Effect of load on structural and frictional properties of alkanethiol self-assembled monolayers on gold: some odd-even effects

We have conducted molecular dynamics simulations to study the frictional properties of alkanethiols CH(3)(CH(2))(n-1)SH (Cn, 12 ≤ n ≤ 15) self-assembled monolayers (SAMs) on Au(111) surfaces, under various loading and shearing conditions. For the examined alkanethiols, we found some evidence of the friction coefficient being dependent on the number of carbon atoms in the molecule being odd or even. Alkanethiols with n = odd show consistently higher friction coefficients than those with n = even. Such odd-even effect seems to be independent of the sliding velocity. However, the effect is significant only at lower loads (<700 MPa). The structural origin of this odd-even effect has been discussed. The effect of loading on the structure is also studied. For dodecanethiol (n = 12) we find the film responds to increased loading initially by increasing the tilt and then by deformation of individual molecules. SAM-Au contacts under shear show periodic storage and release of energy and a clear stick-slip pattern in the shear stress, film thickness, and the tilt and tilt orientation angles.     

Odd-even effects on the structure, stability, and phase transition of alkanethiol self-assembled monolayers

Molecular dynamics simulations were conducted to predict the structural properties and phase transition temperatures of n-alkanethiols CH(3)(CH(2))(n-1)SH (Cn, 4 ≤ n ≤ 22) self-assembled monolayers (SAMs) on Au (111) surfaces. We studied the effects of chain length on the structural properties, including tilt and orientation angles, and on phase transition temperature. We found clear dependence of the structural properties, on both the number of carbon atoms, n; and on n being odd or even. Alkanethiols with n ≤ 7 show liquid-like behavior and large rotational mobility, whereas those with n ≥ 12 are well-ordered and stable. For 12 ≤ n ≤ 15, odd-even effects are observed, where for n = odd, larger tilt angles, oriented in the direction of their next next nearest neighbor (NNNN), and for n = even, lower tilt angles, mostly tilted toward next nearest neighbor (NNN), were observed. For 15 ≤ n ≤ 19, we find tilt angle and orientation to be independent of n. For all alkanethiols, a gradual decrease of the tilt angle occurred by increasing the temperature from 300 to 420 K. Order-disorder phase transitions occurred at a certain temperature. This was signified by abrupt instabilities in the tilt orientation angle. This transition temperature showed an enhancement of ～67-100 °C over the melting point of the corresponding n-alkane bulk system. This enhancement depended on n, and was larger for n = odd. Overall, we found that odd alkanethiols show better structural and thermal stability, and smaller gauche defects.     

Molecular dynamic simulations of eicosanoic acid and 18-methyleicosanoic acid langmuir monolayers

The conformational and dynamical properties of Langmuir monolayers of 18-methyleicosanoic acid (18-MEA) and the parent material, eicosanoic acid (EA), are compared using molecular dynamics simulations. The effects on various properties, including film thickness, tilt angle, and order parameter, of the methyl group at the 18 position in 18-MEA were investigated as a function of film-packing density. NVT simulations were run as a function of decreasing areal-packing density similar to experimental Langmuir-Blodgett film compressions and expansions. We find that the order parameters and film thickness for 18-MEA monolayers were markedly different from those of EA. The order parameters for methylene groups for both 18-MEA and EA are greater in the middle region of the chain than at the ends in high-density films. This trend becomes reversed in lower density films. Significantly, our simulations show that the order parameters for methylene groups near the CH3 and carboxyl termini in 18-MEA are comparatively independent of film density in contrast with those of EA. Our findings show that the presence of the methyl group at the 18-position in 18-MEA induces unique intermolecular structural correlations compared to EA.     

A molecular dynamics study of nanoindentation on a methyl methacrylate ultrathin film on a Au(111) substrate: interface and thickness effects

The molecular dynamics simulation model of nanoindentation is proposed in order to study the mechanical and structural deformation properties of an ultrathin MMA (methyl methacrylate) film on a Au(111) surface. First, the significant differences in the structural arrangement of MMA thin films with different thicknesses are observed. Two layers are apparent in the thinnest MMA thin film next to the Au(111) surface, while three layer structures are apparent in the thicker film. Second, this study examines the indentation tip that penetrates the MMA thin film into the Au(111) substrate in order to understand the influence of the interface on the properties and deformation behavior in both the thin film and substrate. The result shows that the indentation force is influenced both by the layer structure and by the thickness of the MMA film. The thinnest case exhibits different deformation behavior from that of the thicker cases. In addition, the deformation of MMA molecules becomes significant at the interface between the MMA film and the Au(111) surface with the increase of film thickness, and detailed deformation behavior of the Au surface for different thicknesses of MMA film is reported in this paper. Finally, both the rigid and the active models for the indentation tip are utilized in the simulation to examine the interaction differences between the tip and the film and the deformation mechanism.     

Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers

Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25 degrees along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 A to as high as 34 degrees at a=5.3 A at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.     

Odd-even variations in the wettability of n-alkanethiolate monolayers on gold by water and hexadecane: a molecular dynamics simulation study

Molecular dynamics (MD) simulations were performed to investigate odd-even chain length dependencies in the wetting properties of self-assembled monolayers (SAMs) of n-alkanethiols [CH3(CH2)n-1SH] on gold by water and hexadecane. Experimentally, the contact angle of hexadecane on the SAMs depends on whether n is odd or even, while contact angles for water show no odd-even dependence. Our MD simulations of this system included a microscopic droplet of either 256 water molecules or 60 hexadecane molecules localized on an n-alkanethiolate SAM on gold with either an even or odd chain length. Contact angles calculated for these nanoscopic droplets were consistent with experimentally observed macroscopic trends in wettability, namely, that hexadecane is sensitive to structural differences between odd- and even-chained SAMs while water is not. Structural properties for the SAMs (including features such as chain tilt, chain twist, and terminal methyl group tilt) were calculated during the MD simulations and used to generate IR spectra of these films that compared favorably with experimental spectra. MD simulations of SAMs in contact with slabs of water and hexadecane revealed that the effects of these solvents on the structure of the SAM was restricted to the chain terminus and had no effect on the inner structure of the SAM. The density profiles for water and hexadecane on the SAMs were different in that water displayed a significant depletion in its density at the liquid/SAM interface from its bulk value, while no such depletion occurred for hexadecane. This difference in contact may explain the lack of an odd-even variation in the wetting characteristics of water on these surfaces, because the water molecules are positioned further away from the surface and, therefore, are not sensitive to the structural differences in the average orientations for the terminal methyl groups in odd- and even-chained SAMs. In contrast, the differences in the wetting properties of hexadecane on the odd- and even-chained SAMs may reflect the closer proximity of these molecules to the SAM surface and a resulting greater sensitivity to the differences in the terminal methyl group orientations in the SAMs. SAM-solvent interaction energies were calculated during the MD simulations, yielding interaction energies that differed on the even- and odd-chained surfaces by approximately 10% for hexadecane and negligibly for water, in accord with estimates using experimental wetting results.     

Molecular dynamics simulations on the adsorption of 4-n-octyl-4′-cyanobiphenyl (8CB) at the air/water interface

The influence of surface coverage to the structural properties of 4-n-octyl-4´-cyanobiphenyl (8CB) monolayer at the air/water interface was studied by full atomistic molecular dynamics simulations. These properties include density profiles, interface thickness, monolayer width, orientational order parameters, and atom-pair radial distribution functions. The calculated tilt angles of the cyanobiphenyl and alkyl parts are in fairly good agreement with the experiments. The simulation results exhibit the general trends in the previous experimental and simulation data.     

Derivation of class II force fields: V. Quantum force field for amides,peptides, and related compounds

As the field of biomolecular structure advances, there is an ever-growing need for accurate modeling of molecular energy surfaces to simulate and predict the properties of these important systems. To address this need, a second generation amide force field for use in simulations of small organics as well as proteins and peptides has been derived. The critical question of what accuracy can be expected from calculations in general, and with this class II force field in particular, is addressed for structural, dynamic, and energetic properties. The force field is derived from a recent methodology we have developed that involves the systematic use of quantum mechanical observables. Systematic ab initio calculations were carried out for numerous configurations of 17 amide and related compounds. Relative energies and first and second derivatives of the energy of 638 structures of these compounds resulted in 140,970 ab initio quantum mechanical observables. The class II peptide quantum mechanical force field (QMFF), containing 732 force constants and reference values, was parameterized against these observables. A major objective of this work is to help establish the role of anharmonicity and coupling in improving the accuracy of molecular force fields, as these terms have not yet become an agreed upon standard in the ever more extensive simulations being used to probe biomolecular properties. This has been addressed by deriving a class I harmonic diagonal force field (HDFF), which was fit to the same energy surface as the QMFF, thus providing an opportunity to quantify the effects of these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess the range of applicability (transferability) of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcal/mol with the class II force field, and 2.30 kcal/mol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it approaches a (rotational) barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of ever-increasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm⁻¹ was achieved with the coupled anharmonic force field, as compared to 105 cm⁻¹ with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 430–458, 1998     

