Vibrations of a single adsorbed organic molecule: anharmonicity matters!

Vibrational spectroscopy is a powerful tool to identify molecules and to characterise their chemical state. Inelastic electron tunnelling spectroscopy (IETS) combined with scanning tunnelling microscopy (STM) allows the application of vibrational analysis to a single molecule. Up to now, IETS was restricted to small species due to the complexity of vibration spectra for larger molecules. We extend the horizon of IETS for both experiment and theory by measuring the STM-IETS spectra of mercaptopyridine adsorbed on the (111) surface of gold and comparing it to theoretical spectra. Such complex spectra with more than 20 lines can be reliably determined and computed leading to completely new insights. Experimentally, the vibrational spectra exhibit a dependence on the specific adsorption site of the molecules. Theoretically, this dependence is only accessible if anharmonic contributions to the interaction potentials are included. These joint experimental and theoretical advances open new perspectives for structure determination of organic adlayers.     

Optical second-harmonic generation from a monolayer of centrosymmetric molecules adsorbed on silver

An increase in the optical second-harmonic signal arising from an electrochemically treated silver surface upon adsorption of a monolayer of the centrosymmetric molecule pyrazine is reported and an effective second-order non-linear polariz-ability for the adsorbed species deduced. These investigations illustrate the potential of second-harmonic generation in the elucidation of interfaces.     

Electronic and molecular properties of an adsorbed protein monolayer probed by two-color sum-frequency generation spectroscopy

Two-color sum-frequency generation spectroscopy (2C-SFG) is used to probe the molecular and electronic properties of an adsorbed layer of the green fluorescent protein mutant 2 (GFPmut2) on a platinum (111) substrate. First, the spectroscopic measurements, performed under different polarization combinations, and atomic force microscopy (AFM) show that the GFPmut2 proteins form a fairly ordered monolayer on the platinum surface. Next, the nonlinear spectroscopic data provide evidence of particular coupling phenomena between the GFPmut2 vibrational and electronic properties. This is revealed by the occurrence of two doubly resonant sum-frequency generation processes for molecules having both their Raman and infrared transition moments in a direction perpendicular to the sample plane. Finally, our 2C-SFG analysis reveals two electronic transitions corresponding to the absorption and fluorescence energy levels which are related to two different GFPmut2 conformations: the B (anionic) and I forms, respectively. Their observation and wavelength positions attest the keeping of the GFPmut2 electronic properties upon adsorption on the metallic surface.     

Steered molecular dynamics simulation of elastic behavior of adsorbed single polyethylene chains

We investigate the dynamics of the detachment of single polyethylene (PE) chains from a strongly adsorbing surface in vacuum using a united atom model. Various statistical properties, including the mean‐square end‐to‐end distance 〈R²〉, the mean‐square radii of gyration , , the shape factor , the torsion angle distribution, the average surface adsorption energy , the average total energy , and the average force , are analyzed. The relationship between the average force and the pulling velocity v shows two distinctive regions: a weakly dependence region at Å/ps and a strongly dependence region at Å/ps. Remarkably, the PE chain manifests force hysteresis under sequential stretching and releasing. These investigations may provide some insights into the elastic behavior of adsorbed polymer chains. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2322–2332, 2007     

Electrostatic energy of vacancy formation in crystals of polar molecules

An exact expression is derived for the electrostatic energy of a crystal of polar polarizable molecules containing an unrelaxed vacancy. The energy exceeds twice the electrostatic binding energy per molecule L by a polarization energy term, when changes in dielectric response due to the vacancy are ignored. The electrostatic energy of a molecule at a crystal surface is estimated from surface and bulk polarization energy measurements. It can be as high as 1.5 L. making the electrostatic energy of vacancy formation significantly less than L. the value for non-polarizable molecules. This may help to explain anomalous results for certain plastic crystals.     

