Well-ordered Self-assembled Monolayers Research Articles

Cooperative Effect of Electron Spin Polarization in Chiral Molecules Studied with Non-Spin-Polarized Scanning Tunneling Microscopy.

Polyalanine molecules (PA) with an α-helix conformation have recently attracted a great deal of interest, as the propagation of electrons through the chiral backbone structure comes along with spin polarization of the transmitted electrons. By means of scanning tunneling microscopy and spectroscopy under ambient conditions, PA molecules adsorbed on surfaces of epitaxial magnetic Al2O3/Pt/Au/Co/Au nanostructures with perpendicular anisotropy were studied. Thereby, a correlation between the PA molecules ordering at the surface with the electron tunneling across this hybrid system as a function of the substrate magnetization orientation as well as the coverage density and helicity of the PA molecules was observed. The highest spin polarization values, P, were found for well-ordered self-assembled monolayers and with a defined chemical coupling of the molecules to the magnetic substrate surface, showing that the current-induced spin selectivity is a cooperative effect. Thereby, P deduced from the electron transmission along unoccupied molecular orbitals of the chiral molecules is larger as compared to values derived from the occupied molecular orbitals. Apparently, the larger orbital overlap results in a higher electron mobility, yielding a higher P value. By switching the magnetization direction of the Co layer, it was demonstrated that the non-spin-polarized STM can be used to study chiral molecules with a submolecular resolution, to detect properties of buried magnetic layers and to detect the spin polarization of the molecules from the change in the magnetoresistance of such hybrid structures.

A Machine-Learning Approach to Correcting Non-Ideal Background Currents in Disordered Self-Assembled Monolayers

In traditional studies of electroactive molecules tethered to metal surfaces through well-ordered self-assembled monolayers (SAMs), cyclic voltammetry is the primary tool used to measure the coverage of the tethered molecules. The charge under the peak in the voltammogram is directly proportional to the coverage of the redox-active molecules. Accurate coverage measurements are possible because well-ordered SAMs exhibit ideal background currents which are easy to subtract from the total current to isolate the SAMs faradaic current. However, for disordered electroactive SAMs with poor surface blocking properties, specific interactions with the metal substrate create non-ideal background currents which are difficult to separate from the SAMs faradaic current. Although analytical approaches exist to account for background currents in other electrochemical systems, they have some fundamental limitations that impede their practical application to electroactive SAMs. In our work, we propose a simple machine-learning approach to empirically correct for background currents in disordered SAMs, and we apply this approach to determine the surface coverage of partially-desorbed ferrocene-terminated monolayers (Fc-SAMs) from gold surfaces. We use LASSO regression and an ensemble of background scans from partially-desorbed unfunctionalized decanethiol SAMs to approximate the Fc-SAM background currents. Using the approximated background, we estimate the coverage of Fc-SAMs after background correction. This technique allows us to explore Fc-SAM coverage as a function of potential when applying potentials near and beyond the onset of the so-called reductive desorption potential of the SAM which induces non-ideal background currents. To verify the accuracy of the coverages determined using our LASSO method, we used two verification methods: 1) backfilling with decanethiol and 2) chemical stripping of the disordered SAM followed by inductively-coupled plasma-mass spectrometry (ICP-MS). The pros and cons of both confirmation methods will be discussed along with a comparison of error rates and limits of detection between traditional background subtraction method and the LASSO method. We propose that this new approach will enable a more quantitative description of disordered SAM films after reductive desorption events.

From Order to Disorder of Alkanethiol Self-Assembled Monolayers on Complex Au (211), (221), and (311) Surfaces: Impact of the Substrate

We investigate the impact of the substrate on the structural properties and the morphology of alkanethiol self-assembled monolayers (SAMs) on gold, using first principles calculations and atomistic molecular dynamics simulations. We consider hexadecanethiols on Au(211), Au(221) and Au(311) surfaces which contain few-atom wide terraces separated by monoatomic steps similar to the complex Au surfaces used in experiments. The structure of the SAMs is probed via several structural properties including tilt angles, mean C atom heights from the surface, precession angles, gauche defects, gyration tensors and relative shape anisotropy. Comparing these properties to those of the well-studied SAMs on Au(111), we observe similarities but also striking differences. A clear order to disorder transition is observed by changing the substrate: well-ordered SAMs on (111) and (211) surfaces become mixed ordered-disordered structures on (311) and fully disordered on (221). The presence of steps on the Au surfaces also results in preferential tilt orientations with long-range order. Our results show that in addition to the expected grafting density dependence, the transition from order to disorder crucially depends on substrate morphology. The onset of ordering behavior is related to the atomic structure of the surface. The key parameter that affects long-range order is the energy for changing the dihedral angle between Au-S-$\mathrm{C^{(1)}-C^{(2)}}$ of the adsorbed alkanethiol.

