Direct observation of long chain alkane bilayer films on graphite by scanning tunneling microscopy (original) (raw)
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Scanning tunneling microscopy imaging of alkane bilayers adsorbed on graphite: mechanism of contrast
Surface Science, 1993
Thin films of insulating molecules (n-f36H74) absorbed on graphite have been studied using scanning tunneling microscopy (STM). By imaging the boundary of second layer islands in various conditions, we demonstrate that the contrast observed in STM images of these films is dominated by elastic deformations of substrate. The relief in these images may strongly differs from the real topography of the film.
Scanning tunneling microscopy images of alkane derivatives on graphite: role of electronic effects
2008
Scanning tunneling microscopy (STM) images of self-assembled monolayers of close-packed alkane chains on highly oriented pyrolitic graphite often display an alternating bright and dark spot pattern. Classical simulations suggest that a tilt of the alkane backbone is unstable and, therefore, unlikely to account for the contrast variation. First principles calculations based on density functional theory show that an electronic effect can explain the observed alternation. Furthermore, the asymmetric spot pattern associated with the minimum energy alignment is modulated depending on the registry of the alkane adsorbate relative to the graphite surface, explaining the characteristic moiré pattern that is often observed in STM images with close packed alkyl assemblies.
Incommensurate Crystalline phase of n -Alkane Monolayers on Graphite (0001)
The Journal of Physical Chemistry C, 2011
An incommensurate crystalline phase of the (sub)monolayer of n-C 36 H 74 lying on graphite (0001) is observed on cooling the smectic phase using normal incidence near edge X-ray absorption fine structure spectroscopy at the carbon K-edge (NI C K-NEXAFS) and scanning tunneling microscopy (STM). The orientation of the CCC plane of the all-trans alkyl chain with respect to the substrate is confirmed by the 1s f σ CH */R resonance detected by the NI C K-NEXAFS spectra at the absorption edge. Almost all molecules take the parallel (flat-on) orientation in the smectic phase, and at least half of them change to the perpendicular (edge-on) orientation in the incommensurate crystalline phase. A lamellar structure with a width corresponding to the chain length and no internal structure is observed by STM in the smectic phase, whereas that in the incommensurate crystalline phase exhibits a ladder-like structure with a periodicity of ca. 2 nm transverse to the chain direction. The periodicity is incommensurate with the substrate lattice. The molecular orientation in the ladder-like structure is related to the molecular width varying from 0.43 to 0.63 nm in the magnified STM image.
Journal of the American Chemical Society, 2004
The morphology of monolayers formed upon adsorption of prochiral 1,5-substituted anthracene derivatives on highly oriented pyrolytic graphite is investigated using scanning tunneling microscopy at the liquid-solid interface. The adsorption orientation of these prochiral anthracene derivatives positions one of their enantiotopic faces in contact with the graphite. The molecules adsorb in rows with contact between adjacent anthracenes. The anthracene side chains extend perpendicular to the direction of the row repeat. All molecules within a single row adsorb via the same enantiotopic face. Anthracenes with side chains containing an even number of non-hydrogenic atoms (C, S) form monolayers in which molecules in adjacent rows adsorb via opposite enantiotopic faces. Anthracenes with side chains that contain an odd number of non-hydrogenic atoms form two-dimensional chiral domains in which all rows contain molecules adsorbed via the same enantiotopic face. This chain length effect on monolayer morphology represents a generalized example of structural effects previously observed in alkanoic acid monolayers formed on HOPG. The variation of the STM current with position in the vicinity of the anthracenes indicates that the highest occupied molecular orbital is the predominant mediator of tunneling for the aromatic group.
Self-assembly of long chain alkanes and their derivatives on graphite
The Journal of Chemical Physics, 2008
We combine scanning tunneling microscopy ͑STM͒ measurements with ab initio calculations to study the self-assembly of long chain alkanes and related alcohol and carboxylic acid molecules on graphite. For each system, we identify the optimum adsorption geometry and explain the energetic origin of the domain formation observed in the STM images. Our results for the hierarchy of adsorbate-adsorbate and adsorbate-substrate interactions provide a quantitative basis to understand the ordering of long chain alkanes in self-assembled monolayers and ways to modify it using alcohol and acid functional groups.
Materialwissenschaft und Werkstofftechnik, 2011
Highly ordered monolayer films of an n-alkane and arachidic acid were deposited on graphite surface from their solutions in n-tetradecane, and their molecular structure was investigated by scanning tunneling microscopy. Close-packed lamella-like structures with long range order were observed. In alkane monolayers, each lamella is composed by single molecules, while in the case of acid, lamellas consist of dimers formed by acid molecules due to interaction between their carboxylic groups, probably via hydrogen bonds. An increased brightness of carboxyl head in each fifth acid molecule was observed, which is attributed to nonequivalent positions of acid molecules with respect to the substrate carbon atoms.
