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1.  Multi-technique Characterization of Self-assembled Carboxylic Acid Terminated Alkanethiol Monolayers on Nanoparticle and Flat Gold Surfaces 
Gold nanoparticles (AuNPs) with 14, 25 and 40nm diameters were functionalized with different chain length (C6, C8, C11 and C16) carboxylic acid terminated alkanethiol self-assembled monolayers (COOH-SAMs). X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to examine the changes in surface chemistry as both AuNP diameter and SAM chain length were varied. COOH-SAMs on flat gold surfaces were also examined and compared to the COOH-SAM on AuNP results. For a given surface, as the COOH-SAM chain length increased the XPS C/Au atomic ratio increased due to an increased number of carbon atoms per molecule in the overlayer and an increased attenuation of the Au substrate signal. For the C16 COOH-SAMs, as the size of AuNPs decreased the XPS C/Au atomic ratio and the apparent SAM thickness increased due to the increased curvature of the smaller AuNPs. The C16 COOH-SAMs on the flat Au had the lowest XPS C/Au atomic ratio and apparent SAM thickness of any C16 COOH-SAM covered Au surface. The effective take-off angles of the COOH-SAMs were also calculated by comparing the apparent thickness of COOH-SAMs with literature values. The effective take-off angle for C16 COOH-SAM on 14nm, 25nm and 40nm diameter AuNPs and flat Au were found to be 57°, 53°, 51° and 39°, respectively, for data acquired in a mode that collects a wide range of photoelectron take-off angles. The effective take-off angle for C16 COOH-SAM on 14nm AuNP and flat Au decreased to 52° and 0°, respectively, for data acquired in a mode that collects a narrow range of photoelectron take-off angles. The ToF-SIMS results showed similar changes in surface chemistry with COOH-SAM chain length and AuNP size. For example, the ratio of the sum of the C1–4HxOy positive ion intensities to the sum of the Au-containing positive ions intensities increased with decreasing AuNP size and increasing COOH-SAM chain length. Fourier transform IR spectroscopy in the attenuated total reflectance mode (FTIR-ATR) was used to characterize the crystallinity of the COOH-SAMs. The CH2 stretching frequencies decreased with increasing COOH-SAM chain length on flat Au. The C16 COOH-SAM on the 14nm AuNPs exhibited a crystalline-like CH2 stretching frequency. The size, size distribution, shapes and solution stability of AuNPs were investigated with transmission electron microscopy (TEM) and UV/VIS spectroscopy. As the average diameter of the AuNPs decreased the size distribution became narrower and the shape became more spherical.
PMCID: PMC3096993  PMID: 21603069
2.  Improving the Dielectric Properties of Ethylene-Glycol Alkanethiol Self-Assembled Monolayers 
Langmuir  2014;30(5):1321-1326.
Self-assembled monolayers (SAMs) can be formed at the interface between solids and fluids, and are often used to modify the surface properties of the solid. One of the most widely employed SAM systems is exploiting thiol-gold chemistry, which, together with alkane-chain-based molecules, provides a reliable way of SAM formation to modify the surface properties of electrodes. Oligo ethylene-glycol (OEG) terminated alkanethiol monolayers have shown excellent antifouling properties and have been used extensively for the coating of biosensor electrodes to minimize nonspecific binding. Here, we report the investigation of the dielectric properties of COOH-capped OEG monolayers and demonstrate a strategy to improve the dielectric properties significantly by mixing the OEG SAM with small concentrations of 11-mercaptoundecanol (MUD). The monolayer properties and composition were characterized by means of impedance spectroscopy, water contact angle, ellipsometry and X-ray photoelectron spectroscopy. An equivalent circuit model is proposed to interpret the EIS data and to determine the conductivity of the monolayer. We find that for increasing MUD concentrations up to about 5% the resistivity of the SAM steadily increases, which together with a considerable decrease of the phase of the impedance, demonstrates significantly improved dielectric properties of the monolayer. Such monolayers will find widespread use in applications which depend critically on good dielectric properties such as capacitive biosensor.
PMCID: PMC4065163  PMID: 24447311
3.  Nanoscale clustering of carbohydrate thiols in mixed SAMs on gold 
Langmuir  2012;28(17):6950-6959.
Self-assembled monolayers (SAMs) bearing pendant carbohydrate functionality are frequently employed to tailor glycan-specific bioactivity onto gold substrates. The resulting glycoSAMs are valuable for interrogating glycan-mediated biological interactions via surface analytical techniques, microarrays, and label-free biosensors. GlycoSAM composition can be readily modified during assembly using mixed solutions containing thiolated species, including carbohydrates, oligo(ethylene glycol) (OEG) and other inert moieties. This intrinsic tunability of the self-assembled system is frequently used to optimize bioavailability and anti-biofouling properties of the resulting SAM. However, until now, our nanoscale understanding of the behavior of these mixed glycoSAMs has lacked detail. In this study, we examined the time-dependent clustering of mixed sugar+OEG glycoSAMs on ultraflat gold substrates. Composition and surface morphologic changes in the monolayers were analyzed by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), respectively. We provide evidence that the observed clustering is consistent with a phase separation process in which surface-bound glycans self-associate to form dense glycoclusters within the monolayer. These observations have significant implications for the construction of mixed glycoSAMs for use in biosensing and glycomics applications.