Agreement between Experimental and Simulated Circular Dichroic Spectra of a Positively Charged Peptide in Aqueous Solution and on Self-Assembled Monolayers.

Successfully immobilizing functional proteins on inorganic surfaces has long been a challenge to the biophysics and bioengineering communities. This is due, in part, to a lack of understanding of the effect of nonaqueous environments on protein structure from both experimental and computational perspectives. Because most experimental information about protein structure comes from the Protein Data Bank and is collected from an aqueous solvent environment, modern force fields for molecular dynamics (MD) simulations are parameterized against these data. The applicability of such force fields to biomolecules in different environments, including when in contact with surfaces and substrates, must be validated. Here, we present MD folding simulations of a highly charged peptide solvated in water, solvated in a solution of 2:1 t-BuOH/H2O and bound to the surface of a methyl-terminated self-assembled monolayer (SAM), and compare the structures predicted by these simulations to previously reported circular dichroism spectra. We show quantitative agreement between experiments and simulations of solvent- and surface-induced conformational changes of a positively charged peptide in these three environments. We show further that the surface-bound peptide must fold before chemically reacting with the surface. Finally, we demonstrate that a well-ordered SAM is critical to the folding process. These results will guide further simulations of peptides and proteins in diverse and complex environments.

Formation of Highly Ordered Semiconducting Anthracene Monolayer Rigidly Connected to Insulating Alkanethiolate Thin Film

The formation and molecular structure of a self-assembled monolayer (SAM) of anthracene-substituted alkanethiol on Au(111) have been investigated by scanning tunneling microscopy and infrared reflection absorption spectroscopy. A clean and well-ordered SAM composed of densely packed “standing-up” molecules is formed by a wet-chemical process in air, followed by thermal annealing in vacuum. In the SAM, anthracene moieties are arranged in a bulklike in-plane herringbone structure and keep their crystalline ordering above room temperature, which is in contrast to the less ordering in Au nanoclusters ligated by the anthracene-alkanethiolates. In addition, hexagonal arrangement of anthracene dimer is found on the surface of the SAM. These structures remain after annealing at 400 K. Scanning tunneling spectroscopy performed on the surface shows an energy gap of ∼3.6 eV, similar to the band gap of bulk anthracene. The above results demonstrate that the highly ordered semiconducting anthracene monolayer is succes...

Photoisomerization of Self-Assembled Monolayers of Azobiphenyls: Simulations Highlight the Role of Packing and Defects.

We present surface hopping simulations of the photodynamics of self-assembled monolayers (SAMs) of 4'-(biphenyl-4-ylazo)-biphenyl-4-thiol (ABPT) on Au(111). We show that trans → cis photoisomerization is suppressed because of steric hindrance in a well-ordered SAM. Photoisomerization is instead viable in the presence of defects. Two particularly important defects are the boundaries between domains of trans-ABPT molecules leaning in different directions (a line defect) and single cis molecules embedded in a SAM of trans (a point defect). Our findings explain the cooperative behavior observed during the photoisomerization of a trans-ABPT SAM, leading to large domains of pure cis and trans isomers. The line and point defects are predicted to produce different patterns of cis-ABPT molecules during the early stages of the photoconversion.

The role of the crystalline face in the ordering of 6-mercaptopurine self-assembled monolayers on gold.

