Discrete molecular models

This volume of Modem Aspects covers a wide spread of topics presented in an authoritative, informative and instructive manner by some internationally renowned specialists. Professors Politzer and Dr. Murray provide a comprehensive description of the various theoretical treatments of solute-solvent interactions, including ion-solvent interactions. Both continuum and discrete molecular models for the solvent molecules are discussed, including Monte Carlo and molecular dynamics simulations. The advantages and drawbacks of the resulting models and computational approaches are discussed and the impressive progress made in predicting the properties of molecular and ionic solutions is surveyed. 

For ionic as for molecular solutes (Section III.3), some studies have applied the discrete molecular model to the solvent in the immediate environment of the solute, and treated the remainder as a continuum. This can in principle help to deal with the problem of inner-shell structure as well as that of long-range effects. Thus Straatsma and Berendsen used the Bom equation to correct simulation-obtained free energies of hydration for six monatomic ions.174 This helped in some instances but not in others. 

Specific solute-solvent interactions involving the first solvation shell only can be treated in detail by discrete solvent models. The various approaches like point charge models, siipennoleciilar calculations, quantum theories of reactions in solution, and their implementations in Monte Carlo methods and molecular dynamics simulations like the Car-Parrinello method are discussed elsewhere in this encyclopedia. Here only some points will be briefly mentioned that seem of relevance for later sections. 

Over the years there have been many attempts to simulate the behaviour of viscoelastic materials. This has been aimed at (i) facilitating analysis of the behaviour of plastic products, (ii) assisting with extrapolation and interpolation of experimental data and (iii) reducing the need for extensive, time-consuming creep tests. The most successful of the mathematical models have been based on spring and dashpot elements to represent, respectively, the elastic and viscous responses of plastic materials. Although there are no discrete molecular structures which behave like the individual elements of the models, nevertheless... 

Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich El. Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 1998 3 577-87. 

A metal cluster can be considered as a polynuclear compound which contains at least one metal-metal bond. A better definition of cluster catalysis is a reaction in which at least one site of the cluster molecule is mechanistically necessary. Theoretically, homogeneous clusters should be capable of multiple-site catalysis. Many heterogeneous catalytic reactions require multiple-site catalysis and for these reasons discrete molecular metal clusters are often proposed as models of metal surfaces in the processes of chemisorption and catalysis. The use of carbonyl clusters as catalysts for hydrogenation reactions has been the subject of a number of papers, an important question actually being whether the cluster itself is the species responsible for the hydrogenation. Often the cluster is recovered from the catalytic reaction, or is the only species spectroscopically observed under catalytic conditions. These data have been taken as evidence for cluster catalysis. 

The methods used for modeling pure granular flow are essentially borrowed from that of a molecular gas. Similarly, there are two main types of models the continuous (Eulerian) models (Dufty, 2000) and discrete particle (Lagrangian) models (Herrmann and Luding, 1998 Luding, 1998 Walton, 2004). The continuum models are developed for large-scale simulations, where the controlling equations resemble the Navier-Stokes equations for an ordinary gas flow. The discrete particle models (DPMs) are typically used in small-scale simulations or... 

The Gouy-Chapman theory treats the electrolyte as consisting of point ions in a dielectric continuum. This is reasonable when the concentration of the ions is low, and the space charge is so far from the metal surface that the discrete molecular nature of the solution is not important. This is not true at higher electrolyte concentrations, and better models must be used in this case. Improvements on the Gouy-Chapman theory should explain the origin of the Helmholtz capacity. In the last section we have seen that the metal makes a contribution to the Helmholtz capacity other contributions are expected to arise from the molecular structure of the solution. 

Table 7 compares free energies of hydration125 produced by the two types of solvent models that have been presented discrete molecular and continuum. The discrete molecular involved classical force field molecular dynamics (MD) and a free energy perturbation (FEP) technique whereby the solute molecule is annihilated to dummy atoms, so that absolute AGhydration are obtained the continuum were SCRF/PCM calculations, with Claverie-Pierotti Gcavilatlon and Floris-Tomasi Gvdw. The... 

Free Energies of Hydration Predicted by Discrete Molecular (MD/FEP) and Continuum (SCRF/PCM) Solvent Models, in kcal/mole.g... 