PMCID: PMC3350752  PMID: 22435511
Atomic force microscopy; carbohydrates; glycoSAM; phase separation; XPS
4.  Adamantane-Based Tripodal Thioether Ligands Functionalized with a Redox-Active Ferrocenyl Moiety for Self-Assembled Monolayers 
Self-assembled monolayers (SAMs) can decorate surfaces with `smart´ functional units possessing reversible stimulus–response behavior for optical, thermal, magnetic or redox-chemical stimuli. An independent performance of individual functional groups in such a film is desirable, which can be, in particular, ensured by fairly large lateral separations between tailgroups in the SAM. Adsorbate molecules with multiple attachment points are very promising in this context owing to their large surface footprint, which covers a surface area exceeding the lateral dimensions of the functional groups. To address these design constraints, novel tridentate long-chain tripodal thioether ligands with central adamantine units and a redox-active ferrocenyl tailgroup, 1-[4-(ferrocenylethynyl)phenyl]-3,5,7-tri[(4-n-octylsulfanyl)phenyl]adamantine (T8) and 1-[4-(ferrocenylethynyl)phenyl]-3,5,7-tri[(4-n-dodecylsulfanyl)phenyl]adamantine (T12), were synthesized and used as tripodal adsorbate molecules for the fabrication of redox-active ferrocenyl-terminated SAMs on Au(111). These SAMs were characterized by X-ray photoelectron spectroscopy, near edge X-ray absorption fine structure spectroscopy and sum frequency generation spectroscopy. The data suggest that T8 and T12 form almost contamination-free, well-aligned and fairly densely-packed SAMs on Au(111) with laterally separated ferrocenyl units. The SAMs show a homogeneous binding chemistry, an important requirement for high fidelity SAMs. SFG results indicate lateral interactions between neighboring molecules via the long-chain binding units.
PMCID: PMC3049913  PMID: 21399702
5.  Structure and Order of Phosphonic Acid-Based Self-Assembled Monolayers on Si(100) 
Organophosphonic acid self-assembled monolayers (SAMs) on oxide surfaces have recently seen increased use in electrical and biological sensor applications. The reliability and reproducibility of these sensors require good molecular organization in these SAMs. In this regard, packing, order and alignment in the SAMs is important, as it influences the electron transport measurements. In this study, we examine the order of hydroxyl- and methyl- terminated phosphonate films deposited onto silicon oxide surfaces by the tethering by aggregation and growth method using complementary, state-of-art surface characterization tools. Near edge x-ray absorption fine structure (NEXAFS) spectroscopy and in situ sum frequency generation (SFG) spectroscopy are used to study the order of the phosphonate SAMs in vacuum and under aqueous conditions, respectively. X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry results show that these samples form chemically intact monolayer phosphonate films. NEXAFS and SFG spectroscopy showed that molecular order exists in the octadecylphosphonic acid and 11-hydroxyundecylphosphonic acid SAMs. The chain tilt angles in these SAMs were approximately 37° and 45°, respectively.
PMCID: PMC2939309  PMID: 20735054
Phosphonic acid; T-BAG method; NEXAFS; SFG; ToF-SIMS; XPS; surface analysis; order; SAM
6.  Amine Terminated SAMs: Investigating Why Oxygen is Present in these Films 
Self-assembled monolayers (SAMs) on gold prepared from amine-terminated alkanethiols have long been employed as model positively charged surfaces. Yet in previous studies significant amounts of unexpected oxygen containing species are always detected in amine terminated SAMs. Thus, the goal of this investigation was to determine the source of these oxygen species and minimize their presence in the SAM. The surface composition, structure, and order of amine-terminated SAMs on Au were characterized by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectroscopy (ToF-SIMS), sum frequency generation (SFG) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. XPS determined compositions of amine-terminated SAMs in the current study exhibited oxygen concentrations of 2.4 ± 0.4 atomic %, a substantially lower amount of oxygen than reported in previously published studies. High-resolution XPS results from the S2p, C1s and N1s regions did not detect any oxidized species. Angle-resolved XPS indicated that the small amount of oxygen detected was located at or near the amine head group. Small amounts of oxidized nitrogen, carbon and sulfur secondary ions, as well as ions attributed to water, were detected in the ToF-SIMS data due to the higher sensitivity of ToF-SIMS. The lack of N-O, S-O, and C-O stretches in the SFG spectra are consistent with the XPS and ToF-SIMS results and together show that oxidation of the amine-terminated thiols alone can only account for, at most, a small fraction of the oxygen detected by XPS. Both the SFG and angle-dependent NEXAFS indicated the presence of gauche defects in the amine SAMs. However, the SFG spectral features near 2865 cm−1, assigned to the stretch of the methylene group next to the terminal amine unit, demonstrate the SAM is reasonably ordered. The SFG results also show another broad feature near 3200 cm−1 related to hydrogen-bonded water. From this multi-technique investigation it is clear that the majority of the oxygen detected within these amine-terminated SAMs arises from the presence of oxygen containing adsorbates such as tightly bound water.
