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A review with 106 refs. The semiconductor industry has seen a remarkable miniaturization trend, driven by many scientific and technol. innovations. But if this trend is to continue, and provide ever faster and cheaper computers, the size of microelectronic circuit components will soon need to reach the scale of atoms or mols.-a goal that will require conceptually new device structures. The idea that a few mols., or even a single mol., could be embedded between electrodes and perform the basic functions of digital electronics-rectification, amplification and storage-was first put forward in the mid-1970s. The concept is now realized for individual components, but the economic fabrication of complete circuits at the mol. level remains challenging because of the difficulty of connecting mols. to one another. A possible soln. to this problem is 'mono-mol.' electronics, in which a single mol. will integrate the elementary functions and interconnections required for computation.

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A review. The local environment of a functional mol. or nanoscale assembly has tremendous impact on it and thus can be used for functional control. In addn., the local environment is crit. in the interface to the phys., chem., and biol. worlds beyond the assemblies that are the most common applications targeted. Functional measurements without local structural information lack key insight into both the details and the roles of the environment. This Account focuses on progress toward and challenges in the controlled assembly and measurements of functional nanostructures in well-defined environments. The study of single precise supramol. assemblies in well-defined environments offers unique insights into both interactions and function. By designing interactions between mols. and controlling assembly conditions, we can create and place atomically precise nanostructures. The tools to test the structures targeted and to measure the function of these assemblies are just now being developed and becoming available. Advances in this field have depended on gaining access to measurements at this scale. In particular, we recognize but do not yet understand the crit. role of the chem. and phys. environment of the assemblies. Likewise, we are just now realizing the important role that the substrates to which the assemblies are attached play in these processes. In order to develop a predictive understanding and the ability to design and to optimize functional assemblies, we must elucidate the phys., chem., and electronic couplings among the mols. in the assemblies and with their substrates. With a suite of at.- and mol.-resoln. anal. tools, we are able both to ascertain whether the targeted structures have been formed and to measure their function. One of the keys to our ability to det. structure and measure function has been the development and application of methods for the automated acquisition, anal., and assocns. of thousands or tens of thousands of single-mol./particle/assembly structural, dynamic, spectroscopic, and functional data points.

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A review. Supramol. chem. has a very large impact on chem. of current interest and the use of non-covalent but directional forces is appealing for the construction of supramol. architectures. The invention of scanning probe microscopy techniques has opened new doorways to study these concepts on surfaces. This review deals with recent progress in the study of two-dimensional supramol. self-assembly on surfaces probed by STM, with a special emphasis on structure, dynamics, and reactivity of hydrogen bonded systems.

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Proceedings of the National Academy of Sciences of the United States of America (2009), 106 (9), 2995-2999CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

We demonstrate single-mol. fluorescence imaging beyond the optical diffraction limit in 3 dimensions with a wide-field microscope that exhibits a double-helix point spread function (DH-PSF). The DH-PSF design features high and uniform Fisher information and has 2 dominant lobes in the image plane whose angular orientation rotates with the axial (z) position of the emitter. Single fluorescent mols. in a thick polymer sample are localized in single 500-ms acquisitions with 10- to 20-nm precision over a large depth of field (2 μm) by finding the center of the 2 DH-PSF lobes. By using a photoactivatable fluorophore, repeated imaging of sparse subsets with a DH-PSF microscope provides superresoln. imaging of high concns. of mols. in all 3 dimensions. The combination of optical PSF design and digital postprocessing with photoactivatable fluorophores opens up avenues for improving 3D imaging resoln. beyond the Rayleigh diffraction limit.

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Science (Washington, DC, United States) (2006), 311 (5767), 1600-1603CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

We directly obsd. real-time prodn. of single protein mols. in individual Escherichia coli cells. A fusion protein of a fast-maturing yellow fluorescent protein (YFP) and a membrane-targeting peptide was expressed under a repressed condition. The membrane-localized YFP can be detected with single-mol. sensitivity. We found that the protein mols. are produced in bursts, with each burst originating from a stochastically transcribed single mRNA mol., and that protein copy nos. in the bursts follow a geometric distribution. The quant. study of low-level gene expression demonstrates the potential of single-mol. expts. in elucidating the workings of fundamental biol. processes in living cells.

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A review. Single-mol. measurements provide unique information on heterogeneous populations of mols. They give access to the complete distribution of observables (rather than only their 1st moments), allow discrimination between static and dynamic heterogeneity of their properties, and enable the detection of rare events or a succession of events hidden by ensemble averaging and the impossibility to synchronize mols. Here, the authors describe applications of single-mol. fluorescence spectroscopic methods to the elucidation of protein structure, dynamics, and function, and more specifically to protein folding and conformational dynamics studies.

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Annual Review of Biochemistry (2008), 77 (), 51-76CODEN: ARBOAW; ISSN:0066-4154. (Annual Reviews Inc.)

A review. Ever since their introduction two decades ago, single-mol. (SM) fluorescence methods have matured and branched out to address numerous biol. questions, which were inaccessible via ensemble measurements. Among the current arsenal, SM fluorescence techniques have capabilities of probing the dynamic interactions of nucleic acids and proteins via Forster (fluorescence) resonance energy transfer (FRET), tracking single particles over microns of distances, and deciphering the rotational motion of multisubunit systems. In this exciting era of transitioning from in vitro to in vivo and in situ conditions, it is anticipated that SM fluorescence methodol. will become a common tool of mol. biol.

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Moffitt, J. R. ; Chemla, Y. R. ; Smith, S. B. ; Bustamante, C. Recent Advances in Optical Tweezers Annu. Rev. Biochem. 2008 , 77 , 205 – 228

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Recent advances in optical tweezers

Moffitt, Jeffrey R.; Chemla, Yann R.; Smith, Steven B.; Bustamante, Carlos

Annual Review of Biochemistry (2008), 77 (), 205-228CODEN: ARBOAW; ISSN:0066-4154. (Annual Reviews Inc.)

A review. It has been over 20 years since the pioneering work of Arthur Ashkin, and in the intervening years, the field of optical tweezers has grown tremendously. Optical tweezers are now being used in the investigation of an increasing no. of biochem. and biophys. processes, from the basic mech. properties of biol. polymers to the multitude of mol. machines that drive the internal dynamics of the cell. Innovation, however, continues in all areas of instrumentation and technique, with much of this work focusing on the refinement of established methods and on the integration of this tool with other forms of single-mol. manipulation or detection. Although tech. in nature, these developments have important implications for the expanded use of optical tweezers in biochem. research and thus should be of general interest. In this review, we address these recent advances and speculate on possible future developments.

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Muller, D. J. ; Dufrene, Y. F. Atomic Force Microscopy as a Multifunctional Molecular Toolbox in Nanobiotechnology Nat. Nanotechnol. 2008 , 3 , 261 – 269

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Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology

Muller Daniel J; Dufrene Yves F

Nature nanotechnology (2008), 3 (5), 261-9 ISSN:.

There is no expanded citation for this reference.

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Gross, L. ; Mohn, F. ; Moll, N. ; Liljeroth, P. ; Meyer, G. The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy Science 2009 , 325 , 1110 – 1114

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The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy

Gross, Leo; Mohn, Fabian; Moll, Nikolaj; Liljeroth, Peter; Meyer, Gerhard

Science (Washington, DC, United States) (2009), 325 (5944), 1110-1114CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images at.-scale features on surfaces, but resolving single atoms within an adsorbed mol. remains a great challenge because the tunneling current is primarily sensitive to the local electron d. of states close to the Fermi level. The authors demonstrate imaging of mols. with unprecedented at. resoln. by probing the short-range chem. forces with use of noncontact at. force microscopy. The key step is functionalizing the microscope's tip apex with suitable, atomically well-defined terminations, such as CO mols. These exptl. findings are corroborated by ab initio d. functional theory calcns. Comparison with theory shows that Pauli repulsion is the source of the at. resoln., whereas van der Waals and electrostatic forces only add a diffuse attractive background.

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Michl, J. ; Sykes, E. C. H. Molecular Rotors and Motors: Recent Advances and Future Challenges ACS Nano 2009 , 3 , 1042 – 1048

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Molecular Rotors and Motors: Recent Advances and Future Challenges

Michl, Josef; Sykes, E. Charles H.

ACS Nano (2009), 3 (5), 1042-1048CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)

A review. At the "Mol. Rotors and Motors" symposium of the Spring 2009 ACS National Meeting in Salt Lake City (March 22-26), a diverse mix of talks addressed many current issues in the field. Speakers described topics that varied from single-mol. rotors and nanomachines to exquisite synthetic approaches toward building functional materials and math. and computational methods aimed at uncovering design opportunities and highlighting the fundamental limitations of mol. motors. While the realization of building useful nanomachines remains far off, a general consensus abounded that investigating biol. systems and understanding the implications of the laws of thermodn. and quantum mechanics for the behavior of nanostructures will help drive important advances in the quest for mol. machinery. Mol. rotors were demonstrated to have practical applications as probes for microviscosity, and many speakers presented exptl. studies that indicated that highly directed translation and rotation of individual mols., as well as interacting dipolar arrays, are just around the corner. While this Nano Focus is not intended to be a comprehensive review of the subject, it will focus on several key advances that were presented at the ACS meeting and highlight future challenges for the field of mol. rotors and motors.

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Bustamante, C. ; Chemla, Y. R. ; Forde, N. R. ; Izhaky, D. Mechanical Processes in Biochemistry Annu. Rev. Biochem. 2004 , 73 , 705 – 748

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Mechanical processes in biochemistry

Bustamante, Carlos; Chemla, Yann R.; Forde, Nancy R.; Izhaky, David

Annual Review of Biochemistry (2004), 73 (), 705-748CODEN: ARBOAW; ISSN:0066-4154. (Annual Reviews Inc.)

A review. Mech. processes are involved in nearly every facet of the cell cycle. Mech. forces are generated in the cell during processes as diverse as chromosomal segregation, replication, transcription, translation, translocation of proteins across membranes, cell locomotion, and catalyzed protein and nucleic acid folding and unfolding, among others. Because force is a product of all these reactions, biochemists are beginning to directly apply external forces to these processes to alter the extent or even the fate of these reactions hoping to reveal their underlying mol. mechanisms. This review provides the conceptual framework to understand the role of mech. force in biochem.

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Zandvliet, H. J. W. ; van Houselt, A. Scanning Tunneling Spectroscopy Annu. Rev. Anal. Chem. 2009 , 2 , 37 – 55

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Scanning tunneling spectroscopy

Zandvliet, Harold J. W.; van Houselt, Arie

Annual Review of Analytical Chemistry (2009), 2 (), 37-55CODEN: ARACFU; ISSN:1936-1327. (Annual Reviews Inc.)

A review. The scanning tunneling microscope (STM) has revolutionized our ability to explore and manipulate at.-scale solid surfaces. In addn. to its unparalleled spatial power, the STM can study dynamical processes, such as mol. conformational changes, by recording current traces as a function of time. It can also be employed to measure the phys. properties of mols. or nanostructures down to the at. scale. Combining STM imaging with measurement of current-voltage (I-V) characteristics [i.e., scanning tunneling spectroscopy (STS)] at similar resoln. makes it possible to obtain a detailed map of the electronic structure of a surface. For many years, STM lacked chem. specificity; however, the recent development of STM-IETS (inelastic electron tunneling spectroscopy) has allowed us to measure the vibrational spectrum of a single mol. This review introduces and illustrates these recent developments with a few simple scholarly examples.

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Chen, F. ; Hihath, J. ; Huang, Z. F. ; Li, X. L. ; Tao, N. J. Measurement of Single-Molecule Conductance Annu. Rev. Phys. Chem. 2007 , 58 , 535 – 564

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Measurement of single-molecule conductance

Chen, Fang; Hihath, Joshua; Huang, Zhifeng; Li, Xiulan; Tao, N. J.

Annual Review of Physical Chemistry (2007), 58 (), 535-564CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews Inc.)

A review. What is the conductance of a single mol. This basic and seemingly simple question has been a difficult one to answer for both experimentalists and theorists. To det. the conductance of a mol., one must wire the mol. reliably to at least two electrodes. The conductance of the mol. thus depends not only on the intrinsic properties of the mol., but also on the electrode materials. Furthermore, the conductance is sensitive to the at.-level details of the mol.-electrode contact and the local environment of the mol. Creating identical contact geometries has been a challenging exptl. problem, and the lack of at.-level structural information of the contacts makes it hard to compare calcns. with measurements. Despite the difficulties, researchers have made substantial advances in recent years. This review provides an overview of the exptl. advances, discusses the advantages and drawbacks of different techniques, and explores remaining issues.

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Poggio, M. ; Degen, C. L. Force-Detected Nuclear Magnetic Resonance: Recent Advances and Future Challenges Nanotechnology 2010 , 21 , 342001−1 – 13

Maze, J. R. ; Stanwix, P. L. ; Hodges, J. S. ; Hong, S. ; Taylor, J. M. ; Cappellaro, P. ; Jiang, L. ; Dutt, M. V. G. ; Togan, E. ; Zibrov, A. S. et al. Nanoscale Magnetic Sensing with an Individual Electronic Spin in Diamond Nature 2008 , 455 , 644 – 648

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Nanoscale magnetic sensing with an individual electronic spin in diamond

Maze, J. R.; Stanwix, P. L.; Hodges, J. S.; Hong, S.; Taylor, J. M.; Cappellaro, P.; Jiang, L.; Dutt, M. V. Gurudev; Togan, E.; Zibrov, A. S.; Yacoby, A.; Walsworth, R. L.; Lukin, M. D.

Nature (London, United Kingdom) (2008), 455 (7213), 644-647CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Detection of weak magnetic fields with nanoscale spatial resoln. is an outstanding problem in the biol. and phys. sciences. For example, at a distance of 10 nm, the spin of a single electron produces a magnetic field of ∼1 μT, and the corresponding field from a single proton is a few nanoteslas. A sensor able to detect such magnetic fields with nanometer spatial resoln. would enable powerful applications, ranging from the detection of magnetic resonance signals from individual electron or nuclear spins in complex biol. mols. to readout of classical or quantum bits of information encoded in an electron or nuclear spin memory. Here the authors exptl. demonstrate an approach to such nanoscale magnetic sensing, using coherent manipulation of an individual electronic spin qubit assocd. with a nitrogen-vacancy impurity in diamond at room temp. Using an ultra-pure diamond sample, the authors achieve detection of 3 nT magnetic fields at kilohertz frequencies after 100 s of averaging. The authors demonstrate a sensitivity of 0.5 μT Hz-1/2 for a diamond nanocrystal with a diam. of 30 nm.

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Xue, Q. F. ; Yeung, E. S. Differences in the Chemical-Reactivity of Individual Molecules of an Enzyme Nature 1995 , 373 , 681 – 683

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Differences in the chemical reactivity of individual molecules of an enzyme

Xue, Qifeng; Yeung, Edward S.

Nature (London) (1995), 373 (6516), 681-3CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)

Much attention has been focused recently on the detection and phys. characterization of individual mols. Using methods to study chem. properties, such as reactivity, of single mols. offers the potential to investigate how these might vary from mol. to mol., and for individual mols. as a function of time. The complex structures of biomols., such as enzymes, make them particularly attractive targets for studying how subtle changes or differences at the mol. level might influence chem. reactivity. The authors previously showed that very small (zeptomole) amts. of enzymes could be studied using a fluorescence microassay; single enzyme mols. have also been detected in oil-dispersed droplets by fluorescence microscopy. Here, the observation of reactions of individual mols. of lactate dehydrogenase isoenzyme 1 (LDH-1) is reported. When they were present at very low concns. in a narrow capillary, each enzyme mol. produced a discrete zone of NADH; these could be manipulated electrophoretically and monitored by fluorescence spectroscopy. It was found that the activity of individual electrophoretically pure enzyme mols. could vary by up to a factor of 4, and that these activities remained unchanged over a 2-h period. It was suggested that the origin of the activity differences may lie in the presence of several stable forms of the enzyme.

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Lu, H. P. ; Xun, L. Y. ; Xie, X. S. Single-Molecule Enzymatic Dynamics Science 1998 , 282 , 1877 – 1882

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Single-molecule enzymic dynamics

Lu, H. Peter; Xun, Luying; Xie, X. Sunney

Science (Washington, D. C.) (1998), 282 (5395), 1877-1882CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Enzymic turnovers of single cholesterol oxidase mols. were obsd. in real time by monitoring the emission from the enzyme's fluorescent active site, FAD. Statistical analyses of single-mol. trajectories revealed a significant and slow fluctuation in the rate of cholesterol oxidn. by FAD. The static disorder and dynamic disorder of reaction rates, which are essentially indistinguishable in ensemble-averaged expts., were detd. sep. by the real-time single-mol. approach. A mol. memory phenomenon, in which an enzymic turnover was not independent of its previous turnovers because of a slow fluctuation of protein conformation, was evidenced by spontaneous spectral fluctuation of FAD.

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Weiss, S. Measuring Conformational Dynamics of Biomolecules by Single Molecule Fluorescence Spectroscopy Nat. Struct. Mol. Biol. 2000 , 7 , 724 – 729

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Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy

Weiss, Shimon

Nature Structural Biology (2000), 7 (9), 724-729CODEN: NSBIEW; ISSN:1072-8368. (Nature America Inc.)

A review, with 51 refs. Dynamic structural changes of macromols. undergoing biochem. reactions can be studied using novel single mol. spectroscopy tools. Recent advances in applying such distance and orientation mol. rulers to biol. systems are reviewed, and future prospects and challenges are discussed.

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Jaklevic, R. C. ; Lambe, J. Molecular Vibration Spectra by Electron Tunneling Phys. Rev. Lett. 1966 , 17 , 1139 – 1140

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Molecular vibration spectra by electron tunneling

Jaklevic, Robert C.; Lambe, John

Physical Review Letters (1966), 17 (22), 1139-40CODEN: PRLTAO; ISSN:0031-9007.

The conductance of metal-metal oxide-metal tunnel junctions has been observed to increase at certain characteristic bias voltages (0.050-0.5 v.). These voltages are identified with vibrational frequencies of mols. contained in the barrier. Tunneling electrons interact with vibrational states of mols. included at a metal-oxide interface. The tunneling structures studied were Al-Al oxide-Pb, Ta-Ta oxide-Pb, Al-Al oxide-Sn, and Al-Al oxide-Al, at 0.9-300°K.

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Lambe, J. ; Jaklevic, R. C. Molecular Vibration Spectra by Inelastic Electron Tunneling Phys. Rev. 1968 , 165 , 821 – 832

Smith, D. J. The Realization of Atomic Resolution with the Electron Microscope Rep. Prog. Phys. 1997 , 60 , 1513 – 1580

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The realization of atomic resolution with the electron microscope

Smith, David J.

Reports on Progress in Physics (1997), 60 (12), 1513-1580CODEN: RPPHAG; ISSN:0034-4885. (Institute of Physics Publishing)

A review with many refs. The high-resoln. electron microscope has evolved into a sophisticated instrument that is capable of routinely providing quant. structural information on the at. scale. Applications of at.-resoln. imaging can now be found in many scientific fields, and its impact on the knowledge and understanding of atomistic processes has been profound. Better control over instrumental parameters, enhanced reliability of signal recording, and novel methods for imaging and data processing are areas of highly active, ongoing research. Agreement over reliability factors, serious discrepancies in abs. contrast levels, and inversion of crystal scattering are identified as unresolved issues requiring further attention.

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Donhauser, Z. J. ; Mantooth, B. A. ; Kelly, K. F. ; Bumm, L. A. ; Monnell, J. D. ; Stapleton, J. J. ; Price, D. W. ; Rawlett, A. M. ; Allara, D. L. ; Tour, J. M. et al. Conductance Switching in Single Molecules through Conformational Changes Science 2001 , 292 , 2303 – 2307

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Conductance switching in single molecules through conformational changes

Donhauser, Z. J.; Mantooth, B. A.; Kelly, K. F.; Bumm, L. A.; Monnell, J. D.; Stapleton, J. J.; Price, D. W., Jr.; Rawlett, A. M.; Allara, D. L.; Tour, J. M.; Weiss, P. S.

Science (Washington, DC, United States) (2001), 292 (5525), 2303-2307CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

The authors tracked over time the conductance switching of single and bundled phenylene ethynylene oligomers isolated in matrixes of alkanethiolate monolayers. The persistence times for isolated and bundled mols. in either the ON or OFF switch state range from seconds to tens of hours. When the surrounding matrix is well ordered, the rate at which the inserted mols. switch is low. Conversely, when the surrounding matrix is poorly ordered, the inserted mols. switch more often. The switching is a result of conformational changes in the mols. or bundles, rather than electrostatic effects of charge transfer.

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Moerner, W. E. ; Orrit, M. Illuminating Single Molecules in Condensed Matter Science 1999 , 283 , 1670 – 1676

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Illuminating single molecules in condensed matter

Moerner, W. E.; Orrit, Michel

Science (Washington, D. C.) (1999), 283 (5408), 1670-1676CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

A review, with 76 refs. 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 mols. in complex condensed matter environments. This ultimate method for unraveling ensemble avs. leads to the observation of new effects and to direct measurements of stochastic fluctuations. Expts. at cryogenic temps. open new directions in mol. spectroscopy, quantum optics, and solid-state dynamics. Room-temp. studies apply several techniques (polarization microscopy, single-mol. imaging, emission time dependence, energy transfer, Lifetime studies, and the Like) to a growing array of biophys. problems where new insight may be gained from direct observations of hidden static and dynamic inhomogeneity.

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Giepmans, B. N. G. ; Adams, S. R. ; Ellisman, M. H. ; Tsien, R. Y. The Fluorescent Toolbox for Assessing Protein Location and Function Science 2006 , 312 , 217 – 224

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The Fluorescent Toolbox for Assessing Protein Location and Function

Giepmans, Ben N. G.; Adams, Stephen R.; Ellisman, Mark H.; Tsien, Roger Y.

Science (Washington, DC, United States) (2006), 312 (5771), 217-224CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

A review. Advances in mol. biol., org. chem., and materials science have recently created several new classes of fluorescent probes for imaging in cell biol. Here the authors review the characteristic benefits and limitations of fluorescent probes to study proteins. The focus is on protein detection in live vs. fixed cells: detn. of protein expression, localization, activity state, and the possibility for combination of fluorescent light microscopy with electron microscopy. Small org. fluorescent dyes, nanocrystals ("quantum dots"), autofluorescent proteins, small genetic encoded tags that can be complexed with fluorochromes, and combinations of these probes are highlighted.

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Ha, T. ; Enderle, T. ; Chemla, D. S. ; Selvin, P. R. ; Weiss, S. Single Molecule Dynamics Studied by Polarization Modulation Phys. Rev. Lett. 1996 , 77 , 3979 – 3982

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Single molecular dynamics studied by polarization modulation

Ha, T.; Enderle, Th.; Chemla, D. S.; Selvin, P. R.; Weiss, S.

Physical Review Letters (1996), 77 (19), 3979-3982CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

We obsd. and made unambiguous distinctions between abrupt photophys. events of single mols.: a rotational jump of a single dipole, a transition to a dark state (reversible and irreversible photobleaching), and a spectral jump. The study was performed in the far field by modulating the excitation polarization and monitoring the fluorescence in time. This technique also allowed us to measure the in-plane dipole orientation of stationary single mol. dipoles with subdegree accuracy and to resolve desorption and readsorption of fluorophores from and onto a glass surface. In one case, clear evidence was obtained for rapid rotation of the dipole after a desorption process.

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Neuman, K. C. ; Nagy, A. Single-Molecule Force Spectroscopy: Optical Tweezers, Magnetic Tweezers and Atomic Force Microscopy Nat. Methods 2008 , 5 , 491 – 505

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

Neuman, Keir C.; Nagy, Attila

Nature Methods (2008), 5 (6), 491-505CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

A review. Single-mol. force spectroscopy has emerged as a powerful tool to investigate the forces and motions assocd. with biol. mols. and enzymic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and at. force microscopy. Here the authors describe these techniques and illustrate them with examples highlighting current capabilities and limitations.

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Moffitt, J. R. ; Chemla, Y. R. ; Izhaky, D. ; Bustamante, C. Differential Detection of Dual Traps Improves the Spatial Resolution of Optical Tweezers Proc. Natl. Acad. Sci. U.S.A. 2006 , 103 , 9006 – 9011

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Differential detection of dual traps improves the spatial resolution of optical tweezers

Moffitt, Jeffrey R.; Chemla, Yann R.; Izhaky, David; Bustamante, Carlos

Proceedings of the National Academy of Sciences of the United States of America (2006), 103 (24), 9006-9011CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

The drive toward more sensitive single-mol. manipulation techniques has led to the recent development of optical tweezers capable of resolving the motions of biol. systems at the subnanometer level, approaching the fundamental limit set by Brownian fluctuations. One successful approach has been the dual-trap optical tweezers, in which the system of study is held at both ends by microspheres in two sep. optical traps. The authors present here a theor. description of the Brownian limit on the spatial resoln. of such systems and verify these predictions by direct measurement in a Brownian noise-limited dual-trap optical tweezers. The authors find that by detecting the positions of both trapped microspheres, correlations in their motions can be exploited to maximize the resolving power of the instrument. Remarkably, the authors show that the spatial resoln. of dual optical traps with dual-trap detection is always superior to that of more traditional, single-trap designs, despite the added Brownian noise of the second trapped microsphere.

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Danilowicz, C. ; Lee, C. H. ; Kim, K. ; Hatch, K. ; Coljee, V. W. ; Kleckner, N. ; Prentiss, M. Single Molecule Detection of Direct, Homologous, DNA/DNA Pairing Proc. Natl. Acad. Sci. U.S.A. 2009 , 106 , 19824 – 19829

Weiss, P. S. ; Eigler, D. M. Site Dependence of the Apparent Shape of a Molecule in Scanning Tunneling Microscope Images—Benzene on Pt(111) Phys. Rev. Lett. 1993 , 71 , 3139 – 3142

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Scanning tunneling microscopy

Hansma, Paul K.; Tersoff, Jerry

Journal of Applied Physics (1987), 61 (2), R1-R23CODEN: JAPIAU; ISSN:0021-8979.

A review on scanning tunneling microscope (STM) at.-resoln. images of samples in ultra-high vacuum, moderate vacuum, gases including air at atm. pressure, and liqs. including oil, water, liq. nitrogen, and even conductive solns. Images of single-crystal metals, metal films, both elemental and compd. semiconductors, superconductors, layered materials, adsorbed atoms, and even DNA are presented. Lithog. results leads to speculations on a bright future in which STMs may not only observe, but also manipulate surfaces, right down to the at. level. 116 Refs.

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Urban, K. W. Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy Science 2008 , 321 , 506 – 510

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Studying Atomic Structures by Aberration-Corrected Transmission Electron Microscopy

Urban, Knut W.

Science (Washington, DC, United States) (2008), 321 (5888), 506-510CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

A review. Seventy-five years after its invention, TEM has taken a great step forward with the introduction of aberration-cor. electron optics. An entirely new generation of instruments enables studies in condensed-matter physics and materials science to be performed at at.-scale resoln. These new possibilities are meeting the growing demand of nanosciences and nanotechnol. for the at.-scale characterization of materials, nanosynthesized products and devices, and the validation of expected functions. Equipped with electron-energy filters and electron-energy-loss spectrometers, the new instruments allow studies not only of structure but also of elemental compn. and chem. bonding. The energy resoln. is ∼100 milli-eV, and the accuracy of spatial measurements has reached a few picometers. However, understanding the results is generally not straightforward and only possible with extensive quantum-mech. computer calcns.

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Eigler, D. M. ; Weiss, P. S. ; Schweizer, E. K. ; Lang, N. D. Imaging Xe with a Low-Temperature Scanning Tunneling Microscope Phys. Rev. Lett. 1991 , 66 , 1189 – 1192

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Imaging xenon with a low-temperature scanning tunneling microscope

Eigler, D. M.; Weiss, P. S.; Schweizer, E. K.; Lang, N. D.

Physical Review Letters (1991), 66 (9), 1189-92CODEN: PRLTAO; ISSN:0031-9007.

Images were obtained for individual Xe atoms adsorbed on a Ni(110) surface by using a low-temp. scanning tunneling microscope (STM). The atom-on-jellium model was used to calc. the apparent height of a Xe atom as imaged by STM and the result is found to be in good agreement with expt. The Xe 6s resonance, although lying close to the vacuum level, is the origin of the Fermi-level local state d. which renders Xe "visible" in STM.

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Moore, A. M. ; Weiss, P. S. Functional and Spectroscopic Measurements with Scanning Tunneling Microscopy Annu. Rev. Anal. Chem. 2008 , 1 , 857 – 882

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Moore, Amanda M.; Weiss, Paul S.

Annual Review of Analytical Chemistry (2008), 1 (), 857-882CODEN: ARACFU; ISSN:1936-1327. (Annual Reviews Inc.)

A review. Invented as a surface anal. technique capable of imaging individual atoms and mols. in real space, scanning tunneling microscopy (STM) has developed and advanced into a technique able to measure a variety of structural, functional, and spectroscopic properties and relationships at the single-mol. level. Here, we review basic STM operation and image interpretation, techniques developed to manipulate single atoms and mols. with the STM to measure functional properties of surfaces, local spectroscopies used to characterize atoms and mols. at the single-mol. level, and surface perturbations affecting surface coverage and surface reactions. Each section focuses on detg. the identity and function of chem. species so as to elucidate information beyond topog. with STM.

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Modern Surface Science and Surface Technologies: An Introduction

Somorjai, Gabor A.

Chemical Reviews (Washington, D. C.) (1996), 96 (4), 1223-1235CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review with 50 refs. on modern surface science theory and instrumentation. Applications include catalysis, semiconductor technol., chem. sensors, and magnetic disk storage.

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Poirier, G. E. Characterization of Organosulfur Molecular Monolayers on Au(111) Using Scanning Tunneling Microscopy Chem. Rev. 1997 , 97 , 1117 – 1127

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Characterization of Organosulfur Molecular Monolayers on Au(111) using Scanning Tunneling Microscopy

Poirier, Gregory E.

Chemical Reviews (Washington, D. C.) (1997), 97 (4), 1117-1127CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review with 118 refs. on STM characterization of self-assembled monolayers of thiol derivatized hydrocarbons [HS(CH2)nX; 0 ≤ n ≤ 21, X = CH3, OH, COOH, c-C6H5 etc, abbreviated CnX].

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McKie, D.; McKie, C. Essentials of Crystallography; Blackwell Scientific Publications: Oxford, 1986.

Wong, K. ; Kwon, K. Y. ; Rao, B. V. ; Liu, A. W. ; Bartels, L. Effect of Halo Substitution on the Geometry of Arenethiol Films on Cu(111) J. Am. Chem. Soc. 2004 , 126 , 7762 – 7763

Wong, K. L. ; Lin, X. ; Kwon, K. Y. ; Pawin, G. ; Rao, B. V. ; Liu, A. ; Bartels, L. ; Stolbov, S. ; Rahman, T. S. Halogen-Substituted Thiophenol Molecules on Cu(111) Langmuir 2004 , 20 , 10928 – 10934

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Halogen-Substituted Thiophenol Molecules on Cu(111)

Wong, K. L.; Lin, X.; Kwon, K.-Y.; Pawin, G.; Rao, B. V.; Liu, A.; Bartels, L.; Stolbov, S.; Rahman, T. S.

Langmuir (2004), 20 (25), 10928-10934CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)

Para-halosubstituted thiophenols (X-TPs, where X is Br, Cl, or F) form ordered islands and monolayers on Cu(111) at temps. as low as 81 K. At incomplete coverages, all X-TPs adsorb with the dehydrogenated thiol group attached to the substrate and the substituted ring inclined toward the surface, as verified exptl. and theor. The structure of ordered islands has a pronounced dependence on the nature of the halogen substituent: while unsubstituted TP and pentafluoro-TP mols. do not self-assemble into extended ordered patterns at 81 K, X-TP mols. form a range of different structures which depend both on the size and electronegativity of the substituent, as well as on the coverage.

