Fragmentation of dodecanethiol molecules: application to self-assembled monolayer damage in atom lithography

Atom lithography commonly employs self-assem- bled monolayers (SAMs) of alkanethiols which act as resists to protect prepared surfaces. Metastable atomic species such as helium are used to damage the resist, enabling pattern transfer via mask lithography, followed by wet chemical etching. The damage mechanism is, however, not well understood. Here we report studies of fragmentation of dodecanethiol (DDT) molecules embedded in helium nano-droplets that have been irradiated by an electron beam. The results of the charge-transfer fragmentation process provide the first experimental data on the damage mechanisms that occur in the metastable helium/SAM interaction. Received: 20 September 1999 / Revised version: 6 December 1999 / Published online: 8 March 2000     

Spin injection in an organic device with a spin polarized self-assembled monolayer

We propose to achieve spin injection in an organic device by a spin polarized self-assembled monolayer (SPSAM), which is used to tune the spin-dependent coupling between electrode and organic polymer. The results show that spin injection can be realized by both the spin selection and spin manipulation effects of the SPSAM. Interestingly, we found spin polarized wave-packet as a consequence of the spin injection, which is a mix of a normal spin polaron and a spinless bipolaron.     

Nanotribology of self-assembled monolayer with a probe tip investigated using molecular dynamics simulations

The nanotribology of an alkanethiol self-assembled monolayer (SAM) under tilt contact with a scanning probe tip is studied using molecular dynamics (MD) simulations. The tilt contact is described in terms of the tilt angle and the magnitude of the specimen–tip separation. The effects of tilt angle and magnitude of the specimen–tip separation on the normal force, friction force, friction coefficient, shear strength of the tip–SAM junction, and self-recovery characteristics are evaluated during the scanning probe tip process at a temperature of 300 K. The simulation results clearly show that the magnitudes and periods of the normal force and friction force increase with decreasing magnitude of the specimen–tip separation due to a large change of the tilt angle of the SAM chains during the deformation and recovery stages. For scanning and indentation processes, the effect of the tilt angle of the probe tip on the normal force is more significant than that on the friction force for the SAM. The behaviors of interfacial contact forces, friction coefficient, and shear strength strongly depend on the number of interacting atoms and the contact area, which increases with decreasing magnitude of the specimen–tip separation and increasing tilt angle of the probe tip. The self-recovery of SAM is significantly affected by the magnitude of the specimen–tip separation; the recovery ability of SAM is worse for magnitude of the specimen–tip separation below −0.9 nm with a large tilt angle of the probe tip.     

On conjugated molecules with identical topological spectra

Properties of molecular graphs having identical topological spectra are investigated in some detail. It has been established that whole families of isospectral graphs can be derived from a molecular skeleton of vinyl benzene. A pair of isospectral graphs are obtained by an exchange of two non-equivalent residuals attached to particular sites of the skeleton. Additional pairs of isospectral graphs can be derived from related skeletons in which ortho positions of vinyl benzene are occupied by substituents. No constraints have to be imposed on the nature and form of the residuals or the substituting groups. This allows construction of larger isospectral systems including polymeric species. The theoretical foundation for the construction of isospectral graphs described in this work rests on the factorization of the eigenvalue problem of the adjacency matrix associated with molecular graphs which is analogous to a fragmentation of a secular determinant of a Hückel MO problem as outlined some time ago by Heilbronner. A formal proof of the procedure, expressed in a symbolic form, is presented in the Appendix. A discussion of some interesting features of isospectral systems reflected in special properties of topological eigenfunctions is presented.     

Detection and switching of the oxidation state of Fe in a self-assembled monolayer

A self-assembled monolayer of ferrocene-capped alkanethiols is produced in two stable oxidation states of Fe (Fe²⁺ and Fe³⁺). These oxidation states are detected with sub-monolayer sensitivity by the fine structure of the Fe2p absorption edge. The native Fe²⁺ ferrocene layer is converted chemically to Fe³⁺, and the Fe³⁺ layer can be transformed back to Fe²⁺ or possibly Fe⁰ by irradiation with soft X-rays. The results have implications on switching mechanisms in molecular electronics.     

