Structural development of mercaptophenol self-assembled monolayers and the overlying mineral phase during templated CaCO3 crystallization from a transient amorphous film

Formation of biomineral structures is increasingly attributed to directed growth of a mineral phase from an amorphous precursor on an organic matrix. While many in vitro studies have used calcite formation on organothiol self-assembled monolayers (SAMs) as a model system to investigate this process, they have generally focused on the stability of amorphous calcium carbonate (ACC) or maximizing control over the order of the final mineral phase. Little is known about the early stages of mineral formation, particularly the structural evolution of the SAM and mineral. Here we use near-edge X-ray absorption spectroscopy (NEXAFS), photoemission spectroscopy (PES), X-ray diffraction (XRD), and scanning electron microscopy (SEM) to address this gap in knowledge by examining the changes in order and bonding of mercaptophenol (MP) SAMs on Au(111) during the initial stages of mineral formation as well as the mechanism of ACC to calcite transformation during template-directed crystallization. We demonstrate that formation of ACC on the MP SAMs brings about a profound change in the morphology of the monolayers: although the as-prepared MP SAMs are composed of monomers with well-defined orientations, precipitation of the amorphous mineral phase results in substantial structural disorder within the monolayers. Significantly, a preferential face of nucleation is observed for crystallization of calcite from ACC on the SAM surfaces despite this static disorder.     

Effect of bicarbonate ions on the crystallization of calcite on self-assembled monolayers

We use molecular dynamics simulations to investigate the nucleation of calcite crystals on self-assembled monolayers. We show how the presence of bicarbonate ions adsorbed on the monolayer surface can both aid nucleation and control the orientation of the growth of the crystal. Using a simple model of the nucleation process and calculated interfacial energies, we calculate the enhancement (with respect to the homogeneous nucleation rate) of the nucleation of calcite on the (012) and (0001) faces. The calculations show clearly that the (012) face is favored over the (0001) face and that the nucleation rate is enhanced for self-assembled monolayers made from molecules containing an even number of carbon atoms in the alkyl chain over those containing an odd number.     

Molecular dynamics simulation of the structural configuration of binary colloidal monolayers

Molecular dynamics simulations of binary colloidal monolayers, i.e., monolayers consisting of mixtures of two different particle sizes, are presented. In the simulations, the colloid particles are located at an oil-water interface and interact via an effective dipole-dipole potential. In particular, the influence of the particle ratio on the configurations of the binary monolayers is investigated for two different relative interaction strengths between the particles, and the pair correlation functions corresponding to the binary monolayers are calculated. The simulations show that the binary monolayers can only form two-dimensional crystals for certain particle ratios, for example, 2:1, 6:1, etc., while, for example, for a particle ratio of 7:1 the monolayers are found to be in a disordered, glassy state. The calculations also reveal that in analogy to the Wigner lattice the configurations are very sensitive to the relative interaction strength between the particles but not to the absolute magnitude of the interaction strength, even when particle size effects are taken into account. Consequently, it is argued that a comparison between the calculated configurations and actual binary particle monolayer systems could provide useful information on the relative interaction strength between large and small particles. Possible mechanisms giving rise to disparities in the interaction strength between large and small particles are described briefly.     

Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface

The adsorption of trichloroethene, C₂HCl₃, on clay mineral surfaces in the presence of water has been modeled as an example describing a general program that uses molecular dynamics simulations to study the sorption of organic materials at the clay mineral/aqueous solution interface. Surfaces of the clay minerals kaolinite and pyrophyllite were hydrated at different water levels corresponding to partial and complete monolayers of water. In agreement with experimental trends, water was found to outcompete C₂HCl₃ for clay surface sites. The simulations suggest that at least three distinct mechanisms coexist for C₂HCl₃ on clay minerals in the environment. The most stable interaction of C₂HCl₃ with clay surfaces is by full molecular contact, coplanar with the basal surface. This kind of interaction is suppressed by increasing water loads. A second less stable and more reversible interaction involves adsorption through single-atom contact between one Cl atom and the surface. In a third mechanism, adsorbed C₂HCl₃ never contacts the clay directly but sorbs onto the first water layer. To test the efficacy of existing force field parameters of organic compounds in solid state simulations, molecular dynamics simulations of several representative organic crystals were also performed and compared with the experimental crystal structures. These investigations show that, in general, in condensed-phase studies, parameter evaluations are realistic only when thermal motion effects are included in the simulations. For chlorohydrocarbons in particular, further explorations are needed of atomic point charge assignments. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 144–153, 1998     

Inelastic electron tunneling spectroscopy of alkane monolayers with dissimilar attachment chemistry to gold

We compare the low-temperature electron transport properties of alkyl monolayers which utilize different attachment strategies to gold. Inelastic electron tunneling spectroscopy (IETS) and current-voltage analysis were performed on molecular junctions incorporating alkyl-dithiocarbamate and alkanethiolate self-assembled monolayers of similar length. Alkyl-dithiocarbamate monolayers were formed by the condensation of dioctylamine or didecylamine with carbon disulfide in anhydrous ethanol and compared to alkanethiolate SAMs of 1-decanethiol and 1-dodecanethiol, respectively. The electron transport properties of each monolayer were examined using magnetically assembled microsphere junctions under high-vacuum conditions at low temperature. IETS was employed to differentiate the films on the basis of vibrational modes which are characteristic of each method of attachment. We use quantum chemical simulations of model compounds to calculate frequency and intensity of predicted signals arising from molecular vibrations to aid in the accurate assignment of the spectra. A qualitative comparison of our devices also reveals an increase in current density when utilizing dithiocarbamate attachment to gold compared to alkanethiolate molecules of similar length.     