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Shevchenko, E. V. ; Talapin, D. V. ; Kotov, N. A. ; O'Brien, S. ; Murray, C. B. Structural Diversity in Binary Nanoparticle Superlattices Nature 2006 , 439 , 55 – 59

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Structural diversity in binary nanoparticle superlattices

Shevchenko, Elena V.; Talapin, Dmitri V.; Kotov, Nicholas A.; O'Brien, Stephen; Murray, Christopher B.

Nature (London, United Kingdom) (2006), 439 (7072), 55-59CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Assembly of small building blocks such as atoms, mols. and nanoparticles into macroscopic structures-i.e., 'bottom up' assembly-is a theme that runs through chem., biol. and material science. Bacteria, macromols. and nanoparticles can self-assemble, generating ordered structures with a precision that challenges current lithog. techniques. The assembly of nanoparticles of two different materials into a binary nanoparticle superlattice (BNSL) can provide a general and inexpensive path to a large variety of materials (metamaterials) with precisely controlled chem. compn. and tight placement of the components. Maximization of the nanoparticle packing d. is proposed as the driving force for BNSL formation, and only a few BNSL structures were predicted to be thermodynamically stable. Recently, colloidal crystals with micrometre-scale lattice spacings were grown from oppositely charged polymethyl methacrylate spheres. Here the authors demonstrate formation of >15 different BNSL structures, using combinations of semiconducting, metallic and magnetic nanoparticle building blocks. At least ten of these colloidal cryst. structures were not reported previously. Elec. charges on sterically stabilized nanoparticles det. BNSL stoichiometry; addnl. contributions from entropic, van der Waals, steric and dipolar forces stabilize the variety of BNSL structures.

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Schreiber, F. Structure and Growth of Self-Assembling Monolayers Prog. Surf. Sci. 2000 , 65 , 151 – 256

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Structure and growth of self-assembling monolayers

Schreiber, Frank

Progress in Surface Science (2000), 65 (5-6), 151-256CODEN: PSSFBP; ISSN:0079-6816. (Elsevier Science B.V.)

A review with 357 refs. The structural phases and the growth of self-assembled monolayers (SAMs) are reviewed from a surface science perspective, with emphasis on simple model systems. The concept of self-assembly is explained, and different self-assembling materials are briefly discussed. A summary of the techniques used for the study of SAMs is given. Different general scenarios for structures obtained by self-assembly are described. Thiols on Au(111) surfaces are used as an archetypal system to study in detail the structural phase diagram as a function of temp. and coverage, the specific structural features on a mol. level, and the effect of changes of the mol. backbone and the end group on the structure of the SAM. Temp. effects including phase transitions are discussed. Concepts for the prepn. of more complex structures such as multi-component SAMs, laterally structured SAMs, and heterostructures, also with inorg. materials, are outlined. The growth and ways to control it are discussed. Soln. and gas phase deposition and the impact of various parameters such as temp., concn. (in soln.) or partial pressure (in the gas phase) are described. The kinetics and the energetics of self-assembly are analyzed. Several more complex issues of the film formation process including nonequil. issues are discussed. Some general conclusions are drawn concerning the impact of various mol. features on the growth behavior and concerning the relation between growth and structural phase diagram. Finally, the potential of self-assembly as a route for the prepn. of monolayers with pre-designed properties and SAMs as building blocks in heterostructures as well as application strategies are discussed.

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Chidsey, C. E. D. ; Loiacono, D. N. Chemical Functionality in Self-Assembled Monolayers—Structural and Electrochemical Properties Langmuir 1990 , 6 , 682 – 691

Weigelt, S. ; Busse, C. ; Petersen, L. ; Rauls, E. ; Hammer, B. ; Gothelf, K. V. ; Besenbacher, F. ; Linderoth, T. R. Chiral Switching by Spontaneous Conformational Change in Adsorbed Organic Molecules Nat. Mater. 2006 , 5 , 112 – 117

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Chiral switching by spontaneous conformational change in adsorbed organic molecules

Weigelt, Sigrid; Busse, Carsten; Petersen, Lars; Rauls, Eva; Hammer, Bjork; Gothelf, Kurt V.; Besenbacher, Flemming; Linderoth, Trolle R.

Nature Materials (2006), 5 (2), 112-117CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)

Self-assembly of adsorbed org. mols. is a promising route towards functional surface nano-architectures, and our understanding of assocd. dynamic processes has been significantly advanced by several scanning tunnelling microscopy (STM) investigations. Intramol. degrees of freedom are widely accepted to influence ordering of complex adsorbates, but although mol. conformation has been identified and even manipulated by STM, the detailed dynamics of spontaneous conformational change in adsorbed mols. has hitherto not been addressed. Mol. surface structures often show important stereochem. effects as, aside from truly chiral mols., a large class of so-called prochiral mols. become chiral once confined on a surface with an assocd. loss of symmetry. Here, we investigate a model system in which adsorbed mols. surprisingly switch between enantiomeric forms as they undergo thermally induced conformational changes. The assocd. kinetic parameters are quantified from time-resolved STM data whereas mechanistic insight is obtained from theor. modeling. The chiral switching is demonstrated to enable an efficient channel towards formation of extended homochiral surface domains. Our results imply that appropriate prochiral mols. may be induced (for example, by seeding) to assume only one enantiomeric form in surface assemblies, which is of relevance for chiral amplification and asym. heterogeneous catalysis.

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Monnell, J. D. ; Stapleton, J. J. ; Jackiw, J. J. ; Dunbar, T. ; Reinerth, W. A. ; Dirk, S. M. ; Tour, J. M. ; Allara, D. L. ; Weiss, P. S. Ordered Local Domain Structures of Decaneselenolate and Dodecaneselenolate Monolayers on Au{111} J. Phys. Chem. B 2004 , 108 , 9834 – 9841

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Ordered Local Domain Structures of Decaneselenolate and Dodecaneselenolate Monolayers on Au{111}

Monnell, Jason D.; Stapleton, Joshua J.; Jackiw, Jennifer J.; Dunbar, Tim; Reinerth, William A.; Dirk, Shawn M.; Tour, James M.; Allara, David L.; Weiss, Paul S.

Journal of Physical Chemistry B (2004), 108 (28), 9834-9841CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)

Coexisting adsorbate phases in high-coverage decaneselenolate and dodecaneselenolate [Me(CH2)nSe, n = 9 and 11] self-assembled monolayers on Au{111} were characterized by scanning tunneling microscopy and consist of 2 types: a densely packed distorted hexagonal lattice incommensurate to the underlying Au substrate, as revealed by the observation of a Moire pattern, and a commensurate linear missing-row structure. Examn. of the nearest neighbor distances in the tightly packed lattice reveal 2 distinct repeat distances of 4.90 and 5.20 Å, which complements previous surface x-ray data. The linear missing row structure manifests in several variants of the (√3 × 3√3)R30° unit cell differentiated by whether the mols. bind at 2- or 3-fold substrate sites. While the no. of mols. within this unit cell is typically two, in some cases an addnl. alkaneselenolate mol. is located at a site one Au atom lower than the rest. The structural conclusions are supported by excellent agreement of exptl. lattice parameters and those derived from mol. packing models. Comparison of the alkaneselenolate data with analogous structural phases reported for alkanethiolate monolayers on Au{111} shows that differences between the 2 systems can be understood on the basis that self-assembly is guided both by headgroup-headgroup as well as headgroup-substrate interactions.

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Shevchenko, E. V. ; Talapin, D. V. ; Murray, C. B. ; O'Brien, S. Structural Characterization of Self-Assembled Multifunctional Binary Nanoparticle Superlattices J. Am. Chem. Soc. 2006 , 128 , 3620 – 3637

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Structural Characterization of Self-Assembled Multifunctional Binary Nanoparticle Superlattices

Shevchenko, Elena V.; Talapin, Dmitri V.; Murray, Christopher B.; O'Brien, Stephen

Journal of the American Chemical Society (2006), 128 (11), 3620-3637CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

Nanocrystals of different size and functionality (e.g., noble metals, semiconductors, oxides, magnetic alloys) can be induced to self-assemble into ordered binary superlattices (also known as opals or colloidal crystals), retaining the size tunable properties of their constituents. We have built a variety of binary superlattices from monodisperse PbS, PbSe, CoPt3, Fe2O3, Au, Ag, and Pd nanocrystals, mixing and matching these nanoscale building blocks to yield multifunctional nanocomposites (metamaterials). Superlattices with AB, AB2, AB3, AB4, AB5, AB6, and AB13 stoichiometry with cubic, hexagonal, tetragonal, and orthorhombic symmetries have been identified. Assemblies with the same stoichiometry can be produced in several polymorphous forms by tailoring the particle size and deposition conditions. We have identified arrays isostructural with NaCl, CuAu, AlB2, MgZn2, MgNi2, Cu3Au, Fe4C, CaCu5, CaB6, NaZn13, and cub-AB13 compds. emphasizing the parallels between nanoparticle assembly and at. scale crystal growth and providing confidence that many more structures will follow. Recently, we have demonstrated that elec. charges on sterically stabilized nanoparticles in addn. to such parameters as particle size ratio and their concns. can provide the formation of a much broader pallet of binary nanoparticle superlattices1 as compared with the limited no. of possible superlattices formed by hard noninteracting spheres. In this contribution, we demonstrate a large variety of different binary superlattices, provide their detailed structural characterization, and discuss the role of energetic and kinetic factors in the cocrystn. process. We found that Coulomb, van der Waals, charge-dipole, dipole-dipole, and other interactions can contribute equally to cocrystn., allowing superlattice formation to be dependent on a no. of tunable parameters. We present binary superlattices as a new class of materials with a potentially unlimited library of constituents over a wide range of tunable structures.

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Smith, B. W. ; Monthioux, M. ; Luzzi, D. E. Carbon Nanotube Encapsulated Fullerenes: A Unique Class of Hybrid Materials Chem. Phys. Lett. 1999 , 315 , 31 – 36

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Yu, X. K. ; Jin, L. ; Zhou, Z. H. 3.88 Å Structure of Cytoplasmic Polyhedrosis Virus by Cryo-Electron Microscopy Nature 2008 , 453 , 415 – 420

Zhang, X. ; Jin, L. ; Fang, Q. ; Hui, W. H. ; Zhou, Z. H. 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry Cell 2010 , 141 , 472 – 482

Huang, C. S. ; Sadre-Bazzaz, K. ; Shen, Y. ; Deng, B. B. ; Zhou, Z. H. ; Tong, L. A. Crystal Structure of the α₆β₆ Holoenzyme of Propionyl-Coenzyme A Carboxylase Nature 2010 , 466 , 1001 – 1006

Poirier, G. E. ; Tarlov, M. J. Molecular Ordering and Gold Migration Observed in Butanethiol Self-Assembled Monolayers Using Scanning-Tunneling-Microscopy J. Phys. Chem. 1995 , 99 , 10966 – 10970

Xiao, X. D. ; Wang, B. ; Zhang, C. ; Yang, Z. ; Loy, M. M. T. Thermal Annealing Effect of Alkanethiol Monolayers on Au(111) in Air Surf. Sci. 2001 , 472 , 41 – 50

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Thermal annealing effect of alkanethiol monolayers on Au(1 1 1) in air

Xiao, X.; Wang, B.; Zhang, C.; Yang, Z.; Loy, M. M. T.

Surface Science (2001), 472 (1-2), 41-50CODEN: SUSCAS; ISSN:0039-6028. (Elsevier Science B.V.)

We present a systematic study on the effect of air annealing on the structures of alkanethiol (CH3(CH2)n-1SH) self-assembled monolayers (SAMs) on Au(1 1 1) with chain length n = 7, 10, 18. Partial desorption of the monolayers was obsd. by scanning tunneling microscopy (STM) and XPS at relatively low annealing temps. By increasing the annealing time at appropriate temps., the structures of SAMs transform from densely packed (√3×√3)R30° phase to c(4√3×2√3)R30° phase, and then slowly to striped (p×√3) phases with p = 4 and 5. Through the relative C content measurement by XPS and the stripe spacing measurement by STM, we propose a different stripe phase structure than those obsd. for SAMs grown by gas-phase deposition or by vacuum annealed soln.-grown samples.

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Li, X. L. ; Xu, B. Q. ; Xiao, X. Y. ; Yang, X. M. ; Zang, L. ; Tao, N. J. Controlling Charge Transport in Single Molecules Using an Electrochemical Gate Faraday Discuss. 2006 , 131 , 111 – 120

Cyganik, P. ; Buck, M. ; Strunskus, T. ; Shaporenko, A. ; Witte, G. ; Zharnikov, M. ; Woll, C. Influence of Molecular Structure on Phase Transitions: A Study of Self-Assembled Monolayers of 2-(Aryl)-Ethane Thiols J. Phys. Chem. C 2007 , 111 , 16909 – 16919

Lussem, B. ; Muller-Meskamp, L. ; Karthauser, S. ; Waser, R. ; Homberger, M. ; Simon, U. STM Study of Mixed Alkanethiol/Biphenylthiol Self-Assembled Monolayers on Au(111) Langmuir 2006 , 22 , 3021 – 3027

Lewis, P. A. ; Smith, R. K. ; Kelly, K. F. ; Bumm, L. A. ; Reed, S. M. ; Clegg, R. S. ; Gunderson, J. D. ; Hutchison, J. E. ; Weiss, P. S. The Role of Buried Hydrogen Bonds in Self-Assembled Mixed Composition Thiols on Au{111} J. Phys. Chem. B 2001 , 105 , 10630 – 10636

Poirier, G. E. ; Tarlov, M. J. The c(4 × 2) Superlattice of n-Alkanethiol Monolayers Self-Assembled on Au(111) Langmuir 1994 , 10 , 2853 – 2856

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The c(4X2) Superlattice of n-Alkanethiol Monolayers Self-Assembled on Au(111)

Poirier, G. E.; Tarlov, M. J.

Langmuir (1994), 10 (9), 2853-6CODEN: LANGD5; ISSN:0743-7463.

We report the results of an ultrahigh vacuum STM study of n-alkanethiol [CH3(CH2)n-1SH] (Cn) monolayers self-assembled on Au(111) single-crystal surfaces. The STM images show that the satn. coverage self-assembled monolayer (SAM) unit cell measures 0.86 × 1.0 nm and contains four thiolate mols. The obsd. unit cell is consistent with results from recent X-ray, electron, and helium diffraction studies. This unit cell corresponds to a c(4×2) superlattice of a basic (√3×√3)R30 dense-packed monolayer. The domain size ranges from 5.0 to 15 nm with domains sepd. by mol.-width rotational boundaries, antiphase boundaries, and stacking faults. SAMs composed of longer chain thiols (C8 and C10) were stable in vacuum for over 40 days.

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Shuster, M. J. ; Vaish, A. ; Szapacs, M. E. ; Anderson, M. E. ; Weiss, P. S. ; Andrews, A. M. Biospecific Recognition of Tethered Small Molecules Diluted in Self-Assembled Monolayers Adv. Mater. 2008 , 20 , 164 – 167

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Biospecific recognition of tethered small molecules diluted in self-assembled monolayers

Shuster, Mitchell J.; Vaish, Amit; Szapacs, Matthew E.; Anderson, Mary E.; Weiss, Paul S.; Andrews, Anne M.

Advanced Materials (Weinheim, Germany) (2008), 20 (1), 164-167CODEN: ADVMEW; ISSN:0935-9648. (Wiley-VCH Verlag GmbH & Co. KGaA)

The authors describe the first in a series of studies designed to develop and to characterize self-assembled monolayers contg. isolated small-mol. probes. The authors insert tether mols. into preformed oligo(ethylene glycol)-terminated alkanethiolate monolayer matrixes and covalently attach the neurotransmitter serotonin to the tethers. These monolayers selectively recognize serotonin antibodies and resist binding of nonspecific antibodies and proteins. The authors will use these capture materials for biosensor development and functionally-directed proteomics.

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Lewis, P. A. ; Inman, C. E. ; Yao, Y. X. ; Tour, J. M. ; Hutchison, J. E. ; Weiss, P. S. Mediating Stochastic Switching of Single Molecules Using Chemical Functionality J. Am. Chem. Soc. 2004 , 126 , 12214 – 12215

Donhauser, Z. J. ; Price, D. W. ; Tour, J. M. ; Weiss, P. S. Control of Alkanethiolate Monolayer Structure Using Vapor-Phase Annealing J. Am. Chem. Soc. 2003 , 125 , 11462 – 11463

Dameron, A. A. ; Charles, L. F. ; Weiss, P. S. Structures and Displacement of 1-Adamantanethiol Self-Assembled Monolayers on Au{111} J. Am. Chem. Soc. 2005 , 127 , 8697 – 8704

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Structures and Displacement of 1-Adamantanethiol Self-Assembled Monolayers on Au{111}

Dameron, Arrelaine A.; Charles, Lyndon F.; Weiss, Paul S.

Journal of the American Chemical Society (2005), 127 (24), 8697-8704CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

We have designed monolayers with weak intermol. interactions for use as placeholders in intelligent self- and directed-assembly. We have shown that these 1-adamantanethiolate monolayers are labile with respect to displacement by exposing them to dil. solns. of alkanethiols. These self-assembled monolayers (SAMs) of 1-adamantanethiol on Au{111} were probed using ambient scanning tunneling microscopy (STM), and their assembled order was detd. Soln. deposition of the mols. results in a highly ordered hexagonally close-packed mol. lattice with a measured nearest neighbor distance of 6.9 ± 0.4 Å. The SAMs exhibit several rotational domains, but lack the protruding domain boundaries typical of alkanethiolate SAMs, and are similarly stable at room temp. Co-deposition of alkanethiol and 1-adamantanethiol from soln. results in alkanethiolate SAMs, except when using extremely low alkanethiol to 1-adamantanethiol concn. ratios. Facile displacement of low interaction strength SAMs can be exploited to enhance patterning using soft nanolithog.

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Moore, A. M. ; Mantooth, B. A. ; Donhauser, Z. J. ; Maya, F. ; Price, D. W. ; Yao, Y. X. ; Tour, J. M. ; Weiss, P. S. Cross-Step Place-Exchange of Oligo(phenylene-ethynylene) Molecules Nano Lett. 2005 , 5 , 2292 – 2297

Mullen, T. J. ; Dameron, A. A. ; Andrews, A. M. ; Weiss, P. S. Selecting and Driving Monolayer Structures through Tailored Intermolecular Interactions Aldrichimica Acta 2007 , 40 , 21 – 31

Hohman, J. N. ; Zhang, P. P. ; Morin, E. I. ; Han, P. ; Kim, M. ; Kurland, A. R. ; McClanahan, P. D. ; Balema, V. P. ; Weiss, P. S. Self-Assembly of Carboranethiol Isomers on Au{111}: Intermolecular Interactions Determined by Molecular Dipole Orientations ACS Nano 2009 , 3 , 527 – 536

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Self-Assembly of Carboranethiol Isomers on Au{111}: Intermolecular Interactions Determined by Molecular Dipole Orientations

Hohman, J. Nathan; Zhang, Pengpeng; Morin, Elizabeth I.; Han, Patrick; Kim, Moonhee; Kurland, Adam R.; McClanahan, Patrick D.; Balema, Viktor P.; Weiss, Paul S.

ACS Nano (2009), 3 (3), 527-536CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)

Self-assembled monolayer (SAM) structures and properties are dominated by two interactions: those between the substrate and adsorbate and those between the adsorbates themselves. We have fabricated self-assembled monolayers of m-1-carboranethiol (M1) and m-9-carboranethiol (M9) on Au{111}. The two isomers are nearly identical geometrically, but calcd. mol. dipole moments show a sizable difference at 1.06 and 4.08 D for M1 and M9 in the gas phase, resp. These mols. provide an opportunity to investigate the effect of different dipole moments within SAMs without altering the geometry of the assembly. Pure and co-deposited SAMs of these mols. were studied by scanning tunneling microscopy (STM). The mols. are indistinguishable in STM images, and the hexagonally close-packed adlayer structures were found to have (√19 × √19)R23.4° unit cells. Both SAMs display rotational domains without the protruding or depressed features in STM images assocd. with domain boundaries in other SAM systems. Differing orientations of mol. dipole moments influence SAM properties, including the stability of the SAM and the coverage of the carboranethiolate in competitive binding conditions. These properties were investigated by dynamic contact angle goniometry, Kelvin probe force microscopy, and grazing incidence Fourier transform IR spectroscopy.

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Kim, M. ; Hohman, J. N. ; Morin, E. I. ; Daniel, T. A. ; Weiss, P. S. Self-Assembled Monolayers of 2-Adamantanethiol on Au{111}: Control of Structure and Displacement J. Phys. Chem. A 2009 , 113 , 3895 – 3903

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Self-Assembled Monolayers of 2-Adamantanethiol on Au{111}: Control of Structure and Displacement

Kim, Moonhee; Hohman, J. Nathan; Morin, Elizabeth I.; Daniel, Thomas A.; Weiss, Paul S.

Journal of Physical Chemistry A (2009), 113 (16), 3895-3903CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)

We have investigated the formation of 2-adamantanethiolate self-assembled monolayers on Au{111} and their displacement by n-dodecanethiol, using scanning tunneling microscopy, XPS, and IR reflection absorption spectroscopy. Well-ordered 2-adamantanethiolate monolayers undergo rapid and significant mol. exchange upon exposure to n-dodecanethiol solns., but their structures and intermol. interactions template the growth of n-dodecanethiolate domains. Annealing 2-adamantanethiolate monolayers at 78 °C decreases the d. of vacancy islands, while increasing the overall order and the av. domain sizes in the films. This results in slower displacement by n-dodecanethiol mols., as compared to unannealed monolayers. The secondary sulfur position on the adamantyl cage influences the lattice structure and exchange of 2-adamantanethiolate monolayers by alkanethiols.

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Hohman, J. N. ; Claridge, S. A. ; Kim, M. ; Weiss, P. S. Cage Molecules for Self-Assembly Mater. Sci. Eng. Rep. 2010 , 70 , 188 – 208

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Cage molecules for self-assembly

Hohman, J. Nathan; Claridge, Shelley A.; Kim, Moonhee; Weiss, Paul S.

Materials Science & Engineering, R: Reports (2010), R70 (3-6), 188-208CODEN: MIGIEA; ISSN:0927-796X. (Elsevier B.V.)

A review. Self-assembled monolayers using functionalized cage mols. offer distinct advantages because of their symmetry, lack of conformational flexibility, and well-defined chemistries. While these systems have not yet been studied to the extent that linear alkanethiols on Au{1 1 1} have been, early explorations indicate great promise and important differences. For simple cage mols. that bind upright on the substrate, tilt domain boundaries found in linear chain systems are completely eliminated. Cage mols. can be designed to have a great range of intermol. interactions, which thereby define the stabilities of the assemblies. Weakly interacting monolayers, such as those of 1-adamantanethiol on Au{1 1 1} are labile relative to exchange reactions from soln., vapor, or contact, and thus can be used as sacrificial placeholders and diffusion barriers in soft lithog. Such mols. can be further functionalized to serve as mol. resists for chem. patterning. Cage mols. can also be designed with directional interactions, as for carboranethiols, where mols. with identical lattices have dramatically different chem. and phys. properties, and film stabilities. Multifunctional cage mols. enable further directed surface reactions, higher order supramol. assembly, and ultimately, precise three-dimensional assembly off the surface.

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Repp, J. ; Moresco, F. ; Meyer, G. ; Rieder, K. H. ; Hyldgaard, P. ; Persson, M. Substrate Mediated Long-Range Oscillatory Interaction between Adatoms: Cu/Cu(111) Phys. Rev. Lett. 2000 , 85 , 2981 – 2984

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Substrate mediated long-range oscillatory interaction between adatoms: Cu/Cu(111)

Repp, Jascha; Moresco, Francesca; Meyer, Gerhard; Rieder, Karl-Heinz; Hyldgaard, Per; Persson, Mats

Physical Review Letters (2000), 85 (14), 2981-2984CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

A quant. study of the long-range interaction between single copper adatoms on Cu(111) mediated by the electrons in the two-dimensional surface-state band is presented. The interaction potential was detd. by evaluating the distance distribution of 2 adatoms from a series of STM images taken at temps. of 9-21 K. The long-range interaction is oscillatory with a period of half the Fermi wavelength and decays for larger distances d as 1/d2. Five potential min. were identified for sepns. of ≤70 Å. The interaction significantly changes the growth of Cu/Cu(111) at low temps.

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Knorr, N. ; Brune, H. ; Epple, M. ; Hirstein, A. ; Schneider, M. A. ; Kern, K. Long-Range Adsorbate Interactions Mediated by a Two-Dimensional Electron Gas Phys. Rev. B 2002 , 65 , 115420-1-5

Silly, F. ; Pivetta, M. ; Ternes, M. ; Patthey, F. ; Pelz, J. P. ; Schneider, W. D. Creation of an Atomic Superlattice by Immersing Metallic Adatoms in a Two-Dimensional Electron Sea Phys. Rev. Lett. 2004 , 92 , 016101-1-5

Pawin, G. ; Wong, K. L. ; Kwon, K. Y. ; Bartels, L. A Homomolecular Porous Network at a Cu(111) Surface Science 2006 , 313 , 961 – 962

Dougherty, D. B. ; Maksymovych, P. ; Lee, J. ; Yates, J. T. Local Spectroscopy of Image-Potential-Derived States: From Single Molecules to Monolayers of Benzene on Cu(111) Phys. Rev. Lett. 2006 , 97 , 236806-1-4

Nanayakkara, S. U. ; Sykes, E. C. H. ; Fernandez-Torres, L. C. ; Blake, M. M. ; Weiss, P. S. Long-Range Electronic Interactions at a High Temperature: Bromine Adatom Islands on Cu(111) Phys. Rev. Lett. 2007 , 98 , 206108-1-4

Han, P. ; Kurland, A. R. ; Giordano, A. N. ; Nanayakkara, S. U. ; Blake, M. M. ; Pochas, C. M. ; Weiss, P. S. Heads and Tails: Simultaneous Exposed and Buried Interface Imaging of Monolayers ACS Nano 2009 , 3 , 3115 – 3121

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Heads and Tails: Simultaneous Exposed and Buried Interface Imaging of Monolayers

Han, Patrick; Kurland, Adam R.; Giordano, Andrea N.; Nanayakkara, Sanjini U.; Blake, Meaghan M.; Pochas, Chris M.; Weiss, Paul S.

ACS Nano (2009), 3 (10), 3115-3121CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)

The authors have simultaneously imaged the chem. bound head groups and exposed tail groups in bicomponent alkanethiolate self-assembled monolayers on Au{111} with mol. resoln. This has enabled the authors to resolve the controversy of scanning tunneling microscopy image interpretation and to measure the mol. polar tilt and azimuthal angles. The authors' local measurements demonstrate that ordered domains with different superstructures also have varied buried sulfur head group structures.

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Kim, Y. ; Long, E. C. ; Barton, J. K. ; Lieber, C. M. Imaging of Oligonucleotide Metal-Complexes by Scanning Tunneling Microscopy Langmuir 1992 , 8 , 496 – 500

Tanaka, H. ; Kawai, T. Visualization of Detailed Structures within DNA Surf. Sci. 2003 , 539 , L531 – L536

Otero, R. ; Xu, W. ; Lukas, M. ; Kelly, R. E. A. ; Laegsgaard, E. ; Stensgaard, I. ; Kjems, J. ; Kantorovich, L. N. ; Besenbacher, F. Specificity of Watson−Crick Base Pairing on a Solid Surface Studied at the Atomic Scale Angew. Chem., Int. Ed. 2008 , 47 , 9673 – 9676

Feldkamp, U. ; Niemeyer, C. M. Rational Design of DNA Nanoarchitectures Angew. Chem., Int. Ed. 2006 , 45 , 1856 – 1876

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Rational design of DNA nanoarchitectures

Feldkamp, Udo; Niemeyer, Christof M.

Angewandte Chemie, International Edition (2006), 45 (12), 1856-1876CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)

A review. DNA has many phys. and chem. properties that make it a powerful material for mol. constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramol. arrays, scaffolds, and even mech. and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramol. DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.

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Giljohann, D. A. ; Seferos, D. S. ; Daniel, W. L. ; Massich, M. D. ; Patel, P. C. ; Mirkin, C. A. Gold Nanoparticles for Biology and Medicine Angew. Chem., Int. Ed. 2010 , 49 , 3280 – 3294

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Gold Nanoparticles for Biology and Medicine

Giljohann, David A.; Seferos, Dwight S.; Daniel, Weston L.; Massich, Matthew D.; Patel, Pinal C.; Mirkin, Chad A.

Angewandte Chemie, International Edition (2010), 49 (19), 3280-3294CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)

A review. Gold colloids have fascinated scientists for over a century and are now heavily utilized in chem., biol., engineering, and medicine. Today these materials can be synthesized reproducibly, modified with seemingly limitless chem. functional groups, and, in certain cases, characterized with at.-level precision. This Review highlights recent advances in the synthesis, bioconjugation, and cellular uses of gold nanoconjugates. There are now many examples of highly sensitive and selective assays based upon gold nanoconjugates. In recent years, focus has turned to therapeutic possibilities for such materials. Structures which behave as gene-regulating agents, drug carriers, imaging agents, and photoresponsive therapeutics have been developed and studied in the context of cells and many debilitating diseases. These structures are not simply chosen as alternatives to mol.-based systems, but rather for their new phys. and chem. properties, which confer substantive advantages in cellular and medical applications.

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Claridge, S. A. ; Goh, S. L. ; Frechet, J. M. J. ; Williams, S. C. ; Micheel, C. M. ; Alivisatos, A. P. Directed Assembly of Discrete Gold Nanoparticle Groupings Using Branched DNA Scaffolds Chem. Mater. 2005 , 17 , 1628 – 1635

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Directed Assembly of Discrete Gold Nanoparticle Groupings Using Branched DNA Scaffolds

Claridge, Shelley A.; Goh, Sarah L.; Frechet, Jean M. J.; Williams, Shara C.; Micheel, Christine M.; Alivisatos, A. Paul

Chemistry of Materials (2005), 17 (7), 1628-1635CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)

The concept of self-assembled dendrimers is explored for the creation of discrete nanoparticle assemblies. Hybridization of branched DNA trimers and nanoparticle-DNA conjugates results in the synthesis of nanoparticle trimer and tetramer complexes. Multiple tetramer architectures are investigated, utilizing Au-DNA conjugates with varying secondary structural motifs. Hybridization products are analyzed by gel electrophoresis, and discrete bands are obsd. corresponding to structures with increasing nos. of hybridization events. Samples extd. from each band are analyzed by TEM, and statistics compiled from micrographs are used to compare assembly characteristics for each architecture. Asym. structures are also produced in which both 5- and 10-nm Au particles are assembled on branched scaffolds.

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Fu, A. H. ; Micheel, C. M. ; Cha, J. ; Chang, H. ; Yang, H. ; Alivisatos, A. P. Discrete Nanostructures of Quantum Dots/Au with DNA J. Am. Chem. Soc. 2004 , 126 , 10832 – 10833

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Discrete Nanostructures of Quantum Dots/Au with DNA

Fu, Aihua; Micheel, Christine M.; Cha, Jennifer; Chang, Hauyee; Yang, Haw; Alivisatos, A. Paul

Journal of the American Chemical Society (2004), 126 (35), 10832-10833CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

Nanostructures of colloidal CdSe/ZnS core/shell quantum dots (QDs) surrounded by a discrete no. of Au nanoparticles were generated via DNA hybridization and purified by gel electrophoresis. Statistics from TEM anal. showed a high yield of designed structures. The distance between Au particles and QD, the no. of Au around the central QD, and the size of Au and QD can be adjusted. Rationally designed structures such as these hold great promise for researching the phys. interactions between semiconductor and Au nanoparticles and for developing more efficient nanoprobes.

