Stretching-Induced Conductance Variations as Fingerprints of Contact Configurations in Single-Molecule Junctions

Methods for the analysis, interpretation, and prediction of single-molecule junction conductance behaviour

This article offers a broad overview of measurement methods in the field of molecular electronics, with a particular focus on the most common single-molecule junction fabrication techniques, the challenges in data analysis and interpretation of single-molecule junction current-distance traces, and a summary of simulations and predictive models aimed at establishing robust structure-property relationships of use in the further development of molecular electronics.

Evolution of Single-Molecule Electronic Interfaces

Single-molecule electronics can fabricate single-molecule devices via the construction of molecule-electrode interfaces and also provide a unique tool to investigate single-molecule scale physicochemical processes at these interfaces. To investigate single-molecule electronic devices with desired functionalities, an understanding of the interface evolution processes in single-molecule devices is essential. In this review, we focus on the evolution of molecule-electrode interface properties, including the background of interface evolution in single-molecule electronics, the construction of different types of single-molecule interfaces, and the regulation methods. Finally, we discuss the perspective of future characterization techniques and applications for single-molecule electronic interfaces.

Plasmon-Assisted Trapping of Single Molecules in Nanogap

The manipulation of single molecules has attracted extensive attention because of their promising applications in chemical, biological, medical, and materials sciences. Optical trapping of single molecules at room temperature, a critical approach to manipulating the single molecule, still faces great challenges due to the Brownian motions of molecules, weak optical gradient forces of laser, and limited characterization approaches. Here, we put forward localized surface plasmon (LSP)-assisted trapping of single molecules by utilizing scanning tunneling microscope break junction (STM-BJ) techniques, which could provide adjustable plasmonic nanogap and characterize the formation of molecular junction due to plasmonic trapping. We find that the plasmon-assisted trapping of single molecules in the nanogap, revealed by the conductance measurement, strongly depends on the molecular length and the experimental environments, i.e., plasmon could obviously promote the trapping of longer alkane-based molecules but is almost incapable of acting on shorter molecules in solutions. In contrast, the plasmon-assisted trapping of molecules can be ignored when the molecules are self-assembled (SAM) on a substrate independent of the molecular length.

Toward Density-Functional Theory-Based Structure-Conductance Relationships in Single Molecule Junctions

A method is presented that allows for the calculation using density functional theory (DFT) of the tunneling conductance of single molecule junctions for thousands of junction structures. With a single scaling parameter, conductance is evaluated from clusters consisting of the molecule bonded to one Au atom at each end. Junction geometries are obtained without any constraints from ab initio molecular dynamics simulations at room temperature. This method accurately reproduces standard DFT-based conductance values for several molecular and electrode structures while reducing the computational cost by a factor of ∼400×, allowing for the conductance of tens of thousands of geometries to be computed. When applied to a pair of conjugated molecules, these large data sets quantify the effect on conductance of molecular structure or quantum chemical properties. This methodology enables reliable DFT-based conductance calculations at a negligible computational cost and opens the way to quantitative structure-conductance relationships.

Development of Classical Force Fields for Interfaces between Single Molecules and Au

Interfaces between metals and organic materials play an essential role in molecular surface science, photovoltaics, or molecular electronics. Modeling the evolution of interface geometry over sufficiently long timescales requires an accurate parameterization of the relevant metal-molecule interactions. Here, we describe a method for calculating interface parameters from reference density functional theory calculations of small metal-molecule complexes. We apply this method to develop a parameter set for a series of metal-molecule-metal junctions. We study the dynamics of short oligophenyls with amine, methyl-sulfide, or direct Au-C links, which are bonded to Au(111) via small adatom structures. Nanosecond classical molecular dynamics simulations using the generated parameter set reveal insight into molecular degrees of freedom not accessible from ab initio molecular dynamics simulations.

Simultaneous Electrical and Mechanical Characterization of Single-Molecule Junctions Using AFM-BJ Technique

The fabrication and characterization of single-molecule junctions provide a unique platform to study the physical phenomena of a single molecule, and the electrical characterization enables us to understand the electrical transport properties of a single molecule and guide the fabrication of molecular electronic devices. However, the electrical characterization of single-molecule junctions is sometimes insufficient to extract the structural information on single-molecule junctions, and an alternate method to address this problem is to characterize the mechanical properties of single-molecule junctions. Simultaneous measurement of mechanical and electrical properties can provide complementary information on single molecules to analyze the correlations of their electrical and mechanical properties in the evolution of single-molecule junctions. In this mini-review, we summarize the progress on the simultaneous characterizations of mechanical and electrical properties for single-molecule junctions, and discuss the challenges and perspectives of this research area.

