Molecular adsorption onto metallic quantum wires.

We have studied the adsorption of mercaptopropionic acid, 2,2'-bipyridine, and dopamine onto electrochemically fabricated Cu nanowires. The nanowires are atomically thin with conductance quantized near integer multiples of 2e(2)/h. Upon molecular adsorption, the quantized conductance decreases to a fractional value, due to the scattering of the conduction electrons by the adsorbates. The decrease is as high as 50% for the thinnest nanowires whose conductance is at the lowest quantum step, and smaller for thicker nanowires with conductance at higher quantum steps. The adsorbate-induced conductance changes depend on the binding strengths of the molecules to the nanowires, which are in the order of mercaptopropionic acid, 2,2'-bipyridine, and dopamine, from strongest to weakest. The sensitive dependence of the quantized conductance on molecular adsorption may be used for molecular detection.     

Effect of anchoring groups on single-molecule conductance: comparative study of thiol-, amine-, and carboxylic-acid-terminated molecules

We studied the effect of anchoring groups on the conductance of single molecules using alkanes terminated with dithiol, diamine, and dicarboxylic-acid groups as a model system. We created a large number of molecular junctions mechanically and analyzed the statistical distributions of the conductance values of the molecular junctions. Multiple sets of conductance values were found in each case. The I-V characteristics, temperature independence, and exponential decay of the conductance with the molecular length all indicate tunneling as the conduction mechanism for these molecules. The prefactor of the exponential decay function, which reflects the contact resistance, is highly sensitive to the anchoring group, and the decay constant is weakly dependent on the anchoring group. These observations are attributed to different electronic couplings between the molecules and the electrodes and alignments of the molecular energy levels relative to the Fermi energy level of the electrodes introduced by different anchoring groups. For diamine and dicarboxylic-acid groups, the conductance values are sensitive to pH due to protonation and deprotonation of the anchoring groups. Further insight into the binding strengths of these anchoring groups to gold electrodes is obtained by statistically analyzing the stretching length of molecular junctions.     

Conductance studies of salt solutions in the presence of poly(vinylbenzo crown ethers)

The conductance of acetone and methyl ethyl ketone solutions of tetraphenylborate salts in the presence of homopolymers and styrene copolymers of vinylbenzo-15-crown-5 and vinylbenzo-18-crown-6 was studied, and the results compared with data obtained for crown ethers. Polycations are formed on binding cations to the poly(crown ethers), and the conductance behavior of the polyelectrolytes depends on the nature of the cation-crown complex and the spacing between crown moieties which in turn determines the charge density on the polymer chain. The compositions of the crown-cation complexes were determined for crown ethers. The complex formation constants of sodium and potassium cations to poly(vinylbenzo-18-crown-6) were found to change as more cations bind to the chain. This is not the case for the copolymers where the crown ligands are spaced farther apart. A mixture of poly(vinylbenzo-15-crown-5) and 10^?3M potassium tetraphenylborate in methyl ethyl ketone or acetone has a minimum conductance at a crown to cation ratio of 3.0, but the conductance rapidly increases on addition of crown ether. This was used to qualitatively determine the binding efficiency of a series of crown ethers since the rate of increase in the conductance is a measure of the binding ability of the crown ether to the cation.     

In silico engineering of tailored ink-binding ability at molecular printboards.

Molecular recognition between guest ink molecules and beta-cyclodextrin (beta-CD) cavities at self-assembled monolayers provides a molecular printboard for nanopatterning applications. We recently used molecular dynamics (MD) simulations to describe the specificity of ink-printboard binding and here extend the simulations to include charged cyclodextrin hosts, necessary to broaden the chemistry of molecular printboards and bind charged inks such as the ferrocenium cation. Shifting to high pH, or alternatively grafting a charged sidearm onto beta-CD, created three distinct types of anionic beta-CD cavity and we used electronic structure calculations and MD simulations to measure host-guest charge transfer and binding strengths. We find that steric recognition of uncharged organic molecules is retained at the charged printboards, and that improved guest-host electrostatic contacts can strengthen binding of larger inks while penalising small inks, enhancing the level of discrimination. A prudent choice of complementary host-guest shape and charge states thus provides a means of tuning both ink binding strength and specificity at molecular printboards.     