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Micheel, C. M. ; Zanchet, D. ; Alivisatos, A. P. Correlation Analysis of TEM Images of Nanocrystal Molecules Langmuir 2008 , 24 , 10084 – 10088

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Choi, C. L. ; Claridge, S. A. ; Garner, E. C. ; Alivisatos, A. P. ; Mullins, R. D. Protein−Nanocrystal Conjugates Support a Single Filament Polymerization Model in R1 Plasmid Segregation J. Biol. Chem. 2008 , 283 , 28081 – 28086

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Shirai, Y. ; Osgood, A. J. ; Zhao, Y. M. ; Yao, Y. X. ; Saudan, L. ; Yang, H. B. ; Chiu, Y. H. ; Alemany, L. B. ; Sasaki, T. ; Morin, J. F. et al. Surface-Rolling Molecules J. Am. Chem. Soc. 2006 , 128 , 4854 – 4864

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Surface-Rolling Molecules

Shirai, Yasuhiro; Osgood, Andrew J.; Zhao, Yuming; Yao, Yuxing; Saudan, Lionel; Yang, Hanbiao; Chiu, Yu-Hung; Alemany, Lawrence B.; Sasaki, Takashi; Morin, Jean-Francois; Guerrero, Jason M.; Kelly, Kevin F.; Tour, James M.

Journal of the American Chemical Society (2006), 128 (14), 4854-4864CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

Design, syntheses, and testing of new, fullerene-wheeled single mol. nanomachines, namely, nanocars and nanotrucks, are presented. These nanovehicles are composed of three basic components that include spherical fullerene wheels, freely rotating alkynyl axles, and a mol. chassis. The use of spherical wheels based on C60 and freely rotating axles based on alkynes permits directed nanoscale rolling of the mol. structure on gold surfaces. The rolling motion obsd. by STM resembles the same motion performed by macroscopic entities in which rolling occurs perpendicular to the axles. A new synthesis methodol., in situ ethynylation of fullerenes, was developed for the realization of the fullerene-wheeled mol. machines. Four generations of the fullerene-wheeled structures were developed, and the latest fourth generation nanocar, 3b, along with three-wheeled triangular compds., 4a and 4b, provided definitive evidence for fullerene-based wheel-like rolling motion, not stick-slip or sliding translation. The studies here underscore the ability to control directionality of motion in mol.-sized nanostructures through precise mol. design and synthesis.

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Kwon, K. Y. ; Wong, K. L. ; Pawin, G. ; Bartels, L. ; Stolbov, S. ; Rahman, T. S. Unidirectional Adsorbate Motion on a High-Symmetry Surface: "Walking" Molecules Can Stay the Course Phys. Rev. Lett. 2005 , 95 , 166101-1-5

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Wong, K. L. ; Rao, B. V. ; Pawin, G. ; Ulin-Avila, E. ; Bartels, L. Coverage and Nearest-Neighbor Dependence of Adsorbate Diffusion J. Chem. Phys. 2005 , 123 , 201102-1-4

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Pawin, G. ; Solanki, U. ; Kwon, K. Y. ; Wong, K. L. ; Lin, X. ; Jiao, T. ; Bartels, L. A Quantitative Approach to Hydrogen Bonding at a Metal Surface J. Am. Chem. Soc. 2007 , 129 , 12056 – 12057

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Pawin, G. ; Wong, K. L. ; Kwon, K. Y. ; Frisbee, R. J. ; Rahman, T. S. ; Bartels, L. Surface Diffusive Motion in a Periodic and Asymmetric Potential J. Am. Chem. Soc. 2008 , 130 , 15244 – 15245

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Wong, K. L. ; Pawin, G. ; Kwon, K. Y. ; Lin, X. ; Jiao, T. ; Solanki, U. ; Fawcett, R. H. J. ; Bartels, L. ; Stolbov, S. ; Rahman, T. S. A Molecule Carrier Science 2007 , 315 , 1391 – 1393

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Mantooth, B. A. ; Sykes, E. C. H. ; Han, P. ; Moore, A. M. ; Donhauser, Z. J. ; Crespi, V. H. ; Weiss, P. S. Analyzing the Motion of Benzene on Au{111}: Single Molecule Statistics from Scanning Probe Images J. Phys. Chem. C 2007 , 111 , 6167 – 6182

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Sykes, E. C. H. ; Mantooth, B. A. ; Han, P. ; Donhauser, Z. J. ; Weiss, P. S. Substrate-Mediated Intermolecular Interactions: A Quantitative Single Molecule Analysis J. Am. Chem. Soc. 2005 , 127 , 7255 – 7260

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Taranovskyy, A. ; Tansel, T. ; Magnussen, O. M. Quantitative Measurements of Adsorbate-Adsorbate Interactions at Solid-Liquid Interfaces Phys. Rev. Lett. 2010 , 104 , 106101-1-4

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Rost, M. J. ; van Baarle, G. J. C. ; Katan, A. J. ; van Spengen, W. M. ; Schakel, R. ; van Loo, W. A. ; Oosterkamp, T. H. ; Frenken, J. W. M. Video-Rate Scanning Probe Control Challenges: Setting the Stage for a Microscopy Revolution Asian J. Control 2009 , 11 , 110 – 129

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Disseldorp, E. C. M. ; Tabak, F. C. ; Katan, A. J. ; Hesselberth, M. B. S. ; Oosterkamp, T. H. ; Frenken, J. W. M. ; van Spengen, W. M. MEMS-Based High Speed Scanning Probe Microscopy Rev. Sci. Instrum. 2010 , 81 , 043702-1-7

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Williamson, M. J. ; Tromp, R. M. ; Vereecken, P. M. ; Hull, R. ; Ross, F. M. Dynamic Microscopy of Nanoscale Cluster Growth at the Solid−Liquid Interface Nat. Mater. 2003 , 2 , 532 – 536

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Zheng, H. M. ; Claridge, S. A. ; Minor, A. M. ; Alivisatos, A. P. ; Dahmen, U. Nanocrystal Diffusion in a Liquid Thin Film Observed by In Situ Transmission Electron Microscopy Nano Lett. 2009 , 9 , 2460 – 2465

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Nanocrystal Diffusion in a Liquid Thin Film Observed by in Situ Transmission Electron Microscopy

Zheng, Haimei; Claridge, Shelley A.; Minor, Andrew M.; Alivisatos, A. Paul; Dahmen, Ulrich

Nano Letters (2009), 9 (6), 2460-2465CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)

We have directly obsd. motion of inorg. nanoparticles during fluid evapn. using a transmission electron microscope. Tracking real-time diffusion of both spherical (5-15 nm) and rod-shaped (5 × 10 nm) gold nanocrystals in a thin film of water-15% glycerol reveals complex movements, such as rolling motions coupled to large-step movements and macroscopic violations of the Stokes-Einstein relation for diffusion. As drying patches form during the final stages of evapn., particle motion is dominated by the nearby retracting liq. front.

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118

Zheng, H. M. ; Smith, R. K. ; Jun, Y. W. ; Kisielowski, C. ; Dahmen, U. ; Alivisatos, A. P. Observation of Single Colloidal Platinum Nanocrystal Growth Trajectories Science 2009 , 324 , 1309 – 1312

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Observation of Single Colloidal Platinum Nanocrystal Growth Trajectories

Zheng, Haimei; Smith, Rachel K.; Jun, Young-wook; Kisielowski, Christian; Dahmen, Ulrich; Alivisatos, A. Paul

Science (Washington, DC, United States) (2009), 324 (5932), 1309-1312CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Understanding of colloidal nanocrystal growth mechanisms is essential for the syntheses of nanocrystals with desired phys. properties. The classical model for the growth of monodisperse nanocrystals assumes a discrete nucleation stage followed by growth via monomer attachment, but has overlooked particle-particle interactions. Recent studies suggested that interactions between particles play an important role. Using in situ TEM, platinum nanocrystals can grow either by monomer attachment from soln. or by particle coalescence. Through the combination of these two processes, an initially broad size distribution can spontaneously narrow into a nearly monodisperse distribution. Probably colloidal nanocrystals take different pathways of growth based on their size- and morphol.-dependent internal energies.

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119

Balzani, V. ; Gomez-Lopez, M. ; Stoddart, J. F. Molecular Machines Acc. Chem. Res. 1998 , 31 , 405 – 414

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Feringa, B. L. ; van Delden, R. A. ; Koumura, N. ; Geertsema, E. M. Chiroptical Molecular Switches Chem. Rev. 2000 , 100 , 1789 – 1816

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120

Chiroptical Molecular Switches

Feringa, Ben L.; van Delden, Richard A.; Koumura, Nagatoshi; Geertsema, Edzard M.

Chemical Reviews (Washington, D. C.) (2000), 100 (5), 1789-1816CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review, with ∼196 refs., in which chiral photochromic mols., overcrowded alkenes, Multifunctional chiral switches, photochromic polymers, and chiroptical mol. switching of liq.-cryst. phases are discussed.

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Kay, E. R. ; Leigh, D. A. ; Zerbetto, F. Synthetic Molecular Motors and Mechanical Machines Angew. Chem., Int. Ed. 2007 , 46 , 72 – 191

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Synthetic molecular motors and mechanical machines

Kay, Euan R.; Leigh, David A.; Zerbetto, Francesco

Angewandte Chemie, International Edition (2007), 46 (1+2), 72-191CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)

A review with refs. The widespread use of controlled mol.-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic mol. systems, which by and large rely upon electronic and chem. effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of mol.-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodn. were first being formulated. Here we outline the exciting successes in taming mol.-level movement thus far, the underlying principles that all exptl. designs must follow, and the early progress made towards utilizing synthetic mol. structures to perform tasks using mech. motion. We also highlight some of the issues and challenges that still need to be overcome.

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van der Molen, S. J. ; Liljeroth, P. Charge Transport through Molecular Switches J. Phys.: Condens. Matter 2010 , 22 , 1 – 30

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Fabrication, assembly, and characterization of molecular electronic components

Mantooth, Brent A.; Weiss, Paul S.

Proceedings of the IEEE (2003), 91 (11), 1785-1802CODEN: IEEPAD; ISSN:0018-9219. (Institute of Electrical and Electronics Engineers)

A review. One of the ultimate miniaturizations in nanotechnol. is mol. electronics, where devices will consist of individual mols. There are many complications assocd. with the use of mols. in electronic devices, such as the electronic perturbations in the mol. assocd. with being bonded to an electrode, how electrons traverse the metal-mol. junction, and the difficulty of macroscopically addressing single to very few mols. Whether fabricating a test structure or a usable device, the use of self-assembly is fundamental to the fabrication of mol. electronic devices. We will discuss how to fabricate self-assembled monolayers into test assemblies and how to use intermol. interactions to direct mols. into desired positions to create nanostructures and to connect functional mols. to the outside world. These assemblies serve as test structures for measurements on single or bundled mols. The development of several exptl. techniques, including various scanning probes, mercury drop junctions, break junctions, nanopores, crossed wires, and other techniques using nanoparticles have enabled the ability to test these structures and make reproducible measurements on single mols. Many of these methods were developed to test mols. with potential for integration into devices such as oligo (phenylene-ethynylene) mols. and other π-conjugated mols., in ensemble or single-mol. measurements.

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Moore, A. M. ; Dameron, A. A. ; Mantooth, B. A. ; Smith, R. K. ; Fuchs, D. J. ; Ciszek, J. W. ; Maya, F. ; Yao, Y. X. ; Tour, J. M. ; Weiss, P. S. Molecular Engineering and Measurements to Test Hypothesized Mechanisms in Single Molecule Conductance Switching J. Am. Chem. Soc. 2006 , 128 , 1959 – 1967

125

Moore, A. M. ; Mantooth, B. A. ; Donhauser, Z. J. ; Yao, Y. X. ; Tour, J. M. ; Weiss, P. S. Real-Time Measurements of Conductance Switching and Motion of Single Oligo(phenylene ethynylene) Molecules J. Am. Chem. Soc. 2007 , 129 , 10352 – 10353

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125

Real-Time Measurements of Conductance Switching and Motion of Single Oligo(phenylene ethynylene) Molecules

Moore, Amanda M.; Mantooth, Brent A.; Donhauser, Zachary J.; Yao, Yuxing; Tour, James M.; Weiss, Paul S.

Journal of the American Chemical Society (2007), 129 (34), 10352-10353CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

Real-time conductance switching and place-exchange up and down substrate step edges have been measured for oligo(phenylene ethynylene) (OPE) mols. inserted into host dodecanethiolate self-assembled monolayers (SAM). These measurements were obtained by placing a scanning tunneling microscopy tip over individual nitro-functionalized OPE mols. and recording apparent height vs. time. In addn., real-time measurements for the host SAM were acquired and indicated small motions for the monolayer-substrate system.

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Moresco, F. ; Meyer, G. ; Rieder, K. H. ; Tang, H. ; Gourdon, A. ; Joachim, C. Conformational Changes of Single Molecules Induced by Scanning Tunneling Microscopy Manipulation: A Route to Molecular Switching Phys. Rev. Lett. 2001 , 86 , 672 – 675

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126

Conformational Changes of Single Molecules Induced by Scanning Tunneling Microscopy Manipulation: A Route to Molecular Switching

Moresco, Francesca; Meyer, Gerhard; Rieder, Karl-Heinz; Tang, Hao; Gourdon, Andre; Joachim, Christian

Physical Review Letters (2001), 86 (4), 672-675CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

A detailed exptl. and theor. investigation of the processes involved in the manipulation of individual specially designed porphyrin-based mols. by scanning tunneling microscopy at low temp. is presented. On a stepped Cu(211) surface, the interaction between tip and mol. was used to locally modify in a reversible way the internal configuration of a single mol., thus drastically changing the tunneling current passing through it. Model calcns. confirm that this manipulation realizes the principle of a conformational mol. switch.

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Loppacher, C. ; Guggisberg, M. ; Pfeiffer, O. ; Meyer, E. ; Bammerlin, M. ; Luthi, R. ; Schlittler, R. ; Gimzewski, J. K. ; Tang, H. ; Joachim, C. Direct Determination of the Energy Required to Operate a Single Molecule Switch Phys. Rev. Lett. 2003 , 90 , 066107-1-4

128

Alemani, M. ; Peters, M. V. ; Hecht, S. ; Rieder, K. H. ; Moresco, F. ; Grill, L. Electric Field-Induced Isomerization of Azobenzene by STM J. Am. Chem. Soc. 2006 , 128 , 14446 – 14447

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128

Electric Field-Induced Isomerization of Azobenzene by STM

Alemani, Micol; Peters, Maike V.; Hecht, Stefan; Rieder, Karl-Heinz; Moresco, Francesca; Grill, Leonhard

Journal of the American Chemical Society (2006), 128 (45), 14446-14447CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

The elec. field applied between the tip of a scanning tunneling microscope and a metallic surface is shown to induce the reversible trans-cis isomerization of single azobenzene derivs. adsorbed on a Au(111) surface. The studied mol. is sym. equipped with four tert-Bu groups, which decouple the azobenzene core from the metallic surface, facilitating the formation of highly ordered islands. Due to the spatial extension of the elec. field, it is possible to switch many mols. within the same island simultaneously.

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Liljeroth, P. ; Repp, J. ; Meyer, G. Current-Induced Hydrogen Tautomerization and Conductance Switching of Naphthalocyanine Molecules Science 2007 , 317 , 1203 – 1206

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129

Current-Induced Hydrogen Tautomerization and Conductance Switching of Naphthalocyanine Molecules

Liljeroth, Peter; Repp, Jascha; Meyer, Gerhard

Science (Washington, DC, United States) (2007), 317 (5842), 1203-1206CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine mols. constitutes a two-level system that was manipulated and probed by low-temp. scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the mols. can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the mol. and is expressed as considerable changes in the cond. of the mol. The authors also demonstrated a coupling of the switching process so that the charge injection in one mol. induced tautomerization in an adjacent mol.

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Ye, T. ; Kumar, A. S. ; Saha, S. ; Takami, T. ; Huang, T. J. ; Stoddart, J. F. ; Weiss, P. S. Changing Stations in Single Bistable Rotaxane Molecules under Electrochemical Control ACS Nano 2010 , 4 , 3697 – 3701

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130

Changing Stations in Single Bistable Rotaxane Molecules under Electrochemical Control

Ye, Tao; Kumar, Ajeet S.; Saha, Sourav; Takami, Tomohide; Huang, Tony J.; Stoddart, J. Fraser; Weiss, Paul S.

ACS Nano (2010), 4 (7), 3697-3701CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)

We have directly obsd. electrochem. driven single-mol. station changes within bistable rotaxane mols. anchored laterally on gold surfaces. These observations were achieved by employing mol. designs that significantly reduced the mobility and enhanced the assembly of mols. in orientations conducive to direct measurement using scanning tunneling microscopy. The results reveal mol.-level details of the station changes of surface-bound bistable rotaxane mols., correlated with their different redox states. The mech. motions within these mech. interlocked mols. are influenced by their interactions with the surface and with neighboring mols., as well as by the conformations of the dumbbell component.

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Choi, B. Y. ; Kahng, S. J. ; Kim, S. ; Kim, H. ; Kim, H. W. ; Song, Y. J. ; Ihm, J. ; Kuk, Y. Conformational Molecular Switch of the Azobenzene Molecule: A Scanning Tunneling Microscopy Study Phys. Rev. Lett. 2006 , 96 , 156106-1-4

132

Comstock, M. J. ; Levy, N. ; Kirakosian, A. ; Cho, J. W. ; Lauterwasser, F. ; Harvey, J. H. ; Strubbe, D. A. ; Frechet, J. M. J. ; Trauner, D. ; Louie, S. G. Reversible Photomechanical Switching of Individual Engineered Molecules at a Metallic Surface Phys. Rev. Lett. 2007 , 99 , 038301

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132

Reversible Photomechanical Switching of Individual Engineered Molecules at a Metallic Surface

Comstock, Matthew J.; Levy, Niv; Kirakosian, Armen; Cho, Jongweon; Lauterwasser, Frank; Harvey, Jessica H.; Strubbe, David A.; Frechet, Jean M. J.; Trauner, Dirk; Louie, Steven G.; Crommie, Michael F.

Physical Review Letters (2007), 99 (3), 038301/1-038301/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

The authors have obsd. reversible light-induced mech. switching for individual org. mols. bound to a metal surface. Scanning tunneling microscopy (STM) was used to image the features of individual azobenzene mols. on Au(111) before and after reversibly cycling their mech. structure between trans and cis states using light. Azobenzene mols. were engineered to increase their surface photomech. activity by attaching varying nos. of tert-Bu (TB) ligands ("legs") to the azobenzene Ph rings. STM images show that increasing the no. of TB legs "lifts" the azobenzene mols. from the substrate, thereby increasing mol. photomech. activity by decreasing mol.-surface coupling.

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133

Comstock, M. J. ; Levy, N. ; Cho, J. ; Berbil-Bautista, L. ; Crommie, M. F. ; Poulsen, D. A. ; Frechet, J. M. J. Measuring Reversible Photomechanical Switching Rates for a Molecule at a Surface Appl. Phys. Lett. 2008 , 92 , 123107-1-3

134

Kumar, A. S. ; Ye, T. ; Takami, T. ; Yu, B. C. ; Flatt, A. K. ; Tour, J. M. ; Weiss, P. S. Reversible Photo-Switching of Single Azobenzene Molecules in Controlled Nanoscale Environments Nano Lett. 2008 , 8 , 1644 – 1648

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134

Reversible Photo-Switching of Single Azobenzene Molecules in Controlled Nanoscale Environments

Kumar, Ajeet S.; Ye, Tao; Takami, Tomohide; Yu, Byung-Chan; Flatt, Austen K.; Tour, James M.; Weiss, Paul S.

Nano Letters (2008), 8 (6), 1644-1648CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)

The authors drive reversible photoinduced switching of single azobenzene-functionalized mols. isolated in tailored alkanethiolate monolayer matrixes on Au{111}. The authors designed mol. tethers to suppress excited-state quenching from the metal substrate and formed rigid assemblies of single tethered azobenzene mols. in the domains of monolayer to limit steric constraints and tip-induced and stochastic switching effects. Single mols. were reversibly photoisomerized between trans and cis conformations by cycling exposure to visible and UV light. Trans- and cis conformations were imaged as high (2.1 ± 0.3 Å) and low (0.7 ± 0.2 Å) protrusions in STM images and were assigned to the on and off states of the mol., resp.

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135

Yasuda, R. ; Noji, H. ; Kinosita, K. ; Yoshida, M. F-1-ATPase Is a Highly Efficient Molecular Motor that Rotates with Discrete 120° Steps Cell 1998 , 93 , 1117 – 1124

136

Kottas, G. S. ; Clarke, L. I. ; Horinek, D. ; Michl, J. Artificial Molecular Rotors Chem. Rev. 2005 , 105 , 1281 – 1376

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136

Artificial Molecular Rotors

Kottas, Gregg S.; Clarke, Laura I.; Horinek, Dominik; Michl, Josef

Chemical Reviews (Washington, DC, United States) (2005), 105 (4), 1281-1376CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review on properties of mech. conformational motion of org. mols. in soln. and solids and on surfaces by expts. and mol. dynamics.

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Seldenthuis, J. S. ; Prins, F. ; Thijssen, J. M. ; van der Zant, H. S. J. An All-Electric Single-Molecule Motor ACS Nano 2010 , 4 , 6681 – 6686

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137

An All-Electric Single-Molecule Motor

Seldenthuis, Johannes S.; Prins, Ferry; Thijssen, Joseph M.; van der Zant, Herre S. J.

ACS Nano (2010), 4 (11), 6681-6686CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)

Many types of mol. motors are proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chem. reactions. The authors propose a new type of mol. motor based on elec. field actuation and elec. current detection of the rotational motion of a mol. dipole embedded in a three-terminal single-mol. device. The key aspect of this all-electronic design is the conjugated backbone of the mol., which simultaneously provides the potential landscape of the rotor orientation and a real-time measure of that orientation through the modulation of the cond. Using quantum chem. calcns., this approach provides full control over the speed and continuity of motion, thereby combining elec. and mech. control at the mol. level over a wide range of temps. Also, chem. can be used to change all key parameters of the device, enabling a variety of new expts. on mol. motors.

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van Delden, R. A. ; ter Wiel, M. K. J. ; Pollard, M. M. ; Vicario, J. ; Koumura, N. ; Feringa, B. L. Unidirectional Molecular Motor on a Gold Surface Nature 2005 , 437 , 1337 – 1340

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138

Unidirectional molecular motor on a gold surface

van Delden, Richard A.; ter Wiel, Matthijs K. J.; Pollard, Michael M.; Vicario, Javier; Koumura, Nagatoshi; Feringa, Ben L.

Nature (London, United Kingdom) (2005), 437 (7063), 1337-1340CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Mols. capable of mimicking the function of a wide range of mech. devices have been fabricated, with motors that can induce mech. movement attracting particular attention. Such mol. motors convert light or chem. energy into directional rotary or linear motion, and are usually prepd. and operated in soln. But if they are to be used as nanomachines that can do useful work, it seems essential to construct systems that can function on a surface, like a recently reported linear artificial muscle. Surface-mounted rotors have been realized and limited directionality in their motion predicted. Here we demonstrate that a light-driven mol. motor capable of repetitive unidirectional rotation can be mounted on the surface of gold nanoparticles. The motor design uses a chiral helical alkene with an upper half that serves as a propeller and is connected through a carbon-carbon double bond (the rotation axis) to a lower half that serves as a stator. The stator carries two thiol-functionalized 'legs', which then bind the entire motor mol. to a gold surface. NMR spectroscopy reveals that two photo-induced cis-trans isomerizations of the central double bond, each followed by a thermal helix inversion to prevent reverse rotation, induce a full and unidirectional 360° rotation of the propeller with respect to the surface-mounted lower half of the system.

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Zheng, X. L. ; Mulcahy, M. E. ; Horinek, D. ; Galeotti, F. ; Magnera, T. F. ; Michl, J. Dipolar and Nonpolar Altitudinal Molecular Rotors Mounted on an Au(111) Surface J. Am. Chem. Soc. 2004 , 126 , 4540 – 4542

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139

Dipolar and Nonpolar Altitudinal Molecular Rotors Mounted on an Au(111) Surface

Zheng, Xiaolai; Mulcahy, Mary E.; Horinek, Dominik; Galeotti, Francesco; Magnera, Thomas F.; Michl, Josef

Journal of the American Chemical Society (2004), 126 (14), 4540-4542CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

The authors describe the prepn. of a compd. whose mols. consist of two metal sandwich stands carrying tentacles with affinity to metal surfaces and holding an axle that carries a dipolar or a nonpolar rotator. The dipolar rotor exists as three pairs of enantiomers, rapidly interconverting at room temp. When mounted on a Au surface, each mol. represents a chiral altitudinal rotor, with the rotator axle parallel to the surface. The surface-mounted rotor mols. are characterized by several spectroscopic and imaging techniques. At any one time, in ∼1/3 of the dipolar rotors the rotator is free to turn and the direction of its dipole can be flipped by the elec. field applied by an STM tip, as revealed by differential barrier height imaging. Mol. dynamics calcns. suggest that elec. field normal to the surface causes members of one pair of enantiomers to rotate unidirectionally.

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Mulcahy, M. E. ; Magnera, T. F. ; Michl, J. Molecular Rotors on Au(111): Rotator Orientation from IR Spectroscopy J. Phys. Chem. C 2009 , 113 , 20698 – 20704

141

Gimzewski, J. K. ; Joachim, C. ; Schlittler, R. R. ; Langlais, V. ; Tang, H. ; Johannsen, I. Rotation of a Single Molecule within a Supramolecular Bearing Science 1998 , 281 , 531 – 533

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141

Rotation of a single molecule within a supramolecular bearing

Gimzewski, J. K.; Joachhim, C.; Schlittler, R. R.; Langlias, V.; Tang, H.; Johannsen, I.

Science (Washington, D. C.) (1998), 281 (5376), 531-533CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Exptl. visualization and verification of a single-mol. rotor operating within a supramol. bearing is reported. Using a scanning tunneling microscope, single mols. were obsd. to exist in one of two spatially defined states laterally sepd. by 0.26 nm. One was identified as a rotating state and the other as an immobilized state. Calcns. of the energy barrier for rotation of these two states show that it is below the thermal energy at room temp. for the rotating state and above it for the immobilized state.

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142

Stipe, B. C. ; Rezaei, M. A. ; Ho, W. Inducing and Viewing the Rotational Motion of a Single Molecule Science 1998 , 279 , 1907 – 1909

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142

Inducing and viewing the rotational motion of a single molecule

Stipe, B. C.; Rezaei, M. A.; Ho, W.

Science (Washington, D. C.) (1998), 279 (5358), 1907-1909CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Tunneling electrons from the tip of a scanning tunneling microscope were used to induce and monitor the reversible rotation of single mols. of O2 among three equiv. orientations on the Pt(111) surface. Detailed studies of the rotation rates indicate a crossover from a single-electron process to a multielectron process below a threshold tunneling voltage. Values for the energy barrier to rotation and the vibrational relaxation rate of the mol. were obtained by comparing the exptl. data with a theor. mode. The ability to induce the controlled motion of single mols. enhances the authors' understanding of basic chem. processes on surfaces and may lead to useful single-mol. devices.

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143

Baber, A. E. ; Tierney, H. L. ; Sykes, E. C. H. A Quantitative Single-Molecule Study of Thioether Molecular Rotors ACS Nano 2008 , 2 , 2385 – 2391

144

Jewell, A. D. ; Tierney, H. L. ; Baber, A. E. ; Iski, E. V. ; Laha, M. M. ; Sykes, E. C. H. Time-Resolved Studies of Individual Molecular Rotors J. Phys.: Condens. Matter 2010 , 22 , 264006-1-11

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144

Time-resolved studies of individual molecular rotors

Jewell, April D.; Tierney, Heather L.; Baber, Ashleigh E.; Iski, Erin V.; Laha, Michael M.; Sykes, E. Charles H.

Journal of Physics: Condensed Matter (2010), 22 (26), 264006/1-264006/11CODEN: JCOMEL; ISSN:0953-8984. (Institute of Physics Publishing)

Thioether mol. rotors show great promise as nanoscale models for exploring the fundamental limits of thermally and elec. driven mol. rotation. By using time-resolved measurements which increase the time resoln. of the scanning tunneling microscope the authors were able to record the dynamics of individual thioether mol. rotors as a function of surface structure, rotor chem., thermal energy and elec. excitation. The local surface structure can have a dramatic influence on the energy landscape that the mol. rotors experience. In terms of rotor structure, altering the length of the rotor's alkyl tails allowed the origin of the barrier to rotation to be more fully understood. Finally, time-resolved measurement of elec. excited rotation revealed that vibrational excitation of a C-H bond in the rotor's alkyl tail is an efficient channel with which to excite rotation, and that the excitation is a 1-electron process.

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Chiaravalloti, F. ; Gross, L. ; Rieder, K. H. ; Stojkovic, S. M. ; Gourdon, A. ; Joachim, C. ; Moresco, F. A Rack-and-Pinion Device at the Molecular Scale Nat. Mater. 2007 , 6 , 30 – 33

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145

A rack-and-pinion device at the molecular scale

Chiaravalloti, Franco; Gross, Leo; Rieder, Karl-Heinz; Stojkovic, Sladjana M.; Gourdon, Andre; Joachim, Christian; Moresco, Francesca

Nature Materials (2007), 6 (1), 30-33CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)

Mol. machines, and in particular mol. motors with synthetic mol. structures and fuelled by external light, voltage or chem. conversions, have recently been reported. Most of these expts. are carried out in soln. with a large ensemble of mols. and without access to one mol. at a time, a key point for future use of single mol. machines with an at. scale precision. Therefore, to expt. on a single mol.-machine, this mol. has to be adsorbed on a surface, imaged and manipulated with the tip of a scanning tunneling microscope (STM). A few expts. of this type have described mol. mechanisms in which a rotational movement of a single mol. is involved. However, until now, only uncontrolled rotations or indirect signatures of a rotation have been reported. In this work, we present a mol. rack-and-pinion device for which an STM tip drives a single pinion mol. at low temp. The pinion is a 1.8-nm-diam. mol. functioning as a six-toothed wheel interlocked at the edge of a self-assembled mol. island acting as a rack. We monitor the rotation of the pinion mol. tooth by tooth along the rack by a chem. tag attached to one of its cogs.

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Manzano, C. ; Soe, W. H. ; Wong, H. S. ; Ample, F. ; Gourdon, A. ; Chandrasekhar, N. ; Joachim, C. Step-by-Step Rotation of a Molecule-Gear Mounted on an Atomic-Scale Axis Nat. Mater. 2009 , 8 , 576 – 579

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146

Step-by-step rotation of a molecule-gear mounted on an atomic-scale axis

Manzano, C.; Soe, W.-H.; Wong, H. S.; Ample, F.; Gourdon, A.; Chandrasekhar, N.; Joachim, C.

Nature Materials (2009), 8 (7), 576-579CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)

Gears are microfabricated down to diams. of a few micrometres. Natural macromol. motors, of tens of nanometers in diam., also show gear effects. At a smaller scale, the random rotation of a single-mol. rotor encaged in a mol. stator was obsd., demonstrating that a single mol. can be rotated with the tip of a scanning tunnelling microscope (STM). A self-assembled rack-and-pinion mol. machine where the STM tip apex is the rotation axis of the pinion was also tested. Here, we present the mechanics of an intentionally constructed mol.-gear on a Au(111) surface, mounting and centring one hexa--butyl-pyrimidopentaphenylbenzene mol. on one atom axis. The combination of mol. design, mol. manipulation and surface at. structure selection leads to the construction of a fundamental component of a planar single-mol. mech. machine. The rotation of our mol.-gear is step-by-step and totally under control, demonstrating nine stable stations in both directions.

