Dissertations / Theses on the topic 'Single molecule conductance measurements'
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1
Brooke, Carly. "Synthesis, characterisation and single molecule conductance measurements of organic molecules." Thesis, University of Liverpool, 2012. http://livrepository.liverpool.ac.uk/9397/.
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The use of single molecules to construct electronic devices is an exciting prospect, and one that has long provided a driving force for research in the area of molecular scale electronics. In order for this emerging field to advance a deep understanding of the fundamental mechanisms that govern electron conduction at the molecular level is imperative. Recent developments in areas such as scanning tunnelling microscopy, have facilitated the determination of the electrical properties of single molecules tethered between two metallic contacts. The analysis and potentially tailoring of structure-property relationships is hugely important and could lead to new and unforeseen applications for this emerging field. The work presented herein details two major studies. The first is an investigation of the transport properties of a series of analogous molecules, which consist of a single benzene ring sandwiched between two alkyl chains of varying length. Prior to the work in this thesis one such molecule, and various substituted analogues thereof, had shown behaviour similar to what would be expected of a molecular equivalent of a double tunnelling barrier. The data presented here demonstrates a remarkably low dependence of this system on molecular length; this result contradicts the behaviour expected of a coherent transport mechanism. Moreover, the study of the orbital energies and densities of these molecules provides further evidence of a mechanism of conduction that is very different to that previously suggested for this system. The second study centres around the investigation of the conductance behaviour of 4,4’-bipyridine and some substituted analogues thereof; this study is presented in two parts. The first details attempts to synthesise planar analogues of 4,4’-bipyridine, as well the synthesis and reactivity of novel substituted bipyridines. The second part reports conductance data, electrochemical studies and theoretical calculations of properties of these molecules. The data presented provides new information regarding the relationship between electronic structure and conductance behaviour in this type of system.
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Psychogyiopoulou, Krystallia. "Synthesis, surface spectroscopy and single molecule conductance measurements of some metalloporphyrins." Thesis, University of Liverpool, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.422991.
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Lanzilotto, Valeria. "Self-assembling and charge transfer properties of thin organic films." Doctoral thesis, Università degli studi di Trieste, 2012. http://hdl.handle.net/10077/7362.
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2010/2011In the present thesis I dealt the issue of molecular ordering and charge transfer at two types of organic-inorganic interfaces that are representative of the basic constituents of an organic electron device. I investigated i.) the influence of a selected dielectric surface on the ordering of an overlayer of several organic molecules and ii.) the electronic transport properties of a single molecular junction with a metal electrode. Both systems have been characterized by a structural and electronic point of view. Among the techniques available for structural investigation, I made extensive use of Helium Atom Scattering (HAS) and Scanning Tunneling Microscopy (STM). The electronic properties, with particular emphasis to the charge transfer, have been addressed by two methods chosen according to the dimensionality of the system under consideration. For the charge transfer at laterally extended interfaces I used synchrotron based techniques, like Resonant Photoemssion Spectroscopy (RPES), while for the charge transport through a single molecule I used and developed the STM-based break junction technique (STM-BJ). For the first type of interface, I focused on the coupling between the TiO2(110)-1x1 surface and different organic semiconductor molecules: C60, pentacene, perylene-tetracarboxilic-acid-diimide (PTCDI) and perylene. The strong anisotropy of the substrate has been found to drive the adsorption geometry of the molecules leading to the formation of ordered phases (at least for the first layer). In particular pentacene, PTCDI and perylene (polycyclic aromatic hydrocarbons, PAHs) display a common self-assembly mechanism, where the molecules lay on the surface with their long axis oriented parallel to the [001] substrate direction. In the transverse direction [1-10] these molecules are observed to match the substrate periodicity by tilting the molecular plane around the long axis by an angle that depends on the molecular width. Nevertheless the molecule-to-substrate interaction is very weak as indicated by the molecular electronic structure, which is observed by X-ray spectroscopy to remain mostly unperturbed in the first molecular layer. Only PTCDI bears a major interaction with the TiO2(110)-1x1 surface, but confined to the molecular orbitals closest to the gap. The main experimental evidence of this interaction is the appearance of a new molecular filled state in the valence band region close to the Fermi level. By a combined RPES and NEXAFS study we have found that this new electronic state is due to the charge transfer occurring from the substrate Ti defect state (i.e. the excess of electrons associated with oxygen vacancies) to the lowest unoccupied molecular orbital (LUMO). For the second type of hybrid interface, instead, I exploited the nitrogen-link chemistry in order to bridge a phthalocyanine to two gold electrodes and to measure its conductance. In particular, by using the Tetraaza-Cu-Phthalocyanine I investigated the pyridine-gold bond that is relatively weak and insensitive to the local structure, a fundamental requirement for the establishment of well defined and stable transport properties. The weak interaction between the molecule and a representative metal electrode, namely the Au(100) surface, has been confirmed by spectroscopic and STM experiments. At RT the molecules have been found to diffuse on the surface and only at LT (55 K) they can be observed to self-organize into large molecular domains. On these domains, reliable and reproducible single molecule conductance measurements have been performed by using the STM-based break junction method. The conductance value obtained for the Tetraaza-Cu-Phthalocyanine (7x10-4 G0) has been rationalized in terms of the molecular length and degree of conjugation, as well as by correlation to the energy level alignment at the junction.
XXIV Ciclo
1984
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Leary, Edmund. "Single Molecule Conductance of Dithiahexyl-Aryl Compounds." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507724.
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Zhao, Xiaotao. "The synthesis and single-molecule conductance of conjugated molecular wires." Thesis, Durham University, 2014. http://etheses.dur.ac.uk/10634/.
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The past decades have seen the fast development of electronic devices in the industrial sector. There is increasingly rapid growth in the demand for alternative electronic building blocks to compliment, and possibly replace, the conventional silicon-based products. Electronic devices based on organic molecules, especially those based on single molecules, receive intense studies both theoretically and experimentally. In this presented work, a new family of oligo(aryleneethenylene)s (OAE)s with molecular lengths (N…N distance) of ca. 2-6 nm were designed to investigate the length dependence of conductance at the single molecule level. X-ray molecular structures of OAEs with a molecular length up to 5.3 nm were successfully analysed and presented. Secondly, four groups of pyridyl terminated oligo(phenyleneethylene) (OPE) derivatives were studied for the quantum interference effects. A dramatic destructive quantum interference effect was observed which decreased the single molecule conductance by several orders of magnitude. Unsymmetrical molecules with only one anchor group were noticed to form π-π stacking between two molecules. Thirdly, amino terminated OPEs bearing various substituents on the central phenyl rings were explored to present the robustness of the central OPE backbone towards various functionalising substituents. Fourthly, diaryloligoynes with different anchor groups were synthesised and the single-molecule conductances were studied. The stability of the tetrayne compounds is discussed and X-ray crystal structures of the stable tetraynes are presented. Finally, pyridyl terminated OAE derivatives bearing an anthraquinone core were synthesised to investigate the charge transport through the central anthraquinone core, with special purpose of investigating quantum interference effects and the switching process of the central anthraquinone core.
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Pearson, Anita P. "AFM investigation of single molecule force measurements." Thesis, University of Nottingham, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.441016.
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Radiom, Milad. "Correlation Force Spectroscopy for Single Molecule Measurements." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/49677.