Force field development for cofactors in the photosystem II

We present a set of force field (FF) parameters compatible with the AMBER03 FF to describe five cofactors in photosystem II (PSII) of oxygenic photosynthetic organisms: plastoquinone‐9 (three redox forms), chlorophyll‐a, pheophytin‐a, heme‐b, and β‐carotene. The development of a reliable FF for these cofactors is an essential step for performing molecular dynamics simulations of PSII. Such simulations are important for the calculation of absorption spectrum and the further investigation of the electron and energy transfer processes. We have derived parameters for partial charges, bonds, angles, and dihedral‐angles from solid theoretical models using systematic quantum mechanics (QM) calculations. We have shown that the developed FF parameters are in good agreement with both ab initio QM and experimental structural data in small molecule crystals as well as protein complexes. © 2012 Wiley Periodicals, Inc.     

Molecular dynamics of ��-CD in water/co-solvent mixtures

Molecular dynamics (MD) simulations on ??-cyclodextrin (??-CD) in water, ethanol (EtOH), methanol (MeOH) and mixtures of these solvents have been carried out at 300 K over a time period of 15 ns using the AMBER force field. The hydrated X-ray crystallographic structure has four water molecules inside the cavity, defined by a more precise boundary for the ??-CD cavity. From the simulations, 2?C4 encapsulated water molecules are most probably found. In an ethanol co-solvent system, the ??-CD cavity is occupied with one ethanol molecule located in two discrete sites: below and above the O4(n) plane, which is in agreement with experimental results. In all systems, the average values of tilt angles of the obtained structures are higher than the tilt angles of the X-ray structures. The investigations of the alcohol orientations in co-solvent mixtures reveal the hydrophobic environment of the cavity and the hydrophilic atmosphere at both rims of ??-CD.     

Effect of molecule-substrate interaction on thin-film structures and molecular orientation of pentacene on silver and gold

Evaporated pentacene thin films with thicknesses from several nm to 150 nm on gold and silver substrates have been studied by ultraviolet photoelectron spectroscopy (UPS), near-edge X-ray absorption fine structure (NEXAFS), scanning tunneling microscopy (STM), and atomic force microscopy (AFM). It was found that pentacene thin-film structures, particularly their molecular orientations, are strongly influenced by the metal substrates. UPS measurements revealed a distinct change in the valence band structures of pentacene on Au compared to those on Ag, which is attributed to the different packing between adjacent molecules. Using NEXAFS, we observed 74+/-5 degrees and 46+/-5 degrees molecular tilt angles on Ag and Au, respectively, for all measured thicknesses. We propose that pentacene molecules stand up on the surface and form the "thin-film phase" structure on Ag. On Au, pentacene films grow in domains with molecules either lying flat or standing up on the substrate. Such a mixture of two crystalline phases leads to an average tilt angle of 46 degrees for the whole film and the change in valence band structures. STM and distance-voltage (z-V) spectroscopy studies confirm the existence of two crystalline phases on Au with different conducting properties. z-V spectra on the low conducting phase clearly indicate its nature as "thin-film phase".     

Infrared studies of the potential controlled adsorption of sodium dodecyl sulfate at the Au(111) electrode surface

Quantitative subtractively normalized interfacial Fourier transform infrared reflection spectroscopy (SNIFTIRS) was used to determine the conformation and orientation of sodium dodecyl sulfate (SDS) molecules adsorbed at the single crystal Au(111) surface. The SDS molecules form a hemimicellar/hemicylindrical (phase I) structure for the range of potentials between -200 ≤ E < 450 mV and condensed (phase II) film for electrode potentials ≥500 mV vs Ag/AgCl. The SNIFTIRS measurements indicate that the alkyl chains within the two adsorbed states of SDS film are in the liquid-crystalline state rather than the gel state. However, the sulfate headgroup is in an oriented state in phase I and is disordered in phase II. The newly acquired SNIFTIR spectroscopy measurements were coupled with previous electrochemical, atomic force microscopy, and neutron reflectivity data to improve the current existing models of the SDS film adsorbed on the Au(111) surface. The IR data support the existence of a hemicylindrical film for SDS molecules adsorbed at the Au(111) surface in phase I and suggest that the structure of the condensed film in phase II can be more accurately modeled by a disordered bilayer.     

