Lennard—Jones interactions

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))...

Of somewhat more use here is an approximate description of the interactions in terms of the well-known Lennard-Jones interaction (Lennard-Jones, 1924, 1925). This is a two-parameter model that Lennard-Jones fitted to properties of the giiseous phase. This form contained an attractive term proportional to d, in accord with the Van dcr Waals form. The repulsive term rises more rapidly, and a term proportional to d is commonly taken, though most results are not highly sensitive to the exact exponent. The Lennard-Jones overlap interaction is then written... 

For the MM system and QM/MM interaction, Lennard-Jones parameters (Table 1) for argon were drawn from Maitland et al. [47] and those for the ethylene atoms were drawn from the AMBER ff99 force field [48]. For interactions between distinct atom types, the Lennard-Jones a parameter was chosen to be the arithmetic average of the values for the two atom types, while the parameter was the geometric mean of the two values. 

In the other paper, a completely renewed potential energy function for alkanes and cycloalkanes was optimised. In form it is a GVPP with Morse functions for C-C and C-H bond deformations, and with numerous cross terms. Por non-bonded interactions, Lennard-Jones 9-6 plus Coulomb terms were transferred from previous work d... 

Given a chemical species, identify which intermolecular interactions are significant. Given different species, qualitatively compare the magnitude of their dipole moments, polarizabilities, intermolecular interactions, Lennard-Jones parameters s and a, and van derWaals parameters a and b. 

The gradient model for interfacial tension described in Eqs. III-42 and III-43 is limited to interaction potentials that decay more rapidly than r. Thus it can be applied to the Lennard-Jones potential but not to a longer range interaction such as dipole-dipole interaction. Where does this limitation come from, and what does it imply for interfacial tensions of various liquids ... 

We have two interaction potential energies between uncharged molecules that vary with distance to the minus sixth power as found in the Lennard-Jones potential. Thus far, none of these interactions accounts for the general attraction between atoms and molecules that are neither charged nor possess a dipole moment. After all, CO and Nj are similarly sized, and have roughly comparable heats of vaporization and hence molecular attraction, although only the former has a dipole moment. 

Truncation at the first-order temi is justified when the higher-order tenns can be neglected. Wlien pe higher-order tenns small. One choice exploits the fact that a, which is the mean value of the perturbation over the reference system, provides a strict upper bound for the free energy. This is the basis of a variational approach [78, 79] in which the reference system is approximated as hard spheres, whose diameters are chosen to minimize the upper bound for the free energy. The diameter depends on the temperature as well as the density. The method was applied successfiilly to Lennard-Jones fluids, and a small correction for the softness of the repulsive part of the interaction, which differs from hard spheres, was added to improve the results. 

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. 

But the methods have not really changed. The Verlet algorithm to solve Newton s equations, introduced by Verlet in 1967 [7], and it s variants are still the most popular algorithms today, possibly because they are time-reversible and symplectic, but surely because they are simple. The force field description was then, and still is, a combination of Lennard-Jones and Coulombic terms, with (mostly) harmonic bonds and periodic dihedrals. Modern extensions have added many more parameters but only modestly more reliability. The now almost universal use of constraints for bonds (and sometimes bond angles) was already introduced in 1977 [8]. That polarisability would be necessary was realized then [9], but it is still not routinely implemented today. Long-range interactions are still troublesome, but the methods that now become popular date back to Ewald in 1921 [10] and Hockney and Eastwood in 1981 [11]. 

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

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-... 

We consider a Lennard-Jones fluid consisting of atoms interacting with a Lennard-Jones potential given by... 

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. 

Ihi.. same molecule but separated by at least three bonds (i.e. have a 1, h relationship where n > 4). In a simple force field the non-bonded term is usually modelled using a Coulomb piilential term for electrostatic interactions and a Lennard-Jones potential for van der IV.uls interactions. 

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. 

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