Structure Of Self-assembled Monolayers Research Articles

Side-Group-Induced Polymorphism in Self-Assembled Monolayers: 3,5-Bis(trifluoromethyl)benzenethiolate Films on Au(111).

The structure and molecular organization of self-assembled monolayers (SAMs) depend on a complex interplay of intermolecular and molecule-substrate interactions, so that even a small change in molecular composition can result in noticeable changes in the SAM structure. Herein we show that decoration of the most basic aromatic SAM constituent, benzenethiol, with two trifluoromethyl groups leads to distinct polymorphism in the respective SAMs, in which the appearance of a specific structural phase or a combination of several different phases is dependent on the parameters of the preparation procedure. High-quality films with a single crystallographic phase and significantly large domains could only be prepared after a short immersion time (5 min) and an additional re-immersion of the sample in pure ethanol at an elevated temperature. A standard 24 h immersion at room temperature led to poorly defined films with a large defect density and only a small portion of the surface covered by well-ordered molecular domains.

Even the Odd Numbers Help: Failure Modes of SAM-Based Tunnel Junctions Probed via Odd-Even Effects Revealed in Synchrotrons and Supercomputers.

This Account describes a body of research in atomic level design, synthesis, physicochemical characterization, and macroscopic electrical testing of molecular devices made from ferrocene-functionalized alkanethiol molecules, which are molecular diodes, with the aim to identify, and resolve, the failure modes that cause leakage currents. The mismatch in size between the ferrocene headgroup and alkane rod makes waxlike highly dynamic self-assembled monolayers (SAMs) on coinage metals that show remarkable atomic-scale sensitivity in their electrical properties. Our results make clear that molecular tunnel junction devices provide an excellent testbed to probe the electronic and supramolecular structures of SAMs on inorganic substrates. Contacting these SAMs to a eutectic "EGaIn" alloy top-electrode, we designed highly stable long-lived molecular switches of the form electrode-SAM-electrode with robust rectification ratios of up to 3 orders of magnitude. The graphic that accompanies this conspectus displays a computed SAM packing structure, illustrating the lollipop shape of the molecules that gives dynamic SAM supramolecular structures and also the molecule-electrode van der Waals (vdW) contacts that must be controlled to form good SAM-based devices. In this Account, we first trace the evolution of SAM-based electronic devices and rationalize their operation using energy level diagrams. We describe the measurement of device properties using near edge X-ray absorption fine structure spectroscopy, cyclic voltammetry, and X-ray photoelectron spectroscopy complemented by molecular dynamics and electronic structure calculations together with large numbers of electrical measurements. We discuss how data obtained from these combined experimental/simulation codesign studies demonstrate control over the supramolecular and electronic structure of the devices, tuning odd-even effects to optimize inherent packing tendencies of the molecules in order to minimize leakage currents in the junctions. It is now possible, but still very costly to create atomically smooth electrodes and we discuss progress toward masking electrode imperfections using cooperative molecule-electrode contacts that are only accessible by dynamic SAM structures. Finally, the unique ability of SAM devices to achieve simultaneously high and atom-sensitive electrical switching is summarized and discussed. While putting these structures to work as real world electronic devices remains very challenging, we speculate on the scientific and technological advances that are required to further improve electronic and supramolecular structure, toward the creation of high yields of long-lived molecular devices with (very) large, reproducible rectification ratios.

Self-Assembled Monolayers of Oligophenylenecarboxylic Acids on Silver Formed at the Liquid-Solid Interface.

A series of para-oligophenylene mono- and dicarboxylic acids (R-(C6H4)nCOOH, n = 1-3, R = H,COOH) was studied. Adsorbed on Au(111)/mica modified by an underpotential deposited bilayer of Ag, the self-assembled monolayers (SAMs) were analyzed by near-edge X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, and scanning tunneling microscopy. In all cases SAMs are formed with molecules adopting an upright orientation and anchored to the substrate by a carboxylate. Except benzoic acid, all SAMs could be imaged at molecular resolution, which revealed highly crystalline layers with a dense molecular packing. The structures of the SAMs are described by a rectangular (5 × √3) unit cell for the prevailing phase of the monocarboxylic acids and an oblique ([Formula: see text]) unit cell for the dicarboxylic acids, thus evidencing a pronounced influence of the second COOH moiety on the SAM structure. Density functional theory calculations suggest that hydrogen bonding between the SAM-terminating COOH moieties accounts for the difference. Contrasting other classes of SAMs, the systems studied here are determined by intermolecular interactions whereas molecule-substrate interactions play a secondary role. Thus, eliminating problems arising from the mismatch between the molecular and the substrate lattices, coordinatively bonded carboxylic acids on silver should provide considerable flexibility in the design of SAM structures.

