Single-molecule mechanics of protein-labelled DNA handles

• Vivek S. Jadhav,
• Dorothea Brüggemann,
• Florian Wruck and
• Martin Hegner

Beilstein J. Nanotechnol. 2016, 7, 138–148, doi:10.3762/bjnano.7.16

• .7.16 Abstract DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical

• here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition in time-critical molecular motor studies. Keywords: DNA handles; optical tweezers; protein labels; single molecule

• interactions impeded the study of single molecule mechanics. Ideal experimental conditions with protein–DNA handles allowing for single hook-up experiments were then found with 40:1 handle-to-bead coupling ratio (bead diameter 2.9 µm). For smaller beads (0.84 µm diam.) the optimal ratio of PDHs coupling to

Single-molecule magnet behavior in 2,2’-bipyrimidine-bridged dilanthanide complexes

• Wen Yu,
• Frank Schramm,
• Eufemio Moreno Pineda,
• Yanhua Lan,
• Olaf Fuhr,
• Jinjie Chen,
• Hironari Isshiki,
• Wolfgang Wernsdorfer,
• Wulf Wulfhekel and
• Mario Ruben

Beilstein J. Nanotechnol. 2016, 7, 126–137, doi:10.3762/bjnano.7.15

• complexes have been studied comprehensively. The dynamic magnetic behavior of the Dy(III) and Er(III) compounds clearly exhibits single molecule magnet (SMM) characteristics with an energy barrier of 97 and 25 K, respectively. Moreover, micro-SQUID measurements on single crystals confirm their SMM behavior

• ligand field of the metal complex, which is typically of a few nm in dimensions. It is proposed that the ultimate size limits of modern electronics and information processing can be tackled by such device geometry [1][2][3]. Research on compounds with single-molecule magnet (SMM) characteristics

• was measured using AC, DC and micro-SQUID magnetometry techniques. The homo-dinuclear complexes of Dy(III) and Er(III) show single-molecule magnet behavior featuring hysteresis loops. The [Tb(tmhd)3]2bpm was sublimated on Au(111) surfaces and scanning tunneling microscopy results are presented in this

Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore

• Yun Ding and
• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 91–101, doi:10.3762/bjnano.7.11

• such as the α-HL, a modified version of the Mycobacterium smegmatis porin A (MspA), and the Ph29 connector channel have been investigated as single molecule sensing devices for ssDNA, RNA, dsDNA, and proteins [12][13][14]. The advantage of the natural pores is that they are well defined and highly

• information by EM imaging [43][44][45]. The more recent advancement of nanopores as single molecule detection devices and the corresponding progress in manufacturing, parallelization, and commercialization of such platforms [24], supported the idea of testing osmylated DNA as a surrogate for nanopore-based

• plots with R2 exhibit, at least, two populations consistent with other mechanisms operating besides single molecule translocation. pGEX3’-A25 R2 exhibits a third population (not shown) at times longer than 1 s. In all cases the A25-tail facilitates translocation and more so when it is at the 3’-end

Effects of electronic coupling and electrostatic potential on charge transport in carbon-based molecular electronic junctions

• Richard L. McCreery

Beilstein J. Nanotechnol. 2016, 7, 32–46, doi:10.3762/bjnano.7.4

• relevance of electronic coupling in Au/molecule/Au single molecule junctions by calculating 4t2 for the frontier Au orbitals in the contacts, as modulated by the intervening molecular “bridge” [8]. Changing the substituents on the diamine “bridge” varied the junction conductance, and the theoretical 4t2

Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy

• Riccardo Frisenda,
• Mickael L. Perrin and
• Herre S. J. van der Zant

Beilstein J. Nanotechnol. 2015, 6, 2477–2484, doi:10.3762/bjnano.6.257

• Riccardo Frisenda Mickael L. Perrin Herre S. J. van der Zant Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, Netherlands 10.3762/bjnano.6.257 Abstract We study single-molecule oligo(phenylene ethynylene)dithiol junctions by means of inelastic electron

