Effects of Connectivity Isomerization on Electron Transport Through Thiophene Heterocyclic Molecular Junction.

Connectivity isomerization of the same aromatic molecular core with different substitution positions profoundly affects electron transport pathways and single-molecule conductance. Herein, we designed and synthesized all connectivity isomers of a thiophene (TP) aromatic ring substituted by two dihydrobenzo[b]thiophene (BT) groups with ethynyl spacers (m,n-TP-BT, (m,n = 2,3; 2,4; 2,5; 3,4)), to systematically probe how connectivity contributes to single-molecule conductance. Single-molecule conductance measurements using a scanning tunneling microscopy break junction (STM-BJ) technique show ∼12-fold change in conductance values, which follow an order of 10-4.83 G0 (2,4-TP-BT) < 10-4.78 G0 (3,4-TP-BT) < 10-4.06 G0 (2,3-TP-BT) < 10-3.75 G0 (2,5-TP-BT). Electronic structure analysis and theoretical simulations show that the connectivity isomerization significantly changes electron delocalization and HOMO-LUMO energy gaps. Moreover, the connectivity-dependent molecular structures lead to different quantum interference (QI) effects in electron transport, e.g., a strong destructive QI near E = EF leads the smallest conductance value for 2,4-TP-BT. This work proves a clear relationship between the connectivity isomerization and single-molecule conductance of thiophene heterocyclic molecular junctions for the future design of molecular devices.

Visualizing an Electrochemically Induced Radical Cation of Bipyridine at Au(111)/Ionic Liquid Interfaces toward a Single-Molecule Switch.

Room-temperature ionic liquids (RTILs) emerged as ideal solvents, and bipyridine as one of the most used ligands have been widely employed in surface science, catalysis, and molecular electronics. Herein, in situ shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) and STM break junction (STM-BJ) technique has been employed to probe the electrochemical process of bipyridine at Au(111)/IL interfaces. It is interestingly found that these molecules undertake a redox process with a pair of well-defined reversible peaks in cyclic voltammograms (CVs). The spectroscopic evidence shows a radical cation generated with rising new Raman peaks related to parallel CC stretching of a positively charged pyridyl ring. Furthermore, these electrochemically charged bipyridine is also confirmed by electrochemical STM-BJ at the single-molecule level, which displays a binary conductance switch ratio of about 400% at the redox potentials. This present work offers a molecular-level insight into the pyridine-mediated reaction process and electron transport in RTILs.

In Situ Raman Monitoring of Potential-Dependent Adlayer Structures on the Au(111)/Ionic Liquid Interface.

Probing the adlayer structures on an electrode/electrolyte interface is one of the most important tasks in modern electrochemistry for clarifying the electrochemical processes. Herein, we have combined cyclic voltammetry and electrochemical shell-isolated nanoparticle-enhanced Raman spectroscopy techniques to explore the potential-dependent adlayer structures on Au(111) in a room-temperature ionic liquid of 1-butyl-3-methylimidazolium hexafluorophosphate (BMIPF6) without or with pyridine (Py). It is clearly found that the BMI+ cations strongly adsorb on the negatively charged surface with a flat-lying orientation, leaving a little space for Py adsorption. Upon increasing the potentials of the electrode, the variations of Raman band intensities and frequencies reveal that the interaction between the BMI+ cations and the Au surface becomes weak; meanwhile, the Py adsorption becomes strong, and its geometry turns from flat, tilted to vertical. Finally, BMI+ cations desorb and leave plenty of surface sites for Py adsorption in bulk solution, and a N-bonded compact Py adlayer is formed on the very positively charged surface. This causes obvious anodic peaks in cyclic voltammograms, and the peak currents increase with the square root of the scanning rate. The present work provides a fair molecular-level understanding of electrochemical interfaces and molecular adsorption of Py in ionic liquids.

Electrochemically activated carbon-halogen bond cleavage and C-C coupling monitored by in situ shell-isolated nanoparticle-enhanced Raman spectroscopy.