Phase behaviors of binary mixtures composed of electron-rich and electron-poor triphenylene discotic liquid crystals**Project supported by the National Natural Science Foundation of China (Grant Nos. 51273133 and 51443004).

Disk-like liquid crystals (DLCs) can self-assemble to ordered columnar mesophases and are intriguing one-dimensional organic semiconductors with high charge carrier mobility. To improve their applicable property of mesomorphic temperature ranges, we exploit the binary mixtures of electronic donor-acceptor DLC materials. The electron-rich 2,3,6,7,10,11-hexakis(alkoxy)triphenylenes (C4, C6, C8, C10, C12) and an electron-deficient tetrapentyl triphenylene-2,3,6,10-tetracarboxylate have been prepared and their binary mixtures have been investigated. The mesomorphism of the 1:1 (molar ratio) mixtures has been characterized by polarizing optical microscopy (POM), differential scanning calorimetry (DSC), and small angel x-ray scattering (SAXS). The self-assembled monolayer structure of a discogen on a solid-liquid interface has been imaged by the high resolution scanning tunneling microscopy (STM). The match of peripheral chain length has important influence on the mesomorphism of the binary mixtures.

Formation and Structure of Self-Assembled Monolayers by Adsorption of Octaneselenocyanate on Au(111)

Formation and Structure of Self-Assembled Monolayers by Adsorption of Octaneselenocyanate on Au(111)

Atomic Structure of Self-Assembled Monolayer of Thiolates on a Tetragonal Au92 Nanocrystal.

Unveiling the ligand binding mode on the crystalline surfaces is important for deciphering the long-standing structural enigma in self-assembled monolayers (SAMs). Here, the binding and patterning structures of thiolates (SR) on the Au(100) crystalline facet are revealed on the basis of the atomic structure of a highly regular, single crystalline Au92(SR)44 nanocrystal. The six exposed facets of this tetragonal nanocrystal give rise to six pieces of "nanoSAMs". We found that thiolates bind to the planar (100) facets of the nanocrystal via a simple bridge-like mode and are assembled into an overlayer with c(2 × 2) symmetry. The Au-S binding mode and translational symmetry in the kernel and on the surface of the Au92 nanocrystal can be generalized infinitely to construct the bulk two-dimensional SAMs and various tetragonal nanocrystals.

Striped gold nanoparticles: New insights from molecular dynamics simulations.

Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199-3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols' arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper, we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl's chain length, the length difference between the thiol mixtures, and solvent properties.

Effect of Solution Concentration on the Formation of Ordered Domains in Pentachlorobenzenethiol Self-Assembled Monolayers on Au(111).

The surface structures of self-assembled monolayers (SAMs) formed by the adsorption of pentachlorobenzenethiol (PCBT) molecules on Au(111) as a function of solution concentration were examined by means of scanning tunneling microscopy (STM) to understand the effect of concentration on the formation of ordered domains. STM imaging revealed that PCBT SAMs formed in a 0.01 or 1 mM ethanol solution at room temperature for 20 min contained small ordered domains in the range of several to 20 nm2 and disordered phases, while PCBT SAMs formed in a 0.1 mM ethanol solution were composed of long-range ordered domains in the range of 20 to 50 nm2, which can be assigned as a (4 x √3)R45 degrees packing structure. Interestingly, the bright aggregated domains stacked by π-π interactions between PCBT rings were usually observed around boundary regions of ordered domains. In addition, X-ray photoelectron spectroscopy measurements revealed that ordered PCBT SAMs on Au(111) were formed via the chemical interactions between the sulfur atom of PCBT and gold surface. Our results obtained here will be very useful in understanding the formation and structure of PCBT SAMs on gold surfaces.

Self-Assembled Monolayers of Perfluoroanthracenylaminoalkane Thiolates on Gold as Potential Electron Injection Layers.

As a material with relatively small band gap and low lying valence orbitals, perfluoroanthracene (PFA) is of interest for the modification of electrode surfaces, for example, as charge injection layers for n-type organic semiconductors. To covalently attach PFA in the form of self-assembled monolayers (SAMs), we developed a synthesis of derivatives with a sulfur termination, linked to the 2-position of the PFA moieties by an -NH- group and a short alkane chain with two and three methylene groups, respectively. Spectroscopic characterization of the SAMs reveals that the molecules adopt an almost upright orientation on the gold surface, with the packing density mostly determined by the steric demands of the PFA units. The number of the methylene groups in the -NH-alkyl linker has only a minor impact on the SAM structure because of the nonsymmetric attachment of the PFA units, which permits the compensation of the orientational constraints imposed by the bending potential. The investigated SAMs alter the work function of gold by +(0.59-0.64) eV, suggesting comparably strong depolarization effects, affecting the extent of the work function modification.