• electrodes when describing inelastic contributions to transport through single-molecule junctions. Keywords: current–voltage characteristics; DFT calculations; mechanically controllable break junction (MCBJ); molecule–electrode interaction; vibrational modes; Introduction Vibrational degrees of freedom in

• processes occurring at the single-molecule level are dramatically influenced by the environment. Therefore, to understand the role of vibrations, experiments that can study the properties at the single-molecule level are very suited [8], as they do not suffer from collective effects and ensemble averaging

High electronic couplings of single mesitylene molecular junctions

• Yuki Komoto,
• Shintaro Fujii,
• Tomoaki Nishino and
• Manabu Kiguchi

Beilstein J. Nanotechnol. 2015, 6, 2431–2437, doi:10.3762/bjnano.6.251

• electronics on the single molecular scale [1], much efforts have been devoted to understand charge transport in a single molecular junction, in which a single molecule is wired to two metal electrodes. In recent years single molecular junctions with electronic functionalities such as diodes [2][3][4][5][6][7

• electronics. To bind a single molecule to metal electrodes, anchoring groups such as –SH [14] and –NH2 or (R)3–N [15][16] have been used. Such anchoring groups form strong chemical bonds with metal electrodes and the anchoring regions act as resistive space, leading to low electronic conductances of the

Sub-monolayer film growth of a volatile lanthanide complex on metallic surfaces

• Hironari Isshiki,
• Jinjie Chen,
• Kevin Edelmann and
• Wulf Wulfhekel

Beilstein J. Nanotechnol. 2015, 6, 2412–2416, doi:10.3762/bjnano.6.248

• metal-organic molecules with magnetic-ion cores exhibit long spin-relaxation times for the reversal of the localized magnetic moment at low temperatures. These molecules are called single-molecule magnets (SMMs), because the magnetic properties are attributed to the individual single molecules as a

Surface-enhanced Raman scattering by colloidal CdSe nanocrystal submonolayers fabricated by the Langmuir–Blodgett technique

• Alexander G. Milekhin,
• Larisa L. Sveshnikova,
• Tatyana A. Duda,
• Ekaterina E. Rodyakina,
• Volodymyr M. Dzhagan,
• Ovidiu D. Gordan,
• Sergey L. Veber,
• Cameliu Himcinschi,
• Alexander V. Latyshev and
• Dietrich R. T. Zahn

Beilstein J. Nanotechnol. 2015, 6, 2388–2395, doi:10.3762/bjnano.6.245

• substances [2][3][4][5][6][7] down to a single molecule [8][9]. The primary benefit of SERS is that the intensity of Raman scattering by vibrational modes in molecules is drastically increased (typically by a factor of 105–106) when the molecules are placed in the proximity of noble metal nanoclusters or on

Negative differential electrical resistance of a rotational organic nanomotor

• Hatef Sadeghi,
• Sara Sangtarash,
• Qusiy Al-Galiby,
• Rachel Sparks,
• Steven Bailey and
• Colin J. Lambert

Beilstein J. Nanotechnol. 2015, 6, 2332–2337, doi:10.3762/bjnano.6.240

• is potentially of interest for molecular-scale electronic applications such as single-molecule Gunn oscillators. The device studied in this paper utilises C60 terminal groups attached to gold electrodes. These groups reduce the overall magnitude of the current, and therefore, for the future, it would

Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules

• Philipp Leinen,
• Matthew F. B. Green,
• Taner Esat,
• Christian Wagner,
• F. Stefan Tautz and
• Ruslan Temirov

Beilstein J. Nanotechnol. 2015, 6, 2148–2153, doi:10.3762/bjnano.6.220

• .6.220 Abstract Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM) is the only technique that facilitates direct imaging and manipulations of nanometer-sized

• (PTCDA); scanning probe microscopy (SPM); scanning tunnelling microscopy (STM); single-molecule manipulation; virtual reality interface; Introduction The recently introduced scanning probe microscopy (SPM) technique of hand controlled manipulation (HCM) allows the operator of the SPM to manipulate

