Structure-dependent charge transport and storage in self-assembled monolayers of compounds of interest in molecular electronics: effects of tip material, headgroup, and surface concentration

The electrical properties of self-assembled monolayers (SAMs) on a gold surface have been explored to address the relation between the conductance of a molecule and its electronic structure. We probe interfacial electron transfer processes, particularly those involving electroactive groups, of SAMs of thiolates on Au by using shear force-based scanning probe microscopy (SPM) combined with current-voltage (i-V) and current-distance (i-d) measurements. Peak-shaped i-V curves were obtained for the nitro- and amino-based SAMs studied here. Peak-shaped cathodic i-V curves for nitro-based SAMs were observed at negative potentials in both forward and reverse scans and were used to define the threshold tip bias, V(TH), for electric conduction. For a SAM of 2',5'-dinitro-4,4'-bis(phenylethynyl)-1-benzenethiolate, VII, V(TH) was nearly independent of the tip material [Ir, Pt, Ir-Pt (20-80%), Pd, Ni, Au, Ag, In]. For all of the SAMs studied, the current decreased exponentially with increasing distance, d, between tip and substrate. The exponential attenuation factors (beta values) were lower for the nitro-based SAMs studied here, as compared with alkylthiol-based SAMs. Both V(TH) and beta of the nitro-based SAMs also depended strongly on the molecular headgroup on the end benzene ring addressed by the tip. Finally, we confirmed the "memory" effect observed for nitro-based SAMs. For mixed SAMs of VII and hexadecanethiol, I, the fraction of the charge collected in the negative tip bias region that can be read out at a positive tip bias on reverse scan (up to 38%) depended on the film composition and decreased with an increasing fraction of I, suggesting that lateral electron hopping among molecules of VII occurs in the vicinity of the tip.     

Molecular engineering of the polarity and interactions of molecular electronic switches

We have investigated and learned to control switching of oligo(phenylene ethynylene)s embedded in amide-containing alkanethiol self-assembled monolayers on Au{111}. We demonstrate bias-dependent switching of the oligo(phenylene ethynylene)s as a function of the interaction between the dipole moment of the oligo(phenylene ethynylene)s and the electric field applied between the scanning tunneling microscope tip and the substrate. We are able to invert the polarity of the switches by altering their design-inverting their dipole moments. For appropriately designed switches and matrix molecules, the conductance states are stabilized by intermolecular hydrogen bonding. These results further support the hypothesis that conductance switching in these molecules is due to hybridization changes at the molecule-substrate bonds due to tilting of the switch molecules.     

Molecular junctions based on SAMs of cruciform oligo(phenylene ethynylene)s

Cruciform oligo(phenylene ethynylene)s (OPEs) with an extended tetrathiafulvalene (TTF) donor moiety (OPE5-TTF and OPE3-TTF) and their simple analogues (OPE5-S and OPE3) without conjugated substituents were used to form high-quality self-assembled monolayers (SAMs) on ultraflat gold substrates. Molecular junctions based on these SAMs were investigated using conducting-probe atomic force microscopy (CP-AFM). The TTF substituent changes the molecular orbital energy levels and decreases the HOMO-LUMO energy gap, resulting in a 9-fold increase in conductance for both TTF cruciform OPEs compared to the unsubstituted analogues. The difference in electrical transport properties of the SAMs was reproduced by the theoretical transport calculations for the single molecules.     

An effective, orthogonal deprotection strategy for differentially functionalized, linear and Y-shaped oligo phenylene ethynylenes

Several methodologies for the selective deprotection acetylenes have been reported previously. However, as is shown here, they are often not reliable or convenient. Here, an approach is reported that is efficient and general. Use of this approach to synthesize several two- and three-armed oligo(phenylene ethynylene) molecules with differentiated end groups is reported. In addition, preliminary characterization of the fluorescent properties of some of these molecules and their ability to form self-assembled monolayers (SAMs) is reported.     

Synthesis of oligo(phenylene ethynylene)s with dendrimer "shells" for molecular electronics

Two series of oligo(phenylene ethynylene)s (OPEs) with different dendrimer side groups have been designed and synthesized. The molecules contain thiol groups at both ends to enable interconnection between nanoscale gapped metallic electrodes. The different dendrimer groups act as "shells", allowing tailoring to the nanoscopic environment surrounding the OPE "core". Meanwhile, the dendrimer shells also act as spacers for the precise control of the packing density and intermolecular interaction between the OPE cores. [structure: see text].     