An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts. © 2011 Wiley Periodicals, Inc.     

Adsorption of acetaldehyde on ice as seen from computer simulation and infrared spectroscopy measurements

Detailed investigation of the adsorption of acetaldehyde on I(h) ice is performed under tropospheric conditions by means of grand canonical Monte Carlo computer simulations and compared to infrared spectroscopy measurements. The experimental and simulation results are in a clear accordance with each other. The simulations indicate that the adsorption process follows Langmuir behavior in the entire pressure range of the vapor phase of acetaldehyde. Further, it was found that the adsorption layer is strictly monomolecular, and the adsorbed acetaldehyde molecules are bound to the ice surface by only one hydrogen bond, typically formed with the dangling H atoms at the ice surface, in agreement with the experimental results. Besides this hydrogen bonding, at high surface coverages dipolar attraction between neighboring acetaldehyde molecules also contributes considerably to the energy gain of the adsorption. The acetaldehyde molecules adopt strongly tilted orientations relative to the ice surface, the tilt angle being scattered between 50° and 90° (i.e., perpendicular orientation). The range of the preferred tilt angles narrows, and the preference for perpendicular orientation becomes stronger upon saturation of the adsorption layer. The CH(3) group of the acetaldehyde molecules points as straight away from the ice surface within the constraint imposed by the tilt angle adopted by the molecule as possible. The heat of adsorption at infinitely low coverage is found to be -36 ± 2 kJ/mol from the infrared spectroscopy measurement, which is in excellent agreement with the computer simulation value of -34.1 kJ/mol.     

“Hummingbird” Behaviour of N‐Heterocyclic Carbenes Stabilises Out‐of‐Plane Bonding of AuCl and CuCl Units

An N‐heterocyclic carbene substituted by two expanded 9‐ethyl‐9‐fluorenyl groups was shown to bind an AuCl unit in an unusual manner, namely with the Au?X rod sitting out of the plane defined by the heterocyclic carbene unit. As shown by X‐ray studies and DFT calculations, the observed large pitch angle (21°) arises from an easy displacement of the gold(I) atom away from the carbene lone‐pair axis, combined with the stabilisation provided by weak CH???Au interactions involving aliphatic and aromatic H atoms of the NHC wingtips. Weak, intermolecular Cl???H bonds are likely to cooperate with the H???Au interactions to stabilise the out‐of‐plane conformation. A general belief until now was that tilt angles in NHC complexes arise mainly from steric effects within the first coordination sphere.     

Investigations on the field-induced switching behaviour in an antiferroelectric liquid crystal

The switching currents and field-induced apparent tilt angles in an antiferroelectric liquid crystal, (R)-MHPOBC, were measured. The structural differences among different smectic C* subphases may sensitively reflect the field or temperature dependence of the apparent tilt angle. In a thin cell, the apparent tilt angle was found to change in two steps as a function of field strength in the SmC*alpha and SmC* phases: a steep increase at lower fields and a small linear increase at higher fields. The steep increase in apparent tilt angle is divided into two parts via a plateau in the ferrielectric SmC*gamma phase. Stepwise change with a plateau is also seen in the relation of apparent tilt angle versus temperature under various electric fields. Moreover, the apparent tilt angle in the vicinity of the plateau is almost temperature- and field-independent, implying a preferred orientation of the molecules in the ferrielectric state. The influence of the cell thickness on the structural changes was also investigated.     