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This thesis addresses development of a new force spectroscopy tool, correlation force spectroscopy (CFS), for the measurement of the mechanical properties of very small volumes of material (molecular to µm³) at kHz-MHz time-scales. CFS is based on atomic force microscopy (AFM) and the principles of CFS resemble those of dual-trap optical tweezers. CFS consists of two closely-spaced micro-cantilevers that undergo thermal fluctuations. Measurement of the correlation in thermal fluctuations of the two cantilevers can be used to determine the mechanical properties of the soft matter, e.g. a polymeric molecule, that connects the gap between the two cantilevers. Modeling of the correlations yields the effective stiffness and damping of the molecule. The resolution in stiffness is limited by the stiffness of the cantilever and the frequency by the natural frequency of the cantilevers, but, importantly, the damping resolution is not limited by the damping of the cantilever, which has enabled high-resolution measurements of the internal friction of a polymer. The concept of CFS was originally presented by Roukes' group in Caltech [Arlett et al., Lecture Notes in Physics, 2007]; I developed the first practical versions of CFS for experimentation, and have used it in two applications (1) microrheology of Newtonian fluids and (2) single molecule force spectroscopy. To understand the correlation in thermal fluctuations of two cantilevers I initially validated the theoretical approach for analyzing correlation in terms of deterministic model using the fluctuation-dissipation theorem [Paul and Cross, PRL, 2004]. I have shown that the main advantages of such correlation measurements are a large improvement in the ability to resolve stiffness and damping. Use of CFS as a rheometer was validated by comparison between experimental data and finite element modeling of the deterministic vibrations of the cantilevers using the known viscosity and density of fluids. Work in this thesis shows that the data can also be accurately fitted using a simple harmonic oscillator model, which can be used for rapid rheometric measurements, after calibration. The mechanical properties of biomolecules such as dextran and single stranded DNA (ssDNA) are also described. CFS measurements of single molecule properties of ssDNA reveal the internal friction of the molecule in solution.Ph. D.
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Berthoumieu, Olivia. "Single molecule studies of seven transmembrane domain proteins." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:ff7ae71d-5481-4523-812b-2128fe32f5fc.
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This work aimed at studying biophysical properties of two membrane proteins, one of potential nanotechnological use, bacteriorhodopsin, and one potential drug target, the NTS1 neurotensin receptor, at the single molecule scale. Bacteriorhodopsin (BR) is the only protein in the purple membrane (PM) of the halophilic organism Halobacterium salinarium. It is a light-driven proton pump converting light into a transmembrane proton gradient through isomerization of its retinal chromophore. Its stability, as well as its photoactivity remaining in dry protein layers, has made BR an attractive material for biomolecular devices. Numerous studies have been published on this topic; however, they have all used BR within the PM, on relatively large (µm-wide) surfaces. Here, conducting-probe atomic force microscopy (C-AFM) analysis was performed after removing most of the membrane lipids. For the first time, it was shown that the molecular conductance of BR can be reversibly photoswitched with predictable wavelength sensitivity. Intimate and robust coupling to gold electrodes was achieved by using a strategically engineered cysteine which, combined with partial delipidation, generated protein trimers homogenously orientated on the surface. Numerous controls using biophysical (SPR, ellipsometry, Kelvin-probe AFM) and chemical (photocurrent, cyclic voltammetry) techniques confirmed the wavelength specificity of the photoswitch, the anchoring role of the mutation and the homogenous orientation of the protein on the gold surface. Neurotensin is a brain and gastrointestinal 13 amino acid peptide acting as a neuromodulator in the central nervous system and as a hormone in the periphery. Its wide range of biological activities is primarily mediated through its binding to the neurotensin type 1 receptor (NTS1). NTS1 expressed in E.coli was purified and inserted into 100 nm brain polar lipid liposomes in a conformation which retained its ligand-binding capabilities. Initial AFM characterisation was performed as a prelude for ligand-receptor interaction studies, including high resolution imaging, force spectroscopy and solid state NMR approaches.
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Holden, Seamus J. "Improved methods for sub-diffraction-limit single-molecule fluorescence measurements." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543548.
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Portoles, Jose Fernando. "The development of MEMS devices for traceable single-molecule force measurements." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.493321.
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Fraccari, Raquel Leh-na. "Single-molecule DNA detection in nanopipettes using high-speed measurements and surface modifications." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/44085.
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Inspired by transmembrane pores found in cell membranes and the operating principle of the Coulter counter used for cell counting, nanopore biosensors have emerged as a tool for single-molecule detection. This thesis describes single-molecule DNA detection through resistive pulse sensing using nanopipettes, a novel subclass of solid-state nanopores. In the first part of this thesis, double-stranded (ds) DNA-nanopipette surface interactions were probed in 1 M KCl electrolyte using DNA molecules with lengths ranging from 48.5 to 4 kilobase pair (kbp). A custom-built current amplifier was employed for low-noise and high-bandwidth measurements. Results from these experiments were used to theoretically rationalise DNA-surface interactions and suggest that dsDNA adsorption to the nanopipette surface prior to translocation through the pore is likely to be an important factor in the process. Subsequently, initial investigations to probe DNA-surface interactions were carried out by modifying the surface charge of nanopipettes using silanes. Additionally, experiments were performed to detect shorter dsDNA lengths. In 1 M KCl electrolyte, 200 base pair (bp) long dsDNA was successfully detected using the low-noise and high-bandwidth current amplifier. However detection of 100 bp long dsDNA required the use of 2 or 4 M LiCl electrolyte. Attention was finally shifted to the detection of 100 bp dsDNA in 1 M KCl electrolyte using functionalised lipid bilayer coated nanopipettes. Additional techniques were employed to prepare and characterise the lipid bilayers, including atomic force microscopy (AFM) and dynamic light scattering (DLS). The promising preliminary results provide a framework for further experiments using functionalised lipid bilayers to coat nanopipettes. Overall, results of the aforementioned research presented in this thesis demonstrate high-speed single-molecule detection of DNA and provide novel insights into the translocation dynamics of DNA molecules in nanopipettes and the sensing capabilities of nanopipettes.
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Tran-Ba, Khanh-Hoa. "Single-molecule diffusion measurements for material characterization in one-dimensional nanostructured polymer films." Diss., Kansas State University, 2015. http://hdl.handle.net/2097/32791.
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Doctor of PhilosophyDepartment of Chemistry
Takashi Ito
This dissertation describes single-molecule tracking (SMT) measurements for the quantitative characterization of one-dimensional (1D) nanostructures in 200 nm-thick surfactant-templated mesoporous silica (STMS) and cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer (CF-PS-b-PEO) films with a μm-scale thickness. SMT is advantageous for the characterization of nanomaterials over conventional methods because it permits the simultaneous and quantitative assessment of the nanoscale and microscale morphologies, and mass-transport properties of the materials with a high nanometer-scale resolution under ambient conditions. It offers a unique means for the assessment and evaluation of the μm-scale nanostructure alignment in polymer films induced by vertical spin-coating (for STMS films), directional solution flow and solvent-vapor penetration (SVP) methods (both for CF-PS-b-PEO films), highly crucial for many potential technological applications using the materials. Through this work, we have identified suitable sample preparation conditions (e.g. solvent, temperature or solution flow rate) for obtaining highly-ordered mesoporous and microdomain structures over a long-range (> 5 μm). For the quantitative assessment of the 1D SMT data, orthogonal regression analysis was employed, providing assessment of the in-plane orientation and size of individual nanostructures with nanometer-scale precision. The analysis of the 1D trajectory data allowed the radius (ca. 11 nm) of cylindrical PEO microdomains to be estimated, yielding results consistent with the AFM results (ca. 14 nm). The distribution of the trajectory angles offered the estimation of the average orientation and order of the nanostructures in domains/grains for a μm-wide region of the polymer films, revealing the higher efficiency of SVP in the nanostructure alignment as compared to the spin coating and solution flow approaches. Systematic SMT measurements across the film depth and along lateral mm-scale distances afforded valuable insights into the shear- and solvent-evaporation-based alignment mechanisms induced by solution flow and SVP/spin coating approaches, respectively. Fluorescence recovery after photobleaching (FRAP) measurements in a SVP-aligned CF-PS-b-PEO film permitted the longer-range mass-transport properties to be probed, reflecting the effective continuity of the aligned cylindrical nanostructures over > 100 μm in length. In this dissertation, FRAP and more importantly SMT methods have provided a unique and useful means for the in-depth characterization of morphology and mass-transport characteristics in thin polymer films under ambient conditions, in confined spaces, and with a nanometer-scale resolution.
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Sapra, K. Tanuj. "Single-Molecule Measurements of Complex Molecular Interactions in Membrane Proteins using Atomic Force Microscopy." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1175696409847-74867.
