under pulling by an external force. It was found that lower solution pH values and the presence of divalent cations resulted in a lower bending rigidity of the formed aggregates. The information retrieved from the force curves suggests that asphaltene molecules with a structure featuring small aromatic clusters connected by aliphatic chains do exist and that asphaltene aggregation could occur through a linear polymerization mechanism. The current study extends the application scope of SMFS.

  14. Double point contact single molecule absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Howard, John Brooks

    Our primary objective with the presentation of this thesis is to utilize superconducting transport through microscopic objects to both excite and analyze the vibrational degrees of freedom of various molecules of a biological nature. The technique stems from a Josephson junction's ability to generate radiation that falls in the terahertz gap (≈ 10 THz) and consequently can be used to excite vibrational modes of simple and complex molecules. Analysis of the change in IV characteristics coupled with the differential conductance dIdV allows determination of both the absorption spectra and the vibrational modes of biological molecules. Presented here are both the theoretical foundations of superconductivity relevant to our experimental technique and the fabrication process of our samples. Comparisons between our technique and that of other absorption spectroscopy techniques are included as a means of providing a reference upon which to judge the merits of our novel procedure. This technique is meant to improve not only our understanding of the vibrational degrees of freedom of useful biological molecules, but also these molecule's structural, electronic and mechanical properties.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Single-Molecule Spectroscopy and Imaging Over the Decades

    PubMed Central

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

    2016-01-01

    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 1990's, 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. THEORY OF SINGLE-MOLECULE SPECTROSCOPY: Beyond the Ensemble Average

    NASA Astrophysics Data System (ADS)

    Barkai, Eli; Jung, Younjoon; Silbey, Robert

    2004-01-01

    Single-molecule spectroscopy (SMS) is a powerful experimental technique used to investigate a wide range of physical, chemical, and biophysical phenomena. The merit of SMS is that it does not require ensemble averaging, which is found in standard spectroscopic techniques. Thus SMS yields insight into complex fluctuation phenomena that cannot be observed using standard ensemble techniques. We investigate theoretical aspects of SMS, emphasizing (a) dynamical fluctuations (e.g., spectral diffusion, photon-counting statistics, antibunching, quantum jumps, triplet blinking, and nonergodic blinking) and (b) single-molecule fluctuations in disordered systems, specifically distribution of line shapes of single molecules in low-temperature glasses. Special emphasis is given to single-molecule systems that reveal surprising connections to Levy statistics (i.e., blinking of quantum dots and single molecules in glasses). We compare theory with experiment and mention open problems. Our work demonstrates that the theory of SMS is a complementary field of research for describing optical spectroscopy in the condensed phase.

  5. Methods of single-molecule fluorescence spectroscopy and microscopy

    NASA Astrophysics Data System (ADS)

    Moerner, W. E.; Fromm, David P.

    2003-08-01

    Optical spectroscopy at the ultimate limit of a single molecule has grown over the past dozen years into a powerful technique for exploring the individual nanoscale behavior of molecules in complex local environments. Observing a single molecule removes the usual ensemble average, allowing the exploration of hidden heterogeneity in complex condensed phases as well as direct observation of dynamical state changes arising from photophysics and photochemistry, without synchronization. This article reviews the experimental techniques of single-molecule fluorescence spectroscopy and microscopy with emphasis on studies at room temperature where the same single molecule is studied for an extended period. Key to successful single-molecule detection is the need to optimize signal-to-noise ratio, and the physical parameters affecting both signal and noise are described in detail. Four successful microscopic methods including the wide-field techniques of epifluorescence and total internal reflection, as well as confocal and near-field optical scanning microscopies are described. In order to extract the maximum amount of information from an experiment, a wide array of properties of the emission can be recorded, such as polarization, spectrum, degree of energy transfer, and spatial position. Whatever variable is measured, the time dependence of the parameter can yield information about excited state lifetimes, photochemistry, local environmental fluctuations, enzymatic activity, quantum optics, and many other dynamical effects. Due to the breadth of applications now appearing, single-molecule spectroscopy and microscopy may be viewed as useful new tools for the study of dynamics in complex systems, especially where ensemble averaging or lack of synchronization may obscure the details of the process under study.

  6. Coherent spectroscopy in the single molecule limit (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Potma, Eric O.; Crampton, Kevin; Fast, Alex; Alfonso García, Alba; Apkarian, Vartkess A.

    2016-10-01

    Surface enhanced Raman scattering (SERS) is a popular technique for detecting and analyzing molecules at very low concentrations. The sensitivity of SERS is high enough to detect single molecules. It has proven difficult, however, to perform similar measurements in the so-called nonlinear optical regime, a regime in which the molecule is responding to multiple light pulses. Nonetheless, recent experiments indicate that after careful optimization, it is possible to generate signals derived from nonlinear analogs of SERS. Such measurements make it possible to view molecular vibrations in real time, which amounts to the femto- to pico-second range. In this contribution, we discuss in detail under which conditions detectable surface-enhanced coherent Raman signals can be expected, provide experimental evidence of coherent Raman scattering of single molecules, and highlight the unique information that can be attained from such measurements.

  7. Investigating single molecule adhesion by atomic force spectroscopy.

    PubMed

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-02-27

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

  8. Investigating Single Molecule Adhesion by Atomic Force Spectroscopy

    PubMed Central

    Stetter, Frank W. S.; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

    2015-01-01

    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment. PMID:25867282

  9. Optimized free energies from bidirectional single-molecule force spectroscopy.

    PubMed

    Minh, David D L; Adib, Artur B

    2008-05-09

    An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy-valid for biasing potentials of arbitrary stiffness-are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

  10. 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.

  11. Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

    NASA Astrophysics Data System (ADS)

    Malý, Pavel; Gruber, J. Michael; van Grondelle, Rienk; Mančal, Tomáš

    2016-05-01

    We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence-detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.

  12. Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

    PubMed Central

    Malý, Pavel; Gruber, J. Michael; van Grondelle, Rienk; Mančal, Tomáš

    2016-01-01

    We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence-detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII. PMID:27189196

  13. Analysis of DNA interactions using single-molecule force spectroscopy.

    PubMed

    Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

    2013-06-01

    Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

  14. Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems.

    PubMed

    Kondo, Toru; Chen, Wei Jia; Schlau-Cohen, Gabriela S

    2017-01-25

    Photosynthesis begins when a network of pigment-protein complexes captures solar energy and transports it to the reaction center, where charge separation occurs. When necessary (under low light conditions), photosynthetic organisms perform this energy transport and charge separation with near unity quantum efficiency. Remarkably, this high efficiency is maintained under physiological conditions, which include thermal fluctuations of the pigment-protein complexes and changing local environments. These conditions introduce multiple types of heterogeneity in the pigment-protein complexes, including structural heterogeneity, energetic heterogeneity, and functional heterogeneity. Understanding how photosynthetic light-harvesting functions in the face of these fluctuations requires understanding this heterogeneity, which, in turn, requires characterization of individual pigment-protein complexes. Single-molecule spectroscopy has the power to probe individual complexes. In this review, we present an overview of the common techniques for single-molecule fluorescence spectroscopy applied to photosynthetic systems and describe selected experiments on these systems. We discuss how these experiments provide a new understanding of the impact of heterogeneity on light harvesting and thus how these systems are optimized to capture sunlight under physiological conditions.

  15. Single-molecule force spectroscopy approach to enzyme catalysis.

    PubMed

    Alegre-Cebollada, Jorge; Perez-Jimenez, Raul; Kosuri, Pallav; Fernandez, Julio M

    2010-06-18

    Enzyme catalysis has been traditionally studied using a diverse set of techniques such as bulk biochemistry, x-ray crystallography, and NMR. Recently, single-molecule force spectroscopy by atomic force microscopy has been used as a new tool to study the catalytic properties of an enzyme. In this approach, a mechanical force ranging up to hundreds of piconewtons is applied to the substrate of an enzymatic reaction, altering the conformational energy of the substrate-enzyme interactions during catalysis. From these measurements, the force dependence of an enzymatic reaction can be determined. The force dependence provides valuable new information about the dynamics of enzyme catalysis with sub-angstrom resolution, a feat unmatched by any other current technique. To date, single-molecule force spectroscopy has been applied to gain insight into the reduction of disulfide bonds by different enzymes of the thioredoxin family. This minireview aims to present a perspective on this new approach to study enzyme catalysis and to summarize the results that have already been obtained from it. Finally, the specific requirements that must be fulfilled to apply this new methodology to any other enzyme will be discussed.

  16. Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Engel, Andreas; Janovjak, Harald; Fotiadis, Dimtrios; Kedrov, Alexej; Cisneros, David; Müller, Daniel J.

    Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes.

  17. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    PubMed Central

    Pelz, Benjamin; Žoldák, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-01-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis. PMID:26906294

  18. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Pelz, Benjamin; Žoldák, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-02-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis.

  19. Voltage tuning of vibrational mode energies in single-molecule junctions

    PubMed Central

    Li, Yajing; Doak, Peter; Kronik, Leeor; Neaton, Jeffrey B.; Natelson, Douglas

    2014-01-01

    Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule junctions have been used to manipulate electronic structure and related functional properties of molecules, electrical control of vibrational mode energies has remained elusive. Here we use simultaneous transport and surface-enhanced Raman spectroscopy measurements to demonstrate large, reversible, voltage-driven shifts of vibrational mode energies of C60 molecules in gold junctions. C60 mode energies are found to vary approximately quadratically with bias, but in a manner inconsistent with a simple vibrational Stark effect. Our theoretical model instead suggests that the mode shifts are a signature of bias-driven addition of electronic charge to the molecule. These results imply that voltage-controlled tuning of vibrational modes is a general phenomenon at metal–molecule interfaces and is a means of achieving significant shifts in vibrational energies relative to a pure Stark effect. PMID:24474749

  20. Single molecule atomic force microscopy and force spectroscopy of chitosan.

    PubMed

    Kocun, Marta; Grandbois, Michel; Cuccia, Louis A

    2011-02-01

    Atomic force microscopy (AFM) and AFM-based force spectroscopy was used to study the desorption of individual chitosan polymer chains from substrates with varying chemical composition. AFM images of chitosan adsorbed onto a flat mica substrate show elongated single strands or aggregated bundles. The aggregated state of the polymer is consistent with the high level of flexibility and mobility expected for a highly positively charged polymer strand. Conversely, the visualization of elongated strands indicated the presence of stabilizing interactions with the substrate. Surfaces with varying chemical composition (glass, self-assembled monolayer of mercaptoundecanoic acid/decanethiol and polytetrafluoroethylene (PTFE)) were probed with chitosan modified AFM tips and the corresponding desorption energies, calculated from plateau-like features, were attributed to the desorption of individual polymer strands. Desorption energies of 2.0±0.3×10(-20)J, 1.8±0.3×10(-20)J and 3.5±0.3×10(-20)J were obtained for glass, SAM of mercaptoundecanoic/dodecanethiol and PTFE, respectively. These single molecule level results can be used as a basis for investigating chitosan and chitosan-based materials for biomaterial applications.

  1. Pushing the Sample-Size Limit of Infrared Vibrational Nanospectroscopy: From Monolayer toward Single Molecule Sensitivity.

    PubMed

    Xu, Xiaoji G; Rang, Mathias; Craig, Ian M; Raschke, Markus B

    2012-07-05

    While scattering-scanning near-field optical microscopy (s-SNOM) has demonstrated its potential to extend infrared (IR) spectroscopy into the nanometer scale, it has not yet reached its full potential in terms of spectroscopic sensitivity. We combine broadband femtosecond mid-IR excitation with an optimized spectral irradiance of ∼2 W/cm(2)/ cm(-1) (power/area/bandwidth) and a combination of tip- and substrate enhancement to demonstrate single-monolayer sensitivity with exceptional signal-to-noise ratio. Using interferometric time domain detection, the near-field IR s-SNOM spectral phase directly reflects the molecular vibrational resonances and their intrinsic line shapes. We probe the stretching resonance of ∼1000 carbonyl groups at 1700 cm(-1) in a self-assembled monolayer of 16-mercaptohexadecanoic acid (MHDA) on an evaporated gold substrate with spectroscopic contrast and sensitivity of ≲100 vibrational oscillators. From these results we provide a roadmap for achieving true single-molecule IR vibrational spectroscopy in s-SNOM by implementing optical antenna resonant enhancement, increased spectral pump power, and improved detection schemes.

  2. Theoretical analysis of single molecule spectroscopy lineshapes of conjugated polymers

    NASA Astrophysics Data System (ADS)

    Devi, Murali

    Conjugated Polymers(CPs) exhibit a wide range of highly tunable optical properties. Quantitative and detailed understanding of the nature of excitons responsible for such a rich optical behavior has significant implications for better utilization of CPs for more efficient plastic solar cells and other novel optoelectronic devices. In general, samples of CPs are plagued with substantial inhomogeneous broadening due to various sources of disorder. Single molecule emission spectroscopy (SMES) offers a unique opportunity to investigate the energetics and dynamics of excitons and their interactions with phonon modes. The major subject of the present thesis is to analyze and understand room temperature SMES lineshapes for a particular CP, called poly(2,5-di-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (DEH-PPV). A minimal quantum mechanical model of a two-level system coupled to a Brownian oscillator bath is utilized. The main objective is to identify the set of model parameters best fitting a SMES lineshape for each of about 200 samples of DEH-PPV, from which new insight into the nature of exciton-bath coupling can be gained. This project also entails developing a reliable computational methodology for quantum mechanical modeling of spectral lineshapes in general. Well-known optimization techniques such as gradient descent, genetic algorithms, and heuristic searches have been tested, employing an L2 measure between theoretical and experimental lineshapes for guiding the optimization. However, all of these tend to result in theoretical lineshapes qualitatively different from experimental ones. This is attributed to the ruggedness of the parameter space and inadequateness of the L2 measure. On the other hand, when the dynamic reduction of the original parameter space to a 2-parameter space through feature searching and visualization of the search space paths using directed acyclic graphs(DAGs), the qualitative nature of the fitting improved significantly. For a more

  3. Experimental evidence for quantum interference and vibrationally induced decoherence in single-molecule junctions.

    PubMed

    Ballmann, Stefan; Härtle, Rainer; Coto, Pedro B; Elbing, Mark; Mayor, Marcel; Bryce, Martin R; Thoss, Michael; Weber, Heiko B

    2012-08-03

    We analyze quantum interference and decoherence effects in single-molecule junctions both experimentally and theoretically by means of the mechanically controlled break junction technique and density-functional theory. We consider the case where interference is provided by overlapping quasidegenerate states. Decoherence mechanisms arising from electronic-vibrational coupling strongly affect the electrical current flowing through a single-molecule contact and can be controlled by temperature variation. Our findings underline the universal relevance of vibrations for understanding charge transport through molecular junctions.

  4. 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

  5. Multiplexed single-molecule force spectroscopy using a centrifuge

    PubMed Central

    Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P.

    2016-01-01

    We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise. PMID:26984516

  6. 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.

  7. Directly measuring single-molecule heterogeneity using force spectroscopy

    PubMed Central

    Hinczewski, Michael; Thirumalai, D.

    2016-01-01

    One of the most intriguing results of single-molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Although we now have proof of functional heterogeneity in a handful of systems—enzymes, motors, adhesion complexes—identifying and measuring it remains a formidable challenge. Here, we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single-molecule techniques: atomic force microscopy or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying 10 published datasets, we find heterogeneity in 5 of them, all with interconversion rates slower than 10 s−1. Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved crossover regime between heterogeneous and nonheterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity. PMID:27317744

  8. Electrochemical scanning tunneling microscopy and spectroscopy for single-molecule investigation.

    PubMed

    Alessandrini, Andrea; Facci, Paolo

    2013-01-01

    The technique of electrochemical scanning tunneling microscopy (ECSTM) and spectroscopy (ECSTS) for studying electron transport through single redox molecules is here described. Redox molecules of both biological and organic nature have been studied by this technique with the aim of understanding the transport mechanisms ruling the flow of electrons via a single molecule placed in a nanometer-sized gap between two electrodes while elucidating the role of the redox density of states brought about by the molecule. The obtained results provide unique clues to single-molecule transport behavior and support the concept of single-molecule electrochemical gating.

  9. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

    PubMed Central

    Neuman, Keir C.; Nagy, Attila

    2012-01-01

    Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations. PMID:18511917

  10. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy.

    PubMed

    Neuman, Keir C; Nagy, Attila

    2008-06-01

    Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

  11. Surface-enhanced Raman spectroscopy of dyes: from single molecules to the artists' canvas.

    PubMed

    Wustholz, Kristin L; Brosseau, Christa L; Casadio, Francesca; Van Duyne, Richard P

    2009-09-14

    This perspective presents recent surface-enhanced Raman spectroscopy (SERS) studies of dyes, with applications to the fields of single-molecule spectroscopy and art conservation. First we describe the development and outlook of single-molecule SERS (SMSERS). Rather than providing an exhaustive review of the literature, SMSERS experiments that we consider essential for its future development are emphasized. Shifting from single-molecule to ensemble-averaged experiments, we describe recent efforts toward SERS analysis of colorants in precious artworks. Our intention is to illustrate through these examples that the forward development of SERS is dependent upon both fundamental (e.g., SMSERS) and applied (e.g., on-the-specimen SERS of historical art objects) investigations and that the future of SERS is very bright indeed.

  12. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review

    NASA Astrophysics Data System (ADS)

    Laine, Romain F.; Kaminski Schierle, Gabriele S.; van de Linde, Sebastian; Kaminski, Clemens F.

    2016-06-01

    For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.

  13. Single-molecule spectroscopy for plastic electronics: materials analysis from the bottom-up.

    PubMed

    Lupton, John M

    2010-04-18

    pi-conjugated polymers find a range of applications in electronic devices. These materials are generally highly disordered in terms of chain length and chain conformation, besides being influenced by a variety of chemical and physical defects. Although this characteristic can be of benefit in certain device applications, disorder severely complicates materials analysis. Accurate analytical techniques are, however, crucial to optimising synthetic procedures and assessing overall material purity. Fortunately, single-molecule spectroscopic techniques have emerged as an unlikely but uniquely powerful approach to unraveling intrinsic material properties from the bottom up. Building on the success of such techniques in the life sciences, single-molecule spectroscopy is finding increasing applicability in materials science, effectively enabling the dissection of the bulk down to the level of the individual molecular constituent. This article reviews recent progress in single molecule spectroscopy of conjugated polymers as used in organic electronics.

  14. Silicon photon-counting avalanche diodes for single-molecule fluorescence spectroscopy

    PubMed Central

    Michalet, Xavier; Ingargiola, Antonino; Colyer, Ryan A.; Scalia, Giuseppe; Weiss, Shimon; Maccagnani, Piera; Gulinatti, Angelo; Rech, Ivan; Ghioni, Massimo

    2014-01-01

    Solution-based single-molecule fluorescence spectroscopy is a powerful experimental tool with applications in cell biology, biochemistry and biophysics. The basic feature of this technique is to excite and collect light from a very small volume and work in a low concentration regime resulting in rare burst-like events corresponding to the transit of a single molecule. Detecting photon bursts is a challenging task: the small number of emitted photons in each burst calls for high detector sensitivity. Bursts are very brief, requiring detectors with fast response time and capable of sustaining high count rates. Finally, many bursts need to be accumulated to achieve proper statistical accuracy, resulting in long measurement time unless parallelization strategies are implemented to speed up data acquisition. In this paper we will show that silicon single-photon avalanche diodes (SPADs) best meet the needs of single-molecule detection. We will review the key SPAD parameters and highlight the issues to be addressed in their design, fabrication and operation. After surveying the state-of-the-art SPAD technologies, we will describe our recent progress towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. The potential of this approach is illustrated with single-molecule Förster resonance energy transfer measurements. PMID:25309114

  15. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture).

    PubMed

    Moerner, W E William E

    2015-07-06

    The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the 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 90s, many fascinating physical effects were observed for individual molecules, and the imaging of 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 provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging 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. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.

  16. Nobel Lecture: Single-molecule spectroscopy, imaging, and photocontrol: Foundations for super-resolution microscopy*

    NASA Astrophysics Data System (ADS)

    Moerner, W. E. William E.

    2015-10-01

    The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the 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, many fascinating physical effects were observed for individual molecules, and the imaging of 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 provided important forerunners of the later super-resolution microscopy with single molecules. In the room-temperature regime, imaging 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. Because each single fluorophore acts as a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and selected current developments are summarized.

  17. Highlights from Faraday Discussion 184: Single-Molecule Microscopy and Spectroscopy, London, UK, September 2015.

    PubMed

    Gellings, E; Faez, S; Piatkowski, L

    2016-02-07

    The 2015 Faraday Discussion on single-molecule microscopy and spectroscopy brought together leading scientists involved in various topics of single-molecule research. It attracted almost a hundred delegates from a broad spectrum of backgrounds and experience levels - from experimentalists to theoreticians, from biologists to materials scientists, from masters students to Nobel Prize Laureates. The meeting was merely a reflection of how big of an impact the ability to detect individual molecules has had on science over the past quarter of a century. In the following we give an overview of the topics covered during this meeting and briefly highlight the content of each presentation.

  18. Branching out of single-molecule fluorescence spectroscopy: challenges for chemistry and influence on biology.

    PubMed

    Tinnefeld, Philip; Sauer, Markus

    2005-04-29

    In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells.

  19. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    NASA Astrophysics Data System (ADS)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

    2017-03-01

    The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to

  20. Coherent Anti-Stokes Raman Scattering Spectroscopy of Single Molecules in Solution

    SciTech Connect

    Sunney Xie, Wei Min, Chris Freudiger, Sijia Lu

    2012-01-18

    During this funding period, we have developed two breakthrough techniques. The first is stimulated Raman scattering microscopy, providing label-free chemical contrast for chemical and biomedical imaging based on vibrational spectroscopy. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. We developed a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-free and readily interpretable chemical contrast. We demonstrated a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis. This technology offers exciting prospect for medical imaging. The second technology we developed is stimulated emission microscopy. Many chromophores, such as haemoglobin and cytochromes, absorb but have undetectable fluorescence because the spontaneous emission is dominated by their fast non-radiative decay. Yet the detection of their absorption is difficult under a microscope. We use stimulated emission, which competes effectively with the nonradiative decay, to make the chromophores detectable, as a new contrast mechanism for optical microscopy. We demonstrate a variety of applications of stimulated emission microscopy, such as visualizing chromoproteins, non-fluorescent variants of the green fluorescent protein, monitoring lacZ gene expression with a chromogenic reporter, mapping transdermal drug distribu- tions without histological sectioning, and label-free microvascular

  1. Single molecule detection of 4-dimethylaminoazobenzene by surface-enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Z. L.; Yin, Y. F.; Jiang, J. W.; Mo, Y. J.

    2009-02-01

    4-Dimethylaminoazobenzene (DAB) is anticipated to be a human carcinogen based on sufficient evidence of carcinogenicity in experimental animals. The trace detection of DAB is of great significance in environmental protection and safe life of the people. To test the availability of DAB trace detection using surface-enhanced Raman scattering (SERS), the SERS spectra of DAB single molecules adsorbed on the silver particle aggregates in colloid were investigated. The phenomena of blinking, spectral diffusion, and intensity fluctuations of the vibrational lines in the SERS spectra were observed. Statistical analysis of spectral intensity fluctuations indicates a multimodal distribution of some specific Raman bands, which are consistent with the identification of single molecule detection. Our results demonstrated that SERS can be applied to the trace detection of DAB molecules and other azo dyes.

  2. Wafer-scale metasurface for total power absorption, local field enhancement and single molecule Raman spectroscopy.

    PubMed

    Wang, Dongxing; Zhu, Wenqi; Best, Michael D; Camden, Jon P; Crozier, Kenneth B

    2013-10-04

    The ability to detect molecules at low concentrations is highly desired for applications that range from basic science to healthcare. Considerable interest also exists for ultrathin materials with high optical absorption, e.g. for microbolometers and thermal emitters. Metal nanostructures present opportunities to achieve both purposes. Metal nanoparticles can generate gigantic field enhancements, sufficient for the Raman spectroscopy of single molecules. Thin layers containing metal nanostructures ("metasurfaces") can achieve near-total power absorption at visible and near-infrared wavelengths. Thus far, however, both aims (i.e. single molecule Raman and total power absorption) have only been achieved using metal nanostructures produced by techniques (high resolution lithography or colloidal synthesis) that are complex and/or difficult to implement over large areas. Here, we demonstrate a metasurface that achieves the near-perfect absorption of visible-wavelength light and enables the Raman spectroscopy of single molecules. Our metasurface is fabricated using thin film depositions, and is of unprecedented (wafer-scale) extent.

  3. Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics

    PubMed Central

    He, Yufan; Haque, Mohammad Mahfuzul; Stuehr, Dennis J.; Lu, H. Peter

    2015-01-01

    Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS. PMID:26311846

  4. Probing and Manipulating Protein Conformation Changes by Time-Resolved Single-Molecule Spectroscopy and Site-Specific Ultramicroscopy

    DTIC Science & Technology

    2008-04-01

    Biomolecular Recognition with Single Molecule Dynamics,” Phys. Rev. Lett. 98, 128105 (2007). 4. V. Biju, D. Pan, Yuri A. Gorby , Jim Fredrickson, J. Mclean, D...Protein Interactions of Calmodulin by Single-Molecule Spectroscopy," J. Am. Chem. Soc. 128, 10034-10042 ( 2006 ).

  5. Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy.

    PubMed

    Jobst, Markus A; Milles, Lukas F; Schoeler, Constantin; Ott, Wolfgang; Fried, Daniel B; Bayer, Edward A; Gaub, Hermann E; Nash, Michael A

    2015-10-31

    Receptor-ligand pairs are ordinarily thought to interact through a lock and key mechanism, where a unique molecular conformation is formed upon binding. Contrary to this paradigm, cellulosomal cohesin-dockerin (Coh-Doc) pairs are believed to interact through redundant dual binding modes consisting of two distinct conformations. Here, we combined site-directed mutagenesis and single-molecule force spectroscopy (SMFS) to study the unbinding of Coh:Doc complexes under force. We designed Doc mutations to knock out each binding mode, and compared their single-molecule unfolding patterns as they were dissociated from Coh using an atomic force microscope (AFM) cantilever. Although average bulk measurements were unable to resolve the differences in Doc binding modes due to the similarity of the interactions, with a single-molecule method we were able to discriminate the two modes based on distinct differences in their mechanical properties. We conclude that under native conditions wild-type Doc from Clostridium thermocellum exocellulase Cel48S populates both binding modes with similar probabilities. Given the vast number of Doc domains with predicted dual binding modes across multiple bacterial species, our approach opens up new possibilities for understanding assembly and catalytic properties of a broad range of multi-enzyme complexes.

  6. Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy.

    PubMed

    Camunas-Soler, Joan; Ribezzi-Crivellari, Marco; Ritort, Felix

    2016-07-05

    We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.

  7. Hierarchical organization of the plasma membrane: investigations by single-molecule tracking vs. fluorescence correlation spectroscopy.

    PubMed

    Kusumi, Akihiro; Shirai, Yuki M; Koyama-Honda, Ikuko; Suzuki, Kenichi G N; Fujiwara, Takahiro K

    2010-05-03

    Single-molecule tracking and fluorescence correlation spectroscopy (FCS) applied to the plasma membrane in living cells have allowed a number of unprecedented observations, thus fostering a new basic understanding of molecular diffusion, interaction, and signal transduction in the plasma membrane. It is becoming clear that the plasma membrane is a heterogeneous entity, containing diverse structures on nano-meso-scales (2-200 nm) with a variety of lifetimes, where certain membrane molecules stay together for limited durations. Molecular interactions occur in the time-dependent inhomogeneous two-dimensional liquid of the plasma membrane, which might be a key for plasma membrane functions.

  8. Single-molecule bonds characterized by solid-state nanopore force spectroscopy.

    PubMed

    Tabard-Cossa, Vincent; Wiggin, Matthew; Trivedi, Dhruti; Jetha, Nahid N; Dwyer, Jason R; Marziali, Andre

    2009-10-27

    Weak molecular interactions drive processes at the core of living systems, such as enzyme-substrate interactions, receptor-ligand binding, and nucleic acid replication. Single-molecule force spectroscopy is a remarkable tool for revealing molecular scale energy landscapes of noncovalent bonds, by exerting a mechanical force directly on an individual molecular complex and tracking its survival as a function of time and applied force. In principle, force spectroscopy methods can also be used for highly specific molecular recognition assays, by directly characterizing the strength of bonds between probe and target molecules. However, complexity and low throughput of conventional force spectroscopy techniques render such biosensing applications impractical. Here we demonstrate a straightforward single-molecule approach, suitable for both biophysical studies and molecular recognition assays, in which a approximately 3 nm silicon nitride nanopore is used to determine the bond lifetime spectrum of the biotin-neutravidin complex. Thousands of individual molecular complexes are captured and dissociated in the solid-state nanopore under constant applied forces, ranging from 400 to 900 mV, allowing us to extract the location of the energy barrier that governs the interaction, mapped at Deltax approximately 0.5 nm. These results highlight the capacity of a solid-state nanopore to detect and characterize intermolecular interactions and demonstrate how this could be applied to rapid, highly specific molecular detection assays.

  9. Fluorescence spectroscopy of single molecules at room temperature and its applications

    SciTech Connect

    Ha, Taekjip

    1996-12-01

    We performed fluorescence spectroscopy of single and pairs of dye molecules on a surface at room temperature. Near field scanning optical microscope (NSOM) and far field scanning optical microscope with multi-color excitation/detection capability were built. The instrument is capable of optical imaging with 100nm resolution and has the sensitivity necessary for single molecule detection. A variety of dynamic events which cannot be observed from an ensemble of molecules is revealed when the molecules are probed one at a time. They include (1) spectral jumps correlated with dark states, (2) individually resolved quantum jumps to and from the meta-stable triplet state, (3) rotational jumps due to desorption/readsorption events of single molecules on the surface. For these studies, a computer controlled optical system which automatically and rapidly locates and performs spectroscopic measurements on single molecules was developed. We also studied the interaction between closely spaced pairs of molecules. In particular, fluorescence resonance energy transfer between a single resonant pair of donor and acceptor molecules was measured. Photodestruction dynamics of the donor or acceptor were used to determine the presence and efficiency of energy transfer Dual molecule spectroscopy was extended to a non-resonant pair of molecules to obtain high resolution differential distance information. By combining NSOM and dual color scheme, we studied the co-localization of parasite proteins and host proteins on a human red blood cell membrane infected with malaria. These dual-molecule techniques can be used to measure distances, relative orientations, and changes in distances/orientations of biological macromolecules with very good spatial, angular and temporal resolutions, hence opening new capabilities in the study of such systems.

  10. Single-Molecule Studies of Integrins by AFM-Based Force Spectroscopy on Living Cells

    NASA Astrophysics Data System (ADS)

    Eibl, Robert H.

    The characterization of cell adhesion between two living cells at the single-molecule level, i.e., between one adhesion receptor and its counter-receptor, appears to be an experimental challenge. Atomic force microscopy (AFM) can be used in its force spectroscopy mode to determine unbinding forces of a single pair of adhesion receptors, even with a living cell as a probe. This chapter provides an overview of AFM force measurements of the integrin family of cell adhesion receptors and their ligands. A focus is given to major integrins expressed on leukocytes, such as lymphocyte function-associated antigen 1 (LFA-1) and very late antigen 4 (VLA-4). These receptors are crucial for leukocyte trafficking in health and disease. LFA-1 and VLA-1 can be activated within the bloodstream from a low-affinity to a high-affinity receptor by chemokines in order to adhere strongly to the vessel wall before the receptor-bearing leukocytes extravasate. The experimental considerations needed to provide near-physiological conditions for a living cell and to be able to measure adequate forces at the single-molecule level are discussed in detail. AFM technology has been developed into a modern and extremely sensitive tool in biomedical research. It appears now that AFM force spectroscopy could enter, within a few years, medical applications in diagnosis and therapy of cancer and autoimmune diseases.

  11. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding

    NASA Astrophysics Data System (ADS)

    Hughes, Megan L.; Dougan, Lorna

    2016-07-01

    One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.

  12. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology.

    PubMed

    Wang, Yuling; Irudayaraj, Joseph

    2013-02-05

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences.

  13. Plasmonic nano-protrusions: hierarchical nanostructures for single-molecule Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Basuray, Sagnik; Pathak, Avinash; Bok, Sangho; Chen, Biyan; Hamm, Steven C.; Mathai, Cherian J.; Guha, Suchismita; Gangopadhyay, Keshab; Gangopadhyay, Shubhra

    2017-01-01

    Classical methods for enhancing the electromagnetic field from substrates for spectroscopic applications, such as surface-enhanced Raman spectroscopy (SERS), have involved the generation of hotspots through directed self-assembly of nanoparticles or by patterning nanoscale features using expensive nanolithography techniques. A novel large-area, cost-effective soft lithographic technique involving glancing angle deposition (GLAD) of silver on polymer gratings is reported here. This method produces hierarchical nanostructures with high enhancement factors capable of analyzing single-molecule SERS. The uniform ordered and patterned nanostructures provide extraordinary field enhancements that serve as excitatory hotspots and are herein interrogated by SERS. The high spatial homogeneity of the Raman signal and signal enhancement over a large area from a self-assembled monolayer (SAM) of 2-naphthalenethiol demonstrated the uniformity of the hotspots. The enhancement was shown to have a critical dependence on the underlying nanostructure via the surface energy landscape and GLAD angles for a fixed deposition thickness, as evidenced by atomic force microscopy and scanning electron microscopy surface analysis of the substrate. The nanostructured surface leads to an extremely concentrated electromagnetic field at sharp nanoscale peaks, here referred to as ‘nano-protrusions’, due to the coupling of surface plasmon resonance (SPR) with localized SPR. These nano-protrusions act as hotspots which provide Raman enhancement factors as high as 108 over a comparable SAM on silver. Comparison of our substrate with the commercial substrate Klarite™ shows higher signal enhancement and minimal signal variation with hotspot spatial distribution. By using the proper plasmon resonance angle corresponding to the laser source wavelength, further enhancement in signal intensity can be achieved. Single-molecule Raman spectra for rhodamine 6G are obtained from the best SERS substrate (a

  14. Can Dissipative Properties of Single Molecules Be Extracted from a Force Spectroscopy Experiment?

    PubMed

    Benedetti, Fabrizio; Gazizova, Yulia; Kulik, Andrzej J; Marszalek, Piotr E; Klinov, Dmitry V; Dietler, Giovanni; Sekatskii, Sergey K

    2016-09-20

    We performed dynamic force spectroscopy of single dextran and titin I27 molecules using small-amplitude and low-frequency (40-240 Hz) dithering of an atomic force microscope tip excited by a sine wave voltage fed onto the tip-carrying piezo. We show that for such low-frequency dithering experiments, recorded phase information can be unambiguously interpreted within the framework of a transparent theoretical model that starts from a well-known partial differential equation to describe the dithering of an atomic force microscope cantilever and a single molecule attached to its end system, uses an appropriate set of initial and boundary conditions, and does not exploit any implicit suggestions. We conclude that the observed phase (dissipation) signal is due completely to the dissipation related to the dithering of the cantilever itself (i.e., to the change of boundary conditions in the course of stretching). For both cases, only the upper bound of the dissipation of a single molecule has been established as not exceeding 3⋅10(-7)kg/s. We compare our results with previously reported measurements of the viscoelastic properties of single molecules, and we emphasize that extreme caution must be taken in distinguishing between the dissipation related to the stretched molecule and the dissipation that originates from the viscous damping of the dithered cantilever. We also present the results of an amplitude channel data analysis, which reveal that the typical values of the spring constant of a I27 molecule at the moment of module unfolding are equal to 4±1.5mN/m, and the typical values of the spring constant of dextran at the moment of chair-boat transition are equal to 30-50mN/m.

  15. Microfluidic mixing for non-equilibrium single-molecule optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Pfeil, Shawn H.

    We describe a series of experiments made possible by the combination of single-molecule fluorescence spectroscopy and microfluidic mixing. To perform these measurements, a microfluidic sample handling system was developed and characterized. This system allows observation at times as early as 2.4 ms after a reaction is triggered, which is an more than an order of magnitude earlier than previous microfabricated devices. Dilutions as high as 1:19 (v/v) are achieved, allowing measurements of molecular refolding in native conditions. The interconversion of subpopulations, masked by averaging in ensemble measurements, is observed. This technology also facilitates ultra-sensitive chemiluminescence measurements, using only microliters of sample. Microfluidics are designed and fabricated to extend single-molecule measurements to samples out of equilibrium. The system is optimized for sensitive optical detection and experimental convenience. Channels are replica-molded in poly-dimethyl-siloxane (PDMS) elastomer and sealed to coverglass. The resulting devices are compatible with a broad range of chemicals, and exhibit low background fluorescence. The combination of continuous flow, which decouples reaction progress from measurement duration, with low background enables single molecules to be probed at well defined times after a reaction is triggered. Fluid delivery and pressure connections are made using an interface optimized for rapid assembly, rapid sample exchange, and modular device replacement, while providing access for high numerical aperture optics. The kinetics of Csp, the cold shock protein from Thermotoga maritima, are studied with the mixer. An order of magnitude decrease in deadtime puts a new upper limit of 4.6 ms on the time required for collapse after mixing. This result is in agreement with indirect measurements of chain reconfiguration time, which suggest collapse happens on the timescale of 10--100 ns. Measurements of the kinetics of a DNA sequence that

  16. The Citrate Carrier CitS Probed by Single-Molecule Fluorescence Spectroscopy

    PubMed Central

    Kästner, Christopher N.; Prummer, Michael; Sick, Beate; Renn, Alois; Wild, Urs P.; Dimroth, Peter

    2003-01-01

    A prominent region of the Na+-dependent citrate carrier (CitS) from Klebsiella pneumoniae is the highly conserved loop X-XI, which contains a putative citrate binding site. To monitor potential conformational changes within this region by single-molecule fluorescence spectroscopy, the target cysteines C398 and C414 of the single-Cys mutants (CitS-sC398, CitS-sC414) were selectively labeled with the thiol-reactive fluorophores AlexaFluor 546/568 C5 maleimide (AF546, AF568). While both single-cysteine mutants were catalytically active citrate carriers, labeling with the fluorophore was only tolerated at C398. Upon citrate addition to the functional protein fluorophore conjugate CitS-sC398-AF546, complete fluorescence quenching of the majority of molecules was observed, indicating a citrate-induced conformational change of the fluorophore-containing domain of CitS. This quenching was specific for the physiological substrate citrate and therefore most likely reflecting a conformational change in the citrate transport mechanism. Single-molecule studies with dual-labeled CitS-sC398-AF546/568 and dual-color detection provided strong evidence for a homodimeric association of CitS. PMID:12609868

  17. Segmented nanofibers of spider dragline silk: Atomic force microscopy and single-molecule force spectroscopy

    PubMed Central

    Oroudjev, E.; Soares, J.; Arcidiacono, S.; Thompson, J. B.; Fossey, S. A.; Hansma, H. G.

    2002-01-01

    Despite its remarkable materials properties, the structure of spider dragline silk has remained unsolved. Results from two probe microscopy techniques provide new insights into the structure of spider dragline silk. A soluble synthetic protein from dragline silk spontaneously forms nanofibers, as observed by atomic force microscopy. These nanofibers have a segmented substructure. The segment length and amino acid sequence are consistent with a slab-like shape for individual silk protein molecules. The height and width of nanofiber segments suggest a stacking pattern of slab-like molecules in each nanofiber segment. This stacking pattern produces nano-crystals in an amorphous matrix, as observed previously by NMR and x-ray diffraction of spider dragline silk. The possible importance of nanofiber formation to native silk production is discussed. Force spectra for single molecules of the silk protein demonstrate that this protein unfolds through a number of rupture events, indicating a modular substructure within single silk protein molecules. A minimal unfolding module size is estimated to be around 14 nm, which corresponds to the extended length of a single repeated module, 38 amino acids long. The structure of this spider silk protein is distinctly different from the structures of other proteins that have been analyzed by single-molecule force spectroscopy, and the force spectra show correspondingly novel features. PMID:11959907

  18. Mechanisms of small molecule–DNA interactions probed by single-molecule force spectroscopy

    PubMed Central

    Almaqwashi, Ali A.; Paramanathan, Thayaparan; Rouzina, Ioulia; Williams, Mark C.

    2016-01-01

    There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules. PMID:27085806

  19. Single-molecule force spectroscopy of the Aplysia cell adhesion molecule reveals two homophilic bonds.

    PubMed

    Martines, E; Zhong, J; Muzard, J; Lee, A C; Akhremitchev, B B; Suter, D M; Lee, G U

    2012-08-22

    Aplysia californica neurons comprise a powerful model system for quantitative analysis of cellular and biophysical properties that are essential for neuronal development and function. The Aplysia cell adhesion molecule (apCAM), a member of the immunoglobulin superfamily of cell adhesion molecules, is present in the growth cone plasma membrane and involved in neurite growth, synapse formation, and synaptic plasticity. apCAM has been considered to be the Aplysia homolog of the vertebrate neural cell adhesion molecule (NCAM); however, whether apCAM exhibits similar binding properties and neuronal functions has not been fully established because of the lack of detailed binding data for the extracellular portion of apCAM. In this work, we used the atomic force microscope to perform single-molecule force spectroscopy of the extracellular region of apCAM and show for the first time (to our knowledge) that apCAM, like NCAM, is indeed a homophilic cell adhesion molecule. Furthermore, like NCAM, apCAM exhibits two distinct bonds in the trans configuration, although the kinetic and structural parameters of the apCAM bonds are quite different from those of NCAM. In summary, these single-molecule analyses further indicate that apCAM and NCAM are species homologs likely performing similar functions.

  20. Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates

    PubMed Central

    Motlagh, Hesam N.; Toptygin, Dmitri; Kaiser, Christian M.; Hilser, Vincent J.

    2016-01-01

    Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments. PMID:27028638

  1. Single Molecule Manipulation and Spectroscopy of Chlorophyll-a from Spinach

    NASA Astrophysics Data System (ADS)

    Benson, Jessica-Jones

    2005-03-01

    Chlorophyll-a, a molecule produced from `Spinach', adsorbed on a Au(111) surface has been investigated by using an ultra-high-vacuum low-temperature scanning-tunneling-microscope (UHV-LT-STM) at liquid helium temperatures. Studies are carried out both on isolated single molecules and on self-assembled molecular layers. The tunneling I-V and dI-dV spectroscopy of chlorophyll-a elucidate electronic properties of single molecule, such as the HOMO-LOMO gap and molecular orbital states. Mechanical stability of the chlorophyll-a is examined by using STM lateral manipulation (1,2). Here, the STM tip is placed just a few angstrom separation from the molecule to increase the tip-molecule interaction. Then the tip is laterally scanned across the surface resulting in pulling of the molecule. The detailed molecule movement is directly monitored through the corresponding STM-tip height signals. Our results reveal that the spinach molecule is a promising candidate for environmental friendly nano-device applications. (1). S.-W. Hla, K.-H. Rieder, Ann. Rev. Phys. Chem. 54 (2003) 307-330. (2). S.-W. Hla, et al. Phys. Rev. Lett. 93 (2004), 208302. This work is financially supported by the US-DOE grant DE-FG02-02ER46012.

  2. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.

    PubMed

    Schuler, Benjamin; Soranno, Andrea; Hofmann, Hagen; Nettels, Daniel

    2016-07-05

    The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.

  3. Copper nanoparticle heterogeneous catalytic ‘click’ cycloaddition confirmed by single-molecule spectroscopy

    NASA Astrophysics Data System (ADS)

    Decan, Matthew R.; Impellizzeri, Stefania; Marin, M. Luisa; Scaiano, Juan C.

    2014-08-01

    Colloidal or heterogeneous nanocatalysts can improve the range and diversity of Cu(I)-catalysed click reactions and facilitate catalyst separation and reuse. Catalysis by metal nanoparticles raises the question as to whether heterogeneous catalysts may cause homogeneous catalysis through metal ion leaching, since the catalytic process could be mediated by the particle, or by metal ions released from it. The question is critical as unwanted homogeneous processes could offset the benefits of heterogeneous catalysis. Here, we combine standard bench scale techniques with single-molecule spectroscopy to monitor single catalytic events in real time and demonstrate that click catalysis occurs directly at the surface of copper nanoparticles; this general approach could be implemented in other systems. We use ‘from the mole to the molecule’ to describe this emerging idea in which mole scale reactions can be optimized through an intimate understanding of the catalytic process at the single-molecule—single catalytic nanoparticle level.

  4. Unraveling the Electronic Heterogeneity of Charge Traps in Conjugated Polymers by Single-Molecule Spectroscopy.

    PubMed

    Adachi, Takuji; Vogelsang, Jan; Lupton, John M

    2014-02-06

    Charge trapping is taken for granted in modeling the characteristics of organic semiconductor devices, but very few techniques actually exist to spectroscopically pinpoint trap states. For example, trap levels are often assumed to be discrete in energy. Using the well-known keto defect in polyfluorene as a model, we demonstrate how single-molecule spectroscopy can directly track the formation of charge and exciton traps in conjugated polymers in real time, providing crucial information on the energetic distribution of trap sites relative to the polymer optical gap. Charge traps with universal spectral fingerprints scatter by almost 1 eV in depth, implying that substantial heterogeneity must be taken into account when modeling devices.

  5. Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

    PubMed

    Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E; Cole, Daniel G; Clark, Robert L

    2008-10-01

    In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies.

  6. Towards single-molecule NMR detection and spectroscopy using single spins in diamond

    NASA Astrophysics Data System (ADS)

    Perunicic, V. S.; Hall, L. T.; Simpson, D. A.; Hill, C. D.; Hollenberg, L. C. L.

    2014-02-01

    Nanomagnetometry using the nitrogen-vacancy (NV) center in diamond has attracted a great deal of interest due to its unique combination of room temperature operation, nanoscale resolution, and high sensitivity. One of the important goals for nanomagnetometry is to be able to detect nanoscale nuclear magnetic resonance (NMR) in individual molecules. Our theoretical analysis details a method by which a single molecule on the surface of diamond, with characteristic NMR frequencies, can be detected using a proximate NV center on a time scale of an order of seconds with nanometer precision. We perform spatiotemporal resolution optimization and subsequently outline paths to greater sensitivity. Our method is suitable for application in low and relatively inhomogeneous background magnetic fields in contrast to both conventional liquid and solid state NMR spectroscopy.

  7. Minimizing Pulling Geometry Errors in Atomic Force Microscope Single Molecule Force Spectroscopy

    PubMed Central

    Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E.; Cole, Daniel G.; Clark, Robert L.

    2008-01-01

    In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies. PMID:18641069

  8. Ultrasensitive protein detection in blood serum using gold nanoparticle probes by single molecule spectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Jiji; Wang, Chungang; Irudayaraj, Joseph

    2009-07-01

    A one-step rapid and ultrasensitive immunoassay capable of detecting proteins in blood serum is developed using gold nanoprobes and fluorescence correlation spectroscopy (FCS). In this approach we take advantage of the inherent photoluminescence property of gold nanoparticles (GNPs) to develop a fluorophore-free assay to observe binding entities by monitoring the diffusion of bound versus unbound molecules in a limited confocal volume. 40-nm GNPs conjugated separately with rabbit anti-IgG (Fc) and goat anti-IgG (Fab) when incubated in blood serum containing IgG forms a sandwich structure constituting dimers and oligomers that can be differentiated by to detect IgG in blood serum at a limit of detection (LOD) of 5 pg/ml. The novelty of integrating GNPs with FCS to develop a sensitive blood immunoassay brings single molecule methods one step closer to the clinic.

  9. Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy.

    PubMed

    Hofmann, Hagen; Hillger, Frank; Delley, Cyrille; Hoffmann, Armin; Pfeil, Shawn H; Nettels, Daniel; Lipman, Everett A; Schuler, Benjamin

    2014-12-16

    The bacterial chaperonin GroEL/GroES assists folding of a broad spectrum of denatured and misfolded proteins. Here, we explore the limits of this remarkable promiscuity by mapping two denatured proteins with very different conformational properties, rhodanese and cyclophilin A, during binding and encapsulation by GroEL/GroES with single-molecule spectroscopy, microfluidic mixing, and ensemble kinetics. We find that both proteins bind to GroEL with high affinity in a reaction involving substantial conformational adaptation. However, whereas the compact denatured state of rhodanese is encapsulated efficiently upon addition of GroES and ATP, the more expanded and unstructured denatured cyclophilin A is not encapsulated but is expelled into solution. The origin of this surprising disparity is the weaker interactions of cyclophilin A with a transiently formed GroEL-GroES complex, which may serve as a crucial checkpoint for substrate discrimination.