Commensurate-incommensurate transition of 4He adsorbed on a single C60 molecule

Path-integral Monte Carlo calculations have been performed to study (4)He adsorption on a single C(60) molecule. Helium corrugations on the fullerene molecular surface are incorporated with the (4)He-C(60) interaction described by the sum of all (4)He-C interatomic pair potentials. Radial density distributions show a layer-by-layer growth of (4)He with the first adlayer being located at a distance of ~6.3 ? from the center of the C(60) molecule. The monolayer shows different quantum states as the number of (4)He adatoms N varies. For N = 32, we find a commensurate solid, with each of the 32 adsorption sites on the molecular surface being occupied by a single (4)He atom. Various domain-wall structures are observed as more (4)He atoms are added and the first layer crystallizes into an incommensurate solid when it is completely filled. This commensurate-incommensurate transition of the helium monolayer is found to be accompanied by re-entrant superfluid response at a low temperature of 0.31 K with the superfluidity being totally quenched at N = 32, 44, and 48. Finally, the different quantum states observed in the helium monolayer around C(60) are compared with phase diagrams proposed for the corresponding layer on a graphite surface.     

Two-dimensional supercritical behavior of an ethanol monolayer: a molecular dynamics study

The two-dimensional (2D) supercritical behavior of an ethanol monolayer formed at the vapor/liquid interface of an ethanol solution has been investigated by a molecular dynamics (MD) calculations with a combination of the OPLS-UA and SPC/E potential models. A 100 A thick slab of ethanol solution was placed at the volume center of the rectangular unit cell by 10 A thick nonabsorbate water surfaces. With such an initial configuration, five independent 15 ns NVT constant MD calculations were carried out under 298.15 K, in which the initial ethanol mole fraction of the bulk solution layer was set to 0.010, 0.022, 0.045, 0.10, and 0.20, respectively. The 2D radial distribution function (rdf) of an adsorbed ethanol molecule showed that the ethanol monolayer could be regarded as a 2D fluid where the adsorbed ethanol molecule had an effective 2D diameter of 4.65 A. On the basis of the 2D rdf result, 2D cluster analysis was carried out from the perspective of the percolation theory. It is confirmed that the critical area occupation probability density, the critical exponents, and the fractal dimension of both nonpercolating and percolating clusters satisfied their nature of universality. Therefore, we concluded that an ethanol monolayer formed at the vapor/liquid interface of ethanol solution behaves as a 2D supercritical fluid at 298.15 K.     

Bile salt structural effect on the thermodynamic properties of a catanionic mixed adsorbed monolayer

The interfacial effects of two bile salts (sodium deoxycholate (NaDC) and sodium dehydrocholate (NaDHC)) in a catanionic mixed adsorbed monolayer have been investigated at 25 °C. The surfactant interfacial composition, the interfacial orientation of the molecules and the energy changes are analysed to show a thermodynamic evidence of the hydrophobic BSs effect during its intercalation into interfacial adsorbed didodecyldimethyl ammonium bromide (DDAB) molecules. Both mixed systems (NaDC–DDAB and NaDHC–DDAB) have analogous adsorption efficiencies, which are similar from a pure DDAB monolayer and superior to that obtained for both bile salts molecules. Nevertheless, their adsorption effectiveness is different: NaDC causes an increment of Γ while NaDHC produces the opposite effect. The adsorption efficiency in surface tension reduction is due to the existence of interfacial synergistic interactions (confirmed by the analysis of β ^γ and ΔG _ad ⁰ values). Maximum synergistic interaction is seen for α _BSs = 0.4. The hydrophobic steroid backbone of NaDHC molecule presents a deep interfacial penetration than NaDC. This fact causes a great disturbance of DDAB hydrocarbon tails and conduces to a large separation of molecules (high A _m values) which explains the reduction of adsorption effectiveness (low Γ _m values).     

Bulk and adsorbed monolayer phase behavior of binary mixtures of undecanoic acid and undecylamine: catanionic monolayers

Differential scanning calorimetry (DSC) and X-ray powder diffraction (PXRD) have been used to determine the phase behavior of the binary mixtures of undecanoic acid (A) and undecylamine (B) in the bulk. In addition, we report DSC data that indicates very similar behavior for the solid monolayers of these materials adsorbed on the surface of graphite. The two species are found to form a series of stoichiometric complexes of the type AB, A(2)B, and A(3)B on the acid rich side of the phase diagram. Interestingly, no similar series of complexes is evident on the amine rich side. As a result of this complexation, the solid monolayers of the binary mixtures exhibit a very pronounced enhancement in stability relative to the pure adsorbates.     

