Odd-Even Effect in Peptide SAMs-Competition of Secondary Structure and Molecule-Substrate Interaction.

Peptide-based self-assembled monolayers (SAMs) are well known to be crucial for biocompatible surface formation on inorganic substrates applied for implants, biosensors, or tissue engineering. Moreover, recently these bioinspired nanostructures are also considered particularly interesting for molecular electronics applications due to their surprisingly high conductance and thickness-independent capacitance, which make them a very promising element of organic field-effect transistors (OFETs). Our structural analysis conducted for a series of prototypic homooligopeptides based on glycine (Gly) with cysteine (Cys) as a substrate bonding group chemisorbed on Au and Ag metal substrates (GlynCys/Au(Ag), n = 1-9) exhibits the formation by these monolayers secondary structure close to ß-sheet conformation with pronounced odd-even structural effect strongly affecting packing density and conformation of molecules in the monolayer, which depend on the length of molecules and the type of metal substrate. Our experiments indicate that the origin of these structural effects is related to the either cooperative or competitive relationship between the type of secondary structure formed by these molecules and the directional character of their chemical bonding to the metal substrate. The current analysis opens up the opportunity for the rational design of these biologically inspired nanostructures, which is crucial both for mentioned biological and electronic applications.

N-Heterocyclic Carbenes for the Self-Assembly of Thin and Highly Insulating Monolayers with High Quality and Stability.

As an organic nanostructure, self-assembled monolayers (SAMs) play a central role in many aspects of nanotechnology, including molecular electronics. In this work, we show that SAMs based on N-heterocyclic carbenes on a Au(111) substrate offer a high level of crystallinity and also exhibit the highest possible packing density. As a result of this structural optimization, defect concentrations were reduced by 2-3 orders of magnitude and thermal stability was ∼100 K higher than those of any other SAMs on Au. The conductivity of these SAMs is ∼4 orders of magnitude lower than that of standard alkanethiols of comparable length, which together with very low defect concentration and high thermal stability makes them a highly interesting material for potential application in organic thin film transistors. The self-assembly of such dense, highly crystalline, and notably stable structures is associated with strong C-Au bonding and the rational design of assembled molecules, resulting in the high mobility of both adsorbate and substrate atoms, as confirmed by the size of the molecular domains and the adsorbate-driven modification of the Au(111) substrate, respectively.

Preparation of Carbon Nanomembranes without Chemically Active Groups.

The electron-irradiation-induced synthesis of carbon nanomembranes (CNMs) from aromatic thiol-based self-assembled monolayers (SAMs) on gold substrate is a well-established method to form molecular thin nanosheets. These molecular two-dimensional materials can be prepared with tunable properties; therefore, they find a variety of applications in nanotechnology ranging from ultrafiltration to nanobiosensors. However, no chemically inert CNM was fabricated up to now, as the reactive thiol group is present on the membrane surface even after transferring it to other substrates. Here, we study the electron irradiation of carboxylic acid-based SAMs on a silver substrate as an alternative route for CNM formation. Our analysis, based on a combination of X-ray photoelectron spectroscopy and scanning electron microscopy demonstrates that for this type of SAMs, purely carbonaceous CNMs with tunable porosity can be obtained.

Oscillation in the stability of consecutive chemical bonds at the molecule-metal interface - the case of ionic bonding.

Ion-induced desorption was successfully applied for the analysis of the stability of chemical bonds at the molecule-metal interface in the case of ionic bonding. The obtained experimental data combined with the results of the DFT calculations reveal the effect of positional oscillations in the stability of consecutive chemical bonds, which has general character in chemistry.

Photoisomerization of azobenzene-substituted alkanethiolates on Au(111) substrates in the context of work function variation: the effect of structure and packing density.

Photoisomerization of a series of custom-designed, azobenzene-substituted alkanethiolate (AT) self-assembled monolayers (SAMs) on Au(111) substrates was studied in the context of work function variation, using Kelvin probe measurements as a transduction technique. These SAMs featured variable packing density (by ∼14%; due to the odd-even effects) and, as an option, were additionally decorated with the electron donating/withdrawing -CH3 and -CF3 tail group, respectively, which induce additional dipole moments. The efficiency of photoisomerization and the respective extent of work function variation (ΔΦ) were found to be quite low and independent of the packing density in the SAMs, within the given odd-even packing density variation. They could only be increased, up to ca. 40 meV for ΔΦ, by mixing the azobenzene-substituted ATs with shorter "matrix" molecules, which were introduced for a partial release of the sterical constraints. The ΔΦ values for the SAMs decorated with the -CH3 and -CF3 tail groups were found to be lower than those for the monolayers without such a decoration, which correlated well with the theoretical estimates for the change of the dipole moment of the relevant molecules upon the photoisomerization.