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

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

Beilstein J. Nanotechnol. 2015, 6, 2088–2095, doi:10.3762/bjnano.6.213

• 10.3762/bjnano.6.213 Abstract Mechanical methods for single-molecule control have potential for wide application in nanodevices and machines. Here we demonstrate the operation of a single-molecule switch made functional by the motion of a phenyl ring, analogous to the lever in a conventional toggle switch

• accessibility, we propose that phenyl rings are promising components in mechanical molecular devices. Keywords: density functional theory; phenyl rings; quantum transport simulations; scanning tunneling microscopy; single-molecule switches; Introduction Atomic-scale switches are key device components in

Electrospray deposition of organic molecules on bulk insulator surfaces

• Antoine Hinaut,
• Rémy Pawlak,
• Ernst Meyer and
• Thilo Glatzel

Beilstein J. Nanotechnol. 2015, 6, 1927–1934, doi:10.3762/bjnano.6.195

• observed object size fits with a single molecule. The molecule lay flat at the surface and binds through the 3-cyanophenyl groups to the KBr(001) substrate [29][31] indicated by the two symmetric protrusions. The two elongated features are attributable to the four 3,5-di(tert-butyl)phenyl moieties of the

• surfaces. This leads to the possibility to access molecular electronic properties at the single molecule level with scanning probe microscopy. We first demonstrated that solvent deposition from ESI has a weak influence on the KBr(001) surface. Then a complex molecule based on a triply fused diporphyrin was

• characterized theses islands showing molecular assemblies stabilized by π–π stacking organization and anchoring through the cyano group of the molecules and K+ ions of the surface. To achieve single molecule deposition, we added a pumping chamber in the setup that lowered the number of molecules reaching the

Large-voltage behavior of charge transport characteristics in nanosystems with weak electron–vibration coupling

• Tomáš Novotný and
• Wolfgang Belzig

Beilstein J. Nanotechnol. 2015, 6, 1853–1859, doi:10.3762/bjnano.6.188

• applied successfully to single-molecule junctions and provides directly their vibrational frequencies from the position of IETS signals [4][7] and, indirectly from the IETS features such as heights of the peaks, also information about electronic and structural properties [8][9]. Theoretical modeling of

Conductance through single biphenyl molecules: symmetric and asymmetric coupling to electrodes

• Karthiga Kanthasamy and
• Herbert Pfnür

Beilstein J. Nanotechnol. 2015, 6, 1690–1697, doi:10.3762/bjnano.6.171

• through the molecule is still far from being complete, although significant progress has been made [4][5][6]. The main reasons are the complexity of the metal–molecule–metal junctions and their control on the atomic level. Even in the simplest case with a single molecule and well defined atomic contacts

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

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

Beilstein J. Nanotechnol. 2015, 6, 1558–1567, doi:10.3762/bjnano.6.159

• theory combined with non-equlibrium Green’s function calculations help in elucidating the experimental findings. Keywords: anchoring groups; coherent transport; current–voltage; molecular electronics; single molecule; Introduction Molecular-scale electronics is a field that in recent years experienced

• ) break junctions. These create and displace atomic-sized electrodes so that reproducibly single-molecule junctions are formed [4][5][6][7]. In the past years it has been shown that the electronic properties of single-molecule junctions depend both on the molecular core and on the interfaces between

• electronic coupling between the molecule and the metal electrode are essential to characterize charge transport in single-molecule junctions and to create new fundamental devices such as molecular motors or molecular machines [26][27]. Several previous studies have shown that stable and reproducible single

Continuum models of focused electron beam induced processing

• Milos Toth,
• Charlene Lobo,
• Vinzenz Friedli,
• Aleksandra Szkudlarek and
• Ivo Utke

Beilstein J. Nanotechnol. 2015, 6, 1518–1540, doi:10.3762/bjnano.6.157

• etching, respectively, and VD is the volume of a single molecule removed from or added to the substrate in the etch or deposition reaction. The electron flux f can either be fixed at f0, or specified by an r-dependent function such as Equation 8 or Equation 9. Setting f to f0 is justified when simulating

Transformations of PTCDA structures on rutile TiO₂ induced by thermal annealing and intermolecular forces

• Szymon Godlewski,
• Jakub S. Prauzner-Bechcicki,
• Thilo Glatzel,
• Ernst Meyer and
• Marek Szymoński

