Diffusion of a Butanethiolate Molecule on a Au{111} Surface

Simulations of Subnanometer Scale Image Contrast in Atomic Force Microscopy of Self-Assembled Monolayers in Water

Achieving high-resolution images using dynamic atomic force microscopy (AFM) requires understanding how chemical and structural features of the surface affect image contrast. This understanding is particularly challenging when imaging samples in water. An initial step is to determine how well-characterized surface features interact with the AFM tip in wet environments. Here, we use molecular dynamics simulations of a model AFM tip apex oscillating in water above self-assembled monolayers (SAMs) with different chain lengths and functional groups. The amplitude response of the tip is characterized across a range of vertical distances and amplitude set points. Then relative image contrast is quantified as the difference of the amplitude response of the tip when it is positioned directly above a SAM functional group vs positioned between two functional groups. Differences in contrast between SAMs with different lengths and functional groups are explained in terms of the vertical deflection of the SAMs due to interactions with the tip and water during dynamic imaging. The knowledge gained from simulations of these simple model systems may ultimately be used to guide selection of imaging parameters for more complex surfaces.

Metasurface-Enhanced Raman Spectroscopy (mSERS) for Oriented Molecular Sensing

Surface-enhanced Raman spectroscopy (SERS) is a widely used sensing technique for ultrasensitivity chemical sensing, biomedical detection, and environmental analysis. Because SERS signal is proportional to the fourth power of the local electric field, several SERS applications have focused on the design of plasmonic nanogaps to take advantage of the extremely strong near-field enhancement that results from plasmonic coupling, but few designs have focused on how SERS detection is affected by molecular orientation within these nanogaps. Here, we demonstrate a nanoparticle-on-metal metasurface designed for near-perfect optical absorption as a platform for Raman detection of highly oriented molecular analytes, including two-dimensional materials and aromatic molecules. This metasurface platform overcomes challenges in nanoparticle aggregation, which commonly leads to low or fluctuating Raman signals in other colloidal nanoparticle platforms. Our metasurface-enhanced Raman spectroscopy (mSERS) platform is based on a colloidal Langmuir-Schaefer deposition, with up to 32% surface coverage density of nanogaps across an entire sensor chip. In this work, we perform both simulations of the local electric field and experimental characterization of the mSERS signal obtained for oriented molecular layers. We then demonstrate this mSERS platform for the quantitative detection of the drinking-water toxin polybrominated diphenyl ether (BDE-15), with a limit of detection of 0.25 μM under 530 μW excitation. This detection limit is comparable to other SERS-based sensors operating at laser powers over 3 orders of magnitude higher, indicating the promise of our mSERS platform for nondestructive and low-level analyte detection.

Simulations of Friction Anisotropy on Self-Assembled Monolayers in Water

Molecular dynamics simulations were performed to study nanoscale friction on hydrophilic and hydrophobic self-assembled monolayers (SAMs) immersed in water. Sliding was simulated in two different directions to capture anisotropy due to the direction of motion relative to the inherent tilted orientation of the molecules. It was shown that friction depends on both hydrophobicity and sliding direction, with the highest friction observed for sliding on hydrophobic SAM in the direction against the initial orientation of the molecules. The origins of the friction trends were analyzed by differentiating the tip-SAM and tip-water force contributions to friction. The tip-water force was higher on the hydrophilic SAM, and this was shown to be due to the presence of a dense layer of water adjacent to the surface and hydrogen bonding. In contrast, the tip-SAM force was higher on the hydrophobic SAM due to a water depletion layer, which enabled the tip to be closer to the SAM terminal group. The higher-friction cases all exhibited greater penetration of the tip below the surface of the SAM, accommodated by further tilting and reorientation of the SAM molecules.