Cation selective ion channels formed by macrodiolide antibiotic elaiophylin in lipid bilayer membranes

The macrodiolide antibiotic elaiophylin (1) forms stable, long-lasting cation selective ion channels in planar lipid bilayer membranes prepared from soybean phosphatidylcholine. Current of the single ion channel displayed two sublevels corresponding to the two substates of the channel conductance: a slow substate, with about 5 s of mean dwell time in the open state at 40% level of the total amplitude conductance, and a fast substate of higher conductance with dwell times in the open and closed state of about 0.1 s. Amplitude conductances of the single ion channels in 200 mM of LiCl, NaCl, KCl, RbCl and CsCl were 75, 140, 220, 240 and 226 pS, and the conductance was linear function of the electrolyte concentration. Ratios of cation to anion permeabilities of the channel for NaCl and KCl were 8+/-2 and >24, respectively. A molecular model of the channel structure is suggested.     

Single-molecule junctions based on nitrile-terminated biphenyls: a promising new anchoring group

We present a combined experimental and theoretical study of the electronic transport through single-molecule junctions based on nitrile-terminated biphenyl derivatives. Using a scanning tunneling microscope-based break-junction technique, we show that the nitrile-terminated compounds give rise to well-defined peaks in the conductance histograms resulting from the high selectivity of the N-Au binding. Ab initio calculations have revealed that the transport takes place through the tail of the LUMO. Furthermore, we have found both theoretically and experimentally that the conductance of the molecular junctions is roughly proportional to the square of the cosine of the torsion angle between the two benzene rings of the biphenyl core, which demonstrates the robustness of this structure-conductance relationship.     

A new alligator-clip compound for molecular electronics

We used the B3LYP flavor of density functional calculations to study new alligator-clip compounds for molecular electronics with platinum electrodes. First, with commonly used S-based linkage molecule 3-methyl-1,2-dithiolane (MDTL) we find that after chemisorption on Pt(1 1 1) the most stable structure is ring-opened with a binding energy of 32.44 kcal/mol. Among several alternative alligator-clip compounds we find that P-based molecules lead to much higher binding energies. For the ring-closed structure of 3-methyl-1,2-diphospholane (MDPL) a binding energy of 47.72 kcal/mol was calculated and even 54.88 kcal/mol for the ring-opened molecule. Thus, MDPL provides a more stable link to the metal surface and might increase the conductance.     

Structure-Independent Conductance of Thiophene-Based Single-Stacking Junctions

The experimental investigation of intermolecular charge transport in π-conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single-molecule and single-stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single-stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single-molecule junctions with the same building blocks, and the dominant charge-transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.     

The binding sites of carboxylic acid group contacting to Cu electrode

In this work, the binding sites of carboxylic acid binding to Cu electrode are explored by electrochemical jump-to-contact STM break junction. Single molecular conductance of benzene-based molecules with ending groups of carboxylic acid, carbonyl and hydroxyl are measured and compared. The conductance values of 1,4-benzenedicarboxaldehyde can be found in those of 1,4-benzenedicarboxylic acid, which shows that carboxylic acid can bind to Cu electrode through carbonyl group. Carboxylic acid can also bind to the electrode through carboxylate group, and gives out larger conductance values than those of carbonyl group. However, molecule with hydroxyl group is difficult to form single molecular junction with Cu. The current work demonstrates that the carboxylic acid can bind to the electrode through carbonyl and carboxylate groups, and a new anchoring group of carbonyl group can be used to form effective single molecular junction.     

Single-molecule conductance through multiple π-π-stacked benzene rings determined with direct electrode-to-benzene ring connections

Understanding electron transport across π-π-stacked systems will help to answer fundamental questions about biochemical redox processes and benefit the design of new materials and molecular devices. Herein we employed the STM break-junction technique to measure the single-molecule conductance of multiple π-π-stacked aromatic rings. We studied electron transport through up to four stacked benzene rings held together in an eclipsed fashion via a paracyclophane scaffold. We found that the strained hydrocarbons studied herein couple directly to gold electrodes during the measurements; hence, we did not require any heteroatom binding groups as electrical contacts. Density functional theory-based calculations suggest that the gold atoms of the electrodes bind to two neighboring carbon atoms of the outermost cyclophane benzene rings in η(2) fashion. Our measurements show an exponential decay of the conductance with an increasing number of stacked benzene rings, indicating a nonresonant tunneling mechanism. Furthermore, STM tip-substrate displacement data provide additional evidence that the electrodes bind to the outermost benzene rings of the π-π-stacked molecular wires.     