The electroreductive cleavage of carbon-halogen bonds has attracted increasing attention in both electrosynthesis and pollution remediation. Herein, by employing the in situ electrochemical shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) technique, we have successfully investigated the electroreductive dehalogenation process of aryl halides with the thiol group on a smooth Au electrode in aqueous solution at different pH values. The obtained potential-dependent Raman spectra directly reveal a mixture of the reduction products 4,4'-biphenyldithiol (BPDT) and thiophenol (TP). The conversion ratios of the C-Cl and C-Br bonds at pH = 7 are 37% and 55%, respectively. Furthermore, quantitative analysis of the intensity variations of ν(C-Cl), ν(C-Br) and aromatic ν(CC) stretching modes suggests electroreductive dehalogenation via both direct electron transfer reduction and electrocatalytic hydrodehalogenation. Molecular evidence for the C-C cross coupling process through TP reaction with benzene free radical intermediates is found at negative potentials, which leads to the increasing selectivity of biphenyl products.

Substituent-mediated quantum interference toward a giant single-molecule conductance variation.

Quantum interference (QI) in single molecular junctions shows a promising perspective for realizing conceptual nanoelectronics. However, controlling and modulating the QI remains a big challenge. Herein, two-type substituents at different positions ofmeta-linked benzene, namely electron-donating methoxy (-OMe) and electron-withdrawing nitryl (-NO2), are designed and synthesized to investigate the substituent effects on QI. The calculated transmission coefficientsT(E) indicates that -OMe and -NO2could remove the antiresonance and destructive quantum interference (DQI)-induced transmission dips at position 2. -OMe could raise the antiresonance energy at position 4 while -NO2groups removes the DQI features. For substituents at position 5, both of them are nonactive for tuning QI. The conductance measurements by scanning tunneling microscopy break junction show a good agreement with the theoretical prediction. More than two order of magnitude single-molecule conductance on/off ratio could be achieved at the different positions of -NO2substituent groups at room temperature. The present work proves chemical substituents can be used for tuning QI features in single molecular junctions, which provides a feasible way toward realization of high-performance molecular devices.

Probing Interfacial Electronic Effects on Single-Molecule Adsorption Geometry and Electron Transport at Atomically Flat Surfaces.

Clarifying interfacial electronic effects on molecular adsorption is significant in many chemical and biochemical processes. Here, we used STM breaking junction and shell-isolated nanoparticle-enhanced Raman spectroscopy to probe electron transport and adsorption geometries of 4,4'-bipyridine (4,4'-BPY) at Au(111). Modifying the surface with 1-butyl-3-methylimidazolium cation-containing ionic liquids (ILs) decreases surface electron density and stabilizes a vertical orientation of pyridine through nitrogen atom σ-bond interactions, resulting in uniform adsorption configurations for forming molecular junctions. Modulation from vertical, tilted, to flat, is achieved on adding water to ILs, leading to a new peak ascribed to CC stretching of adsorbed pyridyl ring and 316 % modulation of single-molecule conductance. The dihedral angle between adsorbed pyridyl ring and surface decreases with increasing surface electronic density, enhancing electron donation from surface to pyridyl ring.

Direct In Situ Raman Spectroscopic Evidence of Oxygen Reduction Reaction Intermediates at High-Index Pt(hkl) Surfaces.

The study of the oxygen reduction reaction (ORR) at high-index Pt(hkl) single crystal surfaces has received considerable interest due to their well-ordered, typical atomic structures and superior catalytic activities. However, it is difficult to obtain direct spectral evidence of ORR intermediates during reaction processes, especially at high-index Pt(hkl) surfaces. Herein, in situ Raman spectroscopy has been employed to investigate ORR processes at high-index Pt(hkl) surfaces containing the [011̅] crystal zone-i.e., Pt(211) and Pt(311). Through control and isotope substitution experiments, in situ spectroscopic evidence of OH and OOH intermediates at Pt(211) and Pt(311) surfaces was successfully obtained. After detailed analysis based on the Raman spectra and theoretical simulation, it was deduced that the difference in adsorption of OOH at high-index surfaces has a significant effect on the ORR activity. This research illuminates and deepens the understanding of the ORR mechanism on high-index Pt(hkl) surfaces and provides theoretical guidance for the rational design of high activity ORR catalysts.

Achieving Efficient Multichannel Conductance in Through-Space Conjugated Single-Molecule Parallel Circuits.

Constructing single-molecule parallel circuits with multiple conduction channels is an effective strategy to improve the conductance of a single molecular junction, but rarely reported. We present a novel through-space conjugated single-molecule parallel circuit (f-4Ph-4SMe) comprised of a pair of closely parallelly aligned p-quaterphenyl chains tethered by a vinyl bridge and end-capped with four SMe anchoring groups. Scanning-tunneling-microscopy-based break junction (STM-BJ) and transmission calculations demonstrate that f-4Ph-4SMe holds multiple conductance states owing to different contact configurations. When four SMe groups are in contact with two electrodes at the same time, the through-bond and through-space conduction channels work synergistically, resulting in a conductance much larger than those of analogous molecules with two SMe groups or the sum of two p-quaterphenyl chains. The system is an ideal model for understanding electron transport through parallel π-stacked molecular systems and may serve as a key component for integrated molecular circuits with controllable conductance.