Hard-Soft Chemistry Design Principles for Predictive Assembly of Single Molecule-Metal Junctions

The achievement of atomic control over the organic-inorganic interface is key to engineering electronic and spintronic properties of molecular devices. We leverage insights from inorganic chemistry to create hard-soft acid-base (HSAB) theory-derived design principles for incorporation of single molecules onto metal electrodes. A single molecule circuit is assembled via a bond between an organic backbone and an under-coordinated metal atom of the electrode surface, typically Au. Here, we study molecular composition factors affecting the junction assembly of coordination complexes containing transition metals atoms on Au electrodes. We employ hetero- and homobimetallic lantern complexes and systematically change the coordination environment to vary the character of the intramolecular bonds relative to the electrode-molecule interaction. We observe that trends in the robustness and chemical selectivity of single molecule junctions formed with a range of linkers correlate with HSAB principles, which have traditionally been used to guide atomic arrangements in the synthesis of coordination complexes. We find that this similarity between the intermolecular electrode-molecule bonding in a molecular circuit and the intramolecular bonds within a coordination complex has implications for the design of metal-containing complexes compatible with electrical measurements on metal electrodes. Our results here show that HSAB principles determine which intramolecular interactions can be compromised by inter molecule-electrode coordination; in particular on Au electrodes, soft-soft metal-ligand bonding is vulnerable to competition from soft-soft Au-linker bonding in the junction. Neutral donor-acceptor intramolecular bonds can be tuned by the Lewis acidity of the transition metal ion, suggesting future synthetic routes toward incorporation of transition metal atoms into molecular junctions for increased functionality of single molecule devices.

Tolerance to Stretching in Thiol-Terminated Single-Molecule Junctions Characterized by Surface-Enhanced Raman Scattering

We investigated the change in the metal-molecule interaction in a 1,4-benzenedithiol (BDT) single-molecule junction using a combination of surface-enhanced Raman scattering spectra and current-voltage curves. During the stretching process, the conductance of the junction systematically decreased, accompanied by an increase in the vibrational energy of the CC stretching mode. By analyzing the current-voltage curves and Raman spectra, we found that the interaction between the π orbital of BDT and the electronic states of Au was diminished by the orientation change of BDT during the stretching process. A comparison with a 4,4'-bipyridine single-molecule junction revealed that the reduction of coupling of the Au-S contacts was smaller than that of Au-pyridine contacts. Therefore, the electronic states originating from the contact geometry are responsible for the tolerance to the stretching of thiol-terminated molecular junctions.

Multi-Space Excitation as an Alternative to the Landauer Picture for Nonequilibrium Quantum Transport

While the Landauer viewpoint constitutes a modern basis to understand nanoscale electronic transport and to realize first-principles implementations of the nonequilibrium Green's function (NEGF) formalism, seeking an alternative picture can be beneficial for the fundamental understanding and practical calculations of quantum transport processes. Herein, introducing a micro-canonical picture that maps the finite-bias quantum transport process to a drain-to-source or multi-electrode optical excitation, the multi-space constrained-search density functional theory (MS-DFT) formalism for first-principles electronic structure and quantum transport calculations is developed. Performing MS-DFT calculations for the benzenedithiolate single-molecule junction, it is shown that MS-DFT and standard DFT-NEGF calculations produce practically equivalent electronic and transmission data. Importantly, the variational convergence of "nonequilibrium total energy" within MS-DFT is demonstrated, which should have significant implications for in operando studies of nanoscale devices. Establishing a viable alternative to the Landauer viewpoint, the developed formalism should provide valuable atomistic information in the development of next-generation nanodevices.

Quasi-Fermi level splitting in nanoscale junctions from ab initio

The splitting of quasi-Fermi levels (QFLs) represents a key concept utilized to describe finite-bias operations of semiconductor devices, but its atomic-scale characterization remains a significant challenge. Herein, the nonequilibrium QFL or electrochemical potential profiles within single-molecule junctions obtained from the first-principles multispace constrained-search density-functional formalism are presented. Benchmarking the standard nonequilibrium Green's function calculation results, it is first established that algorithmically the notion of separate electrode-originated nonlocal QFLs should be maintained within the channel region during self-consistent finite-bias electronic structure calculations. For the insulating hexandithiolate junction, the QFL profiles exhibit discontinuities at the left and right electrode interfaces and across the molecule the accompanying electrostatic potential drops linearly and Landauer residual-resistivity dipoles are uniformly distributed. For the conducting hexatrienedithiolate junction, on the other hand, the electrode QFLs penetrate into the channel region and produce split QFLs. With the highest occupied molecular orbital entering the bias window and becoming a good transport channel, the split QFLs are accompanied by the nonlinear electrostatic potential drop and asymmetric Landauer residual-resistivity dipole formation. Our findings underscore the importance of the first-principles extraction of QFLs in nanoscale junctions and point to a future direction for the computational design of next-generation semiconductor 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).