Infrared spectroscopy of self-assembled monolayer films on silicon

Infrared vibrational spectroscopy in an attenuated total reflection (ATR) geometry has been employed to investigate the presence of organic thin layers on Si-wafer surfaces. The phenomena have been simulated to show there can be a field enhancement with the presented single-reflection ATR (SR-ATR) approach which is substantially larger than for conventional ATR or specular reflection. In SR-ATR, a discontinuity of the field normal to the film contributes a field enhancement in the lower index thin film causing a two order of magnitude increase in sensitivity. SR-ATR was employed to characterize a single monolayer of undecylenic acid self-assembled on Si(1 1 1) and to investigate a two monolayer system obtained by adding a monolayer of bovine serum albumin protein.     

Spatially defined silver mirror reaction on a micropatterned aldehyde-terminated self-assembled monolayer

A simple microfabrication technique for silver (Ag) based on spatially defined silver mirror reaction using a photolithographically micropatterned aldehyde (CHO)-terminated self-assembled monolayer (SAM) is proposed. First, both a Si substrate covered with native oxide and a quartz glass plate were exposed to a vapor of triethoxysilylundecanal (TESUD) diluted with absolute toluene for 3 h at 403 K. This vapor phase treatment produced a 1.2-nm-thick TESUD-SAM with a flat, homogeneous surface. Several samples were then photolithographically micropatterned using an excimer lamp radiating 172 nm vacuum ultraviolet light, and subsequently employed as templates for area-selective electroless Ag plating. Optical microscopy, atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) confirmed that Ag metal was preferentially deposited on the CHO-terminated regions, resulting in the formation of well-ordered Ag microstructures composed of rectangular 5 μm × 25 μm features. The CHO terminal groups of the TESUD-SAM were found to be effective in reducing Ag ionic species at the solid/liquid interface.     

Current flow through different phases of dodecanethiol self-assembled monolayer

A self-assembled monolayer of dodecanethiol grown on Au(1 1 1) substrate has been annealed to form different structural phases: a higher density phase, a lower density stripe phase, and a disordered mixed phase. The electrical properties of each phases have been studied by using scanning tunneling spectroscopy. The current-voltage curves measured on the disordered phase were less reproducible than those measured on the two well-ordered phases. Molecular resolution STM image obtained on the stripe phase shows that the structural instability of the alkyl chain of the stripe phase affect the current flow through the molecule. Our study shows that the ordering and structural stability of the molecules are very important in stable measurement of the electrical properties of the molecular films.     

Fine-structure fluorescence of conjugated chain molecules

The fine-structure fluorescence spectra of conjugated chain compounds—distyrylbenzene (DSB), its fluorine-substituted derivative (FDSB), 1,4-bis-(5-phenyl-2-oxazolyl) benzene (POPOP), and 1,4-bis-(5-phenyl-2-oxadiazolyl) benzene (PDPDP)—are obtained at 4.2 K using the Shpolskii method. The multiplicity of the spectra is revealed and their vibrational analysis is performed involving Raman scattering data. It is shown that some vibrational frequencies of the fluorescence spectra are common for all the molecules under study, while other frequencies are specific for the spectra of the pairs DSB-FDSB and POPOP-PDPDP. The relation between the spectra of the molecules and their structure is considered.     

