Standing-up Molecules Research Articles

Structural transition in the single layer growth of diindenoperylene on silica.

When forming a film on a substrate, rod shaped organic molecules can order in lying-down or standing-up phases. We have studied the growth of diindenoperylene films on amorphous silicon dioxide by means of molecular dynamics simulations and analyzed the film structure. The vapor deposition process was emulated by depositing single molecules at a fixed rate on the substrate. At 400K, we observed a transition from disordered lying-down to standing-up molecules, which agrees well with experimental observations. This transition, which depends sensitively on the kinetic parameters, requires both a sufficiently high thermal energy to overcome the energy barrier and a sufficiently large cluster size. Our results indicate that a higher degree of initial disorder in the lying-down phase results in a larger probability for the system to undergo the transition to the standing-up phase.

Electrochemical, HR-XPS and SERS study of the self-assembly of biphenyl 4,4′-dithiol on Au(111) from solution phase

We report a comparative study of 4,4′-biphenyldithiol adlayers grown on Au(111) substrates in solution phase by different methods. Layers prepared by immersion in solutions of ethanol and n-hexane, with and without the use of a disulfide reducing agent (tris-carboxyethyl phosphine, TCEP), were characterized by electroreductive desorption, impedance spectroscopy, redox activity, high-resolution photoemission spectroscopy, and surface-enhanced Raman spectroscopy. It is shown that the simple immersion in an ethanolic solution leads to the formation of, at least, a bilayer with a high number of SS bonds. The use of n-hexane as solvent produces a drastic reduction of these undesired bonds, and a similar result is obtained if the substrates prepared in the ethanolic solution are then washed with TCEP. The best results were obtained when the reducing agent was added into the ethanol solution, in which case all the characterizations were coincident in the formation of a single layer of standing-up molecules free of SS bonds. The charge of the desorption peak and the relative intensity of the S2p and Au4f photoemission peaks both indicate a surface coverage θ≈0.2. In the case of multilayers formed by immersion in pure ethanolic solutions, the Raman experiments indicate that intralayer SS bonds are not formed, and hence that all the SS bonds are of the interlayer type.

Growth of 1,4-Benzenedimethanethiol Films on Au, Ag, and Cu: Effect of Surface Temperature on the Adsorption Kinetics and on the Single versus Multilayer Formation

We report a study of 1,4-benzenedimethanethiol (BDMT) adsorption on the (111) surface of the noble metals Au, Ag, and Cu performed from the vapor phase by ion scattering. The better known case of BDMT on the Au(111) surface is used for comparison. Ion scattering carried out in the forward direction to detect both scattering and recoiling atoms allowed us to delineate the two main different film configurations: with both S atoms attached to the surface and with S exposed at the vacuum interface. The experiments were carried out at room temperature (RT) and around 250 K. At RT we found that a monolayer of standing-up molecules can be formed on all of the surfaces at very high exposures, that is, approaching the Mega Langmuir for Au and Ag. Comparison with experiments of adsorption of S2 on the Au(111) bare surface allowed us to estimate that the S content at the BDMT–vacuum interface is ∼0.3 of a monolayer. The adsorption at lower temperatures has two main effects: it enhances the sticking coefficient and results in the formation of a multilayer at lower exposures. The discrimination of the mono- versus the multilayer film formation with the ion scattering technique is discussed. Once the multilayer is formed, the increase of the surface temperature to 270 K is sufficient to obtain a monolayer with spectral features that are similar to those obtained at RT with much higher exposures.

Adlayers of Alkanedithiols on Au(111): Effect of Disulfide Reducing Agent

High-resolution photoemission spectroscopy is used to characterize adlayers of ethane-, hexane-, and nonanedithiol molecules grown on Au(111) surfaces by the immersion method. The effect of using a reducing agent during and after the immersion to inhibit or eliminate S-S bonds is investigated. Our results demonstrate that immersion 24 h in millimolar dithiol ethanolic solutions gives rise to the formation of multilayers; this effect is more pronounced in the case of ethanedithiol, the shortest molecule. A post-treatment with a disulfide reducing agent is effective to produce monolayers of standing-up molecules; this effect is again more pronounced in the case of ethanedithiol. Finally, the immersion 24 h in a solution containing dithiol and the reducing agent gives an unexpected result: most molecules remain adsorbed in the lying-down configuration; in this case, the almost complete suppression of the standing-up phase occurs equally with the three types of molecules, which suggests that the formation of S-S bonds must be important for the lifting of the molecules.