Heat Conduction Performance over a Poly(ethylene glycol) Self-Assembled Monolayer/Water Interface: A Molecular Dynamics Study

This study examined the interfacial heat condition between a poly(ethylene glycol) (PEG) self-assembled monolayer (SAM) and water using molecular dynamics simulation. It was found that the PEG SAM has higher thermal boundary conductance (TBC) than the traditionally used alkane-based SAM. The TBC conditionally varied with the length of the PEG molecules, where interfacial thermal resistance was a key factor. Our results reveal that the TBC of the PEG SAM/water interface is greatly influenced by its structural properties rather than the matching of vibrational properties between the SAM terminal and water. The structural analysis shows that the water structure around the terminal oxygen atom of the SAM plays a vital role in controlling the TBC. In this study, the concept of free volume has also been exploited, and the result suggests that the reduction of the free volume fraction accommodates a higher TBC. The model was precisely validated against experimental data by calculating the tilt angle and dihedral angle of the PEG SAM, the persistence length of the PEG chain in the water medium, and the sulfur position of the PEG SAM headgroup on the gold surface using quantitative scanning transmission electron microscopy image simulation.

Effect of Concentration, Chain Length, Hydrophobicity, and an External Electric Field on the Growth of Mixed Alkanethiol Self-Assembled Monolayers: A Molecular Dynamics Study

Growing functionalized self-assembled monolayers (SAMs) with fewer defects and lower cost is the focus of ongoing investigations. In the present study, molecular dynamics simulations were performed to investigate the process of SAM formation on a gold substrate from mixed alkanethiolates in ethanol solution. Using the mixed-SAM system of 11-mercaptoundecanoic acid (MUA) with either 1-decanethiol (C9CH3) or 6-mercaptohexanol (C6OH) in a 3:7 ratio as the standard SAM model, we systematically investigated the effects of the concentration, chain length, functional group, and an external electric field on SAM growth. The results showed that the initial growth rate and surface coverage of the SAM are dependent on the ligand concentration. At a certain high concentration (about 1.2-1.5 times the minimum concentration), the final surface coverage is optimal. Reducing the chain length and increasing the proportion of hydrophobic diluting molecules are effective ways to improve the surface coverage, but the compositional ligands have to be changed, which may not be desirable for the functional requirements of SAMs. Furthermore, by investigating the behavior of the alkanethiolates and ethanol solvent under an applied external field, we find that a strong electric field with a proper field direction can facilitate the generation of defect-free monolayers. These findings will contribute to the understanding of mixed-SAM formation and provide insight into experimental design for efficient and effective SAM formation.

Modulating catalytic activity of human topoisomerase II α enzyme by fluorescent gold nanoclusters

Precise monitoring of the enzyme activity by a suitable modulator is one of the very fundamental aspects of drug designing that provides the opportunity to overcome the challenges of several diseases. Herein, inhibition of human Topoisomerase IIα enzyme which serves as a potential target site for several anti-cancer drugs is demonstrated by using ultra-small size gold nanoclusters (Au NCs) with the dimension comparable with size of the active site of the enzyme. Molecular dynamics simulation results demonstrate that the Au NCs strongly interact with the human Topo IIα enzyme at its active site or allosteric site depending on forms of enzyme. Additionally, binding energy and interaction profile provides the molecular basis of understanding of interactions of ultra-small size Au NCs and human Topo IIα enzyme. Enthalpy change (ΔH) and binding constant (K) are measured based on a sequential binding model of the Au NCs with the enzyme as demonstrated by the ITC study. Moreover, the in-vitro inhibition study of the catalytic activity of the enzyme and gel electrophoresis indicates that the ultra-small size Au NCs may be used as a potent inhibitor of human Topo IIα enzyme.