Anomalously Rapid Tunneling: Charge Transport across Self-Assembled Monolayers of Oligo(ethylene glycol).

This paper describes charge transport by tunneling across self-assembled monolayers (SAMs) of thiol-terminated derivatives of oligo(ethylene glycol) (HS(CH2CH2O)nCH3; HS(EG)nCH3); these SAMs are positioned between gold bottom electrodes and Ga2O3/EGaIn top electrodes. Comparison of the attenuation factor (ß of the simplified Simmons equation) across these SAMs with the corresponding value obtained with length-matched SAMs of oligophenyls (HS(Ph)nH) and n-alkanethiols (HS(CH2)nH) demonstrates that SAMs of oligo(ethylene glycol) have values of ß (ß(EG)n = 0.29 ± 0.02 natom-1 and ß = 0.24 ± 0.01 Å-1) indistinguishable from values for SAMs of oligophenyls (ß(Ph)n = 0.28 ± 0.03 Å-1), and significantly lower than those of SAMs of n-alkanethiolates (ß(CH2)n = 0.94 ± 0.02 natom-1 and 0.77 ± 0.03 Å-1). There are two possible origins for this low value of ß. The more probable involves hole tunneling by superexchange, which rationalizes the weak dependence of the rate of charge transport on the length of the molecules of HS(EG)nCH3 using interactions among the high-energy, occupied orbitals associated with the lone-pair electrons on oxygen. Based on this mechanism, SAMs of oligo(ethylene glycol)s are good conductors (by hole tunneling) but good insulators (by electron and/or hole drift conduction). This observation suggests SAMs derived from these or electronically similar molecules are a new class of electronic materials. A second but less probable mechanism for this unexpectedly low value of ß for SAMs of S(EG)nCH3 rests on the possibility of disorder in the SAM and a systematic discrepancy between different estimates of the thickness of these SAMs.

Charge Tunneling along Short Oligoglycine Chains.

This work examines charge transport (CT) through self-assembled monolayers (SAMs) of oligoglycines having an N-terminal cysteine group that anchors the molecule to a gold substrate, and demonstrate that CT is rapid (relative to SAMs of n-alkanethiolates). Comparisons of rates of charge transport-using junctions with the structure Au(TS)/SAM//Ga2O3/EGaIn (across these SAMs of oligoglycines, and across SAMs of a number of structurally and electronically related molecules) established that rates of charge tunneling along SAMs of oligoglycines are comparable to that along SAMs of oligophenyl groups (of comparable length). The mechanism of tunneling in oligoglycines is compatible with superexchange, and involves interactions among high-energy occupied orbitals in multiple, consecutive amide bonds, which may by separated by one to three methylene groups. This mechanistic conclusion is supported by density functional theory (DFT).

Thiolate versus Selenolate: Structure, Stability, and Charge Transfer Properties.

Selenolate is considered as an alternative to thiolate to serve as a headgroup mediating the formation of self-assembled monolayers (SAMs) on coinage metal substrates. There are, however, ongoing vivid discussions regarding the advantages and disadvantages of these anchor groups, regarding, in particular, the energetics of the headgroup-substrate interface and their efficiency in terms of charge transport/transfer. Here we introduce a well-defined model system of 6-cyanonaphthalene-2-thiolate and -selenolate SAMs on Au(111) to resolve these controversies. The exact structural arrangements in both types of SAMs are somewhat different, suggesting a better SAM-building ability in the case of selenolates. At the same time, both types of SAMs have similar packing densities and molecular orientations. This permitted reliable competitive exchange and ion-beam-induced desorption experiments which provided unequivocal evidence for a stronger bonding of selenolates to the substrate as compared to the thiolates. Regardless of this difference, the dynamic charge transfer properties of the thiolate- and selenolate-based adsorbates were found to be nearly identical, as determined by the core-hole-clock approach, which is explained by a redistribution of electron density along the molecular framework, compensating the difference in the substrate-headgroup bond strength.

Characterizing the metal-SAM interface in tunneling junctions.