Synthesis and conformational analysis of fructose-derived scaffolds: molecular diversity from a single molecule

Bi- and tricyclic compounds were synthesized starting from fructose. The different hydroxyl groups present in fructose were exploited in the formation of a number of conformationally constrained sugar-based scaffolds, including azido acids. Introduction of an azido group and carboxy terminus into different bicyclic iodo ethers, allowed the synthesis of different conformationally constrained azido acids. Conformational analysis of compounds 10, 11, 17, and 20 by NMR experiments assisted by molecular mechanics, allowed the determination of the distances between the relevant functional groups, that is the azido and carboxy functionalities.     

STM studies of single molecules: molecular orbital aspects

As a fundamental and frequently referred concept in modern chemistry, the molecular orbital plays a vital role in the science of single molecules, which has become an active field in recent years. For the study of single molecules, scanning tunneling microscopy (STM) has been proven to be a powerful scientific technique. Utilizing specific distribution of the molecular orbitals at spatial, energy, and spin scales, STM can explore many properties of single molecule systems, such as geometrical configuration, electronic structure, magnetic polarization, and so on. Various interactions between the substrate and adsorbed molecules are also understood in terms of the molecular orbitals. Molecular engineering methods, such as mode-selective chemistry based on the molecular orbitals, and resonance tunneling between the molecular orbitals of the molecular sample and STM tip, have stimulated new advances of single molecule science.     

Engineering proteins with tailored nanomechanical properties: a single molecule approach

Elastomeric proteins underlie the elasticity of natural adhesives, cell adhesion and muscle proteins. They also serve as structural materials with superb mechanical properties. Single molecule force spectroscopy has made it possible to directly probe the mechanical properties of elastomeric proteins at the single molecule level and revealed insights into the molecular design principles of elastomeric proteins. Combining single molecule atomic force microscopy and protein engineering techniques, it has become possible to engineer proteins with tailored nanomechanical properties. These efforts are paving the way to design artificial elastomeric proteins with well-defined nanomechanical properties for application in nanomechanics and materials sciences.     

Dielectric behavior of some small ketones as ideal polar molecules

The dielectric behaviors of some small symmetric ketone molecules, including acetone, 3-pentanone, cyclopentanone, 4-heptanone, and cyclohexanone, were investigated as a function of temperature (T) over a wide frequency range from 50 MHz (3.14 × 10(8) s(-1), in angular frequency) to 3 THz (1.88 × 10(13) s(-1)). The temperature dependencies of the rotational diffusion times (τ(r)) determined using (17)O NMR spin-lattice relaxation time (T(1)) measurements and viscosities of the ketones were also examined. The obtained temperature dependencies of the parameters for the ketones were compared with those of ideal polar molecules, which obey the Stokes-Einstein-Debye (SED) relationship without the formation of intermolecular dimeric associations and without orientational correlations between dipoles (molecular axes), that is, free rotation. Kirkwood correlation factors (g(K)) of only acetone and 3-pentanone were close to unity over a wide temperature range, whereas those of other ketones were obviously less than unity. These results revealed that no correlations exist between the rotational motions of dipoles in acetone and 3-pentanone, as expected in ideal polar molecules. However, other ketones exhibited orientational correlations in their dipoles because of dipole-dipole interactions via antiparallel configurations. Furthermore, because acetone and 3-pentanone satisfied the SED relationship and because their microscopic dielectric relaxation times (τ(μ)), which were calculated from the determined dielectric relaxation times (τ(D)) via the relationship τ(μ) = τ(D)g(K)(-1), were identical to 3τ(r) and were proportional to Vη(k(B)T)(-1) over the wide temperature range examined, where V, k(B), and η represent the effective molecular volume, Boltzmann's constant, and the viscosity of the liquid molecules, respectively, these two ketone molecules behave as ideal polar molecules. In addition, other ketones not significantly larger than acetone and 3-pentanone in molecular size likely form dimeric intermolecular associations with antiparallel cyclic configurations, which demonstrates the g(K) values less than unity.     

