Conformational changes of single molecules induced by scanning tunneling microscopy manipulation: a route to molecular switching

Simultaneous Ring-Opening and Dehydrogenation of Diarylethene Induced by Tunneling Electrons

Understanding the reversible transformation between two isomeric states of organic molecules under external stimulation is essential for advancing single-molecule device development. Photochromic diarylethene (DAE) derivatives are promising candidates for single molecular switching elements. This study investigates the single-molecule reactions of the closed-form isomer of a DAE derivative on Cu(111) using scanning tunneling microscopy (STM). A novel ring-opening pathway, distinct from the well-known photochromic isomerization, was discovered. Electron injection into the lowest unoccupied molecular orbitals induces the sequential anchoring of molecules to the substrate through the dehydrogenation of a methyl group at the 2-position of the thiophene ring. This mechanism was revealed by density functional theory calculations and STM simulations. The adsorption configurations for singly and doubly dehydrogenated DAEs were identified. Based on these findings, a new reaction mechanism extending beyond reversible isomeric reactions is proposed for DAE on Cu(111). The present work establishes a novel framework for future studies on single-molecule switching phenomena on metal substrates.

Regulation of Reaction Pathways in Coordinated Chains by Directional Mechanical Force

Mechanochemistry refers to chemical reactions induced by mechanical forces. Due to different reaction mechanisms, products obtained through mechanochemistry can be distinct from those produced by thermochemistry and photochemistry. Scanning probe microscopy is a powerful tool for studying single-molecule mechanochemical processes. Mechanical force is a vector that has both magnitude and direction. Previous studies have focused on triggering reactions by forces and measuring their magnitude. In this work, we use the direction of the force to regulate the reaction pathway in a spin-crossover coordinated chain. The chains are prepared via the dehydrogenated coordination reaction between tetrahydroxybenzene molecules and Ni atoms on Au(111). The Ni atoms in the chain alternate between a high-spin state and a low-spin state. By altering Ni-O bond lengths and O-Ni-O angles through the directional mechanical force, a chemical process occurs, and the spin state of Ni undergoes a transition. With the attraction from a Au tip, the Ni atom is pulled from high-spin to low-spin state. With the repulsion from a C60-functionalized tip, the low-spin Ni atom is pushed to the high-spin state. The force to induce the reaction is measured by qPlus atomic force microscopy. This study provides an approach for regulating chemical pathways.

Remote-Controllable Interfacial Electron Tunneling at Heterogeneous Molecular Junctions via Tip-Induced Optoelectrical Engineering

Molecular electronics enables functional electronic behavior via single molecules or molecular self-assembled monolayers, providing versatile opportunities for hybrid molecular-scale electronic devices. Although various molecular junction structures are constructed to investigate charge transfer dynamics, significant challenges remain in terms of interfacial charging effects and far-field background signals, which dominantly block the optoelectrical observation of interfacial charge transfer dynamics. Here, tip-induced optoelectrical engineering is presented that synergistically correlates photo-induced force microscopy and Kelvin probe force microscopy to remotely control and probe the interfacial charge transfer dynamics with sub-10 nm spatial resolution. Based on this approach, the optoelectrical origin of metal-molecule interfaces is clearly revealed by the nanoscale heterogeneity of the tip-sample interaction and optoelectrical reactivity, which theoretically aligned with density functional theory calculations. For a practical device-scale demonstration of tip-induced optoelectrical engineering, interfacial tunneling is remotely controlled at a 4-inch wafer-scale metal-insulator-metal capacitor, facilitating a 5.211-fold current amplification with the tip-induced electrical field. In conclusion, tip-induced optoelectrical engineering provides a novel strategy to comprehensively understand interfacial charge transfer dynamics and a non-destructive tunneling control platform that enables real-time and real-space investigation of ultrathin hybrid molecular systems.

Probing surface properties of organic molecular layers by scanning tunneling microscopy

In view of the relevance of organic thin layers in many fields, the fundamentals, growth mechanisms, and dynamics of thin organic layers, in particular thiol-based self-assembled monolayers (SAMs) on Au(111) are systematically elaborated. From both theoretical and practical perspectives, dynamical and structural features of the SAMs are of great intrigue. Scanning tunneling microscopy (STM) is a remarkably powerful technique employed in the characterization of SAMs. Numerous research examples of investigation about the structural and dynamical properties of SAMs using STM, sometimes combined with other techniques, are listed in the review. Advanced options to enhance the time resolution of STM are discussed. Additionally, we elaborate on the extremely diverse dynamics of various SAMs, such as phase transitions and structural changes at the molecular level. In brief, the current review is expected to supply a better understanding and novel insights regarding the dynamical events happening in organic SAMs and how to characterize these processes.