Vibronic structures in the electronic spectra of oligo(phenylene ethynylene): effect of m-phenylene to the optical properties of poly(m-phenylene ethynylene)

At the low temperature, hidden vibronic structures are successfully resolved in the absorption and emission spectra of oligo(phenylene ethynylene)s 3-5. Identification of the hidden bands allows estimation of the vibrational energy gaps in these molecules, which appears to increase with the oligomer conjugation length. The remarkable similarity between the absorption profiles of diphenylacetylene (3) and 1,3-bis(phenylethynyl)benzene (5), especially at -198 degrees C, confirms the effectiveness of conjugation interruption at m-phenylene. The function of precise conjugation length control via m-phenylene is further demonstrated from poly(m-phenylene ethynylene) (PmPE) (6). Even though the number of recurring unit (phenylene ethynylene) increases from 2 (for 5) to 12 (for 6), the absorption and emission spectra of the latter are nearly identical to that of the former.     

Direct adsorption and monolayer self-assembly of acetyl-protected dithiols

The alpha,omega-dithiols, with sulfur-containing groups at both ends of the molecules, can be used to bridge a metallic gap. Functional self-assembled monolayers (SAMs) of these dithiols must "stand up" on the surface and expose one thiol group for further reaction. However, both parallel and upright surface orientations and multilayer formation can occur for alpha,omega-dithiols. We find SAMs deposited directly from acetyl protected dithiols (i.e., with no de-protection step) overcome these problems. We present a systematic study of adsorption kinetics from in situ surface plasmon resonance spectroscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectroscopy of alkane- and oligo(phenylene ethylnylene)-based alpha,omega-dithioacetates on gold.     

Electrical conductance of conjugated oligomers at the single molecule level

We determine and compare, at the single molecule level and under identical environmental conditions, the electrical conductance of four conjugated phenylene oligomers comprising terminal sulfur anchor groups with simple structural and conjugation variations. The comparison shows that the conductance of oligo(phenylene vinylene) (OPV) is slightly higher than that of oligo(phenylene ethynylene) (OPE). We find that solubilizing side groups do neither prevent the molecules from being anchored within a break junction nor noticeably influence the conductance value.     

Synthesis of nitrile-terminated potential molecular electronic devices

Several potential molecular devices have been synthesized consisting of oligo(phenylene ethynylene) (OPE) backbones containing a terminal nitrile group alligator clip as a means of attachment to a metal surface. The synthesis of four new nitrile-containing OPEs is discussed, including an improved synthesis of an intermediate used in our prior production of OPEs containing acetate-protected thiol alligator clips.     

Improved and new syntheses of potential molecular electronics devices

New syntheses of ethyl and nitro substituted oligo(phenylene ethynylene)s (OPEs) have been developed. To further explore whether the presence of nitro functionality in OPEs leads to switching and memory capabilities, new nitro substituted OPEs have been designed and synthesized. An isatogen-based system, a structure that is isomeric to the nitro OPE, has been synthesized. Additionally, pyridine-based and chromium-based compounds have been synthesized. We surmise that redox reactions of these candidates may impart switching capabilities and electrochemical studies are shown. U-shaped OPEs were synthesized to inhibit leakage of metals deposited during formation of top contacts on self-assembled monolayers (SAMs). The OPEs contain either thiol-based moieties or isonitrile groups to enable formation of SAMs on metal substrates.     

Modular DNA-programmed assembly of linear and branched conjugated nanostructures

A new strategy for self-assembly and covalent coupling of encoded molecular modules into nanostructures with predetermined connectivity has been developed. The method uses DNA-functionalized oligo(phenylene ethynylene)-derived organic modules for controlling the assembly and covalent coupling of multiple modules. Rigid linear modules (LM) and tripoidal modules (TM) were functionalized with short oligonucleotides at each terminus. They can hybridize and thereby link up modules containing complementary sequences. Each terminus of the oligo(phenylene ethynylene) modules also consists of a salicylaldehyde moiety, which can form metal-salen complexes with other modules. The salicylaldehyde groups of two modules are brought in proximity when their adjoining DNA sequences are complementary, and they selectively form a manganese-salen complex in the presence of ethylenediamine and manganese acetate. The resulting structures consist of a matrix of linear and branched oligo(phenylene ethynylene)s which are linked by conjugated and rigid manganese-salen complexes. These nanostructures are potential conductors for applications in molecular electronics.     

