Lennard parameters

Table A2.3.2 Halide-water, alkali metal cation-water and water-water potential parameters (SPC/E model). In the SPC/E model for water, the charges on H are at 1.000 A from the Lennard-Jones centre at O. The negative charge is at the O site and the HOH angle is 109.47°.

McDonald I R and Singer K 1967 Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method Discuss. Faraday Soc. 43 40-9... 

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]. 

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 Lennard-Jones 12-6 potential contains just two adjustable parameters the collision diameter a (the separation for which the energy is zero) and the well depth s. These parameters are graphically illustrated in Figure 4.34. The Lennard-Jones equation may also be expressed in terms of the separation at which the energy passes through a minimum, (also written f ). At this separation, the first derivative of the energy with respect to the internuclear distance is zero (i.e. dvjdr = 0), from which it can easily be shown that v = 2 / cr. We can thus also write the Lennard-Jones 12-6 potential function as follows ... 

The above potential is referred to as a Lennard-Jones or 6-12 potential and is summed over all nonbonded pairs of atoms ij. The first positive term is the short range repulsion and the second negative term is the long range attraction. The parameters of the interaction are Aj and B... The convenient analytical form of the 6-12 potential means that it is often used, although an exponential repulsion term is usually considered to be a more accurate representation of the repulsive forces (as used in MM-t). 

A proportionality between the theoretical spall strength and the bulk modulus is obtained when a two-parameter model is chosen to represent the intermolecular potential. Other two-parameter representations of the intermolecular potential, such as the Lennard-Jones 6-12 potential, will yield a similar proportionality although the numerical coefficients will differ slightly. 

Lennard-Jones parameters are / ,nh,/ in angsU oms and kilocalories per mole, respectively. 

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. 

The second approach is to derive Lennard-Jones parameters for the quantum atoms that are specific to the problem in hand. This is a less common approach but has been shown to improve the quantitative accuracy of the QM-MM approach in specific cases [53,54]. The disadvantage of this approach, however, is that it is necessary to derive Lennard-Jones parameters for the quanmm region for every different study. Since the derivation of Lennard-Jones parameters is not a trivial exercise, this method of finding van der Walls parameters for the QM-MM interaction has not been widely used. 

The issue of the theoretical maximum storage capacity has been the subject of much debate. Parkyns and Quinn [20] concluded that for active carbons the maximum uptake at 3.5 MPa and 298 K would be 237 V/V. This was estimated from a large number of experimental methane isotherms measured on different carbons, and the relationship of these isotherms to the micropore volume of the corresponding adsorbent. Based on Lennard-Jones parameters [21], Dignum [5] calculated the maximum methane density in a pore at 298 K to be 270 mg/ml. Thus an adsorbent with 0.50 ml of micropore per ml could potentially adsorb 135 mg methane per ml, equivalent to about 205 V/ V, while a microporc volume of 0.60 mEml might store 243 V/V. Using sophisticated parallel slit... 

Here Tq are coordinates in a reference volume Vq and r = potential energy of Ar crystals has been computed [288] as well as lattice constants, thermal expansion coefficients, and isotope effects in other Lennard-Jones solids. In Fig. 4 we show the kinetic and potential energy of an Ar crystal in the canonical ensemble versus temperature for different values of P we note that in the classical hmit (P = 1) the low temperature specific heat does not decrease to zero however, with increasing P values the quantum limit is approached. In Fig. 5 the isotope effect on the lattice constant (at / = 0) in a Lennard-Jones system with parameters suitable for Ne atoms is presented, and a comparison with experimental data is made. Please note that in a classical system no isotope effect can be observed, x "" and the deviations between simulations and experiments are mainly caused by non-optimized potential parameters. 

In the Yukawa potential, A is an inverse range parameter. The value A = 1.8 is appropriate for the inert gases. Each of the above potentials has a hard core. Real molecules are hard but not infinitely so. A slightly softer core is more desirable. The Lennard-Jones potential... 

The density functional approach has also been used to study capillary condensation in slit-like pores [148,149]. As in the previous section, a simple model of the Lennard-Jones associating fluid with a single associative site is considered. All the parameters of the interparticle potentials are chosen the same as in the previous section. Our attention has been focused on the influence of association on capillary condensation and the evaluation of the phase diagram [42]. 

Lennard-Jones 12-6 parameters have been deduced over the years, initially for the interactions between identical pairs of inert gas atoms. Over the years, authors have extended such smdies to include simple molecules and some examples are given in Table 1.3. 

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

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