Physical properties of sodium carboxymethyl cellulose molecules adsorbed on a polyacrylonitrile ultrafiltration membrane

Ultrafiltration experiments showed that the graphical relationship between flux and pressure was a straight line through the origin, provided that the wall shear rate of the bulk fluid was higher than a certain critical value or the pressure was below a critical value. A higher critical shear rate corresponded to a higher critical pressure. For these conditions the total hydrodynamic resistance was only slightly greater than the resistance of a clean membrane for pure water. This additional resistance is attributed to a (mono-) molecular layer of macromolecules which is adsorbed on the membrane in the absence of both a concentration polarization layer and a conventional gel layer.At steady state ultrafiltration conditions, an increase of the flux was obtained after replacing the bulk solution by distilled water at constant experimental conditions, which is attributed to the removal of the concentration polarization layer whereas a mono-molecular layer of macromolecules remained adsorbed on the membrane. For these conditions the flux vs. pressure relationship showed a qualitatively similar behaviour as for ultrafiltration conditions.At a constant shear rate the flux vs. pressure relationship was a straight line through the origin for pressures below the critical pressure, the value of which increased with the shear rate. This linear relationship was reversible, showing no hysteresis. However, if the pressure was higher than its critical value, the flux vs. pressure relationship was no longer a straight line as a consequence of the occurrence of an additional hydrodynamic resistance which did not disappear entirely upon lowering the pressure below its critical value. For the explanation of these phenomena it is assumed that freely moveable parts of the adsorbed macromolecules can block the entrance region of the pores in the membrane if the pressure is beyond its critical value.On the other hand, for pressures below the critical pressure or shear rates beyond the critical shear rate, the pores of the membrane are deblocked. This blocking and deblocking of pores by parts of adsorbed macromolecules apparently takes place in a partly reversible way.     

Direct observation of triplet state emission of single molecules: single molecule phosphorescence quenching of metalloporphyrin and organometallic complexes by molecular oxygen and their quenching rate distributions

Single molecules are detected through the phosphorescence emission of their triplet states. Emission of the triplet states of single molecules of Pt octabutoxycarbonyl porphyrin (PtOBCP) and ruthenium(II)-tris-4,7-diphenyl-1,10-phenanthroline dichloride (Ru(dpp)(3)Cl(2)) is reported. The single molecule phosphorescence is very sensitive to molecular oxygen. Each molecule has its own characteristic quenching rate by oxygen, and the distribution of these rates is measured for (Ru(dpp)(3)Cl(2)) on a quartz surface. The large variance of this distribution is presumed to be caused by fluctuations in the pseudobimolecular rate coefficient and the local oxygen concentration. The possibility of creating a quantitative single oxygen molecule sensor is suggested.     

Elastic behavior of single polymer chains adsorbed on rough surfaces

In this paper, elastic behaviors of single polymer chains adsorbed on the rough surfaces with a substrate and some periodically tactic pillars are investigated by the pruned-enriched-Rosenbluth method (PERM). In our simulation, a single polymer chain is firstly adsorbed on the substrate and then pulled along the z-axis direction, which is vertical to the substrate. We investigate the chain size and shape of polymer chains, such as mean-square radii of gyration per bond 〈S²〉_xy/N, 〈S²〉_z/N and shape factor 〈δ^∗〉 in order to show how the size and shape of adsorbed polymer chains change during the desorption process. Due to the occurrences of separation of the chains from the substrate, farther adsorption on the upper surfaces of pillars and complete separation from the whole rough surfaces in the elastic process, the changes of 〈S²〉_xy/N, 〈S²〉_z/N and 〈δ^∗〉 during the process are complicated. On the other hand, some thermodynamic properties such as average energy per bond, average Helmholtz free energy per bond, elastic force f are investigated, and our aim is to study the elastic behaviors of polymer chains adsorbed on the rough surface during the elasticity process. Elastic force f has some plateaus during the desorption process for strong adsorption interaction. If there is no adsorption interaction, the chains can get away from the rough surfaces spontaneously. These investigations can provide some insights into the elastic behaviors of polymer chains adsorbed on the rough surface.