Force Field Parameter Development for the Thiolate/Defective Au(111) Interface

A molecular-level understanding of the interplay between self-assembled monolayers (SAMs) of thiolates and gold surface is of great importance to a wide range of applications in surface science and nanotechnology. Despite theoretical research progress of the past decade, an atomistic model, capable of describing key features of SAMs at reconstructed gold surfaces, is still missing. In this work, periodic ab initio density functional theory (DFT) calculations were utilized to develop a new atomistic force field model for alkanethiolate (AT) SAMs on a reconstructed Au(111) surface. The new force field parameters were carefully trained to reproduce the key features, including vibrational spectra and torsion energy profiles of ethylthiolate (C₂S) in the bridge or staple motif model on the Au(111) surface, wherein, the force constants of the bond and angle terms were trained by matching the vibrational spectra, while the torsion parameters of the dihedral angles were trained via fitting the torsion energy profiles from DFT calculations. To validate the developed force field parameters, we performed classical molecular dynamics (MD) simulations for both pristine and reconstructed Au-S interface models with a (2√3 × 3) unit cell, which includes four dodecanethiolate (C₁₀S) molecules on the Au(111) surface. The simulation results showed that the geometrical features of the investigated Au-S interface models and structural properties of the C₁₀S SAMs are in good agreement with the ab initio MD studies. The newly developed atomistic force field model provides new fundamental insights into AT SAMs on the reconstructed Au(111) surface and adds advancement to the existing interface research knowledge.

Simulation of Subnanometer Contrast in Dynamic Atomic Force Microscopy of Hydrophilic Alkanethiol Self-Assembled Monolayers in Water

Atomic resolution imaging of surfaces in liquid environments using atomic force microscopy (AFM) is challenging in terms of both reproducibility and measurement interpretation. To understand the origins of these challenges, we used molecular dynamics simulations of AFM on hydrophilic self-assembled monolayers (SAMs) in water. The force on the model AFM tip was calculated as a function of lateral and vertical position relative to the SAM surface. The contributions of the water and SAMs to the overall force were analyzed, and the former was correlated to the water density distribution. Then, dynamic AFM was modeled by oscillating the tip at a driving amplitude. It was found that the contrast between amplitudes at different lateral positions on the surface was dependent on the vertical position of the tip. Lastly, amplitude maps were produced for two vertical positions at constant height, and the ability to capture atomic resolution was related to the force on the tip. These results offer an explanation for the observed instability in atomic scale imaging using AFM and more generally provide insight into the contrast mechanisms of surface images obtained in liquid environments.

Computational and Experimental Investigation of Janus-like Monolayers on Ultrasmall Noble Metal Nanoparticles

Detection of monolayer morphology on nanoparticles smaller than 10 nm has proven difficult with traditional visualization techniques. Here matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is used in conjunction with atomistic simulations to detect the formation of Janus-like monolayers on noble metal nanoparticles. Silver metal nanoparticles were synthesized with a monolayer consisting of dodecanethiol (DDT) and mercaptoethanol (ME) at varying ratios. The nanoparticles were then analyzed using MALDI-MS, which gives information on the local ordering of ligands on the surface. The MALDI-MS analysis showed large deviations from random ordering, suggesting phase separation of the DDT/ME monolayers. Atomistic Monte Carlo (MC) calculations were then used to simulate the nanoscale morphology of the DDT/ME monolayers. In order to quantitatively compare the computational and experimental results, we developed a method for determining an expected MALDI-MS spectrum from the atomistic simulation. Experiments and simulations show quantitative agreement, and both indicate that the DDT/ME ligands undergo phase separation, resulting in Janus-like nanoparticle monolayers with large, patchy domains.

Combined Experimental and Simulation Study of Amplitude Modulation Atomic Force Microscopy Measurements of Self-Assembled Monolayers in Water

Atomic force microscopy (AFM) can be used to measure surface properties at the nanoscale. However, interpretation of measurements from amplitude modulation AFM (AM-AFM) in liquid is not straightforward due to the interactions between the AFM tip, the surface being imaged, and the water. In this work, amplitude-distance measurements and molecular dynamics simulations of AM-AFM were employed to study the effect of surface chemistry on the amplitude of tip oscillation in water. The sample surfaces consisted of self-assembled monolayers where the hydrophilicity or hydrophobicity was determined by the terminal group of the alkanethiols. Analysis showed that surface chemical composition influences the hydration structure near the interface which affects the forces experienced by the tip and in turn changes the amplitude profile. This observation could aid our understanding of AM-AFM measurements of interfacial phenomena on various surfaces in water.

