Dimer Junction Research Articles

Thermal transport in fullerene-based molecular junctions: molecular dynamics simulations

We investigate phonon thermal transport of fullerene-based single-molecule junctions by employing classical molecular dynamics (MD) simulations. We compute the thermal conductances of C60 fullerene monomers, dimers, and trimers utilizing three distinct MD methods. We observe the equilibration dynamics in one approach, and employ two other nonequilibrium steady state simulation methods. We discuss technical aspects of each simulation technique, and show that their predictions for the thermal conductance agree. Our simulations reveal that while the thermal conductance of fullerene monomer and dimer junctions remains similar, that of trimer junctions experiences a significant reduction. This study could assist in the design of high-performing thermoelectric junctions, where low thermal conductance is desired.

Rational design to improve the catalytic efficiency and stability of arginine deiminase

Arginine deiminase (ADI) has garnered significant interest because of its ability to objectively eradicate cancer cells and produce L-citrulline. To meet the production demands, this study focused on enhancing the enzyme activity and thermal stability of ADI. In this study, 24 ADI mutants were obtained through computer aid site-specific mutation in the ADI of Enterobacter faecalis. Notably, the specific enzyme activities of F44W, N163P, E220I, E220L, N318E, A336G, T340I, and N382F increased, reaching 1.33–2.53 times that of the original enzyme. This study confirmed that site-specific mutations are critical for optimizing enzyme function. Additionally, the F44W, N163P, E220I, T340I, and A336G mutants demonstrated good thermal stability. The optimal pH for mutant F44W increased to 8, whereas mutants E220I, I244V, A336G, T340I, and N328F maintained an optimal pH of 7.5. Conversely, the M109L, N163P, E220L, I244L, and N318E mutants shad an optimal pH of 7. This study revealed that mutant enzymes with increased activity were more likely to contain mutation sites situated near the four loops associated with catalytic residues, whereas mutations at the dimer junction sites had a higher tendency to enhance enzyme stability. These findings contribute to the development of ADI industrial applications and its modifications.

Molecular dimer junctions forming: Role of disulfide bonds and electrode‐compression‐time

AbstractThanks to their excellent bond strength, phenyl‐based molecules with thiol anchoring groups are extensively employed to form stable single‐molecule junctions. However, two critical questions are still not answered which seriously hinder high‐yield establishing reliable molecular functional devices: (1) Whether molecular dimer junctions will be formed, and if this is the case, whether the dimerization is caused by intermolecular disulfide bonds or π–π stacking of phenyl rings; (2) Upon a mechanical‐compression force, is it possible that both anchoring groups of the molecule bond to the same electrode instead of bridging two opposite electrodes, which would drastically reduce the yield of the molecular junctions. Here, combining UV‐Vis/Raman spectroscopy of bulk molecules and conductance/flicker‐noise measurements of single molecules, we give compelling evidence that molecular dimers naturally form under ambient conditions, primarily via disulfide bonds rather than by π–π stacking. We further proposed a technique, named electrode‐compression‐hold‐on (ECHO), and reveal that the two thiol groups of phenyl‐backboned molecules will bond to the same electrode upon a compression force with a prolongated ECHO time. In contrast, the compression‐time‐dependent phenomenon is not observed for alkyl‐backboned molecules. The underlying mechanism for these unprecedented observations is elucidated, shedding light on the yield of molecular junctions.

Cooperative Self-Assembly of Dimer Junctions Driven by π Stacking Leads to Conductance Enhancement.

We demonstrate enhanced electronic transport through dimer molecular junctions, which self-assemble between two gold electrodes in π-π stabilized binding configurations. Single molecule junction conductance measurements show that benzimidazole molecules assemble into dimer junctions with a per-molecule conductance that is higher than that in monomer junctions. Density functional theory calculations reveal that parallel stacking of two benzimidazoles between electrodes is the most energetically favorable due to the large π system. Imidazole is smaller and has greater conformational freedom to access different stacking angles. Transport calculations confirm that the conductance enhancement of benzimidazole dimers results from the changed binding geometry of dimers on gold, which is stabilized and made energetically accessible by intermolecular π stacking. We engineer imidazole derivatives with higher monomer conductance than benzimidazole and large intermolecular interaction that promote cooperative in situ assembly of more transparent dimer junctions and suggest at the potential of molecular devices based on self-assembled molecular layers.

Intermolecular and Electrode-Molecule Bonding in a Single Dimer Junction of Naphthalenethiol as Revealed by Surface-Enhanced Raman Scattering Combined with Transport Measurements.