The Journal of Physical Chemistry B, 2005
Self-assembled monolayers of chrysene and indene on graphite have been observed and characterized individually with scanning tunneling microscopy (STM) at 80 K under low-temperature, ultrahigh vacuum conditions. These molecules are small, polycyclic aromatic hydrocarbons (PAHs) containing no alkyl chains or functional groups that are known to promote two-dimensional self-assembly. Energy minimization and molecular dynamics simulations performed for small groups of the molecules physisorbed on graphite provide insight into the monolayer structure and forces that drive the self-assembly. The adsorption energy for a single chrysene molecule on a model graphite substrate is calculated to be 32 kcal/mol, while that for indene is 17 kcal/mol. Two distinct monolayer structures have been observed for chrysene, corresponding to highand low-density assemblies. High-resolution STM images taken of chrysene with different bias polarities reveal distinct nodal structure that is characteristic of the molecular electronic state(s) mediating the tunneling process. Density functional theory calculations are utilized in the assignment of the observed electronic states and possible tunneling mechanism. These results are discussed within the context of PAH and soot particle formation, because both chrysene and indene are known reaction products from the combustion of small hydrocarbons. They are also of fundamental interest in the fields of nanotechnology and molecular electronics.
The Journal of Physical Chemistry C, 2008
The structural properties of self-assembled monolayers of short 1-bromoalkanes and n-alkanes on graphite were investigated by a combination of ultrahigh vacuum scanning tunneling microscopy (UHV-STM) at 80 K and theoretical methods. STM images of 1-bromohexane reveal a lamellar packing structure in which the molecules form a 57°(3°lamella-molecular backbone angle and a head-to-head assembly of the bromine atoms (Müller, et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 5315). STM images of 1-bromoheptane also show a head-to-head 60°(3°lamella-molecular backbone pattern; however, the molecules pack in a herringbone structure. The odd/even chain-length alternation in the monolayer morphologies of 1-bromoalkanes is similar to that observed for the self-assembly of short n-alkanes on graphite, suggesting that the bromine atom acts effectively as an extension of the carbon backbone. The analogy, however, is incomplete. Odd and even short n-alkanes (hexane, heptane, octane) display 60°herringbone and rectangular (not 60°) lamellamolecular backbone configurations, respectively. The balance of intermolecular forces and packing considerations responsible for this odd/even alternation in monolayer morphology for short 1-bromoalkanes on graphite is examined here according to classical molecular dynamics simulations and in light of the structural properties of analogous n-alkane assemblies.
Theoretical Description of the STM Images of Alkanes and Substituted Alkanes Adsorbed on Graphite
The Journal of Physical Chemistry B, 1997
A theoretical model based on perturbation theory has been developed to predict the scanning tunneling microscopy (STM) images of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort and provides images that are in qualitative agreement with experimental results. The model predicts that topographic effects will dominate the STM images of alkanes on graphite surfaces. The computations correlate well with the STM data of functionalized alkanes and allow assessment of the structure and orientation of most of the functionalized alkanes that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals of the adsorbed molecules, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals, may play an important role in determining the STM image contrast of such systems.
Physical Chemistry Chemical Physics, 2002
A combination of neutron and X-ray diffraction has been used to structurally characterise the crystalline monolayer structures of all the alkanes with odd number of carbon atoms in their alkyl chains from pentane to pentadecane adsorbed on graphite. The structures of all the molecules investigated at submonolayer coverages are isomorphous with centred rectangular unit cells containing two molecules per cell in a parallel arrangement. This is a completely different structure from the ' herringbone ' arrangement of molecules found for the shorter ' even ' alkanes, such as hexane, octane and decane. The monolayers at sub-monolayer coverages are interpreted as uniaxial commensurate with the underlying graphite while those monolayers coexisting with the liquid, while structurally similar, are fully commensurate. The difference between the two structures is a uniaxial compression in the b-direction with the monolayers coexisting with the liquids significantly more dense than at submonolayer coverages. In the low coverage structures the ' odd ' molecules have an all trans conformation with their extended axes parallel to the surface with the plane of the carbon skeleton also parallel to the graphite surface. At high coverages the carbon skeleton is no longer parallel to the graphite surface but significantly tilted. The longest alkanes, tridecane and pentadecane also show evidence of positional and/or rotational disorder at high coverages.