Self-assembled Monolayer Matrix Research Articles

Substrate roughness influence on the order of nanografted Self-Assembled Monolayers

Adjacent patches of alkanethiol molecules whose chain lengths range from 11 to 15 carbon atoms are fabricated by nanografting within a Self-Assembled Monolayer matrix. Atomic Force Microscopy and Electrostatic Force Microscopy are employed to investigate their structural and electronic properties, highlighting the key role of the substrate roughness. In particular, the topographic phase signal allows to establish an odd–even dependence of the local stiffness versus the alkyl chain length, while the electrostatic force signal provides evidence that the conformational order versus the alkyl chain length follows an asymmetric parabolic trend induced by the substrate roughness.

Genosensor made with a self-assembled monolayer matrix to detect MGMT gene methylation in head and neck cancer cell lines

DNA methylation is involved in the oncogenesis of head and neck squamous cell carcinoma and could be used for early detection of cancer to increase the chances of cure, but unfortunately diagnosis is usually made at late stages of the disease. In this work we developed genosensors to detect DNA methylation of the MGMT gene in head and neck cancer cell lines. The probe for MGMT promoter methylation was immobilized on gold electrodes modified with 11-mercaptoundecanoic acid (11-MUA) self-assembled monolayers (SAM). Detection was performed with electrochemical impedance spectroscopy, with clear distinction between methylated and non-methylated DNA from head and neck cell lines. The genosensor is sensitive with a low detection limit of 0.24 × 10−12 mol L−1. In addition, the cell lines FaDu, JHU28 and SCC25 for the MGMT gene, could be distinguished from the HN13 cell line which has a high degree of MGMT methylation (97%), thus confirming the selectivity. Samples with different percentages of MGMT DNA methylation could be separated in multidimensional projections using the visualization technique interactive document mapping (IDMAP). The genosensor matrix and the immobilization procedures are generic, and can be extended to other DNA methylation biomarkers.

Thermal Effect on Positive Patterned Self-Assembled Monolayer Grown from a Droplet of Alkanethiol.

Atomic force microscope technique is widely used for the spatial narrow deposition of molecules inside the bare space of preexisting self-assembled monolayer (SAM) matrix. Using molecular dynamics simulation, we studied the formation of positively patterned SAM from a globule of 1-octadecanethiol (ODT) on predesigned SAM matrix of 1-dodecanethiol (DDT) and effect of temperature on it. The alkyl chains of ODT SAM were densely packed and ordered by means of chemisorption through sulfur atoms. The circular SAM of ODT contained defects due to the molecules those were standing upside down or trapped inside ODT SAM. We found that with the increase of temperature, these defects moved out by flipping of inverted ODT molecules or building spaces to be adsorbed on Au surface. The ODT molecules on the top of the pile of stable circular SAM or those are upside down and trapped disperse in a unique fashion namely serial pushing through which molecules firstly make a free space to enter inside the adsorbed thiol molecules and then push neighboring molecules to get enough space to be adsorbed on the gold surface. The stability of ODT SAM was confirmed by analyzing different structural properties such as tilt angle, tilt orientation. and backbone orientation. We also calculated the diffusion coefficient of the ODT molecules which were on the top of SAM island. © 2019 Wiley Periodicals, Inc.

Wafer-scale bioactive substrate patterning by chemical lift-off lithography.

The creation of bioactive substrates requires an appropriate interface molecular environment control and adequate biological species recognition with minimum nonspecific attachment. Herein, a straightforward approach utilizing chemical lift-off lithography to create a diluted self-assembled monolayer matrix for anchoring diverse biological probes is introduced. The strategy encompasses convenient operation, well-tunable pattern feature and size, large-area fabrication, high resolution and fidelity control, and the ability to functionalize versatile bioarrays. With the interface-contact-induced reaction, a preformed alkanethiol self-assembled monolayer on a Au surface is ruptured and a unique defect-rich diluted matrix is created. This post lift-off region is found to be suitable for insertion of a variety of biological probes, which allows for the creation of different types of bioactive substrates. Depending on the modifications to the experimental conditions, the processes of direct probe insertion, molecular structure change-required recognition, and bulky biological species binding are all accomplished with minimum nonspecific adhesion. Furthermore, multiplexed arrays via the integration of microfluidics are also achieved, which enables diverse applications of as-prepared substrates. By embracing the properties of well-tunable pattern feature dimension and geometry, great local molecular environment control, and wafer-scale fabrication characteristics, this chemical lift-off process has advanced conventional bioactive substrate fabrication into a more convenient route.