Beilstein J. Nanotechnol. 2015, 6, 1498–1507, doi:10.3762/bjnano.6.155

• outstanding oxygen rows. However, when a higher resolution is achieved the single molecule is imaged as a characteristic double lobe feature, as noted by a dashed circle in Figure 2b. This finding enables us to determine the molecule orientation on the surface, as the lowest unoccupied molecular orbital (LUMO

• on the TiO2(110) surface (a); (b) magnified image showing the position of the PTCDA molecule relative to the surface rows; for clarity, the image contrast inside the rectangle is adjusted to improve the visibility of surface reconstruction rows, and a single molecule STM image (two lobes) is marked

• with a dashed circle. (c) The structural model of the PTCDA molecule on the surface, where two ellipses mimic the STM appearance of a single molecule; all images acquired with 2 pA tunnelling current and 2.0 V bias voltage. 0.7 ML of PTCDA molecules on a TiO2(110) surface; (a), (b) and (c) are empty

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

• Hatef Sadeghi,
• Sara Sangtarash and
• Colin J. Lambert

Beilstein J. Nanotechnol. 2015, 6, 1413–1420, doi:10.3762/bjnano.6.146

• Hatef Sadeghi Sara Sangtarash Colin J. Lambert Quantum Technology Centre, Physics Department, Lancaster University, Lancaster, LA1 4YB, UK 10.3762/bjnano.6.146 Abstract We have studied the charge and thermal transport properties of a porphyrin-based single-molecule transistor with electro-burnt

• configurations at the electrodes. This can lead to rectification in the current–voltage characteristic of the junction. Keywords: electro-burnt graphene electrodes; nanoelectronics; porphyrin; single-molecule transistor; Introduction Transistors are the fundamental building blocks of modern electronic devices

• circuit should double approximately every two years. Since 1974, when the idea of a single-molecule rectifier was proposed by Ratner and Aviram [5], many attempts to realize FETs have failed to deliver the room-temperature reliability, reproducibility and stability required by the electronics industry [6

Alternative types of molecule-decorated atomic chains in Au–CO–Au single-molecule junctions

• Zoltán Balogh,
• Péter Makk and
• András Halbritter

Beilstein J. Nanotechnol. 2015, 6, 1369–1376, doi:10.3762/bjnano.6.141

• Zoltan Balogh Peter Makk Andras Halbritter Department of Physics, Budapest University of Technology and Economics and MTA-BME Condensed Matter Research Group, Budafoki ut 8, 1111 Budapest, Hungary 10.3762/bjnano.6.141 Abstract We investigate the formation and evolution of Au–CO single-molecule

• pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and

• The break junction method is widely used to establish single-molecule nanowires [1][2]. During its controlled rupture a metallic wire thins down to atomic dimensions and finally breaks forming a nanometer-sized gap between the electrodes. This gap can be bridged by single molecules in a self-organized

Can molecular projected density of states (PDOS) be systematically used in electronic conductance analysis?

• Tonatiuh Rangel,
• Gian-Marco Rignanese and
• Valerio Olevano

Beilstein J. Nanotechnol. 2015, 6, 1247–1259, doi:10.3762/bjnano.6.128

• such junctions (including the measurement of their current–voltage characteristics) is, however, still difficult to achieve. In order to obtain a reliable single-molecule zero-bias conductance, it was suggested to resort to a statistically significant sample of tens of thousands of measurements [4

Nano-contact microscopy of supracrystals

• Adam Sweetman,
• Nicolas Goubet,
• Ioannis Lekkas,
• Marie Paule Pileni and
• Philip Moriarty

Beilstein J. Nanotechnol. 2015, 6, 1229–1236, doi:10.3762/bjnano.6.126

• dispersion forces [41]. However, while force–distance measurements of single molecule interactions using this technique are typically highly reproducible [31][33][41][42][43], we observe a very large degree of variation between different F(z) spectra for the nanocrystals. Although the broad trends remain

Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy

• Andrzej J. Kulik,
• Małgorzata Lekka,
• Kyumin Lee,
• Grazyna Pyka-Fościak and
• Wieslaw Nowak

