Molecular Conductance Research Articles

A Molecular Engineering Approach to Conformationally Regulated Conductance Dualism in a Molecular Junction

AbstractOne key aspect for the development of functional molecular electronic devices is the ability to precisely tune and reversibly switch the conductance of individual molecules in electrode‐molecule‐electrode junctions in response to external stimuli. In this work, we present a new approach to access molecular switches by deliberately controlling the flexibility in the molecular backbone. We here describe two new conductance switches based on bis(triarylamines) that rely on the reversible toggling between two conformers, each associated with vastly different conductances. By molecular design, we were able to realize an on/off ratio Ghigh/Glow of ~103, which is one of the largest values reported to date. Flicker noise analysis and molecular transport calculations indicate that on/off switching relies on a change of the conduction pathway and vast differences in molecule‐electrode coupling. We thereby provide a new scaffold for further development of molecular conductance switches that are both efficient and easily refined.

Front Cover: Protein Quakes in Redox Metalloenzymes: Clues to Molecular Enzyme Conductivity Triggered by Binding of Small Substrate Molecules (ChemistryOpen 12/2024)

Front Cover: Protein Quakes in Redox Metalloenzymes: Clues to Molecular Enzyme Conductivity Triggered by Binding of Small Substrate Molecules (ChemistryOpen 12/2024)

Lewis-Acid Mediated Reactivity in Single-Molecule Junctions.

While chemical reactions at a gold electrode can be monitored using molecular conductance and driven by extrinsic stimuli, the intrinsic properties of the nanostructured interface may perform important additional functions that are not yet well understood. Here we evaluate these properties in studies of single-molecule junctions formed from components comprising 4,4'-biphenyl backbones functionalized with 12 different sulfur-based linker groups. With some linkers, we find evidence for in situ S-C(sp3) bond breaking, and C(sp2)-C(sp3) bond forming, reactions consistent with the ex situ transformations expected for those groups in the presence of a Lewis acid. Notably, we also approach the limits of substituent influence on the conductance of physisorbed sulfur-linked junctions. As an illustrative example, we show that a tert-butylthio-functionalized precursor can form both chemisorbed (Au-S) junctions, consistent with heterolytic S-C(sp3) bond cleavage and generation of a stable tert-butyl carbocation, as well as physisorbed junctions that are >1 order of magnitude lower conductance than analogous junctions comprising cyclic "locked" thioether contacts. These findings are supported by a systematic analysis of model thioether components comprising different simple hydrocarbon substituents of intermediate size, which do not form chemisorbed contacts and further clarify the inverse relationship between conductance and substituent steric bulk. First-principles calculations confirm that bulky sulfur-substituents increase the probability of forming junction geometries with reduced electronic coupling between the electrode and π-conjugated molecular backbone. Together, this work helps to rationalize the dual roles that linker chemical structure and metal electrode Lewis character can play in mediating interfacial reactions in break-junction experiments.

Ultra-highly conductive optoelectronic modulated single-molecule nickel bis(dithiolene) junctions with strong molecule-electrode coupling

Strong molecule-electrode coupling originating from orbit hybridization between gold and the delocalized molecular wires in single-molecule junctions facilitates facile transport towards smart molecular devices. In this paper, we report ultra-highly conductive single-molecule circuits based on highly delocalized nickel bis(dithiolene) (NiS4) molecular junctions using scanning tunneling microscope break junction technique. Single-molecule charge transport measurement of both NiS4 reveals they exhibits high conductance of 10−1.49G0 and 10−1.51G0, respectively. Moreover, under intervention of high bias voltage the molecular conductance could be further improved to approximately 10−1.00G0, the highest value reported to date with similar molecular lengths. Theoretical calculations suggest that the strong hybridization of the π-channels and the gold electrodes in both junctions exists and it further extends from molecule-electrode interfaces to metal electrodes as visualized by the isosurface plots of the transmitting eigenstate, which lead to not only a distinct energy shift of the dominated LUMO peaks toward Fermi level, but also broad peaks in the LUMO resonance in the transmission functions. In addition, the both molecular junctions show remarkable photoconductance of approximately 10−1.00G0 under resonant light excitation, due to possible exciton binding in these junctions. Interestingly, the conductance switching of both molecular junctions under optoelectronic modulation is highly reversible, forming a multi-stimulus responsive molecular switch. This work not only provides a building block for fabricating highly conducting molecular wires with strong molecule-electrode coupling, but also lays a foundation for designing optoelectronic modulated functional molecule-scale devices.