Voltage-Modulated van der Waals Interaction in Single-Molecule Junctions

Understanding how molecular geometry affects the electronic properties of single-molecule junctions experimentally has been challenging. Typically, metal-molecule-metal junctions are measured using a break-junction method where electrode separation is mechanically evolving during measurement. Here, to probe the impact of the junction geometry on conductance, we apply a sinusoidal modulation to the molecular junction electrode position. Simultaneously, we probe the nonlinearity of the current-voltage characteristics of each junction through a modulation in the applied bias at a different frequency. In turn, we show that junctions formed with molecules that have different molecule-electrode interfaces exhibit statistically distinguishable Fourier-transformed conductances. In particular, we find a marked bias dependence for the modulation of junctions where transmission is mediated thorough the van der Waals (vdW) interaction. We attribute our findings to voltage-modulated vdW interactions at the single-molecule level.

Advances of Various Heterogeneous Structure Types in Molecular Junction Systems and Their Charge Transport Properties

Molecular electronics that can produce functional electronic circuits using a single molecule or molecular ensemble remains an attractive research field because it not only represents an essential step toward realizing ultimate electronic device scaling but may also expand our understanding of the intrinsic quantum transports at the molecular level. Recently, in order to overcome the difficulties inherent in the conventional approach to studying molecular electronics and developing functional device applications, this field has attempted to diversify the electrical characteristics and device architectures using various types of heterogeneous structures in molecular junctions. This review summarizes recent efforts devoted to functional devices with molecular heterostructures. Diverse molecules and materials can be combined and incorporated in such two- and three-terminal heterojunction structures, to achieve desirable electronic functionalities. The heterojunction structures, charge transport mechanisms, and possible strategies for implementing electronic functions using various hetero unit materials are presented sequentially. In addition, the applicability and merits of molecular heterojunction structures, as well as the anticipated challenges associated with their implementation in device applications are discussed and summarized. This review will contribute to a deeper understanding of charge transport through molecular heterojunction, and it may pave the way toward desirable electronic functionalities in molecular electronics applications.

Three-Bit Digital Comparator Based on Intracell Diffusion of Silver Single Atom

Using a single atom to construct electronic components is a promising route for the microminiaturization of electronic instruments. However, effective control of the intrinsic property in a molecular/atomic prototype component is full of challenges. Here, we present that the intracell diffusion behavior of a target Ag single atom within a unit cell of Si reconstruction is controllably modulated by constructing Ag nanoclusters and arrays in the neighboring cells. Moreover, a three-bit digital comparator device is fabricated on the basis of the diffusion time of a Ag single atom that can be effectively regulated by using the intercoupling between the target Ag monomer and the surrounding metal arrays.

Voltage-dependent plasticity of spin-polarized conductance in phenyl-based single-molecule magnetic tunnel junctions

Synaptic strengths between neurons in brain networks are highly adaptive due to synaptic plasticity. Spike-timing-dependent plasticity (STDP) is a form of synaptic plasticity induced by temporal correlations between the firing activity of neurons. The development of experimental techniques in recent years enabled the realization of brain-inspired neuromorphic devices. Particularly, magnetic tunnel junctions (MTJs) provide a suitable means for the implementation of learning processes in molecular junctions. Here, we first considered a two-neuron motif subjected to STDP. By employing theoretical analysis and computer simulations we showed that the dynamics and emergent structure of the motif can be predicted by introducing an effective two-neuron synaptic conductance. Then, we considered a phenyl-based single-molecule MTJ connected to two ferromagnetic (FM) cobalt electrodes and investigated its electrical properties using the non-equilibrium Green’s function (NEGF) formalism. Similar to the two-neuron motif, we introduced an effective spin-polarized conductance in the MTJ. Depending on the polarity, frequency and strength of the bias voltage applied to the MTJ, the system can learn input signals by adaptive changes of the effective conductance. Interestingly, this voltage-dependent plasticity is an intrinsic property of the MTJ where its behavior is reminiscent of the classical temporally asymmetric STDP. Furthermore, the shape of voltage-dependent plasticity in the MTJ is determined by the molecule-electrode coupling strength or the length of the molecule. Our results may be relevant for the development of single-molecule devices that capture the adaptive properties of synapses in the brain.