Simulations of nanotribology with realistic probe tip models

We present the results of massively parallel molecular dynamics simulations aimed at understanding the nanotribological properties of alkylsilane self-assembled monolayers (SAMs) on amorphous silica. In contrast to studies with opposing flat plates, as found in the bulk of the simulation literature, we use a model system with a realistic AFM tip (radius of curvature ranging from 3 to 30 nm) in contact with a SAM-coated silica substrate. We compare the differences in response between systems in which chains are fully physisorbed, fully chemisorbed, and systems with a mixture of the two. Our results demonstrate that the ubiquitous JKR and DMT models do not accurately describe the contact mechanics of these systems. In shear simulations, we find that the chain length has minimal effects on both the friction force and coefficient. The tip radius affects the friction force only (i.e., the coefficient is unchanged) by a constant shift in magnitude due to the increase in pull-off force with increasing radius. We also find that at extremely low loads, on the order of 10 nN, shearing from the tip causes damage to the physisorbed monolayers by removal of molecules.     

Odd and even model self-assembled monolayers: links between friction and structure

The friction between an amorphous carbon tip and two n-alkane monolayers has been examined using classical molecular dynamics simulations. The two monolayers have the same packing density, but the chains comprising each monolayer differ in length by one -CH2- unit. The simulations show that the monolayers composed of C13 chains have higher friction than those composed of C14 chains when sliding in the direction of chain cant; the difference in friction becomes more pronounced as the load is increased. Examination of the contact forces between the chains and the tip, along with conformational differences between the two chain types, lends insight into the friction differences.     

A Theoretical Analysis on the Oxidation and Water Dissociation Resistance on Group-IV Phosphide Monolayers

Group-IV phosphide monolayers (MP, M=C, Si, Ge and Sn) provide a versatile platform for photocatalysts, as well as optoelectronic and nanoelectronic devices. Herein, comprehensive first-principles calculations and ab initio molecular dynamics (AIMD) simulations were performed to explore their stabilities in the air. We identified that the MP monolayers have excellent mechanical properties and their carrier mobilities are higher than that of phosphorene. The MP monolayers were predicted to possess superior oxidation resistance than the boron phosphide (BP) monolayer based on the proposed donation–backdonation theory. It was observed that the dissociation and chemisorption of a water molecule on the monolayers are kinetically difficult both in the water and in oxygen–water environments involving energy barriers of 1.28–3.48 eV. We also performed AIMD simulations at 300, 1000, 1200 and 1500 K. It is noteworthy that only the carbon phosphide (CP) monolayer can retain an intact structure at 1500 K, while the other three monolayers can just sustain to 1200 K. These results provide a guidance for their practical application and experimental fabrication.     

Thermal Ripples in Model Molybdenum Disulfide Monolayers

Molybdenum disulfide (MoS₂) monolayers have the potential to revolutionize nanotechnology. To reach this potential, it will be necessary to understand the behavior of this two‐dimensional (2D) material on large length scales and under thermal conditions. Herein, we use molecular dynamics (MD) simulations to investigate the nature of the rippling induced by thermal fluctuations in monolayers of the 2H and 1T phases of MoS₂. The 1T phase is found to be more rigid than the 2H phase. Both monolayer phases are predicted to follow long wavelength scaling behavior typical of systems with anharmonic coupling between vibrational modes as predicted by classic theories of membrane‐like systems.     

Monte Carlo simulations of the adsorption of CO2 on the MgO(100) surface

The adsorption of CO2 gas on the MgO (100) crystal surface is investigated using grand canonical Monte Carlo simulations. This allows us to obtain adsorption isotherms that can be compared with experiment, as well as to explore the possible formation of monolayers of different densities. Our model calculations agree reasonably well with the available experimental results. We find a "low-density" adsorbed monolayer where each CO2 molecule is bound to two Mg2+ ions on the MgO substrate. We also observe the formation of monolayers of higher density, where some of the CO2 molecules have rotated and tilted to expose additional binding sites. Low-temperature simulations of both the low- and high-density monolayers reveal that these states are very close in energy, with binding energies of approximately 7 kcal/mol at T=5 K. The high-density monolayer given by our model has a density that is significantly less than the reported experimental value. We discuss this discrepancy and offer suggestions for resolving it.     

