Formation Of Molecular Junctions Research Articles

Total variation denoising-based method of identifying the states of single molecules in break junction data

Break junction (BJ) measurements provide insights into the electrical properties of diverse molecules, enabling the direct assessment of single-molecule conductances. The BJ method displays potential for use in determining the dynamics of individual molecules, single-molecule chemical reactions, and biomolecules, such as deoxyribonucleic acid and ribonucleic acid. However, conductance data obtained via single-molecule measurements may be susceptible to fluctuations due to minute structural changes within the junctions. Consequently, clearly identifying the conduction states of these molecules is challenging. This study aims to develop a method of precisely identifying conduction state traces. We propose a novel single-molecule analysis approach that employs total variation denoising (TVD) in signal processing, focusing on the integration of information technology with measured single-molecule data. We successfully applied this method to simulated conductance traces, effectively denoise the data, and elucidate multiple conduction states. The proposed method facilitates the identification of well-defined plateau lengths and supervised machine learning with enhanced accuracies. The introduced TVD-based analytical method is effective in elucidating the states within the measured single-molecule data. This approach exhibits the potential to offer novel perspectives regarding the formation of molecular junctions, conformational changes, and cleavage.

Large area arrays of discrete single-molecule junctions derived from host-guest complexes.

The desire to continually reduce the lower limits of semiconductor integrated circuit (IC) fabrication methods continues to inspire interest in unimolecular electronics as a platform technology for the realization of future (opto)electronic devices. However, despite successes in developing methods for the construction and measurement of single-molecule and large-area molecular junctions, exercising control over the precise junction geometry remains a significant challenge. Here, host-guest complexes of the wire-like viologen derivative 1,1'-bis(4-(methylthio)-phenyl)-[4,4'-bipyridine]-1,1'-diium chloride ([1][Cl]2) and cucurbit[7]uril (CB[7]) have been self-assembled in a regular pattern over a gold substrate. Subsequently, ligandless gold nanoparticles (AuNPs) synthesized in situ are deposited over the host-guest array. The agreement between the conductance of individual mono-molecular junctions, appropriately chosen as a function of the AuNP diameter, within this array determined by conductive probe atomic force microscope (c-AFM) and true single-molecule measurements for a closely similar host-guest complex within a scanning tunneling microscope break-junction (STM-BJ) indicates the formation of molecular junctions derived from these host-guest complexes without deleterious intermolecular coupling effects.

A new anchoring group to fabricate single-molecule junctions: diphenyl sulfide

A new anchor (–SPh) was confirmed with the ability to enable reproducible molecular junction formation.

Formation of Molecular Junctions by Single-Entity Collision Electrochemistry.

Controlling and understanding the chemistry of molecular junctions is one of the major themes in various fields ranging from chemistry and nanotechnology to biotechnology and biology. Stochastic single-entity collision electrochemistry (SECE) provides powerful tools to study a single entity, such as single cells, single particles, and even single molecules, in a nanoconfined space. Molecular junctions formed by SECE collision show various potential applications in monitoring molecular dynamics with high spatial resolution and high temporal resolution and in feasible combination with hybrid techniques. This Perspective highlights the new breakthroughs, seminal studies, and trends in the area that have been most recently reported. In addition, future challenges for the study of molecular junction dynamics with SECE are discussed.

Local cation-tuned reversible single-molecule switch in electric double layer

The nature of molecule-electrode interface is critical for the integration of atomically precise molecules as functional components into circuits. Herein, we demonstrate that the electric field localized metal cations in outer Helmholtz plane can modulate interfacial Au-carboxyl contacts, realizing a reversible single-molecule switch. STM break junction and I-V measurements show the electrochemical gating of aliphatic and aromatic carboxylic acids have a conductance ON/OFF behavior in electrolyte solution containing metal cations (i.e., Na+, K+, Mg2+ and Ca2+), compared to almost no change in conductance without metal cations. In situ Raman spectra reveal strong molecular carboxyl-metal cation coordination at the negatively charged electrode surface, hindering the formation of molecular junctions for electron tunnelling. This work validates the critical role of localized cations in the electric double layer to regulate electron transport at the single-molecule level.