Effects of a self-assembled monolayer on the sliding friction and adhesion of an Au surface

The friction and adhesion mechanisms with and without a self-assembled monolayer (SAM) in nanotribology were studied using molecular dynamics (MD) simulation. The MD model consisted of two gold planes with and without n-hexadecanethiol SAM chemisorbed to the substrate, respectively. The molecular trajectories, tilt angles, normal forces, and frictional forces of the SAM and gold molecules were evaluated during the frictional and relaxation processes for various parameters, including the number of CH₂ molecules, the interference magnitude, and whether or not the SAM lubricant was used. The various parameters are discussed with regard to frictional and adhesion forces, mechanisms, and molecular or atomic structural transitions. The stick–slip behavior of SAM chains can be completely attributed to the van der Waals forces of the chain/chain interaction. When the number of CH₂ molecules was increased, the SAM chains appeared to have bigger tilt angles at deformation. The magnitude of the strain energy that was saved and relaxed is proportional to the elastic deformable extent of the SAM molecules. The frictional force was higher for long chain molecules. With shorter SAM molecules, the adhesion force behavior was more stable during the compression and relaxation processes. A surface coated with a SAM can increase nano-device lifetimes by avoiding interface effects like friction and adhesion. PACS 52.65.Yy; 81.40.Pq; 81.16; 68.35.-p     

Preparation and medical application of magnetic beads conjugated with bioactive molecules

Ferrite nanobeads were synthesized from an aqueous solution utilizing Fe²⁺ to Fe³⁺ oxidation for use as magnetic carriers in bioscreening, bio-molecular recognition and anti-cancer diagnosis and therapy. The beads had a crystal structure that was intermediate between Fe₃O₄ and γ-Fe₂O₃. Functional biomolecules were strongly conjugated onto the surfaces of the ferrite beads via COOH and SH groups. The addition of ferrite seed crystals (3-8 nm in size) together with a disaccharide enabled the synthesis of monodisperse, spherical ferrite beads with average diameters (d¯) between 50 and 150 nm and relative deviation Δd/d¯=9-16%. Hollow ferrite nano-spheres (d¯=150-450 nm, Δd/d¯≈10%) were prepared using silica spheres as templates, which were dissolved in NaOH solution. Ferrite beads 40 nm in size were encapsulated in polymer spheres of styrene and polymerized glycidyl methacrylate (poly-GMA), 184±9 nm in diameter. They were used for high throughput bioscreening system for affinity purification of target proteins which make specific bindings to anti-cancer drugs, porphyrins, environment hormones, etc.     

Conformational dynamics of photoexcited conjugated molecules

Time-dependent photoexcitation and optical spectroscopy of pi-conjugated molecules is described using a new method for the simulation of excited state molecular dynamics in extended molecular systems with sizes up to hundreds of atoms. Applications are made to poly(p-phenylene vinylene) oligomers. Our analysis shows self-trapping of excitations on about six repeat units in the course of photoexcitation relaxation, identifies specific slow (torsion) and fast (bond-stretch) nuclear motions strongly coupled to the electronic degrees of freedom, and predicts spectroscopic signatures of molecular conformations.     

Cold atoms and molecules in self-assembled dipolar lattices

We study the realization of lattice models, where cold atoms and molecules move as extra particles in a dipolar crystal of trapped polar molecules. The crystal is a self-assembled floating mesoscopic lattice structure with quantum dynamics given by phonons. We show that within an experimentally accessible parameter regime extended Hubbard models with tunable long-range phonon-mediated interactions describe the effective dynamics of dressed particles.     

Chemical and physical interactions at metal/self-assembled organic monolayer interfaces

The purpose of research on metals (M) deposited onto self-assembled monolayers (SAMs) is to understand the interactions between metal (M) and eventually metal oxide overlayers on well-ordered organic substrates. Application of M/SAM and inorganic/SAM research results to the understanding of real inorganic/ organic interfaces in vacuum and under environmental conditions can potentially play a key role in the development of advanced devices with stable interfacial properties. The M/SAM approach to interface research is delineated as a new subfield in surface science in the context of other approaches to inorganic/organic interface research. Current issues in M/SAM research are outlined, including chemical compound formation, the morphology (spreading, clustering, or penetration) of the metal species, the kinetics of the metal morphology, the effect of the metal on the degree of order in the SAM, and the rate of metal penetration into the SAM. Probes are recommended that are suitable for M/SAM research. The results of M/SAM studies to date are reviewed, and M/SAM combinations are ranked according to reactivity and penetration. Key probes for addressing gaps in the research results are identified. The effects of defects, disordering, air exposure, and X-ray and electron beam exposure on the experimental results to date are evaluated. Thus far, the results have successfully revealed qualitative relationships of M/SAM chemistry, temperature, and penetration. The chemical interactions that have been found are applicable to real M/polymer interfaces as formed in vacuum. It has yet to be shown that M/SAM research will yield quantitative understanding of interface formation or that M/SAM interfaces are entirely analogous to M/polymer interfaces in the details of interface formation. The future of this subfield of surface science lies in its expansion from M/SAM interfaces in vacuum to other inorganic/SAM interfaces in vacuum and, eventually, under environmental conditions.     