Modification of Aromatic Self-Assembled Monolayers by Electron Irradiation: Basic Processes and Related Applications

The effect of electron irradiation on aromatic thiolate self-assembled monolayers (SAMs) with oligophenyl, acene, and oligo(phenylene ethynylene) (OPE) backbones, containing from one to three phenyl rings, was studied, with emphasis on the basic irradiation-induced processes and performance of these films as negative resists in electron lithography. All films exhibited similar behavior upon the irradiation, with clear dominance of cross-linking, taking hold of the systems at already very early stages of the treatment. The cross sections for the modification of the SAM matrix and the damage of the SAM–substrate interface were determined for the primary electron energy of 50 eV, frequently used for the fabrication of carbon nanomembranes (CNM). They show only slight dependence on the backbone character as demonstrated by the example of the three-ring films. The two-ring systems exhibited the best performance as lithographic resists, with an optimal dose of 10–20 mC/cm2 at 0.5–1 keV. The performance of the o...

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...

Why Did the Electron Cross the Road? A Scanning Tunneling Microscopy (STM) Study of Molecular Conductance for the Physical Chemistry Lab

A series of experiments employing scanning tunneling microscopy (STM) have been developed for the physical chemistry laboratory. These experiments are designed to engage students in cutting edge research techniques while introducing and reinforcing topics in physical chemistry, quantum mechanics, solid-state chemistry, and the electronic structure of molecules and materials. In the first of three experiments, students are introduced to the basics of STM operation while imaging and conducting spectroscopy on the highly oriented pyrolytic graphite (HOPG) surface. Images of the surface are used to determine the crystal structure of the material, and scanning tunneling spectroscopy is used to determine the electronic properties of the material and study the tunneling phenomenon. In the second experiment, the students image the Au(111) surface as well as a series of alkanethiol self-assembled monolayers (SAMs) of different chains lengths on the Au(111) surface. They examine the structural and electronic properties of the metal surface and the adlattice structure of the film. Finally, in the third experiment, the students examine the conductance of molecules adsorbed onto the Au(111) surface, including the alkanethiol SAMs and a thiol-tethered porphyrin molecule or a dimercaptostilbene embedded into the SAM matrix. By measuring the tunneling efficiency and spectroscopic characteristics of these molecules, the students can explore the relationship between chemical structure and charge transport efficiency. The experiments provide advanced chemistry students an opportunity to view and study materials at the atomic and molecular length scales and provide an opportunity to apply their understanding of quantum mechanical concepts to real systems.

Trapping dynamics of diindenoperylene (DIP) in self-assembled monolayers using molecular simulation

All-atom Molecular Dynamics simulation methods employing a well-tested intermolecular potential model, MM3 (Molecular Mechanics 3), demonstrate the propensity for diindenoperylene (DIP) molecules to insert between molecules of a self-assembled monolayer (SAM) during a deposition process intended to grow a thin film of this organic semiconductor molecule onto the surface of self-assembled monolayers. The tendency to insert between SAM molecules is fairly prevalent at normal growth temperatures and conditions, but is most strongly dependent on the density and the nature of the SAM. We posit the existence of an optimal density to favor surface adsorption over insertion for this system. DIP is less likely to insert in fluorinated SAMs, like FOTS (fluorooctatrichlorosilane), than its unfluorinated analog, OTS (octatrichlorosilane). It is also less likely to insert between shorter SAMs (e.g., less insertion in OTS than ODTS (octadecyltrichlorosilane)). Very short length, surface-coating molecules, like HDMS (hexamethyldisilazane), are more likely to scatter energetic incoming DIP molecules with little insertion on first impact (depending on the incident energy of the DIP molecule). Grazing angles of incidence of the depositing molecules generally favor surface adsorption, at least in the limit of low coverage, but are shown to be dependent on the nature of the SAM. The validity of these predictions is confirmed by comparison of the predicted sticking coefficients of DIP at a variety of incident energies on OTS, ODTS, and FOTS SAMs with results obtained experimentally by Desai et al. (2010) [23]. The simulation predictions of the tendency of DIP to insert can be explained, in large part, in terms of binding energies between SAM and DIP molecules. However, we note that entropic and stochastic events play a role in the deposition outcomes. Preliminary studies of multiple deposition events, emulating growth, show an unexpected diffusion of DIP molecules inserted within the SAM matrix in a clear attempt of the DIP molecules to aggregate together.