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147

Stipe, B. C. ; Rezaei, M. A. ; Ho, W. Coupling of Vibrational Excitation to the Rotational Motion of a Single Adsorbed Molecule Phys. Rev. Lett. 1998 , 81 , 1263 – 1266

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147

Coupling of Vibrational Excitation to the Rotational Motion of a Single Adsorbed Molecule

Stipe, B. C.; Rezaei, M. A.; Ho, W.

Physical Review Letters (1998), 81 (6), 1263-1266CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

The reversible rotation of a single isolated acetylene mol. between 2 diagonal sites on the Cu(100) surface at 8 K was induced and monitored with tunneling electrons from a scanning tunneling microscope (STM). Excitation of the C-H (C-D) stretch mode of C2H 2 (C2D 2) at 358 meV (266 meV) led to a 10-fold (60-fold) increase in the rotation rate. This increase is attributed to energy transfer from the C-H (C-D) stretch mode to the hindered rotational motion of the mol. Inelastic electron tunneling spectroscopy with the STM provides the energies of the stretch modes and allows a quant. detn. of the inelastic tunneling and coupling probabilities.

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148

Sainoo, Y. ; Kim, Y. ; Okawa, T. ; Komeda, T. ; Shigekawa, H. ; Kawai, M. Excitation of Molecular Vibrational Modes with Inelastic Scanning Tunneling Microscopy Processes: Examination through Action Spectra of cis-2-Butene on Pd(110) Phys. Rev. Lett. 2005 , 95 , 246102-1-4

149

Hliwa, M. ; Ami, S. ; Joachim, C. A 3-Terminal Single Molecule Nanoscale Amperometer Chem. Phys. Lett. 2006 , 425 , 356 – 360

150

Scott, G. D. ; Natelson, D. Kondo Resonances in Molecular Devices ACS Nano 2010 , 4 , 3560 – 3579

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150

Kondo Resonances in Molecular Devices

Scott, Gavin David; Natelson, Douglas

ACS Nano (2010), 4 (7), 3560-3579CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)

A review. Mol. electronic devices currently serve as a platform for studying a variety of phys. phenomena only accessible at the nanometer scale. One such phenomenon is the highly correlated electronic state responsible for the Kondo effect, manifested here as a Kondo resonance in the conductance. Because the Kondo effect results from strong electron-electron interactions, it is not captured by the usual quantum chem. approaches traditionally applied to understand chem. electron transfer. In this review, the authors will discuss the origins and phenomenol. of Kondo resonances obsd. in single-mol. devices, focusing primarily on the spin-1/2 Kondo state arising from a single unpaired electron. The authors explore the rich phys. system of a single-mol. device, which offers a unique spectroscopic tool for studying the interplay of emergent Kondo behavior and such properties as MO transitions and vibrational modes. The authors will addnl. address more exotic systems, such as higher spin states in the Kondo regime, and the authors will review recent exptl. advances in the ability to manipulate and exert control over these nanoscale devices.

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Joachim, C. ; Gimzewski, J. K. ; Schlittler, R. R. ; Chavy, C. Electronic Transparency of a Single C₆₀ Molecule Phys. Rev. Lett. 1995 , 74 , 2102 – 2105

152

Nitzan, A. ; Ratner, M. A. Electron Transport in Molecular Wire Junctions Science 2003 , 300 , 1384 – 1389

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Electron Transport in Molecular Wire Junctions

Nitzan, Abraham; Ratner, Mark A.

Science (Washington, DC, United States) (2003), 300 (5624), 1384-1389CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

A review. Mol. conductance junctions are structures in which single mols. or small groups of mols. conduct elec. current between two electrodes. In such junctions, the connection between the mol. and the electrodes greatly affects the current-voltage characteristics. Despite several exptl. and theor. advances, including the understanding of simple systems, there is still limited correspondence between exptl. and theor. studies of these systems.

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153

Ulgut, B. ; Abruna, H. D. Electron Transfer through Molecules and Assemblies at Electrode Surfaces Chem. Rev. 2008 , 108 , 2721 – 2736

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153

Electron Transfer through Molecules and Assemblies at Electrode Surfaces

Ulgut, Burak; Abruna, Hector D.

Chemical Reviews (Washington, DC, United States) (2008), 108 (7), 2721-2736CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review. Both theor. and exptl. methods were developed in the past 2 decades to study electron transport through single mols. and assemblies. The theor. methods are only recently getting to the level of accurately describing mol. assemblies on electrode surfaces. The experience of making exquisitely designed chem. modified electrodes has contributed a great deal to the efforts of measuring conductance of mols. Break and contact junctions are described.

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154

Su, W. P. ; Schrieffer, J. R. ; Heeger, A. J. Solitons in Polyacetylene Phys. Rev. Lett. 1979 , 42 , 1698 – 1701

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154

Solitons in polyacetylene

Su, W. P.; Schrieffer, J. R.; Heeger, A. J.

Physical Review Letters (1979), 42 (25), 1698-701CODEN: PRLTAO; ISSN:0031-9007.

A theor. study is presented of soliton formation in long-chain polyenes, including the energy of formation, length, mass, and activation energy for motion. The results provide an explanation of the mobile neutral defect obsd. in undoped (CH)x. Since the soliton formation energy is less than that need to create band excitation, solitons play a fundamental role in the charge-transfer doping mechanism.

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Aviram, A. ; Ratner, M. A. Molecular Rectifiers Chem. Phys. Lett. 1974 , 29 , 277 – 283

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155

Molecular rectifiers

Aviram, Arieh; Ratner, Mark A.

Chemical Physics Letters (1974), 29 (2), 277-83CODEN: CHPLBC; ISSN:0009-2614.

The construction of a very simple electronic device, a rectifier, based on the use of a single org. mol. is discussed. The mol. rectifier consists of a donor pi system and an acceptor pi system, sepd. by a sigma-bonded (methylene) tunnelling bridge. The response of such a mol. to an applied field is calcd., and rectifier properties indeed appear.

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Park, H. ; Park, J. ; Lim, A. K. L. ; Anderson, E. H. ; Alivisatos, A. P. ; McEuen, P. L. Nanomechanical Oscillations in a Single-C₆₀ Transistor Nature 2000 , 407 , 57 – 60

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156

Nanomechanical oscillations in a single-C60 transistor

Park; Park; Lim; Anderson; Alivisatos; McEuen

Nature (2000), 407 (6800), 57-60 ISSN:.

The motion of electrons through quantum dots is strongly modified by single-electron charging and the quantization of energy levels. Much effort has been directed towards extending studies of electron transport to chemical nanostructures, including molecules, nanocrystals and nanotubes. Here we report the fabrication of single-molecule transistors based on individual C60 molecules connected to gold electrodes. We perform transport measurements that provide evidence for a coupling between the centre-of-mass motion of the C60 molecules and single-electron hopping--a conduction mechanism that has not been observed previously in quantum dot studies. The coupling is manifest as quantized nano-mechanical oscillations of the C60 molecule against the gold surface, with a frequency of about 1.2 THz. This value is in good agreement with a simple theoretical estimate based on van der Waals and electrostatic interactions between C60 molecules and gold electrodes.

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157

Lu, W. ; Lieber, C. M. Nanoelectronics from the Bottom Up Nat. Mater. 2007 , 6 , 841 – 850

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157

Nanoelectronics from the bottom up

Lu, Wei; Lieber, Charles M.

Nature Materials (2007), 6 (11), 841-850CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)

A review. Electronics obtained through the bottom-up approach of mol.-level control of material compn. and structure may lead to devices and fabrication strategies not possible with top-down methods. This review presents a brief summary of bottom-up and hybrid bottom-up/top-down strategies for nanoelectronics with an emphasis on memories based on the crossbar motif. First, we discuss representative electromech. and resistance-change memory devices based on carbon nanotube and core-shell nanowire structures, resp. These device structures show robust switching, promising performance metrics and the potential for terabit-scale d. Second, we review architectures being developed for circuit-level integration, hybrid crossbar/CMOS circuits and array-based systems, including exptl. demonstrations of key concepts such lithog.-independent, chem. coded stochastic demultiplexers. Finally, bottom-up fabrication approaches, including the opportunity for assembly of three-dimensional, vertically integrated multifunctional circuits, is critically discussed.

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Feldman, A. K. ; Steigerwald, M. L. ; Guo, X. F. ; Nuckolls, C. Molecular Electronic Devices Based on Single-Walled Carbon Nanotube Electrodes Acc. Chem. Res. 2008 , 41 , 1731 – 1741

159

Haick, H. ; Cahen, D. Making Contact: Connecting Molecules Electrically to the Macroscopic World Prog. Surf. Sci. 2008 , 83 , 217 – 261

160

Chen, F. ; Tao, N. J. Electron Transport in Single Molecules: From Benzene to Graphene Acc. Chem. Res. 2009 , 42 , 429 – 438

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160

Electron Transport in Single Molecules: From Benzene to Graphene

Chen, F.; Tao, N. J.

Accounts of Chemical Research (2009), 42 (3), 429-438CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)

A review. Electron movement within and between mols.-i.e., electron transfer-is important in many chem., electrochem., and biol. processes. Recent advances, particularly in scanning electrochem. microscopy (SECM), scanning-tunneling microscopy (STM), and at. force microscopy (AFM), permit the study of electron movement within single mols. In this Account, the authors describe electron transport at the single-mol. level. The authors begin by examg. the distinction between electron transport (from semiconductor physic) and electron transfer (a more general term referring to electron movement between donor and acceptor). The relation between these phenomena allows the authors to apply the authors' understanding of single-mol. electron transport between electrodes to a broad range of other electron transfer processes. Electron transport is most efficient when the electron transmission probability via a mol. reaches 100%; the corresponding conductance is then 2e2/h (e is the charge of the electron and h is the Planck const.). This ideal conduction was obsd. in a single metal atom and a string of metal atoms connected between two electrodes. However, the conductance of a mol. connected to two electrodes is often orders of magnitude less than the ideal and strongly depends on both the intrinsic properties of the mol. and its local environment. Mol. length, means of coupling to the electrodes, the presence of conjugated double bonds, and the inclusion of possible redox centers (for example, ferrocene) within the mol. wire have a pronounced effect on the conductance. This complex behavior is responsible for diverse chem. and biol. phenomena and is potentially useful for device applications. Polycyclic arom. hydrocarbons (PAHs) afford unique insight into electron transport in single mols. The simplest one, benzene, has a conductance «2e2/h due to its large LUMO-HOMO gap. At the other end of the spectrum, graphene sheets and carbon nanotubes-consisting of infinite nos. of arom. rings-have small or even zero energy gaps between the conduction and valence bands. Between these two limits are intermediate mols. with rich properties, such as perylene derivs. made of seven arom. rings; the properties of these types of mols. have yet to be fully explored. Studying PAHs is important not only in answering fundamental questions about electron transport but also in the ongoing quest for mol.-scale electronic devices. This line of research also helps bridge the gap between electron transfer phenomena in small redox mols. and electron transport properties in nanostructures.

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161

Xiao, X. Y. ; Xu, B. Q. ; Tao, N. J. Measurement of Single Molecule Conductance: Benzenedithiol and Benzenedimethanethiol Nano Lett. 2004 , 4 , 267 – 271

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161

Measurement of Single Molecule Conductance: Benzenedithiol and Benzenedimethanethiol

Xiao, Xiaoyin; Xu, Bingqian; Tao, Nongjian J.

Nano Letters (2004), 4 (2), 267-271CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)

The authors have studied electron transport properties of benzenedithiol and benzenedimethanethiol covalently bonded to Au electrodes by repeatedly creating a large no. of mol. junctions. For each mol., conductance histogram shows peaks at integer multiples of a fundamental conductance value, which was used to identify the conductance of a single mol. The conductance values of a benzenedithiol and benzenedimethanethiol are 0.011 G0 and 0.0006 G0 (G0 = 2e2/h), resp. The conductance peaks are broad, which reflects variations in the microscopic details of different mol. junctions. The authors have also studied electrochem. gate effect.

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Chen, F. ; Li, X. L. ; Hihath, J. ; Huang, Z. F. ; Tao, N. J. Effect of Anchoring Groups on Single-Molecule Conductance: Comparative Study of Thiol-, Amine-, and Carboxylic-Acid-Terminated Molecules J. Am. Chem. Soc. 2006 , 128 , 15874 – 15881

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162

Effect of Anchoring Groups on Single-Molecule Conductance: Comparative Study of Thiol-, Amine-, and Carboxylic-Acid-Terminated Molecules

Chen, Fang; Li, Xiulan; Hihath, Joshua; Huang, Zhifeng; Tao, Nongjian

Journal of the American Chemical Society (2006), 128 (49), 15874-15881CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

The authors studied the effect of anchoring groups on the conductance of single mols. using alkanes terminated with dithiol, diamine, and dicarboxylic-acid groups as a model system. The authors created a large no. of mol. junctions mech. and analyzed the statistical distributions of the conductance values of the mol. junctions. Multiple sets of conductance values were found in each case. The I-V characteristics, temp. independence, and exponential decay of the conductance with the mol. length all indicate tunneling as the conduction mechanism for these mols. The prefactor of the exponential decay function, which reflects the contact resistance, is highly sensitive to the anchoring group, and the decay const. is weakly dependent on the anchoring group. These observations are attributed to different electronic couplings between the mols. and the electrodes and alignments of the mol. energy levels relative to the Fermi energy level of the electrodes introduced by different anchoring groups. For diamine and dicarboxylic-acid groups, the conductance values are sensitive to pH due to protonation and deprotonation of the anchoring groups. Further insight into the binding strengths of these anchoring groups to gold electrodes was obtained by statistically analyzing the stretching length of mol. junctions.

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Brandbyge, M. ; Schiotz, J. ; Sorensen, M. R. ; Stoltze, P. ; Jacobsen, K. W. ; Norskov, J. K. ; Olesen, L. ; Laegsgaard, E. ; Stensgaard, I. ; Besenbacher, F. Quantized Conductance in Atom-Sized Wires between Two Metals Phys. Rev. B 1995 , 52 , 8499 – 8514

164

Xu, B. Q. ; Tao, N. J. J. Measurement of Single-Molecule Resistance by Repeated Formation of Molecular Junctions Science 2003 , 301 , 1221 – 1223

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164

Measurement of Single-Molecule Resistance by Repeated Formation of Molecular Junctions

Xu, Bingqian; Tao, Nongjian J.

Science (Washington, DC, United States) (2003), 301 (5637), 1221-1223CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

The conductance of a single mol. connected to two gold electrodes was detd. by repeatedly forming thousands of gold-mol.-gold junctions. Conductance histograms revealed well-defined peaks at integer multiples of a fundamental conductance value, which was used to identify the conductance of a single mol. The resistances near zero bias were 10.5 ± 0.5, 51 ± 5, 630 ± 50, and 1.3 ± 0.1MΩs for hexanedithiol, octanedithiol, decanedithiol, and 4,4' bipyridine, resp. The tunneling decay const. (βn) for N-alkanedithiols was 1.0 ± 0.1 per carbon atom and was weakly dependent on the applied bias. The resistance and βn values are consistent with 1st-principles calcns.

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165

Pascual, J. I. ; Mendez, J. ; Gomezherrero, J. ; Baro, A. M. ; Garcia, N. ; Binh, V. T. Quantum Contact in Gold Nanostructures by Scanning-Tunneling-Microscopy Phys. Rev. Lett. 1993 , 71 , 1852 – 1855

166

Krans, J. M. ; Vanruitenbeek, J. M. ; Fisun, V. V. ; Yanson, I. K. ; Dejongh, L. J. The Signature of Conductance Quantization in Metallic Point Contacts Nature 1995 , 375 , 767 – 769

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166

The signature of conductance quantization in metallic point contacts

Krans, J. M.; van Ruitenbeek, J. M.; Fisun, V. V.; Yanson, I. K.; de Jongh, L. J.

Nature (London) (1995), 375 (6534), 767-9CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)

The authors use the fact that the degeneracy of the conduction modes of a three-dimensional point contact should result in a characteristic sequence of conductance values (some integer multiples of 2e2/h are excluded) to distinguish the effects of conductance quantization from those of discrete variations of contact size in a break-junction expt., confirming that conductance quantization does indeed occur. At.-sized copper and sodium contacts were measured at 4.2 K.

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167

Li, X. L. ; He, J. ; Hihath, J. ; Xu, B. Q. ; Lindsay, S. M. ; Tao, N. J. Conductance of Single Alkanedithiols: Conduction Mechanism and Effect of Molecule−Electrode Contacts J. Am. Chem. Soc. 2006 , 128 , 2135 – 2141

168

Kamenetska, M. ; Koentopp, M. ; Whalley, A. C. ; Park, Y. S. ; Steigerwald, M. L. ; Nuckolls, C. ; Hybertsen, M. S. ; Venkataraman, L. Formation and Evolution of Single-Molecule Junctions Phys. Rev. Lett. 2009 , 102 , 126803-1-4

169

Zhou, C. ; Muller, C. J. ; Deshpande, M. R. ; Sleight, J. W. ; Reed, M. A. Microfabrication of a Mechanically Controllable Break Junction in Silicon Appl. Phys. Lett. 1995 , 67 , 1160 – 1162

170

Park, H. ; Lim, A. K. L. ; Alivisatos, A. P. ; Park, J. ; McEuen, P. L. Fabrication of Metallic Electrodes with Nanometer Separation by Electromigration Appl. Phys. Lett. 1999 , 75 , 301 – 303

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170

Fabrication of metallic electrodes with nanometer separation by electromigration

Park, Hongkun; Lim, Andrew K. L.; Alivisatos, A. Paul; Park, Jiwoong; McEuen, Paul L.

Applied Physics Letters (1999), 75 (2), 301-303CODEN: APPLAB; ISSN:0003-6951. (American Institute of Physics)

A simple yet highly reproducible method to fabricate metallic electrodes with nanometer sepn. is presented. The fabrication is achieved by passing a large elec. current through a gold nanowire defined by electron-beam lithog. and shadow evapn. The current flow causes the electromigration of gold atoms and the eventual breakage of the nanowire. The breaking process yields two stable metallic electrodes sepd. by ∼1 nm with high efficiency. These electrodes are ideally suited for electron-transport studies of chem. synthesized nanostructures, and their utility is demonstrated here by fabricating single-electron transistors based on colloidal cadmium selenide nanocrystals.

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Park, J. ; Pasupathy, A. N. ; Goldsmith, J. I. ; Chang, C. ; Yaish, Y. ; Petta, J. R. ; Rinkoski, M. ; Sethna, J. P. ; Abruna, H. D. ; McEuen, P. L. et al. Coulomb Blockade and the Kondo Effect in Single-Atom Transistors Nature 2002 , 417 , 722 – 725

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171

Coulomb blockade and the Kondo effect in single-atom transistors

Park, Jiwoong; Pasupathy, Abhay N.; Goldsmith, Jonas I.; Chang, Connie; Yaish, Yuval; Petta, Jason R.; Rinkoski, Marie; Sethna, James P.; Abruna, Hector D.; McEuen, Paul L.; Ralph, Daniel C.

Nature (London, United Kingdom) (2002), 417 (6890), 722-725CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Using mols. as electronic components is a powerful new direction in the science and technol. of nanometer-scale systems. Expts. to date have examd. a multitude of mols. conducting in parallel, or, in some cases, transport through single mols. The latter includes mols. probed in a two-terminal geometry using mech. controlled break junctions or scanning probes as well as three-terminal single-mol. transistors made from carbon nanotubes, C60 mols., and conjugated mols. dild. in a less-conducting mol. layer. The ultimate limit would be a device where electrons hop on to, and off from, a single atom between two contacts. Here the authors describe transistors incorporating a transition-metal complex designed so that electron transport occurs through well-defined charge states of a single atom. The authors examine two related mols. contg. a Co ion bonded to polypyridyl ligands, attached to insulating tethers of different lengths. Changing the length of the insulating tether alters the coupling of the ion to the electrodes, enabling the fabrication of devices that exhibit either single-electron phenomena, such as Coulomb blockade, or the Kondo effect.

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172

Liang, W. J. ; Shores, M. P. ; Bockrath, M. ; Long, J. R. ; Park, H. Kondo Resonance in a Single-Molecule Transistor Nature 2002 , 417 , 725 – 729

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172

Kondo resonance in a single-molecule transistor

Liang, Wenjie; Shores, Matthew P.; Bockrath, Marc; Long, Jeffrey R.; Park, Hongkun

Nature (London, United Kingdom) (2002), 417 (6890), 725-729CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

When an individual mol., nanocrystal, nanotube or lithog. defined quantum dot is attached to metallic electrodes via tunnel barriers, electron transport is dominated by single-electron charging and energy-level quantization. As the coupling to the electrodes increases, higher-order tunneling and correlated electron motion give rise to new phenomena, including the Kondo resonance. To date, all of the studies of Kondo phenomena in quantum dots were performed on systems where precise control over the spin degrees of freedom is difficult. Mols. incorporating transition-metal atoms provide powerful new systems in this regard, because the spin and orbital degrees of freedom can be controlled through well-defined chem. Here the authors report the observation of the Kondo effect in single-mol. transistors, where an individual divanadium mol. serves as a spin impurity. The Kondo resonance can be tuned reversibly using the gate voltage to alter the charge and spin state of the mol. The resonance persists at temps. up to 30 K and when the energy sepn. between the mol. state and the Fermi level of the metal exceeds 100 meV.

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Joachim, C. ; Martrou, D. ; Rezeq, M. ; Troadec, C. ; Jie, D. ; Chandrasekhar, N. ; Gauthier, S. Multiple Atomic Scale Solid Surface Interconnects for Atom Circuits and Molecule Logic Gates J. Phys.: Condens. Matter 2010 , 22 , 084025-1-18

174

Wang, W. Y. ; Lee, T. ; Kretzschmar, I. ; Reed, M. A. Inelastic Electron Tunneling Spectroscopy of an Alkanedithiol Self-Assembled Monolayer Nano Lett. 2004 , 4 , 643 – 646

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174

Inelastic Electron Tunneling Spectroscopy of an Alkanedithiol Self-Assembled Monolayer

Wang, Wenyong; Lee, Takhee; Kretzschmar, Ilona; Reed, Mark A.

Nano Letters (2004), 4 (4), 643-646CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)

Inelastic electron tunneling spectroscopy (IETS) of an alkanedithiol self-assembled monolayer (SAM) is investigated using a nanometer-scale device. The IETS spectrum of the octanedithiol device clearly shows vibrational signatures of an octanedithiolate, -SC8 H16S-, bonded to gold electrodes. The pronounced IETS peaks correspond to vibrational modes perpendicular to the junction interface, which include the stretching modes of Au-S (at 33 mV) and C-C (at 133 mV) and the wagging mode of CH2 (at 158 mV). The obsd. peak intensities and peak widths are in good agreement with theor. predictions.

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175

Kushmerick, J. G. ; Holt, D. B. ; Yang, J. C. ; Naciri, J. ; Moore, M. H. ; Shashidhar, R. Metal-Molecule Contacts and Charge Transport across Monomolecular Layers: Measurement and Theory Phys. Rev. Lett. 2002 , 89 , 086802-1-4

176

Kushmerick, J. G. ; Lazorcik, J. ; Patterson, C. H. ; Shashidhar, R. ; Seferos, D. S. ; Bazan, G. C. Vibronic Contributions to Charge Transport across Molecular Junctions Nano Lett. 2004 , 4 , 639 – 642

177

Hansma, P. K. Inelastic Electron-Tunneling Phys. Rep. 1977 , 30 , 145 – 206

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Inelastic electron tunneling

Hansma, Paul K.

Physics Reports (1977), 30C (2), 145-206CODEN: PRPLCM; ISSN:0370-1573.

A review with 101 refs. The technique, theor. basis, selection rules, sensitivity, vibrational mode shifts due to surface interactions and supercond., and sample prepn. are discussed. Applications to biochem., radiation physics, surface studies, and catalysis are described.

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178

Lauhon, L. J. ; Ho, W. Single-Molecule Vibrational Spectroscopy and Microscopy: Co on Cu(001) and Cu(110) Phys. Rev. B 1999 , 60 , R8525 – R8528

179

Lorente, N. ; Persson, M. ; Lauhon, L. J. ; Ho, W. Symmetry Selection Rules for Vibrationally Inelastic Tunneling Phys. Rev. Lett. 2001 , 86 , 2593 – 2596

180

Blake, M. M. ; Nanayakkara, S. U. ; Claridge, S. A. ; Fernandez-Torres, L. C. ; Sykes, E. C. H. ; Weiss, P. S. Identifying Reactive Intermediates in the Ullmann Coupling Reaction by Scanning Tunneling Microscopy and Spectroscopy J. Phys. Chem. A 2009 , 113 , 13167 – 13172

181

Pascual, J. I. ; Jackiw, J. J. ; Song, Z. ; Weiss, P. S. ; Conrad, H. ; Rust, H. P. Adsorbate−Substrate Vibrational Modes of Benzene on Ag(110) Resolved with Scanning Tunneling Spectroscopy Phys. Rev. Lett. 2001 , 86 , 1050 – 1053

182

Kim, Y. ; Komeda, T. ; Kawai, M. Single-Molecule Reaction and Characterization by Vibrational Excitation Phys. Rev. Lett. 2002 , 89 , 126104-1-4

183

Berndt, R. ; Gimzewski, J. K. ; Johansson, P. Inelastic Tunneling Excitation of Tip-Induced Plasmon Modes on Noble-Metal Surfaces Phys. Rev. Lett. 1991 , 67 , 3796 – 3799

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183

Inelastic tunneling excitation of tip-induced plasmon modes on noble metal surfaces

Berndt, Richard; Gimzewski, James K.; Johansson, Peter

Physical Review Letters (1991), 67 (27), 3796-9CODEN: PRLTAO; ISSN:0031-9007.

Light emission characteristics from the tunnel gap of a scanning tunneling microscope were used to elucidate the interaction of tunneling electrons with tip-induced plasmon modes on Ag, Au, and Cu surfaces. Enhanced red shifted spectra were obsd. in the tunneling regime. Model calcns. of optical spectra in this range agree well in the exptl. data. Isochromat spectra were used to demonstrate that the principal excitation process occurs via inelastic tunneling.

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184

Berndt, R. ; Schlittler, R. R. ; Gimzewski, J. K. Photon-Emission Scanning Tunneling Microscope J. Vac. Sci. Technol., B 1991 , 9 , 573 – 577

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184

Photon emission scanning tunneling microscope

Berndt, R.; Schlittler, R. R.; Gimzewski, J. K.

Journal of Vacuum Science & Technology, B: Microelectronics and Nanometer Structures (1991), 9 (2, Pt. 2), 573-7CODEN: JVTBD9; ISSN:0734-211X.

The anal. of photons emitted from the tip-surface region of an STM has produced new information on local dissipative processes in tunneling. A key objective to extend the work to a general spectroscopic and microscopic method is to collect and detect photons as efficiently as possible. The exptl. arrangements are described, one of which incorporates an ellipsoidal mirror and the other a lens system to collect the photons. The systems operate in ultrahigh vacuum and have in situ sample and tip transfer facilities. Examples of a variety of photon spectroscopy modes including photon spectra, isochromat spectra, angular distributions, and photon mapping are presented.

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185

McCarty, G. S. ; Weiss, P. S. Scanning Probe Studies of Single Nanostructures Chem. Rev. 1999 , 99 , 1983 – 1990

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185

Scanning Probe Studies of Single Nanostructures

McCarty, G. S.; Weiss, P. S.

Chemical Reviews (Washington, D. C.) (1999), 99 (7), 1983-1990CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review with 59 refs. The authors focus on attempts to couple nanometer-scale imaging with spectroscopic techniques to understand the results obtained by scanning probe microscopes (SPMs) and to glean useful insight into the properties of the nanostructures under study. The authors limit the nanostructures discussed to nanometer-scale particles or distributed structures deposited or created on surfaces. The authors exclude such single-mol. measurements as single C nanotubes single DNA chains or single antigen-antibody complexes. Constructing and probing nanostructures with STM, AFM, and near-field scanning optical microscopy, and hybrid devices are reviewed.

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Cyr, D. M. ; Venkataraman, B. ; Flynn, G. W. ; Black, A. ; Whitesides, G. M. Functional Group Identification in Scanning Tunneling Microscopy of Molecular Adsorbates J. Phys. Chem. 1996 , 100 , 13747 – 13759

187

Moore, A. M. ; Yeganah, S. ; Yao, Y. ; Claridge, S. A. ; Tour, J. M. ; Ratner, M. A. ; Weiss, P. S. Polarizabilities of Adsorbed and Assembled Molecules: Measuring the Conductance through Buried Contacts ACS Nano 2010 , 4 , 7630 – 7636

188

Hirai, M. ; Yamanaka, C. ; Ikeya, M. Some Trials on a New Method of ESR Detection Using Tunneling Current Appl. Radiat. Isot. 1993 , 44 , 385 – 389

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188

Some trials on a new method of ESR detection using tunneling current

Hirai, M.; Yamanaka, C.; Ikeya, M.

Applied Radiation and Isotopes (1993), 44 (1-2), 385-9CODEN: ARISEF; ISSN:0883-2889.

Some trials on a new method of ESR detection using tunneling current are introduced. Magnetic field modulation and microwave amplitude modulation were tested. Modulation was obsd. in the tunneling current, which probably is caused by the (possibly nonresonant) microwave absorption by the sample (graphite). However, the dependence of the modulation on the magnetic field is not clear. The authors developed a new detection system using microwave frequency modulation (FM-ESR). FM-ESR is expected to be useful for the ESR detection using tunneling current.

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Manassen, Y. ; Hamers, R. J. ; Demuth, J. E. ; Castellano, A. J. Direct Observation of the Precession of Individual Paramagnetic Spins on Oxidized Silicon Surfaces Phys. Rev. Lett. 1989 , 62 , 2531 – 2534

190

Manassen, Y. Real-Time Response and Phase-Sensitive Detection to Demonstrate the Validity of ESR-STM Results J. Magn. Reson. 1997 , 126 , 133 – 137

191

Durkan, C. ; Welland, M. E. Electronic Spin Detection in Molecules Using Scanning-Tunneling-Microscopy-Assisted Electron-Spin Resonance Appl. Phys. Lett. 2002 , 80 , 458 – 460

192

Messina, P. ; Mannini, M. ; Caneschi, A. ; Gatteschi, D. ; Sorace, L. ; Sigalotti, P. ; Sandrin, C. ; Prato, S. ; Pittana, P. ; Manassen, Y. Spin Noise Fluctuations from Paramagnetic Molecular Adsorbates on Surfaces J. Appl. Phys. 2007 , 101 , 053916-1-14

193

Mugnaini, V. ; Fabrizioli, M. ; Ratera, I. ; Mannini, M. ; Caneschi, A. ; Gatteschi, D. ; Manassen, Y. ; Veciana, J. Towards the Detection of Single Polychlorotriphenylmethyl Radical Derivatives by Means of Electron Spin Noise STM Solid State Sci. 2009 , 11 , 956 – 960

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193

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

Mugnaini, Veronica; Fabrizioli, Mauro; Ratera, Imma; Mannini, Matteo; Caneschi, Andrea; Gatteschi, Dante; Manassen, Yishay; Veciana, Jaume

Solid State Sciences (2009), 11 (5), 956-960CODEN: SSSCFJ; ISSN:1293-2558. (Elsevier Masson SAS)

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

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Gorini, L. ; Fabrizioli, M. ; Mannini, M. ; Sorace, L. ; Yakovenko, A. Addressing Single Molecules of a Thin Magnetic Film Inorg. Chim. Acta 2008 , 361 , 4089 – 4093

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194

Addressing single molecules of a thin magnetic film

Gorini, Lapo; Fabrizioli, Mauro; Mannini, Matteo; Sorace, Lorenzo; Yakovenko, Anastasiya

Inorganica Chimica Acta (2008), 361 (14-15), 4089-4093CODEN: ICHAA3; ISSN:0020-1693. (Elsevier B.V.)