Revealing conductance variation of molecular junctions based on an unsupervised data analysis approach

For single-molecule electrical junction conductance measurements the data analysis can be a key challenge because of the large datasets and large stochastic variation in junction conformation from one junction formation cycle to the next. Here, a data sorting algorithm was used to analyze the most dominant conductance groups for four molecular systems. The algorithm was applied to data sorting of molecular junctions repetitively formed during STM current-distance (I-s) retraction traces. The data was recorded using the STM I(s) technique to form molecular junctions, which avoids direct contact between the gold STM tip and gold substrate. The algorithm has been employed to identify different dominant conductance features for two saturated molecular bridges and two conjugated molecular bridges. The former molecular targets featured thiolmethyl and isothiocyanate anchoring groups on each respective end of the polymethylene molecular bridge, while the conjugated molecular wires featured thiol anchoring groups. In each case the sorting algorithm is able to identify two main junction conductance groups related to differing molecular junction configurations. This algorithm is demonstrated to effectively sort and rationalize complex molecular junction formation datasets, where junction formation probably can be relatively low, and thereby shows potential to quantify hidden features in single-molecule charge transport data.

Structure Identification for Force-Induced Reaction Using Single-Molecule Conductance Measurement

Structure Identification for Force-Induced Reaction Using Single-Molecule Conductance Measurement

Fabrication of Polyaniline (PANI) through Parallel Nanopores: Charge Transport Properties of PANI@SiO2 Nanopore Molecular Junctions

Aniline is electropolymerized through mesoporous silica nanopores (100 nm-long, 3 nm in diameter) orthogonally oriented on indium-tin oxide (ITO). Only a few polyaniline (PANI) wires are accommodated in the nanochannels and their growth is electrochemically controlled. The electronic transport properties of PANI@SiO2 are studied by Conductive Atomic Force Microscopy (C-AFM), using a Pt-coated C-AFM tip. Three different behaviors are observed. First, linear I/V curves are obtained when PANI is deposited in the nanopores with material spilling over the silica membrane; electron transport occurs through many PANI@SiO2 channels and the overall conductance is high. Second, flat I/V curves are recorded, indicating “insulator” behavior when the SiO2 nanopores are not fully filled by PANI wires. Thirdly, non-linear I/V curves, which are quantitatively highly reproducible and independent of the point probed, are obtained. These are attributed to the formation of molecular junctions where the C-AFM tip in contact with the nanopores acts as the top electrode and vertical PANI wires just fill the SiO2 channels. The size of the top electrode and the reproducilility of the I/V suggest that the C-AFM is seeing about 5 nanopores each filled with one or two PANI wires.

Benchmark Study of Alkane Molecular Chains

Alkanes serve an important role as benchmark system in molecular electronics. However, a large variation in the conductance values is reported in the literature. To better understand these fluctuations, in this study we measure large molecular data sets (up to 100 000 breaking traces) of a series of alkanes with different lengths and anchoring groups using the mechanically controlled break junction (MCBJ) technique. Employing an unsupervised learning algorithm, we investigate both the time evolution and the distance dependence of the measured traces. For all the molecules considered, we have been able to identify the single-molecule conductance value for the fully stretched molecular configuration. For alkanedithiols, the corresponding extracted β decay constant of 1.05 ± 0.08 per CH2 group agrees well with literature values. In the case of the stronger thiol bonding, additional peaks in the conductance histograms are found, suggesting the formation of molecular junctions containing a single molecule plus additional gold/molecule unit(s). The results shine light on the dispersion in reported conductance values and show that the evolution of the molecule as a function of stretching and time contains crucial information in determining the molecular junction configuration in MCBJs.