Formation of Ordered 4-Fluorobenzenethiol Self-Assembled Monolayers on Au(111) from Vapor Phase Deposition.

Self-assembled monolayers (SAMs) were formed by the spontaneous adsorption of 4-fluorobenzenethiol (4-FBT) on Au(111) using both solution and ambient-pressure vapor deposition methods at room temperature. The surface structure and thermal desorption properties of 4-FBT SAMs were examined by scanning tunneling microscopy (STM) and thermal desorption spectroscopy (TDS). STM imaging showed that 4-FBT SAMs formed in solution at room temperature mainly contained disordered phase with gold adatom islands, while those formed by ambient-pressure vapor deposition had well-ordered phase, which can be described as a (2 x 2√13)R45 degrees structure. In addition, thermal desorption spectroscopy (TDS) measurements showed that strong desorption peak for parent mass fragment (m/z = 128, FC6H5SH+) for 4-FBT SAMs on Au(111) was observed at 460 K, as a result of hydrogen abstract reaction of chemisorbed thiolates during desorption.

Experimental and vdW-DFT Study of the Structure, Properties, and Stability of Isonicotinic Acid Self-Assembled Monolayers on Gold

Self-assembling of derivatized aromatic molecules on metals is of interest in the generation of modified surfaces with ionizable groups in order to generate charged surfaces for constructing more complex nanostructured interfaces. In the present contribution we explore the structure, properties, and stability of isonicotinic acid (INA) adsorbed on gold surfaces employing electrochemical and spectroscopic methods as well as DFT calculations at the level of van der Waals interactions (vdW-DFT). Electrochemical results show changes in the kinetics of redox probes due to the self-assembled monolayers (SAMS) formation on the gold surface. Furthermore, SERS experiments indicate that INA species adsorb on gold perpendicularly to the surface through the deprotonated carboxylate group. In addition, due to the ionizable groups involved in the molecular anchorage, some instability of the SAMS of INA is obtained by pH modification of the chemical environment. On the other hand, theoretical calculations indicate that a strong interaction of the carboxylate group to the gold surface at the bridge sites takes place, and the adsorbed species have sufficient mobility at room temperature. The effect of the coverage and the stability of the SAMS are also reported.

From Chaos to Order: Chain-Length Dependence of the Free Energy of Formation of Meso-tetraalkylporphyrin Self-Assembled Monolayer Polymorphs

We demonstrate that systematic errors can be reduced and physical insight gained through investigation of the dependence of free energies for meso-tetraalkylporphyrin self-assembled monolayers (SAMs) polymorphism on the alkyl chain length m. These SAMs form on highly ordered pyrolytic graphite (HOPG) from organic solution, displaying manifold densities and atomic structures. SAMs with m = 11–19 are investigated experimentally while those with m = 6–28 are simulated using density-functional theory (DFT). It is shown that, for m = 15 or more, the alkyl chains “crystallize” to dominate SAM structure. Meso-tetraalkylporphyrin SAMs of length less than 11 have never been observed, a presumed effect of inadequate surface attraction. Instead, we show that free energies of SAM formation actually enhance as the chain length decreases. The inability to image regular SAMs stems from the appearance of many polymorphic forms of similar free energy, preventing SAM ordering. We also demonstrate a significant odd/even eff...

Structure and Phase Behavior of Mixed Self-Assembled Alkanethiolate Monolayers on Gold Nanoparticles: A Monte Carlo Study.

Configurational-bias Monte Carlo (CBMC) simulations are carried out to investigate the structure and phase behavior of self-assembled monolayers consisting of equimolar alkanethiolate mixtures chemisorbed on the surface of gold nanoparticles. The simulations probe the effects of variations in the chain length, nanoparticle curvature, and exchange of alkanethiolates between nanoparticles. The TraPPE-UA force field is used for the alkanethiolates, whereas the nanoparticle is represented by gold atoms placed on the surface of a sphere. CBMC identity exchange moves are used to enhance sampling of the spatial distribution of the different ligands and to ensure that thermodynamic equilibrium is reached. At a temperature of 298 K, mixtures differing in length by four methylene units exhibit some degree of local segregation. In contrast, the hexanethiolate/tetradecanethiolate mixture yields Janus-like arrangement when the ligands are confined to a single nanoparticle but global demixing when the ligands are allowed to distribute between two nanoparticles.

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.

Self-assembly of trithia-9-crown-3 and octathia-24-crown-8 on Au(111) surfaces

Scanning tunneling microscopy images of trithia-9-crown-3 and octathia-24-crown-8 self-assembled monolayers (SAMs) reveal completely different SAM structures for the two kinds of thiacrown molecules at liquid n-tetradecane/Au(111) interface.

Self-assembled monolayer structures of hexadecylamine on Cu surfaces: density-functional theory.