Probing the Origin of Viscosity of Liquid Electrolytes for Lithium Batteries

Viscosity is an extremely important property for ion transport and wettability of electrolytes. Easy access to viscosity values and a deep understanding of this property remain challenging yet critical to evaluating the electrolyte performance and tailoring electrolyte recipes with targeted properties. We proposed a screened overlapping method to efficiently compute the viscosity of lithium battery electrolytes by molecular dynamics simulations. The origin of electrolyte viscosity was further comprehensively probed. The viscosity of solvents exhibits a positive correlation with the binding energy between molecules, indicating viscosity is directly correlated to intermolecular interactions. Salts in electrolytes enlarge the viscosity significantly with increasing concentrations while diluents serve as the viscosity reducer, which is attributed to the varied binding strength from cation–anion and cation–solvent associations. This work develops an accurate and efficient method for computing the electrolyte viscosity and affords deep insight into viscosity at the molecular level, which exhibits the huge potential to accelerate advanced electrolyte design for next-generation rechargeable batteries.     

Complex formation between poly(ethylene oxide) and alkali picrates

The interaction of poly(ethylene oxide) with alkali picrates in tetrahydrofuran and dioxane was studied by optical and NMR spectroscopy and conductance measurements. Evidence was found of the formation of two kinds of solvation complex, differing in the nature of the ion pairs involved. A strong anion effect on cation binding to the polyether was demonstrated.     

Anisotropic Conductivity at the Single‐Molecule Scale

In most junctions built by wiring a single molecule between two electrodes, the electrons flow along only one axis: between the two anchoring groups. However, molecules can be anisotropic, and an orientation‐dependent conductance is expected. Here, we fabricated single‐molecule junctions by using the electrode potential to control the molecular orientation and access individual elements of the conductivity tensor. We measured the conductance in two directions, along the molecular plane as the benzene ring bridges two electrodes using anchoring groups (upright) and orthogonal to the molecular plane with the molecule lying flat on the substrate (planar). The perpendicular (planar) conductance is about 400 times higher than that along the molecular plane (upright). This offers a new method for designing a reversible room‐temperature single‐molecule electromechanical switch that controllably employs the electrode potential to orient the molecule in the junction in either “ON” or “OFF” conductance states.     

Manifestation of electrode surface states in molecular conduction

We present a conduction mechanism across molecular junctions which derives from conductance resonances that are not associated with particular molecular orbitals. Instead, the resonances are induced by states localized at the surface of the electrodes. To this end, we studied the conductance of a C₆₀ molecule bridging two carbon nanotubes. A simple tight-binding model is employed to investigate analytically the basic features of the effect.     

A novel approach to characterize the binding orientation of lysozyme on ion-exchange resins

Much work has been done to qualify and quantify chromatographic adsorption and transportation mechanisms in different adsorber materials. An important aspect in all studies is the understanding of the binding mechanism between protein and resin on a molecular level in order to optimize processes on the level of adsorber design. We established a method to determine the binding orientation of lysozyme for different materials under various experimental conditions enabling us to observe changes in the mode of adsorption. We varied the protein load of two different adsorber types, Source 15S, a conventional cation exchange resin and EMD Fractogel SO(3), a tentacle-type cation exchanger. We found similar preferential binding sites for the interaction between lysozyme and the surface of these adsorbers at low surface coverage, however, the tentacle adsorber exhibited multi-point binding whereas the binding on Source was limited to one binding site only. With increasing protein density on the surface, lysozyme rotates from a space-consuming side-on to a space-saving end-on orientation on Fractogel, explaining a higher maximum binding capacity for Fractogel. This re-orientation could not be observed for Source.     