(Keynote) Conduction Under Potential Control: From Molecules to Proteins

My brilliant former student NJ Tao, to whose memory this symposium is dedicated, showed in a remarkable single-author paper1 that the conductance of a molecule containing a redox center was strongly dependent on surface potential, being a maximum at the redox potential. Some years later, we showed2 that defined contacts and statistical analysis were the keys to measuring molecular conductance quantitatively. NJ Tao came up with a simpler way of implementing our method, now the gold standard in single molecule conductance measurements.3 Gating of single-molecule conductance has now been reliably demonstrated.4 Despite many advances, there have been few real applications for single-molecule electronic devices. Proteins make excellent electronic conductors, as demonstrated by measurements under potential control that eliminate Faradaic contributions to the current.5 A remarkably long electron mean-free path and means for self-assembly give proteins advantages over conventional molecular wires.6 Furthermore, enzyme activity may be followed directly via conductance fluctuations, a possible basis for a new DNA sequencing technology.7 This talk will look at the physics behind these phenomena. Tao, N. J., Probing Potential-Tuned Resonant Tunneling through Redox Molecules with Scanning Tunneling Microscopy. Physical Review Letters 1996, 76 (21), 4066-4069.Cui, X. D.; Primak, A.; Zarate, X.; Tomfohr, J.; Sankey, O. F.; Moore, A. L.; Moore, T. A.; Gust, D.; Harris, G.; Lindsay, S. M., Reproducible Measurement of Single-Molecule Conductivity. Science (New York, N.Y.) 2001, 294 (5542), 571.Xu, B.; Tao, N. J., Measurement of Single-Molecule Resistance by Repeated Formation of Molecular Junctions. Science (New York, N.Y.) 2003, 301 (5637), 1221.Song, H.; Kim, Y.; Jang, Y. H.; Jeong, H.; Reed, M. A.; Lee, T., Observation of molecular orbital gating. Nature 2009, 462 (7276), 1039-1043.Zhang, B.; Song, W.; Pang, P.; Lai, H.; Chen, Q.; Zhang, P.; Lindsay, S., The Role of Contacts in Long-Range Protein Conductance. Proc Natl Acad Sci U S A 2019, 116, 5886-5891.Lindsay, S., Ubiquitous Electron Transport in non-Electron Transfer Proteins. Life 2020, 10, 72Zhang, B.; Deng, H.; Mukherjee, S.; Song, W.; Wang, X.; Lindsay, S., Engineering an Enzyme for Direct Electrical Monitoring of Activity. ACS Nano 2020, 14, 1630-1638.

Probing metal-molecule contact at the atomic scale via conductance jumps

Understanding the formation of metal-molecule contact at the microscopic level is the key towards controlling and manipulating atomic scale devices. Employing two isomers of bipyridine, $4, 4^\prime$ bipyridine and $2, 2^\prime$ bipyridine between gold electrodes, here, we investigate the formation of metal-molecule bond by studying charge transport through single molecular junctions using a mechanically controlled break junction technique at room temperature. While both molecules form molecular junctions during the breaking process, closing traces show the formation of molecular junctions unambiguously for $4, 4^\prime$ bipyridine via a conductance jump from the tunneling regime, referred as `jump to molecular contact', being absent for $2, 2^\prime$ bipyridine. Through statistical analysis of the data, along with, molecular dynamics and first-principles calculations, we establish that contact formation is strongly connected with the molecular structure of the electrodes as well as how the junction is broken during breaking process, providing important insights for using a single-molecule in an electronic device.

Developing Longer-Lived Single Molecule Junctions with a Functional Flexible Electrode.

Creating single-molecule junctions with a long-lived lifetime at room temperature is an open challenge. Finding simple and efficient approaches to increase the durability of single-molecule junction is also of practical value in molecular electronics. Here it is shown that a flexible gold-coated nanopipette electrode can be utilized in scanning tunneling microscope (STM) break-junction measurements to efficiently enhance the stability of molecular junctions by comparing with the measurements using conventional solid gold probes. The stabilizing effect of the flexible electrode displays anchor group dependence, which increases with the binding energy between the anchor group and gold. An empirical model is proposed and shows that the flexible electrode could promote stable binding geometries at the gold-molecule interface and slow down the junction breakage caused by the external perturbations, thereby extending the junction lifetime. Finally, it is demonstrated for the first time that the internal conduit of the flexible STM tip can be utilized for the controlled molecule delivery and molecular junction formation.

Environmental Control of Single-Molecule Junction Evolution and Conductance: A Case Study of Expanded Pyridinium Wiring.

