Diffusion mechanisms of short-chain alkanes on metal substrates: Unique molecular features

Novel Diffusion Mechanism of Polymers Pinned to an Attractive Impurity

Actual substrates unavoidably possess, to some extent, defects and dirt, which motivate understanding the impact due to their presence. The presence of a substrate naturally breaks symmetries. Additionally, it effectively reduces spatial dimensionality, which favors fluctuation-dominated behavior, but it also provides a multitude of possible interactions. We show evidence of novel behavior in the case of polymer mass transport at a crystalline substrate when a single attractive impurity is present. Specifically, we introduce a model system describing how an attractive impurity pins adsorbed polymers on a substrate. We propose a novel mechanism to explain the size scaling dependence of the diffusion coefficient as D∼N−3/2 for polymers with N monomers. Additionally, the size dependence of the diffusion coefficient scales can be described as D∼N−δ, with δ=1.51 as determined from extensive simulations.

Quantifying entropic barriers in single-molecule surface diffusion

The quantitative role of entropy in the surface diffusion of molecules with many degrees of freedom is still not well understood. Here, we quantify entropic diffusion barriers as well as attempt frequencies by performing a systematic decomposition of the Arrhenius equation for single oligophenyl molecules of various lengths (two to six phenyl rings and benzene as the reference) on an amorphous silica surface using extensive molecular dynamics simulations. Attempt frequencies evaluated from velocity auto-correlation functions are found close to k_BT/h, the frequency factor of transition state theory. Importantly, we find large positive entropy contributions to the free energy barrier of diffusion up to 55%, increasing with molecular length with 4.1 kJ/mol/phenyl ring. The entropic barrier is about 40%-60% of the entropy of the molecule surface adsorption free energy, revealing that at the transition states, the molecules can liberate a major part of their conformational states, increasing with length. The substantial role of the internal degrees of freedom for the diffusive dynamics is explicitly demonstrated by studying internally constrained, "rigid" version of the molecules. Finally, we discuss also rotational diffusion and the role of surface vibrations. Our results affirm that it is essential for quantitative studies and interpretation of surface diffusion of complex molecules to consider internal entropic effects.

Understanding n-Octane Behavior near Graphene with Scaled Solvent-Solute Attractions

We employ molecular dynamics simulations of n-octane near a layered graphene surface to study the related phenomena of solvation, density fluctuations, wettability, and structure and dynamics of n-octane molecules in the inhomogeneous interfacial environment. That solvation in bulk n-octane displays a lengthscale-dependent crossover similar to that of hydrophobic solvation in water is known. Here we show that, near an extended graphene interface having attractive interactions with n-octane, lengthscale-dependent solvation is similar to that in the bulk and displays a small to large crossover. However, as the n-octane-graphene interactions are reduced to make the surface increasingly solvophobic, the crossover behavior is modulated and essentially absent near the most solvophobic surfaces, similar to that in water near hydrophobic interfaces. We show that the macroscopic measure of wettability, namely, the contact angle, characterizes n-octane-graphene coupling over a limited range of attractions. In contrast, molecular measures such as the free energy of cavity formation or the local compressibility in the interfacial region provide an effective measure of this coupling over a broader range of attractions. Finally, as n-octane-graphene attractions are increased, the n-octane liquid displays a wetting transition and corresponding change from sigmoidal to layered density profile. Analysis of the local structure shows that n-octane molecules prefer approximately linear conformations and surface-parallel orientations near the graphene surface, and their translational dynamics slow down with increasing n-octane-graphene attractions. Our study highlights molecular scale behavior of n-octane molecules that is relevant to understanding nanoparticle-solvent coupling in composite materials with enhanced mechanical or thermal properties.

Molecular shape and the energetics of chemisorption: from simple to complex energy landscapes

We enumerate all local minima of the energy landscape for model rigid adsorbates characterized by three or four equivalent binding sites (e.g., thiol groups) on a close-packed (111) surface of a face-centered-cubic crystal. We show that the number of energy minima increases linearly with molecular size with a rate of increase that depends on the degree of registry between the molecule shape and the surface structure. The sparseness of energy minima and the large variations in the center-of-mass positions of these minima vs molecular size for molecules that are incommensurate with the surface suggests a strong coupling in these molecules between surface mobility and shape or size fluctuations resulting from molecular vibrations. We also find that the variation in the binding energy with respect to molecular size decreases more rapidly with molecular size for molecules with a higher degree of registry with the surface. This indicates that surface adsorption should be better able to distinguish molecules by size if the molecules are incommensurate with the surface.