Electron spin noise-scanning tunneling microscopy (ESN-STM) represents the most promising technique for single spin centers addressing on surfaces. After a brief introduction on the results previously obtained by using this technique for the detection of both isolated mols. and small aggregates of BDPA, DPPH and TTM free radicals, here the authors' improved results in the single-mol. addressing of thio-functionalized nitronyl nitroxide radicals (NNRs) chem. bound to gold are discussed. ESN-STM spectra of NNRs self-assembled monolayers (SAMs) on Au(1 1 1) surfaces are reported together with the crystal structure of the studied radical NN-Ph-CH2SMe, considered up to now as the best arom. NNR for the obtainment of thin magnetic films.

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195

Wiesendanger, R. Spin Mapping at the Nanoscale and Atomic Scale Rev. Mod. Phys. 2009 , 81 , 1495 – 1550

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195

Spin mapping at the nanoscale and atomic scale

Wiesendanger, Roland

Reviews of Modern Physics (2009), 81 (4), 1495-1550CODEN: RMPHAT; ISSN:0034-6861. (American Physical Society)

A review. The direct observation of spin structures with at.-scale resoln., a long-time dream in condensed matter research, recently became a reality based on the development of spin-sensitive scanning probe methods, such as spin-polarized scanning-tunneling microscopy (SP-STM) and magnetic exchange force microscopy (MExFM). This article reviews the basic principles and methods of SP-STM and MExFM and describes recently achieved milestones in the application of these techniques to metallic and elec. insulating magnetic nanostructures. Discoveries of novel types of magnetic order at the nanoscale are presented as well as challenges for the future, including studies of local spin excitations based on spin-resolved inelastic tunneling spectroscopy and measurements of damping forces in MExFM expts.

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Loth, S. ; Etzkorn, M. ; Lutz, C. P. ; Eigler, D. M. ; Heinrich, A. J. Measurement of Fast Electron Spin Relaxation Times with Atomic Resolution Science 2010 , 329 , 1628 – 1630

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196

Measurement of Fast Electron Spin Relaxation Times with Atomic Resolution

Loth, Sebastian; Etzkorn, Markus; Lutz, Christopher P.; Eigler, D. M.; Heinrich, Andreas J.

Science (Washington, DC, United States) (2010), 329 (5999), 1628-1630CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Single spins in solid-state systems are often considered prime candidates for the storage of quantum information, and their interaction with the environment the main limiting factor for the realization of such schemes. The lifetime of an excited spin state is a sensitive measure of this interaction, but extending the spatial resoln. of spin relaxation measurements to the at. scale was a challenge. A scanning tunneling microscope can measure electron spin relaxation times of individual atoms adsorbed on a surface using an all-electronic pump-probe measurement scheme. The spin relaxation times of individual Fe-Cu dimers vary 50-250 ns. The method can in principle be generalized to monitor the temporal evolution of other dynamical systems.

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Brede, J. ; Atodiresei, N. ; Kuck, S. ; Lazic, P. ; Caciuc, V. ; Morikawa, Y. ; Hoffmann, G. ; Blugel, S. ; Wiesendanger, R. Spin- and Energy-Dependent Tunneling through a Single Molecule with Intramolecular Spatial Resolution Phys. Rev. Lett. 2010 , 105 , 047204-1-4

198

Atodiresei, N. ; Brede, J. ; Lazic, P. ; Caciuc, V. ; Hoffmann, G. ; Wiesendanger, R. ; Blugel, S. Design of the Local Spin Polarization at the Organic-Ferromagnetic Interface Phys. Rev. Lett. 2010 , 105 , 066601-1-4

199

Tinnefeld, P. ; Sauer, M. Branching out of Single-Molecule Fluorescence Spectroscopy: Challenges for Chemistry and Influence on Biology Angew. Chem., Int. Ed. 2005 , 44 , 2642 – 2671

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199

Branching out of single-molecule fluorescence spectroscopy: Challenges for chemistry and influence on biology

Tinnefeld, Philip; Sauer, Markus

Angewandte Chemie, International Edition (2005), 44 (18), 2642-2671CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)

A review. In the last decade emerging single-mol. fluorescence-spectroscopy tools have been developed and adapted to analyze individual mols. under various conditions. Single-mol.-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 biol. 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 detn. of their distance from polymerase mols. in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this review the authors demonstrate that single-mol. fluorescence spectroscopy has become an independent discipline capable of solving problems in mol. biol. The authors outline the challenges and future prospects for optical single-mol. techniques which can be used in combination with smart labeling strategies to yield quant. three-dimensional information about the dynamic organization of living cells.

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200

Alivisatos, P. The Use of Nanocrystals in Biological Detection Nat. Biotechnol. 2004 , 22 , 47 – 52

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200

The use of nanocrystals in biological detection

Alivisatos, Paul

Nature Biotechnology (2004), 22 (1), 47-52CODEN: NABIF9; ISSN:1087-0156. (Nature Publishing Group)

A review. In the coming decade, the ability to sense and detect the state of biol. systems and living organisms optically, elec. and magnetically will be radically transformed by developments in materials physics and chem. The emerging ability to control the patterns of matter on the nanometer length scale can be expected to lead to entirely new types of biol. sensors. These new systems will be capable of sensing at the single-mol. level in living cells, and capable of parallel integration for detection of multiple signals, enabling a diversity of simultaneous expts., as well as better crosschecks and controls.

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201

Gaiduk, A. ; Yorulmaz, M. ; Ruijgrok, P. V. ; Orrit, M. Room-Temperature Detection of a Single Molecule's Absorption by Photothermal Contrast Science 2010 , 330 , 353 – 356

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201

Room-Temperature Detection of a Single Molecule's Absorption by Photothermal Contrast

Gaiduk, A.; Yorulmaz, M.; Ruijgrok, P. V.; Orrit, M.

Science (Washington, DC, United States) (2010), 330 (6002), 353-356CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

So far, single-mol. imaging has predominantly relied on fluorescence detection. The authors imaged single nonfluorescent azo dye mols. in room-temp. glycerol by the refractive effect of the heat that they release in their environment upon intense illumination. This photothermal technique provides contrast for the absorbing objects only, irresp. of scattering by defects or roughness, with a signal-to-noise ratio of ~10 for a single mol. in an integration time of 300 ms. In the absence of O, virtually no bleaching event was obsd., even after >10 min of illumination. In a soln. satd. with O, the av. bleaching time was of the order of 1 min. No blinking was obsd. in the absorption signal. From bleaching steps, the authors obtained an av. absorption cross section of 4 Å2 for a single chromophore.

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202

Chong, S. S. ; Min, W. ; Xie, X. S. Ground-State Depletion Microscopy: Detection Sensitivity of Single-Molecule Optical Absorption at Room Temperature J. Phys. Chem. Lett. 2010 , 1 , 3316 – 3322

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202

Ground-State Depletion Microscopy: Detection Sensitivity of Single-Molecule Optical Absorption at Room Temperature

Chong, Shasha; Min, Wei; Xie, X. Sunney

Journal of Physical Chemistry Letters (2010), 1 (23), 3316-3322CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)

Optical studies of single mols. in ambient environments, which led to broad applications, are primarily based on fluorescence detection. Direct detection of optical absorption with single-mol. sensitivity at room temp. is difficult because absorption is not a background-free measurement and is often complicated by sample scattering. Here the authors report ground-state depletion microscopy for ultrasensitive detection of absorption contrast. The authors image 20 nm Au nanoparticles as an initial demonstration of this microscopy. The authors then demonstrate the detection of an absorption signal from a single chromophore mol. at room temp. This is accomplished by using 2 tightly focused collinear continuous-wave laser beams at different wavelengths, both within a mol. absorption band, 1 of which is intensity modulated at a high frequency (>MHz). The transmission of the other beam is modulated at the same frequency due to ground state depletion. The signal of single chromophore mols. scanned across the common laser foci can be detected with shot-noise limited sensitivity. This measurement represents the ultimate detection sensitivity of nonlinear optical spectroscopy at room temp.

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203

Kukura, P. ; Celebrano, M. ; Renn, A. ; Sandoghdar, V. Single-Molecule Sensitivity in Optical Absorption at Room Temperature J. Phys. Chem. Lett. 2010 , 1 , 3323 – 3327

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203

Single-Molecule Sensitivity in Optical Absorption at Room Temperature

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

Journal of Physical Chemistry Letters (2010), 1 (23), 3323-3327CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)

Sensitive detection of condensed matter is of utmost importance in fundamental research as well as cutting-edge applications such as mol. analytics and diagnostics. Until very recently, all existing methods for the detection of single mols. at room temp. have required highly efficient fluorophores. Here, single mols. can also be detected via std. modulation-free absorption measurements. Work extends single-mol. detection to a huge class of materials that absorb light but do not fluoresce efficiently.

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204

Lu, Z. J. ; Lu, J. Z. ; Wu, Y. Q. ; Chen, L. Y. Introduction to Theories of Several Super-Resolution Fluorescence Microscopy Methods and Recent Advance in the Field Prog. Biochem. Biophys. 2009 , 36 , 1626 – 1634

205

Mujumdar, R. B. ; Ernst, L. A. ; Mujumdar, S. R. ; Lewis, C. J. ; Waggoner, A. S. Cyanine Dye Labeling Reagents—Sulfoindocyanine Succinimidyl Esters Bioconjugate Chem. 1993 , 4 , 105 – 111

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205

Cyanine dye labeling reagents: Sulfoindocyanine succinimidyl esters

Mujumdar, Ratnakar B.; Ernst, Lauren A.; Mujumdar, Swati R.; Lewis, Christopher J.; Waggoner, Alan S.

Bioconjugate Chemistry (1993), 4 (2), 105-11CODEN: BCCHES; ISSN:1043-1802.

The synthesis and properties of a series of new fluorescent labeling reagents based on sulfoindocyanine dyes are described. They contain succinimidyl ester reactive groups and can be readily conjugated to antibodies, avidin, DNA, lipids, polymers, and other amino-group-contg. materials. The labeling reagents are water sol., pH insensitive, and show much reduced dye aggregation under labeling conditions. One of the reagents, Cy3, can be excited with the 488-, 514-, and 532-nm laser lines and is optimally excited with the 546-nm mercury arc line. Another, Cy5, can be excited with the 633-nm HeNe and 647-nm Kr laser lines available with many flow cytometers and confocal laser-scanning microscopes. New laser diodes emitting near 650 nm should also be excellent excitation sources for Cy5.

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206

Kubin, R. F. ; Fletcher, A. N. Fluorescence Quantum Yields of Some Rhodamine Dyes J. Luminesc. 1982 , 27 , 455 – 462

207

Periasamy, A., Ed. Methods in Cellular Imaging; Oxford University Press: Oxford, 2001.

208

Andersen, F. F. ; Stougaard, M. ; Jorgensen, H. L. ; Bendsen, S. ; Juul, S. ; Hald, K. ; Andersen, A. H. ; Koch, J. ; Knudsen, B. R. Multiplexed Detection of Site Specific Recombinase and DNA Topoisomerase Activities at the Single Molecule Level ACS Nano 2009 , 3 , 4043 – 4054

209

Gelles, J. ; Schnapp, B. J. ; Sheetz, M. P. Tracking Kinesin-Driven Movements with Nanometre-Scale Precision Nature 1988 , 331 , 450 – 453

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209

Tracking kinesin-driven movements with nanometer-scale precision

Gelles, Jeff; Schnapp, Bruce J.; Sheetz, Michael P.

Nature (London, United Kingdom) (1988), 331 (6155), 450-3CODEN: NATUAS; ISSN:0028-0836.

Kinesin, a force-generating ATPase involved in microtubule-based intracellular organelle transport, will drive the unidirectional movement of microscopic plastic beads along microtubules in vitro. Under certain conditions, a few (≤10) kinesin mols. may be sufficient to drive either bead movement or organelle transport. A method is described for detg. precise positional information from light-microscope images. The method is applied to measure kinesin-driven bead movements in vitro with a precision of 1-2 nm. Measurements reveal basic mech. features of kinesin-driven movements along the microtubule lattice, and place significant constraints on possible mol. mechanisms of movement.

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210

Sheetz, M. P. ; Turney, S. ; Qian, H. ; Elson, E. L. Nanometer-Level Analysis Demonstrates That Lipid Flow Does Not Drive Membrane Glycoprotein Movements Nature 1989 , 340 , 284 – 288

211

Kusumi, A. ; Nakada, C. ; Ritchie, K. ; Murase, K. ; Suzuki, K. ; Murakoshi, H. ; Kasai, R. S. ; Kondo, J. ; Fujiwara, T. Paradigm Shift of the Plasma Membrane Concept from the Two-Dimensional Continuum Fluid to the Partitioned Fluid: High-Speed Single-Molecule Tracking of Membrane Molecules Annu. Rev. Biophys. Biomol. Struct. 2005 , 34 , 351 – 378

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211

Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: High-speed single-molecule tracking of membrane molecules

Kusumi, Akihiro; Nakada, Chieko; Ritchie, Ken; Murase, Kotono; Suzuki, Kenichi; Murakoshi, Hideji; Kasai, Rinshi S.; Kondo, Junko; Fujiwara, Takahiro

Annual Review of Biophysics and Biomolecular Structure (2005), 34 (), 351-378, 6 platesCODEN: ABBSE4; ISSN:1056-8700. (Annual Reviews Inc.)

A review. Recent advancements in single-mol. tracking methods with nanometer-level precision now allow researchers to observe the movement, recruitment, and activation of single mols. in the plasma membrane in living cells. In particular, on the basis of the observations by high-speed single-particle tracking at a frame rate of 40,000 frames per s, the partitioning of the fluid plasma membrane into submicron compartments throughout the cell membrane and the hop diffusion of virtually all of the mols. have been proposed. This could explain why the diffusion coeffs. in the plasma membrane are considerably smaller than those in artificial membranes, and why the diffusion coeff. is reduced upon mol. complex formation (oligomerization-induced trapping). Here, the authors 1st describe the high-speed single-mol. tracking methods, and then they critically review a new model of a partitioned fluid plasma membrane and the involvement of the actin-based membrane-skeleton "fences" and anchored-transmembrane protein "pickets" in the formation of compartment boundaries.

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212

Yildiz, A. ; Selvin, P. R. Fluorescence Imaging with One Nanometer Accuracy: Application to Molecular Motors Acc. Chem. Res. 2005 , 38 , 574 – 582

213

Kim, S. Y. ; Gitai, Z. ; Kinkhabwala, A. ; Shapiro, L. ; Moerner, W. E. Single Molecules of the Bacterial Actin MreB Undergo Directed Treadmilling Motion in Caulobacter Crescentus Proc. Natl. Acad. Sci. U.S.A. 2006 , 103 , 10929 – 10934

214

Hell, S. W. ; Wichmann, J. Breaking the Diffraction Resolution Limit by Stimulated-Emission—Stimulated-Emission-Depletion Fluorescence Microscopy Opt. Lett. 1994 , 19 , 780 – 782

215

Donnert, G. ; Keller, J. ; Medda, R. ; Andrei, M. A. ; Rizzoli, S. O. ; Lurmann, R. ; Jahn, R. ; Eggeling, C. ; Hell, S. W. Macromolecular-Scale Resolution in Biological Fluorescence Microscopy Proc. Natl. Acad. Sci. U.S.A. 2006 , 103 , 11440 – 11445

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215

Macromolecular-scale resolution in biological fluorescence microscopy

Donnert, Gerald; Keller, Jan; Medda, Rebecca; Andrei, M. Alexandra; Rizzoli, Silvio O.; Luehrmann, Reinhard; Jahn, Reinhard; Eggeling, Christian; Hell, Stefan W.

Proceedings of the National Academy of Sciences of the United States of America (2006), 103 (31), 11440-11445CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

The authors demonstrate far-field fluorescence microscopy with a focal-plane resoln. of 15-20 nm in biol. samples. The 10- to 12-fold multilateral increase in resoln. below the diffraction barrier has been enabled by the elimination of mol. triplet state excitation as a major source of photobleaching of a no. of dyes in stimulated emission depletion microscopy. Allowing for relaxation of the triplet state between subsequent excitation-depletion cycles yields an up to 30-fold increase in total fluorescence signal as compared with reported stimulated emission depletion illumination schemes. Moreover, it enables the redn. of the effective focal spot area by up to ≈140-fold below that given by diffraction. Triplet-state relaxation can be realized either by reducing the repetition rate of pulsed lasers or by increasing the scanning speed such that the build-up of the triplet state is effectively prevented. This resoln. in immunofluorescence imaging is evidenced by revealing nanoscale protein patterns on endosomes, the punctuated structures of intermediate filaments in neurons, and nuclear protein speckles in mammalian cells with conventional optics. The reported performance of diffraction-unlimited fluorescence microscopy opens up a pathway for addressing fundamental problems in the life sciences.

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Gustafsson, M. G. L. Nonlinear Structured-Illumination Microscopy: Wide-Field Fluorescence Imaging with Theoretically Unlimited Resolution Proc. Natl. Acad. Sci. U.S.A. 2005 , 102 , 13081 – 13086

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216

Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution

Gustafsson, Mats G. L.

Proceedings of the National Academy of Sciences of the United States of America (2005), 102 (37), 13081-13086CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

Contrary to the well known diffraction limit, the fluorescence microscope is in principle capable of unlimited resoln. The necessary elements are spatially structured illumination light and a nonlinear dependence of the fluorescence emission rate on the illumination intensity. As an example of this concept, this article exptl. demonstrates satd. structured-illumination microscopy, a recently proposed method in which the nonlinearity arises from satn. of the excited state. This method can be used in a simple, wide-field (nonscanning) microscope, uses only a single, inexpensive laser, and requires no unusual photophys. properties of the fluorophore. The practical resolving power is detd. by the signal-to-noise ratio, which in turn is limited by photobleaching. Exptl. results show that a 2D point resoln. of <50 nm is possible on sufficiently bright and photostable samples.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtVaqu7bK&md5=754d188bc5b86318ffd7b5839c635dc2

217

Betzig, E. ; Chichester, R. J. Single Molecules Observed by Near-Field Scanning Optical Microscopy Science 1993 , 262 , 1422 – 1425

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217

Single molecules observed by near-field scanning optical microscopy

Betzig, Eric; Chichester, Robert J.

Science (Washington, DC, United States) (1993), 262 (5138), 1422-5CODEN: SCIEAS; ISSN:0036-8075.

Individual carbocyanine dye mols. in a sub-monolayer spread were imaged with near-field scanning optical microscopy. Mols. can be repeatedly detected and spatially localized (to ∼λ/50 where λ is the wavelength of light) with a sensitivity of at least 0.005 mols./(Hz)1/2 and the orientation of each mol. dipole can be detd. This information is exploited to map the elec. field distribution in the near-field aperture with mol. spatial resoln.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXht1elur8%253D&md5=9dbb6f52a288bd9e091e6c2ccc562b25

218

Kim, J. ; Song, K. B. Recent Progress of Nano-Technology with NSOM Micron 2007 , 38 , 409 – 426

219

Dickenson, N. E. ; Armendariz, K. P. ; Huckabay, H. A. ; Livanec, P. W. ; Dunn, R. C. Near-Field Scanning Optical Microscopy: A Tool for Nanometric Exploration of Biological Membranes Anal. Bioanal. Chem. 2010 , 396 , 31 – 43

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219

Near-field scanning optical microscopy: a tool for nanometric exploration of biological membranes

Dickenson, Nicholas E.; Armendariz, Kevin P.; Huckabay, Heath A.; Livanec, Philip W.; Dunn, Robert C.

Analytical and Bioanalytical Chemistry (2010), 396 (1), 31-43CODEN: ABCNBP; ISSN:1618-2642. (Springer)

A review. Near-field scanning optical microscopy (NSOM) is an emerging optical technique that enables simultaneous high-resoln. fluorescence and topog. measurements. Here we discuss selected applications of NSOM to biol. systems that help illustrate the utility of its high spatial resoln. and simultaneous collection of both fluorescence and topog. For the biol. sciences, these attributes seem particularly well suited for addressing ongoing issues in membrane organization, such as those regarding lipid rafts, and protein-protein interactions. Here we highlight a few NSOM measurements on model membranes, isolated biol. membranes, and cultured cells that help illustrate some of these capabilities. We finish by highlighting nontraditional applications of NSOM that take advantage of the small probe to create nanometric sensors or new modes of imaging.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtVygsb3O&md5=60b0f851a368e83ed152ab7740098031

220

Eggeling, C. ; Ringemann, C. ; Medda, R. ; Schwarzmann, G. ; Sandhoff, K. ; Polyakova, S. ; Belov, V. N. ; Hein, B. ; von Middendorff, C. ; Schonle, A. et al. Direct Observation of the Nanoscale Dynamics of Membrane Lipids in a Living Cell Nature 2009 , 457 , 1159 – 1163

[Crossref], [PubMed], [CAS], Google Scholar

220

Direct observation of the nanoscale dynamics of membrane lipids in a living cell

Eggeling, Christian; Ringemann, Christian; Medda, Rebecca; Schwarzmann, Guenter; Sandhoff, Konrad; Polyakova, Svetlana; Belov, Vladimir N.; Hein, Birka; von Middendorff, Claas; Schoenle, Andreas; Hell, Stefan W.

Nature (London, United Kingdom) (2009), 457 (7233), 1159-1162CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Cholesterol-mediated lipid interactions are thought to have a functional role in many membrane-assocd. processes such as signaling events. Although several expts. indicate their existence, lipid nanodomains (rafts') remain controversial owing to the lack of suitable detection techniques in living cells. The controversy is reflected in their putative size of 5-200 nm, spanning the range between the extent of a protein complex and the resoln. limit of optical microscopy. Here we demonstrate the ability of stimulated emission depletion (STED) far-field fluorescence nanoscopy to detect single diffusing (lipid) mols. in nanosized areas in the plasma membrane of living cells. Tuning of the probed area to spot sizes ∼70-fold below the diffraction barrier reveals that unlike phosphoglycerolipids, sphingolipids and glycosylphosphatidylinositol-anchored proteins are transiently (∼10-20 ms) trapped in cholesterol-mediated mol. complexes dwelling within <20-nm diam. areas. The non-invasive optical recording of mol. time traces and fluctuation data in tunable nanoscale domains is a powerful new approach to study the dynamics of biomols. in living cells.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXht1ehsLc%253D&md5=1c41be2d8fd36b9105f36e58a9b96d5b

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Sahl, S. J. ; Leutenegger, M. ; Hilbert, M. ; Hell, S. W. ; Eggeling, C. Fast Molecular Tracking Maps Nanoscale Dynamics of Plasma Membrane Lipids Proc. Natl. Acad. Sci. U.S.A. 2010 , 107 , 6829 – 6834

[Crossref], [PubMed], [CAS], Google Scholar

221

Fast molecular tracking maps nanoscale dynamics of plasma membrane lipids

Sahl, Steffen J.; Leutenegger, Marcel; Hilbert, Michael; Hell, Stefan W.; Eggeling, Christian

Proceedings of the National Academy of Sciences of the United States of America (2010), 107 (15), 6829-6834, S6829/1-S6829/6CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

We describe an optical method capable of tracking a single fluorescent mol. with a flexible choice of high spatial accuracy (∼10-20 nm std. deviation or ∼20-40 nm full-width-at-half-max.) and temporal resoln. (<1 ms). The fluorescence signal during individual passages of fluorescent mols. through a spot of excitation light allows the sequential localization and thus spatio-temporal tracking of the mol. if its fluorescence is collected on at least three sep. point detectors arranged in close proximity. We show two-dimensional trajectories of individual, small org. dye labeled lipids diffusing in the plasma membrane of living cells and directly observe transient events of trapping on <20 nm spatial scales. The trapping is cholesterol-assisted and much more pronounced for a sphingo- than for a phosphoglycero-lipid, with av. trapping times of ∼15 ms and <4 ms, resp. The results support previous STED nanoscopy measurements and suggest that, at least for nontreated cells, the transient interaction of a single lipid is confined to macromol. dimensions. Our exptl. approach demonstrates that fast mol. movements can be tracked with minimal invasion, which can reveal new important details of cellular nano-organization.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXltFSjuro%253D&md5=10b30bb013beca3a5b87771aa8061a6d

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Betzig, E. ; Patterson, G. H. ; Sougrat, R. ; Lindwasser, O. W. ; Olenych, S. ; Bonifacino, J. S. ; Davidson, M. W. ; Lippincott-Schwartz, J. ; Hess, H. F. Imaging Intracellular Fluorescent Proteins at Nanometer Resolution Science 2006 , 313 , 1642 – 1645

[Crossref], [PubMed], [CAS], Google Scholar

222

Imaging Intracellular Fluorescent Proteins at Nanometer Resolution

Betzig, Eric; Patterson, George H.; Sougrat, Rachid; Lindwasser, O. Wolf; Olenych, Scott; Bonifacino, Juan S.; Davidson, Michael W.; Lippincott-Schwartz, Jennifer; Hess, Harald F.

Science (Washington, DC, United States) (2006), 313 (5793), 1642-1645CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

The authors introduce a method for optically imaging intracellular proteins at nanometer spatial resoln. Numerous sparse subsets of photoactivatable fluorescent protein mols. were activated, localized (to ∼2 to 25 nm), and then bleached. The aggregate position information from all subsets was then assembled into a superresoln. image. The authors used this method - termed photoactivated localization microscopy - to image specific target proteins in thin sections of lysosomes and mitochondria; in fixed whole cells, the authors imaged vinculin at focal adhesions, actin within a lamellipodium, and the distribution of the retroviral protein Gag at the plasma membrane.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XpsVOktL0%253D&md5=fa03148b24bb913db3ab36bce7e8d378

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Hess, S. T. ; Girirajan, T. P. K. ; Mason, M. D. Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy Biophys. J. 2006 , 91 , 4258 – 4272

[Crossref], [PubMed], [CAS], Google Scholar

223

Ultra-high resolution imaging by fluorescence photoactivation localization microscopy

Hess, Samuel T.; Girirajan, Thanu P. K.; Mason, Michael D.

Biophysical Journal (2006), 91 (11), 4258-4272CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)

Biol. structures span many orders of magnitude in size, but far-field visible light microscopy suffers from limited resoln. A new method for fluorescence imaging has been developed that can obtain spatial distributions of large nos. of fluorescent mols. on length scales shorter than the classical diffraction limit. Fluorescence photoactivation localization microscopy (FPALM) analyzes thousands of single fluorophores per acquisition, localizing small nos. of them at a time, at low excitation intensity. To control the no. of visible fluorophores in the field of view and ensure that optically active mols. are sepd. by much more than the width of the point spread function, photoactivatable fluorescent mols. are used, in this case the photoactivatable green fluorescent protein (PA-GFP). For these photoactivatable mols., the activation rate is controlled by the activation illumination intensity; nonfluorescent inactive mols. are activated by a high-frequency (405-nm) laser and are then fluorescent when excited at a lower frequency. The fluorescence is imaged by a CCD camera, and then the mols. are either reversibly inactivated or irreversibly photobleached to remove them from the field of view. The rate of photobleaching is controlled by the intensity of the laser used to excite the fluorescence, in this case an Ar+ ion laser. Because only a small no. of mols. are visible at a given time, their positions can be detd. precisely; with only ∼100 detected photons per mol., the localization precision can be as much as 10-fold better than the resoln., depending on background levels. Heterogeneities on length scales of the order of tens of nanometers are obsd. by FPALM of PA-GFP on glass. FPALM images are compared with images of the same mols. by wide-field fluorescence. FPALM images of PA-GFP on a terraced sapphire crystal surface were compared with at. force microscopy and show that the full width at half-max. of features ∼86±4 nm is significantly better than the expected diffraction-limited optical resoln. The no. of fluorescent mols. and their brightness distribution have also been detd. using FPALM. This new method suggests a means to address a significant no. of biol. questions that had previously been limited by microscope resoln.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1Khur%252FN&md5=24c6b6e35708d2236c6355db3894a858

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Rust, M. J. ; Bates, M. ; Zhuang, X. W. Sub-Diffraction-Limit Imaging by Stochastic Optical Reconstruction Microscopy (STORM) Nat. Methods 2006 , 3 , 793 – 795

[Crossref], [PubMed], [CAS], Google Scholar

224

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)

Rust, Michael J.; Bates, Mark; Zhuang, Xiaowei

Nature Methods (2006), 3 (10), 793-796CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

The authors have developed a high-resoln. fluorescence microscopy method based on high-accuracy localization of photoswitchable fluorophores. In each imaging cycle, only a fraction of the fluorophores were turned on, allowing their positions to be detd. with nanometer accuracy. The fluorophore positions obtained from a series of imaging cycles were used to reconstruct the overall image. The authors demonstrated an imaging resoln. of 20 nm. This technique can, in principle, reach mol.-scale resoln.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XpvVCmtLY%253D&md5=404479afefd206a6e80aeccec011070b

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Bates, M. ; Huang, B. ; Dempsey, G. T. ; Zhuang, X. W. Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes Science 2007 , 317 , 1749 – 1753

[Crossref], [PubMed], [CAS], Google Scholar

225

Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes

Bates, Mark; Huang, Bo; Dempsey, Graham T.; Zhuang, Xiaowei

Science (Washington, DC, United States) (2007), 317 (5845), 1749-1753CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Recent advances in far-field optical nanoscopy have enabled fluorescence imaging with a spatial resoln. of 20 to 50 nm. Multicolor super-resoln. imaging, however, remains a challenging task. Here, the authors introduce a family of photoswitchable fluorescent probes and demonstrate multicolor stochastic optical reconstruction microscopy (STORM). Each probe consists of a photoswitchable "reporter" fluorophore that can be cycled between fluorescent and dark states, and an "activator" that facilitates photoactivation of the reporter. Combinatorial pairing of reporters and activators allows the creation of probes with many distinct colors. Iterative, color-specific activation of sparse subsets of these probes allows their localization with nanometer accuracy, enabling the construction of a super-resoln. STORM image. Using this approach, the authors demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nm resoln. This technique will facilitate direct visualization of mol. interactions at the nanometer scale.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtVGmsLnE&md5=537b2567934af0a2a9401a31974cc06e

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Shroff, H. ; Galbraith, C. G. ; Galbraith, J. A. ; Betzig, E. Live-Cell Photoactivated Localization Microscopy of Nanoscale Adhesion Dynamics Nat. Methods 2008 , 5 , 417 – 423

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226

Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics

Shroff, Hari; Galbraith, Catherine G.; Galbraith, James A.; Betzig, Eric

Nature Methods (2008), 5 (5), 417-423CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

We demonstrate live-cell super-resoln. imaging using photoactivated localization microscopy (PALM). The use of photon-tolerant cell lines in combination with the high resoln. and mol. sensitivity of PALM permitted us to investigate the nanoscale dynamics within individual adhesion complexes (ACs) in living cells under physiol. conditions for as long as 25 min, with half of the time spent collecting the PALM images at spatial resolns. down to ∼60 nm and frame rates as short as 25 s. We visualized the formation of ACs and measured the fractional gain and loss of individual paxillin mols. as each AC evolved. By allowing observation of a wide variety of nanoscale dynamics, live-cell PALM provides insights into mol. assembly during the initiation, maturation and dissoln. of cellular processes.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXlt1ahtbc%253D&md5=c285cfc8da2eb71f31cc324409e1f0e5

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Huang, B. ; Wang, W. Q. ; Bates, M. ; Zhuang, X. W. Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy Science 2008 , 319 , 810 – 813

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227

Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy

Huang, Bo; Wang, Wenqin; Bates, Mark; Zhuang, Xiaowei

Science (Washington, DC, United States) (2008), 319 (5864), 810-813CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Recent advances in far-field fluorescence microscopy have led to substantial improvements in image resoln., achieving a near-mol. resoln. of 20 to 30 nm in the two lateral dimensions. Three-dimensional (3D) nanoscale-resoln. imaging, however, remains a challenge. We demonstrated 3D stochastic optical reconstruction microscopy (STORM) by using optical astigmatism to det. both axial and lateral positions of individual fluorophores with nanometer accuracy. Iterative, stochastic activation of photoswitchable probes enables high-precision 3D localization of each probe, and thus the construction of a 3D image, without scanning the sample. Using this approach, we achieved an image resoln. of 20 to 30 nm in the lateral dimensions and 50 to 60 nm in the axial dimension. This development allowed us to resolve the 3D morphol. of nanoscopic cellular structures.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsFGhs7s%253D&md5=2d7becd73b0786ad4f2b35dd8045c887

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Manley, S. ; Gillette, J. M. ; Patterson, G. H. ; Shroff, H. ; Hess, H. F. ; Betzig, E. ; Lippincott-Schwartz, J. High-Density Mapping of Single-Molecule Trajectories with Photoactivated Localization Microscopy Nat. Methods 2008 , 5 , 155 – 157

[Crossref], [PubMed], [CAS], Google Scholar

228

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

Manley, Suliana; Gillette, Jennifer M.; Patterson, George H.; Shroff, Hari; Hess, Harald F.; Betzig, Eric; Lippincott-Schwartz, Jennifer

Nature Methods (2008), 5 (2), 155-157CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

We combined photoactivated localization microscopy (PALM) with live-cell single-particle tracking to create a new method termed sptPALM. We created spatially resolved maps of single-mol. motions by imaging the membrane proteins Gag and VSVG, and obtained several orders of magnitude more trajectories per cell than traditional single-particle tracking enables. By probing distinct subsets of mols., sptPALM can provide insight into the origins of spatial and temporal heterogeneities in membranes.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsV2ks7Y%253D&md5=7e2ef0c6e2e5f2d1524e3f6771b03a1e

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Sonnichsen, C. ; Reinhard, B. M. ; Liphardt, J. ; Alivisatos, A. P. A Molecular Ruler Based on Plasmon Coupling of Single Gold and Silver Nanoparticles Nat. Biotechnol. 2005 , 23 , 741 – 745

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229

A molecular ruler based on plasmon coupling of single gold and silver nanoparticles

Sonnichsen Carsten; Reinhard Bjorn M; Liphardt Jan; Alivisatos A Paul

Nature biotechnology (2005), 23 (6), 741-5 ISSN:1087-0156.