Deterministic transfer of optical-quality carbon nanotubes for atomically defined technology

When continued device scaling reaches the ultimate limit imposed by atoms, technology based on atomically precise structures is expected to emerge. Device fabrication will then require building blocks with identified atomic arrangements and assembly of the components without contamination. Here we report on a versatile dry transfer technique for deterministic placement of optical-quality carbon nanotubes. Single-crystalline anthracene is used as a medium which readily sublimes by mild heating, leaving behind clean nanotubes and thus enabling bright photoluminescence. We are able to position nanotubes of a desired chirality with a sub-micron accuracy under in-situ optical monitoring, thereby demonstrating deterministic coupling of a nanotube to a photonic crystal nanobeam cavity. A cross junction structure is also designed and constructed by repeating the nanotube transfer, where intertube exciton transfer is observed. Our results represent an important step towards development of devices consisting of atomically precise components and interfaces.

As device fabrication reach atomic scales, assembly of atomically defined components becomes crucial. Here, the authors demonstrate a low contamination transfer technique, using single-crystalline anthracene as medium, for placement of structure-specific carbon nanotubes with submicron accuracy.

Conformation and Quantum-Interference-Enhanced Thermoelectric Properties of Diphenyl Diketopyrrolopyrrole Derivatives

Manipulating the connectivity of external electrodes to central rings of carbon-based molecules in single molecule junctions is an effective route to tune their thermoelectrical properties. Here we investigate the connectivity dependence of the thermoelectric properties of a series of thiophene-diketopyrrolopyrrole (DPP) derivative molecules using density functional theory and tight-binding modeling, combined with quantum transport theory. We find a significant dependence of electrical conductance on the connectivity of the two thiophene rings attached to the DPP core. Interestingly, for connectivities corresponding to constructive quantum interference (CQI), different isomers obtained by rotating the thiophene rings possess the same electrical conductance while those corresponding to destructive quantum interference (DQI) show huge conductance variations upon ring rotation. Furthermore, we find that DQI connectivity leads to enhanced Seebeck coefficients, which can reach 500-700 μV/K. After including the contribution to the thermal conductance from phonons, the full figure of merit (ZT) for the CQI molecules could reach 1.5 at room temperature and it would further increase to 2 when temperature elevates to 400 K. Finally, we demonstrate that doping with tetracyanoquinodimethane can change the sign of the Seebeck coefficients by forming a charge-transfer system with the DPP.

Structural Memory Effects in Gold-4,4'-Bipyridine-Gold Single-Molecule Nanowires

We study the vulnerability of single-molecule nanowires against a temporary disconnection of the junction. To this end, we compare the room and low-temperature junction formation trajectories along the opening and closing of gold-4,4'-bipyridine-gold single-molecule nanowires. In the low-temperature measurements, the cross-correlations between the opening and subsequent closing conductance traces demonstrate a strong structural memory effect: around half of the molecular opening traces exhibit similar, statistically dependent molecular features as the junction is closed again. This means that the junction stays rigid and the molecule remains protruding from one electrode even after the rupture of the junction, and therefore, the same single-molecule junction can be reestablished if the electrodes are closed again. In the room-temperature measurements, however, weak opening-closing correlations are found, indicating a significant rearrangement of the junction after the rupture and the related loss of structural memory effects.

Switching Quantum Interference in Phenoxyquinone Single Molecule Junction with Light

Quantum interference (QI) can lead to large variations in single molecule conductance. However, controlling QI using external stimuli is challenging. The molecular structure of phenoxyquinone can be tuned reversibly using light stimulus. In this paper, we show that this can be utilized to control QI in phenoxyquinone derivatives. Our calculations indicate that, as a result of such variation in molecular structure of phenoxyquinone, a crossover from destructive to constructive QI is induced. This leads to a significant variation in the single molecule conductance by a couple of orders of magnitude. This control of QI using light is a new paradigm in photosensitive single molecule switches and opens new avenues for future QI-based photoswitches.