Conformational Control of σ-Interference Effects in the Conductance of Permethylated Oligosilanes.

As silicon-based integrated circuits continue to shrink, their molecular characteristics become more pronounced. However, the structure-property relationship of silicon-based molecular junctions remains to be elucidated. Here, an intuitive explanation of the effects of backbone dihedral angles on transport properties in permethylated oligosilanes is presented employing the Ladder C model Hamiltonian combined with nonequilibrium Green's function formalism. Backbone dihedral angles modulate quantum interference (QI), resulting in the change of the transmission coefficient at the Fermi energy (EF) by up to 6 orders of magnitude in Si4Me10. Because the types of QI (constructive or destructive) between molecular conductance orbitals (MCOs) are unchanged, the relative magnitudes of contributions from QI are critical. This quantitative aspect of QI is often neglected in previous theoretical studies. Small backbone dihedral angles lead to localized MCOs near EF and delocalized MCOs further away from EF. As a result, the constructive QI between the MCOs near EF is suppressed, while the destructive QI between other MCOs is enhanced. This insight opens an avenue to harness QI to realize ultrainsulating molecular devices.

Molecular Orientation and Thermal Conductivity in Liquid Crystalline Epoxy Resins by Anionic Ring-Opening Polymerization

Molecular Orientation and Thermal Conductivity in Liquid Crystalline Epoxy Resins by Anionic Ring-Opening Polymerization

Protein Quakes in Redox Metalloenzymes: Clues to Molecular Enzyme Conductivity Triggered by Binding of Small Substrate Molecules.

Multicentre redox metalloproteins undergo conformational changes on electrochemical surfaces, or on enzyme substrate binding. The two-centre copper enzymes, laccase (Type I and TypeII/III Cu) and nitrite reductase (CuNIR) (Type I and Type II Cu) are examples. With some exceptions, these enzymes show no non-turnover voltammetry on Au(111)-surfaces modified by thiol based self-assembled molecular monolayers, but dioxygen or nitrite substrate triggers strong electrocatalytic signals. Scanning tunnelling microscopy also shows high conductivity only when dioxygen or nitrite is present. Atomic force microscopy shows constant CuNIR height but pronounced structural expansion in the electrocatalytic range on nitrite binding. We have recently offered a rationale, based on ab initio quantum chemical studies of water/nitrite substitution in a 740-atom CuNIR fragment. Presently we provide much more detailed structural assignment mapped to single-residue resolution. NO2 --binding induces both a 2 Å Cu-Cu distance increase, and pronounced frontier orbital delocalization strongly facilitating ET between the Cu regions. The conformational changes transmit from the catalytic Type II centre to the electron inlet Type I centre, via the His129-Cys130 ligands, and via Type I-Cys130 or Type I-His129 ending at Type II Asp92. The ET patterns are reflected in different atomic Mulliken charges in the water and nitrite CuNIR fragment.

Boosting the Photoresponse of Azobenzene Single-Molecule Junctions via Mechanical Interlock and Dynamic Anchor.

As the most classic photoisomerization system, azobenzene has been widely utilized as a building unit in various photoswitching applications. However, attempts to build azobenzene-based single-molecule photoswitches have met with limited success, giving low on/off ratios. Herein, we demonstrate two designs of azobenzene-based photoresponsive single-molecule junctions, based on mechanically interlocked diazocine and azobenzene-based dynamic anchors, respectively. Molecular conductance measurements using the scanning tunneling microscope breaking junction (STMBJ) technique revealed dramatic conductance changes upon photoillumination, achieving a high on/off ratio of ∼3.7. Using density functional theory (DFT), we revealed peculiar quantum interference (QI) effects in the diazocine molecular switch, indicating that diazocine is an excellent candidate for molecular photoswitches. The asymmetric azobenzene devices with a dynamic anchor exhibit switching behavior between a fully off state and a highly conductive state associated with the trans/cis conformation transition. The findings of this work not only present the design and development of functional molecular devices based on azobenzene units but also provide insight into the fundamental properties of light-induced quantum interference in azobenzene-based molecular devices.