Plasma modification of self-assembled structures of CoTMPP molecules

Plasma-treated cobalt metalloporphyrins have recently been proposed as electrocatalysts for the oxygen and oxygen peroxide reduction reaction. Whereas the effects of plasma treatment on the elemental composition of the surface of catalysts have been investigated, the effects of plasma treatment on the morphology of catalysts have not yet been studied. In this study, plasma modified nanosized structures of cobalt tetramethoxyphenylporphyrin (CoTMPP) molecules arising from the deposition of a porphyrin solution on an a-C:H film are investigated using an atomic force microscope (AFM). Additionally, the effects of plasma treatment on the structure of porphyrin molecules are studied by using ultra violet visible (UV-vis) absorption analysis. The investigations reveal the morphological changes which accompany the transformation of CoTMPP into the final catalytic material. First, the large CoTMPP aggregates are split into smaller ones. Second, the CoTMPP layer appears to be sublimated after plasma treatment. Sublimated CoTMPP molecules can be decomposed by plasma and after redeposition can form catalytic active fragments.     

Third-order optical polarizability of conjugated organic molecules

We present a theoretical investigation of the π-electron contribution to linear and non-linear polarizabilities of conjugated chains. Using simple models the respective influence of chain length and bond alternation on optical non-linearities are analyzed. The results are applied to symmetrical cyanines and polyenes.     

On the magnetic properties of conjugated molecules

Recent criticisms of the gauge factors usually employed in the ‘test-dipole’ method for the calculation of ‘ring current’ chemical shifts in conjugated molecules, are discussed. It is shown that, in a simple semi-empirical scheme of the London-McWeeny type, insertion of a dipole contribution into the vector potential appearing in the gauge factor, whilst having no effect on the calculated ‘ring current’ intensities, is algebraically analogous (and, at large distances from ring centres, numerically equivalent) to estimating the secondary field at the origin due to a set of classical line currents, as discussed originally by Salem; these ‘line currents’ are of the same magnitude as the quantum-mechanical ‘bond currents’ implicit in the ‘ring currents’ calculated using the simpler gauge factors originally due to London, but their contributions to the secondary magnetic field experienced by the peripheral protons, are estimated classically. Extensive numerical comparison is made between experimentally-observed proton chemical shifts in some conjugated hydrocarbons, and secondary fields estimated by this semi-classical formalism, and its predictions are found to correlate as well with experiment as do those of the original McWeeny approach. It is concluded that any further illegitimacy involved in the procedure of inserting a dipole contribution into the gauge factor, is evidently quite simply compensated for, numerically, by an appropriate empirical parametrization. Such empirical parametrizations are also thought to absorb errors due to all the other various approximations of the ‘ring current’ theories (with apparently unwarranted efficiency), and they should, therefore, be treated with more scepticism than has previously been thought necessary.     

Quantum fluids of self-assembled chains of polar molecules

We study polar molecules in a stack of strongly confined pancake traps. When dipole moments point perpendicular to the planes of the traps and are sufficiently strong, the system is stable against collapse but attractive interaction between molecules in different layers leads to the formation of dipolar chains, analogously to the chaining phenomenon in classical rheological electro- and magnetofluids. We analyze properties of the resulting quantum liquid of dipolar chains and show that only the longest chains undergo Bose-Einstein condensation with a strongly reduced condensation temperature. We discuss several experimental methods for studying chains of polar molecules.