Electron transport through noncovalent interaction is of fundamental and practical importance in nanomaterials and nanodevices. Recent single-molecule studies employing single-molecule junctions have revealed unique electron transport properties through noncovalent interactions, especially those through a π-π interaction. However, the relationship between the junction structure and electron transport remains elusive due to the insufficient knowledge of geometric structures. In this article, we employ surface-enhanced Raman scattering (SERS) synchronized with current-voltage (I-V) measurements to characterize the junction structure, together with the transport properties, of a single dimer and monomer junction of naphthalenethiol, the former of which was formed by the intermolecular π-π interaction. The correlation analysis of the vibrational energy and electrical conductance enables identifying the intermolecular and molecule-electrode interactions in these molecular junctions and, consequently, addressing the transport properties exclusively associated with the π-π interaction. In addition, the analysis achieved discrimination of the interaction between the NT molecule and the Au electrode of the junction, i.e., Au-π interactions through-π coupling and though-space coupling. The power density spectra support the noncovalent character at the interfaces in the molecular junctions. These results demonstrate that the simultaneous SERS and I-V technique provides a unique means for the structural and electrical investigation of noncovalent interactions.

Vibration‐Assisted Charge Transport through Positively Charged Dimer Junctions

AbstractIntermolecular charge transport plays a vital role in the fields of electronics, as well as biochemical systems. Here, we design supramolecular dimer junctions and investigate the effects of charge state and energy level alignment on charge transport under nanoconfinement. Incoherent tunneling caused by thermally‐induced vibrations is enhanced in positively charged systems. The transition between coherent and incoherent tunneling is associated with specific molecular vibration modes. Positively charged systems with smaller torsional barriers and vibrational frequencies result in lower transition temperatures. Multiple thermal effects have a great impact on the conductance in the off‐resonant tunneling, while thermally‐induced vibron‐assisted tunneling contributes more to the transport in the resonant tunneling. These investigations offer a deep mechanism understanding of intermolecular charge transport and facilitate the development of practical functional molecular devices.

Vibration-Assisted Charge Transport through Positively Charged Dimer Junctions.

Intermolecular charge transport plays a vital role in the fields of electronics, as well as biochemical systems. Here, we design supramolecular dimer junctions and investigate the effects of charge state and energy level alignment on charge transport under nanoconfinement. Incoherent tunneling caused by thermally-induced vibrations is enhanced in positively charged systems. The transition between coherent and incoherent tunneling is associated with specific molecular vibration modes. Positively charged systems with smaller torsional barriers and vibrational frequencies result in lower transition temperatures. Multiple thermal effects have a great impact on the conductance in the off-resonant tunneling, while thermally-induced vibron-assisted tunneling contributes more to the transport in the resonant tunneling. These investigations offer a deep mechanism understanding of intermolecular charge transport and facilitate the development of practical functional molecular devices.

Propagation mechanism of surface plasmons coupled with surface-enhanced resonant Raman scattering light through a one-dimensional hotspot along a silver nanowire dimer junction

We investigate the propagation of surface-enhanced resonant Raman scattering (SERRS) light coupled with surface plasmons (SPs) by several micrometers through a one-dimensional hotspot (1D HS) located between a plasmonic nanowire dimer (NWD) by end-type excitations. The propagation exhibits properties, e.g., an effective propagation is induced by excitation and detection polarization orthogonal to the 1D HS long axis, the propagation profiles are composed of bright short and dark long propagations, SERRS spectral shapes are independent of localized plasmon (LP) resonance of NWDs, the SERRS spectra redshifts at the edges of 1D HSs, and considerable NWD-by-NWD variations appear in the propagation lengths. These properties are well reproduced by numerical calculations based on electromagnetism. These calculations reveal the following propagation mechanism: excitation light resonantly coupled with LP at the edges of 1D HSs, and the light energy is transferred to two types of junction SP modes supporting the short and long propagations; these modes are attributed to the upper and lower branches of coupled two-SP modes. This mechanism comprehensively clarifies the abovementioned properties.

The Control of Intramolecular Through-Bond and Through-Space Coupling in Single-Molecule Junctions

The Control of Intramolecular Through-Bond and Through-Space Coupling in Single-Molecule Junctions

Molecular Junctions Inspired by Nature: Electrical Conduction through Noncovalent Nanobelts.