Atomic-scale sliding friction on a contaminated surface

Using non-equilibrium molecular dynamic simulations, we investigate the effect of adsorbates on nanoscopic friction. We find that the interplay between different channels of energy dissipation at the frictional interface may lead to non-monotonic dependence of the friction force on the adsorbate surface coverage and to strongly nonlinear variation of friction with normal load (non-Amontons' behavior). Our simulations suggest that the key parameter controlling the variation of friction force with the normal load, surface coverage and temperature is the time-averaged number of adsorbates confined between the tip and the substrate. Three different regimes of temperature dependence of friction in the presence of adsorbates are predicted. Our findings point on new ways to control friction on contaminated surfaces.

Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles

The self-assembly and self-organization of small molecules on the surface of nanoparticles constitute a potential route toward the preparation of advanced proteinlike nanosystems. However, their structural characterization, critical to the design of bionanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles (GNPs) is developed using experimentally characterized Cys-Ala-Leu-Asn-Asn (CALNN)- and Cys-Phe-Gly-Ala-Ile-Leu-Ser-Ser (CFGAILSS)-capped GNPs as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated using both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on the peptide capping density and on the nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bionanomaterials.

Vibrational mismatch of metal leads controls thermal conductance of self-assembled monolayer junctions

We present measurements of the thermal conductance of self-assembled monolayer (SAM) junctions formed between metal leads (Au, Ag, Pt, and Pd) with mismatched phonon spectra. The thermal conductance obtained from frequency domain thermoreflectance experiments is 65 ± 7 MW/m(2) K for matched Au-alkanedithiol-Au junctions, while the mismatched Au-alkanedithiol-Pd junctions yield a thermal conductance of 36 ± 3 MW/m(2) K. The experimental observation that junction thermal conductance (per molecule) decreases as the mismatch between the lead vibrational spectra increases, paired with results from molecular dynamics (MD) simulations, suggest that phonons scatter elastically at the metal-SAM interfaces. Furthermore, we resolve a known discrepancy between measurements and MD predictions of SAM thermal conductance by using a contact mechanics model to predict 54 ± 15% areal contact in the Au-alkanedithiol-Au experimental junction. This incomplete contact obscures the actual junction thermal conductance of 115 ± 22 MW/m(2) K, which is comparable to that of metal-dielectric interfaces.

Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles

A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.e. hollow, bridge, top, on-top Au adatom and the novel staple motif) for different crystalline facets, i.e. Au(111) and (100). Langevin dynamics simulations have been performed to study the capping effects of alkanethiolates molecules on Au nanoparticles in the range 1-4 nm. The simulation results reveal an enhancement of the coverage degree whilst the nanoparticles diameter decreases. A high surface disorder due to the strong S-Au bond was found, in very good agreement with very recent experimental findings [M. M. Mariscal, J. A. Olmos-Asar, C. Gutierrez-Wing, A. Mayoral and M. J. Yacaman, Phys. Chem. Chem. Phys., 2010, 12, 11785].

DYNAMICS OF SINGLE-MOLECULE ROTATIONS ON SURFACES DEPEND ON SYMMETRY, INTERACTIONS AND MOLECULAR SIZES

Rotating surface-mounted molecules have attracted attention of many research groups as a way to develop new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule level are still not well understood. Theoretical and experimental studies on thioether molecular rotors on gold surfaces suggest that the size of the molecules, their flexibility and steric repulsions with the surface are important for dynamics of the system. A complex combination of these factors leads to the observation that the rotation speeds have not been hindered by increasing the length of the alkyl chains. However, experiments on diferrocene derivatives indicated that a significant increase in the rotational barriers for longer molecules. We present here a comprehensive theoretical study that combines molecular dynamics simulations and simple models to investigate what factors influence single-molecule rotations on the surfaces. Our results suggest that rotational dynamics is determined by the size and by the symmetry of the molecules and surfaces, and by interactions with surfaces. Our theoretical predictions are in excellent agreement with current experimental observations.