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Single-molecule force spectroscopy (SMFS) with atomic force microscope (AFM) has advanced our knowledge of the mechanical aspects of biological processes, and helped us take big strides in the hitherto unexplored areas of protein (un)folding. One such virgin land is that of membrane proteins, where the advent of AFM has not only helped to visualize the difficult to crystallize membrane proteins at the single-molecule level, but also given a new perspective in the understanding of the interplay of molecular interactions involved in the construction of these molecules. My PhD work was tightly focused on exploiting this sensitive technique to decipher the intra- and intermolecular interactions in membrane proteins, using bacteriorhodopsin and bovine rhodopsin as model systems. Using single-molecule unfolding measurements on different bacteriorhodopsin oligomeric assemblies - trimeric, dimeric and monomeric - it was possible to elucidate the contribution of intra- and interhelical interactions in single bacteriorhodopsin molecules. Besides, intriguing insights were obtained into the organization of bacteriorhodopsin as trimers, as deduced from the unfolding pathways of the proteins from different assemblies. Though the unfolding pathways of bacteriorhodopsin from all the assemblies remained the same, the different occurrence probability of these pathways suggested a kinetic stabilization of bacteriorhodopsin from a trimer compared to that existing as a monomer. Unraveling the knot of a complex G-protein coupled receptor, rhodopsin, showed the existence of two structural states, a native, functional state, and a non-native, non-functional state, corresponding to the presence or absence of a highly conserved disulfide bridge, respectively. The molecular interactions in absence of the native disulfide bridge mapped onto the three-dimensional structure of native rhodopsin gave insights into the molecular origin of the neurodegenerative disease retinitis pigmentosa. This presents a novel technique to decipher molecular interactions of a different conformational state of the same molecule in the absence of a high-resolution X-ray crystal structure. Interestingly, the presence of ZnCl2 maintained the integrity of the disulfide bridge and the nature of unfolding intermediates. Moreover, the increased mechanical and thermodynamic stability of rhodopsin with bound zinc ions suggested a plausible role for the bivalent ion in rhodopsin dimerization and consequently signal transduction. Last but not the least, I decided to dig into the mysteries of the real mechanisms of mechanical unfolding with the help of well-chosen single point mutations in bacteriorhodopsin. The monumental work has helped me to solve some key questions regarding the nature of mechanical barriers that constitute the intermediates in the unfolding process. Of particular interest is the determination of altered occurrence probabilities of unfolding pathways in an energy landscape and their correlation to the intramolecular interactions with the help of bioinformatics tools. The kind of work presented here, in my opinion, will not only help us to understand the basic principles of membrane protein (un)folding, but also to manipulate and tune energy landscapes with the help of small molecules, proteins, or mutations, thus opening up new vistas in medicine and pharmacology. It is just a matter of a lot of hard work, some time, and a little bit of luck till we understand the key elements of membrane protein (un)folding and use it to our advantage.
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Doroshenko, Olga [Verfasser]. "Accurate structural determination of biomolecules via single-molecule high-precision FRET measurements / Olga Doroshenko." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2020. http://d-nb.info/1203369786/34.
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Sapra, K. Tanuj. "Single-Molecule Measurements of Complex Molecular Interactions in Membrane Proteins using Atomic Force Microscopy." Doctoral thesis, Technische Universität Dresden, 2006. https://tud.qucosa.de/id/qucosa%3A24922.
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Single-molecule force spectroscopy (SMFS) with atomic force microscope (AFM) has advanced our knowledge of the mechanical aspects of biological processes, and helped us take big strides in the hitherto unexplored areas of protein (un)folding. One such virgin land is that of membrane proteins, where the advent of AFM has not only helped to visualize the difficult to crystallize membrane proteins at the single-molecule level, but also given a new perspective in the understanding of the interplay of molecular interactions involved in the construction of these molecules. My PhD work was tightly focused on exploiting this sensitive technique to decipher the intra- and intermolecular interactions in membrane proteins, using bacteriorhodopsin and bovine rhodopsin as model systems. Using single-molecule unfolding measurements on different bacteriorhodopsin oligomeric assemblies - trimeric, dimeric and monomeric - it was possible to elucidate the contribution of intra- and interhelical interactions in single bacteriorhodopsin molecules. Besides, intriguing insights were obtained into the organization of bacteriorhodopsin as trimers, as deduced from the unfolding pathways of the proteins from different assemblies. Though the unfolding pathways of bacteriorhodopsin from all the assemblies remained the same, the different occurrence probability of these pathways suggested a kinetic stabilization of bacteriorhodopsin from a trimer compared to that existing as a monomer. Unraveling the knot of a complex G-protein coupled receptor, rhodopsin, showed the existence of two structural states, a native, functional state, and a non-native, non-functional state, corresponding to the presence or absence of a highly conserved disulfide bridge, respectively. The molecular interactions in absence of the native disulfide bridge mapped onto the three-dimensional structure of native rhodopsin gave insights into the molecular origin of the neurodegenerative disease retinitis pigmentosa. This presents a novel technique to decipher molecular interactions of a different conformational state of the same molecule in the absence of a high-resolution X-ray crystal structure. Interestingly, the presence of ZnCl2 maintained the integrity of the disulfide bridge and the nature of unfolding intermediates. Moreover, the increased mechanical and thermodynamic stability of rhodopsin with bound zinc ions suggested a plausible role for the bivalent ion in rhodopsin dimerization and consequently signal transduction. Last but not the least, I decided to dig into the mysteries of the real mechanisms of mechanical unfolding with the help of well-chosen single point mutations in bacteriorhodopsin. The monumental work has helped me to solve some key questions regarding the nature of mechanical barriers that constitute the intermediates in the unfolding process. Of particular interest is the determination of altered occurrence probabilities of unfolding pathways in an energy landscape and their correlation to the intramolecular interactions with the help of bioinformatics tools. The kind of work presented here, in my opinion, will not only help us to understand the basic principles of membrane protein (un)folding, but also to manipulate and tune energy landscapes with the help of small molecules, proteins, or mutations, thus opening up new vistas in medicine and pharmacology. It is just a matter of a lot of hard work, some time, and a little bit of luck till we understand the key elements of membrane protein (un)folding and use it to our advantage.
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Janovjak, Harald. "Exploring the Mechanical Stability and Visco-elasticity of Membrane Proteins by Single-Molecule Force Measurements." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2005. http://nbn-resolving.de/urn:nbn:de:swb:14-1135090167025-44737.
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Relatively little is known about the folding and stability of membrane proteins. Conventional thermal or chemical unfolding techniques probe the average behavior of large numbers of molecules and thus cannot resolve co-existing minor and major unfolding pathways and intermediates. Here, I applied single-molecule force measurements based on an atomic force microscope (AFM) to characterize the stability of the membrane protein bacteriorhodopsin (BR). In these mechanical unfolding experiments, an external pulling force played the role of the denaturant and lead to unfolding of the three-dimensional structure of individual proteins. It was found that single BRs unfold step-wise in a well-defined sequence of stable intermediates and in different unfolding pathways. Although single [alpha]-helices were sufficiently stable to unfold in individual steps they also exhibited certain probabilities to unfold in pairs. These observations support the "two-stage" and the "helical-hairpin" model of membrane protein folding. Dynamic force measurements showed that [alpha]-helices and helical hairpins are relatively rigid structures, which are stabilized by narrow energy barriers and have stabilities between 100-10?000 seconds. These forced unfolding experiments were complemented with the development of new force measurement techniques. It is demonstrated that hydrodynamic effects need to be considered to obtain more complete kinetic pictures of single molecules. In addition, two force spectroscopy approaches to measure the complex visco-elastic response of single molecules are presented and applied to BR. These experiments revealed that the unfolding patterns of single proteins are dominated by purely elastic polypeptide extension and determined the dissipative interactions associated with the unfolding of single [alpha]-helices. In addition, it was found that kinks result in a reduced unfolding cooperativity of [alpha]-helices.
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Landry, Matthew. "Analysis of Nanopore Detector Measurements using Machine Learning Methods, with Application to Single-Molecule Kinetics." ScholarWorks@UNO, 2007. http://scholarworks.uno.edu/td/533.