This paper investigates the influence of the interface between a gold or silver metal electrode and an n-alkyl SAM (supported on that electrode) on the rate of charge transport across junctions with structure Met(Au or Ag)(TS)/A(CH2)nH//Ga2O3/EGaIn by comparing measurements of current density, J(V), for Met/AR = Au/thiolate (Au/SR), Ag/thiolate (Ag/SR), Ag/carboxylate (Ag/O2CR), and Au/acetylene (Au/C≡CR), where R is an n-alkyl group. Values of J0 and ß (from the Simmons equation) were indistinguishable for these four interfaces. Since the anchoring groups, A, have large differences in their physical and electronic properties, the observation that they are indistinguishable in their influence on the injection current, J0 (V = 0.5) indicates that these four Met/A interfaces do not contribute to the shape of the tunneling barrier in a way that influences J(V).

Oscillations in the stability of consecutive chemical bonds revealed by ion-induced desorption.

While it is a common concept in chemistry that strengthening of one bond results in weakening of the adjacent ones, no results have been published on if and how this effect protrudes further into the molecular backbone. By binding molecules to a surface in the form of a self-assembled monolayer, the strength of a primary bond can be selectively altered. Herein, we report that by using secondary-ion mass spectrometry, we are able to detect for the first time positional oscillations in the stability of consecutive bonds along the adsorbed molecule, with the amplitudes diminishing with increasing distance from the molecule-metal interface. To explain these observations, we have performed molecular dynamics simulations and DFT calculations. These show that the oscillation effects in chemical-bond stability have a very general nature and break the translational symmetry in molecules.

Formation of highly ordered self-assembled monolayers of alkynes on Au(111) substrate.

Self-assembled monolayers (SAMs), prepared by reaction of terminal n-alkynes (HC≡C(CH2)nCH3, n = 5, 7, 9, and 11) with Au(111) at 60 °C were characterized using scanning tunneling microscopy (STM), infrared reflection absorption spectroscopy (IRRAS), X-ray photoelectron spectroscopy (XPS), and contact angles of water. In contrast to previous spectroscopic studies of this type of SAMs, these combined microscopic and spectroscopic experiments confirm formation of highly ordered SAMs having packing densities and molecular chain orientations very similar to those of alkanethiolates on Au(111). Physical properties, hydrophobicity, high surface order, and packing density, also suggest that SAMs of alkynes are similar to SAMs of alkanethiols. The formation of high-quality SAMs from alkynes requires careful preparation and manipulation of reactants in an oxygen-free environment; trace quantities of O2 lead to oxidized contaminants and disordered surface films. The oxidation process occurs during formation of the SAM by oxidation of the -C≡C- group (most likely catalyzed by the gold substrate in the presence of O2).

Self-assembled monolayers of perfluoroterphenyl-substituted alkanethiols: specific characteristics and odd-even effects.

Self-assembled monolayers (SAMs) formed by perfluoroterphenyl-substituted alkanethiols (C(6)F(5)-C(6)F(4)-C(6)F(4)-(CH(2))(n)-SH, FTPn) with variable length of the aliphatic linker (n = 2 and 3) were prepared on (111) Au and Ag and characterized by a combination of several complementary spectroscopic and microscopic techniques. A specific feature of these systems is the helical conformation of the FTP moieties, which, along with the high electronegativity of fluorine, distinguishes them from the analogous non-fluorinated systems and makes them attractive for different applications. The SAMs were found to be well-defined, highly ordered, and densely packed, which suggests a perfect correlation between the orientations and, in particular, twists of the FTP helices in the adjacent molecules. Significantly, the SAM exhibited pronounced odd-even effects, i.e. a dependence of the molecular orientation and packing density on the length of the aliphatic linker in the target molecules, with parity of n being the decisive parameter and the direction of the effects on Au opposite to that on Ag. The presence of the odd-even effects in the FTPn system brings new aspects into the discussion about the origin and mechanism of these phenomena. Specifically, the helical conformation of the FTP moieties in the dense phase excludes a variation of the intramolecular torsion and molecular twist as the mechanism behind the odd-even effects.

Relative stability of thiol and selenol based SAMs on Au(111) - exchange experiments.