Standing Up versus Looping Over: Controlling the Geometry of Self-Assembled Monolayers of α,ω-Diynes on Gold

It is shown that self-assembled monolayers (SAMs) composed of α,ω-diynes on gold have different structures depending on the concentration of molecules used to make the SAM. Evidence for both hairpinned and standing-up molecules is provided. This behavior is in contrast to SAMs of α,ω-dithiols on gold, which generally form SAMs with only the straight conformation. The looped SAMs composed of α,ω-diynes offer a less densely packed and thus somewhat accessible surface that may be useful when the underlying surface is used as an electrode. Furthermore, biasing the structure of the molecules in the SAM between looped and standing-up may be useful in the design of dynamic surfaces.

Formation of a 1,8-Octanedithiol Self-Assembled Monolayer on Au(111) Prepared in a Lyotropic Liquid-Crystalline Medium

A characterization of the 1,8-octanedithiol (ODT) self-assembled monolayer (SAM) formed from a Triton X-100 lyotropic medium has been conducted by electrochemical techniques. It is found that an ODT layer of standing-up molecules is obtained at short modification time without removing oxygen from the medium. The electrochemical study shows that the ODT layer formed after 15 min of modification time has similar electron-transfer blocking properties to the layers formed from organic solvents at much longer modification times. On the basis of XPS data, it is demonstrated that the inability to bind gold nanoparticles (AuNPs) is due to the presence of extra ODT molecules either interdigited or on top of the layer. Treatment consisting of an acid washing step following the formation of the ODT-Au(111) SAM produces a layer that is able to attach AuNPs as demonstrated by electrochemical techniques and atomic force microscopy (AFM) images.

The structure and phase diagram of chiral alkyl-serine monolayers on mercury

The structure of liquid-mercury-supported Langmuir films (LFs) of chiral serine-modified fatty acid molecules was studied as a function of length, n = 8–22 carbons, temperature, T = 5–25 °C, and surface coverage, A ≈ 40–200 A2 per molecule, for both homochiral and heterochiral compounds. Using surface pressure π-area A isotherms and surface-specific synchrotron X-ray diffraction methods the phase diagram was determined in detail. No lateral order was found for phases comprising surface-parallel molecules, in contrast with unmodified fatty acid LFs on mercury. For phases comprising standing-up molecules, long range lateral order was found for n ≥ 12, but no order for n = 8. The molecules in the ordered phases are extended, and tilt rigidly by ∼40° from the surface normal. The homochiral LFs pack in an oblique, single-molecule, unit cell. The heterochiral LFs pack in a body-centered rectangular unit cell, containing two molecules. Unlike unmodified fatty acid LFs, the structure of the standing-up phase does not vary with n, T or A. The interactions underlying these characteristics, and the role of chirality, are discussed.

Langmuir Films of Chiral Molecules on Mercury

Homo- and heterochiral Langmuir films of a chiral derivative of stearic acid are studied in situ on the surface of liquid mercury as a function of surface coverage by surface tensiometry and surface-specific synchrotron X-ray diffraction and reflectivity. A transition from a phase of surface-parallel molecules to a phase of standing-up molecules is found. The former shows no surface-parallel long-range order. The standing-up phase of both homochiral and heterochiral compositions exhibit long-range order. However, the former has an oblique unit cell with parallel molecular planes, and the later has a centered rectangular unit cell with a herringbone molecular packing. For both cases, the standing-up molecules are tilted by 44 degrees from the surface normal and pack at a density of 19.5 A(2)/molecule in the plane normal to the molecular long axis. Important differences are found, and discussed, between this behavior and that of a Langmuir film of the nonchiral stearic acid on mercury.

Alkyl-thiol Langmuir Films on the Surface of Liquid Mercury

The coverage dependent phase behavior of monolayers of alkyl thiols (CH3(CH2)(n-1)SH, denoted as CnSH) on mercury was studied for chain lengths 9 <or= n <or= 22, using surface tensiometry and surface-specific X-ray scattering methods. At low coverage, a disordered single layer of surface-parallel molecules is found for all n. At high coverage, a monolayer of standing-up molecules is formed, exhibiting well-ordered phases, the structure of which is n- and coverage-dependent. The molecular chains pack in a centered rectangular unit cell, with an approximately 27 degrees tilt from the surface normal toward nearest neighbors. The strong sulfur-mercury bond induces a noncentered unit cell for the headgroups, incorporating one mercury atom per two thiol molecules. The small but significant differences in structure of these films on gold and on mercury are discussed and assigned to the different structure of the subphase: long-range-ordered crystal for gold and short-range-ordered liquid for mercury.

Langmuir films of polycyclic molecules on mercury

Langmuir films (LFs) of biphenyl and anthracene derivatives on the surface of liquid mercury were studied by surface-specific X-ray and surface tension measurements. Phases of lying-down, side-lying and standing-up molecules were found, some of which exhibit long-range lateral order. The molecular symmetry and the position and nature of the side-, end-, and headgroups are shown to dominate the structural evolution of the LFs with surface coverage.