Surface modification of gold electrode with gold nanoparticles and mixed self-assembled monolayers for enzyme biosensors

This paper describes the development and evaluation of a generic method for the immobilization of enzymes onto a gold electrode and its application to amperometric biosensors. The surface of the gold electrode was modified with gold nano-particles (AuNP) and mixed self-assembled monolayers (SAMs) to form an enzyme biosensor matrix. Horseradish peroxidase (HRP) was immobilized on the modified surface to form a biosensor matrix on a gold electrode. After the deposition of gold nano-particles on a bare gold surface, the AuNP-deposited gold electrode and a bare electrode were compared for the surface area and electric current using AFM and cyclic voltammetry (CV). The AuNP strongly adhered to the surface of the gold electrode, had uniform distribution and was very stable. A mixed SAM, composed of two different monolayer molecules, dithiobis-N-succinimidyl propionate (DTSP) and inert tetradecane-1-thiol (TDT), was formed using reductive desorption technique and cyclic voltammetry was used to verify the formation of mixed deposition. First, 3-mercaptopropionic acid (MPA) and TDT were deposited with a specified deposition ratio between the two components. Then, MPA was desorbed by applying electric potential to the surface. Finally, DTSP was deposited where MPA was. The ratios of 20: 80 and 50: 50 between MPA and TDT were examined, and differences in the CV responses were discussed. HRP was immobilized on the mixed SAM surface. The investigated method is regarded as an effective way for stable enzyme attachment, while the presence of gold nanoparticles provides enhanced electrochemical activity; it needs very small amounts of samples and enzymes and the SAM matrix helps avoid enzyme leaking. It is interesting that the mixed SAM shows unique CV characteristics compared to the uni-molecular SAMs. The reaction kinetics of the SAM-immobilized enzyme is discussed with the CV results and is observed to obey the Michaelis-Menten equation.

Potential dependent change in local structure of ferrocenyl-terminated molecular islands by electrochemical frequency modulation atomic force microscopy

Electroactive ferrocenylundecanethiol (FcC11H22SH) islands embedded in a n-heptanethiol (C7H15SH) self-assembled monolayer matrix on Au(111) were studied under potential control in 0.1M HClO4 aqueous solution using electrochemical frequency modulation atomic force microscopy. Signal of local structural change on the Fc islands upon oxidation from Fc0 to Fc+ was obtained in topography as a reversible process; however, the magnitude of the change was far less than expected in contrast to the case of the previous study for FcC11H22SH islands embedded in C10H21SH. Different degrees of freedom for the structures of the Fc islands originating from different molecular lengths for surrounding matrix molecules perhaps provide the distinct contrast between the two systems.

Molecular Friction as a Tool to Identify Functionalized Alkanethiols

By using the nanografting method, well-defined nanoscale patches of alkanethiols were constructed in a self-assembled monolayer (SAM) matrix on an atomically flat gold (Au(111)) surface. A series of nanografted patches, composed of alkanethiols with different end groups (-CH(3), -CF(3), -OH, -SH, -COOH, and -NH(2)), were analyzed in detail by a combination of atomic force microscopy (AFM) height and quantitative lateral friction measurements. By constructing a series of nanografted patches of methyl-terminated thiols with various chain lengths, it was shown that the absolute friction of the nanografted patches was always smaller than that of the surrounding SAM matrix, demonstrating that, because of the spatially confined self-assembly during nanografting, SAMs show less defects. In addition, the friction gradually increased for decreasing alkane chain length as expected, although a subtle odd-even effect was observed. The study of thiols with functionalized end groups (-CF(3), -OH, -SH, -COOH, and -NH(2)) gave specific insights in orientation, packing, and structure of the molecules in the SAMs. Depending on the thiol end groups, these nanografted patches exhibited large and specific differences in lateral friction force, which offers the unique possibility to use the friction as a molecular recognition tool for thiol-based self-assembled monolayers.

Soft-Landing Experiments of Cr(benzene)2 Sandwich Complexes onto a Carboxyl-Terminated Self-Assembled Monolayer Matrix

Gas-phase synthesized Cr(benzene)2 sandwich complexes were soft-landed onto a carboxyl-terminated self-assembled monolayer (C15COOH-SAM) on a gold substrate at hyperthermal collision energy (5−20 e...