Force-Activated Isomerization of a Single Molecule

Understanding and controlling isomerization at the single molecular level should provide new insight into the molecular dynamics and design guidelines of functional devices. Scanning tunneling microscopy (STM) has been demonstrated to be a powerful tool to study isomerization of single molecules on a substrate, by either electric field or inelastic electron tunneling mechanisms. A similar molecular isomerization process can in principle be induced by mechanical force; however, relevant study has remained elusive. Here, we demonstrate that isomerization of a N,N-dimethylamino-dianthryl-benzene molecule on Ag(100) can be mechanically driven by the STM tip. The existence of an out-of-plane dimethylamino group in the molecule is found to play a pivotal role in the isomerization process by providing a steric hindrance effect for asymmetric interaction between the STM tip and the molecule. This underlying mechanism is further confirmed by performing molecular dynamics simulations, which show agreement with experimental results. Our work opens the opportunity to manipulate the molecular configuration on the basis of mechanical force.

Electric-Field-Controllable Conductance Switching of an Overcrowded Ethylene Self-Assembled Monolayer

Molecular isomerism has been discussed from the viewpoint of the tiniest switch and memory elements in electronics. Here, we report an overcrowded ethylene-based molecular conductance switch, which fulfills all the essential requirements for implementation into electronic devices, namely, electric-field-controllable reversible conductance change with a molecular-level spatial resolution, robust conformational bistability under ambient conditions, and ordered monolayer formation on electrode surfaces. The conformational state of this overcrowded ethylene, represented by a folded or twisted conformer, is susceptible to external environments. Nanoscopic measurements using scanning tunneling microscopy techniques, together with theoretical simulations, revealed the electronic properties of each conformer adsorbed on Au(111). While the twisted conformer prevails in the molecularly dispersed state, upon self-assembly into a monolayer, a two-dimensional network structure of the folded conformer is preferentially formed due to particular intermolecular interaction. In the monolayer state, folded-to-twisted and its reverse isomerization can be controlled by the modulation of electric fields.

In Operando Characterization and Control over Intermittent Light Emission from Molecular Tunnel Junctions via Molecular Backbone Rigidity

In principle, excitation of surface plasmons by molecular tunnel junctions can be controlled at the molecular level. Stable electrical excitation sources of surface plasmons are therefore desirable. Herein, molecular junctions are reported where tunneling charge carriers excite surface plasmons in the gold bottom electrodes via inelastic tunneling and it is shown that the intermittent light emission (blinking) originates from conformational dynamics of the molecules. The blinking rates, in turn, are controlled by changing the rigidity of the molecular backbone. Power spectral density analysis shows that molecular junctions with flexible aliphatic molecules blink, while junctions with rigid aromatic molecules do not.

Unravelling the conductance path through single-porphyrin junctions

By studying transport through seven structurally related porphyrin derivatives with a machine learning algorithm we could identify and distinguish three different electronic paths.

Porphyrin derivatives are key components in natural machinery enabling us to store sunlight as chemical energy. In spite of their prominent role in cascades separating electrical charges and their potential as sensitizers in molecular devices, reports concerning their electronic transport characteristics are inconsistent. Here we report a systematic investigation of electronic transport paths through single porphyrin junctions. The transport through seven structurally related porphyrin derivatives was repeatedly measured in an automatized mechanically controlled break-junction set-up and the recorded data were analyzed by an unsupervised clustering algorithm. The correlation between the appearances of similar clusters in particular sub-sets of the porphyrins with a common structural motif allowed us to assign the corresponding current path. The small series of model porphyrins allowed us to identify and distinguish three different electronic paths covering more than four orders of magnitude in conductance.

Unraveling the molecular conformations of a single ruthenium complex adsorbed on the Ag(111) surface by calculations

The tris(dibenzoylmethanato)ruthenium (Ru(dbm)3) molecule has recently been characterized by scanning tunneling microscopy (STM) experiments upon adsorption on Ag(111). The adsorbed Ru(dbm)3 molecule shows two conformations with respect to the [11[combining macron]0] direction of the substrate, one with a three-lobed feature and the other one with a bi-lobed structure. For each of these structures, the molecule can take two geometries (states). Molecular mechanics calculations in a semi-empirical framework and STM calculated images reveal that these states on the substrate originate from the enantiomer of the Ru(dbm)3 molecule in the case of three-lobed structure and from the rotation of the two phenyls in the top dbm moities for the bi-lobed form.