PMCID: PMC2776750  PMID: 20161353
7.  Simulation and Modeling of Self-Assembled Monolayers of Carboxylic Acid Thiols on Flat and Nanoparticle Gold Surfaces 
Analytical chemistry  2011;83(17):6704-6712.
Quantitative analysis of the 16-mercaptohexadecanoic acid self-assembled monolayer (C16 COOH-SAM) layer thickness on gold nanoparticles (AuNPs) was performed using simulation of electron spectra for surface analysis (SESSA) software and x-ray photoelectron spectroscopy (XPS) experimental measurements. XPS measurements of C16 COOH SAMs on flat gold surfaces were made at 9 different photoelectron emission angles (5° to 85° in 10° increments), corrected using geometric weighting factors and then summed together to approximate spherical AuNPs. The SAM thickness and relative surface roughness (RSA) in SESSA were optimized to determine the best agreement between simulated and experimental surface composition. Based on the glancing-angle results, it was found that inclusion of a hydrocarbon contamination layer on top the C16 COOH-SAM was necessary to improve the agreement between the SESSA and XPS results. For the 16 COOH-SAMs on flat Au surfaces, using a SAM thickness of 1.1Å/CH2 group, an RSA of 1.05, and a 1.5Å CH2-contamination overlayer (total film thickness = 21.5Å) for the SESSA calculations provided the best agreement with the experimental XPS data. After applying the appropriate geometric corrections and summing the SESSA flat-surface compositions, the best fit results for the 16 COOH-SAM thickness and surface roughness on the AuNPs indicated a slightly thinner overlayer with parameters of 0.9Å/CH2 group in the SAM, a RSA of 1.06 RSA and a 1.5Å CH2-contamination overlayer (total film thickness = 18.5Å). The three angstrom difference in SAM thickness between the flat Au and AuNP surfaces suggests that the alkyl chains of the SAM are slightly more tilted or disordered on the AuNP surfaces.
PMCID: PMC3165144  PMID: 21744862
8.  XPS and ToF-SIMS Investigation of α-Helical and β-Strand Peptide Adsorption onto SAMs 
14-mer α-helix and a 15-mer β-strand oligopeptides composed of leucine (L) and lysine (K) were used to investigate peptide adsorption and orientation onto well-defined methyl and carboxylic acid terminated self-assembled monolayer (SAM) surfaces with X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). XPS showed both peptides reached monolayer thickness on both SAMs, but significantly higher solution concentrations were required to reach this coverage on the methyl SAMs. This shows that the peptides adsorb more strongly onto the carboxyl-terminated SAMs. The excess oxygen detected by XPS and the H3O+ signal detected by ToF-SIMS for the SAMs with adsorbed peptides indicated that water molecules are associated with the adsorbed peptides, even under ultra-high vacuum conditions. Changes in the amount of L and K fragments detected by ToF-SIMS indicate the β-strand oriented differently on the two SAMs. The L side-chains were preferentially associated with the methyl-terminated SAM and the K side-chains were preferentially associated with the carboxyl SAM. In contrast, little change in the ToF-SIMS K/L ratio was observed for the α-helix peptide absorbed on the two SAMs, indicating ToF-SIMS was not as sensitive to orientation of the α-helix peptide.
PMCID: PMC2827643  PMID: 19891457
9.  Probing Orientation and Conformation of α-Helix and β-Strand Model Peptides on Self-Assembled Monolayers Using Sum Frequency Generation and NEXAFS Spectroscopies 
The structure and orientation of amphiphilic α-helix and β-strand model peptide films on self-assembled monolayers (SAMs) have been studied with sum frequency generation (SFG) vibrational spectroscopy and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The α-helix peptide is a 14-mer and the β-strand is a 15-mer of hydrophilic lysine and hydrophobic leucine residues with hydrophobic periodicities of 3.5 and 2, respectively. These periodicities result the leucine side chains located on one side of the peptides and the lysine side chains on the other side. The SAMs were prepared from assembly of either carboxylic acid or methyl terminated alkyl thiols onto gold surfaces. For SFG studies the deuterated analog of the methyl SAM was used. SFG vibrational spectra in the C-H region of air dried peptides films on both SAMs exhibit strong peaks near 2965 cm−1, 2940 cm−1 and 2875 cm−1 related to ordered leucine side chains. The orientation of the leucine side chains was determined from the phase of these features relative to the non-resonant gold background. The relative phase for both the α-helix and β-strand peptides showed that the leucine side chains were oriented away from the carboxylic acid SAM surface and oriented towards the methyl SAM surface. Amide I peaks observed near 1656 cm−1 for the α-helix peptide confirm that the secondary structure is preserved on both SAMs. A strong linear dichroism related to the amide π* orbital at 400.8 eV was observed in the nitrogen K-edge NEXAFS spectra for the adsorbed β-strand peptides, suggesting that the peptide backbones are oriented parallel to the SAM surface with the side-chains pointing towards or away from the interface. For the α-helix the dichroism of the amide π* is significantly weaker, probably due to the broad distribution of amide bond orientations in the α-helix secondary structure.