Density functional theory study of the adsorption of alkanethiols on Cu(111), Ag(111), and Au(111) in the low and high coverage regimes

The structure, the surface bonding, and the energetics of alkanethiols adsorbed on Cu(111), Ag(111), and Au(111) surfaces were studied under low and high coverages. The potential energy surfaces (PES) for the thiol/metal interaction were investigated in the absence and presence of externally applied electric fields in order to simulate the effect of the electrode potential on the surface bonding. The electric field affects the corrugation of the PES which decreases for negative fields and increases for positive fields. In the structural investigation, we considered the relaxation of the adsorbate and the surface. The highest relaxation in a direction perpendicular to the surface was observed for gold atoms, whereas silver atoms presented the highest relaxation in a plane parallel to the surface. The surface relaxation is more important in the low coverage limit. The surface bonding was investigated by means of the total and projected density of states analysis. The highest ionic character was observed on the copper surface whereas the highest covalent character occurs on gold. This leads to a strong dependence of the PES with the tilt angle of the adsorbate on Au(111) whereas this dependence is less pronounced on the other metals. Thus, the adsorbate-relaxation and the metal-relaxation contributions to the binding energy are more important on gold. The adsorption of thiols on gold was investigated on the 111 surface as well as on a surface with gold adatoms in order to elucidate the effect of thiols on the surface diffusion of gold. The CH(3)CH(2)S radical adsorbs ontop of the gold adatom. The diffusional barrier of the CH(3)CH(2)SAu species is lower than that for a bare gold adatom and is also lower than that for the bare thiol radical. The adsorption of the molecular species CH(3)SH and CH(3)CH(2)SH was also investigated on Au(111). They adsorb via the sulfur atom ontop of a gold atom. On the other hand, the adsorption of the alkanethiol radicals on the perfect 111 surfaces occurs on the face centered cubic (fcc)-bridge site in the low coverage limit for all metals and shifts toward the fcc site at high coverage on copper and silver.     

A Periodic Density Functional Study on Adsorption Properties of Methoxy on Au（111） Surface

1INTRODUCTION Methoxy(CH3O)has been identified as the first intermediate in the decomposition of methanol on extensive list of clean transition metal surfaces,such as Ni(100)[1],Cu(100)[2,3],Cu(111)[4],Ag(111)[5],Au(110)[6],Pd(111)[7]and Ru(0001)[8].The electronic structure of the metal is a determining factor in OH bond scission.In fact,group IB clean surfaces have shown very low activity towards this reaction,al-though there are reports on low amounts of methoxy formed on clean Cu(…     

Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets.

Ab initio quantum mechanical computations of force fields (FF) and atomic polar and axial tensors (APT and AAT) were carried out for triamide strands Ac-A-A-NH-CH(3) clustered into single-, double-, and triple-strand beta-sheet-like conformations. Models with phi, psi, and omega angles constrained to values appropriate for planar antiparallel and parallel as well as coiled antiparallel (two-stranded) and twisted antiparallel and parallel sheets were computed. The FF, APT, and AAT values were transferred to corresponding larger oligopeptide beta-sheet structures of up to five strands of eight residues each, and their respective IR and vibrational circular dichroism (VCD) spectra were simulated. The antiparallel planar models in a multiple-stranded assembly give a unique IR amide I spectrum with a high-intensity, low-frequency component, but they have very weak negative amide I VCD, both reflecting experimental patterns seen in aggregated structures. Parallel and twisted beta-sheet structures do not develop a highly split amide I, their IR spectra all being similar. A twist in the antiparallel beta-sheet structure leads to a significant increase in VCD intensity, while the parallel structure was not as dramatically affected by the twist. The overall predicted VCD intensity is quite weak but predominantly negative (amide I) for all conformations. This intrinsically weak VCD can explain the high variation seen experimentally in beta-forming peptides and proteins. An even larger variation was predicted in the amide II VCD, which had added complications due to non-hydrogen-bonded residues on the edges of the model sheets.     

Spin-crossover and liquid crystal properties in 2D cyanide-bridged Fe(II)-M(I/II) metalorganic frameworks

Novel two-dimensional heterometallic Fe(II)-M(Ni(II), Pd(II), Pt(II), Ag(I), and Au(I)) cyanide-bridged metalorganic frameworks exhibiting spin-crossover and liquid crystal properties, formulated as {FeL(2)[M(I/II)(CN)(x)](y)}·sH(2)O, where L are the ligands 4-(4-alkoxyphenyl)pyridine, 4-(3,4-dialkoxyphenyl)pyridine, and 4-(3,4,5-trisalkoxyphenyl)pyridine, have been synthesized and characterized. The physical characterization has been carried out by means of EXAFS, X-ray powder diffraction, magnetic susceptibility, differential scanning measurements, and Mo?ssbauer spectroscopy. The 2D Fe(II) metallomesogens undergo incomplete and continuous thermally induced spin transition at T(1/2) ≈ 170 K and crystal-to-smectic transition above 370 K.