On the atomic structure of thiol-protected gold nanoparticles: a combined experimental and theoretical study

In the present work new findings on the structure of the S-Au interface are presented. Theoretical calculations using a new semiempirical potential, based on density functional theory and a bond-order Morse potential, are employed to simulate the adsorption process in a more realistic way. The simulation results reveal the formation of gold adatoms on the nanoparticle surface and high surface disorder due to the strong S-Au bond. Experimental data were acquired by aberration (Cs) corrected scanning transmission electron microscopy (STEM) using a high angle annular dark field detector (HAADF) that showed a great similarity with the theory predicted.

Molecular simulation of the water meniscus in dip-pen nanolithography

We report a molecular dynamics simulation of the nanometer water meniscus formed in dip-pen nanolithography (DPN). When an atomic force microscope tip is in contact with a surface, the meniscus is significantly asymmetric around the tip axis. The meniscus as a whole can move away from the tip axis due to surface diffusion. The structure of the meniscus fluctuates and its periphery has a finite thickness as large as 25% of its width. We simulated the transport of nonpolar hydrophobic molecules through a water meniscus. Molecules move on the surface of, not dissolving into the interior of, the meniscus. As a result, an annular pattern forms in DPN. Even if the meniscus is cylindrically symmetric, the molecular flow from the tip and the subsequent pattern growth on the surface are anisotropic at the nanosecond timescale.

Switching in of Ac-(Ala)10-NHMe at a solid surface

Using molecular simulation, we show how Ac-(Ala)(10)-NHMe adsorbed on a solid surface switches between three conformations at distinct surface energies. The first switch is from an alpha-helix to a 3.1(10)-helix. The second involves further stretching to a 2(7)-helix. This switching has several potential applications including memory in molecular computers to motility elements in nanotechnology, and could be relevant to biological activity of proteins near solid surfaces (e.g., nano and aerosol particles) and disease processes induced by such interactions.

Mechano-chemical stability of gold nanoparticles coated with alkanethiolate SAMs

Molecular dynamics simulations are used to probe the structure and stability of alkanethiolate self-assembled monolayers (SAMs) on gold nanoparticles. We observed that the surface of gold nanoparticles becomes highly corrugated by the adsorption of the SAMs. Furthermore, as the temperature is increased, the SAMs dissolve into the gold nanoparticle, creating a liquid mixture at temperatures much lower than the melting temperature of the gold nanoparticle. By analyzing the mechanical and chemical properties of gold nanoparticles at temperatures below the melting point of gold, with different SAM chain lengths and surface coverage properties, we determined that the system is metastable. The model and computational results that provide support for this hypothesis are presented.

Study on nanoscale abrasive interaction between nanoprobe and self-assembled molecular surface for probe-based nanolithography process

Mechano-chemical scanning probe lithography (MC-SPL) is a nanofabrication technique that is based on the nanoscale abrasive interaction between a sharp nanoprobe and an ultrathin organic resist-coated surface. This work reviews the fundamental aspects of the MC-SPL process. The abrasive interaction at the tip-workpiece contact interface that occurs in the MC-SPL process was investigated by experimentally as well as by molecular dynamics simulation. Experimental results showed that severe wear of the tip that can generate just after coming into contact with the sample and the defects on the organic resists lead to the pattern broadening. In addition, the results from the simulation using the tips modeled with various shapes disclosed that the scribed pattern width was largely affected more by the shape of the tip rather than by the tip-surface contact area and thus the severe pattern broadening and large displacement of alkanethiol molecules around the tip could occur in the case of using the tip with large cone angle. It was found that these phenomena were due to the strong van der Waals interactions between the alkanethiol molecules.