Structure‐Independent Conductance of Thiophene‐Based Single‐Stacking Junctions

The experimental investigation of intermolecular charge transport in π‐conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single‐molecule and single‐stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single‐stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single‐molecule junctions with the same building blocks, and the dominant charge‐transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.     

Dynamic devices. Shape switching and substrate binding in ion-controlled nanomechanical molecular tweezers

As examples of supramolecular devices performing chemical (ionic, molecular) control of binding events and models of related natural systems, two molecular conformational switches are described, which display cation-controlled nanomechanical motion coupled to substrate binding and release. The substrate binding relies on donor/acceptor interactions, provided by intercalation between planar sites located at the extremities of the switching units, whereas cation complexation is responsible for conformational regulation. The terpyridine py-py-py-based receptor is activated toward substrate binding upon complexation of a zinc(II) cation and operates in a two-state process. The replacement of the central pyridine by a 4,6-disubstituted pyridimine as in py-pym-py induces a state reversal and yields a new receptor which binds a substrate in the absence of cation, and releases it when copper(I) is introduced, following a three-step process. These systems represent effector-triggered supramolecular switching devices leading toward multistate nanomechanical chemical systems. These two systems illustrate the use of simple conformational switches in the binding site and allosteric regulation of substrate affinity.     

High fidelity kinetic self-sorting in multi-component systems based on guests with multiple binding epitopes

The molecular recognition platforms of natural systems often possess multiple binding epitopes, each of which has programmed functional consequences. We report the dynamic behavior of a system comprising CB[6], CB[7], and guests cyclohexanediammonium (1) and adamantanealkylammonium (2) that we refer to as a two-faced guest because it contains two distinct binding epitopes. We find that the presence of the two-faced guest--just as is observed for protein targeting in vivo--dictates the kinetic pathway that the system follows toward equilibrium. The influence of two-faced guest structure, cation concentration, cation identity, and individual rate and equilibrium constants on the behavior of the system was explored by a combination of experiment and simulation. Deconstruction of this system led to the discovery of an anomalous host-guest complex (CB[6].1) whose dissociation rate constant (k(out) = 8.5 x 10(-10) s(-1)) is approximately 100-fold slower than the widely used avidin.biotin affinity pair. This result, in combination with the analysis of previous systems which uncovered extraordinarily tight binding events (K(a) > or = 10(12) M(-1)), highlights the inherent potential of pursuing a systems approach toward supramolecular chemistry.     

Polarization-corrected molecular electrostatic potential for the cation binding problem

The molecular electrostatic potential (MESP) and polarization-corrected MESP (PMESP) minima for some small molecules are calculated on the surface generated by rolling cations (Li⁺ and Na⁺) on their van der Waals surfaces. The cation binding energies of these molecules are obtained with HF/6-31G^** level ab initio calculations. A noteworthy outcome of the present study is that the plot of these binding energies and the corresponding PMESP surface minimum values turns out to be remarkably linear with a slope close to unity. The PMESP is thus found to work as a powerful tool for unearthing the patterns of cation binding sites and energetics for molecular systems.     

Quantum chemical studies on hydrogen adsorption in carbon-based model systems: role of charged surface and the electronic induction effect

Quantum chemical studies on the molecular hydrogen adsorption in a six-membered carbon ring has been undertaken to mimic the adsorption process in carbon nanotubes, considering the fact that the six-membered carbon ring is found to be one of the basic units of the carbon nanotubes and fullerenes. Our results reveal that the carbon surface as such is not a good candidate for hydrogen adsorption but a charged surface created by doping of an alkali metal atom can play an important role for the improvement in adsorption of molecular hydrogen. The strength of hydrogen interaction as well as the number of hydrogen molecules that can be adsorbed on the system is found to depend on the nature of the cation doped in the system. We have also studied the role of electronic induction by substituting different functional groups in the model system on the hydrogen adsorption energy. The results demonstrate that the binding energy of the cation with the carbon surface as well as the hydrogen adsorption energy can be tuned significantly through the use of suitable substituents. In addition, we have shown that the extended planar or the curved carbon surface of the coronene system alone may not be suitable for an effective molecular hydrogen adsorption. In essence, our results reveal that the ionic surface with a significant degree of curvature will enhance the hydrogen adsorption effectively.