PMCID: PMC2922880  PMID: 20175575
10.  Tripodal Binding Units for Self-Assembled Monolayers on Gold: A Comparison of Thiol and Thioether Headgroups 
Whereas thiols and thioethers are frequently used as binding units of oligodentate precursor molecules to fabricate self-assembled monolayers (SAMs) on coinage metal and semiconductor surfaces, their use for tridentate bonding configuration is still questionable. Against this background, novel tridentate thiol ligands, PhSi(CH2SH)3 (PTT) and p-Ph-C6H4Si(CH2SH)3 (BPTT), were synthesized and used as tripodal adsorbate molecules for the fabrication of SAMs on Au(111). These SAMs were characterized by X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The PTT and BPTT films were compared with the analogous systems comprised of same tripodal ligands with thioether instead of thiol binding units (anchors). XPS and NEXAFS data suggest that the binding uniformity, packing density, and molecular alignment of the thiol-based ligands in the respective SAMs is superior to their thioether counterparts. In addition, the thiol-based films showed significantly lower levels of contamination. Significantly, the quality of the PTT SAMs on Au(111) was found to be even higher than that of the films formed from the respective monodentate counterpart, benzenethiol. The results obtained allow for making some general conclusions on the specific character of molecular self-assembly in the case of tridentate ligands.
PMCID: PMC3102536  PMID: 21625327
11.  Microwave-Accelerated Surface Modification of Plasmonic Gold Thin Films with Self-Assembled Monolayers of Alkanethiols 
A rapid surface modification technique for the formation of self-assembled monolayers (SAMs) of alkanethiols on gold thin films using microwave heating in less than 10 min is reported. In this regard, SAMs of two model alkanethiols, 11-mercaptoundecanoic acid (11-MUDA, to generate a hydrophilic surface) and undecanethiol (UDET, a hydrophobic surface), were successfully formed on gold thin films using selective microwave heating in 1) a semi-continuous and 2) a continuous fashion and at room temperature (24 hours, control experiment, no microwave heating). The formation of SAMs of 11-MUDA and UDET were confirmed by contact angle measurements, Fourier–transform infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The contact angles for water on SAMs formed by the selective microwave heating and conventional room temperature incubation technique (24 hours) were measured to be similar for 11-MUDA and UDET. FT-IR spectroscopy results confirmed that the internal structure of SAMs prepared using both microwave heating and at room temperature were similar. XPS results revealed that the organic and sulfate contaminants found on bare gold thin films were replaced by SAMs after the surface modification process was carried out using both microwave heating and at room temperature.
PMCID: PMC3863588  PMID: 24083414
Alkanethiols; self-assembled monolayers; gold thin films; surface plasmon resonance; surface plasmon fluorescence spectroscopy; microwave-induced temperature gradients
12.  XPS, ToF-SIMS, NEXAFS and SPR Characterization of Nitrilotriacetic Acid-Terminated Self-Assembled Monolayers for Controllable Immobilization of Proteins 
Analytical chemistry  2008;80(7):2564-2573.
For immobilization of proteins onto surfaces in a specific and controlled manner it is important to start with a well-defined surface that contains specific binding sites surrounded by a nonfouling background. For immobilizing histidine-tagged (his-tagged) proteins, surfaces containing nitrilotriacetic acid (NTA) headgroups and oligo(ethylene glycol) (OEG) moieties are a widely used model system. The surface composition, structure and reactivity of mixed NTA/OEG self-assembled monolayers (SAMs) on Au substrates were characterized in detail using x-ray photoelectron spectroscopy (XPS), near-edge x-ray absorption fine structure spectroscopy (NEXAFS), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and surface plasmon resonance (SPR) biosensoring. XPS results for sequential adsorption of NTA thiols followed by OEG thiols showed that OEG molecules were incorporated into an incompletely formed NTA monolayer until a complete mixed SAM was formed. The surface concentration of NTA headgroups was estimated to be 0.9–1.3 molecule/nm2 in the mixed NTA/OEG monolayers, compared to 1.9 molecule/nm2 in pure NTA monolayers. Angle-dependent XPS indicated NTA headgroups were slightly reoriented toward an upright position after OEG incorporation and polarization-dependent NEXAFS results indicated increased ordering of the alkane chains of the molecules. Nitrogen-containing and OEG-related secondary ion fragments from the ToF-SIMS experiments confirmed the presence of NTA headgroups and OEG moieties in the monolayers. A multivariate peak intensity ratio was developed for estimating the relative NTA concentration in the outermost (10 Ǻ) of the monolayers. SPR measurements of a his-tagged, humanized anti-lysozyme variable fragment (HuLys Fv) immobilized onto Ni(II)-treated mixed NTA/OEG and pure NTA monolayers demonstrated the reversible, site-specific immobilization of his-tagged HuLys Fv (108 – 205 ng/cm2) with dissociation rates (koff) between 1.0x10−4 and 2.1x10−5 s−1, both depending on the NTA surface concentration and orientation. The monolayers without Ni(II) treatment exhibited low nonspecific adsorption of his-tagged HuLys Fv ( < 2ng/cm2).