Comparative Study of Single Molecular Junctions with Para-Phthalic Acid and Meta-Phthalic Acid Binding to Different Metal Electrodes.

In this paper, single molecular junctions of Para-phthalic acid and Meta-phthalic acid with Au electrodes were studied by STM break junction approach. Conductance values of 10-3.55 G0 and 10-3.70 G0 were found for Para-phthalic acid and Meta-phthalic acid, respectively. The conductance order between Para-phthalic acid and Meta-phthalic acid with Au is different from that with Cu, which can be contributed to the different coupling between molecules and electrodes; different through-space interaction is proposed for such phenomenon between Cu and Au electrodes. Furthermore, the breaking off distances can reflect the length of molecules. The current work presents the important role of electrode in single molecular junctions with different position anchoring groups.

Remarkable Multichannel Conductance of Novel Single-Molecule Wires Built on Through-Space Conjugated Hexaphenylbenzene.

Through-bond conjugated molecules are the major frameworks for traditional molecular wires, while through-space conjugated units are rarely utilized and studied although they have shown unique conducting potential. Herein, we present novel single-molecule wires built on through-space conjugated hexaphenylbenzene. Their conductance, measured by the scanning tunneling microscopy based break-junction technique, increases with the improvement of through-space conjugation and finally reaches a remarkable value (12.28 nS) which greatly exceeds that of conventional through-bond conjugated counterpart (2.45 nS). The multichannel conducting model by integrating through-space and through-bond conjugations could be a promising strategy for the further design of robust single-molecule wires with advanced conductance and stability.

In†situ Spectroscopic Insight into the Origin of the Enhanced Performance of Bimetallic Nanocatalysts towards the Oxygen Reduction Reaction (ORR).

It is vital to understand the oxygen reduction reaction (ORR) mechanism at the molecular level for the rational design and synthesis of high activity fuel-cell catalysts. Surface enhanced Raman spectroscopy (SERS) is a powerful technique capable of detecting the bond vibrations of surface species in the low wavenumber range, however, using it to probe practical nanocatalysts remains extremely challenging. Herein, shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) was used to investigate ORR processes on the surface of bimetallic Pt3 Co nanocatalyst structures. Direct spectroscopic evidence of *OOH suggests that ORR undergoes an associative mechanism on Pt3 Co in both acidic and basic environments. Density functional theory (DFT) calculations show that the weak *O adsorption arise from electronic effect on the Pt3 Co surface accounts for enhanced ORR activity. This work shows SHINERS is a promising technique for the real-time observation of catalytic processes.

Controlling and Observing Sharp-Valleyed Quantum Interference Effect in Single Molecular Junctions.

The ability to control over the quantum interference (QI) effect in single molecular junctions is attractive in the application of molecular electronics. Herein we report that the QI effect of meta-benzene based molecule with dihydrobenzo[ b]thiophene as the anchoring group ( meta-BT) can be controlled by manipulating the electrode potential of the junctions in electrolyte while the redox state of the molecule does not change. More than 2 orders of magnitude conductance change is observed for meta-BT ranging from <10-6.0 to 10-3.3 G0 with varying the electrode potential, while the upper value is even larger than the conductance of para-BT ( para-benzene based molecule with anchoring group of dihydrobenzo[ b]thiophene). This phenomenon is attributed to the shifting of energy level alignment between the molecule and electrodes under electrode potential control. Calculation is carried out to predict the transmission function of single molecular junction and the work function of Au surface in the presence of the molecule, and good agreement is found between theory and experiments, both showing sharp-valley featured destructive QI effect for the meta-BT. The present work demonstrates that the QI effect can be tuned through electrochemical gating without change of molecular redox states, which provides a feasible way toward realization of effective molecular switches.

Supramolecularly Multicolor DNA Decoding Using an Indicator Competition Assay.

