Long-range sigma-pi interactions in tetrahydro-4H-thiopyran end-capped oligo(cyclohexylidenes). Photo-electron spectroscopy, ab initio SCF MO calculations, and natural bond orbital analyses

Long-range sigma-pi interactions in tetrahydro4H-thiopyran end-capped oligo(cyclohexylidenes) were identified by He(I) photoelectron spectroscopy (PES) and ab initio RHF/6-31G* calculations. The vertical ionization energies Ivj of the highest occupied molecular orbitals (MO's) were assigned using Koopmans' theorem (Iv,j = -epsilonj) and by correlation with the ionizations of related reference compounds. The experimental (PES) and theoretical (RHF/6-31G*) results are in good agreement. For tercyclohexylidene derivatives which contain two nonconjugated pi-bonds splittings deltaIv,j of the pi-bands in the range from approximately 0.5 to 0.7 eV (delta-epsilonj approximately 0.6 to 0.9 eV). For the bi- and tercyclohexylidene compounds containing two sulfur atoms at their alpha- and omega-end positions the pi-type sulfur lone pair bands [Lppi(S)] split significantly by deltaIvj approximately 0.3 to 0.4 eV (delta-epsilonj approximately 0.3 to 0.4 eV), i.e. sigma-pi interactions over distances of ca. 8 and 12 A, respectively, occur. The magnitude of the interactions and the observed splittings are independent of the anti and syn conformations of the oligo(cyclohexylidene) hydrocarbon skeletons. RHF/6-31G* Natural Bond Orbital analyses reveal that the Hax-C-C-Hax precanonical MO's (PCMO's) centered on the cyclohexyl-type rings are paramount for the relay of the through-bond sigma-pi interactions; no through-space sigma-pi interactions were identified.     

Weak distance dependence of through-bond interactions in tetrahydro-4H-thiopyran-4-ylidene end-capped oligo(cyclohexylidenes); a computational survey

Calculations on members of the oligo(cyclohexylidene) series [(n), n = 1-5)] and related tetrahydro-4H-thiopyran end-capped analogues [(n), n = 1-4)] show a strong through-bond coupling between their pi bonds and sulfur lone pairs (Lp(pi)S). This coupling is mediated by an interaction between the H(ax)-C-C-H(ax) structural sub-units and the pi bonds connecting the cyclohexyl moieties. A comparison of the length dependency of the through-bond coupling via an oligo(cyclohexylidene) and an alkane bridge [divinyl alkanes (n)] shows that oligo(cyclohexylidenes) are more efficient in mediating through-bond couplings over large distances. Oligo(cyclohexylidene) bridges exhibit molecular wire characteristics.     

Strong resistance of oligo(phosphorylcholine) self-assembled monolayers to protein adsorption

In this work, we demonstrate the strong resistance of oligo(phosphorylcholine) (OPC) self-assembled monolayers (SAMs) to protein adsorption and cell adhesion. OPC SAMs were characterized using X-ray photoelectron spectroscopy (XPS), and protein adsorption was measured using a surface plasmon resonance (SPR) sensor. Results are compared with those of phosphorylcholine (PC) SAMs. Despite the existence of negative charge on OPC SAMs and the simple synthesis procedure of OPC thiols, OPC SAMs resist protein adsorption as effectively as or better than PC SAMs formed from highly purified PC thiols. The ease of their preparation and the effectiveness of their function make OPC SAMs an attractive alternative for creating nonfouling surfaces.     

In-situ characterization of self-assembled monolayers of water-soluble oligo(ethylene oxide) compounds

In-situ spectroscopic ellipsometry (SE) was utilized to examine the formation of the self-assembled monolayers (SAMs) of the water-soluble oligo(ethylene oxide) [OEO] disulfide [S(CH(2)CH(2)O)(6)CH(3)](2) {[S(EO)(6)](2)} and two analogous thiols - HS(CH(2)CH(2)O)(6)CH(3) {(EO)(6)} and HS(CH(2))(3)O(CH(2)CH(2)O)(5)CH(3) {C(3)(EO)(5)} - on Au from aqueous solutions. Kinetic data for all compounds follow simple Langmuirian models with the disulfide reaching a self-limiting final state (d=1.2nm) more rapidly than the full coverage final states of the thiol analogs (d=2.0nm). The in-situ ellipsometric thicknesses of all compounds were found to be nearly identical to earlier ex-situ ellipsometric measurements suggesting similar surface coverages and structural models in air and under water. Exposure to bovine serum albumin (BSA) shows the self-limiting (d=1.2nm) [S(EO)(6)](2) SAMs to be the most highly protein resistant surfaces relative to bare Au and completely-formed SAMs of the two analogous thiols and octadecanethiol (ODT). When challenged with up to near physiological levels of BSA (2.5mg/mL), protein adsorption on the final state [S(EO)(6)](2) SAM was only 3% of that which adsorbed to the bare Au and ODT SAMs.     