Beilstein J. Nanotechnol. 2015, 6, 1164–1175, doi:10.3762/bjnano.6.118

• its monoclonal antibody. The results obtained using LFM and AFM-based classical force spectroscopies showed similar unbinding forces recorded at similar loading rates. Our studies verify that the proposed lateral force calibration method can be applied to study single molecule interactions. Keywords

• , recently, Dendzik et al. proposed that the stretching of a reference single molecule (e.g., dextran) could be used to determine the normal and lateral AFM cantilever calibration [15]. Although this new method presents a clear improvement over previous attempts to obtain a reliable calibration for lateral

• , Table 1). Discussion The unbinding measurements realized by the conventional AFM-FS method are one of the most tedious experiments due to the necessity of high statistics and the low number of unbinding events corresponding to single molecule interactions in a single experimental run [23]. LFM has high

Electrical characterization of single molecule and Langmuir–Blodgett monomolecular films of a pyridine-terminated oligo(phenylene-ethynylene) derivative

• Henrry M. Osorio,
• Santiago Martín,
• María Carmen López,
• Santiago Marqués-González,
• Simon J. Higgins,
• Richard J. Nichols,
• Paul J. Low and
• Pilar Cea

Beilstein J. Nanotechnol. 2015, 6, 1145–1157, doi:10.3762/bjnano.6.116

• pseudolinear (ohmic) region of the I–V curves. This value is higher than that of the conductance values of LB films of phenylene-ethynylene derivatives contacted by amines, thiols, carboxylate, trimethylsilylethynyl or acetylide groups. In addition, the single molecule I–V curve of 1 determined using the I(s

• molecules within the LB film do not strongly influence the molecule conductance. The results presented here complement earlier studies of single molecule conductance of 1 using STM-BJ methods, and support the growing evidence that the pyridyl group is an efficient and effective anchoring group in sandwiched

• metal–monolayer–metal junctions prepared under a number of different conditions. Keywords: Langmuir–Blodgett films; molecular electronics; STM touch-to-contact method; Introduction Molecular electronics, in which a single molecule or a single layer of molecules is oriented between two electrodes to

Closed-loop conductance scanning tunneling spectroscopy: demonstrating the equivalence to the open-loop alternative

• Chris Hellenthal,
• Kai Sotthewes,
• Martin H. Siekman,
• E. Stefan Kooij and
• Harold J. W. Zandvliet

Beilstein J. Nanotechnol. 2015, 6, 1116–1124, doi:10.3762/bjnano.6.113

• also been applied to tunneling junctions consisting of a single molecule attached to both the STM tip and the sample and to tip-molecule-vacuum-sample junctions [27][41][42]. While a non-unity effective mass does indeed lead to lower apparent barrier heights, the tip–vacuum–sample system described in

Charge carrier mobility and electronic properties of Al(Op)₃: impact of excimer formation

• Andrea Magri,
• Pascal Friederich,
• Bernhard Schäfer,
• Valeria Fattori,
• Xiangnan Sun,
• Timo Strunk,
• Velimir Meded,
• Luis E. Hueso,
• Wolfgang Wenzel and
• Mario Ruben

Beilstein J. Nanotechnol. 2015, 6, 1107–1115, doi:10.3762/bjnano.6.112

• similar trend in the HOMO energies of Al(Op)3 and Alq3, we could, based on this single molecule energy analogy, assume that Al(Op)3, when implemented in a device, would prevent hole diffusion in the same manner as Alq3. In order to confirm the thermal stability of Al(Op)3, the complex was deposited by

• presumed excimer formation within the thin film. Normally, an excimer is caused by a charge-transfer interaction between an electronically excited species and a ground state molecule [30][31]. Often, the excimer possesses observable properties quite distinct from those of the single molecule [30][31]. The

• problem at hand, we performed density functional-based [36][37][38] calculations for both a single molecule in vacuum and molecules embedded in an explicit matrix [39] and compared them to a de facto standard in the field, namely, Alq3. Structurally, Al(Op)3 is formed by symmetric ligands that bind to the