  10. Role of Denatured-State Properties in Chaperonin Action Probed by Single-Molecule Spectroscopy

    PubMed Central

    Hofmann, Hagen; Hillger, Frank; Delley, Cyrille; Hoffmann, Armin; Pfeil, Shawn H.; Nettels, Daniel; Lipman, Everett A.; Schuler, Benjamin

    2014-01-01

    The bacterial chaperonin GroEL/GroES assists folding of a broad spectrum of denatured and misfolded proteins. Here, we explore the limits of this remarkable promiscuity by mapping two denatured proteins with very different conformational properties, rhodanese and cyclophilin A, during binding and encapsulation by GroEL/GroES with single-molecule spectroscopy, microfluidic mixing, and ensemble kinetics. We find that both proteins bind to GroEL with high affinity in a reaction involving substantial conformational adaptation. However, whereas the compact denatured state of rhodanese is encapsulated efficiently upon addition of GroES and ATP, the more expanded and unstructured denatured cyclophilin A is not encapsulated but is expelled into solution. The origin of this surprising disparity is the weaker interactions of cyclophilin A with a transiently formed GroEL-GroES complex, which may serve as a crucial checkpoint for substrate discrimination. PMID:25517154

  11. Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy.

    PubMed

    Lu, Maolin; Lu, H Peter

    2014-10-16

    Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental

  12. Is Single-Molecule Fluorescence Spectroscopy Ready To Join the Organic Chemistry Toolkit? A Test Case Involving Click Chemistry.

    PubMed

    Scaiano, Juan C; Lanterna, Anabel E

    2017-04-06

    Single molecule spectroscopy (SMS) has matured to a point where it can be used as a convenient tool to guide organic synthesis and drug discovery, particularly applicable to catalytic systems where questions related to homogeneous vs heterogeneous pathways are important. SMS can look at intimate mechanistic details that can inspire major improvements of the catalyst performance, its recovery, and reuse. Here, we use the click reaction between alkynes and azides as an example where improvements at the bench have been inspired and validated using single-molecule fluorescence spectroscopy.

  13. Single-molecule force spectroscopy of membrane proteins from membranes freely spanning across nanoscopic pores.

    PubMed

    Petrosyan, Rafayel; Bippes, Christian A; Walheim, Stefan; Harder, Daniel; Fotiadis, Dimitrios; Schimmel, Thomas; Alsteens, David; Müller, Daniel J

    2015-05-13

    Single-molecule force spectroscopy (SMFS) provides detailed insight into the mechanical (un)folding pathways and structural stability of membrane proteins. So far, SMFS could only be applied to membrane proteins embedded in native or synthetic membranes adsorbed to solid supports. This adsorption causes experimental limitations and raises the question to what extent the support influences the results obtained by SMFS. Therefore, we introduce here SMFS from native purple membrane freely spanning across nanopores. We show that correct analysis of the SMFS data requires extending the worm-like chain model, which describes the mechanical stretching of a polypeptide, by the cubic extension model, which describes the bending of a purple membrane exposed to mechanical stress. This new experimental and theoretical approach allows to characterize the stepwise (un)folding of the membrane protein bacteriorhodopsin and to assign the stability of single and grouped secondary structures. The (un)folding and stability of bacteriorhodopsin shows no significant difference between freely spanning and directly supported purple membranes. Importantly, the novel experimental SMFS setup opens an avenue to characterize any protein from freely spanning cellular or synthetic membranes.

  14. Motion of a DNA Sliding Clamp Observed by Single Molecule Fluorescence Spectroscopy*S⃞

    PubMed Central

    Laurence, Ted A.; Kwon, Youngeun; Johnson, Aaron; Hollars, Christopher W.; O'Donnell, Mike; Camarero, Julio A.; Barsky, Daniel

    2008-01-01

    DNA sliding clamps attach to polymerases and slide along DNA to allow rapid, processive replication of DNA. These clamps contain many positively charged residues that could curtail the sliding due to attractive interactions with the negatively charged DNA. By single-molecule spectroscopy we have observed a fluorescently labeled sliding clamp (polymerase III β subunit or β clamp) loaded onto freely diffusing, single-stranded M13 circular DNA annealed with fluorescently labeled DNA oligomers of up to 90 bases. We find that the diffusion constant for the β clamp diffusing along DNA is on the order of 10–14 m2/s, at least 3 orders of magnitude less than that for diffusion through water alone. We also find evidence that the β clamp remains at the 3′ end in the presence of Escherichia coli single-stranded-binding protein. These results may imply that the clamp not only acts to hold the polymerase on the DNA but also prevents excessive drifting along the DNA. PMID:18556658

  15. Single-Molecule Force Spectroscopy of DNA-Based Reversible Polymer Bridges: Surface Robustness and Homogeneity

    PubMed Central

    Serpe, Michael J.; Whitehead, Jason R.; Rivera, Monica; Clark, Robert L.; Craig, Stephen L.

    2011-01-01

    Single-molecule force spectroscopy, as implemented in an atomic force microscope, provides a rarely-used method by which to monitor dynamic processes that occur near surfaces. Here, a methodology is presented and characterized that facilitates the study of polymer bridging across nanometer-sized gaps. The model system employed is that of DNA-based reversible polymers, and an automated procedure is introduced that allows the AFM tip-surface contact point to be automatically determined, and the distance d between opposing surfaces to be actively controlled. Using this methodology, the importance of several experimental parameters was systematically studied, e.g. the frequency of repeated tip/surface contacts, the area of the substrate surface sampled by the AFM, and the use of multiple AFM tips and substrates. Experiments revealed the surfaces to be robust throughout pulling experiments, so that multiple touches and pulls could be carried out on a single spot with no measurable affect on the results. Differences in observed bridging probabilities were observed, both on different spots on the same surface and, more dramatically, from one day to another. Data normalization via a reference measurement allows data from multiple days to be directly compared. PMID:21966095

  16. Design principles of natural light-harvesting as revealed by single molecule spectroscopy

    NASA Astrophysics Data System (ADS)

    Krüger, T. P. J.; van Grondelle, R.

    2016-01-01

    Biology offers a boundless source of adaptation, innovation, and inspiration. A wide range of photosynthetic organisms exist that are capable of harvesting solar light in an exceptionally efficient way, using abundant and low-cost materials. These natural light-harvesting complexes consist of proteins that strongly bind a high density of chromophores to capture solar photons and rapidly transfer the excitation energy to the photochemical reaction centre. The amount of harvested light is also delicately tuned to the level of solar radiation to maintain a constant energy throughput at the reaction centre and avoid the accumulation of the products of charge separation. In this Review, recent developments in the understanding of light-harvesting by plants will be discussed, based on results obtained from single molecule spectroscopy studies. Three design principles of the main light-harvesting antenna of plants will be highlighted: (a) fine, photoactive control over the intrinsic protein disorder to efficiently use intrinsically available thermal energy dissipation mechanisms; (b) the design of the protein microenvironment of a low-energy chromophore dimer to control the amount of shade absorption; (c) the design of the exciton manifold to ensure efficient funneling of the harvested light to the terminal emitter cluster.

  17. Red antenna states of Photosystem I trimers from Arthrospira platensis revealed by single-molecule spectroscopy.

    PubMed

    Brecht, Marc; Hussels, Martin; Schlodder, Eberhard; Karapetyan, Navassard V

    2012-03-01

    Single-molecule fluorescence spectroscopy at 1.4K was used to investigate the spectral properties of red (long-wavelength) chlorophylls in trimeric Photosystem I (PSI) complexes from the cyanobacterium Arthrospira platensis. Three distinct red antenna states could be identified in the fluorescence spectra of single PSI trimers from A. platensis in the presence of oxidized P700. Two of them are responsible for broad emission bands centered at 726 and 760nm. These bands are similar to those found in bulk fluorescence spectra measured at cryogenic temperatures. The broad fluorescence bands at ≅726 and ≅760nm belong to individual emitters that are broadened by strong electron-phonon coupling giving rise to a large Stokes-shift of about 20nm and rapid spectral diffusion. An almost perpendicular orientation of the transition dipole moments of F726 and F760 has to be assumed because direct excitation energy transfer does not occur between F726 and F760. For the first time a third red state assigned to the pool absorbing around 708nm could be detected by its zero-phonon lines. The center of the zero-phonon line distribution is found at ≅714nm. The spectral properties of the three red antenna states show a high similarity to the red antenna states found in trimeric PSI of Thermosynechoccocus elongatus. Based on these findings a similar organization of the red antenna states in PSI of these two cyanobacteria is discussed.

  18. Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

    PubMed Central

    Gensler, Manuel; Eidamshaus, Christian; Taszarek, Maurice; Reissig, Hans-Ulrich

    2015-01-01

    Summary Multivalent biomolecular interactions allow for a balanced interplay of mechanical stability and malleability, and nature makes widely use of it. For instance, systems of similar thermal stability may have very different rupture forces. Thus it is of paramount interest to study and understand the mechanical properties of multivalent systems through well-characterized model systems. We analyzed the rupture behavior of three different bivalent pyridine coordination complexes with Cu2+ in aqueous environment by single-molecule force spectroscopy. Those complexes share the same supramolecular interaction leading to similar thermal off-rates in the range of 0.09 and 0.36 s−1, compared to 1.7 s−1 for the monovalent complex. On the other hand, the backbones exhibit different flexibility, and we determined a broad range of rupture lengths between 0.3 and 1.1 nm, with higher most-probable rupture forces for the stiffer backbones. Interestingly, the medium-flexible connection has the highest rupture forces, whereas the ligands with highest and lowest rigidity seem to be prone to consecutive bond rupture. The presented approach allows separating bond and backbone effects in multivalent model systems. PMID:26124883

  19. Low Temperature STM Manipulation and Spectroscopy of Chlorophyll-a Single Molecules from Spinach

    NASA Astrophysics Data System (ADS)

    Benson, Jessica J.; Iancu, Violeta; Deshpande, Aparna; Hla, Saw-Wai

    2004-04-01

    We interrogate single chlorophyll-a, a molecule produced from Spinach, on Cu(111) surface to check its mechanical stability and electronic properties using an ultra-high-vacuum low-temperature scanning-tunneling-microscope (UHV-LT-STM) at liquid helium temperatures. The measured results of isolated single chlorophyll-a molecules are then compared with that of self-assembled molecular layer. The tunneling I/V and dI/dV spectroscopy techniques are used to probe the electronic properties of the chlorophyll-a molecule with atomic precision (1). These spectroscopic investigations elucidate properties of the single molecule such as the band gap and additional molecular orbital states. Mechanical stability of the chlorophyll-a molecule is examined using lateral manipulation techniques with the STM tip (2). In this procedure, the STM tip is placed in close proximity to the molecule (just a few angstrom separation) to increase the tip-molecule interaction. Then the tip is laterally moved across the surface, which results in pulling of the chlorophyll-a molecule to relocate to the specific surface sites. The detailed molecule movement during this manipulation is directly monitored through the corresponding STM-tip height signals. Our results highlight that the Spinach molecule is a promising candidate for environmental friendly nano-electronic device applications. (1) F. Moresco et al, Phy. Rev. Lett. 86, 672-675, (2001) (2) S-W. Hla, K-H. Rieder, Ann. Phy. Chem. 54, 307-330, (2003)

  20. Time resolved single molecule spectroscopy of semiconductor quantum dot/conjugated organic hybrid nanostructures

    NASA Astrophysics Data System (ADS)

    Odoi, Michael Yemoh

    Single molecule studies on CdSe quantum dots functionalized with oligo-phenylene vinylene ligands (CdSe-OPV) provide evidence of strong electronic communication that facilitate charge and energy transport between the OPV ligands and the CdSe quantum dot core. This electronic interaction greatly modify, the photoluminescence properties of both bulk and single CdSe-OPV nanostructure thin film samples. Size-correlated wide-field fluorescence imaging show that blinking suppression in single CdSe-OPV is linked to the degree of OPV coverage (inferred from AFM height scans) on the quantum dot surface. The effect of the complex electronic environment presented by photoexcited OPV ligands on the excited state property of CdSe-OPV is measured with single photon counting and photon-pair correlation spectroscopy techniques. Time-tagged-time-resolved (TTTR) single photon counting measurements from individual CdSe-OPV nanostructures, show excited state lifetimes an order of magnitude shorter relative to conventional ZnS/CdSe quantum dots. Second-order intensity correlation measurements g(2)(tau) from individual CdSe-OPV nanostructures point to a weak multi-excitonic character with a strong wavelength dependent modulation depth. By tuning in and out of the absorption of the OPV ligands we observe changes in modulation depth from g(2) (0) ≈ 0.2 to 0.05 under 405 and 514 nm excitation respectively. Defocused images and polarization anisotropy measurements also reveal a well-defined linear dipole emission pattern in single CdSe-OPV nanostructures. These results provide new insights into to the mechanism behind the electronic interactions in composite quantum dot/conjugated organic composite systems at the single molecule level. The observed intensity flickering , blinking suppression and associated lifetime/count rate and antibunching behaviour is well explained by a Stark interaction model. Charge transfer from photo-excitation of the OPV ligands to the surface of the Cd

  1. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    SciTech Connect

    Laurence, Ted Alfred

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  2. Unraveling the complexity of the interactions of DNA nucleotides with gold by single molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Bano, Fouzia; Sluysmans, Damien; Wislez, Arnaud; Duwez, Anne-Sophie

    2015-11-01

    Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct adsorption behavior of the deoxyribonucleotides (i.e., a nitrogenous base, a deoxyribose sugar, and a phosphate group) and on the factors that govern the DNA-gold bond strength. Here, using single molecule force spectroscopy, we investigated the interaction of the four individual nucleotides, adenine, guanine, cytosine, and thymine, with gold. Experiments were performed in three salinity conditions and two surface dwell times to reveal the factors that influence nucleotide-Au bond strength. Force data show that, at physiological ionic strength, adenine-Au interactions are stronger, asymmetrical and independent of surface dwell time as compared to cytosine-Au and guanine-Au interactions. We suggest that in these conditions only adenine is able to chemisorb on gold. A decrease of the ionic strength significantly increases the bond strength for all nucleotides. We show that moderate ionic strength along with longer surface dwell period suggest weak chemisorption also for cytosine and guanine.Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct

  3. Optical tweezers for single molecule force spectroscopy on bacterial adhesion organelles

    NASA Astrophysics Data System (ADS)

    Andersson, Magnus; Axner, Ove; Uhlin, Bernt Eric; Fällman, Erik

    2006-08-01

    Instrumentation and methodologies for single molecule force spectroscopy on bacterial adhesion organelles by the use of force measuring optical tweezers have been developed. A thorough study of the biomechanical properties of fimbrial adhesion organelles expressed by uropathogenic E. coli, so-called pili, is presented. Steady-state as well as dynamic force measurements on P pili, expressed by E. coli causing pyelonephritis, have revealed, among other things, various unfolding and refolding properties of the helical structure of P pili, the PapA rod. Based on these properties an energy landscape model has been constructed by which specific biophysical properties of the PapA rod have been extracted, e.g. the number of subunits, the length of a single pilus, bond lengths and activation energies for bond opening and closure. Moreover, long time repetitive measurements have shown that the rod can be unfolded and refolded repetitive times without losing its intrinsic properties. These properties are believed to be of importance for the bacteria's ability to maintain close contact with host cells during initial infections. The results presented are considered to be of importance for the field of biopolymers in general and the development of new pharmaceuticals towards urinary tract infections in particular. The results show furthermore that the methodology can be used to gain knowledge of the intrinsic biomechanical function of adhesion organelles. The instrumentation is currently used for characterization of type 1 pili, expressed by E. coli causing cystitis, i.e. infections in the bladder. The first force spectrometry investigations of these pili will be presented.

  4. Bloch Surface Wave-Coupled Emission from Quantum Dots by Ensemble and Single Molecule Spectroscopy.

    PubMed

    Ray, Krishanu; Badugu, Ramachandram; Lakowicz, Joseph R

    We report the spectral properties and spatial distribution of quantum dot (QD575 ) emission on a one-dimensional photonic crystal (1DPC). Our 1DPC substrate consists of multiple layers of dielectrics with a photonic band gap (PBG) near the QD575 emission maximum. The 1DPC was designed to display a surface-trapped electromagnetic state known as a Bloch surface wave (BSW) at the 1DPC-air (sample) interface. Ensemble angle-dependent emission intensities revealed a sharp angular emission peak near 41° from the normal which is consistent with the BSW resonance at 575 nm. We further examined the emission from single QDs on the 1DPC. A notable increase in fluorescence intensity from QD575 particles was observed on BSW substrate compared to the glass substrate from the scanning confocal fluorescence images and from the intensity-time trajectories of single QD575 particles. The intensity-decays showed substantially faster decay (4-fold decrease in emission lifetime) from the single QD575 particles on 1DPC substrate (∼4.8 nsec) as compared to the glass substrate (∼18 nsec). We observed the spectral characteristics of the individual QD575 particles on 1DPC and glass substrates, by recording the single particle emission spectra through the 1DPC. The emission spectra of the single QD575 particles are similar (with emission maxima around 575 nm) on both substrates except a substantial increase in intensity (over 10-fold) on the BSW substrate. Our results demonstrate that quantum dots can interact with Bloch Surface Waves (BSW) on a 1DPC. To the best of our knowledge, this is the first report on the single particle fluorescence studies on 1DPC substrate. The 10-fold increase in intensity in combination with 4-fold reduction in emission lifetime suggest 1DPCs with BSW modes have potential use in sensing and single molecule spectroscopy.

  5. Probing of Amyloid Aβ (14–23) Trimers by Single-Molecule Force Spectroscopy

    PubMed Central

    Maity, Sibaprasad; Lyubchenko, Yuri L.

    2016-01-01

    Self-assembly and aggregation of amyloid peptides, such as Aβ(1–40) and Aβ(1–42), lead to the development of Alzheimer disease and similar neurodegenerative disorders associated with protein aggregation. The structures of large aggregates, specifically fibrils, are well characterized. However, our understanding about the structure of oligomeric forms of amyloids is incomplete and needs to be expanded, particularly given the finding that oligomeric rather than fibrillar amyloid morphologies are neurotoxic. This lack of knowledge is primarily due to the existence of transient oligomeric forms that require the use of non-traditional approaches capable of probing transiently existing amyloid forms. We have recently developed the Single-Molecule Force Spectroscopy (SMFS) approach enabling us to probe dimeric forms of amyloids. These studies suggest that the assembly of amyloid proteins into dimers leads to extremely stabilized amyloids in non-native, misfolded states [1]. Herein, we applied the SMFS approach to probe amyloid trimers. We used the Aβ(14–23) segment of Aβ42 protein that is responsible for full-size protein aggregation. The dimerization of this peptide was recently characterized [2]. The dimeric form of Aβ (14–23) was assembled by the use of a tandem Aβ(14–23)-YNGK-Aβ(14–23), in which the YNGK motif between the two Aβ(14–23) monomers makes a β turn to form a hairpin loop with an antiparallel arrangement of Aβ(14–23) monomers[3]. The Aβ(14–23) monomer was tethered to the AFM tip, and trimers were formed by approaching the tip to the mica surface on which the Aβ(14–23)-YNGK-Aβ(14–23) dimer was immobilized via a polyethylene glycol tether. We identified trimers by rupture forces that were considerably larger than those for dimers. Models for the trimer assembly process are discussed.

  6. Blinking effect and the use of quantum dots in single molecule spectroscopy

    SciTech Connect

    Rombach-Riegraf, Verena; Oswald, Peter; Bienert, Roland; Petersen, Jan; Domingo, M.P.; Pardo, Julian; Graeber, P.; Galvez, E.M.

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer It is possible to eliminate the blinking effect of a water-soluble QD. Black-Right-Pointing-Pointer We provide a direct method to study protein function and dynamics at the single level. Black-Right-Pointing-Pointer QD, potent tool for single molecule studies of biochemical and biological processes. -- Abstract: Luminescent semiconductor nanocrystals (quantum dots, QD) have unique photo-physical properties: high photostability, brightness and narrow size-tunable fluorescence spectra. Due to their unique properties, QD-based single molecule studies have become increasingly more popular during the last years. However QDs show a strong blinking effect (random and intermittent light emission), which may limit their use in single molecule fluorescence studies. QD blinking has been widely studied and some hypotheses have been done to explain this effect. Here we summarise what is known about the blinking effect in QDs, how this phenomenon may affect single molecule studies and, on the other hand, how the 'on'/'off' states can be exploited in diverse experimental settings. In addition, we present results showing that site-directed binding of QD to cysteine residues of proteins reduces the blinking effect. This option opens a new possibility of using QDs to study protein-protein interactions and dynamics by single molecule fluorescence without modifying the chemical composition of the solution or the QD surface.

  7. Studying the mechanism of CD47-SIRPα interactions on red blood cells by single molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Pan, Yangang; Wang, Feng; Liu, Yanhou; Jiang, Junguang; Yang, Yong-Guang; Wang, Hongda

    2014-08-01

    The interaction forces and binding kinetics between SIRPα and CD47 were investigated by single-molecule force spectroscopy (SMFS) on both fresh and experimentally aged human red blood cells (hRBCs). We found that CD47 experienced a conformation change after oxidation, which influenced the interaction force and the position of the energy barrier between SIRPα and CD47. Our results are significant for understanding the mechanism of phagocytosis of red blood cells at the single molecule level.The interaction forces and binding kinetics between SIRPα and CD47 were investigated by single-molecule force spectroscopy (SMFS) on both fresh and experimentally aged human red blood cells (hRBCs). We found that CD47 experienced a conformation change after oxidation, which influenced the interaction force and the position of the energy barrier between SIRPα and CD47. Our results are significant for understanding the mechanism of phagocytosis of red blood cells at the single molecule level. Electronic supplementary information (ESI) available: Experimental section. See DOI: 10.1039/c4nr02889a

  8. Testing Landscape Theory for Biomolecular Processes with Single Molecule Fluorescence Spectroscopy

    NASA Astrophysics Data System (ADS)

    Truex, Katherine; Chung, Hoi Sung; Louis, John M.; Eaton, William A.

    2015-07-01

    Although Kramers' theory for diffusive barrier crossing on a 1D free energy profile plays a central role in landscape theory for complex biomolecular processes, it has not yet been rigorously tested by experiment. Here we test this 1D diffusion scenario with single molecule fluorescence measurements of DNA hairpin folding. We find an upper bound of 2.5 μ s for the average transition path time, consistent with the predictions by theory with parameters determined from optical tweezer measurements.

  9. The Study of Biomolecule-Substrate Interactions by Single Molecule Force Spectroscopy and Brownian Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Cook, Sara Iliafar

    Hybrids of biomolecules and nanomaterials have been identified as promising candidates in the development of novel therapeutics and electronic devices. Single stranded DNA (ssDNA)-bound Single-walled carbon nanotubes (SWCNTs) are of particular interest as they may be the key to solving the challenges that face the carbon nanotube separation technology and because of their potential application in bio-nanomedicine. The ability of ssDNA to form a stable hybrid with CNTs has been attributed to the structure and amphiphilic nature of this macromolecule, enabling the dispersion, sorting and patterned placement of nanotubes. Considering the significant role of ssDNA-CNTs in future technologies and the potential toxicity of such nanomaterials in biological systems, it is essential to gain a quantitative and fundamental understanding on the interactions that allow, weaken or prevent the formation of these hybrids. In this dissertation, we use both experimental and theoretical methods to systematically investigate the major characteristics of these interactions. The free energy of binding of ssDNA homopolymers to solvated carbon nanotubes is one of the key characteristics that determine the stability of such dispersions. We used single molecule force spectroscopy (SMFS), first on graphite and next on single walled carbon nanotubes, to probe and directly quantify the binding strength of ssDNA homopolymer oligomers to these substrates. The force resisting removal of DNA molecules from these surfaces shows characteristic steady-state force plateaus which were distinguishable for each DNA sequence. The free energy of binding per nucleotide for these oligomers on graphite were ranked as T >= A > G >= C (11.3 +/- 0.8 kT, 9.9 +/- 0.4 kT, 8.3 +/- 0.2 kT, and 7.5 +/- 0.8 kT, respectively). On SWCNTs, these interactions decreased in the following order: A > G > T > C, and their magnitude was much larger than on graphite (38.1 +/- 0.2; 33.9 +/- 0.1; 23.3 +/- 0.1; 17.1 +/- 0.1 k

  10. Review insights into the interactions of amino acids and peptides with inorganic materials using single molecule force spectroscopy.

    PubMed

    Das, Priyadip; Reches, Meital

    2015-09-01

    Understanding the interactions between proteins and inorganic surfaces is important for the development of new biomaterials and implants as they interface with the immune response by proteins. In addition, the adsorption of proteins to inorganic surfaces leads to the formation of a conditioning layer that facilitates bacterial attachments and biofilm formation. As biofilm provides bacterial resistance to antibiotics, biofilm formation is an undesirable process that could be prevented by resisting protein interactions with the substrate. Moreover, the interaction between proteins and inorganic materials is the basis for the formation of composite materials in nature. Understanding the underlying forces that governs these interactions would lead to the design of new and unique composite materials in vitro. This review focuses on the insights gained using single-molecule force spectroscopy by AFM on these interactions. This tool provides molecular information, at the single molecule level, on the interaction between a molecule on the AFM tip and a substrate.

  11. The structure and function of cell membranes examined by atomic force microscopy and single-molecule force spectroscopy.

    PubMed

    Shan, Yuping; Wang, Hongda

    2015-06-07

    The cell membrane is one of the most complicated biological complexes, and long-term fierce debates regarding the cell membrane persist because of technical hurdles. With the rapid development of nanotechnology and single-molecule techniques, our understanding of cell membranes has substantially increased. Atomic force microscopy (AFM) has provided several unprecedented advances (e.g., high resolution, three-dimensional and in situ measurements) in the study of cell membranes and has been used to systematically dissect the membrane structure in situ from both sides of membranes; as a result, novel models of cell membranes have recently been proposed. This review summarizes the new progress regarding membrane structure using in situ AFM and single-molecule force spectroscopy (SMFS), which may shed light on the study of the structure and functions of cell membranes.

  12. Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy.

    PubMed

    Zhang, Zhengyang; Kenny, Samuel J; Hauser, Margaret; Li, Wan; Xu, Ke

    2015-10-01

    By developing a wide-field scheme for spectral measurement and implementing photoswitching, we synchronously obtained the fluorescence spectra and positions of ∼10(6) single molecules in labeled cells in minutes, which consequently enabled spectrally resolved, 'true-color' super-resolution microscopy. The method, called spectrally resolved stochastic optical reconstruction microscopy (SR-STORM), achieved cross-talk-free three-dimensional (3D) imaging for four dyes 10 nm apart in emission spectrum. Excellent resolution was obtained for every channel, and 3D localizations of all molecules were automatically aligned within one imaging path.

  13. Single-molecule spectroscopy of protein folding in a chaperonin cage

    PubMed Central

    Hofmann, Hagen; Hillger, Frank; Pfeil, Shawn H.; Hoffmann, Armin; Streich, Daniel; Haenni, Dominik; Nettels, Daniel; Lipman, Everett A.; Schuler, Benjamin

    2010-01-01

    Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage. PMID:20547872

  14. Spectroscopy and single-molecule emission of a fluorene-terthiophene oligomer.

    PubMed

    Khalil, G E; Adawi, A M; Robinson, B; Cadby, A J; Tsoi, W C; Kim, J-S; Charas, A; Morgado, J; Lidzey, D G

    2011-10-27

    We study the thiophene-based oligomer poly[2,7-(9,9-bis(2'-ethylhexyl)fluorene)-alt-2,5-terthiophene] (PF3T) in solution and when dispersed at low concentration into a polynorbornene matrix. We find that at high concentration in solution the 0-0 electronic transition observed in fluorescence is suppressed, a result indicative of the formation of weakly coupled H-aggregates. At low concentration in a polymer matrix, emission from both single molecules and molecular aggregates is observed. We find that the fluorescence spectra of most PF3T emitters are composed of a number of relatively narrow emission features, indicating that the emission usually occurs from multiple chromophores. A small number of PF3T molecules are however characterized by single chromophore emission, spectral blinking, and narrowed emission peaks.

  15. 2008 Vibrational Spectroscopy

    SciTech Connect

    Philip J. Reid

    2009-09-21

    The conference focuses on using vibrational spectroscopy to probe structure and dynamics of molecules in gases, liquids, and interfaces. The goal is to bring together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of systems.

  16. Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy.

    PubMed

    Das, Priyadip; Duanias-Assaf, Tal; Reches, Meital

    2017-03-06

    The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

  17. Mechanism of amyloid β-protein dimerization determined using single-molecule AFM force spectroscopy

    NASA Astrophysics Data System (ADS)

    Lv, Zhengjian; Roychaudhuri, Robin; Condron, Margaret M.; Teplow, David B.; Lyubchenko, Yuri L.

    2013-10-01

    Aβ42 and Aβ40 are the two primary alloforms of human amyloid β-protein (Aβ). The two additional C-terminal residues of Aβ42 result in elevated neurotoxicity compared with Aβ40, but the molecular mechanism underlying this effect remains unclear. Here, we used single-molecule force microscopy to characterize interpeptide interactions for Aβ42 and Aβ40 and corresponding mutants. We discovered a dramatic difference in the interaction patterns of Aβ42 and Aβ40 monomers within dimers. Although the sequence difference between the two peptides is at the C-termini, the N-terminal segment plays a key role in the peptide interaction in the dimers. This is an unexpected finding as N-terminal was considered as disordered segment with no effect on the Aβ peptide aggregation. These novel properties of Aβ proteins suggests that the stabilization of N-terminal interactions is a switch in redirecting of amyloids form the neurotoxic aggregation pathway, opening a novel avenue for the disease preventions and treatments.

  18. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, Jongone; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

    2014-06-01

    The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic `fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.

  19. Interactions of light with matter: Applications to single molecule spectroscopy and quantum control

    NASA Astrophysics Data System (ADS)

    Brown, Frank Leon Halet

    Two different applications of the interaction between light and matter are discussed. First, we consider the single molecule spectra (SMS) of chromophores embedded in low temperature glasses. We demonstrate that it is possible to rationalize recent experimental results within the framework of the standard tunneling model (STM) for glassy dynamics as proposed by Anderson, Halperin and Varma and Phillips. Our analysis enables insight to be gained as to what features of the model are most important in describing experiment. Implicit in our treatment is the assumption that the two level systems, central to the STM, do not interact. The validity of this assumption is critically examined by extending the model to allow for such interactions. This complication of the theoretical model, beyond the lowest order implications of the STM, is found to influence individual spectra, but not the averaged quantities which are typically reported in the experimental literature. Our second application is a brief foray into the field of quantum control. Within the limit of weak applied fields and quadratic potentials for the control target, we describe a general method capable of determining the best possible field for affecting a desired configuration of the nuclear positions in the target. Several simple models are discussed within this framework to prove the validity of the formulation and its ease of implementation. Possibilities for extension to more complicated applications will be discussed. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307, Ph. 617-253-5668; Fax 617-253- 1690.)

  20. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    PubMed

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  1. Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies.

    PubMed

    Amo, Carlos A; Garcia, Ricardo

    2016-07-26

    Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force-distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50-500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations.

  2. Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies

    PubMed Central

    2016-01-01

    Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force–distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50–500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations. PMID:27359243

  3. Following aptamer-ricin specific binding by single molecule recognition and force spectroscopy measurements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The atomic force microscope (AFM) recognition and dynamic force spectroscopy (DFS) experiments provide both morphology and interaction information of the aptamer and protein, which can be used for the future study on the thermodynamics and kinetics properties of ricin-aptamer/antibody interactions. ...

  4. Spectroscopy and microscopy of single molecules in nanoscopic channels: spectral behavior vs. confinement depth.

    PubMed

    Gmeiner, Benjamin; Maser, Andreas; Utikal, Tobias; Götzinger, Stephan; Sandoghdar, Vahid

    2016-07-20

    We perform high-resolution spectroscopy and localization microscopy to study single dye molecules confined to nanoscopic dimensions in one direction. We provide the fabrication details of our nanoscopic glass channels and the procedure for filling them with organic matrices. Optical data on hundreds of molecules in different channel depths show a clear trend from narrow stable lines in deep channels to broader linewidths in ultrathin matrices. In addition, we observe a steady blue shift of the center of the inhomogeneous band as the channels become thinner. Furthermore, we use super-resolution localization microscopy to correlate the positions and orientations of the individual dye molecules with the lateral landscape of the organic matrix, including cracks and strain-induced dislocations. Our results and methodology are useful for a number of studies in various fields such as physical chemistry, solid-state spectroscopy, and quantum nano-optics.

  5. Conformational rearrangements in the transmembrane domain of CNGA1 channels revealed by single-molecule force spectroscopy

    PubMed Central

    Maity, Sourav; Mazzolini, Monica; Arcangeletti, Manuel; Valbuena, Alejandro; Fabris, Paolo; Lazzarino, Marco; Torre, Vincent

    2015-01-01

    Cyclic nucleotide-gated (CNG) channels are activated by binding of cyclic nucleotides. Although structural studies have identified the channel pore and selectivity filter, conformation changes associated with gating remain poorly understood. Here we combine single-molecule force spectroscopy (SMFS) with mutagenesis, bioinformatics and electrophysiology to study conformational changes associated with gating. By expressing functional channels with SMFS fingerprints in Xenopus laevis oocytes, we were able to investigate gating of CNGA1 in a physiological-like membrane. Force spectra determined that the S4 transmembrane domain is mechanically coupled to S5 in the closed state, but S3 in the open state. We also show there are multiple pathways for the unfolding of the transmembrane domains, probably caused by a different degree of α-helix folding. This approach demonstrates that CNG transmembrane domains have dynamic structure and establishes SMFS as a tool for probing conformational change in ion channels. PMID:25963832

  6. Conformational rearrangements in the transmembrane domain of CNGA1 channels revealed by single-molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Maity, Sourav; Mazzolini, Monica; Arcangeletti, Manuel; Valbuena, Alejandro; Fabris, Paolo; Lazzarino, Marco; Torre, Vincent

    2015-05-01

    Cyclic nucleotide-gated (CNG) channels are activated by binding of cyclic nucleotides. Although structural studies have identified the channel pore and selectivity filter, conformation changes associated with gating remain poorly understood. Here we combine single-molecule force spectroscopy (SMFS) with mutagenesis, bioinformatics and electrophysiology to study conformational changes associated with gating. By expressing functional channels with SMFS fingerprints in Xenopus laevis oocytes, we were able to investigate gating of CNGA1 in a physiological-like membrane. Force spectra determined that the S4 transmembrane domain is mechanically coupled to S5 in the closed state, but S3 in the open state. We also show there are multiple pathways for the unfolding of the transmembrane domains, probably caused by a different degree of α-helix folding. This approach demonstrates that CNG transmembrane domains have dynamic structure and establishes SMFS as a tool for probing conformational change in ion channels.

  7. Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy.

    PubMed

    Borgia, Alessandro; Wensley, Beth G; Soranno, Andrea; Nettels, Daniel; Borgia, Madeleine B; Hoffmann, Armin; Pfeil, Shawn H; Lipman, Everett A; Clarke, Jane; Schuler, Benjamin

    2012-01-01

    Theory, simulations and experimental results have suggested an important role of internal friction in the kinetics of protein folding. Recent experiments on spectrin domains provided the first evidence for a pronounced contribution of internal friction in proteins that fold on the millisecond timescale. However, it has remained unclear how this contribution is distributed along the reaction and what influence it has on the folding dynamics. Here we use a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, microfluidic mixing and denaturant- and viscosity-dependent protein-folding kinetics to probe internal friction in the unfolded state and at the early and late transition states of slow- and fast-folding spectrin domains. We find that the internal friction affecting the folding rates of spectrin domains is highly localized to the early transition state, suggesting an important role of rather specific interactions in the rate-limiting conformational changes.

  8. Confocal sample-scanning microscope for single-molecule spectroscopy and microscopy with fast sample exchange at cryogenic temperatures.

    PubMed

    Hussels, Martin; Konrad, Alexander; Brecht, Marc

    2012-12-01

    The construction of a microscope with fast sample transfer system for single-molecule spectroscopy and microscopy at low temperatures using 2D/3D sample-scanning is reported. The presented construction enables the insertion of a sample from the outside (room temperature) into the cooled (4.2 K) cryostat within seconds. We describe the mechanical and optical design and present data from individual Photosystem I complexes. With the described setup numerous samples can be investigated within one cooling cycle. It opens the possibility to investigate biological samples (i) without artifacts introduced by prolonged cooling procedures and (ii) samples that require preparation steps like plunge-freezing or specific illumination procedures prior to the insertion into the cryostat.

  9. Orientations between Red Antenna States of Photosystem I Monomers from Thermosynechococcus elongatus Revealed by Single-Molecule Spectroscopy.

    PubMed

    Skandary, Sepideh; Konrad, Alexander; Hussels, Martin; Meixner, Alfred J; Brecht, Marc

    2015-10-29

    Single-molecule spectroscopy at low temperature was used to study the spectral properties, heterogeneities, and spectral dynamics of the chlorophyll a (Chl a) molecules responsible for the fluorescence emission of photosystem I monomers (PS I-M) from the cyanobacterium Thermosynechococcus elongatus. The fluorescence spectra of single PS I-M are dominated by several red-shifted chlorophyll a molecules named C708 and C719. The emission spectra show broad spectral distributions and several zero-phonon lines (ZPLs). Compared with the spectra of the single PS I trimers, some contributions are missing due to the lower number of C719 Chl's in monomers. Polarization-dependent measurements show an almost perpendicular orientation between the emitters corresponding to C708 and C719. These contributions can be assigned to chlorophyll dimers B18B19, B31B32, and B32B33.

  10. How does the molecular linker in dynamic force spectroscopy affect probing molecular interactions at the single-molecule level?

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Aizawa, Kota; Hanyu, Tatsuya; Hirano, Yuuichi; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-08-01

    Dynamic force spectroscopy (DFS) based on atomic force microscopy, which enables us to obtain information on the interaction potential between molecules such as antigen-antibody complexes at the single-molecule level, is a key technique for advancing molecular science and technology. However, to ensure the reliability of DFS measurement, its basic mechanism must be well understood. We examined the effect of the molecular linker used to fix the target molecule to the atomic force microscope cantilever, i.e., the force direction during measurement, for the first time, which has not been discussed until now despite its importance. The effect on the lifetime and barrier position, which can be obtained by DFS, was found to be ˜10 and ˜50%, respectively, confirming the high potential of DFS.

  11. Single molecule tunneling spectroscopy investigation of reversibly switched dipolar vanadyl phthalocyanine on graphite

    SciTech Connect

    Zhang, Jialin; Wang, Zhunzhun; Li, Zhenyu E-mail: phycw@nus.edu.sg; Niu, Tianchao; Chen, Wei E-mail: phycw@nus.edu.sg

    2014-03-17

    We report a spatially resolved scanning tunneling spectroscopy (STS) investigation of reversibly switchable dipolar vanadyl phthalocyanine (VOPc) on graphite by using low temperature scanning tunneling microscopy. VOPc molecule can be switched between O-up and O-down configurations by changing the polarity of the pulse voltage applied to the tip, actuated by the inelastic tunneling electrons. The spatially resolved STS measurements allow the identification of the electronic structures of VOPc with different dipole orientation. The present approach provides geometry images and electronic characterization of a molecular switch on surface spontaneously.

  12. Structure-Dependent Electronic Interactions in Ethyne-Bridged Porphyrin Arrays Investigated by Single-Molecule Fluorescence Spectroscopy.

    PubMed

    Lee, Sang Hyeon; Yang, Jaesung; Kim, Dongho

    2016-09-15

    By using single-molecule fluorescence spectroscopy, we have investigated the electronic interaction of ethyne-bridged porphyrin arrays (ZNE) depending on their structure. The fluorescence dynamics of ZNE show a large amount of one-step photobleaching behaviors, indicating the high degree of π-conjugation. The ratio of one-step photobleaching behavior decreased as the number of porphyrin units increased. This behavior indicates that the linear and shortest Z2E shows a strong electronic coupling between constituent porphyrin moieties. Structural properties and orientation of ZNE were also measured by wide-field excitation fluorescence spectroscopy (ExPFS) and defocused wide-field imaging (DWFI). The ExPFS and DWFI show that the structure of absorbing and emitting units of Z2E and Z3E are linear. On the other hand, star-shaped pentamer with five porphyrins acts as an absorbing unit, but unidirectional trimer moiety acts as an emitting unit in the Z5E molecule. Collectively, these studies provide further information on the electronic interaction depending on their structure and length.

  13. Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions

    PubMed Central

    Scholl, Zackary N.; Marszalek, Piotr E.

    2013-01-01

    The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age. PMID:24001740

  14. Atomic force microscopy imaging and single molecule recognition force spectroscopy of coat proteins on the surface of Bacillus subtilis spore.

    PubMed

    Tang, Jilin; Krajcikova, Daniela; Zhu, Rong; Ebner, Andreas; Cutting, Simon; Gruber, Hermann J; Barak, Imrich; Hinterdorfer, Peter

    2007-01-01

    Coat assembly in Bacillus subtilis serves as a tractable model for the study of the self-assembly process of biological structures and has a significant potential for use in nano-biotechnological applications. In the present study, the morphology of B. subtilis spores was investigated by magnetically driven dynamic force microscopy (MAC mode atomic force microscopy) under physiological conditions. B. subtilis spores appeared as prolate structures, with a length of 0.6-3 microm and a width of about 0.5-2 microm. The spore surface was mainly covered with bump-like structures with diameters ranging from 8 to 70 nm. Besides topographical explorations, single molecule recognition force spectroscopy (SMRFS) was used to characterize the spore coat protein CotA. This protein was specifically recognized by a polyclonal antibody directed against CotA (anti-CotA), the antibody being covalently tethered to the AFM tip via a polyethylene glycol linker. The unbinding force between CotA and anti-CotA was determined as 55 +/- 2 pN. From the high-binding probability of more than 20% in force-distance cycles it is concluded that CotA locates in the outer surface of B. subtilis spores.

  15. Optimizing 1-μs-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope.

    PubMed

    Edwards, Devin T; Faulk, Jaevyn K; Sanders, Aric W; Bull, Matthew S; Walder, Robert; LeBlanc, Marc-Andre; Sousa, Marcelo C; Perkins, Thomas T

    2015-10-14

    Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is widely used to mechanically measure the folding and unfolding of proteins. However, the temporal resolution of a standard commercial cantilever is 50-1000 μs, masking rapid transitions and short-lived intermediates. Recently, SMFS with 0.7-μs temporal resolution was achieved using an ultrashort (L = 9 μm) cantilever on a custom-built, high-speed AFM. By micromachining such cantilevers with a focused ion beam, we optimized them for SMFS rather than tapping-mode imaging. To enhance usability and throughput, we detected the modified cantilevers on a commercial AFM retrofitted with a detection laser system featuring a 3-μm circular spot size. Moreover, individual cantilevers were reused over multiple days. The improved capabilities of the modified cantilevers for SMFS were showcased by unfolding a polyprotein, a popular biophysical assay. Specifically, these cantilevers maintained a 1-μs response time while eliminating cantilever ringing (Q ≅ 0.5). We therefore expect such cantilevers, along with the instrumentational improvements to detect them on a commercial AFM, to accelerate high-precision AFM-based SMFS studies.

  16. Stable, non-destructive immobilization of native nuclear membranes to micro-structured PDMS for single-molecule force spectroscopy.

    PubMed

    Rangl, Martina; Nevo, Reinat; Liashkovich, Ivan; Shahin, Victor; Reich, Ziv; Ebner, Andreas; Hinterdorfer, Peter

    2009-07-13

    In eukaryotic cells the nucleus is separated from the cytoplasm by a double-membraned nuclear envelope (NE). Exchange of molecules between the two compartments is mediated by nuclear pore complexes (NPCs) that are embedded in the NE membranes. The translocation of molecules such as proteins and RNAs through the nuclear membrane is executed by transport shuttling factors (karyopherines). They thereby dock to particular binding sites located all over the NPC, the so-called phenylalanine-glycin nucleoporines (FG Nups). Molecular recognition force spectroscopy (MRFS) allows investigations of the binding at the single-molecule level. Therefore the AFM tip carries a ligand for example, a particular karyopherin whereas the nuclear membrane with its receptors is mounted on a surface. Hence, one of the first requirements to study the nucleocytoplasmatic transport mechanism using MRFS is the development of an optimized membrane preparation that preserves structure and function of the NPCs. In this study we present a stable non-destructive preparation method of Xenopus laevis nuclear envelopes. We use micro-structured polydimethylsiloxane (PDMS) that provides an ideal platform for immobilization and biological integrity due to its elastic, chemical and mechanical properties. It is a solid basis for studying molecular recognition, transport interactions, and translocation processes through the NPC. As a first recognition system we investigate the interaction between an important transport shuttling factor, importin beta, and its binding sites on the NPC, the FG-domains.

  17. The nature of the force-induced conformation transition of dsDNA studied by using single molecule force spectroscopy.

    PubMed

    Liu, Ningning; Bu, Tianjia; Song, Yu; Zhang, Wei; Li, Jinjing; Zhang, Wenke; Shen, Jiacong; Li, Hongbin

    2010-06-15

    Single-stranded DNA binding proteins (SSB) interact with single-stranded DNA (ssDNA) specifically. Taking advantage of this character, we have employed Bacillus subtilis SSB protein to investigate the nature of force-induced conformation transition of double-stranded DNA (dsDNA) by using AFM-based single molecule force spectroscopy (SMFS) technique. Our results show that, when a dsDNA is stretched beyond its contour length, the dsDNA is partially melted, producing some ssDNA segments which can be captured by SSB proteins. We have also systematically investigated the effects of stretching length, waiting time, and salt concentration on the conformation transition of dsDNA and SSB-ssDNA interactions, respectively. Furthermore, the effect of proflavine, a DNA intercalator, on the SSB-DNA interactions has been investigated, and the results indicate that the proflavine-saturated dsDNA can be stabilized to the extent that the dsDNA will no longer melt into ssDNA under the mechanical force even up to 150 pN, and no SSB-DNA interactions are detectable.

  18. The Effect of Electrode Coupling on Single Molecule Device Characteristics: An X-Ray Spectroscopy and Scanning Probe Microscopy Study

    NASA Astrophysics Data System (ADS)

    Batra, Arunabh

    This thesis studies electronic properties of molecular devices in the limiting cases of strong and weak electrode-molecule coupling. In these two limits, we use the complementary techniques of X-Ray spectroscopy and Scanning Tunneling Microscopy (STM) to understand the mechanisms for electrode-molecule bond formation, the energy level realignment due to metal-molecule bonds, the effect of coupling strength on single-molecule conductance in low-bias measurements, and the effect of coupling on transport under high-bias. We also introduce molecular designs with inherent asymmetries, and develop an analytical method to determine the effect of these features on high-bias conductance. This understanding of the role of electrode-molecule coupling in high-bias regimes enables us to develop a series of functional electronic devices whose properties can be predictably tuned through chemical design. First, we explore the weak electrode-molecule coupling regime by studing the interaction of two types of paracyclophane derivates that are coupled 'through-space' to underlying gold substrates. The two paracyclophane derivatives differ in the strength of their intramolecular through-space coupling. X-Ray photoemission spectroscopy (XPS) and Near-Edge X-ray Absorbance Fine Structure (NEXAFS) spectroscopy allows us to determine the orientation of both molecules; Resonant Photoemission Spectroscopy (RPES) then allows us to measure charge transfer time from molecule to metal for both molecules. This study provides a quantititative measure of charge transfer time as a function of through-space coupling strength. Next we use this understanding in STM based single-molecule current-voltage measurements of a series of molecules that couple through-space to one electrode, and through-bond to the other. We find that in the high-bias regime, these molecules respond differently depending on the direction of the applied field. This asymmetric response to electric field direction results in

  19. Single-molecule force spectroscopy studies of fibrin 'A-a' polymerization interactions via the atomic force microscope

    NASA Astrophysics Data System (ADS)

    Averett, Laurel E.