Hydration of oligo(ethylene glycol) self-assembled monolayers studied using polarization modulation infrared spectroscopy

The interaction with water of protein-resistant monolayers (SAMs), self-assembled from (triethylene glycol) terminated thiol HS(CH2)11(OCH2CH2)3OMe solutions, was studied using in and ex situ polarization-modulated Fourier transform infrared spectroscopy. In particular, shifts in the position of the characteristic C-O-C stretching vibration were observed after the monolayers had been exposed to water. The shift in frequency increased when the SAM was observed in direct contact with a thin layer of water. It was found that the magnitude of the shift also depended on the surface coverage of the SAM. These findings suggest a rather strong interaction of oligo(ethylene glycol) SAMs with water and indicate the penetration of water into the upper region of the monolayer.     

Structural and chemical characterization of monofluoro-substituted oligo(phenylene-ethynylene) thiolate self-assembled monolayers on gold

Monolayers of oligo(phenylene-ethynylene) (OPE) molecules have exhibited promise in molecular electronic test structures. This paper discusses films formed from a novel molecule within this class, 2-fluoro-4-phenylethynyl-1-[(4-acetylthio)phenylethynyl]benzene (F-OPE). The conditions of self-assembled monolayer (SAM) formation were systematically altered to fabricate reproducible high-quality molecular monolayers from the acetate-protected F-OPE molecule. Detailed characterization of the F-OPE monolayers was performed by using an array of surface probes, including reflection absorbance infrared spectroscopy (RAIRS), contact angle (CA) measurements, spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and atomic force microscopy (AFM). XPS and RAIRS established that the SAM formed without removal of the F substituent and without oxidation of the thiol. The monolayer thickness, determined from SE and AFM based nanolithography, was consistent with the formation of a densely packed monolayer. The valence electronic structure of the SAM was consistent with an aromatic structure shifted by the electron-withdrawing fluorine substituent and intermolecular coupling within an oriented array of molecules.     

Shape-persistent linear, kinked, and cyclic oligo(phenylene-ethynylene-butadiynylene)s: self-assembled monolayers

Shape-persistent rigid phenylene-ethynylene-butadiynylenes form lamellar self-assembled monolayers (SAMs) at the HOPG/TCB interface, which were studied by scanning tunneling microscopy (STM) with submolecular resolution. Substitution of the terminating acetylene functions with polar cyanopropyldimethylsilyl groups leads to 2D phase separation and defined rod-rod interactions, which determine the packing distances between the rigid rods. The results stimulated the connection of rigid rods via septiarylene clamp units. They covalently link two rigid rod units and define the intramolecular rod-rod distance that matches the alkoxy substituent chain lengths. The systems can be described as half-ring structures of two rigid rods connected via a rotatable joint unit. These acetylene-terminated half-ring structures were also oligomerized under Cu and Pd catalysis to yield defined acyclic and cyclic oligomers. Detailed STM studies decoded the molecular origin of the surface patterning of such systems. The dodecyloxy side chains are adsorbed along the HOPG main axes and, together with the alkoxy backbone angle, determine the adsorption direction of the adlayers.     

Covalent attachment of a transition metal coordination complex to functionalized oligo(phenylene-ethynylene) self-assembled monolayers

We have investigated the reaction of tetrakis(dimethylamido)titanium, Ti[N(CH(3))(2)](4), with N-isopropyl-N-[4-(thien-3-ylethynyl) phenyl] amine and N-isopropyl-N-(4-{[4-(thien-3-ylethynyl) phenyl]ethynyl}phenyl) amine self-assembled monolayers (SAMs), on polycrystalline Au substrates. The structure of the SAMs themselves has also been investigated. Both molecules form SAMs on polycrystalline Au bound by the thiophene group. The longer-molecular-backbone molecule forms a denser SAM, with molecules characterized by a smaller tilt angle. X-ray photoelectron spectroscopy (XPS) and angle-resolved XPS have been employed to examine the kinetics of adsorption, the spatial extent of reaction, and the stoichiometry of reaction. For both the SAMs, adsorption is described well by first-order Langmuirian kinetics, and adsorption is self-limiting from T(s) = -50 to 30 degrees C. The use of angle-resolved XPS clearly demonstrates that the Ti[N(CH(3))(2)](4) reacts exclusively with the isopropylamine end group via ligand exchange, and there is no penetration of the SAM, followed by reaction at the SAM-Au interface. Moreover, the SAM molecules remain bound to the Au surface via their thiopene functionalites. From XPS, we have found that, in both cases, approximately one Ti[N(CH(3))(2)](4) is adsorbed per two SAM molecules.     

Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers

Molecular simulations were performed to study a system consisting of protein (e.g., lysozyme) and self-assembled monolayers (SAMs) terminating with different chemical groups in the presence of explicit water molecules and ions. Mixed SAMs of oligo (ethylene glycol) [S(CH2)4(OCH2CH2)4OH, (OEG)] and hydroxyl-terminated SAMs [S(CH2)4OH] with a mole fraction of OEG at chiOEG = 0.2, 0.5, 0.8, and 1.0 were used in this study. In addition, methyl-terminated SAMs [S(CH2)11CH3] were also studied for comparison. The structural and dynamic behavior of hydration water, the flexibility and conformation state of SAMs, and the orientation and conformation of protein were examined. Simulation results were compared with those of experiments. It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around OEG chains and the rapid mobility of hydrated SAM chains.     

Structure and dynamics of water near the interface with oligo(ethylene oxide) self-assembled monolayers

We performed molecular dynamics simulations of the oligo(ethylene oxide) (OEO) self-assembled monolayers in water to determine the nature of the systems' interfacial structure and dynamics. The density profiles, hydrogen bonding, and water dynamics are calculated as a function of the area per molecule A of OEO. At the highest coverages, the interface is hydrophobic, and a density drop is found at the interface. The interfacial region becomes more like bulk water as A increases. The OEO and water become progressively more mixed, and hydrogen bonding increases within the interfacial region. Water mobility is slower within the interfacial region, but not substantially. The implications of our results on the resistance of OEO SAMs to protein adsorption are discussed. Our principal result is that as A increases the increasingly waterlike interfacial region provides a more protein-resistant surface. This finding supports recent experimental measurements that protein resistance is maximal for less than full coverage on Au.     

One-step photochemical introduction of nanopatterned protein-binding functionalities to oligo(ethylene glycol)-terminated self-assembled monolayers

Exposure of oligo(ethylene glycol) (OEG)-terminated self-assembled monolayers (SAMs) to UV light leads to the formation of aldehyde groups, leading to a simple one-step method for the introduction of reactive functional groups to protein-resistant surfaces. X-ray photoelectron spectroscopy has been used to demonstrate binding of amines to the modified surfaces, while surface plasmon resonance has shown that proteins are covalently bound. Modified OEG monolayers bind streptavidin at least as well as N-hydroxysuccinimidyl ester functionalized monolayers. Micrometer and nanometer-scale patterns are conveniently fabricated by exposing the monolayers using, respectively, a mask and a scanning near-field optical microscope.     

Ion recognition at the interface of self-assembled monolayers (SAMs) of bis-thioctic ester derivatives of oligo(ethyleneglycols)

Self-assembled monolayers (SAMs) of bis-thioctic ester derivatives of oligoethylene glycols were prepared. When the number of (-CH2-CH2-O-)n units in these podands was either five or six, the corresponding SAMs showed ion binding properties and selectivities similar to those exhibited by 15-crown-5 or 18-crown-6 in aqueous solution, respectively. Impedance data for the SAMs as a function of metal ion concentrations were fitted by using a Langmuir isotherm to determine the association constants (Ka) with the different ions. The SAM derived from the n = 5 compound is selective for Na+ while that with n = 6 is selective for K+. Results presented here confirm the formation of ion recognition domains during self-assembly of acyclic polyethylene glycol derivatives on gold surfaces; this suggests that surface-confined pseudocrown ether structures are formed.     

Fabrication of biomolecular nanostructures by scanning near-field photolithography of oligo(ethylene glycol)-terminated self-assembled monolayers

The UV photo-oxidation of oligo(ethylene glycol) (OEG)-terminated self-assembled monolayers (SAMs) has been studied using static secondary ion mass spectrometry, X-ray photoelectron spectroscopy, contact angle measurement, and friction force microscopy. OEG-terminated SAMs are oxidized to yield sulfonates, but photodegradation of the OEG chain also occurs on a more rapid time scale, yielding degradation products that remain bound to the surface via gold-sulfur bonds. The oxidation of these degradation products is the rate-limiting step in the process. Photopatterning of OEG-terminated SAMs may be accomplished by using a mask and suitable light source or by using scanning near-field photolithography (SNP) in which the mask is replaced by a scanning near-field optical microscope coupled to a UV laser. Using SNP, it is possible to fabricate patterns in SAMs with a full width at half-maximum height (fwhm) as small as 9 nm, which is approximately 15 times smaller than the conventional diffraction limit. SNP-patterned OEG-terminated SAMs may be used to fabricate protein nanopatterns. By adsorbing carboxylic acid-terminated thiols into oxidized regions and converting these to active ester intermediates, it has been possible to fabricate lines of protein molecules with widths of only a few tens of nanometers.     