Structure of Mercaptobiphenyl Monolayers on Mercury

The molecular-scale structure and phase behavior of single-component Langmuir films of 4'-methyl-4-mercaptobiphenyl (MMB) and 4'-perfluoromethyl-4-mercaptobiphenyl (FMMB) on mercury were studied using surface tensiometry, grazing incidence X-ray diffraction, and X-ray reflectivity. At low coverages, a condensed but in-plane disordered single layer of surface-parallel molecules is found for both compounds. At high coverages, both compounds exhibit in-plane-ordered phases of standing-up molecules. For MMB, the biphenyl core dominates the structure, yielding a centered-rectangular unit cell with an area A(x) of 21.8 A(2)/molecule, with molecules tilted by approximately 14 degrees from the surface normal in the nearest-neighbor direction, and a coherence length xi of >1000 A for the crystalline domains. For FMMB, the perfluoromethyl group dominates the structure, yielding a hexagonal unit cell with untilted molecules, an area A(x) of 24.2 A(2)/molecule, and a much smaller xi of approximately 110 A. The structure is discussed in comparison with self-assembled monolayers of MMB on crystalline Au(111) and similar-length alkanethiolate SAMs on Au(111) and on mercury. The differences in the structure are discussed and traced to the differences in the substrate's surface structure, and in the molecular cross section and rigidity.

Structural and functional characterization of self-assembled monolayers of peptide nucleic acids and its interaction with complementary DNA

Self-assembled monolayers (SAMs) of single-stranded peptide nucleic acid (ssPNA) molecules on gold surfaces, with efficient capability for recognizing complementary ssDNA. In spite of their remarkably long length of 6–7 nm, ssPNA molecules can assemble standing-up on the surface similarly to the SAMs of short alkanethiols. The equilibrium between lying and standing-up molecules on the surface is a function of the molecular coverage. These structural and functional studies have been performed by means of powerful label-free techniques for surface characterization such as synchrotron radiation-based X-ray photoemission spectroscopy and atomic force microscopy.

Spectrum of the interaction potential between He and as-deposited self-assembled monolayers of decanethiol chemisorbed on Au(111)

Abstract In this article, full monolayers of standing-up molecules of decanethiol chemisorbed on Au(1 1 1) have been grown at 275 K in ultrahigh vacuum and studied by low energy He atom scattering in the temperature range between 40 and 60 K. The specular peak intensity has been measured on the as-deposited layer and features associated to resonances with bound states of the He atom interacting with the CH3 groups of the organic molecules have been observed. Through the analysis of the angular position of these features four bound state levels have been determined. The comparison between the levels determined for the as-deposited monolayer and those determined for the annealed one shows that the spectra are sensitive to the annealing process.

Structure of a Langmuir film on a liquid metal surface.

The structure of organic monolayers on liquid surfaces depends sensitively on the details of the molecular interactions. The structure of a stearic acid film on a mercury surface was measured as a function of coverage with angstrom resolution. Unlike monolayers on water, the molecules were found here to undergo a transition from surface-parallel to surface-normal orientation with increasing coverage. At high coverage, two condensed hexatic phases of standing-up molecules were found. At low coverage, a two-dimensional (2D) gas phase and condensed single- and double-layered phases of flat-lying molecular dimers were revealed, exhibiting a 1D longitudinal positional order. This system should provide a broader tunability range for nanostructure construction than solid-supported self-assembled monolayers.

The structure of organic langmuir films on liquid metal surfaces

Langmuir films (LFs) on water have long been studied for their interest for basic science and their numerous applications in chemistry, physics, materials science and biology. We present here Å-resolution synchrotron X-ray studies of the structure of stearic acid LFs on a liquid mercury surface. At low coverage, ⩾110 Å 2/mol, a 2D gas phase of flat-lying molecules is observed. At high coverage, ⩽23 Å 2/mol, two different hexatic phases of standing-up molecules are observed. At intermediate coverage, 52⩽ A⩽110 Å 2/mol, novel single- and double-layered phases of flat-lying molecular dimers are found, exhibiting a 1D in-layer order. Such flat-lying phases were not hitherto observed in any LF. Measurements on LFs of fatty acids of other chain lengths indicate that this structure is generic to chain molecules on mercury, although the existence of some of the flat-lying phases, and the observed phase sequence, depend on the chain length. Organic LFs on Hg, and in particular the new flat-lying phases, should provide a broader nano-structural tunability range for molecular electronic device construction than most solid-supported self-assembled monolayers used at present.