Van der Waals Lennard-Jones

Energy terms bonds, angles, improper torsions, NOE, van der Waals (Lennard-Jones)... 

An approximate approach for computing free-energy changes based on linear response (LR) theory is also implemented in BOSS. In this model, the free energy of interaction of a solute with its environment is given as a function of the electrostatic (Coulombic) energy, van der Waals (Lennard-Jones) energy, and solvent-accessible surface area for the solute scaled by empirical parameters, a, p, and y ... 

Rare-gas clusters can be produced easily using supersonic expansion. They are attractive to study theoretically because the interaction potentials are relatively simple and dominated by the van der Waals interactions. The Lennard-Jones pair potential describes the stmctures of the rare-gas clusters well and predicts magic clusters with icosahedral stmctures [139, 140]. The first five icosahedral clusters occur at 13, 55, 147, 309 and 561 atoms and are observed in experiments of Ar, Kr and Xe clusters [1411. Small helium clusters are difficult to produce because of the extremely weak interactions between helium atoms. Due to the large zero-point energy, bulk helium is a quantum fluid and does not solidify under standard pressure. Large helium clusters, which are liquid-like, have been produced and studied by Toennies and coworkers [142]. Recent experiments have provided evidence of... 

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

The biasing function is applied to spread the range of configurations sampled such that the trajectory contains configurations appropriate to both the initial and final states. For the creation or deletion of atoms a softcore interaction function may be used. The standard Lennard-Jones (LJ) function used to model van der Waals interactions between atoms is strongly repulsive at short distances and contains a singularity at r = 0. This precludes two atoms from occupying the same position. A so-called softcore potential in contrast approaches a finite value at short distances. This removes the sin-... 

Figure 7-12. Plot of the van der Waals interaction energy according to the Lennard-Jones potential given in Eq. (27) (Sj, = 2.0 kcal mol , / (, = 1.5 A). The calculated collision diameter tr is 1.34 A.

Additionally to and a third adjustable parameter a was introduced. For a-values between 14 and 15, a form very similar to the Lennard-Jones [12-6] potential can be obtained. The Buckingham type of potential has the disadvantage that it becomes attractive for very short interatomic distances. A Morse potential may also be used to model van der Waals interactions in a PEF, assuming that an adapted parameter set is available. 

The range of systems that have been studied by force field methods is extremely varied. Some force fields liave been developed to study just one atomic or molecular sp>ecies under a wider range of conditions. For example, the chlorine model of Rodger, Stone and TUdesley [Rodger et al 1988] can be used to study the solid, liquid and gaseous phases. This is an anisotropic site model, in which the interaction between a pair of sites on two molecules dep>ends not only upon the separation between the sites (as in an isotropic model such as the Lennard-Jones model) but also upon the orientation of the site-site vector with resp>ect to the bond vectors of the two molecules. The model includes an electrostatic component which contciins dipwle-dipole, dipole-quadrupole and quadrupole-quadrupole terms, and the van der Waals contribution is modelled using a Buckingham-like function. 

A6-12 function (also known as a Lennard-Jones function) frequently simulates van der Waals interactions in force fields (equation 11). 

The MMh- van der Waals interactions do not use a Lennard-Jones potential but combine an exponential repulsion with an attractive... 

Forces Molecules are attracted to surfaces as the result of two types of forces dispersion-repulsion forces (also called London or van der Waals forces) such as described by the Lennard-Jones potential for molecule-molecule interactions and electrostatic forces, which exist as the result of a molecule or surface group having a permanent electric dipole or quadrupole moment or net electric charge. 

An approximate value for dc in the equation for tire Lennard-Jones potential, quoted above, may be obtained from the van der Waals constant, b, since... 

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. 

Interatomic potentials began with empirical formulations (empirical in the sense that analytical calculations based on them... no computers were being used yet... gave reasonable agreement with experiments). The most famous of these was the Lennard-Jones (1924) potential for noble gas atoms these were essentially van der Waals interactions. Another is the Weber potential for covalent interactions between silicon atoms (Stillinger and Weber 1985) to take into account the directed covalent bonds, interactions between three atoms have to be considered. This potential is well-tested and provides a good description of both the crystalline and... 

It is interesting to note that all three mechanisms contributing to the attractive van der Waals interactions vary as the reciprocal of the separation distance to the sixth power. It is for this reason that the Lennard-Jones potential has been extensively used to model van der Waals forces. 

Obviously, the mean-field treatment of the attraetive van der Waals inter-aetion results in negleet of the influenee of the interpartiele eorrelations on as well as the influenee of attraetive forees on assoeiation effeets (ef. the definition of Eq. (78)). To obtain a more adequate approximation, Johnson and Gubbins (see, e.g., [114]), have developed an aeeurate equation of state for assoeiating Lennard-Jones fluids, or more preeisely for the following nonassoeiative potential... 

The calculations have been carried out for a one-component, Lennard-Jones associating fluid with one associating site. The nonassociative van der Waals potential is thus given by Eq. (87) with = 2.5a, whereas the associative forces are described by means of Eq. (60), with d = 0.5contact with an attracting wall. The fluid-wall potential is given by the Lennard-Jones (9-3) function... 

As the distance between the two particles varies, they are subject to these long-range r " attractive forces (which some authors refer to collectively as van der Waals forces). Upon very close approach they will experience a repulsive force due to electron-electron repulsion. This repulsive interaction is not theoretically well characterized, and it is usually approximated by an empirical reciprocal power of distance of separation. The net potential energy is then a balance of the attractive and repulsive components, often described by Eq. (8-16), the Lennard-Jones 6-12 potential. 

For dilute solutions, the ratio of qx to q2 is given by the ratio of the pure-component critical volumes. This limiting relationship is somewhat arbitrary and is chosen primarily for convenience any other convenient measure of molecular size could be used—for example, van der Waals b or Lennard-Jones a3. 

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