PMCID: PMC3781950  PMID: 18302347
13.  Solid-State Densification of Spun-Cast Self-Assembled Monolayers for Use in Ultra-Thin Hybrid Dielectrics 
Applied surface science  2012;261:10.1016/j.apsusc.2012.09.013.
Ultra-thin self-assembled monolayer (SAM)-oxide hybrid dielectrics have gained significant interest for their application in low-voltage organic thin film transistors (OTFTs). A [8-(11-phenoxy-undecyloxy)-octyl]phosphonic acid (PhO-19-PA) SAM on ultrathin AlOx (2.5 nm) has been developed to significantly enhance the dielectric performance of inorganic oxides through reduction of leakage current while maintaining similar capacitance to the underlying oxide structure. Rapid processing of this SAM in ambient conditions is achieved by spin coating, however, as-cast monolayer density is not sufficient for dielectric applications. Thermal annealing of a bulk spun-cast PhO-19-PA molecular film is explored as a mechanism for SAM densification. SAM density, or surface coverage, and order are examined as a function of annealing temperature. These SAM characteristics are probed through atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure spectroscopy (NEXAFS). It is found that at temperatures sufficient to melt the as-cast bulk molecular film, SAM densification is achieved; leading to a rapid processing technique for high performance SAM-oxide hybrid dielectric systems utilizing a single wet processing step. To demonstrate low-voltage devices based on this hybrid dielectric (with leakage current density of 7.7×10−8 A cm−2 and capacitance density of 0.62 µF cm−2 at 3 V), pentacene thin-film transistors (OTFTs) are fabricated and yield sub 2 V operation and charge carrier mobilites of up to 1.1 cm2 V−1 s−1.
PMCID: PMC3840438  PMID: 24288423
Self Assembled Monolayer (SAM); SAM Dielectric; Hybrid Dielectric; SAM Processing; Organic Field Effect Transistor (OFET); Organic Thin Film Transistor (OTFT)
14.  Patterning discrete stem cell culture environments via localized SAM replacement 
Self-assembled monolayers (SAMs) of alkanethiolates on gold have become an important tool for probing cell-material interactions. Emerging studies in stem cell biology are particularly reliant on well-defined model substrates, and rapid and highly controllable fabrication methods may be necessary to characterize the wide array of stem cell-material interactions. Therefore, this study describes a rapid method to create SAM cell culture substrates with multiple discrete regions of controlled peptide identity and density. The approach uses an NaBH4 solution to selectively remove regions of bio-inert, hydroxyl-terminated oligo(ethylene glycol) alkanethiolate SAM, then locally replace them with mixed SAMs of hydroxyl- and carboxylic acid-terminated oligo(ethylene glycol) alkanethiolates. The cell adhesion peptide Arg-Gly-Asp-Ser-Pro (RGDSP) was then covalently linked to carboxylic acid-terminated mixed SAM regions to create cell adhesive environments within a bio-inert background. SAM preparation and peptide immobilization were characterized using polarization modulation–infrared reflection-absorption spectroscopy (PMIRRAS), as well as assays to monitor conjugation of a fluorescently-labeled peptide. This “localized SAM replacement” method was achieved using an array of microchannels, which facilitated rapid and simple processing. Results indicate that immobilized RGDSP promoted spatially localized attachment of human mesenchymal stem cells (hMSCs) within specified regions, while maintaining a stable, bio-inert background in serum-containing cell culture conditions for up to 14 days. Cell attachment to patterned regions presenting a range of cell adhesion peptide densities demonstrated that peptide identity and density strongly influence hMSC spreading and focal adhesion density. These substrates contain discrete, well-defined microenvironments for stem cell culture, which could ultimately enable high-throughput screening for the effects of immobilized signals on stem cell phenotype.
PMCID: PMC2769026  PMID: 19856996
15.  Molecular Self-Assembly into One-Dimensional Nanostructures 
Accounts of chemical research  2008;41(12):1674-1684.
