Models, molecular monolayers

Guided mode calculations were also carried out to compare the sensor response of several waveguide systems. In these simulations a model molecular monolayer is represented by a 2-nm thick layer with a refractive index of n 1.5. The optical properties of this model layer are typical of a dense layer of organic molecules on a substrate1 41, and are a reasonable approximation for a streptavidin protein layer bound to a biotinylated surface, the experimental model system we use to characterize our sensors. The ambient upper cladding was assumed to be water with a refractive index of n 1.32. For all examples, the lower cladding was assumed to be Si02 with an index of n 1.44. In the simulations, the effective index of... 

Emberly EG, Kirczenow G (2001) Models of electron transport through organic molecular monolayers self-assembled on nanoscale metallic contacts. Phys Rev B 64(23) 235412... 

In the first monolayer of conjugated model material, a model molecular solid or a polymer adsorbate, assume that no chemistry (covalent bonding) occurs, since, in the absence of, for example, mechanical rupturing, the bonds at the surface of the molecular film are completely satisfied. This assumption is supported by the fact that, at least for condensed molecular solids, vapor-deposited films may be re-evaporated (removed) from the surface by gentle heating in UHV. 

Based on this modeling, molecular dynamics simulations [140] for a complete Vs monolayer are carried out from 10 K to 80 K—that is, ranging from the harmonic herringbone solid through the orientationally disordered solid to the fluid. The herringbone transition occurs at around 22 K, below which enhanced 180° head-to-tail flips of the homonuclear molecules occur. The sixfold symmetry in the orientations persists up to about 50 K,... 

This is exactly the same / dependence that one gets for the bending rigidity of a thin solid sheet of thickness / [99]. This result is also consistent with a calculation of bending rigidity from a molecular model of monolayers [62,63,66]. For I smaller than about 20 A, where fiK zz 1, the bending rigidity is found to decrease more rapidly than P [37]. 

Any interpretation of the Type I isotherm must account for the fact that the uptake does not increase continuously as in the Type II isotherm, but comes to a limiting value manifested in the plateau BC (Fig. 4.1). According to the earlier, classical view, this limit exists because the pores are so narrow that they cannot accommodate more than a single molecular layer on their walls the plateau thus corresponds to the completion of the monolayer. The shape of the isotherm was explained in terms of the Langmuir model, even though this had initially been set up for an open surface, i.e. a non-porous solid. The Type I isotherm was therefore assumed to conform to the Langmuir equation already referred to, viz. 

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]. 

The ordered structure and molecule orientation in the monolayers, as suggested by the Hardy model, have been studied by various means. Electron diffraction techniques, for example, including both reflection and transmission, have been employed to examine the molecular orientation of adsorbed monolayers or surface hlms. The observations from these studies can be summarized as follows [3]. 

Novotny et al. [41] used p-polarized reflection and modulated polarization infrared spectroscopy to examine the conformation of 1 -1,000 nm thick liquid polyperfluoropropy-lene oxide (PPFPO) on various solid surfaces, such as gold, silver, and silica surfaces. They found that the peak frequencies and relative intensities in the vibration spectra from thin polymer films were different from those from the bulk, suggesting that the molecular arrangement in the polymer hlms deviated from the bulk conformation. A two-layer model has been proposed where the hlms are composed of interfacial and bulk layers. The interfacial layer, with a thickness of 1-2 monolayers, has the molecular chains preferentially extended along the surface while the second layer above exhibits a normal bulk polymer conformation. 

We review here results of computer simulations of monolayers, with an emphasis on those models that include significant molecular detail to the surfactant molecule. We start with a focus on hydrocarbon chains and simple head groups (typically a COOH group in either the neutral or the ionized state) and a historical focus. A less comprehensive review follows on simulations of surfactants of other types, either nonhydrocarbon chains or different head groups. More detailed descriptions of the general simulation techniques discussed here are available in a book dedicated to simulation techniques, for example, Allen and Tildesley [338] or Frenkel and Smit [339],... 

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. 

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