Solvent Density Effects on the Solvation Behavior and Configurational Structure of Bare and Passivated 38-Atom Gold Nanoparticle in Supercritical Ethane

In exploring the effects of solvent density on the mode and the degree of solvation of the bare and passivated 38-atom gold particle in supercritical ethane, we have extended the molecular dynamics simulations of the system, reported previously,(34) to cover a range of isotherms in the T > T(c) regime, where T(c) is the critical temperature of the solvent. Consonant with our previous observations, the modes of solvation of the bare and the passivated particle, deduced from the radial distribution of the solvent about the metal core center of mass, are found to be vastly different from each other at all solvent densities: while the molecules solvating the bare particle form a well-defined, two-region layer around it, those solvating the passivated particle are loosely dispersed in the passivating layer. For the bare particle, the degree of solvation (vartheta) as a function of solvent density passes through a maximum occurring in the close vicinity of the critical point, consistent with our previous results and in agreement with Debenedetti's theoretical analysis,(22,23) which predicts a solvation enhancement effect in the critical region for systems where the unlike solvent/solute interaction is much stronger than the solvent/solvent interaction. Taking the degree of solvation (vartheta) as a measure of solvent quality, we have investigated how the solvent quality would vary along the solvent-density isotherms. In the solvent-density regime rho > rho(c), the solvent quality is found to be a decreasing function of the density as a result of progressive dominance of the excluded volume effect over the attractive particle/solvent interactions. The particle/solvent affinity is greatly reduced in the presence of the passivating layer, resulting in considerable shrinkage of the good-solvent-quality domain in the supercritical regime. The solvent environment and the presence of the passivating chains produce significant disorder in the equilibrium structure assumed by the nanoparticle core.

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.

Growth Dynamics of Self-Assembled Monolayers in Dip-Pen Nanolithography

Using molecular dynamics simulations, we studied the growth mechanism of self-assembled monolayers in dip-pen nanolithography. A molecule dropping from the tip kicks out a molecule sitting on the substrate, and the displaced molecule in turn kicks out a molecule next to it. This kicking propagates and finally stops when it hits the periphery of the monolayer. This monolayer growth is faster than predicted from the previous diffusion theory. Increasing the molecule-substrate binding strength enhances the molecular deposition rate and makes the monolayer well-ordered.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Dynamic Simulations of Adhesion and Friction in Chemical Force Microscopy

A hybrid molecular simulation approach has been applied to investigate dynamic adhesion and friction between a chemical force microscope (CFM) tip and a substrate, both modified by self-assembled monolayers (SAMs) with hydrophobic methyl (CH(3)) or hydrophilic hydroxyl (OH) terminal groups. The method combines a dynamic model for the CFM tip-cantilever system and a molecular dynamics (MD) relaxation technique for SAMs on Au(111) at room temperature. The hybrid simulation method allows one to simulate force-distance curves (or adhesion) and friction loops (or friction coefficient) in the CFM on the experimental time scale for the first time. The simulation results also provide valuable molecular information at the interface that is not accessible in CFM experiments, such as the actual tip position with respect to the cantilever support position, molecular and hydrogen-bonding structures at the interface, and load distributions among different molecular chains (or single-molecule forces). Results show that the adhesion force and friction coefficient for the OH/OH contact pair are much larger than those for the CH(3)/CH(3) pair due to the formation of hydrogen bonds. During the retraction of a CFM tip from a surface, the CFM tip is away from the sample surface slightly while the spring undergoes dramatic elongation in the normal direction before rupture occurs. Single-molecule forces are distributed unevenly at the contact area. Surface energies calculated for functionalized surfaces compare well with those determined by experiments.