Well-ordered molecular films play an important role in nanotechnology, from device fabrication to surface patterning. Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) on the Au(100)-(1 × 1) and Au(111)-(1 × 1) have been used to understand the interplay of molecule-substrate interactions for heterocyclic thiols capable of binding to the surface by two anchors, which spontaneously form a highly disordered film on Au(111). Our results reveal that for the same surface coverage the simple change of the substrate from Au(111)-(1 × 1) to Au(100)-(1 × 1) eliminates molecular disorder and yields well-ordered SAMs. We discuss these findings in terms of differences in the surface mobility of 6MP species on these surfaces, the energetics of the adsorption sites, and the number of degrees of freedom of these substrates for a molecule with reduced surface mobility resulting from its two surface anchors. These results reveal the presence of subtle molecule-substrate interactions involving the heteroatom that drastically alter SAM properties and therefore strongly impact on our ability to control physical properties and to build devices at the nanoscale.

Bottom-up synthesis of liquid-phase-processable graphene nanoribbons with near-infrared absorption.

Structurally defined, long (>100 nm), and low-band-gap (∼1.2 eV) graphene nanoribbons (GNRs) were synthesized through a bottom-up approach, enabling GNRs with a broad absorption spanning into the near-infrared (NIR) region. The chemical identity of GNRs was validated by IR, Raman, solid-state NMR, and UV-vis-NIR absorption spectroscopy. Atomic force microscopy revealed well-ordered self-assembled monolayers of uniform GNRs on a graphite surface upon deposition from the liquid phase. The broad absorption of the low-band-gap GNRs enables their detailed characterization by Raman and time-resolved terahertz photoconductivity spectroscopy with excitation at multiple wavelengths, including the NIR region, which provides further insights into the fundamental physical properties of such graphene nanostructures.

Detection of calcium ions using gold-coated micro-cantilever sensors using upper- and lower-rim functionalized calix[4]arenes

The use of a bimodal calix[4]arene 2, was investigated as a potential host/guest sensing layer for microcantilever sensors for detecting selected ions in dilute aqueous solutions. It was found that the sensing layers gave the highest microcantilever sensitivity when microcantilevers coated with 5 nm of Inconel and 40 nm of Au were incubated for 1 h in a 1.0 μM dichloromethane:ethanol (1:9) solution of calix[4]arene 2. This calix[4]arene 2 was observed to form well-ordered self-assembled monolayers (SAM) on Au-coated substrates with no sign of bare areas or etch pits. Microcantilever sensor measurements showed that the calix[4]arene 2-functionalized cantilevers were able to detect Ca2+ ions in aqueous solutions of CaCl2 at concentrations as low as 10−12 M. Although this receptor was shown to have a high affinity for CaCl2 in aqueous solutions, it was also found to be able to detect other ionic compounds, however only producing microcantilever deflections ranging from 10% to 30% of those obtained for CaCl2.

Formation of Stabilized Ketene Intermediates in the Reaction of O(3P) with Oligo(phenylene ethynylene) Thiolate Self-Assembled Monolayers on Au(111)

We have taken steps to develop a methodology for quantifying the kinetics and dynamics of bimolecular reactions through spectroscopic monitoring of reactants and products during exposure of well-ordered self-assembled monolayers (SAMs) to supersonic beams of atomic reagents. The use of a SAM stabilizes highly energetic intermediates formed from bimolecular reactions at the vacuum/film interface due to rapid thermal equilibration with the SAM matrix that are otherwise not readily observed under single-collision conditions in the gas phase. In this paper, we will discuss the elucidation of the mechanistic details for the fundamental reaction between O(3P) and phenyl-substituted alkyne bonds by monitoring chemical and structural changes in an oligo(phenylene ethynylene) SAM reacting with O(3P) under collision conditions having specified initial reaction orientation. Utilizing time-resolved reflection–absorption infrared spectroscopy (RAIRS) and scanning tunneling microscopy (STM) under ultrahigh vacuum condi...

Self-assembled organic monolayers on epitaxial graphene with enhanced structural and thermal stability.

Scanning tunnelling microscopy and X-ray reflectivity are used to characterize adlayers of perylenetetracarboxylic diimide (PTCDI) deposited on epitaxial graphene (EG) on SiC(0001). PTCDI adopts a herringbone structural phase on EG/SiC that can accommodate sub-5 nm voids with molecularly defined boundaries and isolated molecular vacancies at room temperature. The PTCDI monolayer remains intact up to substrate temperatures of ~260 °C, thus demonstrating enhanced thermal stability compared to previously studied perylene derivatives on EG/SiC.