Environmental control of single‐molecule junction evolution and conductance was demonstrated for expanded pyridinium molecules by scanning tunneling microscopy break junction method and interpreted by quantum transport calculations including solvent molecules explicitly. Fully extended and highly conducting molecular junctions prevail in water environment as opposed to short and less conducting junctions formed in non‐solvating mesitylene. A theoretical approach correctly models single‐molecule conductance values considering the experimental junction length. Most pronounced difference in the molecular junction formation and conductance was identified for a molecule with the highest stabilization energy on the gold substrate confirming the importance of molecule–electrode interactions. Presented concept of tuning conductance through molecule–electrode interactions in the solvent‐driven junctions can be used in the development of new molecular electronic devices.

Environmental Control of Single‐Molecule Junction Evolution and Conductance: A Case Study of Expanded Pyridinium Wiring

AbstractEnvironmental control of single‐molecule junction evolution and conductance was demonstrated for expanded pyridinium molecules by scanning tunneling microscopy break junction method and interpreted by quantum transport calculations including solvent molecules explicitly. Fully extended and highly conducting molecular junctions prevail in water environment as opposed to short and less conducting junctions formed in non‐solvating mesitylene. A theoretical approach correctly models single‐molecule conductance values considering the experimental junction length. Most pronounced difference in the molecular junction formation and conductance was identified for a molecule with the highest stabilization energy on the gold substrate confirming the importance of molecule–electrode interactions. Presented concept of tuning conductance through molecule–electrode interactions in the solvent‐driven junctions can be used in the development of new molecular electronic devices.

Richness of molecular junction configurations revealed by tracking a full pull-push cycle.

In the field of molecular electronics, the interplay between molecular orientation and the resulting electronic transport is of central interest. At the single molecule level, this topic is extensively studied with the aid of break junction setups. In such experiments, two metal electrodes are brought into contact, and the conductance is typically measured when the electrodes are pulled apart in the presence of molecules, until a molecule bridges the two electrodes. However, the molecular junctions formed in this pull process reflect only part of the rich possible junction configurations. Here, we show that the push process, in which molecular junctions are formed by bringing the electrodes towards each other, allows the fabrication of molecular junction structures that are not necessarily formed in the pull process. We also find that in the extreme case, molecular junctions can be formed only in the push process that is typically ignored. Our findings demonstrate that tracking the two inverse processes of molecular junction formation, reveals a more comprehensive picture of the variety of molecular configurations in molecular junctions.

Giant Conductance Enhancement of Intramolecular Circuits through Interchannel Gating

Summary For neutral intramolecular circuits with two constitutionally identical branches, a maximum 4-fold increase in total conductance can be obtained according to constructive quantum interference (CQI). For charged intramolecular circuits, however, the strong electrostatic interactions entangle the quantum states of these two parallel pathways, thus introducing complicated transport behavior that warrants experimental investigation of the intramolecular circuit rules. Here, we report that a tetracationic cyclophane with parallel channels exhibits a 50-fold conductance enhancement compared with that of a single-channel control, an observation that supplements intramolecular circuit law in systems with strong Coulombic interactions. Flicker noise measurements and theoretical calculations show that strong electrostatic interactions between charged parallel channels—serving as the chemical gate to promote the effective conductance of each channel—and CQI boosts the total conductance of the two-channel circuit. The molecular design presented herein constitutes a proof-of-principle approach to charged intramolecular circuits that are desirable for quantum circuits and devices.

Selective formation of molecular junctions with high and low conductance states by tuning the velocity of electrode displacement.

A single-molecule junction of 1,4-di(4-pyridyl)benzene (DPB) was prepared in a nano-gap between two Au electrodes using the scanning tunnelling microscopy-based break junction method (STM-BJ). Electric conductance and current versus bias voltage (I-V) measurements during the pulling and pushing processes of DPB single-molecule junctions revealed that high (H) and low (L) conductance states formed in both the pulling and pushing processes. Analysis of the I-V curves based on a single-level model indicated that the difference in conductivity of the H and L states mainly arises from high and low metal-molecule electric coupling in the junction. We demonstrated the controllable formation of H and L conductance states by simply tuning the velocity of electrode displacement in the pushing process. In the pulling process, both H and L states formed regardless of the velocity (v) of electrode displacement, while in the pushing process, H and L states could be selectively fabricated by using low (v = 16 nm s-1) and high (v = 64 nm s-1) velocities of displacement, respectively. This study provides a simple approach to selectively fabricate high and low conductance states by fine tuning of the electrode displacement.