    Fibrin, the polymerized form of the soluble plasma protein fibrinogen, plays a critical role in hemostasis as the structural scaffold of blood clots. The primary functions of fibrin are to withstand the shear forces of blood flow and provide mechanical stability to the clot, protecting the wound. While studies have investigated the mechanical properties of fibrin constructs, the response to force of critical polymerization interactions such as the 'A--a' knob--hole interaction remains unclear. Herein, the response of the 'A--a' bond to force was examined at the single-molecule level using the atomic force microscope. Force spectroscopy methodology was developed to examine the 'A--a' interaction while reducing the incidence of both nonspecific and multiple molecule interactions. The rupture of this interaction resulted in a previously unreported characteristic force profile comprised of up to four events. We hypothesized that the first event represented reorientation of the fibrinogen molecule, the second and third represented unfolding of structures in the D region of fibrinogen, and the last event was the rupture of the 'A--a' bond weakened by prior structural unfolding. The configuration, molecular extension, and kinetic parameters of each event in the characteristic pattern were examined to compare the unfolding of fibrin to other proteins unfolded by force. Fitting the pattern with polymer models showed that the D region of fibrinogen could lengthen by ˜50% of the length of a fibrin monomer before rupture of the 'A--a' bond. Analysis showed that the second and third events had kinetic parameters similar to other protein structures unfolded by force. Studies of the dependence of the characteristic pattern on calcium, concentration of sodium chloride, pH, and temperature demonstrated that the incidence of the last event was affected by solution conditions. However, only low pH and high temperatures reduced the probability that an interaction was characteristic

  20. Vibrational Spectroscopy of Ionic Liquids.

    PubMed

    Paschoal, Vitor H; Faria, Luiz F O; Ribeiro, Mauro C C

    2017-01-04

    Vibrational spectroscopy has continued use as a powerful tool to characterize ionic liquids since the literature on room temperature molten salts experienced the rapid increase in number of publications in the 1990's. In the past years, infrared (IR) and Raman spectroscopies have provided insights on ionic interactions and the resulting liquid structure in ionic liquids. A large body of information is now available concerning vibrational spectra of ionic liquids made of many different combinations of anions and cations, but reviews on this literature are scarce. This review is an attempt at filling this gap. Some basic care needed while recording IR or Raman spectra of ionic liquids is explained. We have reviewed the conceptual basis of theoretical frameworks which have been used to interpret vibrational spectra of ionic liquids, helping the reader to distinguish the scope of application of different methods of calculation. Vibrational frequencies observed in IR and Raman spectra of ionic liquids based on different anions and cations are discussed and eventual disagreements between different sources are critically reviewed. The aim is that the reader can use this information while assigning vibrational spectra of an ionic liquid containing another particular combination of anions and cations. Different applications of IR and Raman spectroscopies are given for both pure ionic liquids and solutions. Further issues addressed in this review are the intermolecular vibrations that are more directly probed by the low-frequency range of IR and Raman spectra and the applications of vibrational spectroscopy in studying phase transitions of ionic liquids.

  1. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

    PubMed

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-07-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.

  2. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy

    PubMed Central

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-01-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers. PMID:27363513

  3. Low-temperature spectroscopy of organic molecules in solid matrices: from the Shpol'skii effect to laser luminescent spectromicroscopy for all effectively emitting single molecules

    NASA Astrophysics Data System (ADS)

    Naumov, A. V.

    2013-06-01

    Sixty years ago, in 1952, Prof. E V Shpol'skii and his colleagues were the first to see quasilinear spectra from complex organic compounds in specially selected solvents at low temperatures. Twenty years later, in 1972, a team headed by Prof. R I Personov discovered laser fluorescence line narrowing in the solid solutions of organic dyes. These two discoveries served as the basis for the field of laser selective spectroscopy of impurity centers in solids. The work in this field culminated in the techniques of spectroscopy and luminescence imaging (microscopy) of single molecules in condensed matter. Today, optical spectroscopy of impurity centers in solid solutions has become one of the most popular tools for solving a wide variety of interdisciplinary problems in physics, physical chemistry, optics and spectroscopy, biophysics, quantum optics, and nanotechnology. In this article, the development of this field is briefly reviewed, potentials of the developed methods are discussed, and some research results are highlighted.

  4. 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

  5. Vibrational spectroscopy of resveratrol

    NASA Astrophysics Data System (ADS)

    Billes, Ferenc; Mohammed-Ziegler, Ildikó; Mikosch, Hans; Tyihák, Ernő

    2007-11-01

    In this article the authors deal with the experimental and theoretical interpretation of the vibrational spectra of trans-resveratrol (3,5,4'-trihydroxy- trans-stilbene) of diverse beneficial biological activity. Infrared and Raman spectra of the compound were recorded; density functional calculations were carried out resulting in the optimized geometry and several properties of the molecule. Based on the calculated force constants, a normal coordinate analysis yielded the character of the vibrational modes and the assignment of the measured spectral bands.

  6. Room temperature spectrally resolved single-molecule spectroscopy reveals new spectral forms and photophysical versatility of aequorea green fluorescent protein variants.

    PubMed

    Blum, Christian; Meixner, Alfred J; Subramaniam, Vinod

    2004-12-01

    It is known from ensemble spectroscopy at cryogenic temperatures that variants of the Aequorea green fluorescent protein (GFP) occur in interconvertible spectroscopically distinct forms which are obscured in ensemble room temperature spectroscopy. By analyzing the fluorescence of the GFP variants EYFP and EGFP by spectrally resolved single-molecule spectroscopy we were able to observe spectroscopically different forms of the proteins and to dynamically monitor transitions between these forms at room temperature. In addition to the predominant EYFP B-form we have observed the blue-shifted I-form thus far only seen at cryogenic temperatures and have followed transitions between these forms. Further we have identified for EYFP and for EGFP three more, so far unknown, forms with red-shifted fluorescence. Transitions between the predominant forms and the red-shifted forms show a dark time which indicates the existence of a nonfluorescent intermediate. The spectral position of the newly-identified red-shifted forms and their formation via a nonfluorescent intermediate hint that these states may account for the possible photoactivation observed in bulk experiments. The comparison of the single-protein spectra of the red-shifted EYFP and EGFP forms with single-molecule fluorescence spectra of DsRed suggest that these new forms possibly originate from an extended chromophoric pi-system analogous to the DsRed chromophore.

  7. Binding Strength and Dynamics of Invariant Natural Killer Cell T Cell Receptor/CD1d-Glycosphingolipid Interaction on Living Cells by Single Molecule Force Spectroscopy*

    PubMed Central

    Bozna, Bianca L.; Polzella, Paolo; Rankl, Christian; Zhu, Rong; Salio, Mariolina; Shepherd, Dawn; Duman, Memed; Cerundolo, Vincenzo; Hinterdorfer, Peter

    2011-01-01

    Invariant natural killer T (iNKT) cells are a population of T lymphocytes that play an important role in regulating immunity to infection and tumors by recognizing endogenous and exogenous CD1d-bound lipid molecules. Using soluble iNKT T cell receptor (TCR) molecules, we applied single molecule force spectroscopy for the investigation of the iNKT TCR affinity for human CD1d molecules loaded with glycolipids differing in the length of the phytosphingosine chain using either recombinant CD1d molecules or lipid-pulsed THP1 cells. In both settings, the dissociation of the iNKT TCR from human CD1d molecules loaded with the lipid containing the longer phytosphingosine chain required higher unbinding forces compared with the shorter phytosphingosine lipid. Our findings are discussed in the context of previous results obtained by surface plasmon resonance measurements. We present new insights into the energy landscape and the kinetic rate constants of the iNKT TCR/human CD1d-glycosphingolipid interaction and emphasize the unique potential of single molecule force spectroscopy on living cells. PMID:21454514

  8. Binding strength and dynamics of invariant natural killer cell T cell receptor/CD1d-glycosphingolipid interaction on living cells by single molecule force spectroscopy.

    PubMed

    Bozna, Bianca L; Polzella, Paolo; Rankl, Christian; Zhu, Rong; Salio, Mariolina; Shepherd, Dawn; Duman, Memed; Cerundolo, Vincenzo; Hinterdorfer, Peter

    2011-05-06

    Invariant natural killer T (iNKT) cells are a population of T lymphocytes that play an important role in regulating immunity to infection and tumors by recognizing endogenous and exogenous CD1d-bound lipid molecules. Using soluble iNKT T cell receptor (TCR) molecules, we applied single molecule force spectroscopy for the investigation of the iNKT TCR affinity for human CD1d molecules loaded with glycolipids differing in the length of the phytosphingosine chain using either recombinant CD1d molecules or lipid-pulsed THP1 cells. In both settings, the dissociation of the iNKT TCR from human CD1d molecules loaded with the lipid containing the longer phytosphingosine chain required higher unbinding forces compared with the shorter phytosphingosine lipid. Our findings are discussed in the context of previous results obtained by surface plasmon resonance measurements. We present new insights into the energy landscape and the kinetic rate constants of the iNKT TCR/human CD1d-glycosphingolipid interaction and emphasize the unique potential of single molecule force spectroscopy on living cells.

  9. Cotunneling spectroscopy and the properties of excited-state spin manifolds of Mn12 single molecule magnets

    NASA Astrophysics Data System (ADS)

    Rostamzadeh Renani, Fatemeh; Kirczenow, George

    2014-10-01

    We study charge transport through single molecule magnet (SMM) junctions in the cotunneling regime as a tool for investigating the properties of the excited-state manifolds of neutral Mn12 SMs. This study is motivated by a recent transport experiment [S. Kahle et al., Nano Lett. 12, 518 (2012), 10.1021/nl204141z] that probed the details of the magnetic and electronic structure of Mn12 SMMs beyond the ground-state spin manifold. A giant spin Hamiltonian and master equation approach is used to explore theoretically the cotunneling transport through Mn12-Ac SMM junctions. We identify SMM transitions that can account for both the strong and weak features of the experimental differential conductance spectra. We find the experimental results to imply that the excited spin-state manifolds of the neutral SMM have either different anisotropy constants or different g factors in comparison with its ground-state manifold. However, the latter scenario accounts best for the experimental data.

  10. Single molecule force spectroscopy reveals critical roles of hydrophobic core packing in determining the mechanical stability of protein GB1.

    PubMed

    Bu, Tianjia; Wang, Hui-Chuan Eileen; Li, Hongbin

    2012-08-21

    Understanding molecular determinants of protein mechanical stability is important not only for elucidating how elastomeric proteins are designed and functioning in biological systems but also for designing protein building blocks with defined nanomechanical properties for constructing novel biomaterials. GB1 is a small α/β protein and exhibits significant mechanical stability. It is thought that the shear topology of GB1 plays an important role in determining its mechanical stability. Here, we combine single molecule atomic force microscopy and protein engineering techniques to investigate the effect of side chain reduction and hydrophobic core packing on the mechanical stability of GB1. We engineered seven point mutants and carried out mechanical φ-value analysis of the mechanical unfolding of GB1. We found that three mutations, which are across the surfaces of two subdomains that are to be sheared by the applied stretching force, in the hydrophobic core (F30L, Y45L, and F52L) result in significant decrease in mechanical unfolding force of GB1. The mechanical unfolding force of these mutants drop by 50-90 pN compared with wild-type GB1, which unfolds at around 180 pN at a pulling speed of 400 nm/s. These results indicate that hydrophobic core packing plays an important role in determining the mechanical stability of GB1 and suggest that optimizing hydrophobic interactions across the surfaces that are to be sheared will likely be an efficient method to enhance the mechanical stability of GB1 and GB1 homologues.

  11. Significant Heterogeneity and Slow Dynamics of the Unfolded Ubiquitin Detected by the Line Confocal Method of Single-Molecule Fluorescence Spectroscopy.

    PubMed

    Saito, Masataka; Kamonprasertsuk, Supawich; Suzuki, Satomi; Nanatani, Kei; Oikawa, Hiroyuki; Kushiro, Keiichiro; Takai, Madoka; Chen, Po-Ting; Chen, Eric H-L; Chen, Rita P-Y; Takahashi, Satoshi

    2016-09-01

    The conformation and dynamics of the unfolded state of ubiquitin doubly labeled regiospecifically with Alexa488 and Alexa647 were investigated using single-molecule fluorescence spectroscopy. The line confocal fluorescence detection system combined with the rapid sample flow enabled the characterization of unfolded proteins at the improved structural and temporal resolutions compared to the conventional single-molecule methods. In the initial stage of the current investigation, however, the single-molecule Förster resonance energy transfer (sm-FRET) data of the labeled ubiquitin were flawed by artifacts caused by the adsorption of samples to the surfaces of the fused-silica flow chip and the sample delivery system. The covalent coating of 2-methacryloyloxyethyl phosphorylcholine polymer to the flow chip surface was found to suppress the artifacts. The sm-FRET measurements based on the coated flow chip demonstrated that the histogram of the sm-FRET efficiencies of ubiquitin at the native condition were narrowly distributed, which is comparable to the probability density function (PDF) expected from the shot noise, demonstrating the structural homogeneity of the native state. In contrast, the histogram of the sm-FRET efficiencies of the unfolded ubiquitin obtained at a time resolution of 100 μs was distributed significantly more broadly than the PDF expected from the shot noise, demonstrating the heterogeneity of the unfolded state conformation. The variety of the sm-FRET efficiencies of the unfolded state remained even after evaluating the moving average of traces with a window size of 1 ms, suggesting that conformational averaging of the heterogeneous conformations mostly occurs in the time domain slower than 1 ms. Local structural heterogeneity around the labeled fluorophores was inferred as the cause of the structural heterogeneity. The heterogeneity and slow dynamics revealed by the line confocal tracking of sm-FRET might be common properties of the unfolded

  12. Time-resolved vibrational spectroscopy

    SciTech Connect

    Tokmakoff, Andrei; Champion, Paul; Heilweil, Edwin J.; Nelson, Keith A.; Ziegler, Larry

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE's Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all fiveof DOE's grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  13. Vibrational Spectroscopy and Quantum Localization

    NASA Astrophysics Data System (ADS)

    Fillaux, François

    These lecture-notes are meant to provide newcomers with an overview of the impact of vibrational spectroscopy in the field of nonlinear dynamics of atoms and molecules, in the perspective of energy localization. In the introduction, the terminology of nonlinear excitations and tentative experimental evidences are briefly recalled in a brief historical perspective. The basic principles of vibrational spectroscopy are presented in section 11 for infrared, Raman and inelastic neutron scattering. The potentialities for each technique to probing energy localization are discussed. In section 12, nonlinear dynamics in isolated molecules are treated within the framework of normal versus local mode representations. It is shown that these complementary representations are not necessarily distinctive of weak versus strong anharmonicity, in the context of chemical complexity. It is emphasized that local modes and energy localization are totally independent concepts. In section 4, examples of nonlinear dynamics in crystals are reviewed: multiphonon bound states, strong coupling between phonons and electrons probed with resonance Raman, local modes and quantum rotation in one-dimension probed with inelastic neutron scattering, strong coupling in hydrogen-bonded crystals and self-trapping probed with time-resolved vibrational-spectroscopy. The extended character of eigenstates in crystals free of impurities and disorder, the nature of the interaction of periodic lattices with plane waves, the Franck-Condon principle and the particle-wave duality in the quantum regime are key factors preventing observation of energy localization. It is shown that free spatially-localized nondissipative classical waves give rise to free pseudoparticles that behave as planar waves in the quantum regime. In conclusion, a clear demonstration that energy localization corresponds to eigenstates is eagerly expected for further evidencing these states with vibrational spectroscopy.

  14. Single-Molecule Spectroscopy Unmasks the Lowest Exciton State of the B850 Assembly in LH2 from Rps. acidophila

    PubMed Central

    Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J.; Freiberg, Arvi; Köhler, Jürgen

    2014-01-01

    We have recorded fluorescence-excitation and emission spectra from single LH2 complexes from Rhodopseudomonas (Rps.) acidophila. Both types of spectra show strong temporal spectral fluctuations that can be visualized as spectral diffusion plots. Comparison of the excitation and emission spectra reveals that for most of the complexes the lowest exciton transition is not observable in the excitation spectra due to the cutoff of the detection filter characteristics. However, from the spectral diffusion plots we have the full spectral and temporal information at hand and can select those complexes for which the excitation spectra are complete. Correlating the red most spectral feature of the excitation spectrum with the blue most spectral feature of the emission spectrum allows an unambiguous assignment of the lowest exciton state. Hence, application of fluorescence-excitation and emission spectroscopy on the same individual LH2 complex allows us to decipher spectral subtleties that are usually hidden in traditional ensemble spectroscopy. PMID:24806933

  15. Highly specific identification of single nucleic polymorphism in M. tuberculosis using smart probes and single-molecule fluorescence spectroscopy in combination with blocking oligonucleotides

    NASA Astrophysics Data System (ADS)

    Friedrich, Achim; Müller, Matthias; Nolte, Oliver; Wolfrum, Jürgen; Sauer, Markus; Hoheisel, Jörg D.; Knemeyer, Jens-Peter; Marme, Nicole

    2008-02-01

    In this article we present a method for the highly specific identification of single nucleotide polymorphism (SNP) responsible for rifampicin resistance of Mycobacterium tuberculosis. This approach applies fluorescently labeled hairpin-structured oligonucleotides (smart probes) and confocal single-molecule fluorescence spectroscopy. Smart probes are fluorescently labeled at the 5'-end. The dye's fluorescence is quenched in the closed hairpin conformation due to close proximity of the guanosine residues located at the 3'-end. As a result of the hybridization to the complementary target sequence the hairpin structure and thus fluorescence quenching gets lost and a strong fluorescence increase appears. To enhance the specificity of the SNP detection unlabeled "blocking oligonucleotides" were added to the sample. These oligonucleotides hybridizes to the DNA sequence containing the mismatch thus masking this sequence and hereby preventing the smart probe from hybridizing to the mismatched sequence.

  16. Single molecules: Thermodynamic limits

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    2012-09-01

    Technologies aimed at single-molecule resolution of non-equilibrium systems increasingly require sophisticated new ways of thinking about thermodynamics. An elegant extension to standard fluctuation theory grants access to the kinetic intermediate states of these systems -- as DNA-pulling experiments now demonstrate.

  17. 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.

  18. Correlative Synchrotron Fourier Transform Infrared Spectroscopy and Single Molecule Super Resolution Microscopy for the Detection of Composition and Ultrastructure Alterations in Single Cells.

    PubMed

    Whelan, Donna R; Bell, Toby D M

    2015-12-18

    Single molecule localization microscopy (SMLM) and synchrotron Fourier transform infrared (S-FTIR) spectroscopy are two techniques capable of elucidating unique and valuable biological detail. SMLM provides images of the structures and distributions of targeted biomolecules at spatial resolutions up to an order of magnitude better than the diffraction limit, whereas IR spectroscopy objectively measures the holistic biochemistry of an entire sample, thereby revealing any variations in overall composition. Both tools are currently applied extensively to detect cellular response to disease, chemical treatment, and environmental change. Here, these two techniques have been applied correlatively at the single cell level to probe the biochemistry of common fixation methods and have detected various fixation-induced losses of biomolecular composition and cellular ultrastructure. Furthermore, by extensive honing and optimizing of fixation protocols, many fixation artifacts previously considered pervasive and regularly identified using IR spectroscopy and fluorescence techniques have been avoided. Both paraformaldehyde and two-step glutaraldehyde fixation were identified as best preserving biochemistry for both SMLM and IR studies while other glutaraldehyde and methanol fixation protocols were demonstrated to cause significant biochemical changes and higher variability between samples. Moreover, the potential complementarity of the two techniques was strikingly demonstrated in the correlated detection of biochemical changes as well as in the detection of fixation-induced damage that was only revealed by one of the two techniques.

  19. Soil chemical insights provided through vibrational spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vibrational spectroscopy techniques provide a powerful approach to study environmental materials and processes. These multifunctional analysis tools can be used to probe molecular vibrations of solid, liquid, and gaseous samples for characterizing materials, elucidating reaction mechanisms, and exam...

  20. Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy.

    PubMed

    Banerjee, S; Rakshit, T; Sett, S; Mukhopadhyay, R

    2015-10-22

    One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

  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. Demonstration of specific binding of heparin to Plasmodium falciparum-infected vs. non-infected red blood cells by single-molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Valle-Delgado, Juan José; Urbán, Patricia; Fernàndez-Busquets, Xavier

    2013-04-01

    Glycosaminoglycans (GAGs) play an important role in the sequestration of Plasmodium falciparum-infected red blood cells (pRBCs) in the microvascular endothelium of different tissues, as well as in the formation of small clusters (rosettes) between infected and non-infected red blood cells (RBCs). Both sequestration and rosetting have been recognized as characteristic events in severe malaria. Here we have used heparin and pRBCs infected by the 3D7 strain of P. falciparum as a model to study GAG-pRBC interactions. Fluorescence microscopy and fluorescence-assisted cell sorting assays have shown that exogenously added heparin has binding specificity for pRBCs (preferentially for those infected with late forms of the parasite) vs. RBCs. Heparin-pRBC adhesion has been probed by single-molecule force spectroscopy, obtaining an average binding force ranging between 28 and 46 pN depending on the loading rate. No significant binding of heparin to non-infected RBCs has been observed in control experiments. This work represents the first approach to quantitatively evaluate GAG-pRBC molecular interactions at the individual molecule level.Glycosaminoglycans (GAGs) play an important role in the sequestration of Plasmodium falciparum-infected red blood cells (pRBCs) in the microvascular endothelium of different tissues, as well as in the formation of small clusters (rosettes) between infected and non-infected red blood cells (RBCs). Both sequestration and rosetting have been recognized as characteristic events in severe malaria. Here we have used heparin and pRBCs infected by the 3D7 strain of P. falciparum as a model to study GAG-pRBC interactions. Fluorescence microscopy and fluorescence-assisted cell sorting assays have shown that exogenously added heparin has binding specificity for pRBCs (preferentially for those infected with late forms of the parasite) vs. RBCs. Heparin-pRBC adhesion has been probed by single-molecule force spectroscopy, obtaining an average binding force

  3. 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

  4. Vibrational spectroscopy of HNS degradation

    NASA Astrophysics Data System (ADS)

    Alam, M. Kathleen; Martin, Laura; Schmitt, Randal L.; Ten Eyck, Gregory A.; Welle, Eric

    2008-08-01

    Hexanitrostilbene (HNS) is a widely used explosive, due in part to its high thermal stability. Degradation of HNS is known to occur through UV, chemical exposure, and heat exposure, which can lead to reduced performance of the material. Common methods of testing for HNS degradation include wet chemical and surface area testing of the material itself, and performance testing of devices that use HNS. The commonly used chemical tests, such as volatility, conductivity and contaminant trapping provide information on contaminants rather than the chemical stability of the HNS itself. Additionally, these tests are destructive in nature. As an alternative to these methods, we have been exploring the use of vibrational spectroscopy as a means of monitoring HNS degradation non-destructively. In particular, infrared (IR) spectroscopy lends itself well to non-destructive analysis. Molecular variations in the material can be identified and compared to pure samples. The utility of IR spectroscopy was evaluated using pressed pellets of HNS exposed to DETA (diethylaminetriamine). Amines are known to degrade HNS, with the proposed product being a σ-adduct. We have followed these changes as a function of time using various IR sampling techniques including photoacoustic and attenuated total reflectance (ATR).

  5. Effects of Supramolecular Encapsulation on Photophysics and Photostability of a 9,10-Bis(arylethynyl)anthracene-Based Chromophore Revealed by Single-Molecule Fluorescence Spectroscopy.

    PubMed

    Mitsui, Masaaki; Higashi, Koji; Hirumi, Yohei; Kobayashi, Kenji

    2016-10-18

    The effects of supramolecular encapsulation on the photophysics and photostability of a highly fluorescent dimeric derivative of 2,6-diacetoxy-9,10-bis(arylethynyl)anthracene (G2) were investigated by single-molecule fluorescence spectroscopy (SMFS). The fluorescence properties of free-G2 and its self-assembled boronic ester encapsulation complex, G2@(Cap)2, were compared in solution and a glassy polymer film. The fluorescence spectral characteristics and theoretical calculations suggest that the environment affects the excited-state conformation and subsequent fluorescence emission of G2@(Cap)2. In particular, in the liquid and polymer environments, G2@(Cap)2 emits a fluorescence photon in the planar and twist conformation, respectively, whereas the fluorescence-emitting conformation of free-G2 is planar in both environments. The luminous conformation differences between free-G2 and G2@(Cap)2 in polymer are reflected in the intersystem crossing (ISC) parameters (the ISC quantum yield and triplet lifetime), as determined by fluorescence autocorrelation analysis. The photobleaching yield revealed a 3-fold enhancement in the photostability of encapsulated G2 (relative to free-G2). Under the SMFS measurement conditions, the photostability of the encapsulation complex was independent of the guest's photostability and appeared to be dominated by the thermal stability of the Cap host molecule.

  6. Single molecule magnets with protective ligand shells on gold and titanium dioxide surfaces: in situ electrospray deposition and x-ray absorption spectroscopy.

    PubMed

    Handrup, Karsten; Richards, Victoria J; Weston, Matthew; Champness, Neil R; O'Shea, James N

    2013-10-21

    Two single molecule magnets based on the dodecamanganese (III, IV) cluster with either benzoate or terphenyl-4-carboxylate ligands, have been studied on the Au(111) and rutile TiO2(110) surfaces. We have used in situ electrospray deposition to produce a series of surface coverages from a fraction of a monolayer to multilayer films in both cases. X-ray absorption spectroscopy measured at the Mn L-edge (Mn 2p) has been used to study the effect of adsorption on the oxidation states of the manganese atoms in the core. In the case of the benzoate-functionalised complex reduction of the manganese metal centres is observed due to the interaction of the manganese core with the underlying surface. In the case of terphenyl-4-carboxylate, the presence of this much larger ligand prevents the magnetic core from interacting with either the gold or the titanium dioxide surfaces and the characteristic Mn(3+) and Mn(4+) oxidation states necessary for magnetic behaviour are preserved.

  7. Enhancing single-molecule fluorescence with nanophotonics.

    PubMed

    Acuna, Guillermo; Grohmann, Dina; Tinnefeld, Philip

    2014-10-01

    Single-molecule fluorescence spectroscopy has become an important research tool in the life sciences but a number of limitations hinder the widespread use as a standard technique. The limited dynamic concentration range is one of the major hurdles. Recent developments in the nanophotonic field promise to alleviate these restrictions to an extent that even low affinity biomolecular interactions can be studied. After motivating the need for nanophotonics we introduce the basic concepts of nanophotonic devices such as zero mode waveguides and nanoantennas. We highlight current applications and the future potential of nanophotonic approaches when combined with biological systems and single-molecule spectroscopy.

  8. Single molecule study of silicon quantum dots

    NASA Astrophysics Data System (ADS)

    So, Woong Young; Li, Qi; Jin, Rongchao; Peteanu, Linda

    2016-09-01

    Recently, fluorescent Silicon (Si) Quantum Dots (QDs) have attracted much interest due to their high quantum yield, use of non-toxic and environmentally-benign chemicals, and water-solubility. However, more research is necessary to understand the energy level characteristics and single molecule behavior to enable their development for imaging applications. Therefore, single molecule time-resolved fluorescence spectroscopy of fluorescent Si QDs (cyan, green, and yellow) is needed. A rigorous analysis of time-resolved photon correlation spectroscopy and fluorescence lifetime data on single Si QDs at room temperature is presented.

  9. Gradual disordering of the native state on a slow two-state folding protein monitored by single-molecule fluorescence spectroscopy and NMR.

    PubMed

    Campos, Luis A; Sadqi, Mourad; Liu, Jianwei; Wang, Xiang; English, Douglas S; Muñoz, Victor

    2013-10-24

    Theory predicts that folding free energy landscapes are intrinsically malleable and as such are expected to respond to perturbations in topographically complex ways. Structural changes upon perturbation have been observed experimentally for unfolded ensembles, folding transition states, and fast downhill folding proteins. However, the native state of proteins that fold in a two-state fashion is conventionally assumed to be structurally invariant during unfolding. Here we investigate how the native and unfolded states of the chicken α-spectrin SH3 domain (a well characterized slow two-state folder) change in response to chemical denaturants and/or temperature. We can resolve the individual properties of the two end-states across the chemical unfolding transition employing single-molecule fluorescence spectroscopy (SM-FRET) and across the thermal unfolding transition by NMR because SH3 folds-unfolds in the slow chemical exchange regime. Our results demonstrate that α-spectrin SH3 unfolds in a canonical way in the sense that it converts between the native state and an unfolded ensemble that expands in response to chemical denaturants. However, as conditions become increasingly destabilizing, the native state also expands gradually, and a large fraction of its native intramolecular hydrogen bonds break up. This gradual disordering of the native state takes place in times shorter than the 100 μs resolution of our SM-FRET experiments. α-Spectrin SH3 thus showcases the extreme plasticity of folding landscapes, which extends to the native state of slow two-state proteins. Our results point to the idea that folding mechanisms under physiological conditions might be quite different from those obtained by linear extrapolation from denaturing conditions. Furthermore, they highlight a pressing need for re-evaluating the conventional procedures for analyzing and interpreting folding experiments, which may be based on too-simplistic assumptions.

  10. {beta}-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

    SciTech Connect

    Marchetti, S.; Carla, M.; Gambi, C. M. C.; Sbrana, F.; Vassalli, M.; Toscano, A.; Pacini, A.; Fratini, E.; Tiribilli, B.

    2011-05-15

    The three-dimensional structure and the mechanical properties of a {beta}-connectin fragment from human cardiac muscle, belonging to the I band, from I{sub 27} to I{sub 34}, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I{sub 27}-I{sub 34} fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

  11. Spin resolved photoelectron spectroscopy of [Mn6(III)Cr(III)]3+ single-molecule magnets and of manganese compounds as reference layers.

    PubMed

    Helmstedt, Andreas; Müller, Norbert; Gryzia, Aaron; Dohmeier, Niklas; Brechling, Armin; Sacher, Marc D; Heinzmann, Ulrich; Hoeke, Veronika; Krickemeyer, Erich; Glaser, Thorsten; Bouvron, Samuel; Fonin, Mikhail; Neumann, Manfred

    2011-07-06

    Properties of the manganese-based single-molecule magnet [Mn(6)(III)Cr(III)](3+) are studied. It contains six Mn(III) ions arranged in two bowl-shaped trinuclear triplesalen building blocks linked by a hexacyanochromate and exhibits a large spin ground state of S(t) = 21/2. The dominant structures in the electron emission spectra of [Mn(6)(III)Cr(III)](3+) resonantly excited at the L(3)-edge are the L(3)M(2, 3)M(2, 3), L(3)M(2, 3)V and L(3)VV Auger emission groups following the decay of the primary p(3/2) core hole state. Significant differences of the Auger spectra from intact and degraded [Mn(6)(III)Cr(III)](3+) show up. First measurements of the electron spin polarization in the L(3)M(2, 3)V and L(3)VV Auger emission peaks from the manganese constituents in [Mn(6)(III)Cr(III)](3+) resonantly excited at the L(3)-edge near 640 eV by circularly polarized synchrotron radiation are reported. In addition spin resolved Auger electron spectra of the reference substances MnO, Mn(2)O(3) and Mn(II)(acetate)(2)·4H(2)O are given. The applicability of spin resolved electron spectroscopy for characterizing magnetic states of constituent atoms compared to magnetic circular dichroism (MCD) is verified: the spin polarization obtained from Mn(II)(acetate)(2)·4H(2)O at room temperature in the paramagnetic state compares to the MCD asymmetry revealed for a star-shaped molecule with a Mn(4)(II)O(6) core at 5 K in an external magnetic field of 5 T.

  12. 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.

  13. Vibrational spectroscopy of water interfaces

    SciTech Connect

    Du, Quan

    1994-12-01

    The second order nonlinear optical processes of second harmonic generation and sum frequency generation are powerful and versatile tools for studying all kinds of surfaces. They possess unusual surface sensitivity due to the symmetry properties of the second order nonlinear susceptibility. The technique of infrared-visible sum frequency generation (SFG) is particularly attractive because it offers a viable way to do vibrational spectroscopy on any surfaces accessible to light with submonolayer sensitivity. In this thesis, the author applies SFG to study a number of important water interfaces. At the air/water interface, hydrophobic solid/water and liquid/water interfaces, it was found that approximately 25% of surface water molecules have one of their hydrogen pointing away from the liquid water. The large number of unsatisfied hydrogen bonds contributes significantly to the large interfacial energy of the hydrophobic surfaces. At the hydrophilic fused quartz/water interface and a fatty acid monolayer covered water surface, the structure and orientation of surface water molecules are controlled by the hydrogen bonding of water molecules with the surface OH groups and the electrostatic interaction with the surface field from the ionization of surface groups. A change of pH value in the bulk water can significantly change the relative importance of the two interactions and cause a drastic change in orientation of the surface water molecules. SFG has also been applied to study the tribological response of some model lubricant films. Monolayers of Langmuir-Blodgett films were found to disorder orientationaly under mildly high pressure and recover promptly upon removal of the applied pressure.

  14. Surface-Enhanced Impulsive Coherent Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Juan; Harra, Juha; Virkki, Matti; Mäkelä, Jyrki M.; Leng, Yuxin; Kauranen, Martti; Kobayashi, Takayoshi

    2016-11-01

    Surface-enhanced Raman spectroscopy (SERS) has attracted a lot of attention in molecular sensing because of the remarkable ability of plasmonic metal nanostructures to enhance the weak Raman scattering process. On the other hand, coherent vibrational spectroscopy triggered by impulsive excitation using ultrafast laser pulses provides complete information about the temporal evolution of molecular vibrations, allowing dynamical processes in molecular systems to be followed in “real time”. Here, we combine these two concepts and demonstrate surface-enhanced impulsive vibrational spectroscopy. The vibrational modes of the ground and excited states of poly[2-methoxy-5-(2-ethylhexyloxy)‑1,4-phenylenevinylene] (MEH-PPV), spin-coated on a substrate covered with monodisperse silver nanoparticles, are impulsively excited with a sub-10 fs pump pulse and characterized with a delayed broad-band probe pulse. The maximum enhancement in the spectrally and temporally resolved vibrational signatures averaged over the whole sample is about 4.6, while the real-time information about the instantaneous vibrational amplitude together with the initial vibrational phase is preserved. The phase is essential to determine the vibrational contributions from the ground and excited states.

  15. Surface-Enhanced Impulsive Coherent Vibrational Spectroscopy

    PubMed Central

    Du, Juan; Harra, Juha; Virkki, Matti; Mäkelä, Jyrki M.; Leng, Yuxin; Kauranen, Martti; Kobayashi, Takayoshi

    2016-01-01

    Surface-enhanced Raman spectroscopy (SERS) has attracted a lot of attention in molecular sensing because of the remarkable ability of plasmonic metal nanostructures to enhance the weak Raman scattering process. On the other hand, coherent vibrational spectroscopy triggered by impulsive excitation using ultrafast laser pulses provides complete information about the temporal evolution of molecular vibrations, allowing dynamical processes in molecular systems to be followed in “real time”. Here, we combine these two concepts and demonstrate surface-enhanced impulsive vibrational spectroscopy. The vibrational modes of the ground and excited states of poly[2-methoxy-5-(2-ethylhexyloxy)−1,4-phenylenevinylene] (MEH-PPV), spin-coated on a substrate covered with monodisperse silver nanoparticles, are impulsively excited with a sub-10 fs pump pulse and characterized with a delayed broad-band probe pulse. The maximum enhancement in the spectrally and temporally resolved vibrational signatures averaged over the whole sample is about 4.6, while the real-time information about the instantaneous vibrational amplitude together with the initial vibrational phase is preserved. The phase is essential to determine the vibrational contributions from the ground and excited states. PMID:27812020

  16. Probing vibrational anisotropy with nuclear resonance vibrational spectroscopy.

    SciTech Connect

    Pavlik, J. W.; Barabanschikov, A.; Oliver, A. G.; Alp, E. E.; Sturhahn, W.; Zhao, J.; Sage, J. T.; Scheidt, W. R.

    2010-06-14

    A NRVS single-crystal study (NRVS=nuclear resonance vibrational spectroscopy) has provided detailed information on the in-plane modes of nitrosyl iron porphyrinate [Fe(oep)(NO)] (see picture; oep=octaethylporphyrin). The axial nitrosyl ligand controls the direction of the in-plane iron motion.

  17. Two-dimensional vibrational-electronic spectroscopy

    SciTech Connect

    Courtney, Trevor L.; Fox, Zachary W.; Slenkamp, Karla M.; Khalil, Munira

    2015-10-21

    Two-dimensional vibrational-electronic (2D VE) spectroscopy is a femtosecond Fourier transform (FT) third-order nonlinear technique that creates a link between existing 2D FT spectroscopies in the vibrational and electronic regions of the spectrum. 2D VE spectroscopy enables a direct measurement of infrared (IR) and electronic dipole moment cross terms by utilizing mid-IR pump and optical probe fields that are resonant with vibrational and electronic transitions, respectively, in a sample of interest. We detail this newly developed 2D VE spectroscopy experiment and outline the information contained in a 2D VE spectrum. We then use this technique and its single-pump counterpart (1D VE) to probe the vibrational-electronic couplings between high frequency cyanide stretching vibrations (ν{sub CN}) and either a ligand-to-metal charge transfer transition ([Fe{sup III}(CN){sub 6}]{sup 3−} dissolved in formamide) or a metal-to-metal charge transfer (MMCT) transition ([(CN){sub 5}Fe{sup II}CNRu{sup III}(NH{sub 3}){sub 5}]{sup −} dissolved in formamide). The 2D VE spectra of both molecules reveal peaks resulting from coupled high- and low-frequency vibrational modes to the charge transfer transition. The time-evolving amplitudes and positions of the peaks in the 2D VE spectra report on coherent and incoherent vibrational energy transfer dynamics among the coupled vibrational modes and the charge transfer transition. The selectivity of 2D VE spectroscopy to vibronic processes is evidenced from the selective coupling of specific ν{sub CN} modes to the MMCT transition in the mixed valence complex. The lineshapes in 2D VE spectra report on the correlation of the frequency fluctuations between the coupled vibrational and electronic frequencies in the mixed valence complex which has a time scale of 1 ps. The details and results of this study confirm the versatility of 2D VE spectroscopy and its applicability to probe how vibrations modulate charge and energy transfer in a

  18. 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.

  19. Interplay of hole transfer and host-guest interaction in a molecular dyad and triad: ensemble and single-molecule spectroscopy and sensing applications.

    PubMed

    Wu, Xiangyang; Liu, Fang; Wells, Kym L; Tan, Serena L J; Webster, Richard D; Tan, Howe-Siang; Zhang, Dawei; Xing, Bengang; Yeow, Edwin K L

    2015-02-16

    A new molecular dyad consisting of a Cy5 chromophore and ferrocene (Fc) and a triad consisting of Cy5, Fc, and β-cyclodextrin (CD) are synthesized and their photophysical properties investigated at both the ensemble and single-molecule levels. Hole transfer efficiency from Cy5 to Fc in the dyad is reduced upon addition of CD. This is due to an increase in the Cy5-Fc separation (r) when the Fc is encapsulated in the macrocyclic host. On the other hand, the triad adopts either a Fc-CD inclusion complex conformation in which hole transfer quenching of the Cy5 by Fc is minimal or a quasi-static conformation with short r and rapid charge transfer. Single-molecule fluorescence measurements reveal that r is lengthened when the triad molecules are deposited on a glass substrate. By combining intramolecular charge transfer and competitive supramolecular interaction, the triad acts as an efficient chemical sensor to detect different bioactive analytes such as amantadine hydrochloride and sodium lithocholate in aqueous solution and synthetic urine.

  20. Vibrational Spectroscopy of Chromatographic Interfaces

    SciTech Connect

    Jeanne E. Pemberton

    2011-03-10

    Chromatographic separations play a central role in DOE-supported fundamental research related to energy, biological systems, the environment, and nuclear science. The overall portfolio of research activities in the Separations and Analysis Program within the DOE Office of Basic Energy Sciences includes support for activities designed to develop a molecular-level understanding of the chemical processes that underlie separations for both large-scale and analytical-scale purposes. The research effort funded by this grant award was a continuation of DOE-supported research to develop vibrational spectroscopic methods to characterize the interfacial details of separations processes at a molecular level.

  1. Single-molecule magnets: structural characterization, magnetic properties, and (19)F NMR spectroscopy of a Mn(12) family spanning three oxidation levels.

    PubMed

    Chakov, Nicole E; Soler, Monica; Wernsdorfer, Wolfgang; Abboud, Khalil A; Christou, George

    2005-07-25

    lower temperatures reflects the decreasing magnetic anisotropy upon successive reduction and, hence, the decreasing energy barrier to magnetization relaxation. Relaxation rate vs T data obtained from chi(M)' ' vs AC oscillation frequency studies down to 1.8 K were combined with rate vs T data from DC magnetization decay vs time measurements at lower temperatures to generate an Arrhenius plot from which the effective barrier (U(eff)) to magnetization reversal was obtained; the U(eff) values are 59 K for 2, 49 and 21 K for the slower- and faster-relaxing species of 3, respectively, and 25 K for 4. Hysteresis loops obtained from single-crystal magnetization vs DC field scans are typical of single-molecule magnets with the coercivities increasing with decreasing T and increasing field sweep rate and containing steps caused by the quantum tunneling of magnetization (QTM). The step separations gave D/g values of 0.22 cm(-)(1) for 2, 0.15 and 0.042 cm(-)(1) for the slower- and faster-relaxing species of 3, and 0.15 cm(-)(1) for 4.

  2. Single-molecule spectroscopy and femtosecond transient absorption studies on the excitation energy transfer process in ApcE(1-240) dimers.

    PubMed

    Long, Saran; Zhou, Meng; Tang, Kun; Zeng, Xiao-Li; Niu, Yingli; Guo, Qianjin; Zhao, Kai-Hong; Xia, Andong

    2015-05-28

    ApcE(1-240) dimers with one intrinsic phycocyanobilin (PCB) chromophore in each monomer that is truncated from the core-membrane linker (ApcE) of phycobilisomes (PBS) in Nostoc sp. PCC 7120 show a sharp and significantly red-shifted absorption. Two explanations either conformation-dependent Förster resonance energy transfer (FRET) or the strong exciton coupling limit have been proposed for red-shifted absorption. This is a classic example of the special pair in the photosynthetic light harvesting proteins, but the mechanism of this interaction is still a matter of intense debate. We report the studies using single-molecule and transient absorption spectra on the interaction in the special pair of ApcE dimers. Our results demonstrate the presence of conformation-dependent FRET between the two PCB chromophores in ApcE dimers. The broad distributions of fluorescence intensities, lifetimes and polarization difference from single-molecule measurements reveal the heterogeneity of local protein-pigment environments in ApcE dimers, where the same molecular structures but different protein environments are the main reason for the two PCB chromophores with different spectral properties. The excitation energy transfer rate between the donor and the acceptor about (110 ps)(-1) is determined from transient absorption measurements. The red-shifted absorption in ApcE dimers could result from more extending conformation, which shows another type of absorption redshift that does not depend on strong exciton coupling. The results here stress the importance of conformation-controlled spectral properties of the chemically identical chromophores, which could be a general feature to control energy/electron transfer, widely existing in the light harvesting complexes.

  3. Illuminating single molecules in condensed matter.

    PubMed

    Moerner, W E; Orrit, M

    1999-03-12

    Efficient collection and detection of fluorescence coupled with careful minimization of background from impurities and Raman scattering now enable routine optical microscopy and study of single molecules in complex condensed matter environments. This ultimate method for unraveling ensemble averages leads to the observation of new effects and to direct measurements of stochastic fluctuations. Experiments at cryogenic temperatures open new directions in molecular spectroscopy, quantum optics, and solid-state dynamics. Room-temperature investigations apply several techniques (polarization microscopy, single-molecule imaging, emission time dependence, energy transfer, lifetime studies, and the like) to a growing array of biophysical problems where new insight may be gained from direct observations of hidden static and dynamic inhomogeneity.

  4. Vibrational spectroscopy in shock-compressed liquids

    SciTech Connect

    Schmidt, S.C.; Moore, D.S.

    1992-01-01

    Coherent anti-Stokes Raman spectroscopy is being used to study the structure and energy transfer in simple molecular liquids at the high pressures and temperatures characteristic of explosive detonation. Dense fluids to several thousand degrees temperature and several hundred kilobars pressure are obtained using the shock-compression technique. Vibrational frequencies, third-order susceptibility ratios, and linewidths have been measured for N{sub 2}, O{sub 2}, CO, mixtures of N{sub 2}, O{sub 2}, and CO, and N{sub 2}O. Frequencies are found to increase with pressure. The transition intensity and line-width data suggest that thermal equilibrium of the vibrational levels is attained in less than a few nanoseconds at these high pressures and temperatures. Vibrational temperatures obtained are compared to those derived from equation-of-state calculations.

  5. Vibrational spectroscopy in shock-compressed liquids

    SciTech Connect

    Schmidt, S.C.; Moore, D.S.

    1992-03-01

    Coherent anti-Stokes Raman spectroscopy is being used to study the structure and energy transfer in simple molecular liquids at the high pressures and temperatures characteristic of explosive detonation. Dense fluids to several thousand degrees temperature and several hundred kilobars pressure are obtained using the shock-compression technique. Vibrational frequencies, third-order susceptibility ratios, and linewidths have been measured for N{sub 2}, O{sub 2}, CO, mixtures of N{sub 2}, O{sub 2}, and CO, and N{sub 2}O. Frequencies are found to increase with pressure. The transition intensity and line-width data suggest that thermal equilibrium of the vibrational levels is attained in less than a few nanoseconds at these high pressures and temperatures. Vibrational temperatures obtained are compared to those derived from equation-of-state calculations.

  6. The molecular yo-yo method: Live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions

    NASA Astrophysics Data System (ADS)

    Mack, A. H.; Schlingman, D. J.; Kamenetska, M.; Collins, R.; Regan, L.; Mochrie, S. G. J.

    2013-08-01

    By monitoring multiple molecular transitions, force-clamp, and trap-position-clamp methods have led to precise determinations of the free energies and free energy landscapes for molecular states populated in equilibrium at the same or similar forces. Here, we present a powerful new elaboration of the force-clamp and force-jump methods, applicable to transitions far from equilibrium. Specifically, we have implemented a live jump detection and force-clamp algorithm that intelligently adjusts and maintains the force on a single molecule in response to the measured state of that molecule. We are able to collect hundreds of individual molecular transitions at different forces, many times faster than previously, permitting us to accurately determine force-dependent lifetime distributions and reaction rates. Application of our method to unwinding and rewinding the nucleosome inner turn, using optical tweezers reveals experimental lifetime distributions that comprise a statistically meaningful number of transitions, and that are accurately single exponential. These measurements significantly reduce the error in the previously measured rates, and demonstrate the existence of a single, dominant free energy barrier at each force studied. A key benefit of the molecular yo-yo method for nucleosomes is that it reduces as far as possible the time spent in the tangentially bound state, which minimizes the loss of nucleosomes by dissociation.

  7. The molecular yo-yo method: live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions.

    PubMed

    Mack, A H; Schlingman, D J; Kamenetska, M; Collins, R; Regan, L; Mochrie, S G J

    2013-08-01

    By monitoring multiple molecular transitions, force-clamp, and trap-position-clamp methods have led to precise determinations of the free energies and free energy landscapes for molecular states populated in equilibrium at the same or similar forces. Here, we present a powerful new elaboration of the force-clamp and force-jump methods, applicable to transitions far from equilibrium. Specifically, we have implemented a live jump detection and force-clamp algorithm that intelligently adjusts and maintains the force on a single molecule in response to the measured state of that molecule. We are able to collect hundreds of individual molecular transitions at different forces, many times faster than previously, permitting us to accurately determine force-dependent lifetime distributions and reaction rates. Application of our method to unwinding and rewinding the nucleosome inner turn, using optical tweezers reveals experimental lifetime distributions that comprise a statistically meaningful number of transitions, and that are accurately single exponential. These measurements significantly reduce the error in the previously measured rates, and demonstrate the existence of a single, dominant free energy barrier at each force studied. A key benefit of the molecular yo-yo method for nucleosomes is that it reduces as far as possible the time spent in the tangentially bound state, which minimizes the loss of nucleosomes by dissociation.

  8. Anharmonic Vibrational Spectroscopy on Metal Transition Complexes

    NASA Astrophysics Data System (ADS)

    Latouche, Camille; Bloino, Julien; Barone, Vincenzo

    2014-06-01

    Advances in hardware performance and the availability of efficient and reliable computational models have made possible the application of computational spectroscopy to ever larger molecular systems. The systematic interpretation of experimental data and the full characterization of complex molecules can then be facilitated. Focusing on vibrational spectroscopy, several approaches have been proposed to simulate spectra beyond the double harmonic approximation, so that more details become available. However, a routine use of such tools requires the preliminary definition of a valid protocol with the most appropriate combination of electronic structure and nuclear calculation models. Several benchmark of anharmonic calculations frequency have been realized on organic molecules. Nevertheless, benchmarks of organometallics or inorganic metal complexes at this level are strongly lacking despite the interest of these systems due to their strong emission and vibrational properties. Herein we report the benchmark study realized with anharmonic calculations on simple metal complexes, along with some pilot applications on systems of direct technological or biological interest.

  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. Transport mirages in single-molecule devices

    NASA Astrophysics Data System (ADS)

    Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

    2017-03-01

    Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

  11. 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.