Single-molecule level control of host-guest interactions in metallocycle-C60 complexes

Host−guest interactions are of central importance in many biological and chemical processes. However, the investigation of the formation and decomplexation of host−guest systems at the single-molecule level has been a challenging task. Here we show that the single-molecule conductance of organoplatinum(II) metallocycle hosts can be enhanced by an order of magnitude by the incorporation of a C₆₀ guest molecule. Mechanically stretching the metallocycle-C₆₀ junction with a scanning tunneling microscopy break junction technique causes the release of the C₆₀ guest from the metallocycle, and consequently the conductance switches back to the free-host level. Metallocycle hosts with different shapes and cavity sizes show different degrees of flexibility to accommodate the C₆₀ guest in response to mechanical stretching. DFT calculations provide further insights into the electronic structures and charge transport properties of the molecular junctions based on metallocycles and the metallocycle-C₆₀ complexes.

Studying the single-molecule behavior of host-guest complexes can provide fundamental insights into their supramolecular interactions. Here, the authors use the scanning tunneling microscopy break junction technique to show that encapsulation of a C₆₀ molecule significantly enhances the conductance of an organoplatinum metallocycle; mechanical stretching of the junction releases the guest, returning the conductance to free-host level.

Controlling Contact Configuration of Carboxylic Acid-Based Molecular Junctions Through Side Group

In this paper, the contact configuration of single molecular junction is controlled through side group, which is explored by electrochemical jump-to-contact STM break junction. The conductance values of 2-methoxy-1,3-benzenedicarboxylic acid (2-M-1,3-BDC) is around 10-3.65 G0, which is different from that of 5-methoxy-1,3-benzenedicarboxylic acid (5-M-1,3-BDC) with 10-3.20 G0. Interestingly, the conductance value of 2-M-1,3-BDC is the same as that of 1,3-benzenedicarboxaldehyde (1,3-BDCA), while single molecular junctions of 5-M-1,3-BDC and 1,3-benzenedicarboxylic acid (1,3-BDC) give out similar conductance value. Since 1,3-BDCA binds to the Cu electrode through one oxygen atom, the dominated contact configuration for 1,3-BDC is through two oxygen atoms. The different conductance values between 2-M-1,3-BDC and 5-M-1,3-BDC can be attributed to the different contact configurations caused by the position of the side group. The current work provides a feasible way to control the contact configuration between the anchoring group and the electrode, which may be useful in designing future molecular electronics.

Endohedral Fullerene Fe@C28 Adsorbed on Au(111) Surface as a High-Efficiency Spin Filter: A Theoretical Study

We present a theoretical study on the adsorption and spin transport properties of magnetic Fe@C₂₈ using Ab initio calculations based on spin density functional theory and non-equilibrium Green’s function techniques. Fe@C₂₈ tends to adsorb on the bridge sites in the manner of C–C bonds, and the spin-resolved transmission spectra of Fe@C₂₈ molecular junctions exhibit robust transport spin polarization (TSP). Under small bias voltage, the transport properties of Fe@C₂₈ are mainly determined by the spin-down channel and exhibit a large spin polarization. When compressing the right electrode, the TSP is decreased, but high spin filter efficiency (SFE) is still maintained. These theoretical results indicate that Fe@C₂₈ with a large magnetic moment has potential applications in molecular spintronics.

Non-chemisorbed gold-sulfur binding prevails in self-assembled monolayers

Gold-thiol contacts are ubiquitous across the physical and biological sciences in connecting organic molecules to surfaces. When thiols bind to gold in self-assembled monolayers (SAMs) the fate of the hydrogen remains a subject of profound debate-with implications for our understanding of their physical properties, spectroscopic features and formation mechanism(s). Exploiting measurements of the transmission through a molecular junction, which is highly sensitive to the nature of the molecule-electrode contact, we demonstrate here that the nature of the gold-sulfur bond in SAMs can be probed via single-molecule conductance measurements. Critically, we find that SAM measurements of dithiol-terminated molecular junctions yield a significantly lower conductance than solution measurements of the same molecule. Through numerous control experiments, conductance noise analysis and transport calculations based on density functional theory, we show that the gold-sulfur bond in SAMs prepared from the solution deposition of dithiols does not have chemisorbed character, which strongly suggests that under these widely used preparation conditions the hydrogen is retained.

Data for quantum phonon transport in strained carbon atomic chains bridging graphene and graphene nanoribbon electrodes

The data presented in this article are related to "Odd-even phonon transport effects in strained carbon atomic chains bridging graphene nanoribbon electrodes" (Kim et al., 2019). To provide the information that can be utilized in reproducing our results, we provide the fully optimized graphene nanoribbon (GNR)-carbon chain (CC)-GNR junction atomic configurations at different strain values, the computational setting for quantum phonon transport calculations, and several computational data that were not included in the main manuscript. Data on graphene-CC-graphene junctions are additionally presented.

Probing Lewis acid-base interactions in single-molecule junctions

A novel strategy to regulate the tunneling mechanism for charge transport through an organoborane wire via Lewis acid-base interactions has been developed. A change from LUMO- to HOMO-dominated charge transport upon the addition of the fluoride is verified both experimentally and theoretically.