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At its core, a nanopore detector has a nanometer-scale biological membrane across which a voltage is applied. The voltage draws a DNA molecule into an á-hemolysin channel in the membrane. Consequently, a distinctive channel current blockade signal is created as the molecule flexes and interacts with the channel. This flexing of the molecule is characterized by different blockade levels in the channel current signal. Previous experiments have shown that a nanopore detector is sufficiently sensitive such that nearly identical DNA molecules were classified successfully using machine learning techniques such as Hidden Markov Models and Support Vector Machines in a channel current based signal analysis platform [4-9]. In this paper, methods for improving feature extraction are presented to improve both classification and to provide biologists and chemists with a better understanding of the physical properties of a given molecule.
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VanDelinder, Virginia Alison. "Microfluidics for blood component separation, medium exchange, response latency measurements, and single molecule fluorescence microscopy." Diss., [La Jolla, Calif.] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3344833.
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Thesis (Ph. D.)--University of California, San Diego, 2009.Title from first page of PDF file (viewed Apr. 7, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 133-155).
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Bircher, Roland. "Studies of single-molecule magnets and spin clusters by inelastic neutron scattering and magnetic measurements /." Bern : [s.l.], 2005. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.
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Gelléri, Márton [Verfasser], Philippe I. [Akademischer Betreuer] Bastiaens, and Roland [Gutachter] Winter. "TIRF-anisotropy microscopy: homo-FRET and single molecule measurements / Márton Gelléri. Betreuer: Philippe I. Bastiaens. Gutachter: Roland Winter." Dortmund : Universitätsbibliothek Dortmund, 2013. http://d-nb.info/1104736411/34.
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Düselder, André [Verfasser], Christoph F. [Akademischer Betreuer] Schmidt, and Sarah [Akademischer Betreuer] Köster. "Single-molecule measurements of Kinesin motor proteins / André Düselder. Gutachter: Christoph F. Schmidt ; Sarah Köster. Betreuer: Christoph F. Schmidt." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2014. http://d-nb.info/1048469956/34.
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Teeling-Smith, Richelle Marie. "Single Molecule Electron Paramagnetic Resonance and Other Sensing and Imaging Applications with Nitrogen-Vacancy Nanodiamond." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1424779811.
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Kurz, Anton [Verfasser], and Dirk-Peter [Akademischer Betreuer] Herten. "Characterization and Application of Photon-Statistics in Single-Molecule Measurements for Quantitative Studies of Fluorescently Labeled Samples / Anton Kurz ; Betreuer: Dirk-Peter Herten." Heidelberg : Universitätsbibliothek Heidelberg, 2013. http://d-nb.info/1177247879/34.
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Sendler, Torsten. "Leitwertkontrolle einzelner elektrisch kontaktierter Moleküle." Doctoral thesis, Helmholtz-Zentrum Dresden-Rossendorf, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:d120-qucosa-184190.
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Die molekulare Elektronik setzt sich zum Ziel, passive und aktive Bausteine in integrierten Schaltkreisen auf molekularer Ebene zu realisieren. Dabei ist entscheidend, dass sich der elektrische Leitwert der molekularen Bauelemente hinreichend regulieren lässt. Um zu belegen, dass dies möglich ist, wird in dieser Dissertation die gezielte Leitwertkontrolle einzelner über Nanoelektroden kontaktierter Moleküle nachgewiesen. Die erzielten Ergebnisse ergänzen dabei nahtlos aktuellste Studien.
Zum einen werden kontaktierte molekulare Schalter durch Bestrahlung mit Licht einer bestimmten Wellenlänge in-situ von einem nicht-leitenden in einen leitenden Zustand geschaltet, wobei der Einfluss unterschiedlicher Seitengruppen für eine zusätzliche Modifikation des Leitwerts sorgt. Ausschlaggebend ist hierbei die elektronische Anbindung des Moleküls an die Elektroden. Zum anderen werden Molekül-Metall-Komplexe durch die Einbindung eines Übergangsmetallions von einem isolierenden in einen leitenden Zustand versetzt. In diesem Fall lässt sich der leitende Zustand durch die Wahl des Ions innerhalb einer Größenordnung variieren, was eine völlig neue Möglichkeit der Leitwertkontrolle in molekularen Bausteinen darstellt. Das Ion bestimmt dabei sowohl die mechanische Stabilität als auch die elektronische Struktur des Moleküls.
Für die Kontaktierung einzelner Moleküle kommt die Technik des mechanisch kontrollierten Bruchkontakts zum Einsatz. So lassen sich feine Goldnanoelektroden herstellen, an die Moleküle anbinden. Um eine präzise Analyse durchzuführen, werden über zwei unabhängige Messstrategien Informationen über das elektrische Transportverhalten sowie über die elektronische Struktur der Moleküle erworben.
In dieser Arbeit sind echte Neuentwicklungen auf dem Gebiet der molekularen Elektronik gelungen, die einen wesentlichen Beitrag für die Umsetzung integrierter molekularer Schaltkreise leisten.
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Gross, Linda C. M. "Applications of droplet interface bilayers : specific capacitance measurements and membrane protein corralling." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:0b7ffba6-b86d-499c-a93f-3b2fc46a427b.
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Droplet Interface Bilayers (DIBs) have a number of attributes that distinguish them from conventional artificial lipid bilayers. In particular, the ability to manipulate bilayers mechanically is explored in this thesis. Directed bilayer area changes are used to make precise measurements of the specific capacitance of DIBs and to control the two dimensional concentration of a membrane protein reconstituted in the bilayer. Chapter 1 provides a general introduction to the role of the lipid membrane en- vironment in the function of biological membranes and their integral proteins. An overview of model lipid bilayer systems is given. Chapter 2 introduces work carried out in this laboratory previously and illustrates the experimental setup of DIBs. Some important bilayer biophysical concepts are covered to provide the theoretical background to experiments in this and in later chapters. Results from the characterisation of DIBs are reported, and an account of the development of methods to manipulate the bilayer by mechanical means is given. Chapter 3 describes experiments that apply bilayer area manipulation in DIBs to achieve precise measurement of specific capacitance in a range of lipid systems. Chapter 4 reports results from experiments investigating the response of bilayer specific capacitance to an applied potential. Chapter 5 covers the background and experimental setup for total internal fluo- rescence microscopy experiments in DIBs and describes the expression, purification and characterisation of the bacterial β-barrel membrane protein pore α-Hemolysin. Chapter 6 describes experiments that apply the mechanical manipulation of bilayer area in DIBs to the corralling and control of the surface density of α-Hemolysin.
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Alwan, Monzer. "Etude experimentale de contacts métalliques et moléculaires ponctuels : de l'objet individuel aux statistiques." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM4106/document.
Full textAbstract:
Nous présentons un travail expérimental contribuant à l'étude de contacts ponctuels métalliques et moléculaires à l'aide de dispositifs de jonctions brisées développés dans notre équipe. Ces techniques de jonctions brisées, utilisables dans les conditions ambiantes, sont particulièrement adaptées à deux champs disciplinaires : l'électronique moléculaire et la nano mécanique.Nous avons étudié la durée de vie de contacts métalliques d'or, qui excède rarement la dizaine de millisecondes à température ambiante. Par le biais d'une analyse statistique de mesures de conductance, nous montrons que leur durée de vie est limitée par la contrainte mécanique appliquée à la jonction. Ces résultats nous ont permis de proposer un mécanisme de rupture, et de définir des conditions optimales pour la formation des contacts à température ambiante.Nous présentons ensuite une étude préliminaire de mesure de conductance d'une molécule unique, utilisant un dispositif à jonction brisée ainsi qu'un microscope à effet tunnel.Les résultats obtenus indiquent que, si la mesure de la conductance d'une molécule unique est possible, la stabilité observée est à considérer avant d'envisager des applicationsWe present here an experimental work which contributes to the study of metallic and molecular point contacts using broken junctions-based devices developed in our team. Under ambient environmental conditions, these techniques are particularly adapted to two disciplinary fields: molecular electronics and nano-mechanics.We have studied the lifetime of gold contacts, which rarely exceed ten milliseconds at room temperature.Through statistical analyses of conductance measurements, we show that this lifetime is limited by the mechanical strain applied to the junction. These results allowed us to propose a breaking mechanism, and to define optimal conditions for the formation of the contacts at room temperature. We present then a preliminary study of conductance measurements of a single molecule, using a broken junction device as well as a scanning tunneling microscope.The results indicate that, despite the conductance measure of a single molecule is possible the observed stability should be considered before envisaging applications
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Hemmig, Elisa Alina. "DNA origami structures for artificial light-harvesting and optical voltage sensing." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274005.
