AbstractA key target in molecular electronics has been molecules having switchable electrical properties. Switching between two electrical states has been demonstrated using such stimuli as light, electrochemical voltage, complexation and mechanical modulation. A classic example of the latter is the switching of 4,4′-bipyridine, leading to conductance modulation of around 1 order of magnitude. Here, we describe the use of side-group chemistry to control the properties of a single-molecule electromechanical switch, which can be cycled between two conductance states by repeated compression and elongation. While bulky alkyl substituents inhibit the switching behavior, π-conjugated side-groups reinstate it. DFT calculations show that weak interactions between aryl moieties and the metallic electrodes are responsible for the observed phenomenon. This represents a significant expansion of the single-molecule electronics “tool-box” for the design of junctions with electromechanical properties.

AbstractA key target in molecular electronics has been molecules having switchable electrical properties. Switching between two electrical states has been demonstrated using such stimuli as light, electrochemical voltage, complexation and mechanical modulation. A classic example of the latter is the switching of 4,4′-bipyridine, leading to conductance modulation of around 1 order of magnitude. Here, we describe the use of side-group chemistry to control the properties of a single-molecule electromechanical switch, which can be cycled between two conductance states by repeated compression and elongation. While bulky alkyl substituents inhibit the switching behavior, π-conjugated side-groups reinstate it. DFT calculations show that weak interactions between aryl moieties and the metallic electrodes are responsible for the observed phenomenon. This represents a significant expansion of the single-molecule electronics “tool-box” for the design of junctions with electromechanical properties.

In an effort to exert more precise control over structural features of supramolecules, a series of giant concentric hexagons were assembled as discrete structures using tetratopic terpyridine (tpy) ligands. In preparation of tetratopic ligand, pyrylium and pyridinium salts chemistry significantly facilitated synthesis. The key compounds were obtained by condensation reactions of pyrylium salts with corresponding primary amine derivatives in good yields. These discrete metallo-supramolecular concentric hexagons were fully characterized by NMR, ESI–MS, TWIM–MS, and TEM, establishing their hexagon-in-hexagon architectures. The combination of different tetratopic ligands also assembled hybrid concentric hexagons with increasing diversity and complexity. Furthermore, these concentric hexagon supramolecules with precisely controlled shapes and sizes were utilized as building blocks to hierarchically self-assemble supramolecular metal–organic nanoribbons (SMON) at solid–liquid interfaces. Ambient STM imaging showed the formation of long 1D SMON rather than 2D assembly on the basal plane of highly oriented pyrolytic graphite (HOPG) surface after simple dropcasting of the solution of preassembled concentric hexagons onto a freshly cleaved surface of HOPG. This wet chemical method based on self-assembly may offer simple, economical, and scalable routes to deliver complex materials.

The aggregates of the full-length human recombinant prion protein (PrP) (23–231) on model membranes were investigated by combining the atomic force microscopy (AFM) measurements and theoretical calculations at pH 5.0, showing the great effect of PrP concentration on its supramolecular assemblies on the lipid bilayer.

An advanced understanding of the molecule–electrode contact interfaces of single-molecule junctions is a necessity for real world application of future single-molecule devices. This study aims to elucidate the change in the contact tunnelling barrier induced by junction extension and how this change affects the resulting junction conductance. The contact barrier of Au–octanedithiol/octanediamine–Au junctions was studied under triangle (TRI) mechanical modulations using the modified scanning tunneling microscopy (STM) break junction technique. The experimental results reveal that as the junction separation extends, the contact barrier of octanedithiol follows a unique trend, a linear increase followed by a plateau in barrier height, which is in contrast to that of octanediamine, a nearly rectangle barrier. We propose a modified contact barrier model for the unique barrier shape of octanedithiol, based on which the calculation agrees well with the experimental data. This study shows unprecedented experimental features of the molecule–electrode contact barrier of single-molecule junctions and provides new insights into the nature of contact effect in determining electron transport through single-molecule junctions.