Soft-landing Isolation of Gas-phase-synthesized Transition Metal−Benzene Complexes into a Fluorinated Self-assembled Monolayer Matrix

Gas-phase-synthesized chromium−benzene 1:2 sandwich cation complexes [Cr+(benzene)2] were soft-landed on a self-assembled monolayer (SAM) of fluorinated alkanethiol (C10F-SAM) at a hyperthermal collision energy of ∼20 eV. The adsorption properties and thermal stability of the soft-landed complexes were studied with infrared reflection absorption spectroscopy (IRAS) and temperature-programmed desorption (TPD). The landed complexes were neutralized due to charge transfer from the SAM substrate, but their native sandwich structure remained intact. The hyperthermal collision event resulted in the penetration of the incoming complexes into the C10F-SAM matrix. The embedded complexes then tended to orient their molecular axes approximately along the surface normal. This orientational preference is measurably different from that of complexes isolated in alkanethiol SAM matrices, a discrepancy that might be caused by a repulsive interaction between the π cloud of the capping benzene rings of the complex and the side-chain CF2 groups of the fluorocarbon chains in the C10F-SAM matrix. The thermal desorption study showed that the complexes supported inside the C10F-SAM could resist thermal desorption until the high-temperature region of ∼320 K, a persistence revealing a large desorption activation energy (∼190 kJ/mol).

Length Dependence of Tunneling Current Through Single Phenylene Oligomers Measured by Scanning Tunneling Microscopy at Low Temperature

The length dependence of tunneling current through single phenylene oligomers, i.e., benzenemethanethiol, 4-biphenylmethanethiol and [1,1':4',1''-terphenyl]-4-methanethiol, was determined experimentally by scanning tunneling microscopy (STM). The single phenylene oligomers were isolated in a self-assembled monolayer (SAM) matrix of a disulfide with two spherical bicyclo[2.2.2]octane moieties on Au(111). The STM measurement was conducted at a low temperature to prevent the thermal motions of the isolated molecules that occur at room temperature. The isolated single molecules inserted in the SAM matrix were observed as protrusions in an STM topography using a constant-current mode owing to their higher tunneling ability. The decay constant, β, of the tunneling current through single phenylene oligomers was estimated from the STM heights of the protrusions corresponding to the single phenylene oligomers using a bilayer tunnel junction model. The value of β for tunneling current through single phenylene oligomers was 5.5 ±0.2 nm-1. In a constant-height mode, we measured the conductance of the isolated single molecules. We estimated an averaged single-molecular conductance of the isolated molecules of a biphenyl derivative to be ca. 2 nS. Here, one side of each isolated molecule was bound via an Au–S bond and the other phenyl end was physically in contact with an Au STM tip.

Trapping of V(benzene)2 sandwich clusters in a n-alkanethiol self-assembled monolayer matrix

V(benzene)2 sandwich cluster cations produced in the gas phase were size-selectively deposited onto a self-assembled monolayer of n-hexadecanethiols (HDT-SAM) chemisorbed on a Au(111) surface as well as onto a bare Au(111) surface. The thermal chemistry of the neutralized clusters on each substrate was studied with temperature programmed desorption (TPD). From the analyses of the threshold in the TPD, the desorption activation energies of the clusters deposited were determined to be 64.4 ±12.8 kJ/mol for the Au(111) and 130 ±10 kJ/mol for the HDT-SAM. The remarkably large desorption activation energy from the SAM suggests that the deposited clusters are incorporated into the SAM matrix and firmly trapped inside the alkyl chains of the SAM.

Crystallization of Vaterite Nanowires by the Cooperative Interaction of Tailor-Made Nucleation Surfaces and Polyelectrolytes