PH-regulated release of dopamine from well-ordered self-assembled monolayers: Electrochemical studies

In the present work, gold electrode modified with novel aldehyde-terminated self-assembled monolayers (SAMs) was used for controllable load and release of dopamine molecules by pH triggering. Electrochemical techniques including cyclic voltammetry (CV) and electrochemcial impedance spectroscopy (EIS) were employed to investigate the SAMs characteristic on the gold electrode surface. The electrochemical experiments indicated Faradaic behavior for the electrode surface after its modification with dopamine. Notably, it was observed that decreasing the conditioning pH, results in a decrease of peak currents, presumably due to the hydrolysis of the terminal imine bonds and releasing the dopamine moiety into the solution. Moreover, the preliminary kinetics studies were done for dopamine release from the SAMs surface as a model to design future drug delivery systems. Finally, the rate constant of dopamine release from the SAMs modified surface estimated to be 0.167 day(-1) at pH=3.

Preparation and photolithography of self-assembled monolayers of 10-mercaptodecanylphosphonic acid on glass mediated by zirconium for protein patterning

Self-assembled monolayers (SAMs) formed by adsorption of octadecylphosphonic acid (ODPA) on zirconium mediated glass substrates were prepared. In this sandwich structure, Zr(4+) was used as a bi-linker to bind phosphonic acid head group in ODPA to glass substrates. The contact angle of the as-prepared SAMs was measured to be around 104°. X-ray photoelectron spectroscopy (XPS) characterization indicated the modification of Zr(4+) on glass substrates was critical for the formation of reasonably dense, well-ordered SAMs similar in quality to those typically formed on other metal oxide surfaces. Bifunctional molecule, 10-mercaptodecanylphosphonic acid (MDPA), bearing thiol terminal groups for various chemical reactions, was synthesized and formed SAMs on glass using the same approach, which allowed us to control the surface chemistry and functionality through photooxidation of the thiol terminal group. Photopatterning of proteins was performed first by exposing the SAMs to UV light through a mask, followed by protein immobilization to the masked regions through a heterobifunctional linker, while the exposed areas prohibit nonspecific protein absorption. The present strategy, which combined the SAMs assembly and photolithography, offered a facile approach for the fabrication of biomolecule patterning and could be applied to construction of biochips and other applications.

In vitro stability study of organophosphonic self assembled monolayers (SAMs) on cobalt chromium (Co–Cr) alloy

Surface modification of cobalt chromium (Co-Cr) alloy is being investigated as a possible solution to the biomedical challenges arising from its usage. Self assembled monolayers (SAMs) of organophosphonic octadecylphosphonic acid (ODPA) were formed on the oxide surface of Co-Cr alloy by chemisorption using the solution deposition technique. High quality and well-ordered SAMs were formed which were characterized using Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), contact angle measurements and ellipsometry. The resulting monolayers were then exposed to in vitro conditions using phosphate buffered saline (PBS) solution. The samples were analyzed for a period of 1, 3, 7 and 14 days. The resulting samples were characterized using XPS, AFM and Contact angle measurements. XPS atomic concentrations and detailed high energy elemental scans gave an insight into the trends of elemental concentrations over the duration of the study. SAMs were found to be strongly bound to the oxide surface after PBS exposure. AFM gave the topographic details of SAMs presence by island formation before and after SAM formation and also over the duration of the PBS exposure. Contact Angle Measurements confirmed the hydrophobicity of the surface after SAM formation and indicated a slight disorder of the SAM alkyl chain upon exposure to PBS. Thus, ODPA SAMs were successfully coated on Cobalt Chromium (Co-Cr) alloy surface and were found to be stable and strongly bound after PBS exposure.