Charge transport occurs in a range of biomolecular systems, whose structures have covalent and noncovalent bonds. Understanding from these systems have yet to translate into molecular junction devices. We design junctions which have hydrogen-bonds between the edges of a series of prototype noncovalent nanobelts (NCNs) and vary the number of donor-acceptors to study their electrical properties. From frontier molecular orbitals (FMOs) and projected density of state (DOS) calculations, we found these NCN dimer junctions to have low HOMO-LUMO gaps and states at the Fermi level, suggesting these are metallic-like systems. Their conductance properties were studied with nonequilibrium Green's functions density functional theory (NEGF-DFT) and was found to decrease with cooperative H-bonding, that is, the conductance decreased as the alternating donor-acceptors around the nanobelts attenuates to a uniform distribution in the H-bonding arrays. The latter gave the highest conductance of 51.3 × 10-6 S and the Seebeck coefficient showed n-type (-36 to -39 μV K-1) behavior, while the lower conductors with alternating H-bonds are p-type (49.7 to 204 μV K-1). In addition, the NCNs have appreciable binding energies (19.8 to 46.1 kcal mol-1), implying they could form self-assembled monolayer (SAM) heterojunctions leading to a polymeric network for long-range charge transport.

Noncovalent Molecular Electronics.

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

Thermal conductance and thermoelectric figure of merit of C60 -based single-molecule junctions: Electrons, phonons, and photons

Motivated by recent experiments, we present here an ab initio study of the impact of the phonon transport on the thermal conductance and thermoelectric figure of merit of ${\mathrm{C}}_{60}$-based single-molecule junctions. To be precise, we combine density functional theory with nonequilibrium Green's-function techniques to compute these two quantities in junctions with either a ${\mathrm{C}}_{60}$ monomer or a ${\mathrm{C}}_{60}$ dimer connected to gold electrodes, taking into account the contributions of both electrons and phonons. Our results show that for ${\mathrm{C}}_{60}$ monomer junctions phonon transport plays a minor role in the thermal conductance and, in turn, in the figure of merit, which can reach values on the order of 0.1, depending on the contact geometry. In ${\mathrm{C}}_{60}$ dimer junctions, phonons are transported less efficiently, but they completely dominate the thermal conductance and reduce the figure of merit as compared to monomer junctions. Thus, claims that by stacking ${\mathrm{C}}_{60}$ molecules one could achieve high thermoelectric performance, which have been made without considering the phonon contribution, are not justified. Moreover, we analyze the relevance of near-field thermal radiation for the figure of merit of these junctions within the framework of fluctuational electrodynamics. We conclude that photon tunneling can be another detrimental factor for the thermoelectric performance, which has been overlooked so far in the field of molecular electronics. Our study illustrates the crucial roles that phonon transport and photon tunneling can play, when critically assessing the performance of molecular junctions as potential nanoscale thermoelectric devices.

Host-specific accumulation and temperature effects on the generation of dimeric viral RNA species derived from the S-RNA of members of the Tospovirus genus.

Polygonum ringspot virus (PolRSV) is a recently characterized Tospovirus reported in Italy. Northern blot analyses of PolRSV infections in Nicotiana benthamiana and tomato plants showed that a viral RNA species with nearly twice the length of the Small genomic RNA (S-RNA) accumulated abundantly in the former host, but was not detected in the latter. Additional assays confirmed that biogenesis of this novel RNA species was common to all PolRSV isolates tested and also to an isolate of Tomato spotted wilt virus (TSWV). Given its size, we hypothesized that the novel RNA species was a dimer molecule and we confirmed this hypothesis by RNA sequencing (RNAseq) analysis and reverse transcription (RT)-PCR of putative predicted dimer junction sites in RNA extracts of N. benthamiana challenged with PolRSV isolates Plg6 and Plg13/2. We also confirmed that these molecules are derived from head-to-tail dimers and often contain deletions at their junction sites. We named these novel molecules imperfect dimer RNAs (IMPD-RNAs). PolRSV IMPD-RNAs systemic accumulation in a range of host plants was restricted to N. benthamiana and Nicotiana occidentalis. Notably, IMPD-RNAs accumulation was modulated by temperature and their generation was restricted to late stages of systemic infection (12 days post-inoculation) in N. benthamiana. Differently from all other PolRSV isolates used in this study, Plg13/2 generated more IMPD-RNAs coupled with low amounts of genomic S-RNA and maintained them even at 18 °C, besides having lost the ability to infect tomato plants. This is the first characterization of S-RNA dimers for Tospovirus, and of occurrence of dimers of genomic segments at the whole organism level for Bunyaviridae.

Spin-polarization inversion of transport current and tunnel magnetoresistance through a non-collinear uniaxial-molecule-magnet dimer junction with electrode magnetization

In this paper, we study quantum transport through a tunnel junction embedded with a non-collinear uniaxial molecule-magnet-dimer with the magnetization of ferromagnetic electrodes.