The concepts of template-induced crystallization on self-assembled monolayers (SAMs) and the use of polymer additives are combined into a new strategy, where, through the cooperative interaction of a SAM matrix involved in the nucleation process, poly(acrylic acid), a dissolved polyelectrolyte, and the dissolved ions, hierarchically ordered mineral structures are formed. The adsorption of poly(acrylic acid) to the SAM is monitored using a quartz microbalance. Transmission electron microscopy measurements on samples that are taken from polyacrylate solution in short intervals after the start of the reaction reveals that nanometer-sized particles pre-formed in solution are being attached to the polymer template. These CaCO3 nanoparticles are still amorphous 20 min after the start of the mineralization process; the transformation from the amorphous to the crystalline phase takes place within the first 60 min of the reaction. The morphologies of the crystalline products exhibit characteristic differences from those that are obtained in crystallization experiments on self-assembled monolayers without the polyelectrolyte. This model of cooperative formation of vaterite nanowires represents an alternative to current models of structure formation, where two-phase systems (e.g., microemulsions or foams) act as a structure-directing interface, or the mineralization process is caused by the diffusion of a hydrolyzable component from a non-aqueous into an aqueous phase.

The dynamic behaviour of a single molecule inserted in a self-assembled monolayer matrixat low temperature

We observed the dynamic behaviour of a single conjugated molecule, 4-biphenylmethanethiol(BPMT), inserted in a self-assembled monolayer (SAM) matrix of a bicyclo[2.2.2]octanederivative (BCO) using scanning tunnelling microscopy at . At room temperature (Wakamatsu et al 2003 Nanotechnology 14 258), stochasticswitching of BPNT and lateral movement of the BPMT and the BCO molecules wereobserved even in the well-ordered BCO SAM matrix on Au(111) terraces. Such movementwas, however, rarely observed in the SAM on Au(111) terraces at . Single BPMT molecules were fixed in the well-ordered BCO SAM matrix at , except at step edges and edges of one atom deep pits of the Au(111) substrate. Whena disordered BCO SAM matrix was created intentionally by applying voltagepulses, the stochastic switching of the single BPMT molecule and the lateralmovement of the BCO and the BPMT molecules were observed more frequentlythan those at the step edges and the pit edges at .

Dependence of tunneling current through a single molecule of phenylene oligomers on the molecular length

The electrical properties of single phenylene oligomers were studied in terms of the dependence of the tunneling current on the length of the oligomers using self-assembling techniques and scanning tunneling microscopy (STM). It is important to isolate single molecules in an insulating matrix for the measurement of the conductivity of the single molecule. We demonstrate here a novel self-assembled monolayer (SAM) matrix appropriate for isolation of the single molecules. A bicyclo[2.2.2]octane derivative was used for a SAM matrix, in which the single molecules were inserted at molecular lattice defects. The isolated single molecules of phenylene oligomers inserted in the SAM matrix were observed as protrusions in STM topography using a constant current mode. We measured the topographic heights of the molecular protrusions using STM and estimated the decay constant, β, of the tunneling current through the single phenylene oligomers using a bilayer tunnel junction model.

Precise Positioning of Nanoparticles on Surfaces Using Scanning Probe Lithography

Two new methods have been developed to precisely position gold nanoparticles on surfaces. The surface-active nanoparticles have a shell of a mixed monolayer comprised of alkanethiol and alkanedithiol molecules to anchor particles to gold surfaces via sulfur−gold chemisorption. In the first method, regions of an alkanethiol self-assembled monolayer (SAM) are shaved by the AFM tip under high force in a solution containing nanoparticles. Nanoparticles then adsorb onto the exposed areas defined by the shaving track of the tip. In a second method, the AFM tip is coated with nanoparticles. Under low force, AFM images are acquired and the nanoparticles remain on the tip. When higher load is applied, areas of the SAM matrix are uncovered and nanoparticles are deposited following the scanning track of the AFM tip. Thus, the 3D positions of the nanoparticles are precisely controlled. The nanostructures are characterized in situ with the same tip at reduced load. Individual particles within the nanopatterns can be r...

Motions of single molecules inserted in a self-assembled monolayer matrix of abicyclo[2.2.2]octane derivative on Au(111)

The motion of single conjugated molecules inserted in a self-assembledmonolayer (SAM) matrix composed of a spherical bicyclo[2.2.2]octanederivative was observed using scanning tunnelling microscopy at roomtemperature. Two kinds of conjugated molecules, i.e. benzenemethanethiol and4-biphenylmethanethiol, were inserted in the SAM matrix. It was revealed thatthe isolated single molecules exhibited two types of motions. One was thechange in tilt of the molecular axis at a fixed position, and the other waslateral motion in the SAM matrix. These motions of the single moleculesdue to thermal energy at room temperature were most likely caused bylarge and mobile vacancies of single molecular defects in the SAM matrix.