Modification of Electrode Surfaces by Self‐Assembled Monolayers of Thiol‐Terminated Oligo(Phenyleneethynylene)s

The wire-like properties of four S-(4-{2-[4-(2-phenylethynyl)phenyl]ethynyl}phenyl) thioacetate derivatives, PhC≡CC(6)H(4)C≡CC(6)H(4)SAc (1), H(2)NC(6)H(4)C≡CC(6)H(4)C≡CC(6)H(4)SAc (2), PhC≡CC(6)H(2)(OMe)(2)C≡CC(6)H(4)SAc (3) and AcSC(6)H(4)C≡CC(6)H(4)C≡CC(6)H(4)SAc (4) (Figure 1), all of which possess a high degree of conjugation along the oligo(phenyleneethynylene) (OPE) backbone, were investigated as self-assembled monolayers (SAMs) on gold and platinum electrodes by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The redox probe [Fe(CN)(6)](4)(-) was used in both the CV and impedance experiments. The results indicate that the thiolates derived from thioacetate-protected precursor molecules 1 and 2 form well-ordered monolayers on a gold electrode, whereas SAMs derived from 3 and 4 exhibit randomly distributed pinholes. The electron tunnelling resistance and fractional coverage of SAMs of all four compounds were examined using electron tunnelling theory. The analysis of the results reveal that the well-ordered SAMs of 1 and 2 exhibit higher charge-transfer resistance in comparison to the defect-ridden SAMs of 3 and 4. The additional steric bulk offered by the methoxy groups in 3 is likely to prevent efficient packing within the SAM, leading to a microelectrode behaviour, when assembled on a gold electrode surface. The protected dithiol derivative 4 probably binds to the surface through both terminal groups which prevents dense packing and leads to the formation of a monolayer with randomly distributed pinholes. Atomic force microscopy (AFM) was used to examine the morphology of the monolayers, and height images gave root-mean-square (RMS) roughness's which are in agreement with the proposed SAM structures.

Mixed self-assembled monolayers of azobenzene photoswitches with trifluoromethyl and cyano end groups

Mixed self-assembled monolayers (SAMs) of alkanethiolates carrying azobenzene chromophores with either a trifluoromethyl or a cyano substituent have been studied. High-resolution x-ray photoelectron spectroscopy proves that the ratio of adsorbed molecules can be arbitrarily adjusted via the molar fractions in solution. As a function of these molar fractions core level shifts are observed which are attributed to local work-function changes. By simulating the electric dipole field distribution, the continuous core level shifts are ascribed to a homogeneous mixture of molecules with different end groups adsorbed on adjacent lattice sites. Near-edge x-ray absorption fine structure measurements reveal formation of well-ordered SAMs. Despite the difference in dipole moment of the end groups, the molecular tilt and twist angles are identical for both single-component SAMs and a 1:1 mixed SAM.

Study of Insulating Properties of Alkanethiol Self-Assembled Monolayers Formed Under Prolonged Incubation Using Electrochemical Impedance Spectroscopy

The electrochemical interfacial properties of a well-ordered self-assembled monolayer (SAM) of 1-undecanethiol (UDT) on evaporated gold surface have been investigated by electrochemical impedance spectroscopy (EIS) in electrolytes without a redox couple. Using a constant-phase element (CPE) series resistance model, prolonged incubation times (up to 120 h) show decreasing monolayer capacitance approaching the theoretical value for 1-undecanethiol. Using the CPE exponent α as a measure of ideality, it was found that the monolayer approaches an ideal dielectric (α = 0.992) under prolonged incubation, which is attributed to the reduction of pinholes and defects in the monolayer during coalescence and annealing of SAM chains. The SAMs behave as insulators until a critical potential, Vc, is exceeded in both cathodic and anodic regimes, where electrolyte ions are believed to penetrate the monolayers. Using a Randles circuit model for these cases, the variation of the capacitance and charge transfer resistance with applied dc potential shows decreased permeability to ionic species with prolonged incubation time. The EIS data show that UDT (methylene chain length n = 10), incubated for 120 h, forms a monolayer whose critical voltage range extends from −0.3 to 0.5 V versus Ag/AgCl, previously attained only for alkanethiol at n = 15. At low frequencies where ion diffusion occurs, almost pure capacitive phase (−89 deg) was attained with lengthy incubation.