Directed by increasing the density of coordination sites (DOCS) to increase the stability of assemblies, discrete 2D ring-in-rings and 3D sphere-in-sphere were designed and self-assembled by one tetratopic pyridyl-based ligand with 180° diplatinum(II) acceptors and naked Pd(II), respectively. The high DOCS resulted by multitopic ligand provided more geometric constraints to form discrete structures with high stability. Compared to reported supramolecular hexagons and polyhedra by ditotpic ligands, the self-assembly of such giant architectures using multitopic ligands with all rigid backbone emphasized the structural integrity with precise preorganization of entire architecture, and required elaborate synthetic operations for ligand preparation. In-depth structural characterization was conducted to support desired structures, including multinuclear NMR (1H, 31P, and 13C) analysis, 2D NMR spectroscopy (COSY and NOESY), diffusion-ordered NMR spectroscopy (DOSY), multidimensional mass spectrometry, TEM and AFM. Furthermore, a quantitative definition of DOCS was proposed to compare 2D and 3D structures and correlate the DOCS and stability of assemblies in a quantitative manner. Finally, ring-in-rings in DMSO or DMF could undergo hierarchical self-assembly into the ordered nanostructures and generated translucent supramolecular metallogels.

Aggregations of human prion protein (23–231) were monitored by atomic force microscopy in real-time under pH 4. Prion dimers and trimers were determined as the basic units by AFM images and simulated structures. Aggregates aligned with the herringbone structures of an Au(111) reconstructed surface via Au–S bonds as the first layer, while the second layer was formed by non-covalent interactions.

Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with a wide range of important protein ligands, such as the key anticoagulant factor, antithrombin (AT). The specific interaction of HS with a protein ligand is determined mainly by the sulfation patterns on the HS chain. Here, we reported the probing single-molecule interaction of AT and HS (both wild type and mutated) expressed on the endothelial cell surface under near-physiological conditions by atomic force microscopy (AFM). Functional AFM imaging revealed the uneven distribution of HS on the endothelial cell surface though they are highly expressed. Force spectroscopy measurements using an AT-functionalized AFM tip revealed that AT interacts with endothelial HS on the cell surface through multiple binding sites. The interaction essentially requires HS to be N-, 2-O- and/or 6-O-sulfated. This work provides a new tool to probe the HS-protein ligand interaction at a single-molecular level on the cell surface to elucidate the functional roles of HS.

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL−1). The off-rate values of the ricin–aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10−4 s−1 and (1.82 ± 0.067) × 10−2 s−1, respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

•Early-stage aggregation imaging of prion protein (PrP) on mica and Au(1 1 1) surfaces.•Dimers and trimers were revealed as the basic units of the observed aggregates.•The mechanism relies on surface properties and pH values.•A schematic illustration for PrP aggregations at pH 4.5 is proposed.By in situ time-lapse AFM, we investigated early-stage aggregates of PrP formed at low concentration (100 ng/mL) on mica and Au(1 1 1) surfaces in acetate buffer (pH 4.5). Remarkably different PrP assemblies were observed. Oligomeric structures of PrP aggregates were observed on mica surface, which was in sharp contrast to the multi-layer PrP aggregates yielding parallel linear patterns observed Au(1 1 1) surface. Combining molecular dynamics and docking simulations, PrP monomers, dimers and trimers were revealed as the basic units of the observed aggregates. Besides, the mechanisms of the observed PrP aggregations and the corresponding molecular-substrate and intermolecular interactions were suggested. These interactions involved gold–sulfur interaction, electrostatic interaction, hydrophobic interaction, and hydrogen binding interaction. In contrast, the PrP aggregates observed in pH 7.2 PBS buffer demonstrated similar large ball-like structures on both mica and Au(1 1 1) surfaces. The results indicate that the pH of a solution and the surface of the system can have strong effects on supramolecular assemblies of prion proteins. This study provides in-depth understanding on the structural and mechanistic nature of PrP aggregation, and can be used to study the aggregation mechanisms of other proteins with similar misfolding properties.

We have measured the force and conductance of Au-octanedithiol-Au junctions using a modified conducting atomic force microscopy break junction technique with sawtooth modulations. Force–conductance two-dimensional cross-correlation histogram (FC-2DCCH) analysis for the single-molecule plateaus is demonstrated. Interestingly, four strong correlated regions appear in FC-2DCCHs consistently when modulations with different amplitudes are applied, in sharp contrast to the results under no modulation. These regions reflect the conductance and force changes during the transition of two molecule/electrode contact configurations. As the modulation amplitude increases, intermediate transition states of the contact configurations are discerned and further confirmed by comparing individual traces. This study unravels the relation between force and conductance hidden in the data of a modulated single-molecule break junction system and provides a fresh understanding of electron transport properties at molecule/electrode interfaces.