Forster Resonance Energy Transfer has served as a molecular ruler that reports conformational changes and intramolecular distances of single biomolecules. However, such rulers suffer from low and fluctuating signal intensities, limited observation time due to photobleaching, and an upper distance limit of approximately 10 nm. Noble metal nanoparticles have plasmon resonances in the visible range and do not blink or bleach. They have been employed as alternative probes to overcome the limitations of organic fluorophores, and the coupling of plasmons in nearby particles has been exploited to detect particle aggregation by a distinct color change in bulk experiments. Here we demonstrate that plasmon coupling can be used to monitor distances between single pairs of gold and silver nanoparticles. We followed the directed assembly of gold and silver nanoparticle dimers in real time and studied the kinetics of single DNA hybridization events. These "plasmon rulers" allowed us to continuously monitor separations of up to 70 nm for >3,000 s.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD2M3psVagsA%253D%253D&md5=681772a0a087aa18008be9ae16c35fd6

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Reinhard, B. M. ; Sheikholeslami, S. ; Mastroianni, A. ; Alivisatos, A. P. ; Liphardt, J. Use of Plasmon Coupling to Reveal the Dynamics of DNA Bending and Cleavage by Single EcoRV Restriction Enzymes Proc. Natl. Acad. Sci. U.S.A. 2007 , 104 , 2667 – 2672

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230

Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes

Reinhard, Bjoern M.; Sheikholeslami, Sassan; Mastroianni, Alexander; Alivisatos, A. Paul; Liphardt, Jan

Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (8), 2667-2672CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1- to 100-nm length scale in biol. Here, we substantiate the idea that plasmon rulers can be used to measure dynamical biophys. processes by applying the ruler to a system that has been investigated extensively using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolns. of up to 240 Hz were obtained, and the end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extd. from our single-mol. cleavage trajectories agree well with values obtained in bulk through other methods and confirm well-known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, such as the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resoln., and high signal/noise ratio make the plasmon ruler a unique tool for studying macromol. assemblies and conformational changes at the single-mol. level.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXisVWru70%253D&md5=c48cdb857c527671ba3479bef4b74e8c

231

Bonnell, D. A. Scanning Probe Microscopy and Spectroscopy: Theory, Techniques, and Applications; Wiley: New York, 2001.

232

Reinhard, B. M. ; Siu, M. ; Agarwal, H. ; Alivisatos, A. P. ; Liphardt, J. Calibration of a Dynamic Molecular Ruler Based on Plasmon Coupling between Gold Nanoparticles Nano Lett. 2005 , 5 , 2246 – 2252

233

Stryer, L. ; Haugland, R. P. Energy Transfer—A Spectroscopic Ruler Proc. Natl. Acad. Sci. U.S.A. 1967 , 58 , 719 – 726

234

Kapanidis, A. N. ; Lee, N. K. ; Laurence, T. A. ; Doose, S. ; Margeat, E. ; Weiss, S. Fluorescence-Aided Molecule Sorting: Analysis of Structure and Interactions by Alternating-Laser Excitation of Single Molecules Proc. Natl. Acad. Sci. U.S.A. 2004 , 101 , 8936 – 8941

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234

Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules

Kapanidis, Achillefs N.; Lee, Nam Ki; Laurence, Ted A.; Doose, Soeren; Margeat, Emmanuel; Weiss, Shimon

Proceedings of the National Academy of Sciences of the United States of America (2004), 101 (24), 8936-8941CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

We use alternating-laser excitation to achieve fluorescence-aided mol. sorting (FAMS) and enable simultaneous anal. of biomol. structure and interactions at the level of single mols. This was performed by labeling biomols. with fluorophores that serve as donor-acceptor pairs for Foerster resonance energy transfer, and by using alternating-laser excitation to excite directly both donors and acceptors present in single diffusing mols. Emissions were reduced to the distance-dependent ratio E, and a distance-independent, stoichiometry-based ratio S. Histograms of E and S sorted species based on the conformation and assocn. status of each species. S was sensitive to the stoichiometry and relative brightness of fluorophores in single mols., observables that can monitor oligomerization and local-environment changes, resp. FAMS permits equil. and kinetic anal. of macromol.-ligand interactions; this was validated by measuring equil. and kinetic dissocn. consts. for the interaction of Escherichia coli catabolite activator protein with DNA. FAMS is a general platform for ratiometric measurements that report on structure, dynamics, stoichiometries, environment, and interactions of diffusing or immobilized mols., thus enabling detailed mechanistic studies and ultrasensitive diagnostics.

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235

Deniz, A. A. ; Laurence, T. A. ; Beligere, G. S. ; Dahan, M. ; Martin, A. B. ; Chemla, D. S. ; Dawson, P. E. ; Schultz, P. G. ; Weiss, S. Single-Molecule Protein Folding: Diffusion Fluorescence Resonance Energy Transfer Studies of the Denaturation of Chymotrypsin Inhibitor 2 Proc. Natl. Acad. Sci. U.S.A. 2000 , 97 , 5179 – 5184

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Schuler, B. ; Lipman, E. A. ; Eaton, W. A. Probing the Free-Energy Surface for Protein Folding with Single-Molecule Fluorescence Spectroscopy Nature 2002 , 419 , 743 – 747

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236

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy

Schuler, Benjamin; Lipman, Everett A.; Eaton, William A.

Nature (London, United Kingdom) (2002), 419 (6908), 743-747CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Protein folding is inherently a heterogeneous process because of the very large no. of microscopic pathways that connect the myriad unfolded conformations to the unique conformation of the native structure. In a first step towards the long-range goal of describing the distribution of pathways exptl., Foerster resonance energy transfer (FRET) has been measured on single, freely diffusing mols. Here we use this method to det. properties of the free-energy surface for folding that have not been obtained from ensemble expts. We show that single-mol. FRET measurements of a small cold-shock protein expose equil. collapse of the unfolded polypeptide and allow us to calc. limits on the polypeptide reconfiguration time. From these results, limits on the height of the free-energy barrier to folding are obtained that are consistent with a simple statistical mech. model, but not with the barriers derived from simulations using mol. dynamics. Unlike the activation energy, the free-energy barrier includes the activation entropy and thus has been elusive to exptl. detn. for any kinetic process in soln.

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Kuzmenkina, E. V. ; Heyes, C. D. ; Nienhaus, G. U. Single-Molecule Forster Resonance Energy Transfer Study of Protein Dynamics under Denaturing Conditions Proc. Natl. Acad. Sci. U.S.A. 2005 , 102 , 15471 – 15476

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Majumdar, D. S. ; Smirnova, I. ; Kasho, V. ; Nir, E. ; Kong, X. X. ; Weiss, S. ; Kaback, H. R. Single-Molecule FRET Reveals Sugar-Induced Conformational Dynamics in LacY Proc. Natl. Acad. Sci. U.S.A. 2007 , 104 , 12640 – 12645

239

Jun, Y. W. ; Sheikholeslami, S. ; Hostetter, D. R. ; Tajon, C. ; Craik, C. S. ; Alivisatos, A. P. Continuous Imaging of Plasmon Rulers in Live Cells Reveals Early-Stage Caspase-3 Activation at the Single-Molecule Level Proc. Natl. Acad. Sci. U.S.A. 2009 , 106 , 17735 – 17740

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239

Continuous imaging of plasmon rulers in live cells reveals early-stage caspase-3 activation at the single-molecule level

Jun, Young-wook; Sheikholeslami, Sassan; Hostetter, Daniel R.; Tajon, Cheryl; Craik, Charles S.; Alivisatos, A. Paul

Proceedings of the National Academy of Sciences of the United States of America (2009), 106 (42), 17735-17740, S17735/1-S17735/15CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

The use of plasmon coupling in metal nanoparticles has shown great potential for the optical characterization of many biol. processes. Recently, we have demonstrated the use of "plasmon rulers" to observe conformational changes of single biomols. in vitro. Plasmon rulers provide robust signals without photobleaching or blinking. Here, we show the first application of plasmon rulers to in vivo studies to observe very long trajectories of single biomols. in live cells. We present a unique type of plasmon ruler comprised of peptide-linked gold nanoparticle satellites around a core particle, which was used as a probe to optically follow cell-signaling pathways in vivo at the single-mol. level. These "crown nanoparticle plasmon rulers" allowed us to continuously monitor trajectories of caspase-3 activity in live cells for over 2 h, providing sufficient time to observe early-stage caspase-3 activation, which was not possible by conventional ensemble analyses.

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Gradinaru, C. C. ; Marushchak, D. O. ; Samim, M. ; Krull, U. J. Fluorescence Anisotropy: From Single Molecules to Live Cells Analyst 2010 , 135 , 452 – 459

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240

Fluorescence anisotropy: from single molecules to live cells

Gradinaru, Claudiu C.; Marushchak, Denys O.; Samim, Masood; Krull, Ulrich J.

Analyst (Cambridge, United Kingdom) (2010), 135 (3), 452-459CODEN: ANALAO; ISSN:0003-2654. (Royal Society of Chemistry)

A review. The polarization of light emitted by fluorescent probes is an easily accessible phys. quantity that is related to a multitude of mol. parameters including conformation, orientation, size and the nanoscale environment conditions, such as dynamic viscosity and temp. In anal. biochem. and anal. chem. applied to biol. problems, fluorescence anisotropy is widely used for measuring the folding state of proteins and nucleic acids, and the affinity const. of ligands through titrn. expts. The emphasis of this review is on new multi-parameter single-mol. detection schemes and their bioanal. applications, and on the use of ensemble polarization assays to study binding and conformational dynamics of proteins and aptamers and for high-throughput discovery of small-mol. drugs.

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241

Moerner, W. E. ; Fromm, D. P. Methods of Single-Molecule Fluorescence Spectroscopy and Microscopy Rev. Sci. Instrum. 2003 , 74 , 3597 – 3619

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241

Methods of single-molecule fluorescence spectroscopy and microscopy

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

Review of Scientific Instruments (2003), 74 (8), 3597-3619CODEN: RSINAK; ISSN:0034-6748. (American Institute of Physics)

A review. Optical spectroscopy at the ultimate limit of a single mol. has grown over the past dozen years into a powerful technique for exploring the individual nanoscale behavior of mols. in complex local environments. Observing a single mol. removes the usual ensemble av., allowing the exploration of hidden heterogeneity in complex condensed phases as well as direct observation of dynamical state changes arising from photophysics and photochem., without synchronization. This article reviews the exptl. techniques of single-mol. fluorescence spectroscopy and microscopy with emphasis on studies at room temp. where the same single mol. is studied for an extended period. Key to successful single-mol. detection is the need to optimize signal-to-noise ratio, and the phys. parameters affecting both signal and noise are described. 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. To ext. the max. amt. of information from an expt., 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, photochem., local environmental fluctuations, enzymic activity, quantum optics, and many other dynamical effects. Due to the breadth of applications now appearing, single-mol. spectroscopy and microscopy may be viewed as useful new tools for the study of dynamics in complex systems, esp. where ensemble averaging or lack of synchronization may obscure the details of the process under study.

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Ruiter, A. G. T. ; Veerman, J. A. ; Garcia Parajo, M. F. ; van Hulst, N. F. Single Molecule Rotational and Translational Diffusion Observed by Near-Field Scanning Optical Microscopy J. Phys. Chem. A 1997 , 101 , 7318 – 7323

243

Sosa, H. ; Peterman, E. J. G. ; Moerner, W. E. ; Goldstein, L. S. B. ADP-Induced Rocking of the Kinesin Motor Domain Revealed by Single-Molecule Fluorescence Polarization Microscopy Nat. Struct. Mol. Biol. 2001 , 8 , 540 – 544

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243

ADP-induced rocking of the kinesin motor domain revealed by single-molecule fluorescence polarization microscopy

Sosa, Hernando; Peterman, Erwin J. G.; Moerner, W. E.; Goldstein, Lawrence S. B.

Nature Structural Biology (2001), 8 (6), 540-544CODEN: NSBIEW; ISSN:1072-8368. (Nature America Inc.)

Kinesin is an ATP-driven mol. motor protein that moves processively along microtubules. Despite consider- able research, the detailed mechanism of kinesin motion remains elusive. We applied an enhanced suite of single- and multiple-mol. fluorescence polarization microscopy assays to report the orientation and mobility of kinesin mols. bound to microtubules as a function of nucleotide state. In the presence of analogs of ATP, ADP-Pi or in the absence of nucleotide, the kinesin head maintains a rigid orientation. In the presence of ADP, the motor domain of kinesin, still bound to the microtubule, adopts a previously undescribed, highly mobile state. This state may be general to the chemomech. cycle of motor proteins; in the case of kinesin, the transition from a highly mobile to a rigid state after ADP release may contribute to the generation of the 8 nm step.

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Forkey, J. N. ; Quinlan, M. E. ; Shaw, M. A. ; Corrie, J. E. T. ; Goldman, Y. E. Three-Dimensional Structural Dynamics of Myosin V by Single-Molecule Fluorescence Polarization Nature 2003 , 422 , 399 – 404

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244

Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization

Forkey, Joseph N.; Quinlan, Margot E.; Alexander Shaw, M.; Corrie, John E. T.; Goldman, Yale E.

Nature (London, United Kingdom) (2003), 422 (6930), 399-404CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

The structural change that generates force and motion in actomyosin motility has been proposed to be the tilting of the myosin light chain domain (LCD), which serves as a lever arm. Several exptl. approaches have provided support for the lever arm hypothesis; however, the extent and timing of tilting motions are not well defined in the motor protein complex of functioning actomyosin. Here, the authors report 3-dimensional measurements of the structural dynamics of the LCD of chicken brain myosin V using a single-mol. fluorescence polarization technique that dets. the orientation of individual protein domains with 20-40-ms time resoln. Single fluorescent calmodulin light chains tilted back and forth between 2 well-defined angles as the myosin mol. processively translocated along actin. The results provided evidence for lever arm rotation of the calmodulin-binding domain in myosin V, and supported a 'hand-over-hand' mechanism for the translocation of double-headed myosin V mols. along actin filaments. The technique is also applicable to the study of real-time structural changes in other biol. systems.

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Noji, H. ; Yasuda, R. ; Yoshida, M. ; Kinosita, K. Direct Observation of the Rotation of F-1-ATPase Nature 1997 , 386 , 299 – 302

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Adachi, K. ; Yasuda, R. ; Noji, H. ; Itoh, H. ; Harada, Y. ; Yoshida, M. ; Kinosita, K. Stepping Rotation of F-1-ATPase Visualized through Angle-Resolved Single-Fluorophore Imaging Proc. Natl. Acad. Sci. U.S.A. 2000 , 97 , 7243 – 7247

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Gutierrez-Medina, B. ; Fehr, A. N. ; Block, S. M. Direct Measurements of Kinesin Torsional Properties Reveal Flexible Domains and Occasional Stalk Reversals During Stepping Proc. Natl. Acad. Sci. U.S.A. 2009 , 106 , 17007 – 17012

248

Ferraro, J. R. Introductory Raman Spectroscopy; Academic Press: New York, 1994.

249

Kneipp, K. ; Kneipp, H. ; Itzkan, I. ; Dasari, R. R. ; Feld, M. S. Ultrasensitive Chemical Analysis by Raman Spectroscopy Chem. Rev. 1999 , 99 , 2957 – 2975

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249

Ultrasensitive chemical analysis by Raman spectroscopy

Kneipp, Katrin; Kneipp, Harald; Itzkan, Irving; Dasari, Ramachandra R.; Feld, Michael S.

Chemical Reviews (Washington, D. C.) (1999), 99 (10), 2957-2975CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)

A review with 133 refs. is given on surface-enhanced Raman scattering, single-mol. Raman spectroscopy, crit. anal. and prospects of single-mol. Raman spectroscopy.

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250

Moskovits, M. Surface-Enhanced Spectroscopy Rev. Mod. Phys. 1985 , 57 , 783 – 826

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250

Surface-enhanced spectroscopy

Moskovits, Martin

Reviews of Modern Physics (1985), 57 (3, Pt. 1), 783-826CODEN: RMPHAT; ISSN:0034-6861.

A review with many refs. with emphasis on surface enhanced Raman scattering.

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251

Bailo, E. ; Deckert, V. Tip-Enhanced Raman Scattering Chem. Soc. Rev. 2008 , 37 , 921 – 930

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251

Tip-enhanced Raman scattering

Bailo, Elena; Deckert, Volker

Chemical Society Reviews (2008), 37 (5), 921-930CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)

A review. Tip-enhanced Raman scattering (TERS) is a technique that provides mol. information on the nanometer scale. Using a nanometer-sized metal particle results in a strong signal enhancement and a lateral resoln. similar to the dimensions of the particle. As TERS is in a way the ultimate SERS expt., the theor. background will be briefly discussed with respect to the unique features and the specific effects that occur when only a single nanoparticle is used as a probe. All the major parts of the instrument will be revealed and the specific advantages of the different instrumental set ups will be studied with respect to the particular requirements of the sample. Selected examples ranging from material science to cell biol. applications demonstrate the capabilities and the potential of TERS in this tutorial review.

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Qian, X. M. ; Nie, S. M. Single-Molecule and Single-Nanoparticle SERS: From Fundamental Mechanisms to Biomedical Applications Chem. Soc. Rev. 2008 , 37 , 912 – 920

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252

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

Qian, X.-M.; Nie, S. M.

Chemical Society Reviews (2008), 37 (5), 912-920CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)

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 1014-1015 fold. This enormous enhancement allows spectroscopic detection and identification of single mols. 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-mol. origin of fluctuating SERS signals. For applications, SERS nanoparticle tags have been developed based on the use of embedded reporter mols. 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-IR spectral window. These properties have raised new opportunities for multiplexed mol. diagnosis and in vivo Raman spectroscopy and imaging.

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Michaels, A. M. ; Jiang, J. ; Brus, L. Ag Nanocrystal Junctions as the Site for Surface-Enhanced Raman Scattering of Single Rhodamine 6G Molecules J. Phys. Chem. B 2000 , 104 , 11965 – 11971

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253

Ag Nanocrystal Junctions as the Site for Surface-Enhanced Raman Scattering of Single Rhodamine 6G Molecules

Michaels, Amy M.; Jiang, Jiang; Brus, Louis

Journal of Physical Chemistry B (2000), 104 (50), 11965-11971CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)

At. force microscopy (AFM) measurements show that the Ag nanoparticles that yield surface-enhanced Raman scattering (SERS) of single mols. of Rhodamine (R6G) are all compact aggregates consisting of a min. of two individual particles. Comparison of 514.5 and 632.8 nm excitation shows that the single mol. R6G signal is significantly higher when the excitation wavelength is resonant with the absorption band of R6G and suggests that the Raman excitation spectrum follows the absorption profile for R6G. We have also obsd. an interesting superlinear power dependence of the SERS signal. On av., by increasing the incident power by 2 orders of magnitude and decreasing the integration time by the same factor to maintain const. fluence, increases of 4 to 6 times were obsd. in the SERS intensity. We discuss these results in terms of a model where the R6G mol. that yields single mol. SERS signals is located at the junction of two Ag nanoparticles. We have also modeled the system using mol. resonance Raman theory to provide further insight into the enhancement mechanism.

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254

Brus, L. Noble Metal Nanocrystals: Plasmon Electron Transfer Photochemistry and Single-Molecule Raman Spectroscopy Acc. Chem. Res. 2008 , 41 , 1742 – 1749

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254

Noble Metal Nanocrystals: Plasmon Electron Transfer Photochemistry and Single-Molecule Raman Spectroscopy

Brus, Louis

Accounts of Chemical Research (2008), 41 (12), 1742-1749CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)

A review. The excited electronic states of noble metal Au and Ag nanocrystals are very different than those of mols. Ag and Au nanocrystal optical transitions (plasmons) in the visible can be so intense that they significantly modify the local electromagnetic field. Coherent elastic Rayleigh light scattering is stronger than normal electronic absorption of photons for larger nanocrystals. These 2 facts make Au and Ag nanocrystals ideal nanoantennas, in that they focus incident light into the local neighborhood of subwavelength size. Surface-enhanced Raman scattering (SERS), in which the Raman scattering rate of nearby mols. increases by many orders of magnitude, is a consequence of this nanoantenna effect. Metallic nanocrystals also have no band gap; this makes them extraordinarily polarizable. Their electronic transitions sense the local environment. An extreme case is the interaction of 2 30 nm Ag nanocrystals sepd. by a 1. nm gap. Their mutual polarization completely transforms the nature of the metallic excited electronic state. Single particles have an excited state uniformly distributed throughout the interior, while the nanocrystal dimer has its excited state localized on the metal surface in the junction. This creates an electromagnetic hot spot in the junction, enabling the observation of single-mol. SERS. The fact that surface mols. are typically chemisorbed and exchange electrons with the metal has interesting chem. consequences. The enhanced Raman intensities are controlled by quantum mech. coupling of the mol. LUMO and HOMO with the optically excited electrons in the metal. Charge-transfer photochem. can result from metal plasmon excitation. In cryst. Ag nanocrystals the photochem. quantum yield can be high because the nanocrystal surface dominates plasmon nonradiative relaxation. Colloidal Ag nanocrystals stabilized by Na citrate build up a photovoltage under visible excitation, caused by irreversible hot hole photooxidn. of adsorbed citrate anion. This creates a driving force for photochem. transformation of round 8 nm Ag seeds into 70 nm single-crystal disk prisms under room lights, in a novel type of light-driven Ostwald ripening.

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255

Nie, S. M. ; Emery, S. R. Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering Science 1997 , 275 , 1102 – 1106

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255

Probing single molecules and single nanoparticles by surface-enhanced Raman scattering

Nie, Shuming; Emory, Steven R.

Science (Washington, D. C.) (1997), 275 (5303), 1102-1106CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Optical detection and spectroscopy of single mols. and single nanoparticles were achieved at room temp. using surface-enhanced Raman scattering. Individual Ag colloidal nanoparticles were screened from a large heterogeneous population for special size-dependent properties and were then used to amplify the speculation for special size-dependent properties and were then used to amplify the spectroscopic signatures of adsorbed mols. For single rhodamine 6G mols. adsorbed on the selected nanoparticles, the intrinsic Raman enhancement factors were ∼1014 to 1015, much larger than the ensemble-averaged values derived from conventional measurements. This enormous enhancement leads to vibrational Raman signals that are more intense and more stable than single-mol. fluorescence.

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256

Kneipp, K. ; Wang, Y. ; Kneipp, H. ; Perelman, L. T. ; Itzkan, I. ; Dasari, R. ; Feld, M. S. Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS) Phys. Rev. Lett. 1997 , 78 , 1667 – 1670

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256

Single molecule detection using surface-enhanced Raman scattering (SERS)

Kneipp, Katrin; Wang, Yang; Kneipp, Harald; Perelman, Lev T.; Itzkan, Irving; Dasari, Ramachandra R.; Feld, Michael S.

Physical Review Letters (1997), 78 (9), 1667-1670CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

By exploiting the extremely large effective cross sections (10-17-10-16 cm2/mol.) available from surface-enhanced Raman scattering (SERS), the authors achieved the 1st observation of single mol. Raman scattering. Measured spectra of a single crystal violet mol. in aq. colloidal Ag soln. using one 2nd collection time and ∼2 × 105 W/cm2 nonresonant near-IR excitation show a clear fingerprint of its Raman features between 700 and 1700 cm-1. Spectra obsd. in a time sequence for an av. of 0.6 dye mol. in the probed vol. exhibited the expected Poisson distribution for actually measuring 0, 1, 2, or 3 mols.

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257

Dieringer, J. A. ; Lettan, R. B. ; Scheidt, K. A. ; Van Duyne, R. P. A Frequency Domain Existence Proof of Single-Molecule Surface-Enhanced Raman Spectroscopy J. Am. Chem. Soc. 2007 , 129 , 16249 – 16256

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257

A Frequency Domain Existence Proof of Single-Molecule Surface-Enhanced Raman Spectroscopy

Dieringer, Jon A.; Lettan, Robert B., II; Scheidt, Karl A.; Van Duyne, Richard P.

Journal of the American Chemical Society (2007), 129 (51), 16249-16256CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

The existence of single-mol. surface-enhanced Raman spectroscopy (SMSERS) is proven by employing a frequency-domain approach. This is demonstrated using two isotopologues of Rhodamine 6G that offer unique vibrational signatures. When an av. of one mol. was adsorbed per Ag nanoparticle, only one isotopologue was typically obsd. under dry N2 environment. Addnl., the distribution of vibrational frequencies hidden under the ensemble av. is revealed by examg. the single-mol. spectra. Correlation with TEM reveals that SMSERS active aggregates are composed of multiple randomly sized and shaped nanoparticles. At higher coverage and in a humid environment, adsorbate interchange was detected. Using 2-dimensional cross correlation, vibrational modes from different isotopologues were anti-correlated, indicating that the dynamic behavior was from multiple mols. competing for a single hot spot. This allows hot-spot diffusion to be directly obsd. without analyzing the peak intensity fluctuations.

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258

Bailo, E. ; Deckert, V. Tip-Enhanced Raman Spectroscopy of Single RNA Strands: Towards a Novel Direct-Sequencing Method Angew. Chem., Int. Ed. 2008 , 47 , 1658 – 1661

259

Yeo, B. S. ; Madler, S. ; Schmid, T. ; Zhang, W. H. ; Zenobi, R. Tip-Enhanced Raman Spectroscopy Can See More: The Case of Cytochrome c J. Phys. Chem. C 2008 , 112 , 4867 – 4873

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259

Tip-Enhanced Raman Spectroscopy Can See More: The Case of Cytochrome c

Yeo, Boon-Siang; Maedler, Stefanie; Schmid, Thomas; Zhang, Weihua; Zenobi, Renato

Journal of Physical Chemistry C (2008), 112 (13), 4867-4873CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)

The heme protein, cytochrome c (Cc) has been studied using tip-enhanced Raman spectroscopy (TERS). By virtue of its sensitivity and superior spatial resoln., TERS detected both the heme and amino acid vibrational bands of Cc using resonance excitation at 532 nm. This is in contrast to conventional surface-enhanced Raman spectroscopy (SERS) where ensemble information is obtained, leading to the strongest Raman bands obscuring the weaker ones; i.e., only the resonantly enhanced heme bands are obsd. Matrix-assisted laser desorption/ionization mass spectrometry supported the interpretation of the Raman data by showing that Cc remains intact on Ag surfaces. This work demonstrates the sensitivity of TERS for analyzing proteins (complete with band assignments) and that a collection of TER spectra gives a more complete description of large biomols. The latter is an important advantage usually not found in SERS measurements.

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260

Zhang, J. ; Campbell, R. E. ; Ting, A. Y. ; Tsien, R. Y. Creating New Fluorescent Probes for Cell Biology Nat. Rev. Mol. Cell Biol. 2002 , 3 , 906 – 918

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260

Creating New Fluorescent Probes for Cell Biology

Zhang, Jin; Campbell, Robert E.; Ting, Alice Y.; Tsien, Roger Y.

Nature Reviews Molecular Cell Biology (2002), 3 (12), 906-918CODEN: NRMCBP; ISSN:1471-0072. (Nature Publishing Group)

A review. Fluorescent probes are one of the cornerstones of real-time imaging of live cells and a powerful tool for cell biologists. They provide high sensitivity and great versatility while minimally perturbing the cell under investigation. Genetically-encoded reporter constructs that are derived from fluorescent proteins are leading a revolution in the real-time visualization and tracking of various cellular events. Recent advances include the continued development of 'passive' markers for the measurement of biomol. expression and localization in live cells, and 'active' indicators for monitoring more complex cellular processes such as small-mol.-messenger dynamics, enzyme activation and protein-protein interactions.

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261

Brasselet, S. ; Peterman, E. J. G. ; Miyawaki, A. ; Moerner, W. E. Single-Molecule Fluorescence Resonant Energy Transfer in Calcium Concentration Dependent Cameleon J. Phys. Chem. B 2000 , 104 , 3676 – 3682

262

Yang, H. ; Luo, G. B. ; Karnchanaphanurach, P. ; Louie, T. M. ; Rech, I. ; Cova, S. ; Xun, L. Y. ; Xie, X. S. Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer Science 2003 , 302 , 262 – 266

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262

Protein conformational dynamics probed by single-molecule electron transfer

Yang, Haw; Luo, Guobin; Karnchanaphanurach, Pallop; Louie, Tai-Man; Rech, Ivan; Cova, Sergio; Xun, Luying; Xie, X. Sunney

Science (Washington, DC, United States) (2003), 302 (5643), 262-266CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Electron transfer is used as a probe for angstrom-scale structural changes in single protein mols. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then det. the potential of mean force between the flavin and the tyrosine, and a correlation anal. revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

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263

Kou, S. C. ; Xie, X. S. Generalized Langevin Equation with Fractional Gaussian Noise: Subdiffusion within a Single Protein Molecule Phys. Rev. Lett. 2004 , 93 , 180603-1-4

264

Kohler, J. ; Disselhorst, J. ; Donckers, M. ; Groenen, E. J. J. ; Schmidt, J. ; Moerner, W. E. Magnetic-Resonance of a Single Molecular Spin Nature 1993 , 363 , 242 – 244

265

Wrachtrup, J. ; Vonborczyskowski, C. ; Bernard, J. ; Orrit, M. ; Brown, R. Optical-Detection of Magnetic-Resonance in a Single Molecule Nature 1993 , 363 , 244 – 245

266

Gruber, A. ; Drabenstedt, A. ; Tietz, C. ; Fleury, L. ; Wrachtrup, J. ; von Borczyskowski, C. Scanning Confocal Optical Microscopy and Magnetic Resonance on Single Defect Centers Science 1997 , 276 , 2012 – 2014

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266

Scanning confocal optical microscopy and magnetic resonance on single defect centers

Gruber, A.; Drabenstedt, A.; Tietz, C.; Fleury, L.; Wrachtrup, J.; von Borczyskowski, C.

