United-atom interaction site

Fig. 4.2-5 The approximation made in converting a methyl group into a single united atom interaction site.

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

A modification of the united-atom approach, called the anisotropic united-atom (AUA) model was the focus of extensive work by Karabomi et al. [362-365]. As in the other models of hydrocarbon chains described so far, the AUA approach to monolayers was preceded by work on alkanes [367]. hi the AUA model the interaction site is located at the geometrical mean of the valence electrons of the atoms it represents, while the pseudoatom itself is located at the carbon atom position. The movement of each interaction center depends on the conformation of the molecule as a whole. 

The OPLS model is an example of pair potential where non-bonded interactions are represented through Coulomb and Lennard-Jones terms interacting between sites centred on nuclei (equation (51). Within this model, each atomic nucleus has an interaction site, except CH groups that are treated as united atoms centered on the carbon. It is important to note that no special functions were found to be needed to describe hydrogen bonding and there are no additional interaction sites for lone pairs. Another important point is that standard combining rules are used for the Lennard-Jones interactions such that An = (Ai As )1/2 and Cu = (C Cy)1/2. The A and C parameters may also be expressed in terms of Lennard-Jones o s and e s as A = 4ei Oi and C ... 

Figure 8 Left Schematic graph of the setup for the simulation of rubbing surfaces. Upper and lower walls are separated by a fluid or a boundary lubricant of thickness D. The outermost layers of the walls, represented by a dark color, are often treated as a rigid unit. The bottom most layer is fixed in a laboratory system, and the upper most layer is driven externally, for instance, by a spring of stiffness k. Also shown is a typical, linear velocity profile for a confined fluid with finite velocities at the boundary. The length at which the fluid s drift velocity would extrapolate to the wall s velocity is called the slip length A. Right The top wail atoms in the rigid top layer are set onto their equilibrium sites or coupled elastically to them. The remaining top wall atoms interact through interatomic potentials, which certainly may be chosen to be elastic.

Assuming that the number of specific interacting sites present on the polymer chain coincides with the oxygen atoms, the density of interacting sites per unit of mass of polymer (a = of interacting sites/mass of polymer) is... 

Based on the above observations, evidence exists for the formation of a Ag-O-C species in the early stages of Ag metallization on untreated PET. The degree of interaction is slight and, at most, only one carbonyl oxygen atom per PET repeat unit in the first molecular layer of PET is an interaction site. This corresponds to approximately 7% of the surface atoms. Although the interaction is slight, it can account for the improved adhesion compared to PE where virtually no interaction sites were observed. 

With large molecules, the number of sites is often smaller than that of atoms and the multipoles are located at the center of groups of atoms. For instance, the site-site description of the interactions in hydrocarbons with, say, a LJ potential, can either place an interaction center on each nucleus or just on the carbon of CH3 or CH2 groups (united atom approach). From this point of view, different treatment may be applied to the interaction terms in multipolar expansions. 

The surface can be visualized as built up by cubic units where each side represents an interaction site.35.46 qqjjg allows the surface to be represented by inhomogenities, snch as kinks, steps, vacancies, and ad atoms. The sites by which an adsorbed atom can simultaneonsly be bonded with can be maximally five for fhe vacancy, four for fhe kink, two for the step, and one for the ad atom. Obviously, the molecular adsorption energy is a function of the surface roughness, here represented by... 

In some force field models, even simpler representations are used than the united atom approach, with entire groups of atoms being modelled as single interaction points. For example, a benzene ring might be modelled as a single site with appropriately chosen parameters. 

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