Formation of Highly Ordered and Orientated Gold Islands: Effect of Immersion Time on the Molecular Adlayer Structure of Pentafluorobenzenethiols (PFBT) SAMs on Au(111)

Self-assembled monolayers (SAMs) of pentafluorobenzenethiol (PFBT) on Au(111) substrates, prepared with different immersion times (ITs) at room temperature, were studied using scanning tunneling microscopy (STM) and infrared reflection-absorption spectroscopy (IRRAS). In the present study, the focus was on several important points of interest in the field of SAMs. First, the gold islands formed upon adsorption of PFBT molecules on the gold surface were monitored at different ITs in terms of their size, density, and shape. After short ITs (5 to 30 min), small gold islands with rounded shape were formed. These gold islands were arranged in a rather regular fashion and found to be quite mobile under the influence of the STM-tip during the scanning. When the IT was increased to 16 h, the results revealed the formation of highly ordered and orientated gold islands with very unusual shapes with straight edges meeting at 60° or 120° running preferentially along the [11(-)0] substrate directions. The density of the gold islands was found to decrease with increasing IT until they almost disappeared from the SAMs prepared after 190 h of IT. On top of the gold islands, the PFBT molecules were found to adopt the closely packed (10√3 × 2) structure. Second, a number of structural defects such as disordered regions at the domain boundaries and dark row(s) of molecules within the ordered domains of the PFBT SAMs were observed at different ITs. The SAMs prepared after 190 h of IT were found to be free of these defects. Third, at low and moderate ITs, a variation in the PFBT molecular contrast was observed. This contrast variation was found to depend mainly on the tunneling parameters. Finally, our results revealed that the organization process of PFBT SAMs is IT-dependent. Consequently, a series of structural phases, namely, α, β, γ, δ, and ε were found. The α-, β-, γ-, and δ-phases were typically accompanied by the ε-phase that appeared on top of gold islands. With increasing IT, the α→β→ γ→δ→ε phase transitions took place. The resulting ε-phase, which covered the entire gold surface after 190 h of IT, yielded well-ordered self-assembled monolayers with large domains having a (10√3 × 2) superlattice structure.

Self-assembly of organic acid molecules on the metal oxide surface of a cupronickel alloy

Corrosion of the metal oxide surface of cupronickel (CuNi) alloys is a problem in applications such as household water pipes, industrial pipelines, and marine vessels. On other substrates, thin films have been used as barriers to corrosion. Here, the formation of self-assembled monolayers (SAMs) on the CuNi metal oxide surface has been investigated. Stable, well-ordered SAMs of octadecylphosphonic acid (ODPA) and 16-phosphonohexadecanoic acid (COOH-PA) were formed on the metal oxide surface of CuNi foils (55% Cu/45% Ni) using a solution deposition method. The ODPA modified surfaces could be used to provide a non-reactive barrier that inhibits corrosion of the CuNi metal oxide surface. Meanwhile, COOH-PA films could be used for further surface reactions such as surface initiated polymerization, in which polymer coatings are grown directly from a well-ordered film. Film-modified surfaces were characterized using diffuse reflectance infrared Fourier transform spectroscopy, contact angle analysis, and matrix assisted laser desorption ionization time of flight mass spectrometry. The ability of the films to inhibit corrosion by limiting oxidation of the CuNi surface was assessed using cyclic voltammetry.

Microscopic Wetting of Self-Assembled Monolayers with Different Surfaces: A Combined Molecular Dynamics and Quantum Mechanics Study

Molecular dynamics simulations are used to study the micronature of the organization of water molecules on the flat surface of well-ordered self-assembled monolayers (SAMs) of 18-carbon alkanethiolate chains bound to a silicon (111) substrate. Six different headgroups (-CH(3), -C═C, -OCH(3), -CN, -NH(2), -COOH) are used to tune the character of the surface from hydrophobic to hydrophilic, while the level of hydration is consistent on all six SAM surfaces. Quantum mechanics calculations are employed to optimize each alkyl chain of the different SAMs with one water molecule and to investigate changes in the configuration of each headgroup under hydration. We report the changes of the structure of the six SAMs with different surfaces in the presence of water, and the area of the wetted surface of each SAM, depending on the terminal group. Our results suggest that a corrugated and hydrophobic surface will be formed if the headgroups of SAM surface are not able to form H-bonds either with water molecules or between adjacent groups. In contrast, the formation of hydrogen bonds not only among polar heads but also between polar heads and water may enhance the SAM surface hydrophilicity and corrugation. We explicitly discuss the micromechanisms for the hydration of three hydrophilic SAM (CN-, NH(2)- and COOH-terminated) surfaces, which is helpful to superhydrophilic surface design of SAM in biomimetic materials.