Science (Washington, D. C.) (1997), 276 (5321), 2012-2014CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

The fluorescence of individual nitrogen-vacancy defect centers in diamond was obsd. with room-temp. scanning confocal optical microscopy. The centers were photo-stable, showing no detectable change in their fluorescence emission spectrum as a function of time. Magnetic resonance on single centers at room temp. is feasible. The magnetic resonance spectra revealed marked changes in zero-field splitting parameters among different centers. These changes were attributed to strain-induced differences in the symmetry of the centers.

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267

Prawer, S. ; Greentree, A. D. Diamond for Quantum Computing Science 2008 , 320 , 1601 – 1602

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267

Diamond for Quantum Computing

Prawer, Steven; Greentree, Andrew D.

Science (Washington, DC, United States) (2008), 320 (5883), 1601-1602CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

A review; diamond for quantum computing is discussed.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXnvVKqsrc%253D&md5=d273167810277da8f3af3fdf5572b129

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Childress, L. ; Dutt, M. V. G. ; Taylor, J. M. ; Zibrov, A. S. ; Jelezko, F. ; Wrachtrup, J. ; Hemmer, P. R. ; Lukin, M. D. Coherent Dynamics of Coupled Electron and Nuclear Spin Qubits in Diamond Science 2006 , 314 , 281 – 285

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268

Coherent Dynamics of Coupled Electron and Nuclear Spin Qubits in Diamond

Childress, L.; Dutt, M. V. Gurudev; Taylor, J. M.; Zibrov, A. S.; Jelezko, F.; Wrachtrup, J.; Hemmer, P. R.; Lukin, M. D.

Science (Washington, DC, United States) (2006), 314 (5797), 281-285CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Understanding and controlling the complex environment of solid-state quantum bits is a central challenge in spintronics and quantum information science. Coherent manipulation of an individual electron spin assocd. with a nitrogen-vacancy center in diamond was used to gain insight into its local environment. We show that this environment is effectively sepd. into a set of individual proximal 13C nuclear spins, which are coupled coherently to the electron spin, and the remainder of the 13C nuclear spins, which cause the loss of coherence. The proximal nuclear spins can be addressed and coupled individually because of quantum back-action from the electron, which modifies their energy levels and magnetic moments, effectively distinguishing them from the rest of the nuclei. These results open the door to coherent manipulation of individual isolated nuclear spins in a solid-state environment even at room temp.

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Jiang, L. ; Hodges, J. S. ; Maze, J. R. ; Maurer, P. ; Taylor, J. M. ; Cory, D. G. ; Hemmer, P. R. ; Walsworth, R. L. ; Yacoby, A. ; Zibrov, A. S. et al. Repetitive Readout of a Single Electronic Spin via Quantum Logic with Nuclear Spin Ancillae Science 2009 , 326 , 267 – 272

270

Neumann, P. ; Beck, J. ; Steiner, M. ; Rempp, F. ; Fedder, H. ; Hemmer, P. R. ; Wrachtrup, J. ; Jelezko, F. Single-Shot Readout of a Single Nuclear Spin Science 2010 , 329 , 542 – 544

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270

Single-Shot Readout of a Single Nuclear Spin

Neumann, Philipp; Beck, Johannes; Steiner, Matthias; Rempp, Florian; Fedder, Helmut; Hemmer, Philip R.; Wrachtrup, Joerg; Jelezko, Fedor

Science (Washington, DC, United States) (2010), 329 (5991), 542-544CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Projective measurement of single electron and nuclear spins has evolved from a gedanken expt. to a problem relevant for applications in at.-scale technologies like quantum computing. Although several approaches allow for detection of a spin of single atoms and mols., multiple repetitions of the expt. that are usually required for achieving a detectable signal obscure the intrinsic quantum nature of the spin's behavior. We demonstrated single-shot, projective measurement of a single nuclear spin in diamond using a quantum nondemolition measurement scheme, which allows real-time observation of an individual nuclear spin's state in a room-temp. solid. Such an ideal measurement is crucial for realization of, for example, quantum error correction protocols in a quantum register.

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Balasubramanian, G. ; Chan, I. Y. ; Kolesov, R. ; Al-Hmoud, M. ; Tisler, J. ; Shin, C. ; Kim, C. ; Wojcik, A. ; Hemmer, P. R. ; Krueger, A. et al. Nanoscale Imaging Magnetometry with Diamond Spins under Ambient Conditions Nature 2008 , 455 , 648 – 652

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271

Nanoscale imaging magnetometry with diamond spins under ambient conditions

Balasubramanian, Gopalakrishnan; Chan, I. Y.; Kolesov, Roman; Al-Hmoud, Mohannad; Tisler, Julia; Shin, Chang; Kim, Changdong; Wojcik, Aleksander; Hemmer, Philip R.; Krueger, Anke; Hanke, Tobias; Leitenstorfer, Alfred; Bratschitsch, Rudolf; Jelezko, Fedor; Wrachtrup, Joerg

Nature (London, United Kingdom) (2008), 455 (7213), 648-651CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Magnetic resonance imaging and optical microscopy are key technologies in the life sciences. For microbiol. studies, esp. of the inner workings of single cells, optical microscopy is normally used because it easily achieves resoln. close to the optical wavelength. But in conventional microscopy, diffraction limits the resoln. to about half the wavelength. Recently, it was shown that this limit can be partly overcome by nonlinear imaging techniques, but there is still a barrier to reaching the mol. scale. In contrast, in magnetic resonance imaging the spatial resoln. is not detd. by diffraction; rather, it is limited by magnetic field sensitivity, and so can in principle go well below the optical wavelength. The sensitivity of magnetic resonance imaging has recently been improved enough to image single cells, and magnetic resonance force microscopy has succeeded in detecting single electrons and small nuclear spin ensembles. However, this technique currently requires cryogenic temps., which limit most potential biol. applications. Alternatively, single-electron spin states can be detected optically, even at room temp. in some systems. Here we show how magneto-optical spin detection can be used to det. the location of a spin assocd. with a single nitrogen-vacancy center in diamond with nanometer resoln. under ambient conditions. By placing these nitrogen-vacancy spins in functionalized diamond nanocrystals, biol. specific magnetofluorescent spin markers can be produced. Significantly, we show that this nanometer-scale resoln. can be achieved without any probes located closer than typical cell dimensions. Furthermore, we demonstrate the use of a single diamond spin as a scanning probe magnetometer to map nanoscale magnetic field variations. The potential impact of single-spin imaging at room temp. is far-reaching. It could lead to the capability to probe biol. relevant spins in living cells.

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272

Giessibl, F. J. Advances in Atomic Force Microscopy Rev. Mod. Phys. 2003 , 75 , 949 – 983

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272

Advances in atomic force microscopy

Giessibl, Franz J.

Reviews of Modern Physics (2003), 75 (3), 949-983CODEN: RMPHAT; ISSN:0034-6861. (American Physical Society)

A review. This article reviews the progress of at. force microscopy in ultrahigh vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows one to image surfaces of conductors and insulators in vacuum with at. resoln. The most widely used technique for at.-resoln. force microscopy in vacuum is frequency-modulation at. force microscopy (FM-AFM). This technique, as well as other dynamic methods, is explained in detail. In the last few years many groups have expanded the empirical knowledge and deepened the theor. understanding of frequency-modulation at. force microscopy. Consequently, spatial resoln. and ease of use have been increased dramatically. Vacuum at. force microscopy opens up new classes of expts., ranging from imaging of insulators with true at. resoln. to the measurement of forces between individual atoms.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXmvV2nurY%253D&md5=4c227a2605756f572d45ea8096df3419

273

Crampton, N. ; Brockwell, D. J. Unravelling the Design Principles for Single Protein Mechanical Strength Curr. Opin. Struct. Biol. 2010 , 20 , 508 – 517

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273

Unravelling the design principles for single protein mechanical strength

Crampton, Neal; Brockwell, David J.

Current Opinion in Structural Biology (2010), 20 (4), 508-517CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)

A review. In recent years single mol. manipulation techniques have improved to the extent that measurements of the mech. strength of single proteins can now be undertaken routinely. This powerful new tool, coupled with theor. frameworks to characterize the unfolding process, has enabled significant progress to be made in understanding the phys. mechanisms that underlie protein mech. strength. These design concepts have allowed the search for proteins with novel, mech. strong folds to be automated and for previously mech. characterized proteins to be engineered rationally. Methods to achieve the latter are diverse and include re-engineering of specific hydrophobic core residues, changing solvent conditions and the crosslinking' of side-chains that are sepd. in the rate-limiting unfolding transition. Predicting the mech. behavior of larger proteins and those with more complex structures remains a significant challenge while on-going instrument development is beginning to allow the examn. of mech. strength of protein across a wide range of force loading rates. The integral role of force in biol. and the potential for exploitation of catalytic and structural proteins as functional bio-materials makes this a particularly important area of research.

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Sugimoto, Y. ; Pou, P. ; Abe, M. ; Jelinek, P. ; Perez, R. ; Morita, S. ; Custance, O. Chemical Identification of Individual Surface Atoms by Atomic Force Microscopy Nature 2007 , 446 , 64 – 67

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274

Chemical identification of individual surface atoms by atomic force microscopy

Sugimoto, Yoshiaki; Pou, Pablo; Abe, Masayuki; Jelinek, Pavel; Perez, Ruben; Morita, Seizo; Custance, Oscar

Nature (London, United Kingdom) (2007), 446 (7131), 64-67CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with at. resoln. At cryogenic temps., scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed mols. and of the electronic properties of magnetic impurity atoms, thereby allowing chem. identification. But in many instances, and particularly for insulating systems, detg. the exact chem. compn. of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true at. resoln., by detecting and precisely measuring the short-range forces that arise with the onset of chem. bonding between the tip and surface atoms and that depend sensitively on the chem. identity of the atoms involved. Here the authors report precise measurements of such short-range chem. forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows one to use the chem. force measurements as the basis for at. recognition, even at room temp. The authors illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the 3 constituent at. species Si, Sn and lead, even though these exhibit very similar chem. properties and identical surface position preferences that render any discrimination attempt based on topog. measurements impossible.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXit1arsL0%253D&md5=5f7d3086b09adac56614ef10214340b3

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Ashino, M. ; Wiesendanger, R. ; Khlobystov, A. N. ; Berber, S. ; Tomanek, D. Revealing Subsurface Vibrational Modes by Atom-Resolved Damping Force Spectroscopy Phys. Rev. Lett. 2009 , 102 , 195503-1-4

276

Hinterdorfer, P. ; Dufrene, Y. F. Detection and Localization of Single Molecular Recognition Events Using Atomic Force Microscopy Nat. Methods 2006 , 3 , 347 – 355

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276

Detection and localization of single molecular recognition events using atomic force microscopy

Hinterdorfer, Peter; Dufrene, Yves F.

Nature Methods (2006), 3 (5), 347-355CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

A review. Because of its piconewton force sensitivity and nanometer positional accuracy, the at. force microscope (AFM) has emerged as a powerful tool for exploring the forces and the dynamics of the interaction between individual ligands and receptors, either on isolated mols. or on cellular surfaces. These studies require attaching specific biomols. or cells on AFM tips and on solid supports and measuring the unbinding forces between the modified surfaces using AFM force spectroscopy. In this review, the authors describe the current methodol. for mol. recognition studies using the AFM, with an emphasis on strategies available for prepg. AFM tips and samples, and on procedures for detecting and localizing single mol. recognition events.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XjslSksbg%253D&md5=b23c217bb0ff674681e84b71a867b4c5

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Francius, G. ; Lebeer, S. ; Alsteens, D. ; Wildling, L. ; Gruber, H. J. ; Hols, P. ; De Keersmaecker, S. ; Vanderleyden, J. ; Dufrene, Y. F. Detection, Localization, and Conformational Analysis of Single Polysaccharide Molecules on Live Bacteria ACS Nano 2008 , 2 , 1921 – 1929

278

Ebner, A. ; Kienberger, F. ; Kada, G. ; Stroh, C. M. ; Geretschlager, M. ; Kamruzzahan, A. S. M. ; Wildling, L. ; Johnson, W. T. ; Ashcroft, B. ; Nelson, J. et al. Localization of Single Avidin−Biotin Interactions Using Simultaneous Topography and Molecular Recognition Imaging ChemPhysChem 2005 , 6 , 897 – 900

279

Ashkin, A. ; Dziedzic, J. M. ; Bjorkholm, J. E. ; Chu, S. Observation of a Single-Beam Gradient Force Optical Trap for Dielectric Particles Opt. Lett. 1986 , 11 , 288 – 290

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279

Observation of a single-beam gradient force optical trap for dielectric particles

Ashkin, A.; Dziedzic, J. M.; Bjorkholm, J. E.; Chu, Steven

Optics Letters (1986), 11 (5), 288-90CODEN: OPLEDP; ISSN:0146-9592.

Optical trapping of dielec. particles by a single-beam gradient force trap was demonstrated. This confirms the concept of neg. light pressure due to the gradient force. Trapping was obsd. over the entire range of particle size ∼25-10,000 nm in H2O. Use of the new trap extends the size range of macroscopic particles accessible to optical trapping and manipulation well into the Rayleigh size regime. Application of this trapping principle to atom trapping is considered.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL28Xitlejurs%253D&md5=20ae5975803cbe3c879944d92f9dc27e

280

Grier, D. G. A Revolution in Optical Manipulation Nature 2003 , 424 , 810 – 816

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280

A revolution in optical manipulation

Grier, David G.

Nature (London, United Kingdom) (2003), 424 (6950), 810-816CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

A review. Optical tweezers use the forces exerted by a strongly focused beam of light to trap and move objects ranging in size from tens of nanometers to tens of micrometers. Since their introduction in 1986, the optical tweezer has become an important tool for research in the fields of biol., phys. chem. and soft condensed matter physics. Recent advances promise to take optical tweezers out of the lab. and into the mainstream of manufg. and diagnostics; they may even become consumer products. The next generation of single-beam optical traps offers revolutionary new opportunities for fundamental and applied research.

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281

Visscher, K. ; Schnitzer, M. J. ; Block, S. M. Single Kinesin Molecules Studied with a Molecular Force Clamp Nature 1999 , 400 , 184 – 189

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281

Single kinesin molecules studied with a molecular force clamp

Visscher, Koen; Schnitzer, Mark J.; Block, Steven M.

Nature (London) (1999), 400 (6740), 184-189CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)

Kinesin is a two-headed, ATP-driven motor protein that moves processively along microtubules in discrete steps of 8 nm, probably by advancing each of its heads alternately in sequence. Mol. details of how the chem. energy stored in ATP is coupled to mech. displacement remain obscure. To shed light on this question, a force clamp was constructed, based on a feedback-driven optical trap capable of maintaining const. loads on single kinesin motors. The instrument provides unprecedented resoln. of mol. motion and permits mechanochem. studies under controlled external loads. Anal. of records of kinesin motion under variable ATP concns. and loads revealed several new features. First, kinesin stepping appears to be tightly coupled to ATP hydrolysis over a wide range of forces, with a single hydrolysis per 8-nm mech. advance. Second, the kinesin stall force depends on the ATP concn. Third, increased loads reduce the max. velocity as expected, but also raise the apparent Michaelis-Menten const. The kinesin cycle therefore contains at least one load-dependent transition affecting the rate at which ATP mols. bind and subsequently commit to hydrolysis. It is likely that at least one other load-dependent rate exists, affecting turnover no. Together, these findings will necessitate revisions to our understanding of how kinesin motors function.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXks1KhtbY%253D&md5=c567db4e368fc992eff370d9a9fd0a79

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Lang, M. J. ; Asbury, C. L. ; Shaevitz, J. W. ; Block, S. M. An Automated Two-Dimensional Optical Force Clamp for Single Molecule Studies Biophys. J. 2002 , 83 , 491 – 501

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282

An automated two-dimensional optical force clamp for single molecule studies

Lang, Matthew J.; Asbury, Charles L.; Shaevitz, Joshua W.; Block, Steven M.

Biophysical Journal (2002), 83 (1), 491-501CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)

We constructed a next-generation optical trapping instrument to study the motility of single motor proteins, such as kinesin moving along a microtubule. The instrument can be operated as a two-dimensional force clamp, applying loads of fixed magnitude and direction to motor-coated microscopic beads moving in vitro. Flexibility and automation in exptl. design are achieved by computer control of both the trap position, via acousto-optic deflectors, and the sample position, using a three-dimensional piezo stage. Each measurement is preceded by an initialization sequence, which includes adjustment of bead height relative to the coverslip using a variant of optical force microscopy (to ±4 nm), a two-dimensional raster scan to calibrate position detector response, and adjustment of bead lateral position relative to the microtubule substrate (to ±3 nm). During motor-driven movement, both the trap and stage are moved dynamically to apply const. force while keeping the trapped bead within the calibrated range of the detector. We present details of force clamp operation and preliminary data showing kinesin motor movement subject to diagonal and forward loads.

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283

Lang, M. J. ; Fordyce, P. M. ; Engh, A. M. ; Neuman, K. C. ; Block, S. M. Simultaneous, Coincident Optical Trapping and Single-Molecule Fluorescence Nat. Methods 2004 , 1 , 133 – 139

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283

Simultaneous, coincident optical trapping and single-molecule fluorescence

Lang, Matthew J.; Fordyce, Polly M.; Engh, Anita M.; Neuman, Keir C.; Block, Steven M.

Nature Methods (2004), 1 (2), 133-139CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

We constructed a microscope-based instrument capable of simultaneous, spatially coincident optical trapping and single-mol. fluorescence. The capabilities of this app. were demonstrated by studying the force-induced strand sepn. of a dye-labeled, 15-base-pair region of double-stranded DNA (dsDNA), with force applied either parallel ('unzipping' mode) or perpendicular ('shearing' mode) to the long axis of the region. Mech. transitions corresponding to DNA hybrid rupture occurred simultaneously with discontinuous changes in the fluorescence emission. The rupture force was strongly dependent on the direction of applied force, indicating the existence of distinct unbinding pathways for the two force-loading modes. From the rupture force histograms, we detd. the distance to the thermodn. transition state and the thermal off rates in the absence of load for both processes.

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284

Abbondanzieri, E. A. ; Greenleaf, W. J. ; Shaevitz, J. W. ; Landick, R. ; Block, S. M. Direct Observation of Base-Pair Stepping by RNA Polymerase Nature 2005 , 438 , 460 – 465

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284

Direct observation of base-pair stepping by RNA polymerase

Abbondanzieri, Elio A.; Greenleaf, William J.; Shaevitz, Joshua W.; Landick, Robert; Block, Steven M.

Nature (London, United Kingdom) (2005), 438 (7067), 460-465CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with angstroem-level resoln., which we used to monitor transcriptional elongation by single mols. of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 ± 0.6 Å, a distance equiv. to the mean rise per base found in B-DNA. By combining our results with quant. gel anal., we conclude that RNAP advances along DNA by a single base pair per nucleotide addn. to the nascent RNA. We also detd. the force-velocity relationship for transcription at both satg. and sub-satg. nucleotide concns.; fits to these data returned a characteristic distance parameter equiv. to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.

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285

Fehr, A. N. ; Gutierrez-Medina, B. ; Asbury, C. L. ; Block, S. M. On the Origin of Kinesin Limping Biophys. J. 2009 , 97 , 1663 – 1670

286

Nelson, K. D. ; Li, X. ; Weiss, D. S. Imaging Single Atoms in a Three-Dimensional Array Nat. Phys. 2007 , 3 , 556 – 560

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286

Imaging single atoms in a three-dimensional array

Nelson, Karl D.; Li, Xiao; Weiss, David S.

Nature Physics (2007), 3 (8), 556-560CODEN: NPAHAX; ISSN:1745-2473. (Nature Publishing Group)

A single neutral atom trapped by light is a promising qubit. It has weak, well-understood interactions with the environment, its internal state can be precisely manipulated, interactions that entangle atoms can be varied from negligible to strong and many single atoms can be trapped near each other in an optical lattice. This collection of features would allow for a relatively large quantum computer if each neutral atom qubit could be independently detected and addressed. A quantum computer with even 50 qubits would allow quantum simulations that are out of the reach of classical computers. So far, fewer than 10 single atoms were simultaneously imaged. Here the authors demonstrate trapping and imaging of 250 single atoms in a 3-dimensional optical lattice and show that imaging is highly unlikely to change the pattern of site occupancy. Lattice spacing is large enough that, in principle, individual atoms can be addressed, which in combination with reproducible imaging should allow for verifiable filling of vacancies, execution of site-specific quantum gates and measurement of each atom's final quantum state. The lattice the authors use can readily be scaled to include thousands of trapped atoms.

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287

Neher, E. ; Sakmann, B. Single-Channel Currents Recorded from Membrane of Denervated Frog Muscle-Fibers Nature 1976 , 260 , 799 – 802

288

Meller, A. ; Nivon, L. ; Brandin, E. ; Golovchenko, J. ; Branton, D. Rapid Nanopore Discrimination between Single Polynucleotide Molecules Proc. Natl. Acad. Sci. U.S.A. 2000 , 97 , 1079 – 1084

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288

Rapid nanopore discrimination between single polynucleotide molecules

Meller, Amit; Nivon, Lucas; Brandin, Eric; Golovchenko, Jene; Branton, Daniel

Proceedings of the National Academy of Sciences of the United States of America (2000), 97 (3), 1079-1084CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

A variety of different DNA polymers were electrophoretically driven through the nanopore of an α-hemolysin channel in a lipid bilayer. Single-channel recording of the translocation duration and current flow during traversal of individual polynucleotides yielded a unique pattern of events for each of the several polymers tested. Statistical data derived from this pattern of events demonstrate that in several cases a nanopore can distinguish between polynucleotides of similar length and compn. that differ only in sequence. Studies of temp. effects on the translocation process show that translocation duration scales as ∼T-2. A strong correlation exists between the temp. dependence of the event characteristics and the tendency of some polymers to form secondary structure. Because nanopores can rapidly discriminate and characterize unlabeled DNA mols. at low copy no., refinements of the exptl. approach demonstrated here could eventually provide a low-cost high-throughput method of analyzing DNA polynucleotides.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXpvFegug%253D%253D&md5=aa68cf49ed64eda2970f33d156203795

289

Meller, A. Dynamics of Polynucleotide Transport through Nanometre-Scale Pores J. Phys.: Condens. Matter 2003 , 15 , R581 – R607

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289

Dynamics of polynucleotide transport through nanometre-scale pores

Meller, Amit

Journal of Physics: Condensed Matter (2003), 15 (17), R581-R607CODEN: JCOMEL; ISSN:0953-8984. (Institute of Physics Publishing)

A review. The transport of biopolymers through large membrane channels is a ubiquitous process in biol. It is central to processes such as gene transfer by transduction and RNA transport through nuclear pore complexes. The transport of polymers through nanoscopic channels is also of interest to physicists and chemists studying the effects of steric, hydrodynamic, and electrostatic interactions between polymers and confining walls. Single-channel ion current measurements have been recently used to study the transport of biopolymers, and in particular single-stranded DNA and RNA mols., through nanometer-size channels. Under the influence of an elec. field, the neg. charged polynucleotides can be captured and drawn through the channel in a process termed "translocation". During translocation, the ion current flowing through the channel is mostly blocked, indicating the presence of the polymer inside the channel. The current blockades were found to be sensitive to the properties of the biopolymers such as their nucleotide compn., length, and secondary structure, and to phys. parameters such as the driving field intensity, temp., and ionic strength. These blockades are therefore a rich source of information regarding the dynamics of polynucleotides in the pore. The translocation process is sepd. into its two main steps:. (a) polymer "capture" in which one of the polymer's ends is threaded a small distance through the channel, and. (b) polymer sliding through the channel. The exptl. and theor. efforts to elucidate polymer capture and the transport dynamics of biopolymers in nanoscopic pores are reviewed in this article.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXktFKgsL4%253D&md5=0e0f24f82bea797db850131f7265de10

290

Wilson, N. A. ; Abu-Shumays, R. ; Gyarfas, B. ; Wang, H. ; Lieberman, K. R. ; Akeson, M. ; Dunbar, W. B. Electronic Control of DNA Polymerase Binding and Unbinding to Single DNA Molecules ACS Nano 2009 , 3 , 995 – 1003

291

Li, J. L. ; Gershow, M. ; Stein, D. ; Brandin, E. ; Golovchenko, J. A. DNA Molecules and Configurations in a Solid-State Nanopore Microscope Nat. Mater. 2003 , 2 , 611 – 615

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291

DNA molecules and configurations in a solid-state nanopore microscope

Li, Jiali; Gershow, Marc; Stein, Derek; Brandin, Eric; Golovchenko, J. A.

Nature Materials (2003), 2 (9), 611-615CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)

A nanometer-scale pore in a solid-state membrane provides a new way of electronically probing the structure of single linear polymers, including those of biol. interest in their native environments. Previous work with biol. protein pores wide enough to let through and sense single-stranded DNA mols. demonstrates the power of using nanopores, but many future tasks and applications call for a robust solid-state pore whose nanometer-scale dimensions and properties may be selected, as one selects the lenses of a microscope. Here we demonstrate a solid-state nanopore microscope capable of observing individual mols. of double-stranded DNA and their folding behavior. We discuss extensions of the nanopore microscope concept to alternative probing mechanisms and applications, including the study of mol. structure and sequencing.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXmvVCrsb8%253D&md5=a6c2f67913c578eeb7aeeaa5471210e7

292

Dekker, C. Solid-State Nanopores Nat. Nanotechnol. 2007 , 2 , 209 – 215

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292

Solid-state nanopores

Dekker, Cees

Nature Nanotechnology (2007), 2 (4), 209-215CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)

A review. The passage of individual mols. through nanosized pores in membranes is central to many processes in biol. Previously, expts. have been restricted to naturally occurring nanopores, but advances in technol. now allow artificial solid-state nanopores to be fabricated in insulating membranes. By monitoring ion currents and forces as mols. pass through a solid-state nanopore, it is possible to investigate a wide range of phenomena involving DNA, RNA and proteins. The solid-state nanopore proves to be a surprisingly versatile new single-mol. tool for biophysics and biotechnol.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXjvVOgtrY%253D&md5=e6bb60049955040116b139d49b3b85cf

293

Liu, H. T. ; He, J. ; Tang, J. Y. ; Liu, H. ; Pang, P. ; Cao, D. ; Krstic, P. ; Joseph, S. ; Lindsay, S. ; Nuckolls, C. Translocation of Single-Stranded DNA through Single-Walled Carbon Nanotubes Science 2010 , 327 , 64 – 67

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293

Translocation of Single-Stranded DNA Through Single-Walled Carbon Nanotubes

Liu, Haitao; He, Jin; Tang, Jinyao; Liu, Hao; Pang, Pei; Cao, Di; Krstic, Predrag; Joseph, Sony; Lindsay, Stuart; Nuckolls, Colin

Science (Washington, DC, United States) (2010), 327 (5961), 64-67CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

The authors report the fabrication of devices in which one single-walled carbon nanotube spans a barrier between two fluid reservoirs, enabling direct elec. measurement of ion transport through the tube. A fraction of the tubes pass anomalously high ionic currents. Electrophoretic transport of small single-stranded DNA oligomers through these tubes is marked by large transient increases in ion current and was confirmed by polymerase chain reaction anal. Each current pulse contains about 107 charges, an enormous amplification of the translocated charge. Carbon nanotubes simplify the construction of nanopores, permit new types of elec. measurements, and may open avenues for control of DNA translocation.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhs1WksrbN&md5=b0699b90631d2b50101100b10b6f1c80

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Branton, D. ; Deamer, D. W. ; Marziali, A. ; Bayley, H. ; Benner, S. A. ; Butler, T. ; Di Ventra, M. ; Garaj, S. ; Hibbs, A. ; Huang, X. H. et al. The Potential and Challenges of Nanopore Sequencing Nat. Biotechnol. 2008 , 26 , 1146 – 1153

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294

The potential and challenges of nanopore sequencing

Branton, Daniel; Deamer, David W.; Marziali, Andre; Bayley, Hagan; Benner, Steven A.; Butler, Thomas; Di Ventra, Massimiliano; Garaj, Slaven; Hibbs, Andrew; Huang, Xiaohua; Jovanovich, Stevan B.; Krstic, Predrag S.; Lindsay, Stuart; Ling, Xinsheng Sean; Mastrangelo, Carlos H.; Meller, Amit; Oliver, John S.; Pershin, Yuriy V.; Ramsey, J. Michael; Riehn, Robert; Soni, Gautam V.; Tabard-Cossa, Vincent; Wanunu, Meni; Wiggin, Matthew; Schloss, Jeffery A.

Nature Biotechnology (2008), 26 (10), 1146-1153CODEN: NABIF9; ISSN:1087-0156. (Nature Publishing Group)

A review. A nanopore-based device provides single-mol. detection and anal. capabilities that are achieved by electrophoretically driving mols. in soln. through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small mols. (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique anal. capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for ∼$1,000 in ∼24 h.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXht1aisrzE&md5=1f08524306d35b48c435d675ba0f9b58

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Dudko, O. K. ; Mathe, J. ; Szabo, A. ; Meller, A. ; Hummer, G. Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins Biophys. J. 2007 , 92 , 4188 – 4195

296

Liang, J. ; Fernandez, J. M. Mechanochemistry: One Bond at a Time ACS Nano 2009 , 3 , 1628 – 1645

297

Ternes, M. ; Lutz, C. P. ; Hirjibehedin, C. F. ; Giessibl, F. J. ; Heinrich, A. J. The Force Needed To Move an Atom on a Surface Science 2008 , 319 , 1066 – 1069

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297

The Force Needed to Move an Atom on a Surface

Ternes, Markus; Lutz, Christopher P.; Hirjibehedin, Cyrus F.; Giessibl, Franz J.; Heinrich, Andreas J.

Science (Washington, DC, United States) (2008), 319 (5866), 1066-1069CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Manipulation of individual atoms and mols. by scanning probe microscopy offers the ability of controlled assembly at the single-atom scale. However, the driving forces behind at. manipulation have not yet been measured. The authors used an at. force microscope to measure the vertical and lateral forces exerted on individual adsorbed atoms or mols. by the probe tip. The force that it takes to move an atom depends strongly on the adsorbate and the surface. Results indicate that for moving metal atoms on metal surfaces, the lateral force component plays the dominant role. Also, measuring spatial maps of the forces during manipulation yielded the full potential energy landscape of the tip-sample interaction.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXit1yhsL0%253D&md5=40622bc2fdc27e087681c7a3430c91ff

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Bartels, L. ; Meyer, G. ; Rieder, K. H. Basic Steps of Lateral Manipulation of Single Atoms and Diatomic Clusters with a Scanning Tunneling Microscope Tip Phys. Rev. Lett. 1997 , 79 , 697 – 700

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298

Basic steps of lateral manipulation of single atoms and diatomic clusters with a scanning tunneling microscope tip

Bartels, L.; Meyer, G.; Rieder, K.-H.