Synthesis of terphenyl oligomers as molecular electronic device candidates

Six functionalized bis(phenylene ethynylene)-p,p-terphenyls (BPETs) have been synthesized as potential molecular electronic devices. The molecules containing mono- and dinitro terphenyl cores, were rationally designed based on the electronic properties recently found in oligo(phenylene ethynylene)s (OPEs). From our understanding of the conductance properties in OPEs, improvement of electronic properties may be possible by using BPETs due to a higher rotational barrier between the central aromatic rings of the compounds prepared here. BPETs cores were functionalized with nitro groups and with different metallic adhesion moieties (alligator clips) to provide new compounds for testing in the nanopore and planar testbed structures.     

Fabrication and characterization of metal-molecule-metal junctions by conducting probe atomic force microscopy

Metal-molecule-metal junctions were fabricated by contacting Au-supported alkyl or benzyl thiol self-assembled monolayers (SAMs) with an Au-coated atomic force microscope (AFM) tip. The tip-SAM microcontact is approximately 15 nm(2), meaning the junction contains approximately 75 molecules. Current-voltage (I-V) characteristics of these junctions were probed as a function of SAM thickness and load applied to the microcontact. The measurements showed: (1) the I-V traces were linear over +/-0.3 V, (2) the junction resistance increased exponentially with alkyl chain length, (3) the junction resistance decreased with increasing load and showed two distinct power law scaling regimes, (4) resistances were a factor of 10 lower for junctions based on benzyl thiol SAMs compared to hexyl thiol SAMs having the same thickness, and (5) the junctions sustained fields up to 2 x 10(7) V/cm before breakdown. I-V characteristics determined for bilayer junctions involving alkane thiol-coated tips in contact with alkane thiol SAMs on Au also showed linear I-Vs over +/-0.3 V and the same exponential dependence on thickness. The I-V behavior and the exponential dependence of resistance on alkyl chain length are consistent with coherent, nonresonant electron tunneling across the SAM. The calculated conductance decay constant (beta) is 1.2 per methylene unit ( approximately 1.1 A(-)(1)) for both monolayer and bilayer junctions, in keeping with previous scanning tunneling microscope and electrochemical measurements of electron transfer through SAMs. These measurements show that conducting probe-AFM is a reliable method for fundamental studies of electron transfer through small numbers of molecules. The ability to vary the load on the microcontact is a unique characteristic of these junctions and opens opportunities for exploring electron transfer as a function of molecular deformation.     

Significance of local density of states in the scanning tunneling microscopy imaging of alkanethiol self-assembled monolayers

A systematic scanning tunneling microscopy (STM) study of alkanethiol self-assembled monolayers (SAMs) is presented as a function of the bias voltage, tunneling current, and tip-termini separation. Stable and etch-pit free SAMs of close-packed undecanethiol/Au(111) were obtained after annealing in ultrahigh vacuum. STM revealed two distinct c(4x2) structures with four nonequivalent molecules per unit cell. For both structures, reversible contrast variations occur upon systematically tuning the bias voltage, the current, and the tip-termini distance. These contrast transitions originate from probing the corresponding local density of states (LDOS) of each molecule and not from the reorientation of the alkanethiol chains. The STM contrast is particularly sensitive to the tip-termini separation in the range of 0.5-2.5 A, reflecting the distance-dependence of LDOS. At a fixed tip elevation, the STM contrast is less sensitive to changes in bias within 0.1-1.2 V. For the first time, we demonstrate that LDOS may override the physical height variations in the STM topographic contrast for alkanethiol SAM systems.     