General Comments Discrete Molecular and Continuum Solvent Models... 

The level of accuracy that can be achieved by these different methods may be viewed as somewhat remarkable, given the approximations that are involved. For relatively small organic molecules, for instance, the calculated AGsoivation is now usually within less than 1 kcal/mole of the experimental value, often considerably less. Appropriate parametrization is of key importance. Applications to biological systems pose greater problems, due to the size and complexity of the molecules,66 156 159 161 and require the use of semiempirical rather than ab initio quantum-mechanical methods. In terms of computational expense, continuum models have the advantage over discrete molecular ones, but the latter are better able to describe solvent structure and handle first-solvation-shell effects. 

An interesting combined use of discrete molecular and continuum techniques was demonstrated by Floris et al.181,182 They used the PCM to develop effective pair potentials and then applied these to molecular dynamics simulations of metal ion hydration. Another approach to such systems is to do an ab initio cluster calculation for the first hydration shell, which would typically involve four to eight water molecules, and then to depict the remainder of the solvent as a continuum. This was done by Sanchez Marcos et al. for a group of five cations 183 the continuum model was that developed by Rivail, Rinaldi et al.14,108-112 (Section III.2.ii). Their results are compared in Table 14 with those of Floris et al.,139 who used a similar procedure but PCM-based. In... 

More refined continuum models—for example, the well-known Fumi-Tosi potential with a soft core and a term for attractive van der Waals interactions [172]—have received little attention in phase equilibrium calculations [51]. Refined potentials are, however, vital when specific ion-ion or ion-solvent interactions in electrolyte solutions affect the phase stability. One can retain the continuum picture in these cases by using modified solvent-averaged potentials—for example, the so-called Friedman-Gumey potentials [81, 168, 173]. Specific interactions are then represented by additional terms in (pap(r) that modify the ion distribution in the desired way. Finally, there are models that account for the discrete molecular nature of the solvent—for example, by modeling the solvent as dipolar hard spheres [174, 175]. 

Brady, C.P., Brinkworth, R.I., Dalton, J.P., Dowd, A.J., Verity, C.K. and Brindley, P.J. (2000b) Molecular modelling and substrate specificity of discrete cruzipain-like and cathepsinL-like cysteine proteinases of human blood fluke Schistosoma mansoni. Archives in Biochemistry and Biophysics 380, 46-55. 

It is also interesting to consider charge-transfer models developed primarily for metal surfaces. There are clear parallels to the metal oxide case in that there is an interaction between discrete molecular orbitals on one side, and electronic bands on the other side of the interface. The Newns-Anderson model [118] qualitatively accounts for the interactions between adsorbed atoms and metal surfaces. The model is based on resonance of adatom levels with a substrate band. In particular, the model considers an energy shift in the adatom level, as well as a broadening of that level. The width of the level is taken as a measure of the interaction strength with the substrate bands [118]. Also femtosecond electron dynamics have been studied at electrode interfaces, see e.g. [119]. It needs to be established, however, to what extent metal surface models are valid also for organic adsorbates on metal oxides in view of the differences between the metal an the metal oxide band structures. The significance of the band gap, as well as of surface states in it, must in any case be considered [102]. 

The molecular mechanism of the Hoffmann elimination involving (iV-Cl)-N-methyl-ethanolamine has been theoretically characterized by using DFT at the B3LYP/ 6-31++G computing level.49 The role of water as a solvent has been analysed by using both discrete and hybrid discrete-continuum models. The rearrangement proceeds by a water-assisted asynchronous concerted mechanism. 

Nano-scale and molecular-scale systems are naturally described by discrete-level models, for example eigenstates of quantum dots, molecular orbitals, or atomic orbitals. But the leads are very large (infinite) and have a continuous energy spectrum. To include the lead effects systematically, it is reasonable to start from the discrete-level representation for the whole system. It can be made by the tight-binding (TB) model, which was proposed to describe quantum systems in which the localized electronic states play an essential role, it is widely used as an alternative to the plane wave description of electrons in solids, and also as a method to calculate the electronic structure of molecules in quantum chemistry. 

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