Physical Review Letters (1997), 79 (4), 697-700CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)

Detailed tip height measurements during manipulation of single atoms, mols., and dimers on a Cu(211) surface reveal different manipulation modes depending on tunneling parameters. Both attractive (Cu, Pb, Pb dimers) and repulsive manipulation (CO) are identified. Using attractive forces, discontinuous hopping of Cu and Pb atoms from one adsorption site to the next can be induced ("pulling"). Pb dimers can be pulled with repeated single, double, and triple hops. Pb atoms can also be "slid" continuously. The occurrence of different movement patterns is shown to be a sensitive probe for surface defects.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXltFCmtb0%253D&md5=49a2f1f35fbe368a1438346ab521a620

299

Kellermayer, M. S. Z. ; Smith, S. B. ; Granzier, H. L. ; Bustamante, C. Folding−Unfolding Transitions in Single Titin Molecules Characterized with Laser Tweezers Science 1997 , 276 , 1112 – 1116

300

Rief, M. ; Pascual, J. ; Saraste, M. ; Gaub, H. E. Single Molecule Force Spectroscopy of Spectrin Repeats: Low Unfolding Forces in Helix Bundles J. Mol. Biol. 1999 , 286 , 553 – 561

301

Liphardt, J. ; Onoa, B. ; Smith, S. B. ; Tinoco, I. ; Bustamante, C. Reversible Unfolding of Single RNA Molecules by Mechanical Force Science 2001 , 292 , 733 – 737

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301

Reversible unfolding of single RNA molecules by mechanical force

Liphardt, Jan; Onoa, Bibiana; Smith, Steven B.; Tinoco, Ignacio, Jr.; Bustamante, Carlos

Science (Washington, DC, United States) (2001), 292 (5517), 733-737CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

Here we use mech. force to induce the unfolding and refolding of single RNA mols.: a simple RNA hairpin, a mol. contg. a three-helix junction, and the P5abc domain of the Tetrahymena thermophila ribozyme. All three mols. (P5abc only in the absence of Mg2+) can be mech. unfolded at equil., and when kept at const. force within a crit. force range, are bi-stable and hop between folded and unfolded states. We det. the force-dependent equil. consts. for folding/unfolding these single RNA mols. and the positions of their transition states along the reaction coordinate.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjt1ektb8%253D&md5=61f39c774e91a5ed15c7e843334d4b4d

302

Neuman, K. C. ; Block, S. M. Optical Trapping Rev. Sci. Instrum. 2004 , 75 , 2787 – 2809

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302

Optical trapping

Neuman, Keir C.; Block, Steven M.

Review of Scientific Instruments (2004), 75 (9), 2787-2809CODEN: RSINAK; ISSN:0034-6748. (American Institute of Physics)

A review. Since their invention just over 20 yr ago, optical traps have emerged as a powerful tool with broad-reaching applications in biol. and physics. Capabilities have evolved from simple manipulation to the application of calibrated forces on-and the measurement of nanometer-level displacements of-optically trapped objects. The authors review progress in the development of optical trapping app., including instrument design considerations, position detection schemes and calibration techniques, with an emphasis on recent advances. The authors conclude with a brief summary of innovative optical trapping configurations and applications.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXot1yksb4%253D&md5=8e26e2e8bc253a6d8cb5e3f12beb4e79

303

Moffitt, J. R. ; Chemla, Y. R. ; Aathavan, K. ; Grimes, S. ; Jardine, P. J. ; Anderson, D. L. ; Bustamante, C. Intersubunit Coordination in a Homomeric Ring ATPase Nature 2009 , 457 , 446 – 451

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303

Intersubunit coordination in a homomeric ring ATPase

Moffitt, Jeffrey R.; Chemla, Yann R.; Aathavan, K.; Grimes, Shelley; Jardine, Paul J.; Anderson, Dwight L.; Bustamante, Carlos

Nature (London, United Kingdom) (2009), 457 (7228), 446-450CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Homomeric ring ATPases perform many vital and varied tasks in the cell, ranging from chromosome segregation to protein degrdn. Here we report the direct observation of the intersubunit coordination and step size of such a ring ATPase, the double-stranded-DNA packaging motor in the bacteriophage φ29. Using high-resoln. optical tweezers, we find that packaging occurs in increments of 10 base pairs (bp). Statistical anal. of the preceding dwell times reveals that multiple ATPs bind during each dwell, and application of high force reveals that these 10-bp increments are composed of four 2.5-bp steps. These results indicate that the hydrolysis cycles of the individual subunits are highly coordinated by means of a mechanism novel for ring ATPases. Furthermore, a step size that is a non-integer no. of base pairs demands new models for motor-DNA interactions.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXotlOmuw%253D%253D&md5=8e1c64d50b452597bcaa598c190db1d3

304

Bustamante, C. ; Macosko, J. C. ; Wuite, G. J. L. Grabbing the Cat by the Tail: Manipulating Molecules One by One Nat. Rev. Mol. Cell Biol. 2000 , 1 , 130 – 136

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304

Grabbing the cat by the tail: manipulating molecules one by one

Bustamante, Carlos; Macosko, Jed C.; Wuite, Gijs J. L.

Nature Reviews Molecular Cell Biology (2000), 1 (2), 130-136CODEN: NRMCBP; ISSN:1471-0072. (Nature Publishing Group)

A review with 66 refs. Methods for manipulating single mols. are yielding new information about both the forces that hold biomols. together and the mechanics of mol. motors. We describe here the phys. principles behind these methods, and discuss their capabilities and current limitations.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXivVGjurg%253D&md5=6ad74b32e65da68bcfd8a5b82d5f5523

305

Chiu, D. T. ; Zare, R. N. Biased Diffusion, Optical Trapping, and Manipulation of Single Molecules in Solution J. Am. Chem. Soc. 1996 , 118 , 6512 – 6513

306

Kabata, H. ; Kurosawa, O. ; Arai, I. ; Washizu, M. ; Margarson, S. A. ; Glass, R. E. ; Shimamoto, N. Visualization of Single Molecules of RNA-Polymerase Sliding along DNA Science 1993 , 262 , 1561 – 1563

307

Yamamoto, T. ; Kurosawa, O. ; Kabata, H. ; Shimamoto, N. ; Washizu, M. Molecular Surgery of DNA Based on Electrostatic Micromanipulation IEEE Trans. Ind. Appl. 2000 , 36 , 1010 – 1017

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307

Molecular surgery of DNA based on electrostatic micromanipulation

Yamamoto, Takatoki; Kurosawa, Osamu; Kabata, Hiroyuki; Shimamoto, Nobuo; Washizu, Masao

IEEE Transactions on Industry Applications (2000), 36 (4), 1010-1017CODEN: ITIACR; ISSN:0093-9994. (Institute of Electrical and Electronics Engineers)

A novel method for the space-resolved dissection (mol. surgery) of DNA using electrostatic mol. manipulation is proposed and demonstrated. In conventional biochem., DNA-cutting enzymes and DNA are mixed in water, so the cutting reactions occur only by stochastic chances. In contrast, the present method is based upon a phys. manipulation and enables the reproducible cutting of DNA at any desired position along the DNA mol. In order to realize this space-resolved cutting, the target DNA is stretched straight by electrostatic orientation and anchored on a solid surface by dielectrophoresis, using the high-intensity (1 MV/m) high-frequency (1 MHz) field created in microfabricated electrodes. It is found that, for the enzymic cutting to occur, the DNA strand must be immobilized in such a way as to allow the enzyme to bind and interact with DNA. For this purpose, an electrode system is developed, in which DNA is anchored to the substrate only at the ends of the mol., leaving the middle free. The enzyme, on the other hand, is immobilized on a latex particle having 1-μm diam., and optical tweezers are used to hold it and press it against the stretched and immobilized DNA. The enzymes used are: (1) DNaseI (cuts DNA regardless of the base sequence) and (2) HindIII (a restriction enzyme; cuts DNA at a specific sequence). It is demonstrated that, when a DNaseI-labeled bead is brought into contact with the immobilized DNA, DNA is cut instantaneously. On the other hand, when the restriction enzyme is used, the bead must be moved along the strand for a certain distance until it is finally cut. Our interpretation for this enzyme dependence is that the restriction enzyme has to get into the grooves of DNA to find the restriction sites, so the condition for the mol. contour fitting of the DNA and the enzyme are stricter compared with the case of the simple backbone-cutting enzyme DNaseI. The technique presented in this paper is expected to realize space-resolved mol. surgical operations, not just limited to dissections, but also for chem. modifications, or even insertion of genes.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXmtVeqtb4%253D&md5=830eb3f805cd580b3f7a10d84fb99f65

308

Neuman, K. C. Single-Molecule Measurements of DNA Topology and Topoisomerases J. Biol. Chem. 2010 , 285 , 18967 – 18971

309

Sielaff, H. ; Rennekamp, H. ; Wachter, A. ; Xie, H. ; Hilbers, F. ; Feldbauer, K. ; Dunn, S. D. ; Engelbrecht, S. ; Junge, W. Domain Compliance and Elastic Power Transmission in Rotary F₀F₁-ATPase Proc. Natl. Acad. Sci. U.S.A. 2008 , 105 , 17760 – 17765

310

La Porta, A. ; Wang, M. D. Optical Torque Wrench: Angular Trapping, Rotation, and Torque Detection of Quartz Microparticles Phys. Rev. Lett. 2004 , 92 , 190801-1-4

311

Deufel, C. ; Forth, S. ; Simmons, C. R. ; Dejgosha, S. ; Wang, M. D. Nanofabricated Quartz Cylinders for Angular Trapping: DNA Supercoiling Torque Detection Nat. Methods 2007 , 4 , 223 – 225

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311

Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection

Deufel, Christopher; Forth, Scott; Simmons, Chad R.; Dejgosha, Siavash; Wang, Michelle D.

Nature Methods (2007), 4 (3), 223-225CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

The authors designed and created nanofabricated quartz cylinders well suited for torque application and detection in an angular optical trap. They made the cylinder axis perpendicular to the extraordinary axis of the quartz crystal and chem. functionalized only 1 end of each cylinder for attachment to a DNA mol. They directly measured the torque on a single DNA mol. as it underwent a phase transition from B-form to supercoiled P-form.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXitFChtr8%253D&md5=618f0a2ede11d607ae891fa2ed6d1966

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Forth, S. ; Deufel, C. ; Sheinin, M. Y. ; Daniels, B. ; Sethna, J. P. ; Wang, M. D. Abrupt Buckling Transition Observed during the Plectoneme Formation of Individual DNA Molecules Phys. Rev. Lett. 2008 , 100 , 148301-1-4

313

Degen, C. L. ; Poggio, M. ; Mamin, H. J. ; Rettner, C. T. ; Rugar, D. Nanoscale Magnetic Resonance Imaging Proc. Natl. Acad. Sci. U.S.A. 2009 , 106 , 1313 – 1317

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313

Nanoscale magnetic resonance imaging

Degen, C. L.; Poggio, M.; Mamin, H. J.; Rettner, C. T.; Rugar, D.

Proceedings of the National Academy of Sciences of the United States of America (2009), 106 (5), 1313-1317CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

We have combined ultrasensitive magnetic resonance force microscopy (MRFM) with 3D image reconstruction to achieve magnetic resonance imaging (MRI) with resoln. <10 nm. The image reconstruction converts measured magnetic force data into a 3D map of nuclear spin d., taking advantage of the unique characteristics of the "resonant slice" that is projected outward from a nanoscale magnetic tip. The basic principles are demonstrated by imaging the 1H spin d. within individual tobacco mosaic virus particles sitting on a nanometer-thick layer of adsorbed hydrocarbons. This result, which represents a 100 million-fold improvement in vol. resoln. over conventional MRI, demonstrates the potential of MRFM as a tool for 3D, elementally selective imaging on the nanometer scale.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhvV2qt7k%253D&md5=36e5678f174874787dd91291e080f909

314

Mamin, H. J. ; Poggio, M. ; Degen, C. L. ; Rugar, D. Nuclear Magnetic Resonance Imaging with 90-nm Resolution Nat. Nanotechnol. 2007 , 2 , 301 – 306

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314

Nuclear magnetic resonance imaging with 90-nm resolution

Mamin, H. J.; Poggio, M.; Degen, C. L.; Rugar, D.

Nature Nanotechnology (2007), 2 (5), 301-306CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)

Magnetic resonance imaging (MRI) is a powerful imaging technique that typically operates on the scale of millimeters to micrometers. Conventional MRI is based on the manipulation of nuclear spins with radio-frequency fields, and the subsequent detection of spins with induction-based techniques. An alternative approach, magnetic resonance force microscopy (MRFM), uses force detection to overcome the sensitivity limitations of conventional MRI. Here, we show that the two-dimensional imaging of nuclear spins can be extended to a spatial resoln. better than 100 nm using MRFM. The imaging of 19F nuclei in a patterned CaF2 test object was enabled by a detection sensitivity of roughly 1,200 nuclear spins at a temp. of 600 mK. To achieve this sensitivity, we developed high-moment magnetic tips that produced field gradients up to 1.4 × 106 T m-1, and implemented a measurement protocol based on force-gradient detection of naturally occurring spin fluctuations. The resulting detection vol. was less than 650 zeptoliters. This is 60,000 times smaller than the previous smallest vol. for NMR microscopy, and demonstrates the feasibility of pushing MRI into the nanoscale regime.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXns1Onsbw%253D&md5=4cc8ef6c9ba27ac62ef6c4ad69502d38

315

Rugar, D. ; Budakian, R. ; Mamin, H. J. ; Chui, B. W. Single Spin Detection by Magnetic Resonance Force Microscopy Nature 2004 , 430 , 329 – 332

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315

Single spin detection by magnetic resonance force microscopy

Rugar, D.; Budakian, R.; Mamin, H. J.; Chui, B. W.

Nature (London, United Kingdom) (2004), 430 (6997), 329-332CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)

Magnetic resonance imaging (MRI) is well known as a powerful technique for visualizing subsurface structures with three-dimensional spatial resoln. Pushing the resoln. below 1 μm remains a major challenge, however, owing to the sensitivity limitations of conventional inductive detection techniques. Currently, the smallest vol. elements in an image must contain at least 1012 nuclear spins for MRI-based microscopy, or 107 electron spins for ESR microscopy. Magnetic resonance force microscopy (MRFM) was proposed as a means to improve detection sensitivity to the single-spin level, and thus enable three-dimensional imaging of macromols. (for example, proteins) with at. resoln. MRFM has also been proposed as a qubit readout device for spin-based quantum computers. Here we report the detection of an individual electron spin by MRFM. A spatial resoln. of 25 nm in one dimension was obtained for an unpaired spin in silicon dioxide. The measured signal is consistent with a model in which the spin is aligned parallel or anti-parallel to the effective field, with a rotating-frame relaxation time of 760 ms. The long relaxation time suggests that the state of an individual spin can be monitored for extended periods of time, even while subjected to a complex set of manipulations that are part of the MRFM measurement protocol.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXls1eqs78%253D&md5=289d1d5dc5543fd443fa420e5a96a6d1

316

Eid, J. ; Fehr, A. ; Gray, J. ; Luong, K. ; Lyle, J. ; Otto, G. ; Peluso, P. ; Rank, D. ; Baybayan, P. ; Bettman, B. et al. Real-Time DNA Sequencing from Single Polymerase Molecules Science 2009 , 323 , 133 – 138

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316

Real-time DNA sequencing from single polymerase molecules

Eid, John; Fehr, Adrian; Gray, Jeremy; Luong, Khai; Lyle, John; Otto, Geoff; Peluso, Paul; Rank, David; Baybayan, Primo; Bettman, Brad; Bibillo, Arkadiusz; Bjornson, Keith; Chaudhuri, Bidhan; Christians, Frederick; Cicero, Ronald; Clark, Sonya; Dalal, Ravindra; de Winter, Alex; Dixon, John; Foquet, Mathieu; Gaertner, Alfred; Hardenbol, Paul; Heiner, Cheryl; Hester, Kevin; Holden, David; Kearns, Gregory; Kong, Xiangxu; Kuse, Ronald; Lacroix, Yves; Lin, Steven; Lundquist, Paul; Ma, Congcong; Marks, Patrick; Maxham, Mark; Murphy, Devon; Park, Insil; Pham, Thang; Phillips, Michael; Roy, Joy; Sebra, Robert; Shen, Gene; Sorenson, Jon; Tomaney, Austin; Travers, Kevin; Trulson, Mark; Vieceli, John; Wegener, Jeffrey; Wu, Dawn; Yang, Alicia; Zaccarin, Denis; Zhao, Peter; Zhong, Frank; Korlach, Jonas; Turner, Stephen

Science (Washington, DC, United States) (2009), 323 (5910), 133-138CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

We present single-mol., real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation vol. confinement and enable parallel, simultaneous detection of thousands of single-mol. sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymn. states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known ref. sequence to assay biophys. parameters of polymn. for each template position. Consensus sequences were generated from the single-mol. reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXovF2k&md5=eb80df3838cdf3b370ce54397c9dfa5d

317

Pushkarev, D. ; Neff, N. F. ; Quake, S. R. Single-Molecule Sequencing of an Individual Human Genome Nat. Biotechnol. 2009 , 27 , 847 – 852

318

Chin, C. S. ; Sorenseon, J. ; Harris, J. B. ; Robins, W. P. ; Charles, R. C. ; Jean-Charles, R. R. ; Bullard, J. ; Webster, D. R. ; Kasarskis, A. ; Peluso, P. et al. The Origin of the Haitian Cholera Outbreak Strain N. Engl. J Med. 2011 , 364 , 33 – 42

[Crossref], [PubMed], [CAS], Google Scholar

318

The origin of the Haitian cholera outbreak strain

Chin, Chen-Shan; Sorenson, Jon; Harris, Jason B.; Robins, William P.; Charles, Richelle C.; Jean-Charles, Roger R.; Bullard, James; Webster, Dale R.; Kasarskis, Andrew; Peluso, Paul; Paxinos, Ellen E.; Yamaichi, Yoshiharu; Calderwood, Stephen B.; Mekalanos, John J.; Schadt, Eric E.; Waldor, Matthew K.

New England Journal of Medicine (2011), 364 (1), 33-42CODEN: NEJMAG; ISSN:0028-4793. (Massachusetts Medical Society)

BACKGROUND Although cholera has been present in Latin America since 1991, it had not been epidemic in Haiti for at least 100 years. Recently, however, there has been a severe outbreak of cholera in Haiti. METHODS We used third-generation single-mol. real-time DNA sequencing to det. the genome sequences of 2 clin. Vibrio cholerae isolates from the current outbreak in Haiti, 1 strain that caused cholera in Latin America in 1991, and 2 strains isolated in South Asia in 2002 and 2008. Using primary sequence data, we compared the genomes of these 5 strains and a set of previously obtained partial genomic sequences of 23 diverse strains of V. cholerae to assess the likely origin of the cholera outbreak in Haiti. RESULTS Both single-nucleotide variations and the presence and structure of hypervariable chromosomal elements indicate that there is a close relationship between the Haitian isolates and variant V. cholerae El Tor O1 strains isolated in Bangladesh in 2002 and 2008. In contrast, anal. of genomic variation of the Haitian isolates reveals a more distant relationship with circulating South American isolates. CONCLUSIONS The Haitian epidemic is probably the result of the introduction, through human activity, of a V. cholerae strain from a distant geog. source.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXisVaqsQ%253D%253D&md5=92f63f85b8539c1f89ff0bd375688243

319

van Houselt, A. ; Zandvliet, H. J. W. Time-Resolved Scanning Tunneling Microscopy Rev. Mod. Phys. 2010 , 82 , 1593 – 1605

320

Kim, T. H. ; Wang, Z. H. ; Wendelken, J. F. ; Weitering, H. H. ; Li, W. Z. ; Li, A. P. A Cryogenic Quadraprobe Scanning Tunneling Microscope System with Fabrication Capability for Nanotransport Research Rev. Sci. Instrum. 2007 , 78 , 7

321

Higuchi, S. ; Kuramochi, H. ; Laurent, O. ; Komatsubara, T. ; Machida, S. ; Aono, M. ; Obori, K. ; Nakayama, T. Multiple-Scanning-Probe Tunneling Microscope with Nanoscale Positional Recognition Function Rev. Sci. Instrum. 2010 , 81 , 073706

322

Xu, M. S. ; Fujita, D. ; Hanagata, N. Perspectives and Challenges of Emerging Single-Molecule DNA Sequencing Technologies Small 2009 , 5 , 2638 – 2649

323

de Jonge, N. ; Peckys, D. B. ; Kremers, G. J. ; Piston, D. W. Electron Microscopy of Whole Cells in Liquid with Nanometer Resolution Proc. Natl. Acad. Sci. U.S.A. 2009 , 106 , 2159 – 2164

[Crossref], [PubMed], [CAS], Google Scholar

323

Electron microscopy of whole cells in liquid with nanometer resolution

de Jonge, N.; Peckys, D. B.; Kremers, G. J.; Piston, D. W.

Proceedings of the National Academy of Sciences of the United States of America (2009), 106 (7), 2159-2164CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

Single gold-tagged epidermal growth factor (EGF) mols. bound to cellular EGF receptors of fixed fibroblast cells were imaged in liq. with a scanning transmission electron microscope (STEM). The cells were placed in buffer soln. in a microfluidic device with electron transparent windows inside the vacuum of the electron microscope. A spatial resoln. of 4 nm and a pixel dwell time of 20 μs were obtained. The liq. layer was sufficiently thick to contain the cells with a thickness of 7 ± 1 μm. The exptl. findings are consistent with a theor. calcn. Liq. STEM is a unique approach for imaging single mols. in whole cells with significantly improved resoln. and imaging speed over existing methods.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXitlaqtr0%253D&md5=dc000f4495668de7c798e48f749b1105

324

Bard, A. J. Toward Single Enzyme Molecule Electrochemistry ACS Nano 2008 , 2 , 2437 – 2440

325

Hoeben, F. J. M. ; Meijer, F. S. ; Dekker, C. ; Albracht, S. P. J. ; Heering, H. A. ; Lemay, S. G. Toward Single-Enzyme Molecule Electrochemistry: NiFe -Hydrogenase Protein Film Voltammetry at Nanoelectrodes ACS Nano 2008 , 2 , 2497 – 2504

326

Ji, N. ; Milkie, D. E. ; Betzig, E. Adaptive Optics via Pupil Segmentation for High-Resolution Imaging in Biological Tissues Nat. Methods 2010 , 7 , 141 – 150

[Crossref], [PubMed], [CAS], Google Scholar

326

Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues

Ji, Na; Milkie, Daniel E.; Betzig, Eric

Nature Methods (2010), 7 (2), 141-147CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

Biol. specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction-limited performance from a variety of biol. and nonbiol. samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resoln. to depths of 400 μm.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhs1SktbnJ&md5=c593887502e21ba9d28a3299e95ce2d3

327

Ji, N. ; Magee, J. C. ; Betzig, E. High-Speed, Low-Photodamage Nonlinear Imaging Using Passive Pulse Splitters Nat. Methods 2008 , 5 , 197 – 202

[Crossref], [PubMed], [CAS], Google Scholar

327

High-speed, low-photodamage nonlinear imaging using passive pulse splitters

Ji, Na; Magee, Jeffrey C.; Betzig, Eric

Nature Methods (2008), 5 (2), 197-202CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)

Pulsed lasers are key elements in nonlinear bioimaging techniques such as two-photon fluorescence excitation (TPE) microscopy. Typically, however, only a percent or less of the laser power available can be delivered to the sample before photoinduced damage becomes excessive. Here we describe a passive pulse splitter that converts each laser pulse into a fixed no. of sub-pulses of equal energy. We applied the splitter to TPE imaging of fixed mouse brain slices labeled with GFP and show that, in different power regimes, the splitter can be used either to increase the signal rate more than 100-fold or to reduce the rate of photobleaching by over fourfold. In living specimens, the gains were even greater: a ninefold redn. in photobleaching during in vivo imaging of Caenorhabditis elegans larvae, and a six- to 20-fold decrease in the rate of photodamage during calcium imaging of rat hippocampal brain slices.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsV2ksLk%253D&md5=2b40c93554da05ba3de5a863976c1684

328

Liu, W. ; Howarth, M. ; Greytak, A. B. ; Zheng, Y. ; Nocera, D. G. ; Ting, A. Y. ; Bawendi, M. G. Compact Biocompatible Quantum Dots Functionalized for Cellular Imaging J. Am. Chem. Soc. 2008 , 130 , 1274 – 1284

[ACS Full Text ], [CAS], Google Scholar

328

Compact biocompatible quantum dots functionalized for cellular imaging

Liu, Wenhao; Howarth, Mark; Greytak, Andrew B.; Zheng, Yi; Nocera, Daniel G.; Ting, Alice Y.; Bawendi, Moungi G.

Journal of the American Chemical Society (2008), 130 (4), 1274-1284CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)

The authors present a family of water-sol. quantum dots (QDs) that exhibit low nonspecific binding to cells, small hydrodynamic diam., tunable surface charge, high quantum yield, and good soln. stability across a wide pH range. These QDs are amenable to covalent modification via simple carbodiimide coupling chem., which is achieved by functionalizing the surface of QDs with a new class of heterobifunctional ligands incorporating dihydrolipoic acid, a short poly(ethylene glycol) (PEG) spacer, and an amine or carboxylate terminus. The covalent attachment of mols. is demonstrated by appending a rhodamine dye to form a QD-dye conjugate exhibiting fluorescence resonance energy transfer (FRET). High-affinity labeling is demonstrated by covalent attachment of streptavidin, thus enabling the tracking of biotinylated epidermal growth factor (EGF) bound to EGF receptor on live cells. In addn., QDs solubilized with the heterobifunctional ligands retain their metal-affinity driven conjugation chem. with polyhistidine-tagged proteins. This dual functionality is demonstrated by simultaneous covalent attachment of a rhodamine FRET acceptor and binding of polyhistidine-tagged streptavidin on the same nanocrystal to create a targeted QD, which exhibits dual-wavelength emission. Such emission properties could serve as the basis for ratiometric sensing of the cellular receptor's local chem. environment.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXivF2guw%253D%253D&md5=9df55cae92abb8f9a22ee28165a20530

329

Allen, P. M. ; Liu, W. H. ; Chauhan, V. P. ; Lee, J. ; Ting, A. Y. ; Fukumura, D. ; Jain, R. K. ; Bawendi, M. G. InAs(ZnCdS) Quantum Dots Optimized for Biological Imaging in the Near-Infrared J. Am. Chem. Soc. 2010 , 132 , 470 – 471

330

Claridge, S. A. ; Liang, H. Y. W. ; Basu, S. R. ; Frechet, J. M. J. ; Alivisatos, A. P. Isolation of Discrete Nanoparticle−DNA Conjugates for Plasmonic Applications Nano Lett. 2008 , 8 , 1202 – 1206

331

Fung, R. ; Shneerson, V. ; Saldin, D. K. ; Ourmazd, A. Structure from Fleeting Illumination of Faint Spinning Objects in Flight Nat. Phys. 2009 , 5 , 64 – 67

[Crossref], [CAS], Google Scholar

331

Structure from fleeting illumination of faint spinning objects in flight

Fung, Russell; Shneerson, Valentin; Saldin, Dilano K.; Ourmazd, Abbas

Nature Physics (2009), 5 (1), 64-67CODEN: NPAHAX; ISSN:1745-2473. (Nature Publishing Group)

Moves are afoot to illuminate particles in flight with powerful x-ray bursts, to det. the structure of single mols., viruses and nanoparticles. This would circumvent important limitations of current techniques, including the need to condense mols. into pure crystals. Proposals to reconstruct the mol. structure from diffraction snapshots' of unknown orientation, however, require ∼1,000 times more signal than available from next-generation sources. Using a new approach, the authors demonstrate the recovery of the structure of a weakly scattering macromol. at the anticipated next-generation x-ray source intensities. Work closes a crit. gap in detg. the structure of single mols. and nanoparticles by x-ray methods, and opens the way to reconstructing the structure of spinning, or randomly oriented objects at extremely low signal levels.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXptFyn&md5=01ebc1d1964fdc35e03edfe98b475788

332

Caleman, C.; Huldt, G.; Maia, F. R. N. C.; Ortiz, C.; Parak, F. G.; Hajdu, J.; van der Spoel, D.; Chapman, H. N.; Timneanu, N. On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses. ACS Nano 2011 , 5 , 139− 146

333

Kalinin, S. V. ; Rodriguez, B. J. ; Jesse, S. ; Karapetian, E. ; Mirman, B. ; Eliseev, E. A. ; Morozovska, A. N. Nanoscale Electromechanics of Ferroelectric and Biological Systems: A New Dimension in Scanning Probe Microscopy Annu. Rev. Mater. Res. 2007 , 37 , 189 – 238

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333

Nanoscale electromechanics of ferroelectric and biological systems: a new dimension in scanning probe microscopy

Kalinin, Sergei V.; Rodriguez, Brian J.; Jesse, Stephen; Karapetian, Edgar; Mirman, Boris; Eliseev, Eugene A.; Morozovska, Anna N.

Annual Review of Materials Research (2007), 37 (), 189-238CODEN: ARMRCU; ISSN:1531-7331. (Annual Reviews Inc.)

A review. Functionality of biol. and inorg. systems ranging from non-volatile computer memories and microelectromech. systems to electromotor proteins and cellular membranes is ultimately based on the intricate coupling between elec. and mech. phenomena. In the past decade, piezoresponse force microscopy (PFM) has been established as a powerful tool for nanoscale imaging, spectroscopy, and manipulation of ferroelec. and piezoelec. materials. Here, we give an overview of the fundamental image formation mechanism in PFM and summarize recent theor. and technol. advances. In particular, we show that the signal formation in PFM is complementary to that in the scanning tunneling microscopy (STM) and at. force microscopy (AFM) techniques, and we discuss the implications. We also consider the prospect of extending PFM beyond ferroelec. characterization for quant. probing of electromech. behavior in mol. and biol. systems and high-resoln. probing of static and dynamic polarization switching processes in low-dimensional ferroelec. materials and heterostructures.

https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXptlSlsro%253D&md5=07fd462ab538c879f8ed048fdbc8e56c

334

Degen, C. L. ; Poggio, M. ; Mamin, H. J. ; Rugar, D. Nuclear Spin Relaxation Induced by a Mechanical Resonator Phys. Rev. Lett. 2008 , 100 , 1313 – 1317

335

Lee, J. ; Shen, W. J. ; Payer, K. ; Burg, T. P. ; Manalis, S. R. Toward Attogram Mass Measurements in Solution with Suspended Nanochannel Resonators Nano Lett. 2010 , 10 , 2537 – 2542

336

Halvorsen, K. ; Wong, W. P. Massively Parallel Single-Molecule Manipulation Using Centrifugal Force Biophys. J. 2010 , 98 , L53 – L55

337

Dupres, V. ; Dufrene, Y. F. ; Heinisch, J. J. Measuring Cell Wall Thickness in Living Yeast Cells Using Single Molecular Rulers ACS Nano 2010 , 4 , 5498 – 5504

338

Giessibl, F. J. Atomic Resolution on Si(111)-(7 × 7) by Noncontact Atomic Force Microscopy with a Force Sensor Based on a Quartz Tuning Fork Appl. Phys. Lett. 2000 , 76 , 1470 – 1472

Ntp Origami Orii Sring Dark Night

Source: https://pubs.acs.org/doi/full/10.1021/nn103298x

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