  12. Single-molecule detection with active transport

    NASA Astrophysics Data System (ADS)

    Ball, David Allan

    A glass capillary is used near the focal region of a custom-built confocal microscope to investigate the use of active transport for single-molecule detection in solution, with both one and two-photon laser excitation. The capillary tip has a diameter of several microns and is carefully aligned nearby to the sub-micron laser beam waist, collinear to the optical axis, so that a negative pressure-difference causes molecules to be drawn into the capillary, along the laser beam axis. The flow of solution, which is characterized by fluorescence correlation spectroscopy (FCS), can increase the single-molecule detection rate for slowly diffusing proteins by over a factor of 100, while the mean rate of photons during each burst is similar to that for random diffusional transport. Also, the flow is along the longest axis of the ellipsoidally-shaped confocal volume, which results in more collected photons per molecule than that for transverse flow at the same speed. When transport is dominated by flow, FCS can no longer distinguish molecules with differing translational diffusion, and hence a fluorescence fluctuation spectroscopy method based on differences in fluorescence brightness is investigated as a means for assaying different solution components, for applications in pharmaceutical drug discovery. Multi-channel fluctuation spectroscopy techniques can also be used for assays with the flow system and hence this dissertation also reports the characterization of a prototype 4-channel single-photon detector with a two-wavelength polarization-resolved optical set-up.

  13. Ultrafast time-resolved vibrational spectroscopies of carotenoids in photosynthesis.

    PubMed

    Hashimoto, Hideki; Sugisaki, Mitsuru; Yoshizawa, Masayuki

    2015-01-01

    This review discusses the application of time-resolved vibrational spectroscopies to the studies of carotenoids in photosynthesis. The focus is on the ultrafast time regime and the study of photophysics and photochemistry of carotenoids by femtosecond time-resolved stimulated Raman and four-wave mixing spectroscopies. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

  14. Single-molecule optomechanics in "picocavities".

    PubMed

    Benz, Felix; Schmidt, Mikolaj K; Dreismann, Alexander; Chikkaraddy, Rohit; Zhang, Yao; Demetriadou, Angela; Carnegie, Cloudy; Ohadi, Hamid; de Nijs, Bart; Esteban, Ruben; Aizpurua, Javier; Baumberg, Jeremy J

    2016-11-11

    Trapping light with noble metal nanostructures overcomes the diffraction limit and can confine light to volumes typically on the order of 30 cubic nanometers. We found that individual atomic features inside the gap of a plasmonic nanoassembly can localize light to volumes well below 1 cubic nanometer ("picocavities"), enabling optical experiments on the atomic scale. These atomic features are dynamically formed and disassembled by laser irradiation. Although unstable at room temperature, picocavities can be stabilized at cryogenic temperatures, allowing single atomic cavities to be probed for many minutes. Unlike traditional optomechanical resonators, such extreme optical confinement yields a factor of 10(6) enhancement of optomechanical coupling between the picocavity field and vibrations of individual molecular bonds. This work sets the basis for developing nanoscale nonlinear quantum optics on the single-molecule level.

  15. Photoemission of Mn6Cr single-molecule magnets

    NASA Astrophysics Data System (ADS)

    Heinzmann, U.; Merschjohann, F.; Helmstedt, A.; Gryzia, A.; Winter, A.; Steppeler, S.; Müller, N.; Brechling, A.; Sacher, M.; Richthofen, C.-G. Freiherr v.; Glaser, T.; Voss, S.; Fonin, M.; Rüdiger, U.

    2009-11-01

    We present the status of new experimental studies of X-ray absorption spectroscopy, magnetic circular dichroism in photoemission and spin-resolved photoelectron spectroscopy of Mn6Cr single-molecule magnet systems by use of circularly-polarized synchrotron radiation of the electron storage rings in Maxlab Lund, Sweden und BESSY, Berlin, Germany.

  16. Multidimensional Time-Resolved Spectroscopy of Vibrational Coherence in Biopolyenes

    NASA Astrophysics Data System (ADS)

    Buckup, Tiago; Motzkus, Marcus

    2014-04-01

    Multidimensional femtosecond time-resolved vibrational coherence spectroscopy allows one to investigate the evolution of vibrational coherence in electronic excited states. Methods such as pump-degenerate four-wave mixing and pump-impulsive vibrational spectroscopy combine an initial ultrashort laser pulse with a nonlinear probing sequence to reinduce vibrational coherence exclusively in the excited states. By carefully exploiting specific electronic resonances, one can detect vibrational coherence from 0 cm-1 to over 2,000 cm-1 and map its evolution. This review focuses on the observation and mapping of high-frequency vibrational coherence for all-trans biological polyenes such as β-carotene, lycopene, retinal, and retinal Schiff base. We discuss the role of molecular symmetry in vibrational coherence activity in the S1 electronic state and the interplay of coupling between electronic states and vibrational coherence.

  17. Uncovering hierarchical data structure in single molecule transport

    NASA Astrophysics Data System (ADS)

    Wu, Ben H.; Ivie, Jeffrey A.; Johnson, Tyler K.; Monti, Oliver L. A.

    2017-03-01

    Interpretation of single molecule transport data is complicated by the fact that all such data are inherently highly stochastic in nature. Features are often broad, seemingly unstructured and distributed over more than an order of magnitude. However, the distribution contains information necessary for capturing the full variety of processes relevant in nanoscale transport, and a better understanding of its hierarchical structure is needed to gain deeper insight into the physics and chemistry of single molecule electronics. Here, we describe a novel data analysis approach based on hierarchical clustering to aid in the interpretation of single molecule conductance-displacement histograms. The primary purpose of statistically partitioning transport data is to provide avenues for unbiased hypothesis generation in single molecule break junction experiments by revealing otherwise potentially hidden aspects in the conductance data. Our approach is generalizable to the analysis of a wide variety of other single molecule experiments in molecular electronics, as well as in single molecule fluorescence spectroscopy, force microscopy, and ion-channel conductance measurements.

  18. 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.

  19. Single-molecule strong coupling at room temperature in plasmonic nanocavities

    PubMed Central

    Chikkaraddy, Rohit; de Nijs, Bart; Benz, Felix; Barrow, Steven J.; Scherman, Oren A.; Rosta, Edina; Demetriadou, Angela; Fox, Peter; Hess, Ortwin; Baumberg, Jeremy J.

    2016-01-01

    Emitters placed in an optical cavity experience an environment that changes their coupling to light. In the weak-coupling regime light extraction is enhanced, but more profound effects emerge in the single-molecule strong-coupling regime where mixed light-matter states form1,2. Individual two-level emitters in such cavities become non-linear for single photons, forming key building blocks for quantum information systems as well as ultra-low power switches and lasers3–6. Such cavity quantum electrodynamics has until now been the preserve of low temperatures and complex fabrication, severely compromising their use5,7,8. Here, by scaling the cavity volume below 40 nm3 and using host-guest chemistry to align 1-10 protectively-isolated methylene-blue molecules, we reach the strong-coupling regime at room temperature and in ambient conditions. Dispersion curves from >50 plasmonic nanocavities display characteristic anticrossings, with Rabi frequencies of 300 meV for 10 molecules decreasing to 90 meV for single molecules, matching quantitative models. Statistical analysis of vibrational spectroscopy time-series and dark-field scattering spectra provide evidence of single-molecule strong coupling. This dressing of molecules with light can modify photochemistry, opening up the exploration of complex natural processes such as photosynthesis9 and pathways towards manipulation of chemical bonds10. PMID:27296227

  20. Grafting single molecule magnets on gold nanoparticles.

    PubMed

    Perfetti, Mauro; Pineider, Francesco; Poggini, Lorenzo; Otero, Edwige; Mannini, Matteo; Sorace, Lorenzo; Sangregorio, Claudio; Cornia, Andrea; Sessoli, Roberta

    2014-01-29

    The chemical synthesis and characterization of the first hybrid material composed by gold nanoparticles and single molecule magnets (SMMs) are described. Gold nanoparticles are functionalized via ligand exchange using a tetrairon(III) SMM containing two 1,2-dithiolane end groups. The grafting is evidenced by the shift of the plasmon resonance peak recorded with a UV-vis spectrometer, by the suppression of nuclear magnetic resonance signals, by X-ray photoemission spectroscopy peaks, and by transmission electron microscopy images. The latter evidence the formation of aggregates of nanoparticles as a consequence of the cross-linking ability of Fe4 through the two 1,2-dithiolane rings located on opposite sides of the metal core. The presence of intact Fe4 molecules is directly proven by synchrotron-based X-ray absorption spectroscopy and X-ray magnetic circular dichroism spectroscopy, while a detailed magnetic characterization, obtained using electron paramagnetic resonance and alternating-current susceptibility, confirms the persistence of SMM behavior in this new hybrid nanostructure.

  1. 2010 GRC VIBRATIONAL SPECTROSCOPY AUGUST 1 - AUGUST 6, 2010

    SciTech Connect

    Brooks Pate

    2010-08-06

    The Vibrational Spectroscopy conference focuses on using vibrational spectroscopy to probe structure and dynamics of molecules in gases, liquids, and at interfaces. The conference explores the wide range of state-of-the-art techniques based on vibrational motion. These techniques span the fields of time-domain, high-resolution frequency-domain, spatially-resolved, nonlinear and multidimensional spectroscopies. The conference highlights the application of these techniques in chemistry, materials, biology, and medicine. The theory of molecular vibrational motion and its connection to spectroscopic signatures and chemical reaction dynamics is the third major theme of the meeting. The goal is to bring together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of molecular systems ranging from small polyatomic molecules to large biomolecules and nanomaterials.

  2. Optical microscopy using a single-molecule light source

    PubMed

    Michaelis; Hettich; Mlynek; Sandoghdar

    2000-05-18

    Rapid progress in science on nanoscopic scales has promoted increasing interest in techniques of ultrahigh-resolution optical microscopy. The diffraction limit can be surpassed by illuminating an object in the near field through a sub-wavelength aperture at the end of a sharp metallic probe. Proposed modifications of this technique involve replacing the physical aperture by a nanoscopic active light source. Advances in the spatial and spectral detection of individual fluorescent molecules, using near-field and far-field methods, suggest the possibility of using a single molecule as the illumination source. Here we present optical images taken with a single molecule as a point-like source of illumination, by combining fluorescence excitation spectroscopy with shear-force microscopy. Our single-molecule probe has potential for achieving molecular resolution in optical microscopy; it should also facilitate controlled studies of nanometre-scale phenomena (such as resonant energy transfer) with improved lateral and axial spatial resolution.

  3. 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).

  4. Vibrational spectroscopy at electrolyte/electrode interfaces with graphene gratings

    PubMed Central

    Bie, Ya-Qing; Horng, Jason; Shi, Zhiwen; Ju, Long; Zhou, Qin; Zettl, Alex; Yu, Dapeng; Wang, Feng

    2015-01-01

    Microscopic understanding of physical and electrochemical processes at electrolyte/electrode interfaces is critical for applications ranging from batteries, fuel cells to electrocatalysis. However, probing such buried interfacial processes is experimentally challenging. Infrared spectroscopy is sensitive to molecule vibrational signatures, yet to approach the interface three stringent requirements have to be met: interface specificity, sub-monolayer molecular detection sensitivity, and electrochemically stable and infrared transparent electrodes. Here we show that transparent graphene gratings electrode provide an attractive platform for vibrational spectroscopy at the electrolyte/electrode interfaces: infrared diffraction from graphene gratings offers enhanced detection sensitivity and interface specificity. We demonstrate the vibrational spectroscopy of methylene group of adsorbed sub-monolayer cetrimonium bromide molecules and reveal a reversible field-induced electrochemical deposition of cetrimonium bromide on the electrode controlled by the bias voltage. Such vibrational spectroscopy with graphene gratings is promising for real time and in situ monitoring of different chemical species at the electrolyte/electrode interfaces. PMID:26123807

  5. Single-Molecule Protein Conformational Dynamics in Cell Signaling

    SciTech Connect

    Lu, H PETER.

    2004-08-22

    We have demonstrated the application of single-molecule imaging and ultrafast spectroscopy to probe protein conformational dynamics in solution and in lipid bilayers. Dynamic protein-protein interactions involve significant conformational motions that initiate chain reactions leading to specific cellular responses. We have carried out a single molecule study of dynamic protein-protein interactions in a GTPase intracellular signaling protein Cdc42 in complex with a downstream effector protein, WASP. We were able to probe hydrophobic interactions significant to Cdc42/WASP recognition. Single molecule fluorescence intensity and polarization measurements have revealed the dynamic and inhomogeneous nature of protein-protein interactions within the Cdc42/WASP complex that is characterized by structured distributions of conformational fluctuation rates. Conducting a single-molecule fluorescence anisotropy study of calmodulin (CaM), a regulatory protein for calcium-dependent cell signaling, we were able to probe CaM conformational dynamics at a wide time scale. In this study, CaM contains a site-specifically inserted tetra-cysteine motif that reacted with FlAsH, a biarsenic fluorescein derivative that can be rotationally locked to the host protein. The study provided direct characterization of the nanosecond motions of CaM tethered to a biologically compatible surface under physiological buffer solution. The unique technical approaches are applicable of studying single-molecule dynamics of protein conformational motions and protein-protein interactions at a wide time range without the signal convolution of probe-dye molecule motions

  6. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

    NASA Astrophysics Data System (ADS)

    Wong, Wesley; Halvorsen, Ken

    2011-03-01

    Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

  7. 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.

  8. Geometric Phases in Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Fenochio, Brian Canchola

    The characterization of the material properties of Single Molecule Magnets (SMMs) has grown in importance over the last few decades with the rise of novel applications such as high-density magnetic storage and quantum computation. Many of the applications require the probing of SMMs with spectroscopic methods that make use of electromagnetic radiation. The interaction with these time-dependent fields leads to energy shifts, which can be attributed to the geometric phase acquired by the system or the Bloch-Siegert shift. We model an SMM by a giant spin Hamiltonian, and use Floquet perturbation theory to find the geometric phase shifts. The locations where the phase shift between two levels is zero is useful for performing accurate spectroscopies, whereas the regions where relative phase differences exist are useful in applications like quantum computing. Using the same giant spin Hamiltonian, we can use Floquet theory and Salwen perturbation theory to determine the Bloch-Siegert shift and derive a modified version of the Rabi formula for transition probabilities between the energy states Ealpha → Ealpha+/-1, Ealpha → Ealpha+/-3, and Ealpha → Ealpha+/-5 , where alpha is the index of an arbitrary initial state. The shifted eigenvalues and modified transition probabilities can be useful in spectroscopies where accurate values for the energy-splitting between magnetic states needs to be determined.

  9. 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.

  10. The road to medical vibrational spectroscopy--a history.

    PubMed

    Mantsch, Henry H

    2013-07-21

    The present Editorial chronicles the journey from classical infrared and Raman spectroscopy to medical vibrational spectroscopy, as experienced by a contemporary witness of the times. During the second half of the last century vibrational biospectroscopy became a topic of increasing global interest and has spawned a number of international conferences of which the most recent, SPEC 2012 - Shedding New Light on Disease, constitutes the basis of the present themed issue.

  11. 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.

  12. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.

    to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the conformational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behavior. Next, the single-molecule conductance of a family of oligothiophenes comprising one to six thiophene units was measured. An anomalous behavior was found: the peak of the conductance histogram distribution did not follow a clear exponential decay with increasing number of thiophene units in the chain. The electronic properties of the materials were characterized by optical spectroscopy and electrochemistry to gain an understanding of the factors affecting the conductance of these molecules. Different conformers in the junction were postulated to be a contributing factor to the anomalous trend in the observed conductance as a function of molecule length. Then, the electronic properties of the thiophene-1,1-dioxide unit were investigated. These motifs have become synthetically accessible in the last decade, due to Rozen's unprecedentedly potent oxidizing reagent - HOF˙CH 3CN - which has been shown to be powerful yet selective enough to oxidize thiophenes in various environments. The resulting thiophene-1,1-dioxides show great promise for electronic devices. The oxidation chemistry of thiophenes was expanded and tuning of the frontier energy levels was demonstrated through combining electron poor and electron rich units. Finally, charge carriers in single-molecule junctions were shown to be tunable within a family of molecules containing these thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed in order to increase electron affinity, maintain delocalized frontier orbitals, while significantly decreasing the transport gap. Through thermopower measurements, the dominant charge carriers were shown to change from holes to electrons as the number of

  13. Spectroscopy and reactions of vibrationally excited transient molecules

    SciTech Connect

    Dai, H.L.

    1993-12-01

    Spectroscopy, energy transfer and reactions of vibrationally excited transient molecules are studied through a combination of laser-based excitation techniques and efficient detection of emission from the energized molecules with frequency and time resolution. Specifically, a Time-resolved Fourier Transform Emission Spectroscopy technique has been developed for detecting dispersed laser-induced fluorescence in the IR, visible and UV regions. The structure and spectroscopy of the excited vibrational levels in the electronic ground state, as well as energy relaxation and reactions induced by specific vibronic excitations of a transient molecule can be characterized from time-resolved dispersed fluorescence in the visible and UV region. IR emissions from highly vibrational excited levels, on the other hand, reveal the pathways and rates of collision induced vibrational energy transfer.

  14. Irving Langmuir Prize Talk: Single-Molecule Fluorescence Imaging: Nanoscale Emitters with Photoinduced Switching Enable Superresolution.

    NASA Astrophysics Data System (ADS)

    Moerner, W. E.

    2009-03-01

    In the two decades since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. 62, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. The early years concentrated on high-resolution spectroscopy in solids, which provided observations of lifetime-limited spectra, optical saturation, spectral diffusion, optical switching, vibrational spectra, and magnetic resonance of a single molecular spin. In the mid-1990's, much of the field moved to room temperature, where a wide variety of biophysical effects were subsequently explored, but it is worth noting that several features from the low-temperature studies have analogs at high temperature. For example, in our first studies of yellow-emitting variants of green fluorescent protein (EYFP) in the water-filled pores of a gel (Nature 388, 355 (1997)), optically induced switching of the emission was observed, a room-temperature analog of the earlier low-temperature behavior. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. Recent work has allowed measurement of the shape of single filaments in a living cell simply by allowing a single molecule to move through the filament (PNAS 103, 10929 (2006)). The additional use of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (superresolution) by several novel approaches proposed by different researchers. For example, using photoswitchable EYFP, a novel protein superstructure can now be directly imaged in a living bacterial cell at

  15. Single molecule junction conductance and binding geometry

    NASA Astrophysics Data System (ADS)

    Kamenetska, Maria

    This Thesis addresses the fundamental problem of controlling transport through a metal-organic interface by studying electronic and mechanical properties of single organic molecule-metal junctions. Using a Scanning Tunneling Microscope (STM) we image, probe energy-level alignment and perform STM-based break junction (BJ) measurements on molecules bound to a gold surface. Using Scanning Tunneling Microscope-based break-junction (STM-BJ) techniques, we explore the effect of binding geometry on single-molecule conductance by varying the structure of the molecules, metal-molecule binding chemistry and by applying sub-nanometer manipulation control to the junction. These experiments are performed both in ambient conditions and in ultra high vacuum (UHV) at cryogenic temperatures. First, using STM imaging and scanning tunneling spectroscopy (STS) measurements we explore binding configurations and electronic properties of an amine-terminated benzene derivative on gold. We find that details of metal-molecule binding affect energy-level alignment at the interface. Next, using the STM-BJ technique, we form and rupture metal-molecule-metal junctions ˜104 times to obtain conductance-vs-extension curves and extract most likely conductance values for each molecule. With these measurements, we demonstrated that the control of junction conductance is possible through a choice of metal-molecule binding chemistry and sub-nanometer positioning. First, we show that molecules terminated with amines, sulfides and phosphines bind selectively on gold and therefore demonstrate constant conductance levels even as the junction is elongated and the metal-molecule attachment point is modified. Such well-defined conductance is also obtained with paracyclophane molecules which bind to gold directly through the pi system. Next, we are able to create metal-molecule-metal junctions with more than one reproducible conductance signatures that can be accessed by changing junction geometry. In the

  16. SINGLE MOLECULE ENZYMOLOGY FINDS ITS STRIDE.

    PubMed

    Perkel, Jeffrey

    2015-10-01

    More techniques aimed at probing the nature of single molecules are being developed and advanced in biophysics labs. Jeffrey Perkel takes a look at the scientists leading the charge into the micro-world.

  17. Single-Molecule Fluorescence Spectroscopy of Perylene Diimide Dyes in a γ-Cyclodextrin Film: Manifestation of Photoinduced H-Atom Transfer via Higher Triplet (n, π*) Excited States.

    PubMed

    Mitsui, Masaaki; Fukui, Hiroki; Takahashi, Ryoya; Takakura, Yasushi; Mizukami, Toshinari

    2017-03-02

    Supramolecular complexation of γ-cyclodextrin (γ-CD) with N,N'-bis(2,6-dimethylphenyl)perylene-3,4,9,10-tetracarboxylic diimide (DMP-PDI) or N,N'-bis(2,6-dioctyl)perylene-3,4,9,10-tetracarboxylic diimide (C8-PDI) dye in an aqueous solution and in a γ-CD solid film were investigated via ensemble and single-molecule fluorescence spectroscopy. These two perylene diimide derivatives possess almost the same electronic structure but have different terminal functional groups. This structural difference leads to formation of an inclusion complex of γ-CD with DMP-PDI but not with C8-PDI in aqueous solution. In a γ-CD solid film, the distributions of the wavelengths of emission maximum (λmax(em)) are strikingly different between these two dyes; a much narrower and blue-shifted λmax(em) distribution was observed for C8-PDI relative to DMP-PDI. This difference is attributed to the fact that the C8-PDI molecules are bound at the γ-CD/glass interface as a result of spin-coating of the sample solution, whereas the DMP-PDI molecules form 1:1 and 1:2 inclusion complexes with conformational heterogeneities in the film. In comparison to the case for C8-PDI, more frequent on-off blinking events were observed for DMP-PDI. The blinking statistics of DMP-PDI in the γ-CD film exhibit both single-exponential and nonexponential (i.e., dispersive) kinetics, revealed by robust statistical analysis. Energetic consideration with the aid of theoretical calculations suggests that the underlying photophysics most probably involves hydrogen atom transfer (HAT) between the DMP-PDI guest and γ-CD host via higher excited (n, π*) triplet states. The hypothesis of HAT in the inclusion complex reasonably explains the experimental results; however, a charge transfer hypothesis cannot explain the results. The dispersive kinetics is attributable to the effect of thermal fluctuation in the forward and backward HAT reactions.

  18. Microsecond protein dynamics observed at the single-molecule level

    PubMed Central

    Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

    2015-01-01

    How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767

  19. Methods and applications in single molecule electronics

    NASA Astrophysics Data System (ADS)

    Hihath, Joshua

    In recent years it has become possible to measure charge transport in a single molecule contacted to two metal electrodes. However, a thorough understanding of how a molecule behaves while contacted to two electrodes and how it interacts with its environment is still lacking. This thesis demonstrates various experimental methods for understanding and controlling charge transport in a single molecule junction and the application of these methods to various molecular systems to help elucidate the conduction mechanisms invoked. First, the conductance of DNA is examined in a controlled environment while varying the length, sequence, base-pair matching, bias, temperature, and electrochemical gate of the molecule. These studies show that the conductance of DNA is extremely sensitive to changes in length, sequence, and base-matching, but not as sensitive to temperature and electrochemical gate. Despite the variety of experimental methods applied, the subtleties of the conduction mechanism remain uncertain, and as such necessitate the development of additional tools for understanding the behavior of a single molecule junction. Next, the Conductance Screening Tool for Molecules (CSTM) is described. This is a new tool capable of creating 1000's of single molecules junctions in a matter of minutes. This tool has been used to study the conductance of alkanedithiols, molecules in an array, and single amino acid residues. This system allows for greater speed and flexibility in determining the conductance of a single molecule junction, and provides a capability for performing large-scale systematic studies of molecular systems to determine the conduction mechanism. Finally, an additional experimental method capable of extracting information about the interaction between a molecule and its environment is developed. Here, electron-phonon interactions in a single molecule contacted to two electrodes are studied. This method allows one to obtain a specific, chemical signature of a

  20. Broadband nonlinear vibrational spectroscopy by shaping a coherent fiber supercontinuum

    PubMed Central

    Liu, Yuan; King, Matthew D.; Tu, Haohua; Zhao, Youbo; Boppart, Stephen A.

    2013-01-01

    Vibrational spectroscopy has been widely applied in different fields due to its label-free chemical-sensing capability. Coherent anti-Stokes Raman scattering (CARS) provides stronger signal and faster acquisition than spontaneous Raman scattering, making it especially suitable for molecular imaging. Coherently-controlled single-beam CARS simplifies the conventional multi-beam setup, but the vibrational bandwidth and non-trivial spectrum retrieval have been limiting factors. In this work, a coherent supercontinuum generated in an all-normal-dispersion nonlinear fiber is phase-shaped within a narrow bandwidth for broadband vibrational spectroscopy. The Raman spectra can be directly retrieved from the CARS measurements, covering the fingerprint regime up to 1750 cm−1. The retrieved spectra of several chemical species agree with their spontaneous Raman data. The compact fiber supercontinuum source offers broad vibrational bandwidth with high stability and sufficient power, showing the potential for spectroscopic imaging in a wide range of applications. PMID:23571917

  1. Seventh international conference on time-resolved vibrational spectroscopy

    SciTech Connect

    Dyer, R.B.; Martinez, M.A.D.; Shreve, A.; Woodruff, W.H.

    1997-04-01

    The International Conference on Time-Resolved Vibrational Spectroscopy (TRVS) is widely recognized as the major international forum for the discussion of advances in this rapidly growing field. The 1995 conference was the seventh in a series that began at Lake Placid, New York, 1982. Santa Fe, New Mexico, was the site of the Seventh International Conference on Time-Resolved Vibrational Spectroscopy, held from June 11 to 16, 1995. TRVS-7 was attended by 157 participants from 16 countries and 85 institutions, and research ranging across the full breadth of the field of time-resolved vibrational spectroscopy was presented. Advances in both experimental capabilities for time-resolved vibrational measurements and in theoretical descriptions of time-resolved vibrational methods continue to occur, and several sessions of the conference were devoted to discussion of these advances and the associated new directions in TRVS. Continuing the interdisciplinary tradition of the TRVS meetings, applications of time-resolved vibrational methods to problems in physics, biology, materials science, and chemistry comprised a large portion of the papers presented at the conference.

  2. Directional Raman scattering from single molecules in the feed gaps of optical antennas.

    PubMed

    Wang, Dongxing; Zhu, Wenqi; Best, Michael D; Camden, Jon P; Crozier, Kenneth B

    2013-05-08

    Controlling light from single emitters is an overarching theme of nano-optics. Antennas are routinely used to modify the angular emission patterns of radio wave sources. "Optical antennas" translate these principles to visible and infrared wavelengths and have been recently used to modify fluorescence from single quantum dots and single molecules. Understanding the properties of single molecules, however, would be advanced were one able to observe their vibrational spectra through Raman scattering in a very reproducible manner but it is a hugely challenging task, as Raman scattering cross sections are very weak. Here we measure for the first time the highly directional emission patterns of Raman scattering from single molecules in the feed gaps of optical antennas fabricated on a chip. More than a thousand single molecule events are observed, revealing that an unprecedented near-unity fraction of optical antennas have single molecule sensitivity.

  3. 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

  4. Single molecule fluorescence and force microscopy.

    PubMed

    Schütz, G J; Hinterdorfer, P

    2002-12-01

    The investigation of biomolecules has entered a new age since the development of methodologies capable of studies at the level of single molecules. In biology, most molecules show a complex dynamical behavior, with individual motions and transitions between different states occurring highly correlated in space and time within an arrangement of various elements. Recent advances in the development of new microscopy techniques with sensitivity at the single molecule have gained access to essentially new types of information obtainable from imaging biomolecular samples. These methodologies are described here in terms of their applicability to the in vivo detection and visualization of molecular processes on surfaces, membranes, and cells. First examples of single molecule microscopy on cell membranes revealed new basic insight into the lateral organization of the plasma membrane, providing the captivating perspective of an ultra-sensitive methodology as a general tool to study local processes and heterogeneities in living cells.

  5. Vibrational photodetachment spectroscopy near the electron affinity of S2

    NASA Astrophysics Data System (ADS)

    Barrick, J. B.; Yukich, J. N.

    2016-02-01

    We have conducted laser photodetachment spectroscopy near the detachment threshold of the electron affinity of S2 in a 1.8-T field. The ions are prepared by dissociative electron attachment to carbonyl sulfide. The experiment is conducted in a Penning ion trap and with a narrow-band, tunable, Ti:sapphire laser. A hybrid model for photodetachment in an ion trap is fit to the data using the appropriate Franck-Condon factors. The observations reveal detachment from and to the first few vibrational levels of the anion and the neutral molecule, respectively. Evaporative cooling of the anion ensemble condenses the thermal distribution to the lowest initial vibrational states. The subsequent detachment spectroscopy yields results consistent with a vibrationally cooled anion population.

  6. Life at the Single Molecule Level

    SciTech Connect

    Xie, Xiaoliang Sunny

    2011-03-04

    In a living cell, gene expression—the transcription of DNA to messenger RNA followed by translation to protein—occurs stochastically, as a consequence of the low copy number of DNA and mRNA molecules involved. Can one monitor these processes in a living cell in real time? How do cells with identical genes exhibit different phenotypes? Recent advances in single-molecule imaging in living bacterial cells allow these questions to be answered at the molecular level in a quantitative manner. It was found that rare events of single molecules can have important biological consequences.

  7. Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data

    PubMed Central

    Mabuchi, Hideo; Herschlag, Daniel

    2012-01-01

    Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data. PMID:22363412

  8. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    DOE PAGES

    Dong, Hui; Lewis, Nicholas H. C.; Oliver, Thomas A. A.; ...

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this report, we present a theoretical formalism to demonstrate themore » slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. In conclusion, we also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions« less

  9. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

    Dong, Hui; Lewis, Nicholas H. C.; Oliver, Thomas A. A.; Fleming, Graham R.

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

  10. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy.

    PubMed

    Dong, Hui; Lewis, Nicholas H C; Oliver, Thomas A A; Fleming, Graham R

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

  11. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

    Dong, Hui; Lewis, Nicholas H. C.; Oliver, Thomas A. A.; Fleming, Graham R.

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this report, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. In conclusion, we also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions

  12. Single-molecule techniques for drug discovery.

    PubMed

    Skinner, Gary M; Visscher, Koen

    2004-08-01

    Single-molecule techniques offer a number of key benefits over conventional in vitro assay methods for drug screening, as they use less material and unlock the ability to observe transient states. By observing such states, it should be possible to screen for chemical compounds that isolate these steps. The benefit of this is twofold: (a) inhibitors can be found that target key phases in biochemical processes, e.g., transcription initiation; and (b) the total number of drug targets increases as many biochemical processes consist of many transient steps, e.g., transcription promoter binding, initiation, elongation, and termination. Although single-molecule methods offer exciting opportunities for new ways of discovering drugs, there are a number of obstacles to their adoption for drug screening. The main hurdle is to develop robust apparatus that will allow many thousands of individual single molecule experiments to be performed in parallel. By using recently developed integrated microfluidics technology, this hurdle may be overcome. Here, a number of potential single-molecule approaches to drug screening are presented along with a discussion of the benefits and technical obstacles that must be overcome.

  13. Nanoscience: Single-molecule instant replay

    NASA Astrophysics Data System (ADS)

    Camillone, Nicholas

    2016-11-01

    A nanoscale imaging method that uses ultrashort light pulses to initiate and follow the motion of a single molecule adsorbed on a solid surface opens a window onto the physical and chemical dynamics of molecules on surfaces. See Letter p.263

  14. Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

    PubMed Central

    Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

    2015-01-01

    Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

  15. Single-molecule Michaelis-Menten equations.

    PubMed

    Kou, S C; Cherayil, Binny J; Min, Wei; English, Brian P; Xie, X Sunney

    2005-10-20

    This paper summarizes our present theoretical understanding of single-molecule kinetics associated with the Michaelis-Menten mechanism of enzymatic reactions. Single-molecule enzymatic turnover experiments typically measure the probability density f(t) of the stochastic waiting time t for individual turnovers. While f(t) can be reconciled with ensemble kinetics, it contains more information than the ensemble data; in particular, it provides crucial information on dynamic disorder, the apparent fluctuation of the catalytic rates due to the interconversion among the enzyme's conformers with different catalytic rate constants. In the presence of dynamic disorder, f(t) exhibits a highly stretched multiexponential decay at high substrate concentrations and a monoexponential decay at low substrate concentrations. We derive a single-molecule Michaelis-Menten equation for the reciprocal of the first moment of f(t), 1/, which shows a hyperbolic dependence on the substrate concentration [S], similar to the ensemble enzymatic velocity. We prove that this single-molecule Michaelis-Menten equation holds under many conditions, in particular when the intercoversion rates among different enzyme conformers are slower than the catalytic rate. However, unlike the conventional interpretation, the apparent catalytic rate constant and the apparent Michaelis constant in this single-molecule Michaelis-Menten equation are complicated functions of the catalytic rate constants of individual conformers. We also suggest that the randomness parameter r, defined as <(t - )2> / t2, can serve as an indicator for dynamic disorder in the catalytic step of the enzymatic reaction, as it becomes larger than unity at high substrate concentrations in the presence of dynamic disorder.

  16. Nonlinear Vibrational Spectroscopy: a Method to Study Vibrational Self-Trapping

    NASA Astrophysics Data System (ADS)

    Hamm, Peter; Edler, Julian

    We review the capability of nonlinear vibrational spectroscopy to study vibrational self-trapping in hydrogen-bonded molecular crystals. For that purpose, the two relevant coupling mechanisms, excitonic coupling and nonlinear exciton-phonon coupling, are first introduced separately using appropriately chosen molecular systems as examples. Both coupling mechanisms are subsequently combined, yielding vibrational selftrapping. The experiments unambiguously prove that both the N-H and the C=O band of crystalline acetanilide (ACN), a model system for proteins, show vibrational self-trapping. The C=O band is self-trapped only at low enough temperature, while thermally induced disorder destroys the mechanism at room temperature. The binding energy of the N-H band, on the other hand, is considerably larger and self-trapping survives thermal fluctuations even at room temperature.

  17. Thermal degradation of polyketones. Vibrational spectroscopy studies

    NASA Astrophysics Data System (ADS)

    Conti, G.; Sommazzi, A.

    1993-03-01

    Thermal degradation studies of regular alternating polymers of carbon monoxide and olefin have been followed by FT-IR spectroscopy. The I.R spectra of solid samples, performed in inert atmosphere and in high vacuum, were recorded as a function of time at different temperatures. From the I.R. data it is possible to conclude that the reaction process, near the melting point of the polymers, could consist of intra or intermolecular hydrogen transfer yielding an enol and a small quantity of insaturations. The thermal degradation process, at temperatures higher than melting point, involves the scission of the polymer chain and produces fragments with a large number of insaturations.

  18. Vibrational spectroscopy standoff detection of threat chemicals

    NASA Astrophysics Data System (ADS)

    Ortiz-Rivera, William; Pacheco-Londoño, Leonardo C.; Castro-Suarez, John R.; Felix-Rivera, Hilsamar; Hernandez-Rivera, Samuel P.

    2011-06-01

    Spectroscopy based standoff detection systems: Raman and FTIR have been tested for detection of threat chemicals, including highly energetic materials, homemade explosives, explosives formulations and high explosives mixtures. Other threat chemicals studied included toxic industrial compounds (TIC) and chemical agent simulants. Microorganisms and biological threat agent simulants have also been detected at standoff distances. Open Path FTIR has been used to detect vapors and chemicals deposited on metal surfaces at μg/cm2 levels at distances as far as 30 m in active mode and 60 m in passive mode. In the case of Raman telescope, standoff distances for acetonitrile and ammonium nitrate were 140 m.

  19. Single-Molecule Ion Channel Conformational Dynamics in Living Cells

    NASA Astrophysics Data System (ADS)

    Lu, H. Peter

    2014-03-01

    Stochastic and inhomogeneous conformational changes regulate the function and dynamics of ion channels that are crucial for cell functions, neuronal signaling, and brain functions. Such complexity makes it difficult, if not impossible, to characterize ion channel dynamics using conventional electrical recording alone since that the measurement does not specifically interrogate the associated conformational changes but rather the consequences of the conformational changes. Recently, new technology developments on single-molecule spectroscopy, and especially, the combined approaches of using single ion channel patch-clamp electrical recording and single-molecule fluorescence imaging have provided us the capability of probing ion channel conformational changes simultaneously with the electrical single channel recording. By combining real-time single-molecule fluorescence imaging measurements with real-time single-channel electric current measurements in artificial lipid bilayers and in living cell membranes, we were able to probe single ion-channel-protein conformational changes simultaneously, and thus providing an understanding the dynamics and mechanism of ion-channel proteins at the molecular level. The function-regulating and site-specific conformational changes of ion channels are now measurable under physiological conditions in real-time, one molecule at a time. We will focus our discussion on the new development and results of real-time imaging of the dynamics of gramicidin, colicin, and NMDA receptor ion channels in lipid bilayers and living cells. Our results shed light on new perspectives of the intrinsic interplay of lipid membrane dynamics, solvation dynamics, and the ion channel functions.

  20. Nonequilibrium single molecule protein folding in a coaxial mixer.

    PubMed

    Hamadani, Kambiz M; Weiss, Shimon

    2008-07-01

    We have developed a continuous-flow mixing device suitable for monitoring bioconformational reactions at the single-molecule level with a response time of approximately 10 ms under single-molecule flow conditions. Its coaxial geometry allows three-dimensional hydrodynamic focusing of sample fluids to diffraction-limited dimensions where diffusional mixing is rapid and efficient. The capillary-based design enables rapid in-lab construction of mixers without the need for expensive lithography-based microfabrication facilities. In-line filtering of sample fluids using granulated silica particles virtually eliminates clogging and extends the lifetime of each device to many months. In this article, to determine both the distance-to-time transfer function and the instrument response function of the device we characterize its fluid flow and mixing properties using both fluorescence cross-correlation spectroscopy velocimetry and finite element fluid dynamics simulations. We then apply the mixer to single molecule FRET protein folding studies of Chymotrypsin Inhibitor protein 2. By transiently populating the unfolded state of Chymotrypsin Inhibitor Protein 2 (CI2) under nonequilibrium in vitro refolding conditions, we spatially and temporally resolve the denaturant-dependent nonspecific collapse of the unfolded state from the barrier-limited folding transition of CI2. Our results are consistent with previous CI2 mixing results that found evidence for a heterogeneous unfolded state consisting of cis- and trans-proline conformers.

  1. Vibrational spectroscopy standoff detection of explosives.

    PubMed

    Pacheco-Londoño, Leonardo C; Ortiz-Rivera, William; Primera-Pedrozo, Oliva M; Hernández-Rivera, Samuel P

    2009-09-01

    Standoff infrared and Raman spectroscopy (SIRS and SRS) detection systems were designed from commercial instrumentation and successfully tested in remote detection of high explosives (HE). The SIRS system was configured by coupling a Fourier-transform infrared interferometer to a gold mirror and detector. The SRS instrument was built by fiber coupling a spectrograph to a reflective telescope. HE samples were detected on stainless steel surfaces as thin films (2-30 microg/cm(2)) for SIRS experiments and as particles (3-85 mg) for SRS measurements. Nitroaromatic HEs: TNT, DNT, RDX, C4, and Semtex-H and TATP cyclic peroxide homemade explosive were used as targets. For the SIRS experiments, samples were placed at increasing distances and an infrared beam was reflected from the stainless steel surfaces coated with the target chemicals at an angle of approximately 180 degrees from surface normal. Stainless steel plates containing TNT and RDX were first characterized for coverage distribution and surface concentration by reflection-absorption infrared spectroscopy. Targets were then placed at the standoff distance and SIRS spectra were collected in active reflectance mode. Limits of detection (LOD) were determined for all distances measured for the target HE. LOD values of 18 and 20 microg/cm(2) were obtained for TNT and RDX, respectively, for the SIR longest standoff distance measured. For SRS experiments, as low as 3 mg of TNT and RDX were detected at 7 m source-target distance employing 488 and 514.5 nm excitation wavelengths. The first detection and quantification study of the important formulation C4 is reported. Detection limits as function of laser powers and acquisition times and at a standoff distance of 7 m were obtained.

  2. 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.

  3. Modeling of Single Molecule Cytoplasmic Dynein

    NASA Astrophysics Data System (ADS)

    Yu, Clare

    2010-03-01

    A living cell has an infrastructure much like that of a city. We will describe the transportation system that consists of roads (filaments) and molecular motors (proteins) that haul cargo along these roads. Dynein is one type of motor protein that walks along microtubules towards the nucleus of the cell. Dynein is more complicated in its structure and function than other motors. Experiments have found that, unlike other motors, dynein can take different size steps along microtubules depending on load and ATP concentration. We use Monte Carlo simulations to model the molecular motor function of cytoplasmic dynein at the single molecule level. The theory relates dynein's enzymatic properties to its mechanical force production. Our simulations reproduce the main features of recent single molecule experiments. We make testable predictions that should guide future experiments related to dynein function.

  4. 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

  5. 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.

  6. 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.

  7. Vibrational characterization of pheomelanin and trichochrome F by Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Galván, Ismael; Jorge, Alberto; Solano, Francisco; Wakamatsu, Kazumasa

    2013-06-01

    We characterize for the first time the vibrational state of natural pheomelanin using Raman spectroscopy and model pigment synthesized from 5-S-cysteinyldopa. The shape of the Raman spectrum was very different from that of eumelanin. Four Raman bands were visible in the 500-2000 cm-1 wavenumber region about 500, 1150, 1490 and 2000 cm-1, which we assigned to the out-of-plane deformation and the stretching vibration of the phenyl rings, to the stretching vibration of C-N bonds or the stretching and wagging vibration of CH2, and to overtone or combination bands. Interestingly, we also show that the Raman spectrum of synthetic trichochrome F, a pigment that may be produced along with pheomelanin during pheomelanogenesis, is different from that of pheomelanin and similar to the spectrum of eumelanin. We could detect Raman signal of both eumelanin and pheomelanin in feathers and hairs where both pigments simultaneously occur without the need of isolating the pigment. This indicates that Raman spectroscopy represents a non-invasive method to detect pheomelanin and distinguish it from other pigments. This may be especially relevant to detect pheomelanin in animal skin including humans, where it has been associated with animal appearance and classification, human phototypes, prevention of skin diseases and cancer risk.

  8. Do-it-yourself guide: How to use the modern single molecule toolkit

    PubMed Central

    Walter, Nils G.; Huang, Cheng-Yen; Manzo, Anthony J.; Sobhy, Mohamed A.

    2008-01-01

    Single molecule microscopy has evolved into the ultimate-sensitivity toolkit to study systems from small molecules to living cells, with the prospect of revolutionizing the modern biosciences. Here we survey the current state-of-the-art in single molecule tools including fluorescence spectroscopy, tethered particle microscopy, optical and magnetic tweezers, and atomic force microscopy. Our review seeks to guide the biological scientist in choosing the right approach from the available single molecule toolkit for applications ranging as far as structural biology, enzymology, nanotechnology, and systems biology. PMID:18511916

  9. 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

  10. Electrons, photons, and force: quantitative single-molecule measurements from physics to biology.

    PubMed

    Claridge, Shelley A; Schwartz, Jeffrey J; Weiss, Paul S

    2011-02-22

    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.

  11. Model systems for single molecule polymer dynamics.

    PubMed

    Latinwo, Folarin; Schroeder, Charles M

    2011-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of "ideal" and "real" chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force-extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer-monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of "real" polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena.

  12. 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.

  13. Single-Molecule Imaging of Nuclear Transport

    PubMed Central

    Goryaynov, Alexander; Sarma, Ashapurna; Ma, Jiong; Yang, Weidong

    2010-01-01

    The utility of single molecule fluorescence microscopy approaches has been proven to be of a great avail in understanding biological reactions over the last decade. The investigation of molecular interactions with high temporal and spatial resolutions deep within cells has remained challenging due to the inherently weak signals arising from individual molecules. Recent works by Yang et al. demonstrated that narrow-field epifluorescence microscopy allows visualization of nucleocytoplasmic transport at the single molecule level. By the single molecule approach, important kinetics, such as nuclear transport time and efficiency, for signal-dependent and independent cargo molecules have been obtained. Here we described a protocol for the methodological approach with an improved spatiotemporal resolution of 0.4 ms and 12 nm. The improved resolution enabled us to capture transient active transport and passive diffusion events through the nuclear pore complexes (NPC) in semi-intact cells. We expect this method to be used in elucidating other binding and trafficking events within cells. PMID:20548283

  14. Single molecule thermodynamics in biological motors.

    PubMed

    Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

    2007-04-01

    Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

  15. Model systems for single molecule polymer dynamics

    PubMed Central

    Latinwo, Folarin

    2012-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

  16. Quantitative Analysis of Single-Molecule RNA-Protein Interaction

    PubMed Central

    Fuhrmann, Alexander; Schoening, Jan C.; Anselmetti, Dario; Staiger, Dorothee; Ros, Robert

    2009-01-01

    Abstract RNA-binding proteins impact gene expression at the posttranscriptional level by interacting with cognate cis elements within the transcripts. Here, we apply dynamic single-molecule force spectroscopy to study the interaction of the Arabidopsis glycine-rich RNA-binding protein AtGRP8 with its RNA target. A dwell-time-dependent analysis of the single-molecule data in combination with competition assays and site-directed mutagenesis of both the RNA target and the RNA-binding domain of the protein allowed us to distinguish and quantify two different binding modes. For dwell times <0.21 s an unspecific complex with a lifetime of 0.56 s is observed, whereas dwell times >0.33 s result in a specific interaction with a lifetime of 208 s. The corresponding reaction lengths are 0.28 nm for the unspecific and 0.55 nm for the specific AtGRP8-RNA interactions, indicating formation of a tighter complex with increasing dwell time. These two binding modes cannot be dissected in ensemble experiments. Quantitative titration in RNA bandshift experiments yields an ensemble-averaged equilibrium constant of dissociation of KD = 2 × 10−7 M. Assuming comparable on-rates for the specific and nonspecific binding modes allows us to estimate their free energies as ΔG0 = −42 kJ/mol and ΔG0 = −28 kJ/mol for the specific and nonspecific binding modes, respectively. Thus, we show that single-molecule force spectroscopy with a refined statistical analysis is a potent tool for the analysis of protein-RNA interactions without the drawback of ensemble averaging. This makes it possible to discriminate between different binding modes or sites and to analyze them quantitatively. We propose that this method could be applied to complex interactions of biomolecules in general, and be of particular interest for the investigation of multivalent binding reactions. PMID:19527663

  17. Vibrational spectroscopy of microhydrated conjugate base anions.

    PubMed

    Asmis, Knut R; Neumark, Daniel M

    2012-01-17

    Conjugate-base anions are ubiquitous in aqueous solution. Understanding the hydration of these anions at the molecular level represents a long-standing goal in chemistry. A molecular-level perspective on ion hydration is also important for understanding the surface speciation and reactivity of aerosols, which are a central component of atmospheric and oceanic chemical cycles. In this Account, as a means of studying conjugate-base anions in water, we describe infrared multiple-photon dissociation spectroscopy on clusters in which the sulfate, nitrate, bicarbonate, and suberate anions are hydrated by a known number of water molecules. This spectral technique, used over the range of 550-1800 cm(-1), serves as a structural probe of these clusters. The experiments follow how the solvent network around the conjugate-base anion evolves, one water molecule at a time. We make structural assignments by comparing the experimental infrared spectra to those obtained from electronic structure calculations. Our results show how changes in anion structure, symmetry, and charge state have a profound effect on the structure of the solvent network. Conversely, they indicate how hydration can markedly affect the structure of the anion core in a microhydrated cluster. Some key results include the following. The first few water molecules bind to the anion terminal oxo groups in a bridging fashion, forming two anion-water hydrogen bonds. Each oxo group can form up to three hydrogen bonds; one structural result, for example, is the highly symmetric, fully coordinated SO(4)(2-)(H(2)O)(6) cluster, which only contains bridging water molecules. Adding more water molecules results in the formation of a solvent network comprising water-water hydrogen bonding in addition to hydrogen bonding to the anion. For the nitrate, bicarbonate, and suberate anions, fewer bridging sites are available, namely, three, two, and one (per carboxylate group), respectively. As a result, an earlier onset of water

  18. Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration-vibration two-dimensional infrared spectroscopy.

    PubMed

    Guo, Rui; Fournier, Frederic; Donaldson, Paul M; Gardner, Elizabeth M; Gould, Ian R; Klug, David R

    2009-10-14

    Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species.