Hydrocarbon links in an octet truss

We use the octet truss of R. Buckminster Fuller to develop a geometric placement method for synthesizing braid representations of knots and links of oligo (phenylene ethynylene)s using the 60° ortho, 120° meta or 180° para phenyl ring substitution angles and respecting the van der Waals repulsion constraints. We show that any knot or link can be realized by a phenylene ethynylene oligomer modeled on the octet truss. Use of this lattice is motivated by the structural constraints of these phenylene ethynylene units. Where in bio-organic chemistry, questions often involve identifying existing knots, for example in DNA strands, organic synthesis is concerned with assembling molecular structures that can be verified to exist in a desired knot topology. This physical realization of a knot as a construction of common organic molecular subunits then facilitates further study of the properties of knotted molecules in general.     

Synthesis of rigid homo- and heteroditopic nucleobase-terminated molecules incorporating adenine and/or thymine

A series of homo- and heteroditopic thymine- and/or adenine-terminated molecules incorporating rigid aryl or oligo(phenylene ethynylene) linkers has been efficiently synthesized. The key steps involved in the synthesis are the construction of the N-arylated nucleobases using the Chan-Lam-Evans-modified Ullman coupling and their further elaboration using the Sonogashira coupling. Furthermore, the synthesis of a rigid tripodal thymine derivative is reported.     

Fabrication of carbon nanotube-molecule-silicon junctions

A hybridization strategy for the covalent connection of single wall carbon nanotubes to silicon surfaces via oligo(phenylene ethynylene)s has been demonstrated using an orthogonal bisdiazonium functionalization protocol.     

Nanoscale Biomolecular Structures on Self‐Assembled Monolayers Generated from Modular Pegylated Disulfides

A solid‐phase synthetic strategy was developed that uses modular building blocks to prepare symmetric oligo(ethylene glycol)‐terminated disulfides with a variety of lengths and terminal functionalities. The modular disulfides, composed of alkyl amino groups linked by an amide group to oligoethylene chains were used to generate self‐assembled monolayers (SAMs), which were characterised to determine their applicability for biomolecular applications. X‐ray photoelectron spectroscopy (XPS) of the SAMs obtained from these molecules demonstrated improved stability towards displacement by 16‐hexadecanethiol, while surface plasmon resonance (SPR) analyses of SAMs prepared with the hydroxy‐terminated oligoethylene disulfide showed equal resistance to non‐specific protein adsorption in comparison to 11‐mercaptoundecyl tri(ethylene glycol). SAMs made from these adsorbates were amenable to nanoscale patterning by scanning near‐field photolithography (SNP), facilitating the fabrication of nanopatterned, protein‐functionalised surfaces. Such SAMs may be further developed for bionanotechnology applications such as the fabrication of nanoscale biological arrays and sensor devices.     

Self-assembled monolayers derived from a double-chained monothiol having chemically dissimilar chains

The structure and conformation of self-assembled monolayers (SAMs) derived from the adsorption of a specifically designed double-chained partially fluorinated thiol having the formula 12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,19-heptadecafluoro -2-tetradecylnona-decane-1-thiol ( 2) onto the surface of evaporated gold were examined by ellipsometry, contact angle goniometry, polarization modulation infrared reflection-absorption spectroscopy (PM-IRRAS), and X-ray photoelectron spectroscopy (XPS). The results were compared to those of SAMs generated from normal hexadecanethiol ( 1) and a structurally related single-chained partially fluorinated thiol having the formula 12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,19-heptadecafluorononadecane-1-thiol ( 3). Collectively, the studies demonstrate that the double-chained adsorbate 2 forms SAMs on gold in which the alkyl chains are less densely packed and less conformationally ordered than those in the SAMs derived from each of the single-chained adsorbates. Furthermore, the fluorocarbon moieties in the SAMs derived from 2 are more tilted from the surface normal than those in the SAMs derived from 3. The low values of contact angle hysteresis suggest, however, that the double-chained adsorbate 2 generates homogeneous monolayer films on the surface of gold.     

Synthesis of linear and V-shaped oligo(phenylene ethynylene) derivatives: geometric effects on photophysical properties

<正>A series of linear and V-shaped oligo(phenylene ethynylene) derivatives 1-3 were synthesized through sequent Sonogashira coupling and propargyl alcohol deprotection reaction in high yields.The alkoxy chains(i.e.,n-hexyloxy groups) were introduced to assure good solubility of compounds 1-3 in common solvents.The photophysical properties of 1-3 in solution depend strongly on the geometries of these compounds.