Dimerization boosts one-dimensional mobility of conformationally adapted porphyrins on a hexagonal surface atomic lattice

We employed temperature-controlled fast-scanning tunneling microscopy to monitor the diffusion of tetrapyridylporphyrin molecules on the Cu(111) surface. The data reveal unidirectional thermal migration of conformationally adapted monomers in the 300-360 K temperature range. Surprisingly equally oriented molecules spontaneously form dimers that feature a drastically increased one-dimensional diffusivity. The analysis of the bonding and mobility characteristics indicates that this boost is driven by a collective transport mechanism of a metallosupramolecular complex.

High resolution radially symmetric nanostructures from simultaneous electron beam induced etching and deposition

Electron beam induced etching (EBIE) and deposition (EBID) are promising fabrication techniques in which an electron beam is used to dissociate surface-adsorbed precursor molecules to achieve etching or deposition. Spatial resolution is normally limited by the electron flux distribution at the substrate surface. Here we present simultaneous EBIE and EBID (EBIED) as a method for surpassing this resolution limit by using adsorbate depletion to induce etching and deposition in adjacent regions within the electron flux profile. Our simulation results indicate the possibility of growth control of radially symmetric nanostructures at the sub-1 nm length scale on bulk substrates. The technique is well suited to the fabrication of ring-shaped nanostructures such as those employed in plasmonics, sensing devices, magneto-optics and magnetoelectronics.

Molecular architectonic on metal surfaces

The engineering of highly organized systems from instructed molecular building blocks opens up new vistas for the control of matter and the exploration of nanodevice concepts. Recent investigations demonstrate that well-defined surfaces provide versatile platforms for steering and monitoring the assembly of molecular nanoarchitectures in exquisite detail. This review delineates the principles of noncovalent synthesis on metal substrates under ultrahigh vacuum conditions and briefly assesses the pertaining terminology-self-assembly, self-organization, and self-organized growth. It presents exemplary scanning-tunneling-microscopy observations, providing atomistic insight into the self-assembly of organic clusters, chains, and superlattices, and the metal-directed assembly of low-dimensional coordination architectures. This review also describes hierarchic-assembly protocols leading to intricate multilevel order. Molecular architectonic on metal surfaces represents a versatile rationale to realize structurally complex nanosystems with specific shape, composition, and functional properties, which bear promise for technological applications.

Anisotropic diffusion of n-butane and n-decane on a stepped metal surface

The diffusion of single n-butane and n-decane molecules on a model stepped surface, Pt655, and on a corresponding flat surface, Pt111, is investigated using molecular-dynamics simulations and anisotropic united atom model. The surface step on Pt655 causes the alkane molecules to adsorb on the lower terrace in all-trans conformations with their long molecular axes adjacent and parallel to the step edge, and to diffuse anisotropically along the surface step via a constant wiggly motion without rotation or marked deviation from the parallel adsorption configuration. At relatively high temperatures, the alkane molecules can temporarily break away from the step edge but cannot migrate across the step edge in either the downstair or upstair direction. In comparison with the diffusion on Pt111, the diffusivity of n-decane is reduced by the surface step but its diffusion barrier is hardly affected. In the case of the shorter n-butane, however, the surface step significantly reduces the diffusion energy barrier and gives rise to higher diffusion coefficients at lower temperatures. Important implications of the simulation results are discussed.

n-alkanes on MgO(100). II. Chain length dependence of kinetic desorption parameters for small n-alkanes

Coverage-dependent desorption-kinetics parameters are obtained from high-quality temperature-programmed desorption data for seven small n-alkane molecules on MgO(100). The molecules, CNH2N+2 (N=1-4,6,8,10), were each studied for a set of 29 initial coverages at a heating ramp rate of 0.6 K/s as well as at a set of nine ramp rates in the range of 0.3-10.0 K/s. The inversion analysis method with its least-squares preexponential factor (prefactor) optimization discussed in the accompanying article is applied to these data. This method allows for accurate determination of prefactors and coverage-dependent desorption energies. The prefactor for desorption increases dramatically with chain length from 10(13.1) to 10(19.1) s(-1) over the range of N=1-10. We show that this increase can be physically justified by considering the increase in rotational entropy available to the molecules in the gaslike transition state for desorption. The desorption energy increases with chain length as Ed(N)=6.5+7.1N, which implies an incremental increase of 7.1+/-0.2 kJ/mol per CH2.