A computational study on a multimode spin conductance switching by coordination isomerization in organometallic single-molecule junctions

Single-molecule junctions provide the additional flexibility of tuning the on/off conductance states through molecular design. Here, we focus on a family of organometallic complexes with a conjugated curved buckybowl as the ligand. Using first-principles calculations, a multi-mode reversible spin switching based on the CpFe·corannulene complex is predicted by the temperature control of the CpFe+ coordination position in corannulene. The different spin conductance states for three coordinated modes are ascribed to the different electronic spin states of the organometallic complex due to crystal field effects. The predicted relative stabilities of isomers and the energy barriers of isomerization reactions can ensure that the conversion among the three isomers can occur quickly and, at a specific temperature, a dominant isomer has a higher proportion than the other two isomers. This provides a new framework for understanding transport in organometallic complexes with localized d states. This presents an exciting opportunity for exploiting junctions involving molecular spin switching.

Surface Vacancy-Induced Switchable Electric Polarization and Enhanced Ferromagnetism in Monolayer Metal Trihalides

Monolayer chromium triiodide (CrI₃), as the thinnest ferromagnetic material demonstrated in experiment [ Huang et al. Nature 2017 , 546 , 270 ], opens up new opportunities for the application of two-dimensional (2D) materials in spintronic nanodevices. Atom-thick 2D materials with switchable electric polarization are now urgently needed for their rarity and important roles in nanoelectronics. Herein, we unveil that surface I vacancies not only enhance the intrinsic ferromagnetism of monolayer CrI₃ but also induce switchable electric polarization. I vacancies bring about an out-of-plane polarization without breaking the nonmetallic nature of CrI₃. Meanwhile, the induced polarization can be reversed in a moderate energy barrier, arising from the unique porosity of CrI₃ that contributes to the switch of I vacancies between top and bottom surfaces. Engineering 2D switchable polarization through surface vacancies is also applicable to many other metal trihalides, which opens up a new and general way toward pursuing low-dimensional multifunctional nanodevices.

On-Demand Final State Control of a Surface-Bound Bistable Single Molecule Switch

Modern electronic devices perform their defined action because of the complete reliability of their individual active components (transistors, switches, diodes, and so forth). For instance, to encode basic computer units (bits) an electrical switch can be used. The reliability of the switch ensures that the desired outcome (the component's final state, 0 or 1) can be selected with certainty. No practical data storage device would otherwise exist. This reliability criterion will necessarily need to hold true for future molecular electronics to have the opportunity to emerge as a viable miniaturization alternative to our current silicon-based technology. Molecular electronics target the use of single-molecules to perform the actions of individual electronic components. On-demand final state control over a bistable unimolecular component has therefore been one of the main challenges in the past decade (1-5) but has yet to be achieved. In this Letter, we demonstrate how control of the final state of a surface-supported bistable single molecule switch can be realized. On the basis of the observations and deductions presented here, we further suggest an alternative strategy to achieve final state control in unimolecular bistable switches.

Conformation-based signal transfer and processing at the single-molecule level

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl₂Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

Influence of CH···N Interaction in the Self-Assembly of an Oligo(isoquinolyne-ethynylyne) Molecule with Distinct Conformational States

Molecular conformational flexibility can play an important role in supramolecular self-assembly on surfaces, affecting not least chiral molecular assemblies. To explicitly and systematically investigate the role of molecular conformational flexibility in surface self-assembly, we synthesized a three-bit conformational switch where each of three switching units on the molecules can assume one of two distinct binary positions on the surface. The molecules are designed to promote C-H···N type hydrogen bonds between the switching units. While supramolecular self-assembly based on strong hydrogen-bonding interactions has been widely explored, less is known about the role of such weaker directional interactions for surface self-assembly. The synthesized molecules consist of three nitrogen-containing isoquinoline (IQ) bits connected by ethynylene spokes and terminated by tert-butyl (tBu) groups. Using high-resolution scanning tunnelling microscopy, we investigate the self-assembly of the IQ-tBu molecules on a Au(111) surface under ultrahigh-vacuum conditions. The molecules form extended domains of brick-wall structure where the molecular backbones are packed regularly but without selection of specific molecular conformations. However, statistical analysis of the extended network demonstrates alignment/correlation for the orientations of the switching units indicating specific interactions. The primary interaction motifs in the structure are quantified from DFT calculations, showing that the brick-wall structure is indeed stabilized by two types of weak C-H···N bonds, involving either aromatic hydrogens on the IQ groups or nonaromatic hydrogens on the tBu groups. Analysis of the C-H···N interactions in the brick-wall structure explains the observed distribution and alignment of molecular conformations as well as the overall organization of the molecular surface structures.