Experimental study of the charge transport properties associated with structural variations due to a change in the ionic environment will provide essential physical information in determining the nature of DNA molecules. This work reports an experimental study of the change in electronic transport properties induced by the conformational transition of a poly d(GC)4 DNA. By gradually increasing the concentration of MgCl2 in the buffer solution from 0 M to 4 M, the conductance of the single DNA molecule decreased by two orders of magnitude. Circular dichroism (CD) measurements confirmed that a B to Z conformational transition caused the reduction in conductance. Using a stretch-hold mode scanning probe microscopy break junction (SPMBJ) technique, this B–Z transition process was monitored and a transition trend line was successfully achieved from conductance measurements alone. The transition midpoint occurred at a MgCl2 concentration of 0.93 M for this DNA sequence. This method provides a general tool to study transitions of molecular properties associated with conductance differences.

Force and conductance, measured across 4,4′-bipyridine simultaneously, are crosscorrelated using a two dimensional (2D) histogram method. The result is a 2D multivariate statistical analysis superior to current one dimensional histogram techniques for exploring significant conductance and force modulations within SMBJs. This method is sensitive enough to crosscorrelate signal modulations between force and conductance traces associated with contact geometry perturbations predicted in literature such as Au–molecule contact twisting and slipping during junction elongation.

We studied the binding kinetics of family 3 carbohydrate-binding module (CBM3a) molecules to crystalline cellulose fibrils extracted from the poplar cell wall by atomic force microscopy (AFM) recognition imaging. The free CBM3a molecules of different concentrations were added to the buffer solution to bind to the crystalline cellulose sample immobilized on the AFM substrate. During in-situ AFM imaging, the CBM molecules were observed to bind to cellulose efficiently and regularly, especially in the first 60–120 min. A 1:1 single-molecule binding model was used to study the kinetics of the CBM3a–cellulose interaction. The saturation time when the concentration of occupied binding sites is 99% of the maximum bound CBM3a concentration at the end of reaction, t(0.99), was determined by fitting different concentrations of CBM3a against reaction time using the high resolution AFM images and the single-molecule kinetics equations. Based on the experimental data and kinetics calculations, the minimal effective initial CBM3a concentration was estimated to be 5.1 × 10–7 M at 287 min reaction time. This study provides an in-depth understanding of the binding mechanism of CBM with crystalline cellulose at single molecule level.

Negative differential resistance (NDR) behaviors of single molecule junctions composed of a thiol-terminated Ru(II) bis-terpyridine (Ru(tpy-SH)2) molecule sandwiched between two gold electrodes are measured using a specifically modified scanning probe microscope break junction technique (SPMBJ) at room temperature. The low-bias (0.623 ± 0.135 V) NDR observed for one of the three conductance groups is contact specific and is caused by a bias induced electrode–molecule coupling changes.

Combining atomic force microscopy (AFM) recognition imaging and single molecule dynamic force spectroscopy (SMDFS), we studied the single molecule affinity interactions between the carbohydrate-binding module (CBM) and plant cell wall cellulose using the CBM3a (from Clostridium thermocellum) and CBM2a (from Cellvibrio japonicus) functionalized AFM tips. The binding efficiencies of the CBMs to the cellulose were determined by the binding areas on the crystalline cellulose fibrils surface using the recognition imaging. Several dynamic and kinetic parameters, such as the reconstructed free energy change, energy barrier and bond lifetime constant, were also obtained based on the measured single molecule unbinding forces, which are used to illuminate the affinity of the CBMs binding to the natural and single cellulose surface from a totally different aspect. It was found that CBM3a has a little higher binding efficiency and affinity than CBM2a to both natural and extracted cellulose surfaces and both the CBMs have higher affinities to the natural cell wall cellulose compared to the extracted single cellulose. The in-depth understanding of the binding mechanisms of the CBM–cellulose interactions of this study may pave the way for more efficient plant cell wall degradation and eventually facilitate biofuel production.

Heparin, a functionalized polysaccharide, is observed under a scanning tunneling microscope, which shows atomic scale conformational details. The peptide FX06 is found to bind to five consecutive sugar units of heparin and this interaction is directly revealed by atomic force microscopy and dynamic force spectroscopy measurements. The determined free energy change agrees well with the dynamic calculation result.

Single molecule recognition imaging and dynamic force spectroscopy (DFS) analysis showed strong binding affinity between an aptamer and ricin, which was comparable with antibody–ricin interaction. Molecular simulation showed a ricin binding conformation with aptamers and gave different ricin conformations immobilizing on substrates that were consistent with AFM images.