Full textAbstract:
In the past decade, DNA origami self-assembly has been widely applied for creating customised nanostructures with base-pair precision. In this technique, the unique chemical addressability of DNA can be harnessed to create programmable architectures, using components ranging from dye or protein molecules to metallic nanoparticles. In this thesis, we apply DNA nanotechnology for developing novel light-harvesting and optical voltage sensing nano-devices. We use the programmable positioning of dye molecules on a DNA origami plate as a mimic of a light-harvesting antenna complex required for photosynthesis. Such a structure allows us to systematically analyse optimal design concepts using different dye arrangements. Complementary to this, we use the resistive-pulse sensing technique in a range of electrolytes to characterise the mechanical responses of DNA origami structures to the electric field applied. Based on this knowledge, we assemble voltage responsive DNA origami structures labelled with a FRET pair. These undergo controlled structural changes upon application of an electric field that can be detected through a change in FRET efficiency. Such a DNA-based device could ultimately be used as a sensitive voltage sensor for live-cell imaging of transmembrane potentials.
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Tsai, Miao-Ling, and 蔡妙伶. "Molecular Junctions Stabilized Manually via Tactile Feedback for the Measurements of Single–Molecule Conductance." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/24919375857256461151.
Full textAbstract:
碩士國立臺灣大學
化學研究所
98
The ultimate goal of molecular electronics is the construction of electronic circuit devices from individual molecules and the electron transport through single molecules is crucial to molecular devices. The factors that influence electron transport depend not only on molecules themself but also the detail of molecule-electrode contacts. The latter is considered to be the least controllable aspect of experiments would cause conductance variability due to the contact geometry in molecular junctions. In the scanning tunneling microscopy break junction (STM BJ) method, continuous tip retraction would lead to contact conformation changes, we try to establish a stable contact between the molecule and metal probes and ensure that not the properties of an ensemble but a single molecule are been found. The results presented here is the studies of the single molecular conductance for the self-assembled monolayers (SAMs) of hexanedithiol and octanedithiol (SH-(CH2)n-HS, n=6 and 8) molecules onto Au electrodes by the conductive atomic force microscopy and the PicoAngler. By utilizing the PicoAngler with a force-feedback knob for manual control of the fixed tip-substrate spacing, which can stabilize the molecular junction, our method can not only construct the conductance histogram without the preselection process, but also receive the experimental results similar to the previous reports.
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Chang, Wei-Hsuan, and 張瑋軒. "Measurements of Single-Molecule Conductance by Conductive Atomic Force Microscopy with Tactile Feedback: the Effect of the Cantilever Force Constant." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/38430640100520236824.
Full textAbstract:
碩士國立臺灣大學
化學研究所
99
Abstract In the field of molecular electronics, c-AFM BJ (conductive atomic force microscopy break junction) is one of the methods employed to create molecular junctions of metal–molecule–metal configurations through which single-molecule conductance can be measured. Reported in this thesis work is, for the first time, the acquisition of single-molecule conductance can be correlated with the applied stretching force at the molecular junction by taking advantage of a tensile sensor integrated in the c-AFM. Alkanedithiols (HS(CH2)nSH, n = 6, 8, and 10) are the model compounds and the consistence of their conductance values with literature reports validates this methodology. We construct two-dimensional (2D) histograms from the conductance and force traces using three kinds of force constant of tip (k = 40, 0.3, 0.03 N/m). We have found that (1) The conductance is independent of stretching force at k = 40 N/m. (2) The distribution of conductance become narrow with increasing stretching force at k = 0.3, 0.03 N/m. (3) Multi sets of conductance values are found at k = 0.3, reflecting the reduction of thermal fluctuation by using smaller force constant of tip. A force feedback system, PicoAngler, for fixing tip-substrate spacing to monitor the conductance of single molecular junction with a long lifetime (≈ 450 s) that enables detailed nature of the conductance of single molecules to be gained. When the stretching force is small (0.2 (± 0.1) nN), multi sets of conductance in I-t and I-V curves are produced due to change of conformation in an alkylene chain and binding sites (bridge or the hollow site) of thiolates on gold. On the contract, when the stretching force is large (0.8 (± 0.1) nN), conductance is centralized, resulted from only elongated conformers and the atop binding site.
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"Measurements and Control of Charge Transport through Single DNA Molecules via STM Break Junction Technique." Doctoral diss., 2016. http://hdl.handle.net/2286/R.I.38368.
Full textAbstract:
abstract: Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base.
First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory.
Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations.
Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases.Dissertation/Thesis
Doctoral Dissertation Chemistry 2016
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Dell, Emma Jane. "Single Molecule Conductance of Oligothiophene Derivatives." Thesis, 2015. https://doi.org/10.7916/D8TX3D71.
Full textAbstract:
This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these advanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein.
First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes
in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction to sample similar conformers. This work demonstrates that the conductance of bithiophene displays a strong dependence on the confor- mational fluctuations accessible within a given junction configuration, and that the symmetry of such small molecules can significantly influence their conductance behavior.
Next, the single-molecule conductance of a family of oligothiophenes comprising one to six thiophene units was measured. An anomalous behavior was found: the peak of the conduc- tance histogram distribution did not follow a clear exponential decay with increasing number of thiophene units in the chain. The electronic properties of the materials were characterized by optical spectroscopy and electrochemistry to gain an understanding of the factors affecting the conductance of these molecules. Different conformers in the junction were postulated to be a contributing factor to the anomalous trend in the observed conductance as a function of molecule length.
Then, the electronic properties of the thiophene-1,1-dioxide unit were investigated. These motifs have become synthetically accessible in the last decade, due to Rozen's unprecedentedly potent oxidizing reagent - HOF·CH3CN - which has been shown to be powerful yet selective enough to oxidize thiophenes in various environments. The resulting thiophene-1,1-dioxides show great promise for electronic devices. The oxidation chemistry of thiophenes was expanded and tuning of the frontier energy levels was demonstrated through combining electron poor and electron rich units.
Finally, charge carriers in single-molecule junctions were shown to be tunable within a family
of molecules containing these thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed in order to increase electron affinity, maintain delocalized frontier orbitals, while significantly decreasing the transport gap. Through thermopower measurements, the dominant charge carriers were shown to change from holes to electrons as the number of TDO units was increased. This resulted in a unique system in which the charge carrier depends on backbone length, providing a new means to tune p- and n-type transport in organic materials.
Taken together, the results presented in this thesis offer an insight into how molecular symme- try and the accessible conformers within a junction have important consequences on conductance behavior. Additionally, thiophene-1,1-dioxide is shown to be an exciting unit for single molecule devices, especially when combined with electron rich thiophene flanking groups. By demon- strating, for the first time, a change in conductance pathway with molecular length, this work provides a framework for using frontier orbital levels to strategically design electronic building blocks.
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Kamenetska, Maria. "Single Molecule Junction Conductance and Binding Geometry." Thesis, 2012. https://doi.org/10.7916/D82N587J.