Measuring Single-Molecule Conductance at An Ultra-Low Molecular Concentration in Vacuum.

We report on systematic investigation of single-molecule detection mechanisms in break junction experiments in vacuum. We found molecular feature in the conductance traces at an extremely low concentration of molecules of 10 nM. This was attributed to condensation of the molecular solution on the junction surface upon evaporation of the solvent during evacuation. Furthermore, statistical analyses of the temporal dependence of molecular junction formation probabilities suggested accumulation effects of the contact mechanics to concentrate molecules absorbed on a remote area to the tunneling current sensing zone, which also contributed to the capability of molecular detections at the low concentration condition. The present findings can be used as a useful guide to implement break junction measurements for studying electron and heat transport through single molecules in vacuum.

(Invited) Welding of Nickel Nanowires By Ions Beam Irradiation: From Small to Large Scale

In order to replace conventional transparent conducting electrodes, metal nanowires (MNWs) networks have long been act as promising contenders due to their high mechanical flexibility. However, nanowire-nanowire contact resistance is main technical obstruction in terms of improvement in their performance. To reduce nanowire-nanowire contact resistance, welding of nanowires (NWs) is essential. In this work, MeV proton and argon ions beam irradiation induced nanoscale welding technique to fabricate X-, Y-, II- and T-shaped molecular junctions between nickel nanowires (Ni-NWs) is presented. Ni-NWs are irradiated by 2.75 MeV proton ions and 3.5 MeV argon ions at doses 1x1016ions/cm2 and 5x1015 respectively while temperature is kept constant. Transmission electron microscopy (TEM), scanning electron microscopy (SEM) and x-ray diffraction (XRD) results reveal that Ni-NWs are welded without losing stability in crystal structures of NWs. Afterward, a two-dimensional large scale random network of Ni-NWs is fabricated by 3 MeV proton ions beam irradiation induced nanoscale welding of Ni-NWs at crossing positions. Proton ion beam induced large scale network fabrication is confirmed by TEM and SEM techniques. Moreover, these networks are characterized optically using UV-VIS spectroscopy. It is observed that at a beam fluence of 5x1015 ions/cm2, perfect molecular junctions between Ni-NWs in X-, II-, and V-shapes are achieved and a large scale welded network of Ni-NWs is obtained without distorting the morphology of NWs. Moreover, structure of Ni-NWs remains stable under 3MeV proton ions beam irradiation and networks are found to be optically transparent. The results exhibit that fabrication of Ni-NWs network precede through three steps: i- High energy ions beam irradiation induced heat spikes lead to locally heat and fuse Ni-NWs, ii- Formation of molecular junctions on small scale, iii- Formation of large scale network Ions beam irradiation induced welding of Ni-NWs can improve performance of NWs networks by reducing contact resistance between NWs for application as transparent conducting electrodes. These high quality welded MNWs networks may potentially be applied as transparent conducting electrodes in optoelectronic devices.

Charge Transport through a Single Molecule of trans-1-bis-Diazofluorene [60]fullerene

Fullerenes have attracted interest for their possible applications in various electronic, biological, and optoelectronic devices. However, for efficient use in such devices, a suitable anchoring group has to be employed that forms well-defined and stable contacts with the electrodes. In this work, we propose a novel fullerene tetramalonate derivate functionalized with trans-1 4,5-diazafluorene anchoring groups. The conductance of single-molecule junctions, investigated in two different setups with the mechanically controlled break junction technique, reveals the formation of molecular junctions at three conductance levels. We attribute the conductance peaks to three binding modes of the anchoring groups to the gold electrodes. Density functional theory calculations confirm the existence of multiple binding configurations and calculated transmission functions are consistent with experimentally determined conductance values.