Towards Stable Helical Structures with Enhanced Molecular Conductance by Strengthening Through‐Space Conjugation

AbstractDeveloping long‐chain molecules with stable helical structures is of significant importance for understanding and modulating the properties and functions of helical biological macromolecules, but challenging. In this work, an effective and facile approach to stabilize folded helical structures by strengthening through‐space conjugation is proposed, using new ortho‐hexaphenylene (o‐HP) derivatives as models. The structure–activity relationship between the through‐space conjugation and charge‐transport behavior of the prepared folded helical o‐HP derivatives is experimentally and theoretically investigated. It is demonstrated that the through‐space conjugation within o‐HP derivatives can be strengthened by introducing electron‐withdrawing pyridine and pyrazine rings, which can effectively stabilize the helical structures of o‐HP derivatives. Moreover, scanning tunneling microscopy‐break junction measurements reveal that the stable regular helical structures of o‐HP derivatives open‐up dominant through‐space charge‐transport pathways, and the single‐molecule conductance is enhanced by more than 70 % by strengthening through‐space conjugation with pyridine and pyrazine. However, the through‐bond charge transport pathways contribute much less to the conductance of o‐HP derivatives. These results not only provide a new method for exploring stable helical molecules, but also provide a stepping stone for deciphering and modulating the charge‐transport behavior of helical systems at the single‐molecule level.

Towards Stable Helical Structures with Enhanced Molecular Conductance by Strengthening Through-Space Conjugation.

Developing long-chain molecules with stable helical structures is of significant importance for understanding and modulating the properties and functions of helical biological macromolecules, but challenging. In this work, an effective and facile approach to stabilize folded helical structures by strengthening through-space conjugation is proposed, using new ortho-hexaphenylene (o-HP) derivatives as models. The structure-activity relationship between the through-space conjugation and charge-transport behavior of the prepared folded helical o-HP derivatives is experimentally and theoretically investigated. It is demonstrated that the through-space conjugation within o-HP derivatives can be strengthened by introducing electron-withdrawing pyridine and pyrazine rings, which can effectively stabilize the helical structures of o-HP derivatives. Moreover, scanning tunneling microscopy-break junction measurements reveal that the stable regular helical structures of o-HP derivatives open-up dominant through-space charge-transport pathways, and the single-molecule conductance is enhanced by more than 70 % by strengthening through-space conjugation with pyridine and pyrazine. However, the through-bond charge transport pathways contribute much less to the conductance of o-HP derivatives. These results not only provide a new method for exploring stable helical molecules, but also provide a stepping stone for deciphering and modulating the charge-transport behavior of helical systems at the single-molecule level.

Acid-Mediated Modulation of the Conductance of Diazapentalene Molecular Junctions.

We report an acid-mediated regulation of single-molecule junction conductance achieved using an electron-deficient unit, diazapentalene, functionalized with thiophene extending units and thiomethyl aurophilic terminal groups. This diazapentalene derivative exhibits a protonation reaction in the presence of trifluoroacetic acid, as characterized by UV-vis absorption spectroscopy, and the protonated species shows a voltage-dependent single-molecule conductance, which is not observed for the pristine molecules. Specifically, under a high bias voltage of 850 mV, we observe a conductance value for the protonated molecule larger than that for the deprotonated one by a factor of 4. Density functional theory-based transport calculations show a slight broadening of the HOMO and LUMO frontier orbitals, as well as a reduced HOMO-LUMO gap when the molecule becomes protonated; this implies an increased conductance under protonation that is consistent with the experimental conductance data. Our work demonstrates a new molecular design for versatile control of molecular conductance through the use of acid in the solvent environment.

Shape-persistent ladder molecules exhibit nanogap-independent conductance in single-molecule junctions.

Molecular electronic devices require precise control over the flow of current in single molecules. However, the electron transport properties of single molecules critically depend on dynamic molecular conformations in nanoscale junctions. Here we report a unique strategy for controlling molecular conductance using shape-persistent molecules. Chemically diverse, charged ladder molecules, synthesized via a one-pot multicomponent ladderization strategy, show a molecular conductance (d[log(G/G0)]/dx ≈ -0.1 nm-1) that is nearly independent of junction displacement, in stark contrast to the nanogap-dependent conductance (d[log(G/G0)]/dx ≈ -7 nm-1) observed for non-ladder analogues. Ladder molecules show an unusually narrow distribution of molecular conductance during dynamic junction displacement, which is attributed to the shape-persistent backbone and restricted rotation of terminal anchor groups. These principles are further extended to a butterfly-like molecule, thereby demonstrating the strategy's generality for achieving gap-independent conductance. Overall, our work provides important avenues for controlling molecular conductance using shape-persistent molecules.

Single-Molecule Cross-Plane Conductance of Polycyclic Aromatic Hydrocarbon Derivatives.