Full textAbstract:
This Thesis addresses the fundamental problem of controlling transport through a metal-organic interface by studying electronic and mechanical properties of single organic molecule-metal junctions. Using a Scanning Tunneling Microscope (STM) we image, probe energy-level alignment and perform STM-based break junction (BJ) measurements on molecules bound to a gold surface. Using Scanning Tunneling Microscope-based break-junction (STM-BJ) techniques, we explore the effect of binding geometry on single-molecule conductance by varying the structure of the molecules, metal-molecule binding chemistry and by applying sub-nanometer manipulation control to the junction. These experiments are performed both in ambient conditions and in ultra high vacuum (UHV) at cryogenic temperatures. First, using STM imaging and scanning tunneling spectroscopy (STS) measurements we explore binding configurations and electronic properties of an amine-terminated benzene derivative on gold. We find that details of metal-molecule binding affect energy-level alignment at the interface. Next, using the STM-BJ technique, we form and rupture metal-molecule-metal junctions ~104 times to obtain conductance-vs-extension curves and extract most likely conductance values for each molecule. With these measurements, we demonstrated that the control of junction conductance is possible through a choice of metal-molecule binding chemistry and sub-nanometer positioning. First, we show that molecules terminated with amines, sulfides and phosphines bind selectively on gold and therefore demonstrate constant conductance levels even as the junction is elongated and the metal-molecule attachment point is modified. Such well-defined conductance is also obtained with paracyclophane molecules which bind to gold directly through the ð system. Next, we are able to create metal-molecule-metal junctions with more than one reproducible conductance signatures that can be accessed by changing junction geometry. In the case of pyridine-linked molecules, conductance can be reliably switched between two distinct conductance states using sub-nanometer mechanical manipulation. Using a methyl sulfide linker attached to an oligoene backbone, we are able to create a 3-nm-long molecular potentiometer, whose resistance can be tuned exponentially with Angstom-scale modulations in metal-molecule configuration. These experiments points to a new paradigm for attaining reproducible electrical characteristics of metal-organic devices which involves controlling linker-metal chemistry rather than fabricating identically structured metal-molecule interfaces. By choosing a linker group which is either insensitive to or responds reproducibly to changes in metal-molecule configuration, one can design single molecule devices with functionality more complex than a simple resistor. These ambient temperature experiments were combined with UHV conductance measurements performed in a commercial STM on amine-terminated benzene derivatives which conduct through a non-resonant tunneling mechanism, at temperatures varying from 5 to 300 Kelvin. Our results indicate that while amine-gold binding remains selective irrespective of environment, conductance is not temperature independent, in contrast to what is expected for a tunneling mechanism. Furthermore, using temperature-dependent measurements in ambient conditions we find that HOMO-conducting amines and LUMO-conducting pyridines show opposite dependence of conductance on temperature. These results indicate that energy-level alignment between the molecule and the electrodes changes as a result of varying electrode structure at different temperatures. We find that temperature can serve as a knob with which to tune transport properties of single molecule-metal junctions.
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Frei, Michael. "Force and Conductance Spectroscopy of Single Molecule Junctions." Thesis, 2012. https://doi.org/10.7916/D8H70NS8.
Full textAbstract:
Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.
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Kocun, Marta. "Single molecule force measurements of chitosan." Thesis, 2007. http://spectrum.library.concordia.ca/975687/1/MR40858.pdf.
Full textAbstract:
Chitosan, a glucosamine polysaccharide derived form chitin, was studied by AFM-based single molecule force spectroscopy. The goal of this study was to investigate chitosan's adhesive properties to various surfaces ( i.e. mica, glass, quartz, polytetrafluoroethylene and self-assembled monolayers) as well as obtaining its mechanical constants. The results obtained were in the form of force-extension curves and mathematical fits. Well-defined features, characteristic of single molecule adhesion and stretching, such as constant force plateaus and peaks, were observed in the force curves. The lengths of the constant force plateaus obtained are consistent with the lengths of chitosan strands observed in high resolution AFM images. The energy of desorption of single glucosamine residues from various surfaces was calculated. The values obtained were: 1.8 x 10 -20 J/glucosamine residue on self-assembled monolayers of mercaptoundecanoic acid:dodecanethiol (1:1000), 2.0 x 10 -20 J/glucosamine residue on quartz, 3.5 x 10 -20 J/glucosamine residue on polytetrafluoroethylene and 3.9 x 10 -20 J/glucosamine residue on self-assembled monolayers of dithiobis(succinimidyl undecanoate). The Kuhn length of chitosan (DDA 92%) was calculated, using the freely jointed chain model, to be 2.1 ± 0.9 nm which corresponds to a stiffness of approximately 4 glucosamine residues. These single molecule level results could be applied towards the preparation of novel, chitosan-based biomaterials.
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Kim, Nathaniel T. "Single Molecule Conductance and Junction Breakdown of Strained Cyclic Disilanes." Thesis, 2016. https://doi.org/10.7916/D8BR8SP7.
Full textAbstract:
A long-standing research interest of the Leighton group has been the utilization of strained silanes in the rapid and efficient synthesis of polyketides. Recently, we have been interested in how the effects of strain might manifest itself in the conductance and functionality of silicon-based molecular junctions. As electronic components continue to miniaturize to the point where transistor size and structure begin to resemble small molecules, understanding the principles that guide charge transport in single molecule junctions will be crucial. Herein, we describe our studies on a series of single molecule junctions formed by strained silicon wires. We demonstrate that high conductance pathways are accessed for the cis diastereomers of conformationally locked 1,2-disilaacenaphthenes via a bipodal binding motif which provides a stable electrical contact between the Si—Si bond and the gold electrodes. We then elucidate the mechanism of voltage-induced breakdown in silicon-based single molecule junctions. We show that the naphthalene bridge provides a parallel conductance pathway to the silicon backbone, altering bond rupture behavior of the Si—Si bond. We further investigate the bond rupture mechanism through DFT and molecular dynamics calculations and conclude that breakdown occurs by the excitation of vibrational modes in the molecular junction by tunneling electrons, leading to homolytic Si—Si bond rupture.
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Pan, Xiaoyun. "Single molecule conductance of biological building blocks purines and imidazole." Thesis, 2019. https://hdl.handle.net/2144/36040.
Full textAbstract:
In the last decade, biological molecules such as Deoxyribonucleic acid (DNA) and some proteins have attracted attention as material candidates for molecular electronics applications. Yet, despite numerous studies of electron transport in DNA in particular, inconsistencies in experimental results persist. As a result, both the degree and mechanism of charge transport in these biological molecules remain disputed. To understand if different binding configurations of DNA on metal electrodes through unexpected moieties could be responsible for experimental inconsistencies in the literature, we investigate whether small molecules ubiquitous in both nucleic acids and amino acids, such as purines and imidazole, bind to gold electrodes and produce conductance signature. In this study, we use the Scanning Probe Microscope-based Break Junctions approach method to study single molecule conductance and binding geometry of the purine bases of DNA, particularly adenine and guanine. In addition, the Conductive Atomic Force Microscope-based Break Junction (CAFMBJ) platform has been created to simultaneously measure both electrical and mechanical properties of these single molecule junctions. Our measurements indicate that purines bind in the junction and display several robust conductance signatures on gold. We find that both purine and adenine bind through the imidazole, which is identified, for the first time, as a new linker group for single molecule conductance measurements.
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Düselder, André. "Single-molecule measurements of Kinesin motor proteins." Doctoral thesis, 2013. http://hdl.handle.net/11858/00-1735-0000-0022-5E5D-1.
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Kao, Jing-Yao, and 高靖堯. "Thermal conductance and thermoelectric figure of merit of Single-Molecule junctions." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/78u2c4.
Full textAbstract:
碩士國立交通大學
電子物理系所
104
We investigate the phonon’s thermal current in nanoscale junctions using classical nonequilibrium molecular dynamics simulations(NEMD). The quantum mechanical corrections due to Bose-Einstein distributions are also considered in low-temperature regime.We calculate the thermal conductance of single-molecule junctions connecting to two temperature reservoirs. We systematically investigate the dependence of thermal conductance on lengths and strain in nanowires in a wide range of temperatures. We also investigate its electronic transport properties in the framework of parameter-free density functional theory combined with the Lippmann-Schwinger formalism in scattering approach.We observe that the thermal conductance is proportional to temperature in the low-temperature regime, while the dependence of thermal conductivity on temperature is relatively weak in the high-temperature regime. In atomic junctions, the thermal conductance increases with the increasing compressive stress, and tensile stress can result in a cone shape structure which decrease the magnitudes of thermal. Differently, the thermal conductance only decrease with compressive stress in the molecular junction.In metal nanowire, electronic thermal conductance dominate the total thermal conductance and conversely, the phonon transport dominates the contribution to the thermal conductance in molecular junctions. In addition, we investigate the phonon’s thermal conductance using week-link model in the low-temperature regime and NEMD simulation in the high-temperature regime. We observe that the value of ZT reveals the power law behavior that falls into four phases, ZT∝T^x,x=2,0,2.26,3.
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Ting, Ta-Cheng, and 丁大成. "Tuning the Single-molecule Conductance of Metal String Complexes by Electrochemical Gating." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/39214636188149388162.
