Surface representation, intermolecular interaction

P.R.P. Barreto, A.F. Albemaz, F. Palazzetti, A. Lombardi, G. Grossi, V. Aquilanti, Hyperspherical representation of potential energy surfaces intermolecular interactions in tetra-atomic and penta-atomic systems, Phys. Scr. 84 (2011) 028111. 

The pioneering finite temperature Monte Carlo study [282] of the orientational disordering of commensurate and incommensurate monolayers of CO on graphite was based on empirical potentials and 64 molecules in a rectangular periodic cell. The CO-surface interactions were modeled with the Fourier representation [324, 326], and the necessary Lennard-Jones parameters were obtained from a fit to the measured isosteric heats of adsorption [287]. The nonelectrostatic CO-CO intermolecular interactions were based on Buckingham-type potentials as parameterized in Refs. 238 and 287. The electrostatics was represented by a three-site point-charge distribution located on the molecular axis [282]. The chosen values yield a reasonable representation of the moments up to the hexadecapole the dipole moment, however, is larger than the experimental value. These interactions... 

The preceding has illustrated some of the considerations involved in the representation of intermolecular interactions. Needless to say, the models used so far in molecular dynamics are empirical and are dictated more by convenience than by detailed experimental knowledge. However, a good deal of information has been gained from the use of these models, and it is to be hoped that molecular dynamics will soon reap the benefits of current research into the nature of intermolecular potential surfaces. 

As a first illustration we consider the model discussed in Section 1.3.3, namely a fluid of simple molecules confined between chemically striped solid surfaces (see Fig. 5.2). As before in Section 5.4 we treat the confined fluid as a thermodynamically open system. Hence, equilibrium states correspond to minima of the grand potential 11 introduced in Eqs. (1.66) and (1.67). The fluid fluid interaction is described by the intermolecular potential ug (r) introduced in Eq. (5.38) where the associated shifted-force potential is introduced in Eq. (5.39). The fluid substrate interaction is described by 1 1 (x, z) in the continuum representation [see Eq. (5.68)], where x replaces x because of the misaligmncnt of the sul)stratcs relative to each other [see Eq. (5.103)]. 

Figure 2.5 Schematic representation of interatomic (or intermolecular) forces (a) in the solid before splitting, (b) at a separation H when the atoms on each surface still interact with those on the opposite surface, and (c) at infinite separation where the surface atoms interact only with the bulk atoms below the surface.

The terms within the parentheses are simply probabilities. The first term is the probability of finding the CSP in a given conformational state, the second term is the probability that the analyte is in a particular conformation and the last term is the probability that the two molecules are positioned and oriented in a particular way with respect to each other. Note that because the authors locate all the minima on the complex s intermolecular potential energy surfaces they can derive the entropy of the system as well. Therefore E is actually a good representation of the macroscopic free energy of interaction, which in this case corresponds to a Gibbs free energy. 

Through filler experiments, it is possible to detect exclusively crosspeaks between protons that are attached, e.g., to a N or and protons that are not attached to N or [51]. Now, if one investigates a complex between two molecules, of which one is labelled with N and C, and the other one not, this allows to detect intermolecular H,H proximity exclusively and thus allows mapping of the contact surfaces in macromolecular assemblages. The mapping yields the amino acids in both molecules that interact with each other in the molecular-recognition process. As an example, the filtered NOESY spectrum between CaM and C20W (Fig. 19) is shown, as well as the contacts between the two moieties in a schematic representation derived from the NOESY cross peaks (Fig. 20). 

LSER characterization Ionic liquids can easily adsorb onto solid surfaces and may form a strongly structured interface at the supvport surface. This interface may induce the adsorption of polar solutes. For this reason, it was decided to use the above-described experimental procedure that allows the separation of the adsorption contribution. To quantify intermolecular solute-IL interactions, we used the LSER equation developed by Abraham et al. (Abraham et al., 1987,1990,1991, Abraham, 1993). This method allows one to correlate thermodynamic properties of phase transfer processes. The most recent representation of the LSER model is given by (Mutelet, 2008) ... 

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