Simulated monolayers molecular dynamics

Effects on the Adhesion and Friction between Alkanethiol Monolayers Molecular Dynamics Simulations. 

A number of molecular dynamics (MD) simulations of surfactant monolayers have been published during the last decade. In these studies, the water surface was often modelled as a flat, amorphous plane. Due to severe computer power restrictions, there have been only a few attempts in which the surface was modelled in all atomic details. Monolayers of trimethylammonium chloride at the air/water interface and the properties of tetradecyltrimethylammonium bromide monolayers have been simulated. In addition to these computer experiments, the structures of phenol, p-n-pentylphenol and A,V -diethyl-p-nitroaniline adsorbed on water have been investigated by MD simulations. Recently, molecular dynamics simulations of sodium dodecyl sulfate at the water/vapour and the water/CCU interfaces in regimes of small surface concentrations have been performed (4). 

If D B, D J Tildesley, MRS Pinches, J B Kingdon, T Madden and A Clark 1995. Molecular Dynamics Simulations of Dioctadecyldimethylammonium Chloride Monolayers. Langmuir 11 237-246. 

Kim K S, M A Moller, D J Tildesley and N Quirke 1994a. Molecular Dynamics Simulations Langmuir-Blodgett Monolayers with Explicit Head-group Interactions. Molecular Simidati 13 77-99. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

Thus the formation of tilted analogues of the smectic A phases, i.e. monolayer Cl and bilayer C2, is possible for mesogens with relatively large electric quadrupoles. In the case of strongly sterically asymmetric molecules (e.g., zigzag shaped or dumbell shaped molecules, Fig. 3b) these quadrupolar interactions may be steric in origin. From this point of view observation of molecular tilt in the molecular dynamics simulations for a one-layer film of DOBAMBC in the absence of electrostatic interactions is not so surprising [106]. 

Hu, Y. Z., Zhang, T., and Wang, H., "Molecular Dynamics Simulations on Atomic Friction Between Self-Assembled Monolayers Commensurate and Incommensurate Sliding," Comp. Mater. Sci., Vol. 38,2006, pp. 98-104. 

Tarek et al. [388] studied a system with some similarities to the work of Bocker et al. described earlier—a monolayer of n-tetradecyltrimethylammonium bromide. They also used explicit representations of the water molecules in a slab orientation, with the mono-layer on either side, in a molecular dynamics simulation. Their goal was to model more disordered, liquid states, so they chose two larger molecular areas, 0.45 and 0.67 nm molecule Density profiles normal to the interface were calculated and compared to neutron reflectivity data, with good agreement reported. The hydrocarbon chains were seen as highly disordered, and the diffusion was seen at both areas, with a factor of about 2.5 increase from the smaller molecular area to the larger area. They report no evidence of a tendency for the chains to aggregate into ordered islands, so perhaps this work can be seen as a realistic computer simulation depiction of a monolayer in an LE state. 

Stimulated by these observations, Odelius et al. [73] performed molecular dynamic (MD) simulations of water adsorption at the surface of muscovite mica. They found that at monolayer coverage, water forms a fully connected two-dimensional hydrogen-bonded network in epitaxy with the mica lattice, which is stable at room temperature. A model of the calculated structure is shown in Figure 26. The icelike monolayer (actually a warped molecular bilayer) corresponds to what we have called phase-I. The model is in line with the observed hexagonal shape of the boundaries between phase-I and phase-II. Another result of the MD simulations is that no free OH bonds stick out of the surface and that on average the dipole moment of the water molecules points downward toward the surface, giving a ferroelectric character to the water bilayer. 

FIG. 26 Optimized structure of a water monolayer on mica obtained from molecular dynamic simulations by Odelius et al. The water molecules and the first layer of sihca tetrahedra of the mica substrate are shown in a side view in the top. K ions are the large dark balls. The bottom drawing shows a top view of the water. Oxygen atoms are dark, hydrogen atoms light. Notice the ordered icelike structure and the absence of free OH groups. All the H atoms in the water are involved in a hydrogen bond to another water molecule or to the mica substrate. (From Ref. 73.)... 

Membrane-Interaction (MI)-QSAR approach developed by Iyer et al. was used to develop predictive models of some organic compounds through BBB, and to simulate the interaction of a solute with the phospholipide-rich regions of cellular membranes surrounded by a layer of water. Molecular dynamics simulations were used to determine the explicit interaction of each test compound with the DMPC-water model (a model of dimyristoylphosphatidylcholine membrane monolayer, constructed using the software Material Studio according to the work done by van der Ploeg and Berendsen). Six MI-QSAR equations were constructed (Eqs. 74-79) ... 

In a different approach to this problem, Brenner and Garrison used molecular dynamics to examine the chemical mechanisms which lead to reordering of the atom-pairing reconstruction during atom deposition . This simulation incorporated a dissociative valence-force field potentiaF and consisted essentially of a high-temperature anneal of monolayers of silicon atoms which had been deposited on a silicon (001) reconstructed surface. 

The interpretation of the Langmuir experiments with the carbosilane den-drimers is supported by the results of molecular dynamics simulation. Figure 14 shows snapshots of a dumbbell-like conformation of carbosilane dendximers observed during lateral compression of a dendrimer monolayer on a polar sub-... 

AUds S, Cao C, Cheng HP, Krause JL (2009) Molecular dynamics simulations of Au penetration through alkanethiol monolayers on the Au(lll) surface. J Phys Chem C 113 6360-6366... 

Molecular dynamics simulations have been performed to investigate the interactions between CPZ (9) and DPPC in Langmuir monolayers [48]. The results of computer simulations revealed that the unprotonated form of the... 

The structure and molecular orientation of the monolayers have been studied taking in account the different conformations of the repeating unit in the collapse area. Molecular Dynamic Simulation (MDS) has been also reported. The MDS un-... 

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