Two fully analogue homologue series of thiol and selenol based aromatic self-assembled monolayers (SAMs) on Au(111) in the form of CH(3)-(C(6)H(4))(2)-(CH(2))(n)-S-Au(111) (BPnS/Au(111), n = 2-6) and CH(3)-(C(6)H(4))(2)-(CH(2))(n)-Se-Au(111) (BPnSe/Au(111), n = 2-6), respectively, have been used to elucidate the relative stability of the S-Au(111) and Se-Au(111) bonding by monitoring their exchange by alkanethiol and alkaneselenol molecules from their respective solutions. The exchange process was monitored using infrared reflection absorption spectroscopy (IRRAS). Two main results obtained by these study are: (1) the selenium-based BPnSe/Au(111) series is significantly more stable than their sulfur analogues; (2) a clear odd-even effect exists for the stability of both BPnS/Au(111) and BPnSe/Au(111) SAMs towards exchange processes with the even-numbered systems being less stable. The results obtained are discussed in view of previously reported microscopic and spectroscopic data of the same SAMs addressing the issue of the relative stability of S-Au(111) and Se-Au(111) bonding, which is an important factor for the rational design of SAMs.

Surface structure of metal-organic framework grown on self-assembled monolayers revealed by high-resolution atomic force microscopy.

The surface structure of an individual metal-organic framework (MOF) microcrystal grown on a functionalized surface has been successfully investigated for the first time in air and vacuum using high-resolution atomic force microscopy. Moreover, this detailed surface analysis has been utilized to optimize the MOF formation procedure to obtain a defect-free surface structure. Comparison of obtained data with recent microscopic studies performed on the same MOF crystal but grown by a conventional procedure clearly shows a much higher quality of crystals produced by surface oriented growth. Importantly, this method of preparing crystals suitable for microscopic analysis is also much faster (3 days compared to 2 years) and, in contrast to the conventional method, produces material suitable for in situ study. These results thus demonstrate for the first time the possibility of nanoscale investigation/modification of MOF surface structure.

Competition as a design concept: polymorphism in self-assembled monolayers of biphenyl-based thiols.

Self-assembled monolayers (SAMs) of two omega-(4'-methylbiphenyl-4-yl)alkanethiols (CH(3)(C(6)H(4))(2)(CH(2))(n)SH, BPn, n = 4, 6) on Au(111) substrates, prepared from solution at room temperature and subsequently annealed at temperatures up to 493 K under a nitrogen atmosphere, were studied using scanning tunneling microscopy (STM), high-resolution X-ray photoelectron spectroscopy (HRXPS), and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). In striking contrast to BPn SAMs with n = odd, for which only one phase is observed, the even-numbered BPn SAMs exhibit polymorphism. Irreversible phase transitions occur which involve three phases differing substantially in density and stability. Upon annealing, BP4 and BP6 transform into a beta-phase, which is characterized by an exceptionally high structural quality with virtually defect-free domains exceeding 500 nm in diameter. Exchange experiments, monitored by contact angle measurement, reveal that the beta-phase exhibits a dramatically improved stability. The fundamental differences in the phase behavior of even- and odd-numbered BPn SAMs are discussed in terms of two design strategies based on cooperative and competitive effects.

A comprehensive study of self-assembled monolayers of anthracenethiol on gold: solvent effects, structure, and stability.

The formation and molecular structure of self-assembled monolayers (SAMs) of anthracene-2-thiol (AnT) on Au(111) have been characterized by reflection adsorption infrared spectroscopy, thermal desorption spectroscopy, X-ray photoelectron spectroscopy, near-edge X-ray absorption spectroscopy, scanning tunneling microscopy, and low energy electron diffraction. It is demonstrated that highly ordered monolayer films are formed upon immersion, but their quality depends critically on the choice of solvents and rinsing conditions. The saturated monolayer is characterized by a closed packed arrangement of upright standing molecules forming a (2 x 4)rect unit cell. At about 450 K a partial desorption takes place and the remaining molecules form a dilute (4 x 2)-phase with an almost planar adsorption geometry, while further heating above 520 K causes a thermally induced fragmentation. According to their different densities both phases reveal very diverse chemical reactivities. Whereas the saturated monolayer is stable and inert under ambient conditions, the dilute phase does not warrant any protection of the sulfur headgroups which oxidize rapidly in air.

Stress in self-assembled monolayers: omega-biphenyl alkane thiols on Au(111).

Self-assembled monolayers of omega-(4'-methylbiphenyl-4-yl) alkane thiols CH3(C6H4)2(CH2)(n)SH (BPn, n = 2, 3, and 5) on Au(111) substrates, prepared at room and elevated temperatures, were studied using scanning tunneling microscopy. In contrast to the biphenyl thiol analogues with n = 0 or 1, ordered domains of large size are formed which exhibit small, periodic height variations on a length scale of several nanometers. These are attributed to solitons (or domain walls), resulting from structural mismatch between the molecular adlayer and the gold substrate. The implications of these results for the design of aromatic thiols to cope with stress and yield low-defect density self-assembled monolayers are discussed.