Lennard-Jones interaction energy

Here the atoms in the system are numbered by i, j, k, l = 1,..., N. The distance between two atoms i, j is ry, q is the (partial) charge on an atom, 6 is the angle defined by the coordinates (i, j, k) of three consecutive atoms, and 4> is the dihedral angle defined by the positions of four consecutive atoms, e0 is the dielectric permittivity of vacuum, n is the dihedral multiplicity. The potential function, as given in equation (6), has many parameters that depend on the atoms involved. The first term accounts for Coulombic interactions. The second term is the Lennard-Jones interaction energy. It is composed of a strongly repulsive term and a van der Waals-like attractive term. The form of the repulsive term is chosen ad hoc and has the function of defining the size of the atom. The Ay coefficients are a function of the van der Waals radii of the... 

It was pointed out in Chapter 1 that it is usually assumed that the overall interaction energy between an adsorbate molecule and the adsorbent is given by the summation of the pairwise interactions. Furthermore, if the assemblage of discrete force centres in the solid can be treated as a continuum, the summation can be replaced by integration (Hill, 1952). In this case, the non-specific Lennard-Jones interaction energy between a single molecule and a semi-infinite slab of solid takes the 9-3 form (Steele, 1974) ... 

Some molecular properties of polar solvents are summarized in table 4.3. The dipole moment and molecular polarizability are the molecular parameters which lead to the solvent permittivity. The other parameters listed are the molecular diameter and the Lennard-Jones interaction energy, Elj. These are of interest in assessing the role of van der Waals forces in determining the properties of a polar liquid. 

This discontinuity may result in numerical instabilities during a simulation, because the value of the force may be computed to be much larger than the largest number understood by the computer. In order to avoid the discontinuity the entire potential can be shifted by a constant M(rc). As a result, the Lennard-Jones interaction energy becomes zero at fc in a smooth, continuous way (Fig. 14.2). A long-range correction is then needed, because the potential is actually not zero at the cutoff... 

A few groups replace the Lennard-Jones interactions by interactions of a different form, mostly ones with a much shorter interaction range [144,146]. Since most of the computation time in an off-lattice simulation is usually spent on the evaluation of interaction energies, such a measure can speed up the algorithm considerably. For example, Viduna et al. use a potential in which the interaction range can be tuned... 

Thermodynamic information can also be obtained from simulations. Currently we are measuring the differences in chemical potential of various small molecules in dimethylimidazolium chloride. This involves gradually transforming one molecule into another and is a computationally intensive process. One preliminary result is that the difference in chemical potential of propane and dimethyl ether is about 17.5 kj/mol. These molecules are similar in size, but differ in their polarity. Not surprisingly, the polar ether is stabilized relative to the non-polar propane in the presence of the ionic liquid. One can also investigate the local arrangement of the ions around the solute and the contribution of different parts of the interaction to the energy. Thus, while both molecules have a favorable Lennard-Jones interaction with the cation, the main electrostatic interaction is that between the chloride ion and the ether molecule. 

The interaction of hydrogen (deuterium) molecules with a transition metal surface c an be conveniently described in terms of a Lennard--Jones potential energy diagram (Pig. 1). It cxxislsts of a shallcw molecular precursor well followed by a deep atomic chemisorption potential. Depending on their relative depths and positions the wells m or may not be separated by an activation energy barrier E as schematically Indicated by the dotted cur e in Fig. 1. 

We assume for simplicity that the solvent is pure water, and that only the water-oxygen atoms have explicit Lennard-Jones interactions with the solute (this is typical of several common water models). We have seen that AWnp can be viewed as the free energy to change A from zero to one. Therefore, a well-known thermodynamic integration formula gives... 

Fig. 5.1 A schematic projection of the 3n dimensional (per molecule) potential energy surface for intermolecular interaction. Lennard-Jones potential energy is plotted against molecule-molecule separation in one plane, the shifts in the position of the minimum and the curvature of an internal molecular vibration in the other. The heavy upper curve, a, represents the gas-gas pair interaction, the lower heavy curve, p, measures condensation. The lighter parabolic curves show the internal vibration in the dilute gas, the gas dimer, and the condensed phase. For the CH symmetric stretch of methane (3143.7 cm-1) at 300 K, RT corresponds to 8% of the oscillator zpe, and 210% of the LJ well depth for the gas-gas dimer (Van Hook, W. A., Rebelo, L. P. N. and Wolfsberg, M. /. Phys. Chem. A 105, 9284 (2001))...

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