Multi-orbital charge transfer at highly oriented organic/metal interfaces

The molecule-substrate interaction plays a key role in charge injection organic-based devices. Charge transfer at molecule-metal interfaces strongly affects the overall physical and magnetic properties of the system, and ultimately the device performance. Here, we report theoretical and experimental evidence of a pronounced charge transfer involving nickel tetraphenyl porphyrin molecules adsorbed on Cu(100). The exceptional charge transfer leads to filling of the higher unoccupied orbitals up to LUMO+3. As a consequence of this strong interaction with the substrate, the porphyrin's macrocycle sits very close to the surface, forcing the phenyl ligands to bend upwards. Due to this adsorption configuration, scanning tunneling microscopy cannot reliably probe the states related to the macrocycle. We demonstrate that photoemission tomography can instead access the Ni-TPP macrocycle electronic states and determine the reordering and filling of the LUMOs upon adsorption, thereby confirming the remarkable charge transfer predicted by density functional theory calculations.Charge transfer at molecule-metal interfaces affects the overall physical and magnetic properties of organic-based devices, and ultimately their performance. Here, the authors report evidence of a pronounced charge transfer involving nickel tetraphenyl porphyrin molecules adsorbed on copper.

Adsorption and switching properties of nitrospiropyran on Bi(1 1 4)

Spiropyrans are prototype molecular switches, which undergo a reversible photoinduced ring-opening/-closure reaction between the closed three-dimensional spiropyran (SP) and the open, planar merocyanine (MC) form. In solution the SP isomer is the thermodynamically stable form. Using high resolution electron energy loss spectroscopy, we resolve a thermally-activated irreversible ring-opening reaction of nitrospiropyran resulting in the MC form for coverages above one monolayer. Thus, the situation found in solution is reversed for the adsorbed molecules, since the MC form is more stable due to the modified energetics by the presence of the substrate. In addition, illumination with blue light (445 nm) induced also the ring-opening, while the photostimulated back-reaction could not be observed. The photoisomerization is driven by a substrate-mediated process, i.e. a charge transfer from the substrate into molecular states. The situation changes completely in the monolayer regime. Neither a thermally-assisted nor a photoinduced ring-opening reaction has been identified. We ascribe the suppression to sterical effects stabilizing the SP form due to the surface structure of Bi(1 1 4), which consists of straight atomic rows separated by rough valleys.

Molecular Seesaw: Intricate Dynamics and Versatile Chemistry of Heteroaromatics on Metal Surfaces

The design of novel elementary surface processes is important for applications in catalysis, single-molecule junctions, molecular sensors, switches, and surface-mounted molecular machines. Here we demonstrate by van der Waals inclusive density functional theory calculations that a small and relatively simple heteroaromatic compound s-triazine (C₃H₃N₃) unexpectedly possesses five metastable states when adsorbed on the Pt(111) surface. This diversity of the adsorption states stems from an interplay between versatile molecule/surface chemical bonding and van der Waals interactions and from "softening" of the aromatic ring by nitrogen substitution, which makes folding of the aromatic ring energetically much less demanding as compared to benzene. The intricate seesaw-like surface dynamics and tunable electronic structure of s-triazine show promise for applications in molecular sensors and switches. The broad implications of our findings are demonstrated for triazine- and pyrimidine-based heteroaromatic compounds and other metal surfaces.

Stereoelectronic Effect-Induced Conductance Switching in Aromatic Chain Single-Molecule Junctions

Biphenyl, as the elementary unit of organic functional materials, has been widely used in electronic and optoelectronic devices. However, over decades little has been fundamentally understood regarding how the intramolecular conformation of biphenyl dynamically affects its transport properties at the single-molecule level. Here, we establish the stereoelectronic effect of biphenyl on its electrical conductance based on the platform of graphene-molecule single-molecule junctions, where a specifically designed hexaphenyl aromatic chain molecule is covalently sandwiched between nanogapped graphene point contacts to create stable single-molecule junctions. Both theoretical and temperature-dependent experimental results consistently demonstrate that phenyl twisting in the aromatic chain molecule produces different microstates with different degrees of conjugation, thus leading to stochastic switching between high- and low-conductance states. These investigations offer new molecular design insights into building functional single-molecule electrical devices.