In the cross-plane single-molecule junctions, the correlation between molecular aromaticity and conductance remained puzzling. Cross-plane break junction (XPBJ) provides new insight into understanding the role of aromaticity and conjugation to molecules on charge transport through the planar molecules. In this work, we investigated the modulation of cross-plane charge transport in pyrene derivatives by hydrogenation and substituents based on the XPBJ method that differs from those used in-plane transport. We measured the electrical conductance of the hydrogenated derivatives of the pyrenes and found that hydrogenation reduces conductance, and the fully hydrogenated molecule has the lowest conductance. Conductance of pyrene derivatives increased after substitution by both electron-donating and electron-withdrawing groups. By calculating, the trend in decreased conductance of hydrogenated pyrene was found to be consistent with the change in aromaticity. Electron-withdrawing substituents reduce the aromaticity of the molecule and narrow the HOMO-LUMO gap, while electron-donating groups increase the aromaticity but also narrow the gap. Our work reveals the potential of fine-tuning the structure of the pyrene molecule to control the cross-plane charge transport through the single-molecule junctions.

Quantifying the conductivity of a single polyene chain by lifting with an STM tip

Conjugated polymers are promising candidates for molecular wires in nanoelectronics, with flexibility in mechanics, stability in chemistry and variety in electrical conductivity. Polyene, as a segment of polyacetylene, is a typical conjugated polymer with straightforward structure and wide-range adjustable conductance. To obtain atomic scale understanding of charge transfer in polyene, we have measured the conductance of a single polyene-based molecular chain via lifting it up with scanning tunneling microscopy tip. Different from semiconducting characters in pristine polyene (polyacetylene), high conductance and low decay constant are obtained, along with an electronic state around Fermi level and characteristic vibrational mode. These observed phenomena result from pinned molecular orbital owing to molecule-electrode coupling at the interface, and weakened bond length alternation due to electron-phonon coupling inside single molecular chain. Our findings emphasize the interfacial characteristics in molecular junctions and promising properties of polyene, with single molecular conductance as a vital tool for bringing insights into the design and construction of nanodevices.

Quantum rate electrodynamics and resonant junction electronics of heterocyclic molecules

The quantum rate theory provides a framework to understand electron-transfer reactions by correlating the electron-transfer rate constant (ν) with the quantum capacitance (Cq) and the molecular conductance (G). This theory, which is rooted in relativistic quantum electrodynamics, predicts a fundamental frequency ν=E/h for electron-transfer reactions, where E is the energy associated with the density of states Cq/e2. This work demonstrates the applicability of the quantum rate theory to the intermolecular charge transfer of push-pull heterocyclic compounds assembled over conducting electrodes. Remarkably, the observed differences between molecular junction electronics formed by push-pull molecules and the electrodynamics of electrochemical reactions on redox-active modified electrodes can be attributed solely to the adiabatic setting of the quantum conductance in push-pull molecular junctions. The electrolyte field-effect screening environment plays a crucial role in modulating the resonant quantum conductance dynamics of the molecule-bridge-electrode structure. In this context, the intermolecular electrodynamics within the frontier molecular orbital of push-pull heterocyclic molecules adhere to relativistic quantum mechanics, consistent with the predictions of the quantum rate theory.

Correlating structure, self-assembly chemistry and conductivity of trithiocyanuric acid on Au(111)

The majority of candidates for simple model molecular-electronic components consist of a conductive π-conjugated hydrocarbon linker attached to at least two anchoring groups, such as thiols or isocyanides. It has been found that select molecules self-assemble on gold surfaces, creating one-dimensional conductive structures that act as “molecular wires”. Furthermore, these oligomers can form molecular bridges between gold nanoparticles, leading to the creation of simple molecular-electronic devices. This raises the question whether other π-conjugated molecular linkers could exhibit similar behavior that might offer a broader range of candidates for fabricating electronic devices. Trithiocyanuric acid (1,3,5-triazine-2,4,6-trithiol, TTCA) provides a possible candidate. TTCA (C3N3(SH)3) can exist as a trithiol or as a trithione in which hydrogens transfer to the sulfurs so that they are present with three C=N groups within the ring. TTCA exists naturally in the trithione form but converts into a trithiol when adsorbed onto an Ag(111) where it is vertically oriented. The structure of TTCA adsorbed on Au(111) is studied here using reflection-absorption infrared spectroscopy (RAIRS) where it is found to remain as the trithione isomer, but changes orientation as the coverage increases. Scanning-tunneling microscopy (STM) reveals that TTCA oligomerizes on Au(111) to form chains and triangular structures. The influence on molecular conductivity due to the differences in the adsorbate's isomeric structure was investigated using devices comprising either silver or gold nanoparticles deposited in the gap between gold nanoelectrodes. Both devices were found to conduct when dosed with TTCA, but the devices fabricated using silver were about 13 time more conductive than those made from gold nanoparticles, consistent with the π-conjugated structure formed on silver but not on gold. This implies that oligomers form both on silver and on gold and potentially increases the range of molecule-metal combinations that might be used to fabricate molecular-electronic devices.