Self-assembly of small molecules into one-dimensional nanostructures offers many potential applications in electronically and biologically active materials. The recent advances discussed in this Account demonstrate how researchers can use the fundamental principles of supramolecular chemistry to craft the size, shape, and internal structure of nanoscale objects. In each system described here, we used atomic force microscopy (AFM) and transmission electron microscopy (TEM) to study the assembly morphology. Circular dichroism, nuclear magnetic resonance, infrared, and optical spectroscopy provided additional information about the self-assembly behavior in solution at the molecular level.
Dendron rod–coil molecules self-assemble into flat or helical ribbons. They can incorporate electronically conductive groups and can be mineralized with inorganic semiconductors. To understand the relative importance of each segment in forming the supramolecular structure, we synthetically modified the dendron, rod, and coil portions. The self-assembly depended on the generation number of the dendron, the number of hydrogen-bonding functions, and the length of the rod and coil segments. We formed chiral helices using a dendron–rod–coil molecule prepared from an enantiomerically enriched coil.
Because helical nanostructures are important targets for use in biomaterials, nonlinear optics, and stereoselective catalysis, researchers would like to precisely control their shape and size. Tripeptide-containing peptide lipid molecules assemble into straight or twisted nanofibers in organic solvents. As seen by AFM, the sterics of bulky end groups can tune the helical pitch of these peptide lipid nanofibers in organic solvents. Furthermore, we demonstrated the potential for pitch control using trans-to-cis photoisomerization of a terminal azobenzene group. Other molecules called peptide amphiphiles (PAs) are known to assemble in water into cylindrical nanostructures that appear as nanofiber bundles. Surprisingly, TEM of a PA substituted by a nitrobenzyl group revealed assembly into quadruple helical fibers with a braided morphology. Upon photocleavage of this the nitrobenzyl group, the helices transform into single cylindrical nanofibers.
Finally, inspired by the tobacco mosaic virus, we used a dumbbell-shaped, oligo(phenylene ethynylene) template to control the length of a PA nanofiber self-assembly (<10 nm). AFM showed complete disappearance of long nanofibers in the presence of this rigid-rod template. Results from quick-freeze/deep-etch TEM and dynamic light scattering demonstrated the templating behavior in aqueous solution. This strategy could provide a general method to control size the length of non-spherical supramolecular nanostructures.
PMCID: PMC2645948  PMID: 18754628
16.  Role of SAM Chain Length in Enhancing the Sensitivity of Nanopillar Modified Electrodes for Glucose Detection 
Sensors (Basel, Switzerland)  2009;9(3):1295-1305.
In this report, alkanethiol self assembled monolayers (SAM) with two different chain lengths were used to immobilize the functionalizing enzyme (glucose oxidase) onto gold nanopillar modified electrodes and the electrochemical processes of these functionalized electrodes in glucose detection were investigated. First, the formation of these SAMs on the nanopillar modified electrodes was characterized by the cyclic voltammetry and electrochemical impedance spectroscopy techniques, and then the detection sensitivity of these functionalized electrodes to glucose was evaluated by the amperometry technique. Results showed that the SAM of alkanethiols with a longer chain length resulted in a higher degree of surface coverage with less defect and a higher electron transfer resistance, whereas the SAM of alkanethiols with a shorter chain length gave rise to a higher detection sensitivity to glucose. This study sheds some new insight into how to enhance the sensing performance of nanopillar modified electrodes.
PMCID: PMC3345854  PMID: 22573954
Gold nanopillar modified electrodes; self assembled monolayer; alkanethiols; electrochemical processes; glucose detection; biosensors
17.  Molecular suction pads: Self-assembled monolayers of subphthalocyaninatoboron complexes [BCl{Subpc’(SR)6}] on gold 
Subphthalocyaninatoboron complexes with six long-chain alkylthio substituents in their periphery are applicable for the formation of self-assembled monolayers (SAMs) on gold. Such films were prepared from solution with the axially chlorido substituted derivatives and characterised by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results are in accord with the formation of SAMs assembled by the chemisorption of both covalently bound thiolate-type as well as coordinatively bound thioether units. The adsorbate molecules adopt an essentially ‘flat’ adsorption geometry on the substrate, resembling a suction pad on a surface.
Graphical Abstract
PMCID: PMC4618680  PMID: 23526805
subphthalocyaninatoboron complexes; monolayers; NEXAFS spectroscopy; self-assembly; XPS
18.  Synthesis and Photophysical and Electroluminescent Properties of Poly(1,4-phenylene–ethynylene)-alt-poly(1,4-phenylene–vinylene)s with Various Dissymmetric Substitution of Alkoxy Side Chains 
Macromolecules  2016;49(2):455-464.