Structure and electrochemistry of 4,4'-dithiodipyridine self-assembled monolayers in comparison with 4-mercaptopyridine self-assembled monolayers on Au(111)

4,4'-Dithiodipyridine (PySSPy) monolayers on Au(111) were investigated by cyclic voltammetry, X-ray photoelectron spectroscopy (XPS) and in situ scanning tunneling microscopy (STM). The studies were performed in solutions of different anions and pHs (0.1 M H2SO4, 0.1 M HClO4, 0.1 and 0.01 M Na2SO4, 0.1 and 0.01 M NaOH). The cyclic current-potential curves in H2SO4 show current peaks at about 0.4 V, which are absent for all other electrolytes at this potential. The XPS data suggest that PySSPy adsorbs via the S endgroup on the gold surface and the S-S bond breaks during adsorption. From the chemical shift of the N(ls) peak, it is concluded that in acidic media the self-assembled monolayer (SAM) is fully protonated, whereas in basic solution it is not. The pKa is estimated to be 5.3. STM studies reveal the existence of highly ordered superstructures for the SAM. In Na2SO4 and H2SO4, a (7 x mean square root of 3) structure is proposed. However, whereas in Na2SO4 solutions the superstructure does not change with potential, in 0.1 M H2SO4 the superstructure is observed only negative of the current peak at +0.4 V. At more positive potentials, the film becomes disordered. The results are compared to those for 4-mercaptopyridine (PyS) SAMs. XPS experiments and current-potential curves indicate that both molecules adsorb in the same manner on Au(111), that is, even in the case of PySSPy the adspecies is PyS. The STM results, however, call for a more subtle interpretation. While in Na2SO4 solutions the observed superstructures are the same for both SAMs, markedly different structures are found for PySSPy and PyS SAMs in 0.1 M H2SO4.     

Self-assembled monolayers of clamped oligo(phenylene-ethynylene-butadiynylene)s

Rigid rod oligo(phenylene-ethynylene-butadiynylene)s (oPEBs), "half-rings" of two rigid rods connected via a molecular clamp unit, and shape-persistent macrocycles (cyclic "half-ring dimers") are synthesized and their self-assembled monolayers (SAMs) are investigated by scanning tunneling microscopy (STM) at the interface of 1,2,4-trichlorobenzene (TCB)/highly oriented pyrolytic graphite (HOPG). The results are important for the design of molecular building blocks for two-dimensional nanoscale architectures on solid surfaces.     

Structural characterization of 4-bromostyrene self-assembled monolayers on si(111)

Organic functionalization of silicon holds promise for a variety of applications ranging from molecular electronics to biosensing. Because the performance and reliability of organosilicon devices will be intimately tied to the detailed structure of the organic adlayers, it is imperative to develop systematic strategies for forming and characterizing self-assembled monolayers (SAMs) on silicon with submolecular spatial resolution. In this study, we use 4-bromostyrene for the photochemical growth of Br-terminated SAMs on Si(111). A variety of experimental and theoretical techniques including atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), X-ray reflectivity (XRR), X-ray standing waves (XSW), X-ray fluorescence (XRF), and density functional theory (DFT) have been employed to determine the coverage and conformation of the 4-bromostryene molecules within the SAM. In particular, AFM verifies a continuous and atomically flat SAM, and the XRR data indicate a SAM thickness of 8.50 A and a molecular coverage of 46% of the surface silicon atoms. Because the DFT calculations indicate a molecular length of 8.89 A, the measured XRR thickness implies a molecular tilt angle of approximately 17 degrees. The XRR analysis also suggests that the Br atoms are preserved on top of the SAM in agreement with XPS measurements that show bromine bound solely to carbon and not to silicon. XRF reveals a Br atomic coverage of 50%, again in close agreement to that found by XRR. Single-crystal Bragg diffraction XSW is used to generate a three-dimensional map of the Br distribution within the SAM, which in conjunction with the XRR result suggests that the 4-bromostyrene molecules are tilted such that the Br atoms are located over the T4 sites at a height of 8.50 A above the top bulklike Si(111) layer. The direction of molecular tilt toward the T4 sites is consistent with that predicted by the DFT calculation. Overall, through this unique suite of complementary structural characterization techniques, it is concluded that the Br functional handle is preserved at the top of the SAM and is available for further substitutional chemistry.     