Full textAbstract:
碩士國立臺灣大學
物理研究所
103
The single-molecule conductance is affected by the electron transport through the electrode–molecule–electrode junctions. One of the most important factors is the energy-level difference between the electrode Fermi level and the frontier molecular orbitals. This energy difference can be controlled by electrochemical gating, which means pushing the potential of the working electrode toward the redox potential of the molecule. The compounds here are extended metal-atom chains (EMACs), which have well-defined one-electron oxidation reactions, to study the effect of energy-level alignment on the single-molecule conductance. For the scans of electrochemical potential, the single-molecule conductance is measured at a fixed bias and monitored as a function of electrochemical potential. On the other hand, single-molecule i–V curves are obtained at fixed electrochemical potentials. Transition voltages derived from the corresponding Fowler-Nordheim plots are well correlated with the energy barrier heights. Larger conductance and smaller energy barrier heights were found when electrochemical potential was just about the redox potential, indicating the effect of energy-level alignment.
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"Electronic Single Molecule Measurements with the Scanning Tunneling Microscope." Doctoral diss., 2016. http://hdl.handle.net/2286/R.I.38718.
Full textAbstract:
abstract: Richard Feynman said “There’s plenty of room at the bottom”. This inspired the techniques to improve the single molecule measurements. Since the first single molecule study was in 1961, it has been developed in various field and evolved into powerful tools to understand chemical and biological property of molecules. This thesis demonstrates electronic single molecule measurement with Scanning Tunneling Microscopy (STM) and two of applications of STM; Break Junction (BJ) and Recognition Tunneling (RT). First, the two series of carotenoid molecules with four different substituents were investigated to show how substituents relate to the conductance and molecular structure. The measured conductance by STM-BJ shows that Nitrogen induces molecular twist of phenyl distal substituents and conductivity increasing rather than Carbon. Also, the conductivity is adjustable by replacing the sort of residues at phenyl substituents. Next, amino acids and peptides were identified through STM-RT. The distribution of the intuitive features (such as amplitude or width) are mostly overlapped and gives only a little bit higher separation probability than random separation. By generating some features in frequency and cepstrum domain, the classification accuracy was dramatically increased. Because of large data size and many features, supporting vector machine (machine learning algorithm for big data) was used to identify the analyte from a data pool of all analytes RT data. The STM-RT opens a possibility of molecular sequencing in single molecule level. Similarly, carbohydrates were studied by STM-RT. Carbohydrates are difficult to read the sequence, due to their huge number of possible isomeric configurations. This study shows that STM-RT can identify not only isomers of mono-saccharides and disaccharides, but also various mono-saccharides from a data pool of eleven analytes. In addition, the binding affinity between recognition molecule and analyte was investigated by comparing with surface plasmon resonance. In present, the RT technique is applying to chip type sequencing device onto solid-state nanopore to read out glycosaminoglycans which is ubiquitous to all mammalian cells and controls biological activities.Dissertation/Thesis
Doctoral Dissertation Physics 2016
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Benesch, Claudia [Verfasser]. "Charge transport in single molecule junctions : vibronic effects and conductance switching / Claudia Benesch." 2008. http://d-nb.info/988165627/34.
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Huang, Min-Jie, and 黃敏傑. "Single-Molecule Conductance of Heteropentanuclear Metal String Complexes: Electronic Coupling at Molecule-Electrode Contact and Negative Differential Resistance Behavior." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/91380980853210217452.
Full textAbstract:
博士國立臺灣大學
化學研究所
101
The development of ideal molecule−electrode contacts and the design of functional molecular wires are critical for the realization of molecular electronics. The good molecule−electrode contacts exhibit efficient charge transportation and thus confer large single-molecule conductance. To derive the intrinsic properties of the MMM contact, the conductance of a series of alkanes terminated with–SH, –NCS, and –CN on Au, Pd and Pt were carried out by using the method of STM-bj. The results show the single-molecule conductance via Pt contact is 2~5-fold superior to those via Au contact. Among the three headgroups, –SH bears the largest contact conductance and –CN is smallest. Such disparity in their conductance can be ascribed to the degree of the headgroup–electrode coupling. Simulated bond angles and Mayer bond order at the contact suggest that π characters are significantly involved at Pt and Pd contacts, while σ characters is preferably adopted at Au contacts. These findings demonstrate that the electronic coupling at the contact plays an important factor on contact conductance and on the measured single-molecule conductance. Moreover, we purpose that the resistance of molecular backbone can be extracted via Landauer formula. The resistance values for the same framework are found to be independent of teminal headgroup and electrode material, manifesting that this approach can evaluate quantitatively the resistance of functional moieties from the measured value. To tune electric conductance of extended metal atom chains, the first pentametal EMAC (extended metal-atom chain) of heteronuclear backbone was synthesized by mixing a weakly coupled nickel-atom chain with an Ru2 unit, which has strong metal-metal interactions. The resulted Ni‒Ru‒Ru‒Ni‒Ni is 4-fold more conductive than that of its pentanickel analogue. DFT/UB3LYP analysis shows that the incorporation of the Ru2 unit enhances metal-metal interaction and thus results in the conductance superior to that of pentanickel EMAC. Single-molecule I-V characteristic of NiRu2Ni2(tpda)4(NCS)2 exhibits NDR (negative differential resistance) behavior, unobserved for pentanickel or pentaruthenium complexes. A plausible explanation is derived based on the simulation of energy level and the correlation of the NDR peak positions with the EFermi of Au, Pd, and Pt. The energy levels contributed by the Ru2 moiety make the frontier orbitals discrete such that the molecular conductance decreases upon ramping the electrode EFermi from where aligned with the MOs to nonresonant regimes. Thus, the discrete levels near HOMO are accounted for NDR phenomena.
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Chang, Wei-Cheng, and 張惟程. "Syntheses and Studies of Nonhelical Trinuclear (Mo2/M)Heterometallic String Complexes with High Single-Molecule Conductance." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/5k77gc.
Full textAbstract:
博士國立臺灣大學
化學研究所
106
The concept of single-molecule electronics has attracted the interest of many scientists across various disciplines on the platform of nanotechnology. Among these molecular systems, molecules featuring chains of transition-metal atoms are of great interest for their potential applications in molecular electronic devices, because these complexes resemble macroscopic metal wires in a miniature form at the atomic scale. The development of heteronuclear metal string complexes (HMSCs) provides an ideal system for the investigation of the nature of heterometallic electronic effects and molecular electronic applications. Here we report the synthesis and characterization of three HMSCs with planar 1,8-naphthyridin-2(1H)-one (Hnpo) ligand-stabilized tri-metal cores. The frameworks of these HMSCs 1-13, Mo2M(npo)4X2, M= Mn, Fe, Co, Ni, Cu, Zn, X = Cl, NCS were determined to be nonsymmetric by X-ray diffraction, in spite of disordered metal centers. These HMSCs are isostructural (2,2)-trans structure. Unlike those supported by dpa–, these npo-based HMSCs are not helical. A smaller dihedral angle of ∠N-Mo-Mo-N is envisaged to be more favourable for inter-molybdenum dx2-y2 interactions, leading to a larger Mo–Mo bond order. Measurements of the magnetic properties were carried out on a SQUID magnetometer. The members of this new series of HMSCs are paramagnetic due to the terminal 3d-metal ions. The conductance of the complexes was studied by the method of STM-BJ (scanning tunnelling microscopy-based break junction) in which the molecular junctions of electrode-molecule-electrode configurations were generated by breaking the fused tip-substrate contact. The conductance of metal strings was found correlated strongly with metal-metal interactions or bond orders. HMSCs 4, 6 and 8 exhibit higher conductance than homometallic predecessors like [Ni3(dpa)4(NCS)2] and [Cr3(dpa)4(NCS)2]. The increase can be attributed to the Mo Mo quadruple bond of these complexes. The transformation of MoMoFe to MoMoNi and MoMoCo heteronuclear complexes can be achieved by direct metal replacement. The metal substitution method improves not only the purity but also the yield. In addition to the high electric conductance for the potential applications as molecular wires, these new HMSCs are the first series of non-helical metal strings in which the ligands are co-planar with the metal-atom chain. In the second part, we also successfully synthesized triruthenium metal string, [Ru3(npo)4Cl2][PF6] (22) and [Ru3(npo)4(NCS)2] (23) supported by Hnpo ligands. X-ray single crystal analysis shows that compound 22 and 23 exhibits a nonlinear [Ru3]7+ and [Ru3]6+ backbone (∠= 172.72° and ∠=170.62°) with Ru–Ru bond lengths (2.324 and 2.303 Å). We propose compound 22 is paramagnetic species and compound 23 is diamagnetic species.