The synthesis and characterization of a set of conjugated polymers, poly(1,4-phenylene–ethynylene)-alt-poly(1,4-phenylene–vinylene)s (PPE–PPVs), with a dissymmetrical configuration (partial or total) of alkoxy side chains is reported. Five new polymers bearing octyloxy and/or octadecyloxy side chains at the phenylene–ethynylene and phenylene–vinylene segments, respectively, were obtained. Two symmetrical substituted polymers were used for comparison. Polymers with weight-average molecular weight, Mw, up to 430 000 g/mol and degree of polymerization between 17 and 322 were obtained by a Horner–Wadsworth–Emmons olefination polycondensation reaction of the respective luminophoric dialdehydes and bisphosphonates. As expected, identical conjugated backbones in all polymers results in very similar photophysical response in dilute solution, with high fluorescence quantum yields between 50% and 80%. In contrast, the thin film properties are dependent on the combinatorial effects of side chain configuration, molecular weight, and film thickness parameters, which are the basis of the resulting comparison and discussion.
PMCID: PMC4730230  PMID: 26877550
19.  Molecular Rotors as Switches 
Sensors (Basel, Switzerland)  2012;12(9):11612-11637.
The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene) monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V) revealed a temperature-dependent negative differential resistance (NDR) associated with the device. The analysis of the device I–V characteristics suggests the source of the observed switching effects to be the result of the redox-induced ligand rotation around the copper metal center and this attribution of switching is consistent with the observed temperature dependence of the switching behavior as well as the proposed energy diagram of the device. The observed resistance switching shows the potential for future non-volatile memories and logic devices applications. This review will discuss the progress and provide a perspective of molecular motion for nanoelectronics and other applications.
PMCID: PMC3478801
molecular rotor; molecular devices; switching; memory; crossbar architecture
20.  Bacterial adhesion to hydroxyl- and methyl-terminated alkanethiol self-assembled monolayers. 
Journal of Bacteriology  1995;177(8):1959-1966.
The attachment of bacteria to solid surfaces is influenced by substratum chemistry, but to determine the mechanistic basis of this relationship, homogeneous, well-defined substrata are required. Self-assembled monolayers (SAMs) were constructed from alkanethiols to produce a range of substrata with different exposed functional groups, i.e., methyl and hydroxyl groups and a series of mixtures of the two. Percentages of hydroxyl groups in the SAMs and substratum wettability were measured by X-ray photoelectron spectroscopy and contact angles of water and hexadecane, respectively. SAMs exhibited various substratum compositions and wettabilities, ranging from hydrophilic, hydroxyl-terminated monolayers to hydrophobic, methyl-terminated monolayers. The kinetics of attachment of an estuarine bacterium to these surfaces in a laminar flow chamber were measured over periods of 120 min. The initial rate of net adhesion, the number of cells attached after 120 min, the percentage of attached cells that adsorbed or desorbed between successive measurements, and the residence times of attached cells were quantified by phase-contrast microscopy and digital image processing. The greatest numbers of attached cells occurred on hydrophobic surfaces, because (i) the initial rates of adhesion and the mean numbers of cells that attached after 120 min increased with the methyl content of the SAM and the contact angle of water and (ii) the percentage of cells that desorbed between successive measurements (ca. 2 min) decreased with increasing substratum hydrophobicity. With all surfaces, 60 to 80% of the cells that desorbed during the 120-min exposure period had residence times of less than 10 min, suggesting that establishment of firm adhesion occurred quickly on all of the test surfaces.
PMCID: PMC176836  PMID: 7721687
21.  First-Principles Surface Stress Calculations and Multiscale Deformation Analysis of a Self-Assembled Monolayer Adsorbed on a Micro-Cantilever 
Sensors (Basel, Switzerland)  2014;14(4):7435-7450.
Micro-cantilever sensors are widely used to detect biomolecules, chemical gases, and ionic species. However, the theoretical descriptions and predictive modeling of these devices are not well developed, and lag behind advances in fabrication and applications. In this paper, we present a novel multiscale simulation framework for nanomechanical sensors. This framework, combining density functional theory (DFT) calculations and finite element method (FEM) analysis, is capable of analyzing molecular adsorption-induced deformation and stress fields in the sensors from the molecular scale to the device scale. Adsorption of alkanethiolate self-assembled monolayer (SAM) on the Au(111) surface of the micro-cantilever sensor is studied in detail to demonstrate the applicability of this framework. DFT calculations are employed to investigate the molecular adsorption-induced surface stress upon the gold surface. The 3D shell elements with initial stresses obtained from the DFT calculations serve as SAM domains in the adsorption layer, while FEM is employed to analyze the deformation and stress of the sensor devices. We find that the micro-cantilever tip deflection has a linear relationship with the coverage of the SAM domains. With full coverage, the tip deflection decreases as the molecular chain length increases. The multiscale simulation framework provides a quantitative analysis of the displacement and stress fields, and can be used to predict the response of nanomechanical sensors subjected to complex molecular adsorption.
PMCID: PMC4029703  PMID: 24763217
multiscale modeling; density functional theory; finite element method; micro-cantilever sensors
22.  Probing the Orientation of Electrostatically Immobilized Protein G B1 by Time of Flight Secondary Ion Spectrometry, Sum Frequency Generation and Near-edge X-Ray Adsorption Fine Structure Spectroscopy 
Langmuir  2011;28(4):2107-2112.