We used dispersion-corrected density-functional theory to probe possible structures for adsorbed layers of hexadecylamine (HDA) on Cu(100) and Cu(111). HDA forms self-assembled layers on these surfaces, analogous to alkanethiols on various metal surfaces, and it binds by donating electrons in the amine group to the Cu surface atoms, consistent with experiment. van der Waals interactions between the alkyl tails of HDA molecules are stronger than the interaction between the amine group and the Cu surfaces. Strong HDA-tail interactions lead to coverage-dependent tilting of the HDA layers, such that the tilt angle is larger for lower coverages. At full monolayer coverage, the energetically preferred binding configuration for HDA on Cu(100) is a (5 × 3) pattern - although we cannot rule out incommensurate structures - while the pattern is preferred on Cu(111). A major motivation for this study is to understand the experimentally observed capability of HDA as a capping agent for producing {100}-faceted Cu nanocrystals. Consistent with experiment, we find that HDA binds more strongly to Cu(100) than to Cu(111). This strong binding stems from the capability of HDA to form more densely packed layers on Cu(100), which leads to stronger HDA-tail interactions, as well as the stronger binding of the amine group to Cu(100). We estimate the surface energies of HDA-covered Cu(100) and Cu(111) surfaces and find that these surfaces are nearly isoenergetic. By drawing analogies to previous theoretical work, it seems likely that HDA-covered Cu nanocrystals could have kinetic shapes that primarily express {100} facets, as is seen experimentally.

On the relationship between the structure of self-assembled carboxylic acid monolayers on alumina and the organization and electrical properties of a pentacene thin film

The modification of insulating surfaces by self-assembled monolayers (SAMs) is an elegant way of tailoring the gate dielectric of organic field effect transistors (OFET) to pentacene and is commonly used to improve electrical performance. A SAM based on an alkylcarboxylic acid deposited on a thin layer of alumina, serving as the gate dielectric is considered. The relationship between carrier mobility and (i) the length of the carboxylic acid (CH3(CH2)nCOOH; n=9, 14, 18), (ii) substrate preparation and (iii) the SAM and pentacene thin film structures is considered. The size and boundaries of pentacene grains are not limiting factors for carrier mobility, and the most relevant parameter, which depends on whether there is a SAM or not, is the organization of the first pentacene layers in contact with the gate dielectric. The variation of the interplanar distance d(001) of the pentacene layers close to the alumina surface is much greater without SAM than with, and this could explain the lower carrier mobility observed in the case of a bare alumina dielectric. The relationship between the disorder associated with this variation and mobility is discussed.

Surface Structure and Chemistry of Alkanethiols on Au(100)-(1 × 1) Substrates

The surface structure of self-assembled monolayers of hexanethiolate (HT) on the Au(100)-(1 × 1) surface has been studied by density functional theory (DFT) calculations and their results compared to scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) data. We have found two novel surface structure models consisting of adsorbed thiolates on the Au(100)-(1 × 1) surface that fairly account for experimental STM and XPS observations. Surprisingly, these models exhibit better thermodynamic stability than those consisting of thiolate–Auad–thiolate moieties on a reconstructed Au(100)-(1 × 1) surface. Also these proposed models are more stable than the thiolate–Auad–thiolate containing c(4 × 2) lattice on the reconstructed Au(111) suggesting a surface dependent chemistry for thiolates on Au. However, the possible existence of other models with similar or better stability than those proposed in this work and also the possible coexistence of different surface structures and chemistry on t...

The Porter-Whitesides Discrepancy: Revisiting Odd-Even Effects in Wetting Properties of n-Alkanethiolate SAMs

This review discusses the Porter-Whitesides discrepancy in wetting properties of n-alkanethiolate self-assembled monolayers (SAMs). About 25 years ago, Whitesides and coworker failed to observe any odd-even effect in wetting, however, Porter and his coworker did, albeit in select cases. Most previous studies agreed with Whitesides’ results, suggesting the absence of the odd-even effect in hydrophobicity of n-alkanethiolate SAMs. Recent reports have, however, found the odd-even effect in hydrophobicity of n-alkanethiolate SAMs on smooth substrates, indicating that hydrophobicity, and analogous interfacial properties, of n-alkanethiolate SAMs significantly depends on the properties of substrate. Unfortunately, the Whitesides and Porter papers do not report on the quality of the surfaces used. Based on recent work, we inferred that the original discrepancy between Whitesides and Porter can be attributed to the quality of the surface. Odd-even effect of SAMs in charge transport, capacitance, friction, and SAM structure are also discussed in this review to inform the general discussion. The discrepancy between Porter's group and Whitesides’ group could be due to surface roughness, morphology, oxidation, and adventitious contaminants.

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual–Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual–Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future.