Lennard-Jones, generally parameter

Finally, the parametrization of the van der Waals part of the QM-MM interaction must be considered. This applies to all QM-MM implementations irrespective of the quantum method being employed. From Eq. (9) it can be seen that each quantum atom needs to have two Lennard-Jones parameters associated with it in order to have a van der Walls interaction with classical atoms. Generally, there are two approaches to this problem. The first is to derive a set of parameters, e, and G, for each common atom type and then to use this standard set for any study that requires a QM-MM study. This is the most common aproach, and the derived Lennard-Jones parameters for the quantum atoms are simply the parameters found in the MM force field for the analogous atom types. For example, a study that employed a QM-MM method implemented in the program CHARMM [48] would use the appropriate Lennard-Jones parameters of the CHARMM force field [52] for the atoms in the quantum region. 

In Fig. 1, various elements involved with the development of detailed chemical kinetic mechanisms are illustrated. Generally, the objective of this effort is to predict macroscopic phenomena, e.g., species concentration profiles and heat release in a chemical reactor, from the knowledge of fundamental chemical and physical parameters, together with a mathematical model of the process. Some of the fundamental chemical parameters of interest are the thermochemistry of species, i.e., standard state heats of formation (A//f(To)), and absolute entropies (S(Tq)), and temperature-dependent specific heats (Cp(7)), and the rate parameter constants A, n, and E, for the associated elementary reactions (see Eq. (1)). As noted above, evaluated compilations exist for the determination of these parameters. Fundamental physical parameters of interest may be the Lennard-Jones parameters (e/ic, c), dipole moments (fi), polarizabilities (a), and rotational relaxation numbers (z ,) that are necessary for the calculation of transport parameters such as the viscosity (fx) and the thermal conductivity (k) of the mixture and species diffusion coefficients (Dij). These data, together with their associated uncertainties, are then used in modeling the macroscopic behavior of the chemically reacting system. The model is then subjected to sensitivity analysis to identify its elements that are most important in influencing predictions. 

In reality, molecules each occupy some space, so the empty volume of the container decreases as the concentration N/ V increases. In addition, there is generally some attraction even at distances substantially larger than the nominal diameter of the molecules, and the repulsive part is somewhat soft so that collisions are not instantaneous. The exact form of this interaction must be calculated by quantum mechanics, and it depends on a number of atomic and molecular properties as discussed in Chapter 3. For neutral, nonpolar molecules, a convenient approximate potential is the Lennard-Jones 6-12 potential, discussed in Chapter 3 Table 3.5 listed parameters for some common atoms and molecules. 

The force fields used in the QM/MM methods are typically adopted from fully classical force fields. While this is in general suitable for the solvent-solvent interactions it is not clear how to model, e.g., the van der Waals interaction between the solute and the solvent. The van der Waals interactions are typically treated as Lennard-Jones (LJ) potentials with parameters for the quantum atoms taken from the classical force field or optimized for the particular QM/MM method for some molecular complexes. However, it is not certain that optimizing the (dispersion and short-range repulsion) parameters on small complexes will improve the results in a QM/MM simulation of liquids [37],... 

Thus we again assume a Lennard-Jones form, where now the well depth and range parameters depend on the solute s internal vibrational coordinates. Without loss of generality we can define these coordinates so that q = Q = 0 corresponds to the minimum in the intramolecular potential. The solute-solvent potential in Hb above is actually then

(r, 0, 0), where clearly e = e(0, 0) and a = cr(0, 0). The oscillator-bath interaction term is... 

We illustrate the behavior for a first order transition between a vapor and a dense liquid in the framework of a simple Lennard-Jones model. The condensation of a vapor into a dense liquid upon cooling is a prototype of a phase transition that is characterized by a single scalar order parameter - the density, p. The thermodynamically conjugated field is the chemical potential, p. The qualitative features, however, are general and carry over to other types of phase coexistence, e.g., Sect. 3.4. 

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