We studied the molecular details of DNA aptamer–ricin interactions. The toxic protein ricin molecules were immobilized on a Au(111) surface using a N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in situ using the AFM tip modified with an antiricin aptamer. Computer simulation was used to illustrate the protein and aptamer structures, the single-molecule ricin images on a Au(111) surface, and the binding conformations of ricin–aptamer and ricin–antibody complexes. The various ricin conformations on a Au(111) surface were caused by the different lysine residues reacting with the NHS ester. It was also observed that most of the binding sites for aptamer and antibody on the A chains of ricin molecules were not interfered by the immobilization reaction. The different locations of the ricin binding sites to aptamer and antibody were also distinguished by AFM recognition images and interpreted by simulations.

The affinitive interaction between a carbohydrate-binding module (CBM3a) and natural crystalline cellulose was visualized and measured at the single-molecule level. Noncontact high resolution imaging by atomic force microscopy (AFM) was used to follow the binding process, in real time, of CBM3a-functionalized 6 nm gold nanoparticles (GNPs) to the cell wall polymers on poplar stem sections. The GNP–CBM3a complexes were found to bind to the cellulose surface, closely aligning along the cellulose fibril axis. The binding details were further confirmed and studied by single-molecule recognition imaging and AFM single-molecule dynamic force spectroscopy (SMDFS) using a CBM3a-functionalized AFM tip. The unbinding force was measured to be 44.96 ± 18.80 pN under a loading rate of 67.2 nN/s. This research provides a radical method for the study of single-molecule affinity between CBM and cellulose that is critical to the engineering of novel cellulolytic enzymes.

Presented here is an in-depth study to exploit the molecule−electrode interface effects on electronic transport properties in stabilized molecular junctions under controlled mechanical modulations. By monitoring and analyzing the conductance and force changes corresponding to the modulations, we isolated the effects of both the molecule terminating groups and the different contact configurations on electronic transport properties. The experimental results can be understood by our calculations developed based on simple and straightforward models. The results would be helpful not only to resolve the discrepancies of the recent scanning tunneling microscopy molecular break junction experiment results but also to add new insights into the understanding of the electronic transport mechanisms of molecular junctions.

We demonstrated a new comprehensive method to combine scanning probe microscopy (SPM) nanolithography and modified SPM break junction techniques to fabricate and characterize single molecular break junction devices. By patterning alkanedithiol and alkanediamine molecules in the alkanethiol template and measuring the conductance of the two kinds of molecular junctions, we have shown the following: (1) the new “stretch-hold” approach produced four groups of conductance values for each molecular junction, for the first time realizing the less populated conductance values that correspond to different contact configurations; (2) the electronic transport mechanism for such molecular junctions is electronic tunneling with similar decay constants for each conductance group of the same kind of molecules. The conductance differences among different groups are due to the molecule−electrode contact configuration difference, which was shown by the extrapolated contact resistances. This new approach also allows one to eliminate, or at least minimize, the variations of experimental conditions and enables the measurement of multiple molecules under the same experiment with exactly the same experimental conditions.

A simple two-step protocol for modification of atomic force microscopy (AFM) tip and substrate by using a “click reaction” has been developed. The modified tip and substrate would be applied to detect trace amounts of ricin by using atomic force microscopy. A key feature of the approach is the use of a PEG (polyethylene glycol) derivative functionalized with one thiol and one azide ending group. One end of the PEG was attached to the gold-coated AFM tip by a strong Au−thiol bond. The azide group hanging at the other end of the immobilized PEG was used for the attachment of an antiricin antibody modified with an alkyne group using a “click reaction”. The latter reaction is highly efficient, compatible with the presence of many functional groups and could proceed under mild reaction conditions. In a separate step, ricin was immobilized on the gold substrate surface that was modified by active esters. For this process, a novel bifunctional reagent was employed containing an active ester and a thioctic acid moiety. By these modification processes, AFM recognition imaging was used to detect the toxin molecules and the results show fg/mL detection sensitivity, surpassing the existing detection techniques. With measurement of the unbinding force between the antiricin antibody and ricin, which was statistically determined to be 64.89 ± 1.67 pN, the single molecular specificity of this sensing technique is realized.

Combining atomic force microscopy (AFM) recognition imaging and single molecule dynamic force spectroscopy (SMDFS), we studied the single molecule affinity interactions between the carbohydrate-binding module (CBM) and plant cell wall cellulose using the CBM3a (from Clostridium thermocellum) and CBM2a (from Cellvibrio japonicus) functionalized AFM tips. The binding efficiencies of the CBMs to the cellulose were determined by the binding areas on the crystalline cellulose fibrils surface using the recognition imaging. Several dynamic and kinetic parameters, such as the reconstructed free energy change, energy barrier and bond lifetime constant, were also obtained based on the measured single molecule unbinding forces, which are used to illuminate the affinity of the CBMs binding to the natural and single cellulose surface from a totally different aspect. It was found that CBM3a has a little higher binding efficiency and affinity than CBM2a to both natural and extracted cellulose surfaces and both the CBMs have higher affinities to the natural cell wall cellulose compared to the extracted single cellulose. The in-depth understanding of the binding mechanisms of the CBM–cellulose interactions of this study may pave the way for more efficient plant cell wall degradation and eventually facilitate biofuel production.

Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with a wide range of important protein ligands, such as the key anticoagulant factor, antithrombin (AT). The specific interaction of HS with a protein ligand is determined mainly by the sulfation patterns on the HS chain. Here, we reported the probing single-molecule interaction of AT and HS (both wild type and mutated) expressed on the endothelial cell surface under near-physiological conditions by atomic force microscopy (AFM). Functional AFM imaging revealed the uneven distribution of HS on the endothelial cell surface though they are highly expressed. Force spectroscopy measurements using an AT-functionalized AFM tip revealed that AT interacts with endothelial HS on the cell surface through multiple binding sites. The interaction essentially requires HS to be N-, 2-O- and/or 6-O-sulfated. This work provides a new tool to probe the HS-protein ligand interaction at a single-molecular level on the cell surface to elucidate the functional roles of HS.

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL−1). The off-rate values of the ricin–aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10−4 s−1 and (1.82 ± 0.067) × 10−2 s−1, respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

An advanced understanding of the molecule–electrode contact interfaces of single-molecule junctions is a necessity for real world application of future single-molecule devices. This study aims to elucidate the change in the contact tunnelling barrier induced by junction extension and how this change affects the resulting junction conductance. The contact barrier of Au–octanedithiol/octanediamine–Au junctions was studied under triangle (TRI) mechanical modulations using the modified scanning tunneling microscopy (STM) break junction technique. The experimental results reveal that as the junction separation extends, the contact barrier of octanedithiol follows a unique trend, a linear increase followed by a plateau in barrier height, which is in contrast to that of octanediamine, a nearly rectangle barrier. We propose a modified contact barrier model for the unique barrier shape of octanedithiol, based on which the calculation agrees well with the experimental data. This study shows unprecedented experimental features of the molecule–electrode contact barrier of single-molecule junctions and provides new insights into the nature of contact effect in determining electron transport through single-molecule junctions.

Experimental study of the charge transport properties associated with structural variations due to a change in the ionic environment will provide essential physical information in determining the nature of DNA molecules. This work reports an experimental study of the change in electronic transport properties induced by the conformational transition of a poly d(GC)4 DNA. By gradually increasing the concentration of MgCl2 in the buffer solution from 0 M to 4 M, the conductance of the single DNA molecule decreased by two orders of magnitude. Circular dichroism (CD) measurements confirmed that a B to Z conformational transition caused the reduction in conductance. Using a stretch-hold mode scanning probe microscopy break junction (SPMBJ) technique, this B–Z transition process was monitored and a transition trend line was successfully achieved from conductance measurements alone. The transition midpoint occurred at a MgCl2 concentration of 0.93 M for this DNA sequence. This method provides a general tool to study transitions of molecular properties associated with conductance differences.

Single molecule recognition imaging and dynamic force spectroscopy (DFS) analysis showed strong binding affinity between an aptamer and ricin, which was comparable with antibody–ricin interaction. Molecular simulation showed a ricin binding conformation with aptamers and gave different ricin conformations immobilizing on substrates that were consistent with AFM images.

Heparin, a functionalized polysaccharide, is observed under a scanning tunneling microscope, which shows atomic scale conformational details. The peptide FX06 is found to bind to five consecutive sugar units of heparin and this interaction is directly revealed by atomic force microscopy and dynamic force spectroscopy measurements. The determined free energy change agrees well with the dynamic calculation result.

Aggregations of human prion protein (23–231) were monitored by atomic force microscopy in real-time under pH 4. Prion dimers and trimers were determined as the basic units by AFM images and simulated structures. Aggregates aligned with the herringbone structures of an Au(111) reconstructed surface via Au–S bonds as the first layer, while the second layer was formed by non-covalent interactions.

The aggregates of the full-length human recombinant prion protein (PrP) (23–231) on model membranes were investigated by combining the atomic force microscopy (AFM) measurements and theoretical calculations at pH 5.0, showing the great effect of PrP concentration on its supramolecular assemblies on the lipid bilayer.