  19. Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing

    PubMed Central

    Boujday, Souhir; Lamy de la Chapelle, Marc; Srajer, Johannes; Knoll, Wolfgang

    2015-01-01

    In this short summary we summarize some of the latest developments in vibrational spectroscopic tools applied for the sensing of (small) molecules and biomolecules in a label-free mode of operation. We first introduce various concepts for the enhancement of InfraRed spectroscopic techniques, including the principles of Attenuated Total Reflection InfraRed (ATR-IR), (phase-modulated) InfraRed Reflection Absorption Spectroscopy (IRRAS/PM-IRRAS), and Surface Enhanced Infrared Reflection Absorption Spectroscopy (SEIRAS). Particular attention is put on the use of novel nanostructured substrates that allow for the excitation of propagating and localized surface plasmon modes aimed at operating additional enhancement mechanisms. This is then be complemented by the description of the latest development in Surface- and Tip-Enhanced Raman Spectroscopies, again with an emphasis on the detection of small molecules or bioanalytes. PMID:26343666

  20. 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.

  1. Single-molecule optomechanics in “picocavities”

    NASA Astrophysics Data System (ADS)

    Benz, Felix; Schmidt, Mikolaj K.; Dreismann, Alexander; Chikkaraddy, Rohit; Zhang, Yao; Demetriadou, Angela; Carnegie, Cloudy; Ohadi, Hamid; de Nijs, Bart; Esteban, Ruben; Aizpurua, Javier; Baumberg, Jeremy J.

    2016-11-01

    Trapping light with noble metal nanostructures overcomes the diffraction limit and can confine light to volumes typically on the order of 30 cubic nanometers. We found that individual atomic features inside the gap of a plasmonic nanoassembly can localize light to volumes well below 1 cubic nanometer (“picocavities”), enabling optical experiments on the atomic scale. These atomic features are dynamically formed and disassembled by laser irradiation. Although unstable at room temperature, picocavities can be stabilized at cryogenic temperatures, allowing single atomic cavities to be probed for many minutes. Unlike traditional optomechanical resonators, such extreme optical confinement yields a factor of 106 enhancement of optomechanical coupling between the picocavity field and vibrations of individual molecular bonds. This work sets the basis for developing nanoscale nonlinear quantum optics on the single-molecule level.

  2. Toward Single-Molecule Nanomechanical Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Roukes, Michael

    2009-03-01

    Mass spectrometry (MS) has become a preeminent methodology of proteomics since it provides rapid and quantitative identification of protein species with relatively low sample consumption. Yet with the trend toward biological analysis at increasingly smaller scales, ultimately down to the volume of an individual cell, MS with few-to-single molecule resolution will be required. We report the first realization of MS based on single-biological-molecule detection with nanoelectromechanical systems (NEMS). NEMS provide unparalleled mass resolution, now sufficient for detection of individual molecular species in real time. However, high sensitivity is only one of several components required for MS. We demonstrate a first complete prototype NEMS-MS system for single-molecule mass spectrometry providing proof-of-principle for this new technique. Nanoparticles and protein species are introduced by electrospray injection from the fluid phase in ambient conditions into vacuum and subsequently delivered to the NEMS detector by hexapole ion optics . Mass measurements are then recorded in real-time as analytes adsorb, one-by-one, onto a phase-locked, ultrahigh frequency (UHF) NEMS resonator. These first NEMS-MS spectra, obtained with modest resolution from only several hundred mass adsorption events, presage the future capabilities of this methodology. We outline the substantial improvements feasible in near term, through recent advances and technological avenues that are unique to NEMS-MS.

  3. Single molecule and single cell epigenomics.

    PubMed

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

    2015-01-15

    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.

  4. Surface sum-frequency vibrational spectroscopy of nonpolar media

    SciTech Connect

    Sun, Shumei; Tian, Chuanshan; Shen, Y. Ron

    2015-04-27

    Sum-frequency generation spectroscopy is surface specific only if the bulk contribution to the signal is negligible. Negligible bulk contribution is, however, not necessarily true, even for media with inversion symmetry. The inevitable challenge is to find the surface spectrum in the presence of bulk contribution, part of which has been believed to be inseparable from the surface contribution. Here, we show that, for nonpolar media, it is possible to separately deduce surface and bulk spectra from combined phase-sensitive sum-frequency vibrational spectroscopic measurements in reflection and transmission. Finally, the study of benzene interfaces is presented as an example.

  5. Vibrational spectroscopy of cinnamaldehyde on graphite and supported Pd islands

    NASA Astrophysics Data System (ADS)

    Grimaud, C.-M.; Radosavkic, D.; Ustaze, S.; Palmer, R. E.

    2001-07-01

    We report the first experimental study of the adsorption of cinnamaldehyde on surfaces under ultra high vacuum (UHV) conditions. Cinnamaldehyde is an α,β-unsaturated aldehyde with important applications in the fine chemicals sector. High-resolution electron energy loss spectroscopy (HREELS) is employed to investigate the vibrational modes of cinnamaldehyde condensed on graphite at 100 K and absorbed on the surface of a Pd islands film (supported on graphite), also at 100 K. In the case of the Pd film, we find strong evidence for a parallel orientation of the phenyl ring consistent with theoretical calculations.

  6. 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

  7. Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis.

    PubMed

    Zhu, Zhi; Yang, Chaoyong James

    2017-01-17

    Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single

  8. The information content in single-molecule Raman nanoscopy

    SciTech Connect

    El-Khoury, Patrick Z.; Abellan, Patricia; Chantry, Ruth L.; Gong, Yu; Joly, Alan G.; Novikova, Irina V.; Evans, James E.; Aprà, Edoardo; Hu, Dehong; Ramasse, Quentin M.; Hess, Wayne P.

    2016-01-02

    Nowadays, it is possible to establish the chemical identity of a substance at the ultimate detection limit of a single molecule, i.e. the sensitivity required to probe 1.66 yoctomoles (1/NA), using surface-enhanced Raman scattering (SERS). It is also possible to image within an individual molecule, all while retaining chemical selectivity, using tip-enhanced Raman scattering (TERS). The potential applications of ultrasensitive SERS and TERS in chemical and biological detection and imaging are evident, and have attracted significant attention over the past decade. Rather than focusing on conventional single/few-molecule SERS and TERS experiments, where the objective is ultrasensitive spectroscopy and nanoscale chemical imaging, we consider the reverse problem herein. Namely, we review recent efforts ultimately aimed at probing different aspects of a molecule’s local environment through a detailed analysis of its SERS and TERS signatures. Particular attention is devoted to local electric field imaging using TERS; we describe how the vector components and absolute magnitude of a local electric field may be inferred from molecular Raman spectra and images. We also propose experiments that can potentially be used to cross-check the insights gained from the described SERS and TERS measurements. The ultimate goal of this review is to demonstrate that there is much more to single molecule Raman scattering than mere ultrasensitive chemical nanoscopy.

  9. Studying the Nucleated Mammalian Cell Membrane by Single Molecule Approaches

    PubMed Central

    Wang, Feng; Wu, Jiazhen; Gao, Jing; Liu, Shuheng; Jiang, Junguang; Jiang, Shibo; Wang, Hongda

    2014-01-01

    The cell membrane plays a key role in compartmentalization, nutrient transportation and signal transduction, while the pattern of protein distribution at both cytoplasmic and ectoplasmic sides of the cell membrane remains elusive. Using a combination of single-molecule techniques, including atomic force microscopy (AFM), single molecule force spectroscopy (SMFS) and stochastic optical reconstruction microscopy (STORM), to study the structure of nucleated cell membranes, we found that (1) proteins at the ectoplasmic side of the cell membrane form a dense protein layer (4 nm) on top of a lipid bilayer; (2) proteins aggregate to form islands evenly dispersed at the cytoplasmic side of the cell membrane with a height of about 10–12 nm; (3) cholesterol-enriched domains exist within the cell membrane; (4) carbohydrates stay in microdomains at the ectoplasmic side; and (5) exposed amino groups are asymmetrically distributed on both sides. Based on these observations, we proposed a Protein Layer-Lipid-Protein Island (PLLPI) model, to provide a better understanding of cell membrane structure, membrane trafficking and viral fusion mechanisms. PMID:24806512

  10. Biophysical characterization of DNA binding from single molecule force measurements

    NASA Astrophysics Data System (ADS)

    Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.

    2010-09-01

    Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.

  11. Biophysical characterization of DNA binding from single molecule force measurements

    PubMed Central

    Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.

    2010-01-01

    Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function. PMID:20576476

  12. Single molecule study of a processivity clamp sliding on DNA

    SciTech Connect

    Laurence, T A; Kwon, Y; Johnson, A; Hollars, C; O?Donnell, M; Camarero, J A; Barsky, D

    2007-07-05

    Using solution based single molecule spectroscopy, we study the motion of the polIII {beta}-subunit DNA sliding clamp ('{beta}-clamp') on DNA. Present in all cellular (and some viral) forms of life, DNA sliding clamps attach to polymerases and allow rapid, processive replication of DNA. In the absence of other proteins, the DNA sliding clamps are thought to 'freely slide' along the DNA; however, the abundance of positively charged residues along the inner surface may create favorable electrostatic contact with the highly negatively charged DNA. We have performed single-molecule measurements on a fluorescently labeled {beta}-clamp loaded onto freely diffusing plasmids annealed with fluorescently labeled primers of up to 90 bases. We find that the diffusion constant for 1D diffusion of the {beta}-clamp on DNA satisfies D {le} 10{sup -14} cm{sup 2}/s, much slower than the frictionless limit of D = 10{sup -10} cm{sup 2}/s. We find that the {beta} clamp remains at the 3-foot end in the presence of E. coli single-stranded binding protein (SSB), which would allow for a sliding clamp to wait for binding of the DNA polymerase. Replacement of SSB with Human RP-A eliminates this interaction; free movement of sliding clamp and poor binding of clamp loader to the junction allows sliding clamp to accumulate on DNA. This result implies that the clamp not only acts as a tether, but also a placeholder.

  13. [Structure analysis of disease-related proteins using vibrational spectroscopy].

    PubMed

    Hiramatsu, Hirotsugu

    2014-01-01

    Analyses of the structure and properties of identified pathogenic proteins are important for elucidating the molecular basis of diseases and in drug discovery research. Vibrational spectroscopy has advantages over other techniques in terms of sensitivity of detection of structural changes. Spectral analysis, however, is complicated because the spectrum involves a substantial amount of information. This article includes examples of structural analysis of disease-related proteins using vibrational spectroscopy in combination with additional techniques that facilitate data acquisition and analysis. Residue-specific conformation analysis of an amyloid fibril was conducted using IR absorption spectroscopy in combination with (13)C-isotope labeling, linear dichroism measurement, and analysis of amide I band features. We reveal a pH-dependent property of the interacting segment of an amyloidogenic protein, β2-microglobulin, which causes dialysis-related amyloidosis. We also reveal the molecular mechanisms underlying pH-dependent sugar-binding activity of human galectin-1, which is involved in cell adhesion, using spectroscopic techniques including UV resonance Raman spectroscopy. The decreased activity at acidic pH was attributed to a conformational change in the sugar-binding pocket caused by protonation of His52 (pKa 6.3) and the cation-π interaction between Trp68 and the protonated His44 (pKa 5.7). In addition, we show that the peak positions of the Raman bands of the C4=C5 stretching mode at approximately 1600 cm(-1) and the Nπ-C2-Nτ bending mode at approximately 1405 cm(-1) serve as markers of the His side-chain structure. The Raman signal was enhanced 12 fold using a vertical flow apparatus.

  14. Increased throughput single molecule detection of DNA

    NASA Astrophysics Data System (ADS)

    Gurjar, Rajan; Seetamraju, Madhavi; Kolodziejski, Noah; Myers, Richard; Staples, Christopher; Christian, James; Squillante, Michael R.; Entine, Gerald

    2007-09-01

    In this work, we present research in using confocal optical techniques with femtolitre focal volumes and obtain very high signal-to-noise and signal-to-background ratios for single molecule detection (SMD). We were able to achieve improved signal strength by using highly fluorescent quantum dots and nanopatterned substrates to obtain plasmon induced resonant fluorescence enhancement. A method to simultaneously using multiple excitation spots without the use of confocal apertures and an array of single photon sensitive Geiger mode avalanche photodiodes was used to increase the throughput of the detection system. Using this highly sensitive SMD system, we detect small quantities of synthetic DNA through hybridization eliminating the need of polymerase chain reaction.

  15. Single molecule measurements and biological motors.

    PubMed

    Knight, Alex E; Mashanov, Gregory; Molloy, Justin E

    2005-12-01

    Recent technological advances in lasers and optical detectors have enabled a variety of new, single molecule technologies to be developed. Using intense and highly collimated laser light sources in addition to super-sensitive cameras, the fluorescence of single fluorophores can now be imaged in aqueous solution. Also, laser optical tweezers have enabled the piconewton forces produced by pair of interacting biomolecules to be measured directly. However, for a researcher new to the field to begin to use such techniques in their own research might seem a daunting prospect. Most of the equipment that is in use is custom-built. However, most of the equipment is essence fairly simple and the aim of this article is to provide an entry point to the field for a newcomer. It focuses mainly on those practical aspects which are not particularly well covered in the literature, and aims to provide an overview of the field as a whole with references and web links to more detailed sources elsewhere. Indeed, the opportunity to publish an article such as this on the Internet affords many new opportunities (and more space!) for presenting scientific ideas and information. For example, we have illustrated the nature of optical trap data with an interactive Java simulation; provided links to relevant web sites and technical documents, and included a large number of colour figures and plots. Our group's research focuses on molecular motors, and the bias of this article reflects this. It turns out that molecular motors have been a paradigm (or prototype) for single molecule research and the field has seen a rapid development in the techniques. It is hoped that the methods described here will be broadly applicable to other biological systems.

  16. VLT-CRIRES: ``Good Vibrations'' Rotational-vibrational molecular spectroscopy in astronomy

    NASA Astrophysics Data System (ADS)

    Käufl, H. U.

    2010-05-01

    Near-Infrared high spectral and spatial resolution spectroscopy offers new and innovative observing opportunities for astronomy. The ``traditional'' benefits of IR-astronomy - strongly reduced extinction and availability of adaptive optics - more than offset for many applications the compared to CCD-based astronomy strongly reduced sensitivity. Especially in high resolution spectroscopy interferences by telluric lines can be minimized. Moreover for abundance studies many important atomic lines can be accessed in the NIR. A novel spectral feature available for quantitative spectroscopy are the molecular rotational-vibrational transitions which allow for fundamentally new studies of condensed objects and atmospheres. This is also an important complement to radio-astronomy, especially with ALMA, where molecules are generally only observed in the vibrational ground state. Rot-vib transitions also allow high precision abundance measurements - including isotopic ratios - fundamental to understand the thermo-nuclear processes in stars beyond the main sequence. Quantitative modeling of atmospheres has progressed such that the unambiguous interpretation of IR-spectra is now well established. In combination with adaptive optics spectro-astrometry is even more powerful and with VLT-CRIRES a spatial resolution of better than one milli-arcsecond has been demonstrated. Some highlights and recent results will be presented: our solar system, extrasolar planets, star- and planet formation, stellar evolution and the formation of galactic bulges.

  17. Structural dynamics in complex liquids studied with multidimensional vibrational spectroscopy

    SciTech Connect

    Tokmakoff, Andrei

    2013-08-31

    The development of new sustainable energy sources is linked to our understanding of the molecular properties of water and aqueous solutions. Energy conversion, storage, and transduction processes, particularly those that occur in biology, fuel cells, and batteries, make use of water for the purpose of moving energy in the form of charges and mediating the redox chemistry that allows this energy to be stored as and released from chemical bonds. To build our fundamental knowledge in this area, this project supports work in the Tokmakoff group to investigate the molecular dynamics of water’s hydrogen bond network, and how these dynamics influence its solutes and the mechanism of proton transport in water. To reach the goals of this grant, we developed experiments to observe molecular dynamics in water as directly as possible, using ultrafast multidimensional vibrational spectroscopy. We excite and probe broad vibrational resonances of water, molecular solutes, and protons in water. By correlating how molecules evolve from an initial excitation frequency to a final frequency, we can describe the underlying molecular dynamics. Theoretical modeling of the data with the help of computational spectroscopy coupled with molecular dynamics simulations provided the atomistic insight in these studies.

  18. Spectroscopic characterization of Venus at the single molecule level.

    PubMed

    David, Charlotte C; Dedecker, Peter; De Cremer, Gert; Verstraeten, Natalie; Kint, Cyrielle; Michiels, Jan; Hofkens, Johan

    2012-02-01

    Venus is a recently developed, fast maturating, yellow fluorescent protein that has been used as a probe for in vivo applications. In the present work the photophysical characteristics of Venus were analyzed spectroscopically at the bulk and single molecule level. Through time-resolved single molecule measurements we found that single molecules of Venus display pronounced fluctuations in fluorescence emission, with clear fluorescence on- and off-times. These fluorescence intermittencies were found to occupy a broad range of time scales, ranging from milliseconds to several seconds. Such long off-times can complicate the analysis of single molecule counting experiments or single-molecule FRET experiments.

  19. Microfluidics for biological measurements with single-molecule resolution.

    PubMed

    Streets, Aaron M; Huang, Yanyi

    2014-02-01

    Single-molecule approaches in biology have been critical in studies ranging from the examination of physical properties of biological macromolecules to the extraction of genetic information from DNA. The variation intrinsic to many biological processes necessitates measurements with single-molecule resolution in order to accurately recapitulate population distributions. Microfluidic technology has proven to be useful in the facilitation and even enhancement of single-molecule studies because of the precise liquid handling, small volume manipulation, and high throughput capabilities of microfluidic devices. In this review we survey the microfluidic "toolbox" available to the single-molecule specialist and summarize some recent biological applications of single-molecule detection on chip.

  20. Exploiting the diagnostic potential of biomolecular fingerprinting with vibrational spectroscopy.

    PubMed

    Kendall, Catherine; Hutchings, Joanne; Barr, Hugh; Shepherd, Neil; Stone, Nicholas

    2011-01-01

    There is immense clinical need for techniques that can detect the biochemical changes associated with pre-malignancy. The ideal diagnostic test would provide rapid, non-invasive diagnosis at the point of care with high throughput and without prior tissue processing. Over the past decade vibrational spectroscopy techniques have demonstrated their ability to provide non-destructive, rapid, clinically relevant diagnostic information. Biochemical fingerprints of tissues measured using Raman and infrared spectroscopy analysed in conjunction with advanced chemometrics have shown great potential in the diagnostic assessment of biological material. Development of Raman probes is enabling the potential of in vivo clinical measurements to be realised. A novel probe design has been evaluated in clinical studies to identify and classify the subtle pre-malignant biochemical changes related to the carcinogenesis process. Exciting recent developments have enabled the probing of tissue samples at depth with huge potential for breast and prostate cancer diagnostics. Furthermore, the potential of vibrational spectroscopy to provide prognostic information is tantalising. Raman spectral data acquired on oesophageal biopsy samples analysed in conjunction with patient outcome data has shown the power of spectral biomolecular fingerprinting in predicting the outcome of patients with high-grade dysplasia in Barrett's oesophagus. Raman mapping can also be used to analyse thin tissue sections on calcium fluoride slides enabling the distribution of tissue constituents to be realised. The spectral data acquired effectively enables multiplexing of digital tissue stains since a whole array of information is gathered simultaneously. Technological developments are bringing the technologies closer to the clinical reality of spectral pathology and high-throughput non-destructive measurement with high resolution.

  1. SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

    SciTech Connect

    Professor William Moerner

    2010-07-09

    The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in

  2. Monitoring Cellular Interactions during T Cell Activation at the Single Molecule Level Using Semiconductor Quantum-Dots

    DTIC Science & Technology

    2005-05-10

    correlation spectroscopy (FCS); (5) testing the lipid raft hypothesis by single molecule imaging of targeted peptide-coated quantum dots; and (6) molecular cloning and fusion of avidin to immunological synapse (IS) components.

  3. Force-induced tautomerization in a single molecule

    NASA Astrophysics Data System (ADS)

    Ladenthin, Janina N.; Frederiksen, Thomas; Persson, Mats; Sharp, John C.; Gawinkowski, Sylwester; Waluk, Jacek; Kumagai, Takashi

    2016-10-01

    Heat transfer, electrical potential and light energy are common ways to activate chemical reactions. Applied force is another way, but dedicated studies for such a mechanical activation are limited, and this activation is poorly understood at the single-molecule level. Here, we report force-induced tautomerization in a single porphycene molecule on a Cu(110) surface at 5 K, which is studied by scanning probe microscopy and density functional theory calculations. Force spectroscopy quantifies the force needed to trigger tautomerization with submolecular spatial resolution. The calculations show how the reaction pathway and barrier of tautomerization are modified in the presence of a copper tip and reveal the atomistic origin of the process. Moreover, we demonstrate that a chemically inert tip whose apex is terminated by a xenon atom cannot induce the reaction because of a weak interaction with porphycene and a strong relaxation of xenon on the tip as contact to the molecule is formed.

  4. 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

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

    PubMed

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

    2015-02-10

    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.

  6. Quantitative single-molecule imaging by confocal laser scanning microscopy.

    PubMed

    Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

    2008-11-25

    A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed.

  7. Detection of Steps in Single Molecule Data

    PubMed Central

    Aggarwal, Tanuj; Materassi, Donatello; Davison, Robert; Hays, Thomas; Salapaka, Murti

    2013-01-01

    Over the past few decades, single molecule investigations employing optical tweezers, AFM and TIRF microscopy have revealed that molecular behaviors are typically characterized by discrete steps or events that follow changes in protein conformation. These events, that manifest as steps or jumps, are short-lived transitions between otherwise more stable molecular states. A major limiting factor in determining the size and timing of the steps is the noise introduced by the measurement system. To address this impediment to the analysis of single molecule behaviors, step detection algorithms incorporate large records of data and provide objective analysis. However, existing algorithms are mostly based on heuristics that are not reliable and lack objectivity. Most of these step detection methods require the user to supply parameters that inform the search for steps. They work well, only when the signal to noise ratio (SNR) is high and stepping speed is low. In this report, we have developed a novel step detection method that performs an objective analysis on the data without input parameters, and based only on the noise statistics. The noise levels and characteristics can be estimated from the data providing reliable results for much smaller SNR and higher stepping speeds. An iterative learning process drives the optimization of step-size distributions for data that has unimodal step-size distribution, and produces extremely low false positive outcomes and high accuracy in finding true steps. Our novel methodology, also uniquely incorporates compensation for the smoothing affects of probe dynamics. A mechanical measurement probe typically takes a finite time to respond to step changes, and when steps occur faster than the probe response time, the sharp step transitions are smoothed out and can obscure the step events. To address probe dynamics we accept a model for the dynamic behavior of the probe and invert it to reveal the steps. No other existing method addresses

  8. Redox-Dependent Franck-Condon Blockade and Avalanche Transport in a Graphene-Fullerene Single-Molecule Transistor.

    PubMed

    Lau, Chit Siong; Sadeghi, Hatef; Rogers, Gregory; Sangtarash, Sara; Dallas, Panagiotis; Porfyrakis, Kyriakos; Warner, Jamie; Lambert, Colin J; Briggs, G Andrew D; Mol, Jan A

    2016-01-13

    We report transport measurements on a graphene-fullerene single-molecule transistor. The device architecture where a functionalized C60 binds to graphene nanoelectrodes results in strong electron-vibron coupling and weak vibron relaxation. Using a combined approach of transport spectroscopy, Raman spectroscopy, and DFT calculations, we demonstrate center-of-mass oscillations, redox-dependent Franck-Condon blockade, and a transport regime characterized by avalanche tunnelling in a single-molecule transistor.

  9. Single-molecule mechanics of mussel adhesion

    NASA Astrophysics Data System (ADS)

    Lee, Haeshin; Scherer, Norbert F.; Messersmith, Phillip B.

    2006-08-01

    The glue proteins secreted by marine mussels bind strongly to virtually all inorganic and organic surfaces in aqueous environments in which most adhesives function poorly. Studies of these functionally unique proteins have revealed the presence of the unusual amino acid 3,4-dihydroxy-L-phenylalanine (dopa), which is formed by posttranslational modification of tyrosine. However, the detailed binding mechanisms of dopa remain unknown, and the chemical basis for mussels' ability to adhere to both inorganic and organic surfaces has never been fully explained. Herein, we report a single-molecule study of the substrate and oxidation-dependent adhesive properties of dopa. Atomic force microscopy (AFM) measurements of a single dopa residue contacting a wet metal oxide surface reveal a surprisingly high strength yet fully reversible, noncovalent interaction. The magnitude of the bond dissociation energy as well as the inability to observe this interaction with tyrosine suggests that dopa is critical to adhesion and that the binding mechanism is not hydrogen bond formation. Oxidation of dopa, as occurs during curing of the secreted mussel glue, dramatically reduces the strength of the interaction to metal oxide but results in high strength irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role of dopa emerges from these studies, in which dopa exploits a remarkable combination of high strength and chemical multifunctionality to accomplish adhesion to substrates of widely varying composition from organic to metallic. 3,4-dihydroxylphenylalanine | atomic force microscopy | mussel adhesive protein

  10. Isotopic hydration of cellobiose: vibrational spectroscopy and dynamical simulations.

    PubMed

    Pincu, Madeleine; Cocinero, Emilio J; Mayorkas, Nitzan; Brauer, Brina; Davis, Benjamin G; Gerber, R Benny; Simons, John P

    2011-09-01

    The conformation and structural dynamics of cellobiose, one of the fundamental building blocks in nature, its C4' epimer, lactose, and their microhydrated complexes, isolated in the gas phase, have been explored through a combination of experiment and theory. Their structures at low temperature have been determined through double resonance, IR-UV vibrational spectroscopy conducted under molecular beam conditions, substituting D(2)O for H(2)O to separate isotopically, the carbohydrate (OH) bands from the hydration (OD) bands. Car-Parrinello (CP2K) simulations, employing dispersion corrected density functional potentials and conducted "on-the-fly" from ∼20 to ∼300 K, have been used to explore the consequences of raising the temperature. Comparisons between the experimental data, anharmonic vibrational self-consistent field calculations based upon ab initio potentials, and the CP2K simulations have established the role of anharmonicity; the reliability of classical molecular dynamics predictions of the vibrational spectra of carbohydrates and the accuracy of the dispersion corrected (BLYP-D) force fields employed; the structural consequences of increasing hydration; and the dynamical consequences of increasing temperature. The isolated and hydrated cellobiose and lactose units both present remarkably rigid structures: their glycosidic linkages adopt a "cis" (anti-ϕ and syn-ψ) conformation bound by inter-ring hydrogen bonds. This conformation is maintained when the temperature is increased to ∼300 K and it continues to be maintained when the cellobiose (or lactose) unit is hydrated by one or two explicitly bound water molecules. Despite individual fluctuations in the intra- and intermolecular hydrogen bonding pattern and some local structural motions, the water molecules remain locally bound and the isolated carbohydrates remain trapped within the cis potential well. The Car-Parrinello dynamical simulations do not suggest any accessible pathway to the trans

  11. Single-molecule strong coupling at room temperature in plasmonic nanocavities.

    PubMed

    Chikkaraddy, Rohit; de Nijs, Bart; Benz, Felix; Barrow, Steven J; Scherman, Oren A; Rosta, Edina; Demetriadou, Angela; Fox, Peter; Hess, Ortwin; Baumberg, Jeremy J

    2016-07-07

    Photon emitters placed in an optical cavity experience an environment that changes how they are coupled to the surrounding light field. In the weak-coupling regime, the extraction of light from the emitter is enhanced. But more profound effects emerge when single-emitter strong coupling occurs: mixed states are produced that are part light, part matter1, 2, forming building blocks for quantum information systems and for ultralow-power switches and lasers. Such cavity quantum electrodynamics has until now been the preserve of low temperatures and complicated fabrication methods, compromising its use. Here, by scaling the cavity volume to less than 40 cubic nanometres and using host–guest chemistry to align one to ten protectively isolated methylene-blue molecules, we reach the strong-coupling regime at room temperature and in ambient conditions. Dispersion curves from more than 50 such plasmonic nanocavities display characteristic light–matter mixing, with Rabi frequencies of 300 millielectronvolts for ten methylene-blue molecules, decreasing to 90 millielectronvolts for single molecules—matching quantitative models. Statistical analysis of vibrational spectroscopy time series and dark-field scattering spectra provides evidence of single-molecule strong coupling. This dressing of molecules with light can modify photochemistry, opening up the exploration of complex natural processes such as photosynthesis and the possibility of manipulating chemical bonds.

  12. Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Libing; Fu, Li; Wang, Hong-Fei; Yang, Bin

    2017-03-01

    Significant questions remain in respect to cellulose’s structure and polymorphs, particularly the cellulose surface layers and the bulk crystalline core as well as the conformational differences. Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with conventional SFG-VS (non-TIR) enables selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose, revealing their differences for the first time. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous while the surface layers of Iβ cellulose are crystalline but with different structural and spectroscopic signatures compared with its crystalline core. The differences between hydrogen bonding networks of cellulose surface and crystalline core were also shown by the SFG signal. The discovery here represents yet another instance of the importance of spectroscopic observations in transformative advances to understand the structure of the cellulosic biomass.

  13. Cross-Propagation Sum-Frequency Generation Vibrational Spectroscopy

    SciTech Connect

    Fu, Li; Chen, Shun-li; Gan, Wei; Wang, Hong-fei

    2016-02-27

    Here we report the theory formulation and the experiment realization of sum-frequency generation vibrational spectroscopy (SFG-VS) in the cross-propagation (XP) geometry or configuration. In the XP geometry, the visible and the infrared (IR) beams in the SFG experiment are delivered to the same location on the surface from visible and IR incident planes perpendicular to each other, avoiding the requirement to have windows or optics to be transparent to both the visible and IR frequencies. Therefore, the XP geometry is applicable to study surfaces in the enclosed vacuum or high pressure chambers with far infrared (FIR) frequencies that can directly access the metal oxide and other lower frequency surface modes, with much broader selection of visible and IR transparent window materials.

  14. Vibrational and Rotational Spectroscopy of CD_2H^+

    NASA Astrophysics Data System (ADS)

    Asvany, Oskar; Jusko, Pavol; Brünken, Sandra; Schlemmer, Stephan

    2016-06-01

    The lowest rotational levels (J=0-5) of the CD_2H^+ ground state have been probed by high-resolution rovibrational and pure rotational spectroscopy in a cryogenic 22-pole ion trap. For this, the ν_1 rovibrational band has been revisited, detecting 107 transitions, among which 35 are new. The use of a frequency comb system allowed to measure the rovibrational transitions with high precision and accuracy, typically better than 1 MHz. The high precision has been confirmed by comparing combination differences in the ground and vibrationally excited state. For the ground state, this allowed for equally precise predictions of pure rotational transitions, 24 of which have been measured directly by a novel IR - mm-wave double resonance method. M.-F. Jagod et al, J. Molec. Spectrosc. 153, 666, 1992 S. Gartner et al, J. Phys. Chem. A 117, 9975, 2013

  15. Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy

    PubMed Central

    Zhang, Libing; Fu, Li; Wang, Hong-fei; Yang, Bin

    2017-01-01

    Significant questions remain in respect to cellulose’s structure and polymorphs, particularly the cellulose surface layers and the bulk crystalline core as well as the conformational differences. Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with conventional SFG-VS (non-TIR) enables selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose, revealing their differences for the first time. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous while the surface layers of Iβ cellulose are crystalline but with different structural and spectroscopic signatures compared with its crystalline core. The differences between hydrogen bonding networks of cellulose surface and crystalline core were also shown by the SFG signal. The discovery here represents yet another instance of the importance of spectroscopic observations in transformative advances to understand the structure of the cellulosic biomass. PMID:28290542

  16. Liquid Space Lubricants Examined by Vibrational Micro-Spectroscopy

    NASA Technical Reports Server (NTRS)

    Street, Kenneth W., Jr.

    2008-01-01

    Considerable effort has been expended to develop liquid lubricants for satellites and space exploration vehicles. These lubricants must often perform under a range of harsh conditions such as vacuum, radiation, and temperature extremes while in orbit or in transit and in extremely dusty environments at destinations such as the Moon and Mars. Historically, oil development was guided by terrestrial application, which did not provide adequate space lubricants. Novel fluids such as the perfluorinated polyethers provided some relief but are far from ideal. With each new fluid proposed to solve one problem, other problems have arisen. Much of the work performed at the National Aeronautics and Space Administration (NASA) Glenn Research Center (GRC) in elucidating the mechanisms by which chemical degradation of space oils occur has been done by vibrational micro-spectroscopic techniques such as infrared and Raman, which this review details. Presented are fundamental lubrication studies as well as actual case studies in which vibrational spectroscopy has led to millions of dollars in savings and potentially prevented loss of mission.

  17. Structural characterization and vibrational spectroscopy of the arsenate mineral wendwilsonite.

    PubMed

    Frost, Ray L; Scholz, Ricardo; López, Andrés; Belotti, Fernanda Maria; Xi, Yunfei

    2014-01-24

    In this paper, we have investigated on the natural wendwilsonite mineral with the formulae Ca2(Mg,Co)(AsO4)2⋅2(H2O). Raman spectroscopy complimented with infrared spectroscopy has been used to determine the molecular structure of the wendwilsonite arsenate mineral. A comparison is made with the roselite mineral group with formula Ca2B(AsO4)2⋅2H2O (where B may be Co, Fe(2+), Mg, Mn, Ni, Zn). The Raman spectra of the arsenate related to tetrahedral arsenate clusters with stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. The Raman arsenate (AsO4)(3-) stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. In the infrared spectra complexity exists of multiple to tetrahedral (AsO4)(3-) clusters with antisymmetric stretching vibrations observed indicating a reduction of the tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong Raman bands around 450 cm(-1) are assigned to ν4 bending modes. Multiple bands in the 350-300 cm(-1) region assigned to ν2 bending modes provide evidence of symmetry reduction of the arsenate anion. Three broad bands for wendwilsonite found at 3332, 3119 and 3001 cm(-1) are assigned to OH stretching bands. By using a Libowitzky empirical equation, hydrogen bond distances of 2.65 and 2.75Å are estimated. Vibrational spectra enable the molecular structure of the wendwilsonite mineral to be determined and whilst similarities exist in the spectral patterns with the roselite mineral group, sufficient differences exist to be able to determine the identification of the minerals.

  18. Determining the elastic properties of aptamer-ricin single molecule multiple pathways

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ricin and an anti-ricin aptamer showed three stable binding conformations with their special chemomechanical properties. The elastic properties of the ricin-aptamer single-molecule interactions were investigated by the dynamic force spectroscopy (DFS). The worm-like-chain model and Hook’s law were ...

  19. Vibrationally resolved anion photoelectron spectroscopy of metal clusters

    NASA Astrophysics Data System (ADS)

    Miller, Stephen R.

    Vibrationally resolved anion photoelectron spectroscopy of metal clusters Vibrationally resolved anion photoelectron spectroscopy (APES) and density functional theory (DFT) are applied to the study of structure and reactivity in small metal containing molecules. The studies described fall into two general categories: the study of bare metal clusters and the study of metal/organic ligand reactions. The current lack of spectroscopic data for small, bare gas-phase metal compounds makes the experimental study of such compounds important for understanding structure and bonding in open-shell metallic species. The heteronuclear diatomic anions MCu- (M = Cr, Mo) were prepared in a flowing afterglow ion-molecule reactor, and studied experimentally with APES. Anion and neutral vibrational frequencies and MCu electron affinities were obtained for both systems. The experiments were supplemented by DFT calculations. The combined use of experiment and theory allows for the assignment of both photoelectron spectra, including a reassignment of the CrCu ground state reported in the literature. Similarly, DFT was used to assign the anionic/neutral electronic states observed in the photoelectron spectra of Al3- and Al3O-. The study of partially ligated organometallic complexes offers a means of examining the interactions between metal atoms and individual ligand molecules. DFT was used to assign electronic states observed in the photoelectron spectra of NbC2H2-, NbC4H4 -NbC6H6- and VC6H 6-. Comparison of the NbnHn - (n = 2, 4, 6) spectra (obtained through the reaction of C2 H4 and Nb) with DFT results provides the first direct spectroscopic evidence of the conversion of ethylene to benzene by a gas phase metal atom. Experiments were used to probe the reactivity of Y with C2H 4 in an effort to examine the generality of the metal induced C 2H4 dehydrogenation/cyclization reactions. Some of the key products in the Y reactions were YC2H-, YC 2H2-, and YC6H5 -. However, the results

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

    PubMed

    Riveline, Daniel

    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'.

  1. '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

  2. 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.

  3. A brief introduction to single-molecule fluorescence methods.

    PubMed

    van den Wildenberg, Siet M J L; Prevo, Bram; Peterman, Erwin J G

    2011-01-01

    One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which is the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches are addressed, we first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.

  4. Single-molecule interfacial electron transfer dynamics in solar energy conversion

    NASA Astrophysics Data System (ADS)

    Dhital, Bharat

    This dissertation work investigated the parameters affecting the interfacial electron transfer (ET) dynamics in dye-semiconductor nanoparticles (NPs) system by using single-molecule fluorescence spectroscopy and imaging combined with electrochemistry. The influence of the molecule-substrate electronic coupling, the molecular structure, binding geometry on the surface and the molecule-attachment surface chemistry on interfacial charge transfer processes was studied on zinc porphyrin-TiO2 NP systems. The fluorescence blinking measurement on TiO2 NP demonstrated that electronic coupling regulates dynamics of charge transfer processes at the interface depending on the conformation of molecule on the surface. Moreover, semiconductor surface charge induced electronic coupling of molecule which is electrostatically adsorbed on the semiconductor surface also predominantly alters the ET dynamics. Furthermore, interfacial electric field and electron accepting state density dependent ET dynamics has been dissected in zinc porphyrin-TiO2 NP system by observing the single-molecule fluorescence blinking dynamics and fluorescence lifetime with and without applied bias. The significant difference in fluorescence fluctuation and lifetime suggested the modulation of charge transfer dynamics at the interface with external electric field perturbation. Quasi-continuous distribution of fluorescence intensity with applied negative potential was attributed to the faster charge recombination due to reduced density of electron accepting states. The driving force and electron accepting state density ET dependent dynamics has also been probed in zinc porphyrin-TiO2 NP and zinc porphyrin-indium tin oxide (ITO) systems. Study of a molecule adsorbed on two different semiconductors (ITO and TiO2), with large difference in electron densities and distinct driving forces, allows us to observe the changes in rates of back electron transfer process reflected by the suppressed fluorescence blinking of

  5. Theoretical Study of the Vibrational Spectroscopy of the Ethyl Radical

    NASA Astrophysics Data System (ADS)

    Tabor, Daniel P.; Sibert, Edwin. L. Sibert, Iii

    2013-06-01

    The rich spectroscopy of the ethyl radical has attracted the attention of several experimental and theoretical investigations. The purpose of these studies was to elucidate the signatures of hyperconjugation, torsion, inversion, and Fermi coupling in the molecular spectra. Due to the number of degrees of freedom in the system, previous theoretical studies have implemented reduced-dimensional models. Our ultimate goal is a full-dimensional theoretical treatment of the vibrations using both Van Vleck and variational approaches. The methods will be combined with the potential that we have calculated using the CCSD(T) method on the cc-pVTZ basis set. In this talk we will discuss our initial work, which builds up from these reduced-dimensional models. Our calculations use coordinates that exploit the system's G_{12} PI symmetry in a simple fashion. By systematically adding more degrees of freedom to our model, we can determine the effects of specific couplings on the spectroscopy. T. Häber, A. C. Blair, D. J. Nesbitt and M. D. Schuder J. Chem. Phys. {124}, 054316, (2006). G .E. Douberly, unpublished. R. S. Bhatta, A. Gao and D. S. Perry J. Mol. Struct.: THEOCHEM {941}, 22, (2010).

  6. Intersystem Crossing Mechanisms and Single Molecule Fluorescence: Terrylene in Anthracene Crystals

    SciTech Connect

    Kol'chenko, M.A.; Nicolet, A.; Orrit, M.; Kozankiewicz, B.

    2005-05-15

    Single molecule spectroscopy requires molecules with low triplet yields and/or short triplet lifetimes. The intersystem crossing (ISC) rate may be dramatically enhanced by the host matrix. Comparing the fluorescence intensity of single terrylene molecules in para-terphenyl, naphthalene, and anthracene crystals, we found a reduction of the saturation intensity by three orders of magnitude in the latter case. The fluorescence autocorrelation function indicates that the bottleneck state is the terrylene triplet. We propose a ping-pong mechanism between host and guest. This intermolecular ISC mechanism, which can open whenever the host triplet lies lower than the guest singlet, was overlooked in previous single molecule investigations.

  7. Development of Single-Molecule DNA Sequencing Platform Based on Single-Molecule Electrical Conductance

    DTIC Science & Technology

    2015-05-25

    indicate that they are nearly harmless to cultured cells (17-20). The bio-distribution of injected GNPs has shown a size-dependent accumulation in liver ...Animals” of National Chiao Tung University. Four-week-old male BALB/C mice were housed at 22±2 C with a 12-h light/dark cycle and fed standard...Conference, Protein Folding Dynamics, 5-10 Jan, 2014, Hotel Galvez in Galveston TX, United States Guewha Steven Huang , Single-Molecule Kinetics of

  8. Red light, green light: probing single molecules using alternating-laser excitation.

    PubMed

    Santoso, Yusdi; Hwang, Ling Chin; Le Reste, Ludovic; Kapanidis, Achillefs N

    2008-08-01

    Single-molecule fluorescence methods, particularly single-molecule FRET (fluorescence resonance energy transfer), have provided novel insights into the structure, interactions and dynamics of biological systems. ALEX (alternating-laser excitation) spectroscopy is a new method that extends single-molecule FRET by providing simultaneous information about structure and stoichiometry; this new information allows the detection of interactions in the absence of FRET and extends the dynamic range of distance measurements that are accessible through FRET. In the present article, we discuss combinations of ALEX with confocal microscopy for studying in-solution and in-gel molecules; we also discuss combining ALEX with TIRF (total internal reflection fluorescence) for studying surface-immobilized molecules. We also highlight applications of ALEX to the study of protein-nucleic acid interactions.

  9. Deciphering the scaling of single-molecule interactions using Jarzynski's equality.

    PubMed

    Raman, Sangeetha; Utzig, Thomas; Baimpos, Theodoros; Ratna Shrestha, Buddha; Valtiner, Markus

    2014-11-21

    Unravelling the complexity of the macroscopic world relies on understanding the scaling of single-molecule interactions towards integral macroscopic interactions. Here, we demonstrate the scaling of single acid-amine interactions through a synergistic experimental approach combining macroscopic surface forces apparatus experiments and single-molecule force spectroscopy. This experimental framework is ideal for testing the well-renowned Jarzynski's equality, which relates work performed under non-equilibrium conditions with equilibrium free energy. Macroscopic equilibrium measurements scale linearly with the number density of interfacial bonds, providing acid-amine interaction energies of 10.9 ± 0.2 kT. Irrespective of how far from equilibrium single-molecule experiments are performed, the Jarzynski's free energy converges to 11 ± 1 kT. Our results validate the applicability of Jarzynski's equality to unravel the scaling of non-equilibrium single-molecule experiments to scenarios where large numbers of molecules interacts simultaneously in equilibrium. The developed scaling strategy predicts large-scale properties such as adhesion or cell-cell interactions on the basis of single-molecule measurements.

  10. Capabilities for measuring the diffusivity of a single molecule by recycling it in a nanochannel

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Davis, Lloyd

    2014-03-01

    Analysis of the fractions of fluorescently labeled molecules with different diffusivities within a microliter drop of solution is often used for high-throughput screening of molecular binding interactions in pharmaceutical drug discovery research. Assays frequently employ fluorescence correlation spectroscopy, an ensemble technique that is able to resolve fast diffusing small ligands from those bound to much larger biomolecules with considerably slower diffusion. Single-molecule measurements have the potential to resolve species with different diffusivities and to count the numbers of molecules of each species. Single-molecule recycling in a nanochannel, which entails detection of bursts of fluorescence photons from the repeated passage of a molecule through a focused laser beam as the flow along a nanochannel is periodically alternated, can be used to determine the diffusivity of a single molecule from the fluctuations in the intervals between successive detections. We discuss Monte Carlo studies to determine favorable experimental conditions for determining single-molecule diffusivities, together with a weighted-sliding-sum photon burst detection algorithm for flow-control and maximum-likelihood based analysis of recycle times. We also discuss incorporation of the algorithms into our experimental apparatus for single-molecule recycling, which uses a LabView real-time system for photon count analysis and flow control.

  11. Graphene-porphyrin single-molecule transistors.

    PubMed

    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

    2015-08-21

    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.

  12. Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy--interpretation by molecular mechanics.

    PubMed

    Tan, Ming-Liang; Bizzarri, Anna Rita; Xiao, Yuming; Cannistraro, Salvatore; Ichiye, Toshiko; Manzoni, Cristian; Cerullo, Giulio; Adams, Michael W W; Jenney, Francis E; Cramer, Stephen P

    2007-03-01

    We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.

  13. 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.

  14. 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

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

    NASA Astrophysics Data System (ADS)

    Zimbovskaya, Natalya A.

    2016-07-01

    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.

  16. Investigating buried polymer interfaces using sum frequency generation vibrational spectroscopy

    PubMed Central

    Chen, Zhan

    2010-01-01

    This paper reviews recent progress in the studies of buried polymer interfaces using sum frequency generation (SFG) vibrational spectroscopy. Both buried solid/liquid and solid/solid interfaces involving polymeric materials are discussed. SFG studies of polymer/water interfaces show that different polymers exhibit varied surface restructuring behavior in water, indicating the importance of probing polymer/water interfaces in situ. SFG has also been applied to the investigation of interfaces between polymers and other liquids. It has been found that molecular interactions at such polymer/liquid interfaces dictate interfacial polymer structures. The molecular structures of silane molecules, which are widely used as adhesion promoters, have been investigated using SFG at buried polymer/silane and polymer/polymer interfaces, providing molecular-level understanding of polymer adhesion promotion. The molecular structures of polymer/solid interfaces have been examined using SFG with several different experimental geometries. These results have provided molecular-level information about polymer friction, adhesion, interfacial chemical reactions, interfacial electronic properties, and the structure of layer-by-layer deposited polymers. Such research has demonstrated that SFG is a powerful tool to probe buried interfaces involving polymeric materials, which are difficult to study by conventional surface sensitive analytical techniques. PMID:21113334

  17. Vibrational Spectroscopy of CO2- Radical Anion in Water

    NASA Astrophysics Data System (ADS)

    Janik, Ireneusz; Tripathi, G. N. R.

    2016-06-01

    The reductive conversion of CO2 into industrial products (e.g., oxalic acid, formic acid, and methanol) can occur via aqueous CO2- as a transient intermediate. While the formation, structure and reaction pathways of this radical anion have been modelled for decades using various spectroscopic and theoretical approaches, we present here, for the first time, a vibrational spectroscopic investigation in liquid water, using pulse radiolysis time-resolved resonance Raman spectroscopy for its preparation and observation. Excitation of the radical in resonance with its 235 nm absorption displays a transient Raman band at 1298 wn, attributed to the symmetric CO stretch, which is at 45 wn higher frequency than in inert matrices. Isotopic substitution at C (13CO2-) shifts the frequency downwards by 22 wn which confirms its origin and the assignment. A Raman band of moderate intensity compared to the stronger 1298 wn band also appears at 742 wn, and is assignable to the OCO bending mode. A reasonable resonance enhancement of this mode is possible only in a bent CO2-(C2v/Cs) geometry. These resonance Raman features suggest a strong solute-solvent interaction, the water molecules acting as constituents of the radical structure, rather than exerting a minor solvent perturbation. However, there is no evidence of the non-equivalence (Cs) of the two CO bonds. A surprising resonance Raman feature is the lack of overtones of the symmetric CO stretch, which we interpret due to the detachment of the electron from the CO2- moiety towards the solvation shell. Electron detachment occurs at the energies of 0.28+/-0.03 eV or higher with respect to the zero point energy of the ground electronic state. The issue of acid-base equilibrium of the radical which has been in contention for decades, as reflected in a wide variation in the reported pKa (-0.2 to 3.9), has been resolved. A value of 3.4+/-0.2 measured in this work is consistent with the vibrational properties, bond structure and charge

  18. Breaking the concentration limit of optical single-molecule detection.

    PubMed

    Holzmeister, Phil; Acuna, Guillermo P; Grohmann, Dina; Tinnefeld, Philip

    2014-02-21

    Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach.

  19. Characterizing Anharmonic Vibrational Modes of Quinones with Two-Dimensional Infrared Spectroscopy.

    PubMed

    Cyran, Jenée D; Nite, Jacob M; Krummel, Amber T

    2015-07-23

    Two-dimensional infrared (2D IR) spectroscopy was used to study the vibrational modes of three quinones--benzoquinone, naphthoquinone, and anthraquinone. The vibrations of interest were in the spectral range of 1560-1710 cm(-1), corresponding to the in-plane carbonyl and ring stretching vibrations. Coupling between the vibrational modes is indicated by the cross peaks in the 2D IR spectra. The diagonal and off-diagonal anharmonicities range from 4.6 to 17.4 cm(-1) for the quinone series. In addition, there is significant vibrational coupling between the in-plane carbonyl and ring stretching vibrations. The diagonal anharmonicity, off-diagonal anharmonicity, and vibrational coupling constants are reported for benzoquinone, naphthoquinone, and anthraquinone.