Adsorption and Reactions of C6 Hydrocarbons at High Pressures on Pt(111) Single-Crystal Surfaces Studied by Sum Frequency Generation Vibrational Spectroscopy: Mechanisms of Isomerization and Dehydrocyclization of n-Hexane

The adsorption geometries and surface reactions of various C(6) hydrocarbons (n-hexane, 2-methylpentane, 3-methylpentane, and 1-hexene) adsorbed on Pt(111) were investigated using sum frequency generation (SFG) surface vibrational spectroscopy. The adsorptions and reactions were carried out in 1.5 Torr of C(6) hydrocarbons in the absence and presence of excess hydrogen (15 Torr) and in the temperature range 296-453 K. At 296 K and in the presence of excess hydrogen, n-hexane and 3-methylpentane adsorbed molecularly on Pt(111) mostly in "flat-lying" geometries. Upon heating the sample up to 453 K, the molecules underwent dehydrogenation to form new surface species in "standing-up" geometries, such as hexylidyne and metallacyclic species. However, 2-methylpentane and 1-hexene were dehydrogenated to metallacyclobutane and hexylidyne, respectively, at 296 K in the presence of excess hydrogen. The dehydrogenated species remained unreacted on the surface upon heating the sample up to 453 K. The absence of excess hydrogen enhanced dehydrogenation of n-hexane and 3-methylpentane to form pi-allyl c-C(6)H(9) and metallacyclohexane, respectively, at 296 K. Upon heating to 453 K, the pi-allyl c-C(6)H(9) species underwent irreversible dehydrogenation, while hexylidyne and metallacyclic species remained unreacted. On the basis of these results, the mechanisms for catalytic isomerization and dehydrocyclization of n-hexane, which are the important "reforming" reactions to produce high-octane fuels over platinum, were discussed.

Spectroscopy of the conformational disorder in molecular films: Tetracosane and squalane on Pt(111)

The spectroscopic investigation of the molecular vibrations of adsorbed branched and unbranched alkane molecules using helium atom scattering (HAS) provides evidence for the thermal formation of gauche defects in tetracosane (C24H50) monolayers above 200 K. HAS results for the vibration of tetracosane molecules perpendicular to the Pt(111) surface reveal a strong frequency decrease and peak broadening above the transition temperature which can be related to a reduction of the force holding the molecules to the surface. This reduction of the force is interpreted as being due to the thermal formation of gauche defects within the tetracosane molecules.

Thermal desorption of large molecules from solid surfaces

We use molecular-dynamics simulations and importance sampling to obtain transition-state-theory rate constants for thermal desorption of an n-alkane series from Au(111). We find that the binding of a large molecule to a solid surface involves different types of local minima. The preexponential factors increase with increasing chain length and can be substantially larger than typical estimates for small molecules. Our results match recent experimental studies and indicate that a proper treatment of conformational isomerism and entropy, heretofore not found in coarse-grained models, is essential to quantitatively describe the thermal desorption of large molecules from solid surfaces.

Long jumps in the surface diffusion of large molecules

We have studied the diffusion of the two organic molecules DC and HtBDC on the Cu(110) surface by scanning tunneling microscopy. Surprisingly, we find that long jumps, spanning multiple lattice spacings, play a dominating role in the diffusion of these molecules--the root-mean-square jump lengths are as large as 3.9 and 6.8 lattice spacings, respectively. The presence of long jumps is revealed by a new and simple method of analysis, which is tested by kinetic Monte Carlo simulations.

Molecule length-induced reentrant self-organization of alkanes in monolayers adsorbed on Au(111)

We report the observation by scanning tunneling microscopy of the reentrant self-organization of n-alkanes (C(n)H(2n+2)) in monolayers adsorbed on Au(111) induced by a variation of the chain length. In the investigated range of lengths ( 10</=n</=38 with even n values), the presence of self-assembled monolayers which consist of a close-packed arrangement of molecules lying flat on the surface is evidenced except for alkanes with 18</=n</=26. The unexpected transition between ordered and disordered phases is related to the mismatch between Au(111) lattice and the CH2-group period along the chain.

Monte Carlo simulation of diffusion of adsorbed proteins

We present the results of three-dimensional lattice Monte Carlo simulations of protein diffusion on the liquid-solid interface in a wide temperature range including the most interesting temperatures (from slightly below T(f) and up to T(c), where T(f) and T(c) are the folding and collapse temperatures). For the model under consideration (27 monomers of two types), the temperature dependence of the diffusion coefficient is found to obey the Arrhenius law with the normal value (approximately 10(-2)-10(-3) cm(2)/s) of the preexponential factor. Proteins 2000;39:76-81.