Anisotropy Effects on the Plasmonic Response of Nanoparticle Dimers.

We present an ab initio study of the anisotropy and atomic relaxation effects on the optical properties of nanoparticle dimers. Special emphasis is placed on the hybridization process of localized surface plasmons, plasmon-mediated photoinduced currents, and electric-field enhancement in the dimer junction. We show that there is a critical range of separations between the clusters (0.1-0.5 nm) in which the detailed atomic structure in the junction and the relative orientation of the nanoparticles have to be considered to obtain quantitative predictions for realistic nanoplasmonic devices. It is worth noting that this regime is characterized by the emergence of electron tunneling as a response to the driven electromagnetic field. The orientation of the particles not only modifies the attainable electric field enhancement but can lead to qualitative changes in the optical absorption spectrum of the system.

Plasmon excitation in C60 fullerene dimers

Plasmon resonances in C60 fullerene dimers are investigated using time-dependent density functional theory. Owing to larger separation between molecules, there exist capacitive coupling plasmon modes in fullerene dimers. With the decrease of the gap distance, low-energy capacitive coupling plasmon modes show red shift. When the gap distance further decreases, because of the electrons tunneling across the dimer junction, plasmon resonance modes of C60 fullerene dimers are significantly modified, and the charge transfer plasmon modes occur. C60 fullerene dimer is different from metallic nanostructures dimmer. As the gap distance is again reduced, the charge transfer plasmon modes are not blue-shifted, but they are further red-shifted. In the range of the visible spectrum, C60 fullerene dimmers have strong absorption peaks.

Plasmon resonances and the plasmon-induced field enhancement in nanoring dimers

Plasmon resonances and the plasmon-induced field enhancement (FE) in sodium nanoring dimers are investigated by time-dependent density functional theory. For larger separations, the optical absorption, the induced charge response and the frequency dependent current demonstrate that there are two capacitive coupling plasmon modes. One feature of FE is that, in the surface region of the nanoring, it has a very large maximum. Another feature of FE is that, along the perpendicular bisector of the line segment joining the two nanoring center points in the middle region of the nanoring dimers, it has maxima. With the decrease of the gap distance, because of the electrons tunneling across the dimer junction and screening, collective excitation modes are changed, and the charge transfer plasmon modes emerge in the nanoring dimers. FE induced by any plasmon modes decreases in the gap region. Moreover, corresponding to different gap distances, the high-energy plasmon resonance peak almost does not shift, because this plasmon mode is mainly the collective excitation as a result of interactions among degenerate individual electronic states.

Large Low Bias Negative Differential Resistance in an Endohedral Li@C60 Dimer Junction

By applying the nonequilibrium Green function formalism combined with density functional theory, we have investigated the electronic transport properties of the C60 dimer and its endohedral complex Li@C60 dimer. Our results show that the doping of Li atoms significantly changes the transport properties of the C60 dimer. Negative differential resistance is found in such systems. Especially, the doping of Li atoms can lead to a much larger negative differential resistance at much lower bias, and it is quite evident from the plot of differential conductance versus bias. The negative differential resistance behavior is understood in terms of the evolution of the transmission spectrum and projected density of states spectrum with applied bias combined with molecular projected self-consistent Hamiltonian states analyses.

Surface-Enhanced Raman Spectroscopy: Investigations at the Nanorod Edges and Dimer Junctions

Raman signal enhancement of two analyte molecules, containing bipyridine and phenyl moieties, were investigated by linking them (i) onto the edges of Au nanorods using monothiol derivatives and (ii) at the junctions of two Au nanorods using dithiol derivatives. Edges of Au nanorods are regions of high electric field, and specific interaction of the thiol molecules on the {111} planes at the edges resulted in an enhanced Raman signal. When two Au nanorods are brought together in a linear fashion through dithiol linkages, their longitudinal plasmon oscillations couple each other, creating regions of enhanced electric field (hot spots) at the junctions. Interestingly, dimerization leads to a spontaneous enhancement in the intensity of Raman signals (enhancement factor of ∼1.4 × 105) due to the localization of molecules at the junctions of Au nanorod dimers.

Quantum mechanical study of the coupling of plasmon excitations to atomic-scale electron transport

The coupling of optical excitation and electron transport through a sodium atom in a plasmonic dimer junction is investigated using time-dependent density functional theory. The optical absorption and dynamic conductance is determined as a function of gap size. Surface plasmons are found to couple to atomic-scale transport through several different channels including dipolar, multipolar, and charge transfer plasmon modes. These findings provide insight into subnanoscale couplings of plasmons and atoms, a subject of general interest in plasmonics and molecular electronics.