Covalently modified silicon and diamond surfaces: resistance to nonspecific protein adsorption and optimization for biosensing

We report the direct covalent functionalization of silicon and diamond surfaces with short ethylene glycol (EG) oligomers via photochemical reaction of the hydrogen-terminated surfaces with terminal vinyl groups of the oligomers, and the use of these monolayers to control protein binding at surfaces. Photochemical modification of Si(111) and polycrystalline diamond surfaces produces EG monolayers linked via Si-C bond formation (silicon) or C-C bond formation (diamond). X-ray photoelectron spectroscopy was used to characterize the monolayer composition. Measurements using fluorescently labeled proteins show that the EG-functionalized surfaces effectively resist nonspecific adsorption of proteins. Additionally, we demonstrate the use of mixed monolayers on silicon and diamond and apply these surfaces to control specific versus nonspecific binding to optimize a model protein sensing assay.     

Modeling the properties of self-assembled monolayers terminated by carboxylic acids

Self-assembled monolayers of long-chain carboxylic acids are often used as substrates to promote the growth of oriented crystals. Recent work has shown that the length of the chain (odd or even number of carbon atoms) determines whether oriented growth is observed. We use molecular dynamics simulations to investigate whether the configuration of the headgroups is significantly different in the two cases. We conclude that there are differences between odd- and even-length chains, even at 300 K and in the presence of water for some packings of the monolayer. We discuss whether these differences are large enough to account for the different behavior.     

New electroanalytical applications of self-assembled monolayers

New applications of self-assembled monolayers of thiol compounds on gold electrodes are reviewed. They include: (i) exploitation of electrical control of self-assembly of thiol compounds for electrically-addressable immobilization of receptor molecules onto sensor arrays; (ii) a spreader-bar technique for formation of stable nanostructures; and, (iii) use of self-assembled monolayers as selective filters for chemical sensors.     

Contact forces at the sliding interface: mixed versus pure model alkane monolayers

Classical molecular dynamics simulations of an amorphous carbon tip sliding against monolayers of n-alkane chains are presented. The tribological behavior of tightly packed, pure monolayers composed of chains containing 14 carbon atoms is compared to mixed monolayers that randomly combine equal amounts of 12- and 16-carbon-atom chains. When sliding in the direction of chain cant under repulsive (positive) loads, pure monolayers consistently show lower friction than mixed monolayers. The distribution of contact forces between individual monolayer chain groups and the tip shows pure and mixed monolayers resist tip motion similarly. In contrast, the contact forces "pushing" the tip along differ in the two monolayers. The pure monolayers exhibit a high level of symmetry between resisting and pushing forces which results in a lower net friction. Both systems exhibit a marked friction anisotropy. The contact force distribution changes dramatically as a result of the change in sliding direction, resulting in an increase in friction. Upon continued sliding in the direction perpendicular to chain cant, both types of monolayers are often capable of transitioning to a state where the chains are primarily oriented with the cant along the sliding direction. A large change in the distribution of contact forces and a reduction in friction accompany this transition.     

Assessing the role of chirality in the formation of rosette-like supramolecular assemblies on surfaces

Molecular modeling simulations reveal the role of stereogenic centers in the formation of enantiomorphous surface-confined supramolecular rosette-like assemblies in monolayers of oligophenylene vinylene oligomers adsorbed at the graphite/solvent interface.     

Spreading dynamics of chain-like monolayers: a molecular dynamics study

Using large-scale molecular dynamics simulations, we have shown previously that the spreading dynamics of sessile drops on solid surfaces can be described in detail using the molecular-kinetic theory of dynamic wetting. Here we present our first steps in extending this approach to investigate the spreading dynamics of Langmuir-Blodgett monolayers. We make use of a monolayer model originally developed by Karaborni and Toxvaerd, but somewhat simplified to facilitate large-scale simulations. Our preliminary results are in good agreement with recent experimental observations and also support a molecular-kinetic interpretation in which the driving force for spreading is the lateral pressure in the monolayer. Away from equilibrium, initial spreading rates are constant and logarithmically dependent on pressure. However, near equilibrium, spreading is pseudo-diffusive and follows the square root of time. In both regimes the controlling factor is the equilibrium frequency of molecular displacements within the monolayer.     

Interfacial modification of organic photovoltaic devices by molecular self-organization

This feature article focuses on the relationship between the interfacial structures constructed by molecular self-organization and the properties of organic photovoltaic devices. The use of self-assembled monolayers (SAMs) is reviewed for metal and metal oxide/organic interfaces, while surface-segregated monolayers (SSMs) are introduced as a new method for the modification of organic/organic interfaces. Research up to now has clearly demonstrated the effectiveness of the control of energy levels and other properties at the interfaces to enhance photovoltaic performance. The possibility of more precise control of the interfacial structures is also discussed.     

Simulations of calcite crystallization on self-assembled monolayers

This paper presents simulations of calcium carbonate ordering in contact with self-assembled monolayers. The calculations use potential-based molecular dynamics to model the crystallization of calcium carbonate to calcite expressing both the (00.1) and (01.2) surfaces. The effect of monolayer properties: ionization; epitaxial matching; charge density; and headgroup orientation on the crystallization process are examined in detail. The results demonstrate that highly charged surfaces are vital to stimulate ordering and crystallization. Template directed crystallization requires charge epitaxy between both the crystal surface and the monolayer. The orientation of the headgroup appears to make no contribution to the selection of the crystal surface.