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Ko, Chih-Hung, and 柯志宏. "Superior Contact for Single-Molecule Conductance: Electronic Coupling of Thiolate and Isothiocyanate on Pt, Pd, and Au." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/72957989893864861031.
Full textAbstract:
碩士國立臺灣大學
化學研究所
97
One of the critical issues for molecular electronics is the development of optimal molecule-electrode contacts which have long been expected to substantially influence the measured single-molecule conductance. However, other than gold, systematic studies of a homologous series of molecules to extract the headgroup-metal barrier have not been reported. This thesis work scrutinizes the effect of electrode materials on single-molecule conductance by examining alkanedithiols anchored onto Au and Pt electrodes as well as alkanediisothiocyanates on Au, Pd, and Pt. STM-BJ (scanning tunneling microscopy break junction) was employed to create thousands of molecular junctions and to obtain single-molecule conductance. The results show that all molecule-electrode combination exhibits high- and low-conductance datasets (HC and LC). Compared to the contact resistance measured using Au electrodes, alkanediisothiocyanates are about 20% ~ 60% less resistive on Pd and Pt and alkanedithiols are about 50% less resistive on Pt. The difference is ascribed to their Fermi energies and the pi characters of the atoms at the contact. The dependence of single-molecule conductance on the electrode materials is also true for a linear trimetal complex, [Ni3(dpa)4(NCS)2] (dpa = 2,2''-dipyridylamide), suggesting the generality of the findings for both saturated and highly conductive molecular wires. For alkanediisothiocyanates, the probability of acquiring staircase-like traces among all i-s traces increases from 27% on Au to 37-42% on Pd or Pt electrodes. Using density functional theory (DFT), adsorption energies on three-fold hollow site and ontop site are in agreement with probabilities of HC and LC. Calculations of transmission function and comformation of headgroup-metal interface are also carried out to facilitate the rationalization using HOMO-LUMO gap and electronic coupling at the contact.
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Tsai, Feng-Jen, and 蔡豐任. "Single-Molecule Conductance of Rh and Ni Heterometallic String Complexes in Mixed Solvents of Dichloromethane and 1,2,4-Trichlorobenzene." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/27324345896886006881.
Full textAbstract:
碩士國立臺灣大學
化學研究所
101
Metal string complexes (MSCs), in which the metal centers are co-linear and stably coordinated by four oligopyridylamido ligands, have been demonstrated a unique category of conductive molecular wires. Bond orders which describe the strength of metal-metal interactions are qualitatively well correlated with the single-molecule conductance of the MSCs. Previous examples are limited to homometallic string complexes in which the metal centers are composed of the same element. Explored in this thesis work are the conductive properties of heterometallic string complexes (HMSCs). Specifically, the sequences of the metal cores are RhRhNi, NiRhNi, RhRhNiNiNi, and RhRhRhNiNi. Also examined are Ni3 and Ni5 MSCs. Methods of compound purification and crystallization are improved. The experimental protocols and data analysis are also modified. The conductance measurements are carried out through electrode-molecule-electrode junctions created by an STM (scanning tunneling microscope) tip which repeatedly impinges into and retracts from the substrate. In this study, the tip-substrate contact is ensured by an external device, while it was not monitored in our earlier work. The conductance histograms are prepared by pooling all acquired conductance traces while, in the past, only those with step-like features were selectively used. The results show that the conductance histograms are featureless and that it is very difficult to determine the conductance values for pentametallic string complexes, even for Ni5 MSC. X-ray crystallographic data reveal that solvent molecules, present in the unit cell by previous purification methods, are absent for the new samples. Accordingly, mixed solvents exhibiting a range of polarity are utilized to improve the solubility of MSCs. The conductance peaks are slightly more pronounced in a more polar environment. The conductance peaks of Ni3, Ni5, and NiRhNi are solvent-independent, while the peak positions of asymmetric RhRhNi, RhRhNiNiNi, and RhRhRhNiNi shift associated with the solvent utilized. According to published researches in the effect of environment on molecular junction, we proposed that solvent molecules will affect the head group and alter gold-sulfur contact.
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傅明棟. "Studies of Single-Molecule Conductance: Headgroup-Electrode Contact and Negative Differential Resistance Behavior of [Ru2Ni3(tpda)4(NCS)2] Complex." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/93106096588913094967.
Full textAbstract:
博士國立清華大學
化學系
98
The realization of molecular electronics requires comprehension of single molecular I-V characteristics. Aside from the electron transporting properties of the molecular framework, the molecule-electrode binding contributes significantly to the contact resistance, Rn=0, and thus to the values of single-molecule resistance. Isothiocyanate (–NCS) and cyanate (–CN), versatile ligands for EMACs (Extended Metal-Atom Chains), can bind onto metal substrate to complete a metal-molecule-metal configuration for the external measurements. To isolate the contact effect of contact between headgroup and electrode from other factors, alkanediisothiocyanates and alkanedicyanates are studied because the large HOMO-LUMO gap of alkyl chains is not sensitive to the number of methylene units. The conductance at the single molecular level has long been expected to be matched strongly with the Fermi level of metal electrodes. Another factor to affect the electron transporting characteristic of EMACs is varying the metel center. By incorporating a diruthenium moiety into a string of nickel cores, the heteropentanuclear Ni-Ru-Ru-Ni-Ni EMAC has a single-molecule conductance of 6.3 ± 1.0 MΩ, 4-fold superior to that of the pentanickel analogue (23.3 ± 4.1 MΩ) at the ohmic region and results in NDR characteristics, unobserved for its analogues of pentanickel or pentaruthenium EMACs. The diruthenium unit is accounted for discrete HOMO levels that lead to the NDR behavior as a result of the energy alignment with the electrode Fermi. From the Landauer equation, we only focused on the resistance of molecular without the contact. The resistance of trinickel EMAC is 330 kΩ, one order less than hexamethylene.
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Janovjak, Harald [Verfasser]. "Exploring the mechanical stability and visco-elasticity of membrane proteins by single-molecule force measurements / vorgelegt von Harald Janovjak." 2005. http://d-nb.info/978344677/34.
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Sapra, K. Tanuj [Verfasser]. "Single molecule measurements of complex molecular interactions in membrane proteins using atomic force microscopy / vorgelegt von K. Tanuj Sapra." 2007. http://d-nb.info/983900051/34.
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Nejedlý, Jindřich. "Syntéza π-elektronových systémů vhodných pro přenos a retenci náboje." Doctoral thesis, 2021. http://www.nusl.cz/ntk/nusl-437757.
Full textAbstract:
The aim of my Thesis was to develop a general synthetic methodology for the preparation of long helicenes equipped with suitable functional groups that control their solubility or serve as anchoring groups for attachment to metallic surfaces, especially gold. The well-established transition metal catalyzed [2+2+2] cyclotrimerization of triynes was selected as the key scaffold-forming transformation in the synthesis of long helicenes because of its high regioselectivity, atom efficiency, functional group tolerance and general robustness. A modular approach was used for the preparation of the starting oligoynes, thus enabling a high level of their structural diversity. Individual resorcinol- based aromatic building blocks were interconnected by Sonogashira cross-coupling reactions, providing complex cyclization precursors encompassing up to twelve alkyne units pre-arranged for the multiple [2+2+2] cycloisomerization to produce three six- membered rings from each set of three neighboring alkyne units. Thus, a small series of long helicenes with up to 19 rings constituting the helical scaffold was synthesized. The quadruple cyclization leading to the longest oxahelicene prepared to date was performed in a high-temperature-high-pressure flow reactor at 250 řC in the presence of CpCo(CO)2. The set of...