  20. Vibrationally-resolved polyatomic photoelectron spectroscopy: Mode-specific behavior

    NASA Astrophysics Data System (ADS)

    Rathbone, G. J.; Poliakoff, E. D.; Bozek, J. D.; Lucchese, R. R.

    2002-05-01

    We report the first vibrationally-resolved photoelectron spectra for polyatomic molecules performed over a broad spectral range. Such studies elucidate vibrationally mode-specific aspects of the photoelectron scattering dynamics. Three linear triatomic systems (CO_2, N_2O, and CS_2) are studied, and the results exhibit striking differences for alternative modes. For CO_2^+(C^2Σ_g^+), a continuum resonance results in a 15 eV wide dip for the symmetric stretch branching ratio, while strong peaks are observed for vibrational branching ratios associated with the two symmetry forbidden modes. For CS_2^+(B^2Σ_u^+), mode-specific behavior is displayed, as resonance enhancement of a single quantum excitation is weak for the symmetric stretch, but strong for the bending vibration. For N_2O^+(A^2Σ^+), many vibrational excitations are observed and families of vibrational branching ratio spectra emerge.

  1. Manipulating Kondo temperature via single molecule switching.

    PubMed

    Iancu, Violeta; Deshpande, Aparna; Hla, Saw-Wai

    2006-04-01

    Two conformations of isolated single TBrPP-Co molecules on a Cu(111) surface are switched by applying +2.2 V voltage pulses from a scanning tunneling microscope tip at 4.6 K. The TBrPP-Co has a spin-active cobalt atom caged at its center, and the interaction between the spin of this cobalt atom and free electrons from the Cu(111) substrate can cause a Kondo resonance. Tunneling spectroscopy data reveal that switching from the saddle to a planar molecular conformation enhances spin-electron coupling, which increases the associated Kondo temperature from 130 to 170 K. This result demonstrates that the Kondo temperature can be manipulated just by changing molecular conformation without altering chemical composition of the molecule.

  2. 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.

  3. Stochastic single-molecule dynamics of synaptic membrane protein domains

    NASA Astrophysics Data System (ADS)

    Kahraman, Osman; Li, Yiwei; Haselwandter, Christoph A.

    2016-09-01

    Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.

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

    DOE PAGES

    Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; ...

    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.

  5. 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.

  6. Vibrational predissociation spectroscopy of Ar-tagged, trisubstituted silyl cations

    NASA Astrophysics Data System (ADS)

    DeBlase, Andrew F.; Scerba, Michael T.; Lectka, Thomas; Johnson, Mark A.

    2013-05-01

    Vibrational predissociation spectra of the (CH3)2RSi+·Arn, (R = H and CH3, n = 1 and 2) ions are compared with harmonic calculations to structurally characterize these putative reactive intermediates. Although the vibrational photofragmentation behavior indicates that the Ar-Si bond is quite strong relative to that found in closed shell ions, formation of the Ar adducts is calculated to cause only minor perturbations to the intrinsic vibrational band patterns of the isolated ions. In both (R = H and CH3) cases, the vibrational spectra are very simple, consisting entirely of sharp features readily assigned to fundamentals anticipated by their harmonic spectra.

  7. Probing Single Molecules with a Tunable Femtosecond Laser Coupled RF-STM

    NASA Astrophysics Data System (ADS)

    Cao, Weicai

    Scanning Tunneling Microscope (STM) has become a powerful tool in nanoscience for imaging, manipulation and electronic spectroscopy. STM inelastic electron tunneling spectroscopy (IETS) first achieved chemical identification of molecular species by characterizing vibrational energies. Recently, with the STM itProbe and H2 rotational spectromicroscopy, molecular structure and chemical bonds are observed with the STM. Despite these successes in spatial resolution, various efforts have been made to combine fs laser with STM to overcome the temporal resolution limitation of STM, there is so far no clear evidence of simultaneous fs and A resolution. Electronic properties of organic molecules are of central importance to applications such as molecular electronics, organic LEDs, and solar cells. Properties of these molecules can be probed by the scanning tunneling microscope (STM) at the single molecule level and with sub-A spatial resolution. The molecular orbital of 4, 7-Di ([2, 20-bithiophen]-5-yl) benzo[c] [1, 2, 5] thiadiazole (4T-BTD) with intramolecular donor-acceptor-donor sites is probed with the electronic state dI/dV imaging and H2 rotational and vibrational spectromicroscopy. 1, 4-Phenylene Diisocyanide (PDI) is probed by imaging with a CO-terminated tip and H2. PDI can self-assemble on noble metal surfaces to form nanostructures, which could have potential applications in molecular electronics and catalysis. Further combination of a RF-STM with a tunable femtosecond laser enables the investigation of light-molecule interactions. In this dissertation, efforts are spent to setup a new tunable fs laser (220 nm˜1040 nm) to couple with the RF-STM. The effects of the femtosecond laser are followed by detecting photo induced electron emission and photochemistry. A new double lock-in technique is applied to detect the weak laser-induced signal in the tunneling regime. To sharpen the energy width and increase the lifetime of the excited states of molecules, thin

  8. Single-molecule imaging of cell surfaces using near-field nanoscopy.

    PubMed

    Hinterdorfer, Peter; Garcia-Parajo, Maria F; Dufrêne, Yves F

    2012-03-20

    responses upon cell activation. We anticipate that the next steps in the evolution of single-molecule near-field nanoscopy will involve combining single-molecule imaging with single-molecule force spectroscopy to simultaneously measure the localization, elasticity, and interactions of cell surface molecules. In addition, progress in high-speed AFM should allow researchers to image single cell surface molecules at unprecedented temporal resolution. In parallel, exciting advances in the fields of photonic antennas and plasmonics may soon find applications in cell biology, enabling true nanoimaging and nanospectroscopy of individual molecules in living cells.

  9. Observation of the Interference Effect in Vibrationally Resolved Electron Momentum Spectroscopy of H2

    NASA Astrophysics Data System (ADS)

    Zhang, Zhe; Shan, Xu; Wang, Tian; Wang, Enliang; Chen, Xiangjun

    2014-01-01

    We report the first measurement on vibrationally resolved electron momentum spectroscopy of H2 by using a high-resolution (e, 2e) spectrometer. The vibrational-specific experimental momentum profiles have been obtained and shown to be in agreement with calculations of (e, 2e) ionization cross sections taking into account the vibrational wave functions. Distinct deviations from Franck-Condon predictions have been observed in vibrational ratios of cross sections, which can readily be ascribed to the Young-type two-center interference. Unlike previous (e, 2e) work, the present observation of an interference effect does not rely on the comparison with the one-center atomic cross section.

  10. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications.

    PubMed

    Roy, Tapta Kanchan; Gerber, R Benny

    2013-06-28

    This review describes the vibrational self-consistent field (VSCF) method and its other variants for computing anharmonic vibrational spectroscopy of biological molecules. The superiority and limitations of this algorithm are discussed with examples. The spectroscopic accuracy of the VSCF method is compared with experimental results and other available state-of-the-art algorithms for various biologically important systems. For large biological molecules with many vibrational modes, the scaling of computational effort is investigated. The accuracy of the vibrational spectra of biological molecules using the VSCF approach for different electronic structure methods is also assessed. Finally, a few open problems and challenges in this field are discussed.

  11. 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.

  12. 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.

  13. Single-molecule emulsion PCR in microfluidic droplets.

    PubMed

    Zhu, Zhi; Jenkins, Gareth; Zhang, Wenhua; Zhang, Mingxia; Guan, Zhichao; Yang, Chaoyong James

    2012-06-01

    The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis.

  14. 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

  15. Single molecule conformational analysis of DNA G-quadruplexes

    PubMed Central

    Shirude, Pravin S.; Balasubramanian, Shankar

    2008-01-01

    Single molecule fluorescence resonance energy transfer (FRET) can be employed to study conformational heterogeneity and real-time dynamics of biological macromolecules. Here we present single molecule studies on human genomic DNA G-quadruplex sequences that occur in the telomeres and in the promoter of a proto-oncogene. The findings are discussed with respect to the proposed biological function(s) of such motifs in living cells. PMID:18295608

  16. Probing molecular choreography through single-molecule biochemistry.

    PubMed

    van Oijen, Antoine M; Dixon, Nicholas E

    2015-12-01

    Single-molecule approaches are having a dramatic impact on views of how proteins work. The ability to observe molecular properties at the single-molecule level allows characterization of subpopulations and acquisition of detailed kinetic information that would otherwise be hidden in the averaging over an ensemble of molecules. In this Perspective, we discuss how such approaches have successfully been applied to in vitro-reconstituted systems of increasing complexity.

  17. Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging

    NASA Astrophysics Data System (ADS)

    Ha, Taekjip; Tinnefeld, Philip

    2012-05-01

    Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own “personalities” regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching. Understanding photophysics is critical in the design and interpretation of single-molecule experiments.

  18. Photophysics of Fluorescence Probes for Single Molecule Biophysics and Super-Resolution Imaging

    PubMed Central

    Ha, Taekjip; Tinnefeld, Philip

    2013-01-01

    Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of certain color and brightness but instead have their own ‘personalities’ regarding spectroscopic parameters, redox properties, size and water solubility, photostability and several more. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single molecule biophysical studies which was later overcome using Trolox through reducing/oxidizing system, but a boon for super-resolution imaging due to the controllable photoswitching. Understanding photophysics is critical in design and interpreting single molecule experiments. PMID:22404588

  19. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    SciTech Connect

    Mandal, Aritra; Tokmakoff, Andrei

    2015-11-21

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm{sup −1}. We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.

  20. Application of THz Vibrational Spectroscopy to Molecular Characterization and the Theoretical Fundamentals: An Illustration Using Saccharide Molecules.

    PubMed

    Zhang, Feng; Wang, Houng-Wei; Tominaga, Keisuke; Hayashi, Michitoshi; Hasunuma, Tomohisa; Kondo, Akihiko

    2017-02-01

    This work illustrates several theoretical fundamentals for the application of THz vibrational spectroscopy to molecular characterization in the solid state using two different types of saccharide systems as examples. Four subjects have been specifically addressed: (1) the qualitative differences in the molecular vibrational signatures monitored by THz and mid-IR vibrational spectroscopy; (2) the selection rules for THz vibrational spectroscopy as applied to crystalline and amorphous systems; (3) a normal mode simulation, using α-l-xylose as an example; and (4) a rigorous mode analysis to quantify the percentage contributions of the intermolecular and intramolecular vibrations to the normal mode of interest.

  1. Intermolecular vibrations and vibrational dynamics of a phenol⋯methanol binary complex studied by LIF spectroscopy

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Deb Pratim; Biswas, Souvick; Chakraborty, Tapas

    2017-04-01

    Low-frequency intermolecular vibrations in S0 and S1 states of p-fluorophenol (pFP) methanol binary complex have been studied using laser induced fluorescence (LIF) spectroscopy in a supersonic jet expansion. Vibrational fundamentals of five such modes show up in fluorescence excitation (FE) spectrum, and corresponding ground state frequencies are obtained measuring disperse fluorescence (DF) spectra. Signatures of strong coupling between the hydrogen bond stretching fundamental (σ01) and a ring mode of pFP moiety in S1 state are revealed. In comparison with the analogous pFP-water complex, the present system displays very low threshold (∼170 cm-1) for vibrational energy relaxation in S1 state.

  2. Isotope-Resolved and Charge-Sensitive Force Imaging Using Scanned Single Molecules

    NASA Astrophysics Data System (ADS)

    Sun, Yan; Rastawicki, Dominik; Liu, Yang; Mar, Warren; Manoharan, Hari; Miglio, Anna; Melinte, Sorin; Charlier, Jean-Christophe; Rignanese, Gian-Marco; He, Lianhua; Liu, Fang; Zhou, Aihui

    Originally conceived as surface imaging instruments, the scanning tunnelling microscope (STM) and the atomic force microscope (AFM) were recently used to probe molecular chemical bonds with exquisite sensitivity. Remarkably, molecule-functionalized scanning tips can also provide direct access to the inelastic electron tunneling spectrum (IETS) of the terminal molecule. Here we report atomic manipulation experiments addressing carbon monoxide (CO) isotopes at low temperatures. The unique and quantifiable dependence of the CO vibrational modes offers insight into tip-controlled force and charge sensing of surface adsorbates, subsurface defects, and quantum nanostructures. The specific behavior of the monitored vibrational modes originates from the interplay of interaction forces between the top electrode--a scanned tip functionalized with a single molecule--and the atomic scale force field surrounding the target atomically-assembled nanostructure. We also present density functional theory (DFT) computations that have been performed in order to scrutinize and visualize the vibrational spectroscopic fingerprints and local force fields.

  3. Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET.

    PubMed

    Le Reste, Ludovic; Hohlbein, Johannes; Gryte, Kristofer; Kapanidis, Achillefs N

    2012-06-06

    Dark quenchers are chromophores that primarily relax from the excited state to the ground state nonradiatively (i.e., are dark). As a result, they can serve as acceptors for Förster resonance energy transfer experiments without contributing significantly to background in the donor-emission channel, even at high concentrations. Although the advantages of dark quenchers have been exploited for ensemble bioassays, no systematic single-molecule study of dark quenchers has been performed, and little is known about their photophysical properties. Here, we present the first systematic single-molecule study of dark quenchers in conjunction with fluorophores and demonstrate the use of dark quenchers for monitoring multiple interactions and distances in multichromophore systems. Specifically, using double-stranded DNA standards labeled with two fluorophores and a dark quencher (either QSY7 or QSY21), we show that the proximity of a fluorophore and dark quencher can be monitored using the stoichiometry ratio available from alternating laser excitation spectroscopy experiments, either for single molecules diffusing in solution (using a confocal fluorescence) or immobilized on surfaces (using total-internal-reflection fluorescence). The latter experiments allowed characterization of the dark-quencher photophysical properties at the single-molecule level. We also use dark-quenchers to study the affinity and kinetics of binding of DNA Polymerase I (Klenow fragment) to DNA. The measured properties are in excellent agreement with the results of ensemble assays, validating the use of dark quenchers. Because dark-quencher-labeled biomolecules can be used in total-internal-reflection fluorescence experiments at concentrations of 1 μM or more without introducing a significant background, the use of dark quenchers should permit single-molecule Förster resonance energy transfer measurements for the large number of biomolecules that participate in interactions of moderate

  4. 2012 Gordon Research Conference on Vibrational Spectroscopy - Formal Schedule and Speaker/Poster Program

    SciTech Connect

    Geiger, Franz

    2012-08-10

    The Vibrational Spectroscopy conference brings together experimentalists and theoreticians working at the frontiers of modern vibrational spectroscopy, with a special emphasis on spectroscopies that probe the structure and dynamics of molecules in gases, liquids, and at interfaces. The conference explores the wide range of state-of-the-art techniques based on vibrational motion. These techniques span the fields of time-domain, high-resolution frequency-domain, spatially-resolved, nonlinear, and multidimensional spectroscopies. The conference highlights both the application of these techniques in chemistry, materials, biology, the environment, and medicine as well as the development of theoretical models that enable one to connect spectroscopic signatures to underlying molecular motions including chemical reaction dynamics. The conference goal is to advance the field of vibrational spectroscopy by bringing together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of molecular systems ranging from small polyatomic molecules to large biomolecules, nanomaterials, and environmental systems.

  5. Single-molecule manipulation experiments to explore friction and adhesion

    NASA Astrophysics Data System (ADS)

    Pawlak, R.; Kawai, S.; Meier, T.; Glatzel, T.; Baratoff, A.; Meyer, E.

    2017-03-01

    Friction forces, which arise when two bodies that are in contact are moved with respect to one another, are ubiquitous phenomena. Although various measurement tools have been developed to study these phenomena at all length scales, such investigations are highly challenging when tackling the scale of single molecules in motion on a surface. This work reviews the recent advances in single-molecule manipulation experiments performed at low temperature with the aim of understanding the fundamental frictional response of single molecules. Following the advent of ‘nanotribology’ in the field based on the atomic force microscopy technique, we will show the technical requirements to direct those studies at the single-molecule level. We will also discuss the experimental prerequisites needed to obtain and interpret the phenomena, such as the implementation of single-molecule manipulation techniques, the processing of the experimental data or their comparison with appropriate numerical models. Finally, we will report examples of the controlled vertical and lateral manipulation of long polymeric chains, graphene nanoribbons or single porphyrin molecules that systematically reveal friction-like characteristics while sliding over atomically clean surfaces.

  6. Complex formation dynamics in a single-molecule electronic device

    PubMed Central

    Wen, Huimin; Li, Wengang; Chen, Jiewei; He, Gen; Li, Longhua; Olson, Mark A.; Sue, Andrew C.-H.; Stoddart, J. Fraser; Guo, Xuefeng

    2016-01-01

    Single-molecule electronic devices offer unique opportunities to investigate the properties of individual molecules that are not accessible in conventional ensemble experiments. However, these investigations remain challenging because they require (i) highly precise device fabrication to incorporate single molecules and (ii) sufficient time resolution to be able to make fast molecular dynamic measurements. We demonstrate a graphene-molecule single-molecule junction that is capable of probing the thermodynamic and kinetic parameters of a host-guest complex. By covalently integrating a conjugated molecular wire with a pendent crown ether into graphene point contacts, we can transduce the physical [2]pseudorotaxane (de)formation processes between the electron-rich crown ether and a dicationic guest into real-time electrical signals. The conductance of the single-molecule junction reveals two-level fluctuations that are highly dependent on temperature and solvent environments, affording a nondestructive means of quantitatively determining the binding and rate constants, as well as the activation energies, for host-guest complexes. The thermodynamic processes reveal the host-guest binding to be enthalpy-driven and are consistent with conventional 1H nuclear magnetic resonance titration experiments. This electronic device opens up a new route to developing single-molecule dynamics investigations with microsecond resolution for a broad range of chemical and biochemical applications. PMID:28138528

  7. Towards physiological complexity with in vitro single-molecule biophysics

    PubMed Central

    Duzdevich, Daniel; Greene, Eric C.

    2013-01-01

    Single-molecule biology has matured in recent years, driven to greater sophistication by the development of increasingly advanced experimental techniques. A progressive appreciation for its unique strengths is attracting research that spans an exceptionally broad swath of physiological phenomena—from the function of nucleosomes to protein diffusion in the cell membrane. Newfound enthusiasm notwithstanding, the single-molecule approach is limited to an intrinsically defined set of biological questions; such limitation applies to all experimental approaches, and an explicit statement of the boundaries delineating each set offers a guide to most fruitfully orienting in vitro single-molecule research in the future. Here, we briefly describe a simple conceptual framework to categorize how submolecular, molecular and intracellular processes are studied. We highlight the domain of single-molecule biology in this scheme, with an emphasis on its ability to probe various forms of heterogeneity inherent to populations of discrete biological macromolecules. We then give a general overview of our high-throughput DNA curtain methodology for studying protein–nucleic acid interactions, and by contextualizing it within this framework, we explore what might be the most enticing avenues of future research. We anticipate that a focus on single-molecule biology's unique strengths will suggest a new generation of experiments with greater complexity and more immediately translatable physiological relevance. PMID:23267187

  8. Measuring correlated electronic and vibrational spectral dynamics using line shapes in two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

    Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.; Fleming, Graham R.

    2015-05-07

    Two-dimensional electronic-vibrational (2DEV) spectroscopy is an experimental technique that shows great promise in its ability to provide detailed information concerning the interactions between the electronic and vibrational degrees of freedom in molecular systems. The physical quantities 2DEV is particularly suited for measuring have not yet been fully determined, nor how these effects manifest in the spectra. In this work, we investigate the use of the center line slope of a peak in a 2DEV spectrum as a measure of both the dynamic and static correlations between the electronic and vibrational states of a dye molecule in solution. We show how this center line slope is directly related to the solvation correlation function for the vibrational degrees of freedom. We also demonstrate how the strength with which the vibration on the electronic excited state couples to its bath can be extracted from a set of 2DEV spectra. These analytical techniques are then applied to experimental data from the laser dye 3,3′-diethylthiatricarbocyanine iodide in deuterated chloroform, where we determine the lifetime of the correlation between the electronic transition frequency and the transition frequency for the backbone C = C stretch mode to be ∼1.7 ps. Furthermore, we find that on the electronic excited state, this mode couples to the bath ∼1.5 times more strongly than on the electronic ground state.

  9. ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

    NASA Astrophysics Data System (ADS)

    Nibbering, Erik T. J.; Fidder, Henk; Pines, Ehud

    2005-05-01

    Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

  10. Single molecule dynamics at a mechanically controllable break junction in solution at room temperature.

    PubMed

    Konishi, Tatsuya; Kiguchi, Manabu; Takase, Mai; Nagasawa, Fumika; Nabika, Hideki; Ikeda, Katsuyoshi; Uosaki, Kohei; Ueno, Kosei; Misawa, Hiroaki; Murakoshi, Kei

    2013-01-23

    The in situ observation of geometrical and electronic structural dynamics of a single molecule junction is critically important in order to further progress in molecular electronics. Observations of single molecular junctions are difficult, however, because of sensitivity limits. Here, we report surface-enhanced Raman scattering (SERS) of a single 4,4'-bipyridine molecule under conditions of in situ current flow in a nanogap, by using nano-fabricated, mechanically controllable break junction (MCBJ) electrodes. When adsorbed at room temperature on metal nanoelectrodes in solution to form a single molecule junction, statistical analysis showed that nontotally symmetric b(1) and b(2) modes of 4,4'-bipyridine were strongly enhanced relative to observations of the same modes in solid or aqueous solutions. Significant changes in SERS intensity, energy (wavenumber), and selectivity of Raman vibrational bands that are coincident with current fluctuations provide information on distinct states of electronic and geometrical structure of the single molecule junction, even under large thermal fluctuations occurring at room temperature. We observed the dynamics of 4,4'-bipyridine motion between vertical and tilting configurations in the Au nanogap via b(1) and b(2) mode switching. A slight increase in the tilting angle of the molecule was also observed by noting the increase in the energies of Raman modes and the decrease in conductance of the molecular junction.

  11. Vibrational levels of p-xylene cation determined by mass-analyzed threshold ionization spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Bing; Aigner, Udo; Ludwig Selzle, Heinrich; William Schlag, Edward

    2003-10-01

    Mass-analyzed threshold ionization (MATI) spectroscopy and two-color resonant two-photon ionization method were used for the determination of the vibrational levels of the p-xylene cation. The MATI spectrum was recorded via the 0 0 vibrationless level of the S 1 state of p-xylene. The spectrum shows a rich structure and some vibrational frequencies of the cation are determined. The experimental findings are well supported by ab initio calculation.

  12. A practical guide for nuclear resonance vibrational spectroscopy (NRVS) of biochemical samples and model compounds.

    PubMed

    Wang, Hongxin; Alp, Esen Ercan; Yoda, Yoshitaka; Cramer, Stephen P

    2014-01-01

    Nuclear resonance vibrational spectroscopy (NRVS) has been used by physicists for many years. However, it is still a relatively new technique for bioinorganic users. This technique yields a vibrational spectrum for a specific element, which can be easily interpreted. Furthermore, isotopic labeling allows for site-specific experiments. In this chapter, we discuss how to access specific beamlines, what kind of equipment is used in NRVS, and how the sample should be prepared and the data collected and analyzed.

  13. Manipulation and Motion of Organelles and Single Molecules in Living Cells.

    PubMed

    Norregaard, Kamilla; Metzler, Ralf; Ritter, Christine M; Berg-Sørensen, Kirstine; Oddershede, Lene B

    2017-03-08

    The biomolecule is among the most important building blocks of biological systems, and a full understanding of its function forms the scaffold for describing the mechanisms of higher order structures as organelles and cells. Force is a fundamental regulatory mechanism of biomolecular interactions driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function. In vivo studies are, however, challenged by the complexity of the cell. In this review, we start with presenting relevant theoretical tools for analyzing single molecule data obtained in intracellular environments followed by a description of state-of-the art visualization techniques. The most commonly used force spectroscopy techniques, namely optical tweezers, magnetic tweezers, and atomic force microscopy, are described in detail, and their strength and limitations related to in vivo experiments are discussed. Finally, recent exciting discoveries within the field of in vivo manipulation and dynamics of single molecule and organelles are reviewed.

  14. Systems nanobiology: from quantitative single molecule biophysics to microfluidic-based single cell analysis.

    PubMed

    Martini, Joerg; Hellmich, Wibke; Greif, Dominik; Becker, Anke; Merkle, Thomas; Ros, Robert; Ros, Alexandra; Toensing, Katja; Anselmetti, Dario

    2007-01-01

    Detailed and quantitative information about structure-function relation, concentrations and interaction kinetics of biological molecules and subcellular components is a key prerequisite to understand and model cellular organisation and temporal dynamics. In systems nanobi-ology, cellular processes are quantitatively investigated at the sensitivity level of single molecules and cells. This approach provides direct access to biomolecular information without being statistically ensemble-averaged, their associated distribution functions, and possible subpopulations. Moreover at the single cell level, the interplay of regulated genomic information and proteomic variabilities can be investigated and attributed to functional peculiarities. These requirements necessitate the development of novel and ultrasensitive methods and instruments for single molecule detection, microscopy and spectroscopy for analysis without the need of amplification and preconcentration. In this chapter, we present three methodological applications that demonstrate how quantitative informations can be accessed that are representative for cellular processes or single cell analysis like gene expression regulation, intracellular protein translocation dynamics, and single cell protein fingerprinting. First, the interaction kinetics of transcriptionally regulated DNA-protein interaction can be quantitatively investigated with single molecule force spectroscopy allowing a molecular affinity ranking. Second, intracellular protein dynamics for a transcription regulator migrating form the nucleus to the cytoplasm can be quantitatively monitored by photoactivable GFP and two-photon laser scanning microscopy. And third, a microfluidic-based method for label-free single cell proteomics and fingerprinting and first label-free single cell electropherograms are presented which include the manipulation and steering of single cells in a microfluidic device.

  15. 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.

  16. Tracking single molecules at work in living cells.

    PubMed

    Kusumi, Akihiro; Tsunoyama, Taka A; Hirosawa, Kohichiro M; Kasai, Rinshi S; Fujiwara, Takahiro K

    2014-07-01

    Methods for imaging and tracking single molecules conjugated with fluorescent probes, called single-molecule tracking (SMT), are now providing researchers with the unprecedented ability to directly observe molecular behaviors and interactions in living cells. Current SMT methods are achieving almost the ultimate spatial precision and time resolution for tracking single molecules, determined by the currently available dyes. In cells, various molecular interactions and reactions occur as stochastic and probabilistic processes. SMT provides an ideal way to directly track these processes by observing individual molecules at work in living cells, leading to totally new views of the biochemical and molecular processes used by cells whether in signal transduction, gene regulation or formation and disintegration of macromolecular complexes. Here we review SMT methods, summarize the recent results obtained by SMT, including related superresolution microscopy data, and describe the special concerns when SMT applications are shifted from the in vitro paradigms to living cells.

  17. 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.

  18. Single-molecule mechanochemical sensing using DNA origami nanostructures.

    PubMed

    Koirala, Deepak; Shrestha, Prakash; Emura, Tomoko; Hidaka, Kumi; Mandal, Shankar; Endo, Masayuki; Sugiyama, Hiroshi; Mao, Hanbin

    2014-07-28

    While single-molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single-molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7-tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet-derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single-molecule sensing with improved throughput.

  19. 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.

  20. Extending single-molecule microscopy using optical Fourier processing.

    PubMed

    Backer, Adam S; Moerner, W E

    2014-07-17

    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.

  1. 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

  2. Quantum dots find their stride in single molecule tracking

    PubMed Central

    Bruchez, Marcel P.

    2011-01-01

    Thirteen years after the demonstration of quantum dots as biological imaging agents, and nine years after the initial commercial introduction of bioconjugated quantum dots, the brightness and photostability of the quantum dots has enabled a range of investigations using single molecule tracking. These materials are being routinely utilized by a number of groups to track the dynamics of single molecules in reconstituted biophysical systems and on living cells, and are especially powerful for investigations of single molecules over long timescales with short exposure times and high pointing accuracy. New approaches are emerging where the quantum dots are used as “hard-sphere” probes for intracellular compartments. Innovations in quantum dot surface modification are poised to substantially expand the utility of these materials. PMID:22055494

  3. 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.

  4. Single-molecule chemistry and physics explored by low-temperature scanning probe microscopy.

    PubMed

    Swart, Ingmar; Gross, Leo; Liljeroth, Peter

    2011-08-28

    It is well known that scanning probe techniques such as scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) routinely offer atomic scale information on the geometric and the electronic structure of solids. Recent developments in STM and especially in non-contact AFM have allowed imaging and spectroscopy of individual molecules on surfaces with unprecedented spatial resolution, which makes it possible to study chemistry and physics at the single molecule level. In this feature article, we first review the physical concepts underlying image contrast in STM and AFM. We then focus on the key experimental considerations and use selected examples to demonstrate the capabilities of modern day low-temperature scanning probe microscopy in providing chemical insight at the single molecule level.

  5. Single-molecule and single-nanoparticle SERS: from fundamental mechanisms to biomedical applications.

    PubMed

    Qian, X-M; Nie, S M

    2008-05-01

    This tutorial review discusses a new class of colloidal metal nanoparticles that is able to enhance the efficiencies of surface-enhanced Raman scattering (SERS) by as much as 10(14)-10(15) fold. This enormous enhancement allows spectroscopic detection and identification of single molecules located on the nanoparticle surface or at the junction of two particles under ambient conditions. Considerable progress has been made in understanding the enhancement mechanisms, including definitive evidence for the single-molecule origin of fluctuating SERS signals. For applications, SERS nanoparticle tags have been developed based on the use of embedded reporter molecules and a silica or polymer encapsulation layer. The SERS nanoparticle tags are capable of providing detailed spectroscopic information and are much brighter than semiconductor quantum dots in the near-infrared spectral window. These properties have raised new opportunities for multiplexed molecular diagnosis and in vivo Raman spectroscopy and imaging.

  6. Vibrational energy dynamics of water studied with ultrafast Stokes and anti-Stokes Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Zhaohui; Pang, Yoonsoo; Dlott, Dana D.

    2004-10-01

    The transient Stokes Raman spectroscopy method is introduced to study the dynamics of OH-stretching vibrations in water excited by ultrashort infrared pulses. The combination of Stokes and anti-Stokes Raman probing allows the the absorption and emission contributions to be measured separately. Experiments with 3400 cm -1 pumping of OH-stretching of HOD solute in D 2O solvent are reported. The Stokes Raman method is used to study the delay between the excited-state decay and the ground-state recovery, the vibrational Stokes shift, and the generation of weakened hydrogen bonding due to heat released by vibrational relaxation.

  7. Surface Vibrational Spectroscopy on Shear-Aligned Poly(tetrafluoroethylene) Films

    NASA Astrophysics Data System (ADS)

    Ji, Na; Ostroverkhov, Victor; Lagugné-Labarthet, Francois; Shen, Y. R.

    2004-03-01

    Sum-frequency vibrational spectroscopy was used to obtain the first surface vibrational spectra of shear-deposited highly-oriented poly(tetrafluoroethylene) (PTFE) thin films. The analysis of spectra taken with different polarization combinations of the input and output beams allowed us to assess orientation of the polymer chains on the film surface. The surface PTFE chains appeared to lie along the shearing direction. Vibrational modes observed at 1142 and 1204 cm-1 were found to have the E1 symmetry, in support of some earlier analysis in the long-lasting controversy over the assignment of these modes.

  8. Theoretical and experimental vibrational spectroscopy study on rotational isomer of 4-phenylbutylamine

    NASA Astrophysics Data System (ADS)

    Ünal, A.; Okur, M.

    2017-02-01

    The possible four stable rotational isomers of 4-phenylbutylamine (4PBA) molecule were experimentally and theoretically studied by vibrational spectroscopy. The FT-IR (4000-400 cm-1) and Raman (3700-60 cm-1) spectra of 4PBA were recorded at room temperature in liquid phase. The complete vibrational wavenumbers and corresponding vibrational assignments of 4PBA molecule were discussed assisted with B3LYP/6-311++G(d,p) level of theory along with scaled quantum mechanics force field (SQM-FF) method. Results from experimental and theoretical data the most stable form of 4PBA molecule was obtained.

  9. Inversion vibration of PH3+(X~ 2A2'') studied by zero kinetic energy photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Li, Juan; Hao, Yusong; Zhou, Chang; Mo, Yuxiang

    2006-08-01

    We report the first rotationally resolved spectroscopic studies on PH3+(X˜A2″2) using zero kinetic energy photoelectron spectroscopy and coherent VUV radiation. The spectra about 8000cm-1 above the ground vibrational state of PH3+(X˜A2″2) have been recorded. We observed the vibrational energy level splittings of PH3+(X˜A2″2) due to the tunneling effect in the inversion (symmetric bending) vibration (ν2+). The energy splitting for the first inversion vibrational state (0+/0-) is 5.8cm-1. The inversion vibrational energy levels, rotational constants, and adiabatic ionization energies (IEs) for ν2+=0-16 have been determined. The bond angles between the neighboring P-H bonds and the P-H bond lengths are also obtained using the experimentally determined rotational constants. With the increasing of the inversion vibrational excitations (ν2+), the bond lengths (P-H) increase a little and the bond angles (H-P-H) decrease a lot. The inversion vibrational energy levels have also been calculated by using one dimensional potential model and the results are in good agreement with the experimental data for the first several vibrational levels. In addition to inversion vibration, we also observed firstly the other two vibrational modes: the symmetric P-H stretching vibration (ν1+) and the degenerate bending vibration (ν4+). The fundamental frequencies for ν1+ and ν4+ are 2461.6 (±2) and 1043.9 (±2)cm-1, respectively. The first IE for PH3 was determined as 79670.9 (±1)cm-1.

  10. Separation of overlapping vibrational peaks in terahertz spectra using two-dimensional correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Hoshina, Hiromichi; Ishii, Shinya; Otani, Chiko

    2014-07-01

    In this study, the terahertz (THz) absorption spectra of poly(3-hydroxybutyrate) (PHB) were measured during isothermal crystallization at 90-120 °C. The temporal changes in the absorption spectra were analyzed using two-dimensional correlation spectroscopy (2DCOS). In the asynchronous plot, cross peaks were observed around 2.4 THz, suggesting that two vibrational modes overlap in the raw spectrum. By comparing this to the peak at 2.9 THz corresponding to the stretching mode of the helical structure of PHB and the assignment obtained using polarization spectroscopy, we concluded that the high-frequency band could be attributed to the vibration of the helical structure and the low-frequency band to the vibration between the helical structures. The exact frequencies of the overlapping vibrational bands and their assignments provide a new means to inspect the thermal behavior of the intermolecular vibrational modes. The large red-shift of the interhelix vibrational mode suggests a large anharmonicity in the vibrational potential.

  11. Vibrational spectroscopy and the development of new force fields for biological molecules.

    PubMed

    Gerber, R B; Chaban, G M; Gregurick, S K; Brauer, B

    2003-03-01

    The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy.

  12. Multicolour single molecule imaging on cells using a supercontinuum source

    PubMed Central

    Webb, Stephen E. D.; Zanetti-Domingues, Laura; Coles, Benjamin C.; Rolfe, Daniel J.; Wareham, Richard J.; Martin-Fernandez, Marisa L.

    2012-01-01

    Multicolour single molecule fluorescence imaging enables the study of multiple proteins in the membranes of living cells. We describe the use of a supercontinuum laser as the excitation source, show its comparability with multiplexed single-wavelength lasers and demonstrate that it can be used to study membrane proteins such as the ErbB receptor family. We discuss the benefits of white-light sources for single molecule fluorescence, in particular their ease of use and the freedom to use the most appropriate dye without being constrained by available laser wavelengths. PMID:22435089

  13. An improved surface passivation method for single-molecule studies.

    PubMed

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

    2014-12-01

    We report a surface passivation method based on dichlorodimethylsilane (DDS)-Tween-20 for in vitro single-molecule studies, which, under the conditions tested here, more efficiently prevented nonspecific binding of biomolecules than the standard poly(ethylene glycol) surface. The DDS-Tween-20 surface was simple and inexpensive to prepare and did 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.

  14. Strongly enhanced field-dependent single-molecule electroluminescence

    NASA Astrophysics Data System (ADS)

    Lee, Tae-Hee; Gonzalez, Jose I.; Dickson, Robert M.

    2002-08-01

    Individual, strongly electroluminescent Agn molecules (n = 28 atoms) have been electrically written within otherwise nonemissive silver oxide films. Exhibiting characteristic single-molecule behavior, these individual room-temperature molecules exhibit extreme electroluminescence enhancements (>104 vs. bulk and dc excitation on a per molecule basis) when excited with specific ac frequencies. Occurring through field extraction of electrons with subsequent reinjection and radiative recombination, single-molecule electroluminescence is enhanced by a general mechanism that avoids slow bulk material response. Thus, while we detail strong electroluminescence from single, highly fluorescent Agn molecules, this mechanism also yields strong ac-excited electroluminescence from similarly prepared, but otherwise nonemissive, individual Cu nanoclusters.

  15. Vibrational spectroscopy and intramolecular dynamics of 1-butyne.

    PubMed

    Portnov, Alexander; Rosenwaks, Salman; Bar, Ilana

    2004-09-22

    Photodissociation of jet-cooled vibrationally excited 1-butyne, C(2)H(5)C[Triple Bond]C[Single Bond]H, coupled with mass spectrometric detection of H photofragments, facilitated measurements of action spectra and Doppler profiles, expressing the yield of the ensuing fragments versus the vibrational excitation and UV probe lasers, respectively. Both the action spectra and the simultaneously measured room temperature photoacoustic spectra in the 2nu(1), 3nu(1), and 4nu(1) C[Single Bond]H acetylenic stretch regions exhibit unresolved rotational envelopes with significant narrowing of the former due to temperature-related change in the rotational structure. The narrowing of the action spectrum in the 3nu(1) region exposed a resonance splitting, implying intramolecular vibrational energy redistribution (IVR) time of approximately 1 ps. Asymmetric rotor simulation of the band contours provided the rotational constants and estimates for the homogeneous broadening arising from IVR to the bath vibrational states. The homogenous linewidth of 4nu(1) is anomalously narrower than that of 2nu(1) and 3nu(1), indicating a longer lived 4nu(1) state despite the increasing background state density, suggestive of a lack of low-order resonances or of mode-specific coupling with the bath states. The Doppler profiles indicate that the H photofragments are released with low average translational energies, pointing to an indirect dissociation process occurring after internal conversion (IC) to the ground electronic state or after IC and isomerization to butadiene.

  16. Hydrogen Bonding and Vibrational Spectroscopy: A Theoretical Study

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.

    2005-01-01

    Effects of hydrogen bonding on vibrational spectra are studied for several hydrogen-bonded complexes, in which hydrogen bonding ranges from weak (<5 kcal/mol) to very strong (>25 kcal/mol). The systems studied include complexes of inorganic acids and salts with water and ammonia, as well as complexes of several organic molecules (nitriles and amino acids) with water. Since anharmonic effects are very strong in hydrogen-bonded systems, anharmonic vibrational frequencies and infrared intensities are computed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. The most common spectral effects induced by hydrogen bonding are red shifts of stretching vibrational frequencies ranging from approx.200/cm to over 2000/cm and significant increases of infrared intensities for those bonds that participate in hydrogen bonding. However, some systems (e.g. nitrile-water complexes) exhibit shifts in the opposite direction (to the blue) upon formation of hydrogen bonds.

  17. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  18. Electron-vibron coupling effects on electron transport via a single-molecule magnet

    NASA Astrophysics Data System (ADS)

    McCaskey, Alexander; Yamamoto, Yoh; Warnock, Michael; Burzurí, Enrique; van der Zant, Herre S. J.; Park, Kyungwha

    2015-03-01

    We investigate how the electron-vibron coupling influences electron transport via an anisotropic magnetic molecule, such as a single-molecule magnet (SMM) Fe4, by using a model Hamiltonian with parameter values obtained from density-functional theory (DFT). The magnetic anisotropy parameters, vibrational energies, and electron-vibron coupling strengths of the Fe4 are computed using DFT. A giant spin model is applied to the Fe4 with only two charge states, specifically a neutral state with a total spin S =5 and a singly charged state with S =9 /2 , which is consistent with our DFT result and experiments on Fe4 single-molecule transistors. In sequential electron tunneling, we find that the magnetic anisotropy gives rise to new features in the conductance peaks arising from vibrational excitations. In particular, the peak height shows a strong, unusual dependence on the direction as well as magnitude of applied B field. The magnetic anisotropy also introduces vibrational satellite peaks whose position and height are modified with the direction and magnitude of applied B field. Furthermore, when multiple vibrational modes with considerable electron-vibron coupling have energies close to one another, a low-bias current is suppressed, independently of gate voltage and applied B field, although that is not the case for a single mode with a similar electron-vibron coupling. In the former case, the conductance peaks reveal a stronger B -field dependence than in the latter case. The new features appear because the magnetic anisotropy barrier is of the same order of magnitude as the energies of vibrational modes with significant electron-vibron coupling. Our findings clearly show the interesting interplay between magnetic anisotropy and electron-vibron coupling in electron transport via the Fe4. Similar behavior can be observed in transport via other anisotropic magnetic molecules.

  19. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid

    NASA Astrophysics Data System (ADS)

    Shaw, Daniel J.; Adamczyk, Katrin; Frederix, Pim W. J. M.; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Hoskisson, Paul A.; Hunt, Neil T.

    2015-06-01

    The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm-1 region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

  20. Fourier transform spectroscopy in the vibrational fingerprint region with a birefringent interferometer.

    PubMed

    Réhault, J; Borrego-Varillas, R; Oriana, A; Manzoni, C; Hauri, C P; Helbing, J; Cerullo, G

    2017-02-20

    We introduce a birefringent interferometer for Fourier transform (FT) spectroscopy in the mid-infrared, covering the vibrational fingerprint region (5-10 µm, 1000-2000 cm-1), which is crucial for molecular identification. Our interferometer employs the crystal calomel (Hg2Cl2), which combines high birefringence (ne-no≈0.55) with a broad transparency range (0.38-20 µm). We adopt a design based on birefringent wedges, which is simple and compact and guarantees excellent delay accuracy and long-term stability. We demonstrate FTIR spectroscopy, with a frequency resolution of 3 cm-1, as well as two-dimensional IR (2DIR) spectroscopy. Our setup can be extended to other spectroscopic modalities such as vibrational circular dichroism and step-scan FT spectroscopy.

  1. A plutonium-based single-molecule magnet.

    PubMed

    Magnani, N; Colineau, E; Griveau, J-C; Apostolidis, C; Walter, O; Caciuffo, R

    2014-08-04

    The magnetic properties of the 5f(5) [tris-(tri-1-pyrazolylborato)-plutonium(III)] complex have been investigated by ac susceptibility measurements, showing it to be the first plutonium single-molecule magnet; its magnetic relaxation slows down with decreasing temperature through a thermally activated mechanism followed by a quantum tunnelling regime below 5 K.

  2. Fast temporal fluctuations in single-molecule junctions.

    PubMed

    Ochs, Roif; Secker, Daniel; Elbing, Mark; Mayor, Marcel; Weber, Heiko B

    2006-01-01

    The noise within the electrical current through single-molecule junctions is studied cryogenic temperature. The organic sample molecules were contacted with the mechanically controlled break-junction technique. The noise spectra refer to a where only few Lorentzian fluctuators occur in the conductance. The frequency dependence shows qualitative variations from sample to sample.

  3. Single-molecule choreography between telomere proteins and G quadruplexes.

    PubMed

    Hopfner, Karl-Peter

    2014-06-10

    Telomeric DNA binds proteins to protect chromosome ends, but it also adopts G quadruplex (GQ) structures. Two new studies by Hwang and colleagues (in this issue of Structure) and Ray and colleagues (published elsewhere) use single molecule imaging to reveal how GQs affect the binding of different telomere associated proteins. The data suggest that GQs play important roles in regulating accessibility of telomeres.

  4. Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose

    SciTech Connect

    Liu, Y.-S.; Luo, Y.; Baker, J. O.; Zeng, Y.; Himmel, M. E.; Smith, S.; Ding, S.-Y.

    2009-12-01

    This report seeks to elucidate the role of cellobiohydrolase-I (CBH I) in the hydrolysis of crystalline cellulose. A single-molecule approach uses various imaging techniques to investigate the surface structure of crystalline cellulose and changes made in the structure by CBH I.

  5. The properties and applications of single-molecule DNA sequencing

    PubMed Central

    2011-01-01

    Single-molecule sequencing enables DNA or RNA to be sequenced directly from biological samples, making it well-suited for diagnostic and clinical applications. Here we review the properties and applications of this rapidly evolving and promising technology. PMID:21349208

  6. Statistics and Related Topics in Single-Molecule Biophysics

    PubMed Central

    Qian, Hong; Kou, S. C.

    2014-01-01

    Since the universal acceptance of atoms and molecules as the fundamental constituents of matter in the early twentieth century, molecular physics, chemistry and molecular biology have all experienced major theoretical breakthroughs. To be able to actually “see” biological macromolecules, one at a time in action, one has to wait until the 1970s. Since then the field of single-molecule biophysics has witnessed extensive growth both in experiments and theory. A distinct feature of single-molecule biophysics is that the motions and interactions of molecules and the transformation of molecular species are necessarily described in the language of stochastic processes, whether one investigates equilibrium or nonequilibrium living behavior. For laboratory measurements following a biological process, if it is sampled over time on individual participating molecules, then the analysis of experimental data naturally calls for the inference of stochastic processes. The theoretical and experimental developments of single-molecule biophysics thus present interesting questions and unique opportunity for applied statisticians and probabilists. In this article, we review some important statistical developments in connection to single-molecule biophysics, emphasizing the application of stochastic-process theory and the statistical questions arising from modeling and analyzing experimental data. PMID:25009825

  7. Single molecule thermodynamics and nanopore-based thermometry

    NASA Astrophysics Data System (ADS)

    Reiner, Joseph E.; Robertson, Joseph W. F.; Burden, Lisa K.; Burden, Daniel L.; Kasianowicz, John J.

    2012-02-01

    The nanopore-based resistive pulse method measures the reduction in ionic current caused by the interaction of single molecules with the pore. It has great promise in addressing problems across a range of fields that include biomedicine and genomics. The technique requires the residence time of the molecules in the pore to exceed the inverse bandwidth of the detection system (˜ 10 μs). Efforts are underway to improve this by molecular modification of the pore wall, but little effort has focused on modifying the solution conditions in and around the pore. We address this issue by precisely controlling the solution temperature around a protein ion channel (alpha hemolysin) via laser-induced heating of gold nanoparticles. In this technique, the nanopore serves dual roles as both a highly local thermometer and single molecule sensor. Preliminary data suggests that the solution temperature can be controlled over a wide range, the nanopore conductance can be used to directly measure rapid changes in temperature, and the temperature change can dramatically alter the interaction kinetics of single molecules with the nanopore. The method will improve the development of biochip sensors and lead to a new platform for single molecule thermodynamic studies.

  8. 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.

  9. Single Molecule Fluorescence Microscopy on Planar Supported Bilayers

    PubMed Central

    Axmann, Markus; Schütz, Gerhard J.; Huppa, Johannes B.

    2015-01-01

    In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background in optics and laser physics to a discipline that is now enjoying vivid attention by life-scientists of all venues 1. This is because single molecule imaging has the unique potential to reveal protein behavior in situ in living cells and uncover cellular organization with unprecedented resolution below the diffraction limit of visible light 2. Glass-supported planar lipid bilayers (SLBs) are a powerful tool to bring cells otherwise growing in suspension in close enough proximity to the glass slide so that they can be readily imaged in noise-reduced Total Internal Reflection illumination mode 3,4. They are very useful to study the protein dynamics in plasma membrane-associated events as diverse as cell-cell contact formation, endocytosis, exocytosis and immune recognition. Simple procedures are presented how to generate highly mobile protein-functionalized SLBs in a reproducible manner, how to determine protein mobility within and how to measure protein densities with the use of single molecule detection. It is shown how to construct a cost-efficient single molecule microscopy system with TIRF illumination capabilities and how to operate it in the experiment. PMID:26555335

  10. Vibrational Spectroscopy of the CCl[subscript 4] v[subscript 1] Mode: Theoretical Prediction of Isotopic Effects

    ERIC Educational Resources Information Center

    Gaynor, James D.; Wetterer, Anna M.; Cochran, Rea M.; Valente, Edward J.; Mayer, Steven G.