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Impact of Solvent Electrostatic Environment on Molecular Junctions Probed via Electrochemical Impedance Spectroscopy.

The electrostatic environment around nanoscale molecular junctions modulates charge transport; solvents alter this environment. Methods to directly probe solvent effects require correlating measurements of the local electrostatic environment with charge transport across the metal-molecule-metal junction. Here, we measure the conductance and current-voltage characteristics of molecular wires using a scanning tunneling microscope-break junction (STM-BJ) setup in two commonly used solvents. Our results show that the solvent environment induces shifts in molecular conductance, which we quantify, but more importantly we find that the solvent also impacts the magnitude of current rectification in molecular junctions. By incorporating electrochemical impedance spectroscopy into the STM-BJ setup, we measure the capacitance of the dipole layer formed at the metal-solvent interface and show that rectification can be correlated with solvent capacitance. These results provide a method of quantifying the impact of the solvent environment and a path toward improved environmental control of molecular devices.

Evidence for NMR Relaxation Enhancement in a Protic Ionic Liquid by the Movement of Protons Independent of the Translational Diffusion of Cations.

The molecular dynamics, thermal stability, and ionic conductivity were studied in the protic ionic liquid 1-methylimidazolium bis(trifluoromethylsulfonyl)imide ([MIm][TFSI]). The relaxation of the 1H spin-lattice of cations in the measured frequency range (10 kHz to 20 MHz) and temperature (298 to 343 K) is sensitive mainly to slow processes occurring in the molecular dynamics of protic ionic liquid and dominated by the contribution of intermolecular translational diffusion. Molecular rotations give only a constant contribution and become significant in the higher frequency range. An interesting feature is the observed enhancement of the 1H spin-lattice relaxation below 0.03 MHz attributed to the exchange of protons (order of 10-5 s) between imidazolium cations. The measurements of the self-diffusion coefficient of hydrogen atoms of cation from 298 to 343 K additionally confirm the observed phenomenon. The coefficient for exchangeable protons -NH is higher than for the cation. The nuclear magnetic resonance (NMR) experiments provide unambiguous evidence for proton transport decoupled from molecular diffusion of ions and support the conclusion that the charge transport mechanism in the studied PIL includes contributions from both the vehicular and Grotthus mechanisms. The protic ionic liquid is thermally stable to about 573 K as shown by thermogravimetric analysis and its electrical conductivity is 5 × 10-2 S/cm at 423 K.

Precision Basecalling of Single DNA Nucleotide from Overlapped Transmission Readouts with Machine Learning Aided Solid-State Nanogap.

DNA sequencing with the quantum tunneling technique heralds a paradigm shift in genetic analysis, promising rapid and accurate identification for diverging applications ranging from personalized medicine to security issues. However, the widespread distribution of molecular conductance, conduction orbital alignment for resonant transport, and decoding crisscrossing conductance signals of isomorphic nucleotides have been persistent experimental hurdles for swift and precise identification. Herein, we have reported a machine learning (ML)-driven quantum tunneling study with solid-state model nanogap to determine nucleotides at single-base resolution. The optimized ML basecaller has demonstrated a high predictive basecalling accuracy of all four nucleotides from seven distinct data pools, each containing complex transmission readouts of their different dynamic conformations. ML classification of quaternary, ternary, and binary nucleotide combinations is also performed with high precision, sensitivity, and F1 score. ML explainability unravels the evidence of how extracted normalized features within overlapped nucleotide signals contribute to classification improvement. Moreover, electronic fingerprints, conductance sensitivity, and current readout analysis of nucleotides have promised practical applicability with significant sensitivity and distinguishability. Through this ML approach, our study pushes the boundaries of quantum sequencing by highlighting the effectiveness of single nucleotide basecalling with promising implications for advancing genomics and molecular diagnostics.