Relative to the individual intensity-dependent strategy, the multicolor fluorescence sensor has promise to achieve a high signaling contrast. In this work, we develop a cucurbituril-based supramolecular and multicolor DNA recognition rationale via indicator competition assay (ICA). Alkaloids of coptisine (COP) and palmatine (PAL) are identified as the proof-of-principle indicators with a lighting-up fluorescence upon supramolecular complexation to cucurbit[7]uril (CB[7]). With an introduced abasic site (AP site) as the contestant, DNAs having pyrimidines opposite this site can compete for COP with CB[7] to bring an emission color change from green to yellow brown, while those having purines opposite the AP site do not compete for COP and still have the green emission, indicative of a high selectivity for the multicolor nucleotide transversion recognition. However, because of the relatively weaker binding of PAL with CB[7], the AP site-containing DNA can take away PAL from its CB[7] complex and resultantly bring a blue-to-green emission color change independent of the AP site-opposite nucleotide identity, dissimilar to the remaining blue color for the fully matched DNA without the AP site, suggesting a preferable strategy for the AP site biomarker detection. Our method demonstrates a new way to develop an ICA-based multicolor DNA sensor with the supramolecular cucurbituril complexation to ensure a highly selective performance.

G-Quadruplex DNA with an Apurinic Site as a Soft Molecularly Imprinted Sensing Platform.

Molecularly imprinted polymers (MIPs) provide versatile sensor platforms to recognize targets by shape complementarity. However, the rigid structure of the classic MIPs compromises the signal transduction with necessary polymer and target modifications. Herein, we tried to use a flexible DNA that has a perfectly structured folding as the soft molecularly imprinted polymer (SMIP) for a straightforward sensor. As a proof of concept, the guanosine SMIP recognition was achieved by removal of a guanosine from a G-quadruplex-forming sequence (G4). The G4 folding structure with such an apurinic site (AP site) provides a well-defined MIP binding accommodation for guanosine according to the shape complementarity. The guanosine binding at the AP site subsequently leads to a conformation change suitable for remote readout using a G4-specific fluorescent ligand. The G4 sequence and AP site position were optimized for this SMIP behavior. Due to the G4 compact structure and the remaining hydrogen bonding pattern, nucleosides other than guanosine and negatively charged nucleotides exhibit no binding with the AP site, suggesting a high selectivity in the SMIP recognition. The proposed rationale was then convinced by the alkaline phosphatase-catalyzed GMP hydrolysis. Our work will inspire more interest in exploring nucleic acids as the SMIP frameworks due to their variant conformations and well-established molecular engineering.

Conductance Measurement of Pyrazine Molecular Junction with Cu and Ag Electrodes.

We have measured the conductance of pyrazine molecular junction contacting with Cu and Ag electrodes by using an electrochemical jump-to-contact based scanning tunneling microscopy break junction (ECSTM-BJ). While conductance values of 10-2.8 and 10-3.7 G0 are measured for pyrazineCu electrode, 10-2.1 and 10-3.3 G0 are found for pyrazine-Ag contact. The result shows that the conductance of pyrazine with Ag electrode is larger than that with Cu electrode, which can contribute to the different efficiency of electron transport along the molecular junction between Ag and Cu electrodes. The current work shows the important role for the electrode material in electron transport.

Target-switched triplex nanotweezer and synergic fluorophore translocation for highly selective melamine assay.

This paper describes a triplex DNA nanotweezer to specifically capture melamine (MEL). The triplex-forming oligonucleotide (TFO) arm can be switched from the open state to the closed state once MEL binds to the abasic site (AP site) in duplex via the bifacial hydrogen bonding with thymines. Following this nanotweezer operation, the AP site-bound fluorophore is translocated to the terminal triplet to subsequently light up the nanotweezer. The TFO arm is found to be pivotal for permitting the AP site binding. The synergic processes of target competition and fluorophore translocation support a high selectivity for the MEL assay even against the inherent adenosine and the MEL hydrolysis products. Chelerythrine is employed as the fluorescent probe. The detection limit of MEL was estimated to be about 140 nM assuming a signal-to-noise ratio of 3. It was applied to the determination of MEL in spiked milk samples without any separation procedure. Conceivably, this method opens a new avenue towards highly selective triplex-based sensors by making use of other commercially available DNA modifications for recognizing other analytes. Graphical abstract Schematic presentation of a triplex nanotweezer with an open-to-close conversion upon the abasic site binding of melamine. The assay is based on a synergic fluorophore translocation. The corresponding duplex otherwise shows no binding with melamine. Chelerythrine (CHE) with a yellow-green emission peaking at 544 nm is employed as the fluorescent probe.

Probing Interfacial Electronic and Catalytic Properties on Well-Defined Surfaces by Using In†Situ Raman Spectroscopy.