    2015-01-01

    Raman spectroscopy is a powerful experimental technique, yet it is often missing from the undergraduate physical chemistry laboratory curriculum. Tetrachloromethane (CCl[subscript 4]) is the ideal molecule for an introductory vibrational spectroscopy experiment and the symmetric stretch vibration contains fine structure due to isotopic variations…

  11. Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

    NASA Astrophysics Data System (ADS)

    Meroz, Yasmine

    2015-06-01

    In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

  12. Single Molecule Study of DNA Organization and Recombination

    NASA Astrophysics Data System (ADS)

    Xiao, Botao

    We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force

  13. The optics inside an automated single molecule array analyzer

    NASA Astrophysics Data System (ADS)

    McGuigan, William; Fournier, David R.; Watson, Gary W.; Walling, Les; Gigante, Bill; Duffy, David C.; Rissin, David M.; Kan, Cheuk W.; Meyer, Raymond E.; Piech, Tomasz; Fishburn, Matthew W.

    2014-02-01

    Quanterix and Stratec Biomedical have developed an instrument that enables the automated measurement of multiple proteins at concentration ~1000 times lower than existing immunoassays. The instrument is based on Quanterix's proprietary Single Molecule Array technology (Simoa™ ) that facilitates the detection and quantification of biomarkers previously difficult to measure, thus opening up new applications in life science research and in-vitro diagnostics. Simoa is based on trapping individual beads in arrays of femtoliter-sized wells that, when imaged with sufficient resolution, allows for counting of single molecules associated with each bead. When used to capture and detect proteins, this approach is known as digital ELISA (Enzyme-linked immunosorbent assay). The platform developed is a merger of many science and engineering disciplines. This paper concentrates on the optical technologies that have enabled the development of a fully-automated single molecule analyzer. At the core of the system is a custom, wide field-of-view, fluorescence microscope that images arrays of microwells containing single molecules bound to magnetic beads. A consumable disc containing 24 microstructure arrays was developed previously in collaboration with Sony DADC. The system cadence requirements, array dimensions, and requirement to detect single molecules presented significant optical challenges. Specifically, the wide field-of-view needed to image the entire array resulted in the need for a custom objective lens. Additionally, cost considerations for the system required a custom solution that leveraged the image processing capabilities. This paper will discuss the design considerations and resultant optical architecture that has enabled the development of an automated digital ELISA platform.

  14. Single-Molecule Fluorescence Imaging for Studying Organic, Organometallic, and Inorganic Reaction Mechanisms

    SciTech Connect

    Blum, Suzanne A.

    2016-05-24

    The reactive behavior of individual molecules is seldom observed, because we usually measure the average properties of billions of molecules. What we miss is important: the catalytic activity of less than 1% of the molecules under observation can dominate the outcome of a chemical reaction seen at a macroscopic level. Currently available techniques to examine reaction mechanisms (such as nuclear magnetic resonance spectroscopy and mass spectrometry) study molecules as an averaged ensemble. These ensemble techniques are unable to detect minor components (under ~1%) in mixtures or determine which components in the mixture are responsible for reactivity and catalysis. In the field of mechanistic chemistry, there is a resulting heuristic device that if an intermediate is very reactive in catalysis, it often cannot be observed (termed “Halpern’s Rule” ). Ultimately, the development of single-molecule imaging technology could be a powerful tool to observe these “unobservable” intermediates and active catalysts. Single-molecule techniques have already transformed biology and the understanding of biochemical processes. The potential of single-molecule fluorescence microscopy to address diverse chemical questions, such as the chemical reactivity of organometallic or inorganic systems with discrete metal complexes, however, has not yet been realized. In this respect, its application to chemical systems lags significantly behind its application to biophysical systems. This transformative imaging technique has broad, multidisciplinary impact with the potential to change the way the chemistry community studies reaction mechanisms and reactivity distributions, especially in the core area of catalysis.

  15. Single-stranded DNA scanning and deamination with Single molecule resolution

    NASA Astrophysics Data System (ADS)

    Rueda, David

    2012-04-01

    Over the past decade, single-molecule fluorescence resonance energy transfer spectroscopy (smFRET) has become an increasingly popular tool to study the structural dynamics of biopolymers, such as DNA, RNA and proteins. The most attractive aspect of single-molecule experiments is that, unlike ensemble-averaged techniques, they directly reveal the structural dynamics of individual molecules, which would otherwise be hidden in ensemble-averaged experiments. Here, we will present a novel single molecule assay to study, for the first time, scanning of an enzyme (APOBEC3G, involved in the defense against HIV) on single stranded DNA (ssDNA). We have investigated the ssDNA scanning and activity of Apo3G with smFRET. Our data show that Apo3G scans ssDNA randomly and bidirectionally with average excursion lengths of ˜ 10 å and ˜1 s-1 scanning rates. Apo3G quasi-localization is observed on highly reactive motifs located near the one end of the ssDNA. Motif-dependent ssDNA bending is also observed, where the bending is maximal for highly reactive targets located near the DNA end. Interestingly, both the Apo3G scanning and Apo3G-induced ssDNA bending is reduced with lowered ionic strength, indicating that Apo3G motion on ssDNA is facilitated by salt by reducing `electrostatic friction'. Although scanning is random, asymmetric catalytic orientation may be the reason for Apo3G directional activity.

  16. Development of new photon-counting detectors for single-molecule fluorescence microscopy

    PubMed Central

    Michalet, X.; Colyer, R. A.; Scalia, G.; Ingargiola, A.; Lin, R.; Millaud, J. E.; Weiss, S.; Siegmund, Oswald H. W.; Tremsin, Anton S.; Vallerga, John V.; Cheng, A.; Levi, M.; Aharoni, D.; Arisaka, K.; Villa, F.; Guerrieri, F.; Panzeri, F.; Rech, I.; Gulinatti, A.; Zappa, F.; Ghioni, M.; Cova, S.

    2013-01-01

    Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level. PMID:23267185

  17. Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics.

    PubMed

    Holmstrom, Erik D; Dupuis, Nicholas F; Nesbitt, David J

    2014-01-07

    Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10(-11) liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20-100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation.

  18. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    SciTech Connect

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-03-10

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies o1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. Furthermore, the technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ~10nm, simultaneously combined with imaging in the electron microscope.

  19. Expanded Choices for Vibration-Rotation Spectroscopy in the Physical Chemistry Teaching Laboratory

    NASA Astrophysics Data System (ADS)

    Schmitz, Joel R.; Dolson, David A.

    2015-06-01

    Many third-year physical chemistry laboratory students in the US analyze the vibration-rotation spectrum of HCl in support of lecture concepts in quantum theory and molecular spectroscopy. Contemporary students in physical chemistry teaching laboratories increasingly have access to FTIR spectrometers with 1/8th wn resolution, which allows for expanded choices of molecules for vibration-rotation spectroscopy. Here we present the case for choosing HBr/DBr for such a study, where the 1/8th wn resolution enables the bromine isotopic lines to be resolved. Vibration-rotation lines from the fundamental and first-overtone bands of four hydrogen bromide isotopomers are combined in a global analysis to determine molecular spectroscopic constants. Sample production, spectral appearance, analysis and results will be presented for various resolutions commonly available in teaching laboratories.

  20. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    PubMed Central

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-01-01

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope. PMID:26961578

  1. Vibrational Spectroscopy in Ion-Irradiated Carbon-Based Thin Films

    NASA Astrophysics Data System (ADS)

    Compagnini, Giuseppe; Puglisi, Orazio; Baratta, Giuseppe A.; Strazzulla, Giovanni

    In this work we present and discuss some selected experiments on ion-irradiated carbon-based thin films. Vibrational spectroscopy is used to investigate the materials structure and to explore the mechanisms of ion beam-induced modifications in many carbon solids such as crystalline carbon and carbon alloys, hydrocarbon molecules and exotic carbon species.

  2. Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy

    PubMed Central

    Fu, Li; Wang, Zhuguang; Yan, Elsa C.Y.

    2011-01-01

    We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces. PMID:22272140

  3. Vibrational sum frequency generation spectroscopy using inverted visible pulses.

    PubMed

    Weeraman, Champika; Mitchell, Steven A; Lausten, Rune; Johnston, Linda J; Stolow, Albert

    2010-05-24

    We present a broadband vibrational sum frequency generation (BB-VSFG) scheme using a novel ps visible pulse shape. We generate the fs IR pulse via standard procedures and simultaneously generate an 'inverted' time-asymmetric narrowband ps visible pulse via second harmonic generation in the pump depletion regime using a very long nonlinear crystal which has high group velocity mismatch (LiNbO3). The 'inverted' ps pulse shape minimally samples the instantaneous nonresonant response but maximally samples the resonant response, maintaining high spectral resolution. We experimentally demonstrate this scheme, presenting SFG spectra of canonical organic monolayer systems in the C-H stretch region (2800-3000 cm(-1)).

  4. Visualization of Vibrational Modes in Real Space by Tip-Enhanced Non-Resonant Raman Spectroscopy.

    PubMed

    Duan, Sai; Tian, Guangjun; Luo, Yi

    2016-01-18

    We present a general theory to model the spatially resolved non-resonant Raman images of molecules. It is predicted that the vibrational motions of different Raman modes can be fully visualized in real space by tip-enhanced non-resonant Raman scattering. As an example, the non-resonant Raman images of water clusters were simulated by combining the new theory and first-principles calculations. Each individual normal mode gives rise its own distinct Raman image, which resembles the expected vibrational motions of the atoms very well. The characteristics of intermolecular vibrations in supermolecules could also be identified. The effects of the spatial distribution of the plasmon as well as nonlinear scattering processes were also addressed. Our study not only suggests a feasible approach to spatially visualize vibrational modes, but also provides new insights in the field of nonlinear plasmonic spectroscopy.

  5. Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy.

    PubMed

    Peng, Chunte Sam; Jones, Kevin C; Tokmakoff, Andrei

    2011-10-05

    Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.

  6. Vibration spectroscopy of a sessile drop and its contact line.

    PubMed

    Mettu, S; Chaudhury, M K

    2012-10-02

    Resonance frequencies of small sessile liquid drops (1-20 μL) were estimated from the power spectra of their height fluctuations after subjecting them to white noise vibration. Various resonance modes could be identified with this method as a function of the mass of the drop. Studies with water drops on such supports as polystyrene (θ ≈ 80°) and a superhydrophobic surface of microfibrillar silicone rubber (θ ≈ 162°) demonstrated that the resonant frequency decreases with the contact angle, θ. This trend is in remarkable agreement with the current models of the resonant vibration of sessile drops. A novel aspect of this study is the analysis of the modes of a slipping contact line that indicated that its higher frequency modes are more severely damped than its lower ones. Another case is with the glycerol-water solutions, where the resonance frequency decreases with the concentration of glycerol purely due to the capillary effects. The interface fluctuation, on the other hand, is strongly correlated with the kinematic viscosity of the liquid. Thus, these experiments provide a means to measure the surface tension and the viscosity of very small droplets.

  7. Activated vibrational modes and Fermi resonance in tip-enhanced Raman spectroscopy.

    PubMed

    Sun, Mengtao; Fang, Yurui; Zhang, Zhenyu; Xu, Hongxing

    2013-02-01

    Using p-aminothiophenol (PATP) molecules on a gold substrate and high-vacuum tip-enhanced Raman spectroscopy (HV-TERS), we show that the vibrational spectra of these molecules are distinctly different from those in typical surface-enhanced Raman spectroscopy. Detailed first-principles calculations help to assign the Raman peaks in the TERS measurements as Raman-active and IR-active vibrational modes of dimercaptoazobenzene (DMAB), providing strong spectroscopic evidence for the dimerization of PATP molecules to DMAB under the TERS setup. The activation of the IR-active modes is due to enhanced electromagnetic field gradient effects within the gap region of the highly asymmetric tip-surface geometry. Fermi resonances are also observed in HV-TERS. These findings help to broaden the versatility of TERS as a promising technique for ultrasensitive molecular spectroscopy.

  8. Vibrational spectroscopy and density functional theory study of 4-mercaptophenol

    NASA Astrophysics Data System (ADS)

    Li, Ran; Ji, Wei; Chen, Lei; Lv, Haiming; Cheng, Jianbo; Zhao, Bing

    2014-03-01

    In this paper, 4-mercaptophenol (4-MPH) was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. All FTIR and Raman bands of the compound obtained experimentally were assigned based on the modeling results obtained at the B3LYP/6-311 + G** level. Our calculated vibrational frequencies are in good agreement with the experimental vales. The molecular electrostatic potential surface calculation was performed and the result suggested that the 4-MPH has two hydrogen bond donors and three hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311 + G** level.

  9. Nonlinear vibrational spectroscopy of surfactants at liquid interfaces

    SciTech Connect

    Miranda, Paulo B.

    1998-12-14

    Surfactants are widely used to modify physical and chemical properties of interfaces. They play an important role in many technological problems. Surfactant monolayer are also of great scientific interest because they are two-dimensional systems that may exhibit a very rich phase transition behavior and can also be considered as a model system for biological interfaces. In this Thesis, we use a second-order nonlinear optical technique (Sum-Frequency Generation - SFG) to obtain vibrational spectra of surfactant monolayer at Iiquidhapor and solid/liquid interfaces. The technique has several advantages: it is intrinsically surface-specific, can be applied to buried interfaces, has submonolayer sensitivity and is remarkably sensitive to the confirmational order of surfactant monolayers.

  10. Applying Semiconductor Technologies and Metrology Tools to Biomedical Research: Manipulation and Detection of Single Molecules

    NASA Astrophysics Data System (ADS)

    Berlin, Andrew A.; Sundararajan, Narayan; Koo, Tae-Woong

    2005-09-01

    Intel's Precision Biology research effort is working to combine Intel's expertise in nanotechnology with aspects of biology and medicine to create highly sensitive instrumentation for biomolecular analysis. The ability to manipulate, detect, and identify biological molecules at ultra-low concentrations is important for applications ranging from whole-genome DNA sequencing to protein-based early disease detection. In this paper we describe our work to develop a molecular labeling system based on Surface-Enhanced Raman Spectroscopy (SERS), to enable highly sensitive protein detection. We also present a set of microfluidic and spectroscopic techniques that our team has developed for transporting and identifying single molecules in solution.

  11. Fluorescence Quenching by TEMPO: A Sub-30 Å Single-Molecule Ruler

    PubMed Central

    Zhu, Peizhi; Clamme, Jean-Pierre; Deniz, Ashok A.

    2005-01-01

    A series of DNA molecules labeled with 5-carboxytetramethylrhodamine (5-TAMRA) and the small nitroxide radical TEMPO were synthesized and tested to investigate whether the intramolecular quenching efficiency can be used to measure short intramolecular distances in small ensemble and single-molecule experiments. In combination with distance calculations using molecular mechanics modeling, the experimental results from steady-state ensemble fluorescence and fluorescence correlation spectroscopy measurements both show an exponential decrease in the quenching rate constant with the dye-quencher distance in the 10–30 Å range. The results demonstrate that TEMPO-5-TAMRA fluorescence quenching is a promising method to measure short distance changes within single biomolecules. PMID:16199509

  12. Electrical Measurement of Single Molecule Catalysis using Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Goldsmith, Brett R.; Kane, Alexander A.; Khalap, Vaikunth; Coroneus, John; Weiss, Gregory A.; Collins, Philip G.

    2008-03-01

    We demonstrate single molecule chemical sensors based on single-walled carbon nanotubes (SWNT). The architecture uses a SWNT conductor having a single, reactive species covalently bonded to the sidewall [1]. Dynamics of the molecule are electrically transduced as it interacts with its surrounding environment. As a test case, we investigate the catalytic modification of EDC by a carboxylate. After creating a carboxylate terminus on the SWNT, the circuit is monitored for several hours and through hundreds of individual EDC reactions. Statistical analysis determines the lifetime of the carboxyl-EDC complex, as well as the catalytic turnover rate, from discrete events. Because the carboxylate site can be readily derivatized with proteins, peptides, or other functional molecules, the technique shows promise as a tool for single molecule research independent of optics and scanning probe microscopy. 1. B.R. Goldsmith, et al. Science 315, 77 (2007).

  13. High thermopower of mechanically stretched single-molecule junctions

    PubMed Central

    Tsutsui, Makusu; Morikawa, Takanori; He, Yuhui; Arima, Akihide

    2015-01-01

    Metal-molecule-metal junction is a promising candidate for thermoelectric applications that utilizes quantum confinement effects in the chemically defined zero-dimensional atomic structure to achieve enhanced dimensionless figure of merit ZT. A key issue in this new class of thermoelectric nanomaterials is to clarify the sensitivity of thermoelectricity on the molecular junction configurations. Here we report simultaneous measurements of the thermoelectric voltage and conductance on Au-1,4-benzenedithiol (BDT)-Au junctions mechanically-stretched in-situ at sub-nanoscale. We obtained the average single-molecule conductance and thermopower of 0.01 G0 and 15 μV/K, respectively, suggesting charge transport through the highest occupied molecular orbital. Meanwhile, we found the single-molecule thermoelectric transport properties extremely-sensitive to the BDT bridge configurations, whereby manifesting the importance to design the electrode-molecule contact motifs for optimizing the thermoelectric performance of molecular junctions. PMID:26112999

  14. High thermopower of mechanically stretched single-molecule junctions.

    PubMed

    Tsutsui, Makusu; Morikawa, Takanori; He, Yuhui; Arima, Akihide; Taniguchi, Masateru

    2015-06-26

    Metal-molecule-metal junction is a promising candidate for thermoelectric applications that utilizes quantum confinement effects in the chemically defined zero-dimensional atomic structure to achieve enhanced dimensionless figure of merit ZT. A key issue in this new class of thermoelectric nanomaterials is to clarify the sensitivity of thermoelectricity on the molecular junction configurations. Here we report simultaneous measurements of the thermoelectric voltage and conductance on Au-1,4-benzenedithiol (BDT)-Au junctions mechanically-stretched in-situ at sub-nanoscale. We obtained the average single-molecule conductance and thermopower of 0.01 G0 and 15 μV/K, respectively, suggesting charge transport through the highest occupied molecular orbital. Meanwhile, we found the single-molecule thermoelectric transport properties extremely-sensitive to the BDT bridge configurations, whereby manifesting the importance to design the electrode-molecule contact motifs for optimizing the thermoelectric performance of molecular junctions.

  15. Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry

    PubMed Central

    2016-01-01

    Protein engineering has been used to remodel pores for applications in biotechnology. For example, the heptameric α-hemolysin pore (αHL) has been engineered to form a nanoreactor to study covalent chemistry at the single-molecule level. Previous work has been confined largely to the chemistry of cysteine side chains or, in one instance, to an irreversible reaction of an unnatural amino acid side chain bearing a terminal alkyne. Here, we present four different αHL pores obtained by coupling either two or three fragments by native chemical ligation (NCL). The synthetic αHL monomers were folded and incorporated into heptameric pores. The functionality of the pores was validated by hemolysis assays and by single-channel current recording. By using NCL to introduce a ketone amino acid, the nanoreactor approach was extended to an investigation of reversible covalent chemistry on an unnatural side chain at the single-molecule level. PMID:27537396

  16. Carbon tips for all-carbon single-molecule electronics.

    PubMed

    Dappe, Y J; González, C; Cuevas, J C

    2014-06-21

    We present here an exhaustive ab initio study of the use of carbon-based tips as electrodes in single-molecule junctions. Motivated by recent experiments, we show that carbon tips can be combined with other carbon nanostructures, such as graphene, to form all-carbon molecular junctions with molecules like benzene or C60. Our results show that the use of carbon tips can lead to relatively conductive molecular junctions. However, contrary to junctions formed with standard metals, the conductance traces recorded during the formation of the all-carbon single-molecule junctions do not exhibit clear conductance plateaus, which can be attributed to the inability of the hydrogenated carbon tips to form chemical bonds with the organic molecules. Additionally, we explore here the use of carbon tips for scanning tunneling microscopy and show that they are well suited for obtaining sample images with atomic resolution.

  17. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis

    NASA Astrophysics Data System (ADS)

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-10-01

    The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

  18. Intermittent Single-Molecule Interfacial Electron Transfer Dynamics

    SciTech Connect

    Biju, Vasudevan P.; Micic, Miodrag; Hu, Dehong; Lu, H. Peter

    2004-08-04

    We report on single molecule studies of photosensitized interfacial electron transfer (ET) processes in Coumarin 343 (C343)-TiO2 nanoparticle (NP) and Cresyl Violet (CV+)-TiO2 NP systems, using time-correlated single photon counting coupled with scanning confocal fluorescence microscopy. Fluorescence intensity trajectories of individual dye molecules adsorbed on a semiconductor NP surface showed fluorescence fluctuations and blinking, with time constrants distributed from sub-milliseconds to several seconds.

  19. Probing Nanoparticle Reactivity at the Single-Molecule Level

    DTIC Science & Technology

    2014-02-15

    doi: Xiaochun Zhou, Weilin Xu, Guokun Liu, Debashis Panda , Peng Chen. Size-Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the...Debashis Panda , Peng Chen. Size Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the Single-Molecule Level, (12 2009) Books...Bibliography 1 X. Zhou, W. Xu, G. Liu, D. Panda & P. Chen. Size dependent catalytic activity and dynamics of gold nanoparticles at the single

  20. 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.

  1. Quantum Chemical Characterization of Single Molecule Magnets Based on Uranium.

    PubMed

    Spivak, Mariano; Vogiatzis, Konstantinos D; Cramer, Christopher J; Graaf, Coen de; Gagliardi, Laura

    2017-03-02

    Multiconfigurational electronic structure theory calculations including spin-orbit coupling effects were performed on four uranium-based single-molecule-magnets. Several quartet and doublet states were computed and the energy gaps between spin-orbit states were then used to determine magnetic susceptibility curves. Trends in experimental magnetic susceptibility curves were well reproduced by the calculations, and key factors affecting performance were identified.

  2. Single-molecule studies of actin assembly and disassembly factors.

    PubMed

    Smith, Benjamin A; Gelles, Jeff; Goode, Bruce L

    2014-01-01

    The actin cytoskeleton is very dynamic and highly regulated by multiple associated proteins in vivo. Understanding how this system of proteins functions in the processes of actin network assembly and disassembly requires methods to dissect the mechanisms of activity of individual factors and of multiple factors acting in concert. The advent of single-filament and single-molecule fluorescence imaging methods has provided a powerful new approach to discovering actin-regulatory activities and obtaining direct, quantitative insights into the pathways of molecular interactions that regulate actin network architecture and dynamics. Here we describe techniques for acquisition and analysis of single-molecule data, applied to the novel challenges of studying the filament assembly and disassembly activities of actin-associated proteins in vitro. We discuss the advantages of single-molecule analysis in directly visualizing the order of molecular events, measuring the kinetic rates of filament binding and dissociation, and studying the coordination among multiple factors. The methods described here complement traditional biochemical approaches in elucidating actin-regulatory mechanisms in reconstituted filamentous networks.

  3. Single-molecule imaging of hyaluronan in human synovial fluid

    NASA Astrophysics Data System (ADS)

    Kappler, Joachim; Kaminski, Tim P.; Gieselmann, Volkmar; Kubitscheck, Ulrich; Jerosch, Jörg

    2010-11-01

    Human synovial fluid contains a high concentration of hyaluronan, a high molecular weight glycosaminoglycan that provides viscoelasticity and contributes to joint lubrication. In osteoarthritis synovial fluid, the concentration and molecular weight of hyaluronan decrease, thus impairing shock absorption and lubrication. Consistently, substitution of hyaluronan (viscosupplementation) is a widely used treatment for osteoarthritis. So far, the organization and dynamics of hyaluronan in native human synovial fluid and its action mechanism in viscosupplementation are poorly characterized at the molecular level. Here, we introduce highly sensitive single molecule microscopy to analyze the conformation and interactions of fluorescently labeled hyaluronan molecules in native human synovial fluid. Our findings are consistent with a random coil conformation of hyaluronan in human synovial fluid, and point to specific interactions of hyaluronan molecules with the synovial fluid matrix. Furthermore, single molecule microscopy is capable of detecting the breakdown of the synovial fluid matrix in osteoarthritis. Thus, single molecule microscopy is a useful new method to probe the structure of human synovial fluid and its changes in disease states like osteoarthritis.

  4. Improved Glass Surface Passivation for Single-Molecule Nanoarrays.

    PubMed

    Cai, Haogang; Wind, Shalom J

    2016-10-04

    Single-molecule fluorescence techniques provide a critical tool for probing biomolecular and cellular interactions with unprecedented resolution and precision. Unfortunately, many of these techniques are hindered by a common problem, namely, the nonspecific adsorption of target biomolecules. This issue is mostly addressed by passivating the glass surfaces with a poly(ethylene glycol) (PEG) brush. This is effective only at low concentrations of the probe molecule because there are defects inherent to polymer brushes formed on glass coverslips due to the presence of surface impurities. Tween-20, a detergent, is a promising alternative that can improve surface passivation, but it is incompatible with living cells, and it also possesses limited selectivity for glass background over metallic nanoparticles, which are frequently used as anchors for the probe molecules. To address these issues, we have developed a more versatile method to improve the PEG passivation. A thin film of hydrogen silsesquioxane (HSQ) is spin-coated and thermally cured on glass coverslips in order to cover the surface impurities. This minimizes the formation of PEG defects and reduces nonspecific adsorption, resulting in an improvement comparable to Tween-20 treatment. This approach was applied to single-molecule nanoarrays of streptavidin bound to AuPd nanodots patterned by e-beam lithography (EBL). The fluorescence signal to background ratio (SBR) on HSQ-coated glass was improved by ∼4-fold as compared to PEG directly on glass. This improvement enables direct imaging of ordered arrays of single molecules anchored to lithographically patterned arrays of metallic nanodots.

  5. Decoding Single Molecule Time Traces with Dynamic Disorder

    PubMed Central

    Hwang, Wonseok; Lee, Il-Buem; Hong, Seok-Cheol

    2016-01-01

    Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm—Variational Bayes-double chain Markov model (VB-DCMM)—to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA. PMID:28027304

  6. Predicting single-molecule conductance through machine learning

    NASA Astrophysics Data System (ADS)

    Lanzillo, Nicholas A.; Breneman, Curt M.

    2016-10-01

    We present a robust machine learning model that is trained on the experimentally determined electrical conductance values of approximately 120 single-molecule junctions used in scanning tunnelling microscope molecular break junction (STM-MBJ) experiments. Quantum mechanical, chemical, and topological descriptors are used to correlate each molecular structure with a conductance value, and the resulting machine-learning model can predict the corresponding value of conductance with correlation coefficients of r 2 = 0.95 for the training set and r 2 = 0.78 for a blind testing set. While neglecting entirely the effects of the metal contacts, this work demonstrates that single molecule conductance can be qualitatively correlated with a number of molecular descriptors through a suitably trained machine learning model. The dominant features in the machine learning model include those based on the electronic wavefunction, the geometry/topology of the molecule as well as the surface chemistry of the molecule. This model can be used to identify promising molecular structures for use in single-molecule electronic circuits and can guide synthesis and experiments in the future.

  7. Field Regulation of Single Molecule Conductivity by a Charged Atom

    NASA Astrophysics Data System (ADS)

    Wolkow, Robert

    2006-03-01

    A new concept for a single molecule transistor is demonstrated [1]. A single chargeable atom adjacent to a molecule shifts molecular energy levels into alignment with electrode levels, thereby gating current through the molecule. Seemingly paradoxically, the silicon substrate to which the molecule is covalently attached provides 2, not 1, effective contacts to the molecule. This is achieved because the single charged silicon atom is at a substantially different potential than the remainder of the substrate. Charge localization at one dangling bond is ensured by covalently capping all other surface atoms. Dopant level control and local Fermi level control can change the charge state of that atom. The same configuration is shown to be an effective transducer to an electrical signal of a single molecule detection event. Because the charged atom induced shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. [1] Paul G. Piva1,Gino A. DiLabio, Jason L. Pitters, Janik Zikovsky, Moh'd Rezeq, Stanislav Dogel, Werner A. Hofer & Robert A. Wolkow, Field regulation of single-molecule conductivity by a charged surface atom, NATURE 435, 658-661 (2005)

  8. 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.

  9. Towards Single-Molecule Optical Mapping of the Epigenome

    PubMed Central

    Levy-Sakin, Michal; Grunwald, Assaf; Kim, Soohong; Gassman, Natalie R.; Gottfried, Anna; Antelman, Josh; Kim, Younggyu; Ho, Sam; Samuel, Robin; Michalet, Xavier; Lin, Ron R.; Dertinger, Thomas; Kim, Andrew S.; Chung, Sangyoon; Colyer, Ryan A.; Weinhold, Elmar; Weiss, Shimon; Ebenstein, Yuval

    2014-01-01

    The last decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity on the population level. The complex composition of the genome has made it an ideal system to study on the single-molecule level and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nano-scale and enhanced optical resolving power for analysis of genomic information. In the very last years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation. PMID:24328256

  10. Molecular electronics: the single-molecule switch and transistor

    NASA Astrophysics Data System (ADS)

    Sotthewes, Kai; Geskin, Victor; Heimbuch, Rene; Kumar, Avijit; Zandvliet, Harold

    2014-03-01

    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.

  11. Single molecule microscopy in 3D cell cultures and tissues.

    PubMed

    Lauer, Florian M; Kaemmerer, Elke; Meckel, Tobias

    2014-12-15

    From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.

  12. Single Molecule Electrochemical Detection in Aqueous Solutions and Ionic Liquids.

    PubMed

    Byers, Joshua C; Paulose Nadappuram, Binoy; Perry, David; McKelvey, Kim; Colburn, Alex W; Unwin, Patrick R

    2015-10-20

    Single molecule electrochemical detection (SMED) is an extremely challenging aspect of electroanalytical chemistry, requiring unconventional electrochemical cells and measurements. Here, SMED is reported using a "quad-probe" (four-channel probe) pipet cell, fabricated by depositing carbon pyrolytically into two diagonally opposite barrels of a laser-pulled quartz quadruple-barreled pipet and filling the open channels with electrolyte solution, and quasi-reference counter electrodes. A meniscus forms at the end of the probe covering the two working electrodes and is brought into contact with a substrate working electrode surface. In this way, a nanogap cell is produced whereby the two carbon electrodes in the pipet can be used to promote redox cycling of an individual molecule with the substrate. Anticorrelated currents generated at the substrate and tip electrodes, at particular distances (typically tens of nanometers), are consistent with the detection of single molecules. The low background noise realized in this droplet format opens up new opportunities in single molecule electrochemistry, including the use of ionic liquids, as well as aqueous solution, and the quantitative assessment and analysis of factors influencing redox cycling currents, due to a precisely known gap size.

  13. Improved Dye Stability in Single-Molecule Fluorescence Experiments

    NASA Astrophysics Data System (ADS)

    EcheverrÍa Aitken, Colin; Marshall, R. Andrew; Pugi, Joseph D.

    Complex biological systems challenge existing single-molecule methods. In particular, dye stability limits observation time in singlemolecule fluorescence applications. Current approaches to improving dye performance involve the addition of enzymatic oxygen scavenging systems and small molecule additives. We present an enzymatic oxygen scavenging system that improves dye stability in single-molecule experiments. Compared to the currently-employed glucose-oxidase/catalase system, the protocatechuate-3,4-dioxygenase system achieves lower dissolved oxygen concentration and stabilizes single Cy3, Cy5, and Alexa488 fluorophores. Moreover, this system possesses none of the limitations associated with the glucose oxidase/catalase system. We also tested the effects of small molecule additives in this system. Biological reducing agents significantly destabilize the Cy5 fluorophore as a function of reducing potential. In contrast, anti-oxidants stabilize the Cy3 and Alexa488 fluorophores. We recommend use of the protocatechuate-3,4,-dioxygenase system with antioxidant additives, and in the absence of biological reducing agents. This system should have wide application to single-molecule fluorescence experiments.

  14. Correlating the motion of electrons and nuclei with two-dimensional electronic–vibrational spectroscopy

    PubMed Central

    Oliver, Thomas A. A.; Lewis, Nicholas H. C.; Fleming, Graham R.

    2014-01-01

    Multidimensional nonlinear spectroscopy, in the electronic and vibrational regimes, has reached maturity. To date, no experimental technique has combined the advantages of 2D electronic spectroscopy and 2D infrared spectroscopy, monitoring the evolution of the electronic and nuclear degrees of freedom simultaneously. The interplay and coupling between the electronic state and vibrational manifold is fundamental to understanding ensuing nonradiative pathways, especially those that involve conical intersections. We have developed a new experimental technique that is capable of correlating the electronic and vibrational degrees of freedom: 2D electronic–vibrational spectroscopy (2D-EV). We apply this new technique to the study of the 4-(di-cyanomethylene)-2-methyl-6-p-(dimethylamino)styryl-4H-pyran (DCM) laser dye in deuterated dimethyl sulfoxide and its excited state relaxation pathways. From 2D-EV spectra, we elucidate a ballistic mechanism on the excited state potential energy surface whereby molecules are almost instantaneously projected uphill in energy toward a transition state between locally excited and charge-transfer states, as evidenced by a rapid blue shift on the electronic axis of our 2D-EV spectra. The change in minimum energy structure in this excited state nonradiative crossing is evident as the central frequency of a specific vibrational mode changes on a many-picoseconds timescale. The underlying electronic dynamics, which occur on the hundreds of femtoseconds timescale, drive the far slower ensuing nuclear motions on the excited state potential surface, and serve as a excellent illustration for the unprecedented detail that 2D-EV will afford to photochemical reaction dynamics. PMID:24927586

  15. Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

    PubMed

    Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

    2017-03-14

    We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

  16. Edge chlorination of hexa-peri-hexabenzocoronene investigated by density functional theory and vibrational spectroscopy.

    PubMed

    Maghsoumi, Ali; Narita, Akimitsu; Dong, Renhao; Feng, Xinliang; Castiglioni, Chiara; Müllen, Klaus; Tommasini, Matteo

    2016-04-28

    We investigate the molecular structure and vibrational properties of perchlorinated hexa-peri-hexabenzocoronene (HBC-Cl) by density functional theory (DFT) calculations and IR and Raman spectroscopy, in comparison to the parent HBC. The theoretical and experimental IR and Raman spectra demonstrated very good agreement, elucidating a number of vibrational modes corresponding to the observed peaks. Compared with the parent HBC, the edge chlorination significantly alters the planarity of the molecule. Nevertheless, the results indicated that such structural distortion does not significantly impair the π-conjugation of such polycyclic aromatic hydrocarbons.

  17. Femtosecond time-resolved spectroscopy of coherent vibrational and electronic excitations in solids

    NASA Astrophysics Data System (ADS)

    Williams*, Leah Ruby; Nelson, Keith A.

    1986-08-01

    ``Impulsive'' stimulated scattering (ISS) of femtosecond laser pulses was used to coherently excite and probe a low-lying (61-cm-1) electronic excitation in the cooperative Jahn-Teller crystal, terbium vanadate. Coherent terahertz oscillations and their dephasing were observed in the time domain. ISS is a general aspect of ultrashort-pulse interactions with matter, through which coherent excitations are produced whenever a sufficiently short laser pulse enters a Raman-active medium. Its use for measurement of vibrational and electronic dephasing and lifetimes, and for time-resolved spectroscopy of vibrationally distorted crystals and molecules, is discussed.

  18. Torsional vibrational modes of tryptophan studied by terahertz time-domain spectroscopy.

    PubMed

    Yu, B; Zeng, F; Yang, Y; Xing, Q; Chechin, A; Xin, X; Zeylikovich, I; Alfano, R R

    2004-03-01

    The low-frequency torsional modes, index of refraction, and absorption of a tryptophan film and pressed powders from 0.2 to 2.0 THz (6.6-66 cm(-1)) were measured by terahertz time-domain spectroscopy at room temperature. It was found that there were two dominated torsional vibrational modes at around 1.435 and 1.842 THz. The associated relaxation lifetimes ( approximately 1 ps) for these modes of the tryptophan molecule were measured. Using a density-functional calculation, the origins of the observed torsional vibrations were assigned to the chain and ring of the tryptophan molecule.

  19. Contact and Length Dependent Effects in Single-Molecule Electronics

    NASA Astrophysics Data System (ADS)

    Hines, Thomas

    Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition

  20. Vibrational spectroscopy and DFT calculations of flavonoid derriobtusone A

    NASA Astrophysics Data System (ADS)

    Marques, A. N. L.; Mendes Filho, J.; Freire, P. T. C.; Santos, H. S.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Leite, R. V.; Braz-Filho, R.; Gusmão, G. O. M.; Nogueira, C. E. S.; Teixeira, A. M. R.

    2017-02-01

    Flavonoids are secondary metabolites of plants which perform various functions. One subclass of flavonoid is auronol that can present immunostimulating activity. In this work Fourier-Transform Infrared with Attenuated Total Reflectance (FTIR-ATR) and Fourier-Transform Raman (FT-Raman) spectra of an auronol, derriobtusone A (C18H12O4), were obtained at room temperature. Theoretical calculations using Density Functional Theory (DFT) were performed in order to assign the normal modes and to interpret the spectra of the derriobtusone A molecule. The FTIR-ATR and FT-Raman spectra of the crystal, were recorded at room temperature in the regions 600 cm-1 to 4000 cm-1 and 40 cm-1 to 4000 cm-1, respectively. The normal modes of vibrations were obtained using Density Functional Theory with B3LYP functional and 6-31G+ (d,p) basis set. The calculated frequencies are in good agreement with those obtained experimentally. Detailed assignments of the normal modes present in both the Fourier-Transform infrared and the Fourier-Transform Raman spectra of the crystal are given.

  1. Vibrational spectroscopy for online monitoring of extraction solvent degradation products

    SciTech Connect

    Peterson, J.; Robinson, T.; Bryan, S.A.; Levitskaia, T.G.

    2013-07-01

    In our research, we are exploring the potential of online monitoring of the organic solvents for the flowsheets relevant to the used nuclear fuel reprocessing and tributyl phosphate (TBP)- based extraction processes in particular. Utilization of vibrational spectroscopic techniques permits the discrimination of the degradation products from the primary constituents of the loaded extraction solvent. Multivariate analysis of the spectral data facilitates development of the regression models for their quantification in real time and potentially enables online implementation of a monitoring system. Raman and FTIR spectral databases were created and used to develop the regression partial least squares (PLS) chemometric models for the quantitative prediction of HDBP (dibutyl phosphoric acid) degradation product, TBP, and UO{sub 2}{sup 2+} extraction organic product phase. It was demonstrated that both these spectroscopic techniques are suitable for the quantification of the Purex solvent components in the presence of UO{sub 2}(NO{sub 3}){sub 2}. Developed PLS models successfully predicted HDBP and TBP organic concentrations in simulated Purex solutions.

  2. Vibrational neutron spectroscopy of collagen and model polypeptides.

    PubMed Central

    Middendorf, H D; Hayward, R L; Parker, S F; Bradshaw, J; Miller, A

    1995-01-01

    A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views of the proton-dominated modes of a protein over a wide energy range from the low frequency phonon region to the rich spectrum of localized high frequency modes. Several bands show a level of fine structure approaching that of optical data. The principal features of the spectra are assigned. A difference spectrum is obtained for protein associated water, which displays an acoustic peak similar to pure ice and a librational band shifted to lower frequency by the influence of the protein. Hydrogen-weighted densities of states are extracted for collagen and the model polypeptides, and compared with published calculations. Proton mean-square displacements are calculated from Debye-Waller factors measured in parallel quasi-elastic neutron-scattering experiments. Combined with the collagen density of states function, these yield an effective mass of 14.5 a.m.u. for the low frequency harmonic oscillators, indicating that the extended atom approximation, which simplifies analyses of low frequency protein dynamics, is appropriate. PMID:8527680

  3. Investigating Microbial (Micro)colony Heterogeneity by Vibrational Spectroscopy

    PubMed Central

    Choo-Smith, L.-P.; Maquelin, K.; van Vreeswijk, T.; Bruining, H. A.; Puppels, G. J.; Thi, N. A. Ngo; Kirschner, C.; Naumann, D.; Ami, D.; Villa, A. M.; Orsini, F.; Doglia, S. M.; Lamfarraj, H.; Sockalingum, G. D.; Manfait, M.; Allouch, P.; Endtz, H. P.

    2001-01-01

    Fourier transform infrared and Raman microspectroscopy are currently being developed as new methods for the rapid identification of clinically relevant microorganisms. These methods involve measuring spectra from microcolonies which have been cultured for as little as 6 h, followed by the nonsubjective identification of microorganisms through the use of multivariate statistical analyses. To examine the biological heterogeneity of microorganism growth which is reflected in the spectra, measurements were acquired from various positions within (micro)colonies cultured for 6, 12, and 24 h. The studies reveal that there is little spectral variance in 6-h microcolonies. In contrast, the 12- and 24-h cultures exhibited a significant amount of heterogeneity. Hierarchical cluster analysis of the spectra from the various positions and depths reveals the presence of different layers in the colonies. Further analysis indicates that spectra acquired from the surface of the colonies exhibit higher levels of glycogen than do the deeper layers of the colony. Additionally, the spectra from the deeper layers present with higher RNA levels than the surface layers. Therefore, the 6-h colonies with their limited heterogeneity are more suitable for inclusion in a spectral database to be used for classification purposes. These results also demonstrate that vibrational spectroscopic techniques can be useful tools for studying the nature of colony development and biofilm formation. PMID:11282591

  4. Two-photon vibrational spectroscopy for biosciences based on surface-enhanced hyper-Raman scattering

    PubMed Central

    Kneipp, Janina; Kneipp, Harald; Kneipp, Katrin

    2006-01-01

    Two-photon excitation is gaining rapidly in interest and significance in spectroscopy and microscopy. Here we introduce a new approach that suggests versatile optical labels suitable for both one- and two-photon excitation and also two-photon-excited ultrasensitive, nondestructive chemical probing. The underlying spectroscopic effect is the incoherent inelastic scattering of two photons on the vibrational quantum states called hyper-Raman scattering (HRS). The rather weak effect can be strengthened greatly if HRS takes place in the local optical fields of gold and silver nanostructures. This so-called surface-enhanced HRS (SEHRS) is the two-photon analogue to surface-enhanced Raman scattering (SERS). SEHRS provides structurally sensitive vibrational information complementary to those obtained by SERS. SEHRS combines the advantages of two-photon spectroscopy with the structural information of vibrational spectroscopy and the high-sensitivity and nanometer-scale local confinement of plasmonics-based spectroscopy. We infer effective two-photon cross-sections for SEHRS on the order of 10−46 to 10−45 cm4·s, similar to or higher than the best “action” cross-sections (product of the two-photon absorption cross-section and fluorescence quantum yield) for two-photon fluorescence, and we demonstrate HRS on biological structures such as single cells after incubation with gold nanoparticles. PMID:17088534

  5. OH-stretch vibrational spectroscopy of hydroxymethyl hydroperoxide.

    PubMed

    Fry, Juliane L; Matthews, Jamie; Lane, Joseph R; Roehl, Coleen M; Sinha, Amitabha; Kjaergaard, Henrik G; Wennberg, Paul O

    2006-06-08

    We report measurement and analysis of the photodissociation spectrum of hydroxymethyl hydroperoxide (HOCH(2)OOH) and its partially deuterated analogue, HOCD(2)OOH, in the OH-stretching region. Spectra are obtained by Fourier transform infrared spectroscopy in the 1nu(OH) and 2nu(OH) regions, and by laser induced fluorescence detection of the OH fragment produced from dissociation of HOCH(2)OOH initiated by excitation of the 4nu(OH) and 5nu(OH) overtone regions (action spectroscopy). A one-dimensional local-mode model of each OH chromophore is used with ab initio calculated OH-stretching potential energy and dipole moment curves at the coupled-cluster level of theory. Major features in the observed absorption and photodissociation spectra are explained by our local-mode model. In the 4nu(OH) region, explanation of the photodissocation spectrum requires a nonuniform quantum yield, which is estimated by assuming statistical energy distribution in the excited state. Based on the estimated dissociation threshold, overtone photodissociation is not expected to significantly influence the atmospheric lifetime of hydroxymethyl hydroperoxide.

  6. Spectroscopic properties of photosystem II core complexes from Thermosynechococcus elongatus revealed by single-molecule experiments.

    PubMed

    Brecht, Marc; Skandary, Sepideh; Hellmich, Julia; Glöckner, Carina; Konrad, Alexander; Hussels, Martin; Meixner, Alfred J; Zouni, Athina; Schlodder, Eberhard

    2014-06-01

    In this study we use a combination of absorption, fluorescence and low temperature single-molecule spectroscopy to elucidate the spectral properties, heterogeneities and dynamics of the chlorophyll a (Chla) molecules responsible for the fluorescence emission of photosystem II core complexes (PS II cc) from the cyanobacterium Thermosynechococcus elongatus. At the ensemble level, the absorption and fluorescence spectra show a temperature dependence similar to plant PS II. We report emission spectra of single PS II cc for the first time; the spectra are dominated by zero-phonon lines (ZPLs) in the range between 680 and 705nm. The single-molecule experiments show unambiguously that different emitters and not only the lowest energy trap contribute to the low temperature emission spectrum. The average emission spectrum obtained from more than hundred single complexes shows three main contributions that are in good agreement with the reported bands F685, F689 and F695. The intensity of F695 is found to be lower than in conventional ensemble spectroscopy. The reason for the deviation might be due to the accumulation of triplet states on the red-most chlorophylls (e.g. Chl29 in CP47) or on carotenoids close to these long-wavelength traps by the high excitation power used in the single-molecule experiments. The red-most emitter will not contribute to the fluorescence spectrum as long as it is in the triplet state. In addition, quenching of fluorescence by the triplet state may lead to a decrease of long-wavelength emission.

  7. Vibrational Coupling at the Topmost Surface of Water Revealed by Heterodyne-Detected Sum Frequency Generation Spectroscopy.

    PubMed

    Suzuki, Yudai; Nojima, Yuki; Yamaguchi, Shoichi

    2017-03-15

    Unraveling vibrational coupling is the key to consistently interpret vibrational spectra of complex molecular systems. The vibrational spectrum of the water surface heavily suffers from vibrational coupling, which hinders complete understanding of the molecular structure and dynamics of the water surface. Here we apply heterodyne-detected sum frequency generation spectroscopy to the water surface and accomplish the assignment of a weak vibrational band located at the lower energy side of the free OH stretch. We find that this band is due to a combination mode of the hydrogen-bonded OH stretch and a low-frequency intermolecular vibration, and this combination band appears in the surface vibrational spectrum through anharmonic vibrational coupling that takes place exclusively at the topmost surface.

  8. Communication: Vibrational and vibronic coherences in the two dimensional spectroscopy of coupled electron-nuclear motion

    SciTech Connect

    Albert, Julian; Falge, Mirjam; Hildenbrand, Heiko; Engel, Volker; Gomez, Sandra; Sola, Ignacio R.

    2015-07-28

    We theoretically investigate the photon-echo spectroscopy of coupled electron-nuclear quantum dynamics. Two situations are treated. In the first case, the Born-Oppenheimer (adiabatic) approximation holds. It is then possible to interpret the two-dimensional (2D) spectra in terms of vibrational motion taking place in different electronic states. In particular, pure vibrational coherences which are related to oscillations in the time-dependent third-order polarization can be identified. This concept fails in the second case, where strong non-adiabatic coupling leads to the breakdown of the Born-Oppenheimer-approximation. Then, the 2D-spectra reveal a complicated vibronic structure and vibrational coherences cannot be disentangled from the electronic motion.

  9. Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy.

    PubMed

    Fischer, B M; Walther, M; Uhd Jepsen, P

    2002-11-07

    The far-infrared dielectric function of a wide range of organic molecules is dominated by vibrations involving a substantial fraction of the atoms forming the molecule and motion associated with intermolecular hydrogen bond vibrations. Due to their collective nature such modes are highly sensitive to the intra- and intermolecular structure and thus provide a unique fingerprint of the conformational state of the molecule and effects of its environment. We demonstrate the use of terahertz time-domain spectroscopy (THz-TDS) for recording the far-infrared (0.5-4.0 THz) dielectric function of the four nucleobases and corresponding nucleosides forming the building blocks of deoxyribose nucleic acid (DNA). We observe numerous distinct spectral features with large differences between the molecules in both frequency-dependent absorption coefficient and index of refraction. Assisted by results from density-functional calculations we interpret the origin of the observed resonances as vibrations of hydrogen bonds between the molecules.

  10. High-resolution vibrational and rotational spectroscopy of CD2H+ in a cryogenic ion trap

    NASA Astrophysics Data System (ADS)

    Jusko, Pavol; Stoffels, Alexander; Thorwirth, Sven; Brünken, Sandra; Schlemmer, Stephan; Asvany, Oskar

    2017-02-01

    The low-lying rotational states (J = 0, … , 5) of CD2H+ have been probed by high-resolution ro-vibrational and pure rotational spectroscopy, applying several action spectroscopic methods in a cryogenic 22-pole ion trap. For this, the ν1 ro-vibrational band has been revisited, detecting 108 transitions, among which 36 are new. The use of a frequency comb system allowed us to measure the ro-vibrational transitions with high precision and accuracy, typically better than 1 MHz. The high precision has been confirmed by comparing equal combination differences in the ground and excited state. Moreover, precise predictions of pure rotational transitions were possible for the ground state. Twenty-five rotational transitions have been detected directly by a novel IR-mm-wave double resonance method, giving rise to highly accurate ground state spectroscopic parameters.