To fully develop techniques that provide an accurate description of protein structure at a surface, we must start with a relatively simple model system before moving on to increasingly complex systems. In this study, x-ray photoelectron spectroscopy (XPS), sum frequency generation spectroscopy (SFG), near-edge x-ray adsorption fine structure (NEXAFS) spectroscopy, and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to probe the orientation of Protein G B1 (6 kDa) immobilized onto both amine (NH3+) and carboxyl (COO−) functionalized gold. Previously, we have shown that we could successful control orientation of a similar Protein G fragment via a cysteine-maleimide bond. In this investigation, to induce opposite end-on orientations, a charge distribution was created within the Protein G B1 fragment by first substituting specific negatively charged amino acids with neutral amino acids and then immobilizing the protein onto two oppositely charged self-assembled monolayer (SAM) surfaces (NH3+ and COO−). Protein coverage, on both surfaces, was monitored by the change in the atomic % N, as determined by XPS. Spectral features within the SFG spectra, acquired for the protein adsorbed onto a NH3+-SAM surface, indicates that this electrostatic interaction does induce the protein to form an oriented monolayer on the SAM substrate. This corresponded to the polarization dependence of the spectral feature related to the NEXAFS N1s to π* transition of the β-sheet peptide bonds within the protein layer. ToF-SIMS data demonstrated a clear separation between the two samples based on the intensity differences of secondary ions stemming from amino acids located asymmetrically within Protein G B1 (Methionine: 62 and 105 m/z; Tyrosine: 107 and 137 m/z; Leucine: 86 m/z). For a more quantitative examination of orientation, we developed a ratio comparing the sum of the intensities of secondary-ions stemming from the amino acid residues at either end of the protein. The two-fold increase in this ratio, observed between the protein covered NH3+ and COO− SAMs, indicates opposite orientations of the Protein G B1 fragment on the two different surfaces.
PMCID: PMC3269520  PMID: 22148958
23.  Salt-Mediated Self Assembly of Thioctic Acid on Gold Nanoparticles 
ACS nano  2011;5(6):4570-4580.
Self-assembled monolayer (SAM) modification is a widely used method to improve the functionality and stability of bulk and nanoscale materials. For instance, the chemical compatibility and utility of solution-phase nanoparticles are often improved using covalently bound SAMs. Herein, solution-phase gold nanoparticles are modified with thioctic acid SAMs in the presence and absence of salt. Molecular packing density on the nanoparticle surfaces is estimated using X-ray photoelectron spectroscopy and increases by ~20% when molecular self-assembly occurs in the presence vs. the absence of salt. We hypothesize that as the ionic strength of the solution increases, pinhole and collapsed-site defects in the SAM are more easily accessible as the electrostatic interaction energy between adjacent molecules decreases thereby facilitating the subsequent assembly of additional thioctic acid molecules. Significantly, increased SAM packing densities increase the stability of functionalized gold nanoparticles by a factor of two relative to nanoparticles functionalized in the absence of salt. These results are expected to improve the reproducible functionalization of solution-phase nanomaterials for various applications.
PMCID: PMC3125453  PMID: 21524135
Gold nanoparticles; self-assembled monolayers; thioctic acid; nanoparticle stability
24.  Stability of Phosphonic Self Assembled Monolayers (SAMs) on Cobalt Chromium (Co-Cr) Alloy under Oxidative conditions 
Applied surface science  2011;257(13):5605-5612.
Cobalt Chromium (Co-Cr) alloys has been widely used in the biomedical arena for cardiovascular, orthopedic and dental applications. Surface modification of the alloy allows us to tailor the interfacial properties to address critical challenges of Co-Cr alloy in medical applications. Self assembled monolayers (SAMs) of Octadecylphosphonic acid (ODPA) have been used to form thin films on the oxide layer of the Co-Cr alloy surface by solution deposition technique. The SAMs formed were investigated for their stability to oxidative conditions of ambient laboratory environment over periods of 1, 3, 7 and 14 days. The samples were then characterized for their stability using X-ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM) and Contact Angle Measurements. Detailed high energy XPS elemental scans confirmed the presence of the phosphonic monolayer after oxidative exposure which suggested that the SAMs were firmly attached to the oxide layer of Co-Cr alloy. AFM images gave topographical data of the surface and showed islands of SAMs on Co-Cr alloy surface, before and after SAM formation and also over the duration of the oxidative exposure. Contact angle measurements confirmed the hydrophobicity of the surface over 14 days. Thus the SAMs were found to be stable for the duration of the study. These SAMs could be subsequently tailored by modifying the terminal functional groups and could be used for various potential biomedical applications such as drug delivery, biocompatibility and tissue integration
PMCID: PMC3097514  PMID: 21603056
surface modification; self assembled monolayers (SAMs); phosphonic acids; cobalt chromium alloy
25.  Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance 
A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH2)12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm2 V−1 s−1. It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm2 V−1 s−1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed.
PMCID: PMC3786186  PMID: 24086795

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