Heterogeneous metal interfaces play a key role in determining the mechanism and performance of catalysts. However, in situ characterization of such interfaces at the molecular level is challenging. Herein, two model interfaces, Pd and Pt overlayers on Au single crystals, were constructed. The electronic structures of these interfaces as well as effects of crystallographic orientation on them were analyzed by shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) using phenyl isocyanide (PIC) as a probe molecule. A clear red shift in the frequency of the C≡N stretch (νNC ) was observed, which is consistent with X-ray photoelectron spectroscopy (XPS) data and indicates that the ultrathin Pt and Pd layers donate their free electrons to the Au substrates. Furthermore, in situ electrochemical SHINERS studies showed that the electronic effects weaken Pt-C/Pd-C bonds, leading to improved surface activity towards CO electrooxidation.

Adaptively Recognizing Parallel-Stranded Duplex Structure for Fluorescent DNA Polarity Analysis.

Besides the canonical Watson-Crick (WC) linked antiparallel-stranded duplex (aps-DNA), DNA is also able to form bioactive parallel-stranded duplex (ps-DNA) with the two involving strands adopting the equal 5'-3' polarity. Discriminating ps-DNA from aps-DNA with an ideal selectivity is more challenging because of their comparable duplex topologies. Herein, we designed a unique probe of HPIN to fluorescently recognize ps-DNA but to keep an almost nonfluorescent response in binding with aps-DNA. The success of the Hoogsteen hydrogen bonding pattern in lighting up the HPIN fluorescence over the reverse Watson-Crick (rWC) one suggests the critical role of HPIN in structurally adaptive recognition to the strand polarity-determined base-pairing peculiarity. The turn-on fluorescence should result from restriction of the HPIN cis/trans isomerization upon the adaptive Hoogsteen base pair binding. Such high performance in recognizing ps-DNA against aps-DNA demonstrates the promising applications of HPIN in developing unique DNA polarity-based sensors.

Detecting Electron Transport of Amino Acids by Using Conductance Measurement.

The single molecular conductance of amino acids was measured by a scanning tunneling microscope (STM) break junction. Conductance measurement of alanine gives out two conductance values at 10-1.85 G0 (1095 nS) and 10-3.7 G0 (15.5 nS), while similar conductance values are also observed for aspartic acid and glutamic acid, which have one more carboxylic acid group compared with alanine. This may show that the backbone of NH2-C-COOH is the primary means of electron transport in the molecular junction of aspartic acid and glutamic acid. However, NH2-C-COOH is not the primary means of electron transport in the methionine junction, which may be caused by the strong interaction of the Au-SMe (methyl sulfide) bond for the methionine junction. The current work reveals the important role of the anchoring group in the electron transport in different amino acids junctions.

Shell-isolated nanoparticle-enhanced Raman spectroscopy.

Surface-enhanced Raman scattering (SERS) is a powerful spectroscopy technique that can provide non-destructive and ultra-sensitive characterization down to single molecular level, comparable to single-molecule fluorescence spectroscopy. However, generally substrates based on metals such as Ag, Au and Cu, either with roughened surfaces or in the form of nanoparticles, are required to realise a substantial SERS effect, and this has severely limited the breadth of practical applications of SERS. A number of approaches have extended the technique to non-traditional substrates, most notably tip-enhanced Raman spectroscopy (TERS) where the probed substance (molecule or material surface) can be on a generic substrate and where a nanoscale gold tip above the substrate acts as the Raman signal amplifier. The drawback is that the total Raman scattering signal from the tip area is rather weak, thus limiting TERS studies to molecules with large Raman cross-sections. Here, we report an approach, which we name shell-isolated nanoparticle-enhanced Raman spectroscopy, in which the Raman signal amplification is provided by gold nanoparticles with an ultrathin silica or alumina shell. A monolayer of such nanoparticles is spread as 'smart dust' over the surface that is to be probed. The ultrathin coating keeps the nanoparticles from agglomerating, separates them from direct contact with the probed material and allows the nanoparticles to conform to different contours of substrates. High-quality Raman spectra were obtained on various molecules adsorbed at Pt and Au single-crystal surfaces and from Si surfaces with hydrogen monolayers. These measurements and our studies on yeast cells and citrus fruits with pesticide residues illustrate that our method significantly expands the flexibility of SERS for useful applications in the materials and life sciences, as well as for the inspection of food safety, drugs, explosives and environment pollutants.