Micropatterning gradients and controlling surface densities of photoactivatable biomolecules on self-assembled monolayers of oligo(ethylene glycol) alkanethiolates

Background: Bioactive molecules that are covalently immobilized in patterns on surfaces have previously been used to control or study cell behavior such as adhesion, spreading, movement or differentiation. Photoimmobilization techniques can be used, however, to control not only the spatial pattern of molecular immobilization, termed the micropattern, but also the surface density of the molecules — a characteristic that has not been previously exploited.Results: Oligopeptides containing the bioactive Arg-Gly-Asp cell-adhesion sequence were immobilized upon self-assembled monolayers of an oligo(ethylene glycol) alkanethiolate in patterns that were visualized and quantified by autoradiography. The amount and pattern of immobilized peptide were controlled by manipulating the exposure of the sample to a LIV lamp or a laser beam. Patterns of peptides, including a density gradient, were used to control the location and number of adherent cells and also the cell shape.Conclusions: A photo immobilization technique for decorating surfaces with micropatterns that consist of variable densities of bioactive molecules is described. The efficacy of the patterns for controlling cell adhesion and shape has been demonstrated. This technique is useful for the study of cell behavior on micropatterns.     

Interaction of self-assembled monolayers of oligo(ethylene glycol)-terminated alkanethiols with water studied by vibrational sum-frequency generation

Vibrational sum-frequency generation (VSFG) was used to investigate the conformational changes in self-assembled monolayers (SAMs) of (1-mercaptoundec-11-yl) hexa(ethylene glycol) monomethylether (EG6-OMe) on gold when exposed to liquid water. VSFG spectra of the EG6-OMe SAMs were recorded before, during, and after exposure of the films to water and after a subsequent evacuation step. While in contact with water the entire ethylene glycol chains are found in a random, solvated state, after removal from the fluid water molecules remain absorbed only at the terminal groups of the film giving rise to distinct conformational changes. After evacuation, the structure of the EG6-OMe SAM reverts to its original state, indicating that water has been removed from the monolayer. Our findings support recent ab initio calculations and Monte Carlo simulations on the interaction of ethylene glycol-terminated monolayers with water.     

Globotriose- and oligo(ethylene glycol)-terminated self-assembled monolayers: surface forces, wetting, and surfactant adsorption

A set of oligo(ethylene glycol)-terminated and globotriose-terminated self-assembled monolayers (SAMs) has been prepared on gold substrates. Such model surfaces are well defined and have good stability due to the strong binding of thiols and disulfides to the gold substrate. They are thus very suitable for addressing questions related to effects of surface composition on wetting properties, surface interactions, and surfactant adsorption. These issues are addressed in this report. Accurate wetting tension measurements have been performed as a function of temperature using the Wilhelmy plate technique. The results show that the nonpolar character of oligo(ethylene glycol)-terminated SAMs increases slightly but significantly with temperature in the range 20-55 degrees C. On the other hand, globotriose-terminated SAMs are fully wetted by water at room temperature. Surface forces measurements have been performed and demonstrated that the interactions between oligo(ethylene glycol)-terminated SAMs are purely repulsive and similar to those determined between adsorbed surfactant layers with the same terminal headgroup. On the other hand, the interactions between globotriose-terminated SAMs include a short-range attractive force component that is strongly affected by the packing density in the layer. In some cases it is found that the attractive force component increases with contact time. Both these observations are rationalized by an orientation- and conformation-dependent interaction between globotriose headgroups, and it is suggested that hydrogen-bond formation, directly or via bridging water molecules, is the molecular origin of these effects.     

Novel synthesis of protected thiol end-capped stilbenes and oligo(phenylenevinylene)s (OPVs)

The first general procedures for preparation of thiol end-capped stilbenes and oligo(phenylenevinylene)s (OPVs) with tert-butyl- and acetyl-protected thiol termini have been developed. These reactions proceed via Br/Li exchange, McMurry, and Wittig-type reactions. The thiol functionality is protected against strong basic and acidic reaction conditions as a t-Bu sulfide. As a key point in the method, reprotection of the thiol group is accomplished by means of acetyl chloride and boron tribromide. The novel strategy forms the basis for stepwise introduction of 4-mercaptostyryl units in OPVs. The new mono-, di-, and trimercapto OPVs have potential applications as one, two, and three terminal molecular devices in gold nanoparticle clusters, self-assembled monolayers, and optoelectronic devices.