  11. Communication: Vibrational and vibronic coherences in the two dimensional spectroscopy of coupled electron-nuclear motion

    NASA Astrophysics Data System (ADS)

    Albert, Julian; Falge, Mirjam; Gomez, Sandra; Sola, Ignacio R.; Hildenbrand, Heiko; Engel, Volker

    2015-07-01

    We theoretically investigate the photon-echo spectroscopy of coupled electron-nuclear quantum dynamics. Two situations are treated. In the first case, the Born-Oppenheimer (adiabatic) approximation holds. It is then possible to interpret the two-dimensional (2D) spectra in terms of vibrational motion taking place in different electronic states. In particular, pure vibrational coherences which are related to oscillations in the time-dependent third-order polarization can be identified. This concept fails in the second case, where strong non-adiabatic coupling leads to the breakdown of the Born-Oppenheimer-approximation. Then, the 2D-spectra reveal a complicated vibronic structure and vibrational coherences cannot be disentangled from the electronic motion.

  12. Vibrational Spectroscopy of Transient Dipolar Radicals via Autodetachment of Dipole-Bound States of Cold Anions

    NASA Astrophysics Data System (ADS)

    Huang, Dao-Ling; Liu, Hong-Tao; Dau, Phuong Diem; Wang, Lai-Sheng

    2014-06-01

    High-resolution vibrational spectroscopy of transient species is important for determining their molecular structures and understanding their chemical reactivity. However, the low abundance and high reactivity of molecular radicals pose major challenges to conventional absorption spectroscopic methods. The observation of dipole-bound states (DBS) in anions extend autodetachment spectroscopy to molecular anions whose corresponding neutral radicals possess a large enough dipole moment (>2.5 D).1,2 However, due to the difficulty of assigning the congested spectra at room temperature, there have been only a limited number of autodetachment spectra via DBS reported. Recently, we have built an improved version of a cold trap3 coupled with high-resolution photoelectron imaging.4 The first observation of mode-specific auotodetachment of DBS of cold phenoxide have shown that not only vibrational hot bands were completely suppressed, but also rotational profile was observed.5 The vibrational frequencies of the DBS were found to be the same as those of the neutral radical, suggesting that vibrational structures of dipolar radicals can be probed via DBS.5 More significantly, the DBS resonances allowed a number of vibrational modes with very weak Frank-Condon factors to be "lightened" up via vibrational autodetachment.5 Recently, our first high-resolution vibrational spectroscopy of the dehydrogenated uracil radical, with partial rotational resolution, via autodetachment from DBS of cold deprotonated uracil anions have been reported.6 Rich vibrational information is obtained for this important radical species. The resolved rotational profiles also allow us to characterize the rotational temperature of the trapped anions for the first time.6 1 K. R. Lykke, D. M. Neumark, T. Andersen, V. J. Trapa, and W. C. Lineberger, J. Chem. Phys. 87, 6842 (1987). 2 D. M. Wetzel, and J. I. Brauman, J. Chem. Phys. 90, 68 (1989). 3 P. D. Dau, H. T. Liu, D. L. Huang, and L. S. Wang, J. Chem. Phys

  13. All-Dielectric Silicon Nanogap Antennas To Enhance the Fluorescence of Single Molecules.

    PubMed

    Regmi, Raju; Berthelot, Johann; Winkler, Pamina M; Mivelle, Mathieu; Proust, Julien; Bedu, Frédéric; Ozerov, Igor; Begou, Thomas; Lumeau, Julien; Rigneault, Hervé; García-Parajó, María F; Bidault, Sébastien; Wenger, Jérôme; Bonod, Nicolas

    2016-08-10

    Plasmonic antennas have a profound impact on nanophotonics as they provide efficient means to manipulate light and enhance light-matter interactions at the nanoscale. However, the large absorption losses found in metals can severely limit the plasmonic applications in the visible spectral range. Here, we demonstrate the effectiveness of an alternative approach using all-dielectric nanoantennas based on silicon dimers to enhance the fluorescence detection of single molecules. The silicon antenna design is optimized to confine the near-field intensity in the 20 nm nanogap and reach a 270-fold fluorescence enhancement in a nanoscale volume of λ(3)/1800 with dielectric materials only. Our conclusions are assessed by combining polarization resolved optical spectroscopy of individual antennas, scanning electron microscopy, numerical simulations, fluorescence lifetime measurements, fluorescence burst analysis, and fluorescence correlation spectroscopy. This work demonstrates that all-silicon nanoantennas are a valid alternative to plasmonic devices for enhanced single molecule fluorescence sensing, with the additional key advantages of reduced nonradiative quenching, negligible heat generation, cost-efficiency, and complementary metal-oxide-semiconductor (CMOS) compatibility.

  14. Hollow-core photonic crystal fiber probe for remote fluorescence sensing with single molecule sensitivity.

    PubMed

    Ghenuche, Petru; Rigneault, Hervé; Wenger, Jérôme

    2012-12-17

    Current optical fiber probes for fluorescence spectroscopy struggle with large luminescence background and low detection sensitivities that challenge the detection of fluorescent molecules at sub-micromolar concentration. Here we report the demonstration of a hollow-core photonic crystal fiber (HC-PCF) probe for remote fluorescence sensing with single molecule sensitivity down to nanomolar concentrations, where both the excitation and fluorescence beams are counter-propagating through the same fiber. A 20 μm polystyrene microsphere is used to efficiently excite and collect the fluorescence from the sample solution thanks to a photonic nanojet effect. Compared to earlier work with silica fibers, the new HC-PCF-microsphere probe achieves a 200x improvement of the signal-to-noise ratio for a single molecule detection event, and a 1000x reduction of the minimum detectable concentration. The device is implemented with fluorescence correlation spectroscopy to distinguish between molecules of similar fluorescence spectra based on the analysis of their translational diffusion properties, and provides similar performance as conventional confocal microscopes.

  15. Chitosan-coated anisotropic silver nanoparticles as a SERS substrate for single-molecule detection

    NASA Astrophysics Data System (ADS)

    Potara, Monica; Baia, Monica; Farcau, Cosmin; Astilean, Simion

    2012-02-01

    Surface-enhanced Raman spectroscopy (SERS) is a technique that has become widely used for identifying and providing structural information about molecular species in low concentration. There is an ongoing interest in finding optimum particle size, shape and spatial distribution for optimizing the SERS substrates and pushing the sensitivity toward the single-molecule detection limit. This work reports the design of a novel, biocompatible SERS substrate based on small clusters of anisotropic silver nanoparticles embedded in a film of chitosan biopolymer. The SERS efficiency of the biocompatible film is assessed by employing Raman imaging and spectroscopy of adenine, a significant biological molecule. By combining atomic force microscopy with SERS imaging we find that the chitosan matrix enables the formation of small clusters of silver nanoparticles, with junctions and gaps that greatly enhance the Raman intensities of the adsorbed molecules. The study demonstrates that chitosan-coated anisotropic silver nanoparticle clusters are sensitive enough to be implemented as effective plasmonic substrates for SERS detection of nonresonant analytes at the single-molecule level.

  16. Microwave Spectroscopy of the Excited Vibrational States of Methanol

    NASA Astrophysics Data System (ADS)

    Pearson, John; Daly, Adam M.; Bermúdez, Celina

    2015-06-01

    Methanol is the simplest molecule with a three-fold internal rotation and the observation of its νb{8} band served the primary catalyst for the development of internal rotation theory(a,b). The 75 subsequent years of investigation into the νb{8} band region have yielded a large number assignments, numerous high precision energy levels and a great deal of insight into the coupling of νb{t}=3 & 4 with νb{8}, νb{7}, νb{11} and other nearby states(c). In spite of this progress numerous assignment mysteries persist, the origin of almost half the far infrared laser lines remain unknown and all attempts to model the region quantum mechanically have had very limited success. The C3V internal rotation Hamiltonian has successfully modeled the νb{t}=0,1 & 2 states of methanol and other internal rotors(d). However, successful modeling of the coupling between torsional bath states and excited small amplitude motion remains problematic and coupling of multiple interacting excited small amplitude vibrations featuring large amplitude motions remains almost completely unexplored. Before such modeling can be attempted, identifying the remaining low lying levels of νb{7} and νb{11} is necessary. We present an investigation into the microwave spectrum of νb{7}, νb{8} and νb{11} along with the underlying torsional bath states in νb{t}=3 and νb{t}= 4. (a) A. Borden, E.F. Barker J. Chem. Phys., 6, 553 (1938). (b) J. S. Koehler and D. M. Dennison, Phys. Rev. 57, 1006 (1940). (c) R. M. Lees, Li-Hong Xu, J. W. C. Johns, B. P. Winnewisser, and M. Lock, J. Mol. Spectrosc. 243, 168 (2007). (d) L.-H. Xu, J. Fisher, R.M. Lees, H.Y. Shi, J.T. Hougen, J.C. Pearson, B.J. Drouin, G.A. Blake, R. Braakman J. Mol. Spectrosc., 251, 305 (2008).

  17. VSI@ESS: Case study for a vibrational spectroscopy instrument at the european spallation source

    NASA Astrophysics Data System (ADS)

    Zoppi, Marco; Fedrigo, Anna; Celli, Milva; Colognesi, Daniele

    2015-01-01

    Neutron Vibrational Spectroscopy is a well-established experimental technique where elementary excitations at relatively high frequency are detected via inelastic neutron scattering. This technique attracts a high interest in a large fraction of the scientific community in the fields of chemistry, materials science, physics, and biology, since one of its main applications exploits the large incoherent scattering cross section of the proton with respect to all the other elements, whose dynamics can be spectroscopically detected, even if dissolved in very low concentration in materials composed of much heavier atoms. We have proposed a feasibility study for a Vibrational Spectroscopy Instrument (VSI) at the European Spallation Source ESS. Here, we will summarize the preliminary design calculations and the corresponding McStas simulation results for a possible ToF, Inverted Geometry, VSI beamline.

  18. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals

    PubMed Central

    Guo, Yisong; Brecht, Eric; Aznavour, Kristen; Nix, Jay C.; Xiao, Yuming; Wang, Hongxin; George, Simon J.; Bau, Robert; Keable, Stephen; Peters, John W.; Adams, Michael W.W.; Jenney, Francis; Sturhahn, Wolfgang; Alp, Ercan E.; Zhao, Jiyong; Yoda, Yoshitaka; Cramer, Stephen P.

    2014-01-01

    We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure. PMID:26052177

  19. High throughput single molecule detection for monitoring biochemical reactions

    PubMed Central

    Okagbare, Paul I.; Soper, Steven A.

    2009-01-01

    The design, performance and application of a novel optical system for high throughput single molecule detection (SMD) configured in a continuous flow format using microfluidics is reported. The system consisted of a microfabricated polymer-based multi-channel fluidic network situated within the optical path of a laser source (λex = 660 nm) with photon transduction accomplished using an electron-multiplying charge coupled device (EMCCD) operated in a frame transfer mode that allowed tracking single molecules as they passed through a large field-of-view (FoV) illumination zone. The microfluidic device consisted of 30 microchannels possessing dimensions of 30 μm (width) × 20 μm (depth) with a 25 mm pitch. Individual molecules were electrokinetically driven through the fluidic network and excited within the wide-field illumination area with the resulting fluorescence collected via an objective and imaged onto the EMCCD camera. The detection system demonstrated sufficient sensitivity to detect single DNA molecules labeled with a fluorescent tag (AlexaFluor 660) identified through their characteristic emission wavelength and the burst of photons produced during their transit through the excitation volume. In its present configuration and fluidic architecture, the sample processing throughput was ∼4.02 × 105 molecules s−1, but could be increased dramatically through the use of narrower channels and a smaller pitch. The system was further evaluated using a single molecule-based fluorescence quenching assay for measuring the population differences between duplexed and single-stranded DNA molecules as a function of temperature for determining the duplex melting temperature, Tm. PMID:19082181

  20. Phthalocyanine adsorption to graphene on Ir(111): Evidence for decoupling from vibrational spectroscopy

    SciTech Connect

    Endlich, M. Gozdzik, S.; Néel, N.; Kröger, J.; Rosa, A. L. da; Frauenheim, T.; Wehling, T. O.

    2014-11-14

    Phthalocyanine molecules have been adsorbed to Ir(111) and to graphene on Ir(111). From a comparison of scanning tunneling microscopy images of individual molecules adsorbed to the different surfaces alone it is difficult to discern potential differences in the molecular adsorption geometry. In contrast, vibrational spectroscopy using inelastic electron scattering unequivocally hints at strong molecule deformations on Ir(111) and at a planar adsorption geometry on graphene. The spectroscopic evidence for the different adsorption configurations is supported by density functional calculations.

  1. Single molecule studies of RNA polymerase II transcription in vitro.

    PubMed

    Horn, Abigail E; Goodrich, James A; Kugel, Jennifer F

    2014-01-01

    Eukaryotic mRNA transcription by RNA polymerase II (RNAP II) is the first step in gene expression and a key determinant of cellular regulation. Elucidating the mechanism by which RNAP II synthesizes RNA is therefore vital to determining how genes are controlled under diverse biological conditions. Significant advances in understanding RNAP II transcription have been achieved using classical biochemical and structural techniques; however, aspects of the transcription mechanism cannot be assessed using these approaches. The application of single-molecule techniques to study RNAP II transcription has provided new insight only obtainable by studying molecules in this complex system one at a time.

  2. DNA-psoralen interaction: A single molecule experiment

    NASA Astrophysics Data System (ADS)

    Rocha, M. S.; Viana, N. B.; Mesquita, O. N.

    2004-11-01

    By attaching one end of a single λ-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the λ-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particulary interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

  3. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.

  4. Advances in magnetic tweezers for single molecule and cell biophysics.

    PubMed

    Kilinc, Devrim; Lee, Gil U

    2014-01-01

    Magnetic tweezers (MTW) enable highly accurate forces to be transduced to molecules to study mechanotransduction at the molecular or cellular level. We review recent MTW studies in single molecule and cell biophysics that demonstrate the flexibility of this technique. We also discuss technical advances in the method on several fronts, i.e., from novel approaches for the measurement of torque to multiplexed biophysical assays. Finally, we describe multi-component nanorods with enhanced optical and magnetic properties and discuss their potential as future MTW probes.

  5. Supramolecular 3d-4f single-molecule magnet architectures.

    PubMed

    Schmitz, Sebastian; van Leusen, Jan; Izarova, Natalya V; Lan, Yanhua; Wernsdorfer, Wolfgang; Kögerler, Paul; Monakhov, Kirill Yu

    2016-10-18

    The nanosized self-assemblies {[{Ln(III)}{H2O⊂CrLn}]2(H2O)} (Ln = Dy, 1 and Tb, 2) based on new 3d-4f mixed-metal coordination topologies are formed via extensive intramolecular hydrogen bonding that is directed by enclosed water molecules. Compounds 1 and 2 show single-molecule magnet characteristics manifested by hysteresis loops up to 1.6 K (Ueff = 8.3 cm(-1)) and 1 K (Ueff = 3.4 cm(-1)), respectively.

  6. Single molecule studies of helicases with magnetic tweezers.

    PubMed

    Hodeib, Samar; Raj, Saurabh; Manosas, M; Zhang, Weiting; Bagchi, Debjani; Ducos, Bertrand; Allemand, Jean-François; Bensimon, David; Croquette, Vincent

    2016-08-01

    Helicases are a broad family of enzymes that perform crucial functions in DNA replication and in the maintenance of DNA and RNA integrity. A detailed mechanical study of helicases on DNA and RNA is possible using single molecule manipulation methods. Among those, magnetic tweezers (or traps) present a convenient, moderate throughput assay (tens of enzymes can be monitored simultaneously) that allow for high resolution (single base-pair) studies of these enzymes in various conditions and on various substrates (double and single stranded DNA and RNA). Here we discuss various implementation of the basic assay relevant for these studies.

  7. Detection of pathogenic DNA at the single-molecule level

    NASA Astrophysics Data System (ADS)

    Yahiatène, Idir; Klamp, Tobias; Schüttpelz, Mark; Sauer, Markus

    2011-03-01

    We demonstrate ultrasensitive detection of pathogenic DNA in a homogeneous assay at the single-molecule level applying two-color coincidence analysis. The target molecule we quantify is a 100 nucleotide long synthetic single-stranded oligonucleotide adapted from Streptococcus pneumoniae, a bacterium causing lower respiratory tract infections. Using spontaneous hybridization of two differently fluorescing Molecular Beacons we demonstrate a detection sensitivity of 100 fM (10-13M) in 30 seconds applying a simple microfluidic device with a 100 μm channel and confocal two-color fluorescence microscopy.

  8. 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

  9. The statistics of single molecule detection: An overview

    SciTech Connect

    Enderlein, J.; Robbins, D.L.; Ambrose, W.P.

    1995-12-31

    An overview of our recent results in modeling single molecule detection in fluid flow is presented. Our mathematical approach is based on a path integral representation. The model accounts for all experimental details, such as light collection, laser excitation, hydrodynamics and diffusion, and molecular photophysics. Special attention is paid to multiple molecule crossings through the detection volume. Numerical realization of the theory is discussed. Measurements of burst size distributions in single B-phycoerythrin molecule detection experiments are presented and compared with theoretical predictions.

  10. Single Molecule Studies on Dynamics in Liquid Crystals

    PubMed Central

    Täuber, Daniela; von Borczyskowski, Christian

    2013-01-01

    Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC. PMID:24077123

  11. How fissors works: observing vibrationally adiabatic conformational change through femtosecond stimulated Raman spectroscopy.

    PubMed

    Cina, Jeffrey A; Kovac, Philip A

    2013-07-25

    With the help of a two-dimensional model system comprising a slow conformational degree of freedom and a higher-frequency vibration, we investigate the molecular-level origin and dynamical information content of femtosecond stimulated Raman spectroscopy (fissors) signals. Our treatment avails itself of the time scale separation between conformational and vibrational modes by incorporating a vibrationally adiabatic approximation to the conformational dynamics. We derive an expression for the fissors signal without resort to the macroscopic concepts of light- and phonon-wave propagation employed in prior coupled-wave analyses. Numerical calculations of fissors spectra illustrate the case of relatively small conformational mass (still large enough that conformational motion does not induce any change in the vibrational quantum number) in which conformational sidebands accompany a central peak in the Raman gain at a conformationally averaged vibrational transition frequency, and the case of a larger conformational mass in which the sidebands merge with the central peak and the frequency of the latter tracks the time-evolving conformational coordinate.

  12. Vibrational spectroscopy studies of formalin-fixed cervix tissues.

    PubMed

    Krishna, C M; Sockalingum, G D; Vadhiraja, B M; Maheedhar, K; Rao, A C K; Rao, L; Venteo, L; Pluot, M; Fernandes, D J; Vidyasagar, M S; Kartha, V B; Manfait, M

    2007-02-15

    Optical histopathology is fast emerging as a potential tool in cancer diagnosis. Fresh tissues in saline are ideal samples for optical histopathology. However, evaluation of suitability of ex vivo handled tissues is necessitated because of severe constraints in sample procurement, handling, and other associated problems with fresh tissues. Among these methods, formalin-fixed samples are shown to be suitable for optical histopathology. However, it is necessary to further evaluate this method from the point of view discriminating tissues with minute biochemical variations. A pilot Raman and Fourier transform infrared (FTIR) microspectroscopic studies of formalin-fixed tissues normal, malignant, and after-2-fractions of radiotherapy from the same malignant cervix subjects were carried out, with an aim to explore the feasibility of discriminating these tissues, especially the tissues after-2-fractions of radiotherapy from other two groups. Raman and FTIR spectra exhibit large differences for normal and malignant tissues and subtle differences are seen between malignant and after-2-fractions of radiotherapy tissues. Spectral data were analyzed by principal component analysis (PCA) and it provided good discrimination of normal and malignant tissues. PCA of data of three tissues, normal, malignant, and 2-fractions after radiotherapy, gave two clusters corresponding to normal and malignant + after-2-fractions of radiotherapy tissues. A second step of PCA was required to achieve discrimination between malignant and after-2-fractions of radiotherapy tissues. Hence, this study not only further supports the use of formalin-fixed tissues in optical histopathology, especially from Raman spectroscopy point of view, it also indicates feasibility of discriminating tissues with minute biochemical differences such as malignant and after-2-fractions of radiotherapy.

  13. Vibrational spectral signatures of crystalline cellulose using high resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS)

    DOE PAGES

    Zhang, Libing; Lu, Zhou; Velarde, Luis; ...

    2015-03-03

    Both the C–H and O–H region spectra of crystalline cellulose were studied using the sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) for the first time. The resolution of HR-BB-SFG-VS is about 10-times better than conventional scanning SFG-VS and has the capability of measuring the intrinsic spectral lineshape and revealing many more spectral details. With HR-BB-SFG-VS, we found that in cellulose samples from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the O–H region were unique for the two allomorphs, i.e. Iα and Iβ, while the spectral signaturesmore » in the C–H regions varied in all samples examined. Even though the origin of the different spectral signatures of the crystalline cellulose in the O–H and C–H vibrational frequency regions are yet to be correlated to the structure of cellulose, these results lead to new spectroscopic methods and opportunities to classify and to understand the basic crystalline structures, as well as variations in polymorphism of the crystalline cellulose.« less

  14. Vibrational Spectral Signatures of Crystalline Cellulose Using High Resolution Broadband Sum Frequency Generation Vibrational Spectroscopy (HR-BB-SFG-VS)

    SciTech Connect

    Zhang, Libing; Lu, Zhou; Velarde Ruiz Esparza, Luis A.; Fu, Li; Pu, Yunqiao; Ding, Shi-You; Ragauskas, Art J.; Wang, Hongfei; Yang, Bin

    2015-03-03

    Here we reported the first sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) study on both the C-H and O-H region spectra of crystalline cellulose. HR-BB-SFG-VS has about 10 times better resolution than the conventional scanning SFG-VS and is known to be able to measure the intrinsic spectral lineshape and to resolve much more spectral details. With HR-BB-SFG-VS, we found that in cellulose from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the OH regions were unique for different allomorphs, i.e. Iα and Iβ, while the spectral signatures in the C-H regions varied in all samples examined. Even though the origin of the different behaviors of the crystalline cellulose in the O-H and C-H vibrational frequency regions is yet to be correlated to the structure of cellulose, these results provided new spectroscopic methods and opportunities to classify and understand the basic crystalline structure, as well as variations, in polymorphism of the crystalline cellulose structure.

  15. Vibrational Spectra and Adsorption of Trisiloxane Superspreading Surfactant at Air/Water Interface Studied with Sum Frequency Generation Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Feng, Jun; Wu, Dan; Wen, Jia; Liu, Shi-lin; Wang, Hong-fei

    2008-08-01

    The C-H stretch vibrational spectra of the trisiloxane superspreading surfactant Silwet L-77 ((CH3)3Si-O-Si(CH3)(C3H6)(OCH2CH2)7-8OCH3)-O-Si(CH3)3) at the air/water interface are measured with the surface Sum Frequency Generation Vibrational Spectroscopy (SFG-VS). The spectra are dominated with the features from the -Si-CH3 groups around 2905 cm-1 (symmetric stretch or SS mode) and 2957 cm-1 (mostly the asymmetric stretch or AS mode), and with the weak but apparent contribution from the -O-CH2- groups around 2880 cm-1 (symmetric stretch or SS mode). Comparison of the polarization dependent SFG spectra below and above the critical aggregate or micelle concentration (CAC) indicates that the molecular orientation of the C-H related molecular groups remained unchanged at different surface densities of the Silwet L-77 surfactant. The SFG-VS adsorption isotherm suggested that there was no sign of Silwet L-77 bilayer structure formation at the air/water interface. The Gibbs adsorption free energy of the Silwet surfactant to the air/water interface is -42.2±0.8kcal/mol, indicating the unusually strong adsorption ability of the Silwet L-77 superspreading surfactant.

  16. Vibrational spectral signatures of crystalline cellulose using high resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS)

    SciTech Connect

    Zhang, Libing; Lu, Zhou; Velarde, Luis; Fu, Li; Pu, Yunqiao; Ding, Shi-You; Ragauskas, Arthur; Wang, Hong-Fei; Yang, Bin

    2015-03-03

    Both the C–H and O–H region spectra of crystalline cellulose were studied using the sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) for the first time. The resolution of HR-BB-SFG-VS is about 10-times better than conventional scanning SFG-VS and has the capability of measuring the intrinsic spectral lineshape and revealing many more spectral details. With HR-BB-SFG-VS, we found that in cellulose samples from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the O–H region were unique for the two allomorphs, i.e. Iα and Iβ, while the spectral signatures in the C–H regions varied in all samples examined. Even though the origin of the different spectral signatures of the crystalline cellulose in the O–H and C–H vibrational frequency regions are yet to be correlated to the structure of cellulose, these results lead to new spectroscopic methods and opportunities to classify and to understand the basic crystalline structures, as well as variations in polymorphism of the crystalline cellulose.

  17. Mechanism for Si–Si Bond Rupture in Single Molecule Junctions

    SciTech Connect

    Li, Haixing; Kim, Nathaniel T.; Su, Timothy A.; Steigerwald, Michael L.; Nuckolls, Colin; Darancet, Pierre; Leighton, James L.; Venkataraman, Latha

    2016-12-14

    The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si–Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si–Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si–Si bond is ruptured using an applied voltage. We investigate this voltage induced Si–Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation of molecular vibrational modes by tunneling electrons leads to homolytic Si–Si bond rupture.

  18. DCDHF Fluorophores for Single-Molecule Imaging in Cells**

    PubMed Central

    Lord, Samuel J.; Conley, Nicholas R.; Lee, Hsiao-lu D.; Nishimura, Stefanie Y.; Pomerantz, Andrea K.; Willets, Katherine A.; Lu, Zhikuan; Wang, Hui; Liu, Na; Samuel, Reichel; Weber, Ryan; Semyonov, Alexander; He, Meng; Twieg, Robert J.; Moerner, W. E.

    2009-01-01

    There is a persistent need for small-molecule fluorescent labels optimized for single-molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red-shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed “DCDHF” fluorophores, for use in live-cell imaging based on the push–pull design: an amine donor group and a 2-dicyanomethylene-3-cyano-2,5-dihydrofuran (DCDHF) acceptor group, separated by a π-rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red-emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low-intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small-molecule fluorophores, which are needed for super-resolution imaging schemes that require active control (here turning-on) of single-molecule emission. PMID:19025732

  19. Visualizing helicases unwinding DNA at the single molecule level.

    PubMed

    Fili, Natali; Mashanov, Gregory I; Toseland, Christopher P; Batters, Christopher; Wallace, Mark I; Yeeles, Joseph T P; Dillingham, Mark S; Webb, Martin R; Molloy, Justin E

    2010-07-01

    DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes.

  20. 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

  1. Identifying mechanisms of interfacial dynamics using single-molecule tracking.

    PubMed

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

    2012-08-28

    The "soft" (i.e., noncovalent) interactions between molecules and surfaces are complex and highly varied (e.g., hydrophobic, hydrogen bonding, and ionic), often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from the spatial variation of the surface/interface itself or from molecular configurations (i.e., conformation, orientation, aggregation state, etc.). By observing the 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 track the molecular configuration and simultaneously 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.

  2. Multiplexed single-molecule force proteolysis measurements using magnetic tweezers.

    PubMed

    Adhikari, Arjun S; Chai, Jack; Dunn, Alexander R

    2012-07-25

    The generation and detection of mechanical forces is a ubiquitous aspect of cell physiology, with direct relevance to cancer metastasis(1), atherogenesis(2) and wound healing(3). In each of these examples, cells both exert force on their surroundings and simultaneously enzymatically remodel the extracellular matrix (ECM). The effect of forces on ECM has thus become an area of considerable interest due to its likely biological and medical importance(4-7). Single molecule techniques such as optical trapping(8), atomic force microscopy(9), and magnetic tweezers(10,11) allow researchers to probe the function of enzymes at a molecular level by exerting forces on individual proteins. Of these techniques, magnetic tweezers (MT) are notable for their low cost and high throughput. MT exert forces in the range of ~1-100 pN and can provide millisecond temporal resolution, qualities that are well matched to the study of enzyme mechanism at the single-molecule level(12). Here we report a highly parallelizable MT assay to study the effect of force on the proteolysis of single protein molecules. We present the specific example of the proteolysis of a trimeric collagen peptide by matrix metalloproteinase 1 (MMP-1); however, this assay can be easily adapted to study other substrates and proteases.

  3. Single molecule studies of the neuronal SNARE fusion machinery

    PubMed Central

    Brunger, Axel T.; Weninger, Keith; Bowen, Mark; Chu, Steven

    2010-01-01

    SNAREs are essential components of the machinery for Ca2+-triggered fusion of synaptic vesicles with the plasma membrane, resulting in neurotransmitter release into the synaptic cleft. While much is known about their biophysical and structural properties and their interactions with accessory proteins such as the Ca2+ sensor synaptotagmin, their precise role in membrane fusion remains an enigma. Ensemble studies of liposomes with reconstituted SNAREs have demonstrated that SNAREs and accessory proteins can trigger lipid mixing/fusion, but the inability to study individual fusion events has precluded molecular insights into the fusion process. Thus, this field is ripe for studies with single molecule methodology. In this review we discuss first applications of single-molecule approaches to observe reconstituted SNAREs, their complexes, associated proteins, and their effect on biological membranes. Some of the findings are provocative, such the possibility of parallel and anti-parallel SNARE complexes, or vesicle docking with only syntaxin and synaptobrevin, but have been confirmed by other experiments. PMID:19489736

  4. Dual-Colored DNA Comb Polymers for Single Molecule Rheology

    NASA Astrophysics Data System (ADS)

    Mai, Danielle; Marciel, Amanda; Schroeder, Charles

    2014-03-01

    We report the synthesis and characterization of branched biopolymers for single molecule rheology. In our work, we utilize a hybrid enzymatic-synthetic approach to graft ``short'' DNA branches to ``long'' DNA backbones, thereby producing macromolecular DNA comb polymers. The branches and backbones are synthesized via polymerase chain reaction with chemically modified deoxyribonucleotides (dNTPs): ``short'' branches consist of Cy5-labeled dNTPs and a terminal azide group, and ``long'' backbones contain dibenzylcyclooctyne-modified (DBCO) dNTPs. In this way, we utilize strain-promoted, copper-free cycloaddition ``click'' reactions for facile grafting of azide-terminated branches at DBCO sites along backbones. Copper-free click reactions are bio-orthogonal and nearly quantitative when carried out under mild conditions. Moreover, comb polymers can be labeled with an intercalating dye (e.g., YOYO) for dual-color fluorescence imaging. We characterized these materials using gel electrophoresis, HPLC, and optical microscopy, with atomic force microscopy in progress. Overall, DNA combs are suitable for single molecule dynamics, and in this way, our work holds the potential to improve our understanding of topologically complex polymer melts and solutions.

  5. High contrast single molecule tracking in the pericellular coat

    NASA Astrophysics Data System (ADS)

    Scrimgeour, Jan; McLane, Louis T.; Curtis, Jennifer E.

    2014-03-01

    The pericellular coat is a robust, hydrated, polymer brush-like structure that can extend several micrometers into the extracellular space around living cells. By controlling access to the cell surface, acting as a filter and storage reservoir for proteins, and actively controlling tissue-immune system interactions, the cell coat performs many important functions at scales ranging from the single cell to whole tissues. The cell coat consists of a malleable backbone - the large polysaccharide hyaluronic acid (HA) - with its structure, material properties, and ultimately its bio-functionality tuned by a diverse set of HA binding proteins. These proteins add charge, cross-links and growth factor-like ligands to the coat To probe the dynamic behavior of this soft biomaterial we have used high contrast single molecule imaging, based on highly inclined laser illumination, to observe individual fluorescently labeled HA binding proteins within the cell coat. Our work focuses on the cell coat of living chondrocyte (cartilage) cells, and in particular the effect of the large, highly charged, protein aggrecan on the properties of the coat. Through single molecule imaging we observe that aggrecan is tightly tethered to HA, and plays an important role in cell coat extension and stiffening.

  6. Temperature-cycle single-molecule FRET microscopy on polyprolines.

    PubMed

    Yuan, Haifeng; Xia, Ted; Schuler, Benjamin; Orrit, Michel

    2011-02-07

    Accessing the microsecond dynamics of a single fluorescent molecule in real time is difficult because molecular fluorescence rates usually limit the time resolution to milliseconds. We propose to apply single-molecule temperature-cycle microscopy to probe molecular dynamics at microsecond timescales. Here, we follow donor and acceptor signals of single FRET-labeled polyprolines in glycerol to investigate their conformational dynamics. We observe a steady-state FRET efficiency distribution which differs from theoretical distributions for isotropically orientated fluorescent labels. This may indicate that the orientation of fluorescent labels in glycerol is not isotropic and may reflect the influence of the dye linkers. With proper temperature-cycle parameters, we observed large FRET changes in long series of cycles of the same molecule. We attribute the main conformational changes to reorientations of the fluorescent labels with respect to the oligopeptide chain, which take place in less than a few microseconds at the highest temperature of the cycle (250 K). We were able to follow the FRET efficiency of a particular construct for more than 2000 cycles. This trajectory displays switching between two conformations, which give rise to maxima in the FRET efficiency histogram. Our experiments open the possibility to study biomolecular dynamics at a time scale of a few microseconds at the single-molecule level.

  7. Single-Molecule Electrical Random Resequencing of DNA and RNA

    NASA Astrophysics Data System (ADS)

    Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

    2012-07-01

    Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

  8. Single-molecule enzymology à la Michaelis-Menten.

    PubMed

    Grima, Ramon; Walter, Nils G; Schnell, Santiago

    2014-01-01

    Over the past 100 years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years, sophisticated experimental techniques have been developed that begin to allow the measurement of enzyme-catalysed and other biopolymer-mediated reactions inside single cells at the single-molecule level. Time-course data obtained using these methods are considerably noisy because molecule numbers within cells are typically quite small. As a consequence, the interpretation and analysis of single-cell data requires stochastic methods, rather than deterministic rate equations. Here, we concisely review both experimental and theoretical techniques that enable single-molecule analysis, with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid-20th century to its modern-day status. We discuss the differences between stochastic and deterministic rate equation models, how these depend on enzyme molecule numbers and substrate inflow into the reaction compartment, and how estimation of rate constants from single-cell data is possible using recently developed stochastic approaches.

  9. Single-molecule microscopy using tunable nanoscale confinement

    NASA Astrophysics Data System (ADS)

    McFaul, Christopher M. J.; Leith, Jason; Jia, Bojing; Michaud, François; Arsenault, Adriel; Martin, Andrew; Berard, Daniel; Leslie, Sabrina

    2013-09-01

    We present the design, construction and implementation of a modular microscopy device that transforms a basic inverted fluorescence microscope into a versatile single-molecule imaging system. The device uses Convex Lens- Induced Confinement (CLIC) to improve background rejection and extend diffusion-limited observation time. To facilitate its integration into a wide range of laboratories, this implementation of the CLIC device can use a standard flow-cell, into which the sample is loaded. By mechanically deforming the flow-cell, the device creates a tunable, wedge-shaped imaging chamber which we have modeled using finite element analysis simulations and characterized experimentally using interferometry. A powerful feature of CLIC imaging technology is the ability to examine single molecules under a continuum of applied confinement, from the nanometer to the micrometer scale. We demonstrate, using freely diffusing λ-phage DNA, that when the imposed confinement is on the scale of individual molecules their molecular conformations and diffusivity are altered significantly. To improve the flow-cell stiffness, seal, and re-usability, we have innovated the fabrication of thin PDMS-bonded flow-cells. The presented flow-cell CLIC technology can be combined with surface-lithography to provide an accessible and powerful approach to tune, trap, and image individual molecules under an extended range of imaging conditions. It is well-suited to tackling open problems in biophysics, biotechnology, nanotechnology, materials science, and chemistry.

  10. 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

  11. Mechanobiology of Short DNA Molecules: A Single Molecule Perspective

    NASA Astrophysics Data System (ADS)

    Raghunathan, Krishnan

    Mechanical properties of DNA are known to play a significant role in several biological processes like wrapping of DNA around histones and looping. Most of these cellular events occur on a DNA length scale of a few hundred basepairs. Single molecule methods have been highly successful in directly investigating heterogeneity in different biomolecular systems and serve as ideal tools to study the mechanical properties of DNA. However, their use in studying DNA of contour lengths less than a kilobase are fraught with experimental difficulties. The research presented in this thesis explores the behavior of short stretches of DNA (≤ 500bp) using existing and novel single molecule methods. We have quantified the variation in persistence lengths between sequences having different elasticity using a constant force axial optical tweezers. Our experiments have also revealed that this difference in persistence lengths manifests itself as a difference in looping lifetimes of lac repressor, in sequences having the aforementioned constructs as the intervening sequence between the operator sites. We have also developed a system to probe DNA dynamics in vivo. We have found that the active processes in the cell have distinct effects on dynamics of DNA and eliminating the active processes causes a 'phase transition' like behavior in the inside the cell. We are currently extending this technique to understand DNA dynamics inside bacterial systems. Our results provide vital insights into mechanical properties of DNA and the effect of athermal fluctuations on DNA dynamics.

  12. Exciton-vibrational coupling in the dynamics and spectroscopy of Frenkel excitons in molecular aggregates

    NASA Astrophysics Data System (ADS)

    Schröter, M.; Ivanov, S. D.; Schulze, J.; Polyutov, S. P.; Yan, Y.; Pullerits, T.; Kühn, O.

    2015-03-01

    The influence of exciton-vibrational coupling on the optical and transport properties of molecular aggregates is an old problem that gained renewed interest in recent years. On the experimental side, various nonlinear spectroscopic techniques gave insight into the dynamics of systems as complex as photosynthetic antennae. Striking evidence was gathered that in these protein-pigment complexes quantum coherence is operative even at room temperature conditions. Investigations were triggered to understand the role of vibrational degrees of freedom, beyond that of a heat bath characterized by thermal fluctuations. This development was paralleled by theory, where efficient methods emerged, which could provide the proper frame to perform non-Markovian and non-perturbative simulations of exciton-vibrational dynamics and spectroscopy. This review summarizes the state of affairs of the theory of exciton-vibrational interaction in molecular aggregates and photosynthetic antenna complexes. The focus is put on the discussion of basic effects of exciton-vibrational interaction from the stationary and dynamics points of view. Here, the molecular dimer plays a prominent role as it permits a systematic investigation of absorption and emission spectra by numerical diagonalization of the exciton-vibrational Hamiltonian in a truncated Hilbert space. An extension to larger aggregates, having many coupled nuclear degrees of freedom, becomes possible with the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method for wave packet propagation. In fact it will be shown that this method allows one to approach the limit of almost continuous spectral densities, which is usually the realm of density matrix theory. Real system-bath situations are introduced for two models, which differ in the way strongly coupled nuclear coordinates are treated, as a part of the relevant system or the bath. A rather detailed exposition of the Hierarchy Equations Of Motion (HEOM) method will be

  13. Bunching effect in single-molecule T4 lysozyme nonequilibrium conformational dynamics under enzymatic reactions.

    PubMed

    Wang, Yuanmin; Lu, H Peter

    2010-05-20

    The bunching effect, implying that conformational motion times tend to bunch in a finite and narrow time window, is observed and identified to be associated with substrate-enzyme complex formation in T4 lysozyme conformational dynamics under enzymatic reactions. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. On the basis of the single-molecule spectroscopic results, molecular dynamics simulation, and a random walk model analysis, multiple intermediate states have been estimated in the evolution of T4 lysozyme enzymatic reaction active complex formation (Chen, Y.; Hu, D.; Vorpagel, E. R.; Lu, H. P. Probing single-molecule T4 lysozyme conformational dynamics by intramolecular fluorescence energy transfer. J. Phys. Chem. B 2003, 107, 7947-7956). In this Article, we report progress on the analysis of the reported experimental results, and we have identified the bunching effect of the substrate-enzyme active complex formation time in T4 lysozyme enzymatic reactions. We show that the bunching effect, a dynamic behavior observed for the catalytic hinge-bending conformational motions of T4 lysozyme, is a convoluted outcome of multiple consecutive Poisson rate processes that are defined by protein functional motions under substrate-enzyme interactions; i.e., convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. We suggest that the bunching effect is likely common in protein conformational dynamics involved in conformation-gated protein functions.

  14. Investigation of organometallic reaction mechanisms with one and two dimensional vibrational spectroscopy

    SciTech Connect

    Cahoon, James Francis

    2008-12-01

    One and two dimensional time-resolved vibrational spectroscopy has been used to investigate the elementary reactions of several prototypical organometallic complexes in room temperature solution. The electron transfer and ligand substitution reactions of photogenerated 17-electron organometallic radicals CpW(CO)3 and CpFe(CO)2 have been examined with one dimensional spectroscopy on the picosecond through microsecond time-scales, revealing the importance of caging effects and odd-electron intermediates in these reactions. Similarly, an investigation of the photophysics of the simple Fischer carbene complex Cr(CO)5[CMe(OMe)] showed that this class of molecule undergoes an unusual molecular rearrangement on the picosecond time-scale, briefly forming a metal-ketene complex. Although time-resolved spectroscopy has long been used for these types of photoinitiated reactions, the advent of two dimensional vibrational spectroscopy (2D-IR) opens the possibility to examine the ultrafast dynamics of molecules under thermal equilibrium conditions. Using this method, the picosecond fluxional rearrangements of the model metal carbonyl Fe(CO)5 have been examined, revealing the mechanism, time-scale, and transition state of the fluxional reaction. The success of this experiment demonstrates that 2D-IR is a powerful technique to examine the thermally-driven, ultrafast rearrangements of organometallic molecules in solution.

  15. 2012 SINGLE MOLECULE APPROACHES TO BIOLOGY GORDON RESEARCH CONFERENCE (JULY 15-20, 2012 - MOUNT SNOW RESORT, WEST DOVER VT)

    SciTech Connect

    Fernandez, Julio

    2012-04-20

    Single molecule techniques are rapidly occupying a central role in biological research at all levels. This transition was made possible by the availability and dissemination of robust techniques that use fluorescence and force probes to track the conformation of molecules one at a time, in vitro as well as in live cells. Single-molecule approaches have changed the way many biological problems are studied. These novel techniques provide previously unobtainable data on fundamental biochemical processes that are essential for all forms of life. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of the molecular systems that underpin the functioning of living cells. Hence, our conference seeks to disseminate the implementation and use of single molecule techniques in the pursuit of new biological knowledge. Topics covered include: Molecular Motors on the Move; Origin And Fate Of Proteins; Physical Principles Of Life; Molecules and Super-resolution Microscopy; Nanoswitches In Action; Active Motion Or Random Diffusion?; Building Blocks Of Living Cells; From Molecular Mechanics To Physiology; Tug-of-war: Force Spectroscopy Of Single Proteins.

  16. Double resonant absorption measurement of acetylene symmetric vibrational states probed with cavity ring down spectroscopy

    NASA Astrophysics Data System (ADS)

    Karhu, J.; Nauta, J.; Vainio, M.; Metsälä, M.; Hoekstra, S.; Halonen, L.

    2016-06-01

    A novel mid-infrared/near-infrared double resonant absorption setup for studying infrared-inactive vibrational states is presented. A strong vibrational transition in the mid-infrared region is excited using an idler beam from a singly resonant continuous-wave optical parametric oscillator, to populate an intermediate vibrational state. High output power of the optical parametric oscillator and the strength of the mid-infrared transition result in efficient population transfer to the intermediate state, which allows measuring secondary transitions from this state with a high signal-to-noise ratio. A secondary, near-infrared transition from the intermediate state is probed using cavity ring-down spectroscopy, which provides high sensitivity in this wavelength region. Due to the narrow linewidths of the excitation sources, the rovibrational lines of the secondary transition are measured with sub-Doppler resolution. The setup is used to access a previously unreported symmetric vibrational state of acetylene, ν 1 + ν 2 + ν 3 + ν4 1 + ν5 - 1 in the normal mode notation. Single-photon transitions to this state from the vibrational ground state are forbidden. Ten lines of the newly measured state are observed and fitted with the linear least-squares method to extract the band parameters. The vibrational term value was measured to be at 9775.0018(45) cm-1, the rotational parameter B was 1.162 222(37) cm-1, and the quartic centrifugal distortion parameter D was 3.998(62) × 10-6 cm-1, where the numbers in the parenthesis are one-standard errors in the least significant digits.

  17. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    DOE PAGES

    Rez, Peter; Aoki, Toshihiro; March, Katia; ...

    2016-03-10

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies o1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with nomore » observable radiation damage. Furthermore, the technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ~10nm, simultaneously combined with imaging in the electron microscope.« less

  18. Femtosecond Broadband Stimulated Raman: A New Approach for High-Performance Vibrational Spectroscopy

    PubMed Central

    McCAMANT, DAVID W.; KUKURA, PHILIPP; MATHIES, RICHARD A.

    2005-01-01

    Femtosecond stimulated Raman spectroscopy (FSRS) is a new technique that produces high-quality vibrational spectra free from background fluorescence. FSRS combines a narrow-bandwidth picosecond Raman pump pulse with an ∼80 fs continuum probe pulse to produce stimulated Raman spectra from the pump-induced gain in the probe spectrum. The high intensity of the Raman pump combined with the broad bandwidth of the probe produces high signal-to-noise vibrational spectra with very short data acquisition times. FSRS spectra of standard solutions and solvents such as aqueous Na2SO4, aqueous KNO3, methanol, isopropanol, and cyclohexane are collected in seconds. Furthermore, stimulated Raman spectra can be obtained using just a single pump–probe pulse pair that illuminates the sample for only ∼1 ps. Fluorescence rejection is demonstrated by collecting FSRS spectra of dyes (rhodamine 6G, chlorophyll a, and DTTCI) with varying degrees of fluorescence background and resonance enhancement. The high signal-to-noise, short data acquisition time, fluorescence rejection, and high spectral and temporal resolution of femtosecond stimulated Raman spectroscopy make it a valuable new vibrational spectroscopic technique. PMID:14658143

  19. Interpreting nonlinear vibrational spectroscopy with the classical mechanical analogs of double-sided Feynman diagrams.

    PubMed

    Noid, W G; Loring, Roger F

    2004-10-15

    Observables in coherent, multiple-pulse infrared spectroscopy may be computed from a vibrational nonlinear response function. This response function is conventionally calculated quantum-mechanically, but the challenges in applying quantum mechanics to large, anharmonic systems motivate the examination of classical mechanical vibrational nonlinear response functions. We present an approximate formulation of the classical mechanical third-order vibrational response function for an anharmonic solute oscillator interacting with a harmonic solvent, which establishes a clear connection between classical and quantum mechanical treatments. This formalism permits the identification of the classical mechanical analog of the pure dephasing of a quantum mechanical degree of freedom, and suggests the construction of classical mechanical analogs of the double-sided Feynman diagrams of quantum mechanics, which are widely applied to nonlinear spectroscopy. Application of a rotating wave approximation permits the analytic extraction of signals obeying particular spatial phase matching conditions from a classical-mechanical response function. Calculations of the third-order response function for an anharmonic oscillator coupled to a harmonic solvent are compared to numerically correct classical mechanical results.

  20. Single-molecule pulling and the folding of donor-acceptor oligorotaxanes: Phenomenology and interpretation

    NASA Astrophysics Data System (ADS)

    Franco, Ignacio; Schatz, George C.; Ratner, Mark A.

    2009-09-01

    The thermodynamic driving force in the folding of a class of oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy by atomic force microscopy experiments. The oligorotaxanes consist of cyclobis(paraquat-p-phenylene) rings threaded onto an oligomer of 1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in a high dielectric medium using MM3 as the force field. The resulting force versus extension isotherms show a mechanically unstable region in which the molecule unfolds and, for selected extensions, blinks in the force measurements between a high-force and a low-force regime. From the force versus extension data the molecular potential of mean force is reconstructed using the weighted histogram analysis method and decomposed into energetic and entropic contributions. The simulations indicate that the folding of the oligorotaxanes is energetically favored but entropically penalized, with the energetic contributions overcoming the entropy penalty and effectively driving the folding. In addition, an analogy between the single-molecule folding/unfolding events driven by the atomic force microscope (AFM) tip and the thermodynamic theory of first-order phase transitions is discussed. General conditions (on the molecule and the AFM cantilever) for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are also presented. In particular, it is shown that the mechanical stability properties observed during the extension are intimately related to the fluctuations in the force measurements.