Self-formed nanogap junctions for electronic detection and characterization of molecules and quantum dots

Fabrication of self-forming nanojunction devices is demonstrated using positioning of nanofloret-like building blocks that bridge the gap between two large micron scale electrodes.

On the shuttling mechanism of a chlorine atom in a chloroaluminum phthalocyanine based molecular switch

A ClAlPc-based molecular switch works via the mechanism in which Cl is squeezed in between Al and an inner N-containing ring.

Direct Identification and Determination of Conformational Response in Adsorbed Individual Nonplanar Molecular Species Using Noncontact Atomic Force Microscopy

In recent years atomic force microscopy (AFM) at highest resolution was widely applied to mostly planar molecules, while its application toward exploring species with structural flexibility and a distinct 3D character remains a challenge. Herein, the scope of noncontact AFM is widened by investigating subtle conformational differences occurring in the well-studied reference systems 2H-TPP and Cu-TPP on Cu(111). Different saddle-shape conformations of both species can be recognized in conventional constant-height AFM images. To unambiguously identify the behavior of specific molecular moieties, we extend data acquisition to distances that are inaccessible with constant-height measurements by introducing vertical imaging, that is, AFM mapping in a plane perpendicular to the sample surface. Making use of this novel technique the vertical displacement of the central Cu atom upon tip-induced conformational switching of Cu-TPP is quantified. Further, for 2H-TPP two drastically different geometries are observed, which are systematically characterized. Our results underscore the importance of structural flexibility in adsorbed molecules with large conformational variability and, consequently, the objective to characterize their geometry at the single-molecule level in real space.

Bias-induced conductance switching in single molecule junctions containing a redox-active transition metal complex

ABSTRACT

The paper provides a comprehensive theoretical description of electron transport through transition metal complexes in single molecule junctions, where the main focus is on an analysis of the structural parameters responsible for bias-induced conductance switching as found in recent experiments, where an interpretation was provided by our simulations. The switching could be theoretically explained by a two-channel model combining coherent electron transport and electron hopping, where the underlying mechanism could be identified as a charging of the molecule in the junction made possible by the presence of a localized electronic state on the transition metal center. In this article, we present a framework for the description of an electron hopping-based switching process within the semi-classical Marcus-Hush theory, where all relevant quantities are calculated on the basis of density functional theory (DFT). Additionally, structural aspects of the junction and their respective importance for the occurrence of irreversible switching are discussed.

GRAPHICAL ABSTRACT

Control of Molecule-Metal Interaction by Hydrogen Manipulation in an Organic Molecule

Free-base porphyrin molecules offer appealing options to tune the interaction with their environment via the manipulation of their inner hydrogen atoms and molecular conformation. Using scanning tunneling microscopy we show, through a systematic study, that the molecular conformation, electronic gap, wave function, and molecule-substrate interaction are modified by hydrogen switch or removal. Experimental results in combination with ab initio calculations provide an understanding of the underlying physical process.

Prediction and clarification of structures of (bio)molecules on surfaces

The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.

Manipulation resolves non-trivial structure of corrole monolayer on Ag(111)

Non-trivial arrangement of molecules within a molecular network complicates structure determination due to interdigitation, partial overlap, or stacking. We demonstrate that combined imaging and lateral manipulation with a scanning tunneling microscope resolves the intricate structure of a molecular network in two-dimensions in a straightforward manner. The network, formed by a monolayer of 5,10,15-tris(pentafluorophenyl)-corrole molecules on Ag(111), is manipulated for the first time with single-molecule precision. Our results reveal a shingle-like packing of partially overlapping corrole molecules. Density functional theory calculations support our findings.

The spin-dependent transport of transition metal encapsulated B40fullerene

Two-probe systems of transition metal atom (X)-encapsulated B₄₀fullerene contacted with Au electrodes, where X = Fe, Mn, Ni, and Co.