Phase simulation

Ciccotti G and Ferrario M 1998 Constrained and nonequilibrium molecular dynamics Classical and Quantum Dynamics In Condensed Phase Simulations ed B J Berne, G Ciccotti and D F Coker (Singapore World Scientific) pp 157-77... 

Berne B J, Ciccotti G and Coker D F (ed) 1998 Classical and Quantum Dynamics in Condensed Phase Simulations Proc. Euroconference (Lerici, Italy, 7-18 July, 1997) (Singapore World Scientific)... 

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

Tliroughout this chapter and in Table 1 the inclusion of QM results as target data is evident, with the use of such data in the optimization of empirical forces fields leading to many improvements. Use of QM data alone, however, is insufficient for the optimization of parameters for condensed phase simulations. This is due to limitations in the ability to perform QM calculations at an adequate level combined with limitations in empirical force fields. As discussed above, QM data are insufficient for the treatment of dispersion... 

Improper and Urey-Bradley terms 4C) Condensed phase simulations... 

Figure 2 Outline of the steps involved in the preparation of a force field for the inclusion of new molecules and optimization of the associated parameters. Iterative loops (1) over individual external terms, (11) over individual internal terms, (111) over the external and internal terms. In loop (IV) over the condensed phase simulations, both external terms and internal terms are included.

It is clear from the forgoing discussions that the important material properties of liquid crystals are closely related to the details of the structure and bonding of the individual molecules. However, emphasis in computer simulations has focused on refining and implementing intermolecular interactions for condensed phase simulations. It is clear that further work aimed at better understanding of molecular electronic structure of liquid crystal molecules will be a major step forward in the design and application of new materials. In the following section we outline a number of techniques for predictive calculation of molecular properties. 

The fiuid-phase simulation approach with the longest tradition is the simulation of large numbers of the molecules in boxes with artificial periodic boundary conditions. Since quantum chemical calculations typically are unable to treat systems of the required size, the interactions of the molecules have to be represented by classical force fields as a prerequisite for such simulations. Such force fields have analytical expressions for all forces and energies, which depend on the distances, partial charges and types of atoms. Due to the overwhelming importance of the solvent water, an enormous amount of research effort has been spent in the development of good force field representations for water. Many of these water representations have additional interaction sites on the bonds, because the representation by atom-centered charges turned out to be insufficient. Unfortunately it is impossible to spend comparable parameterization work for every other solvent and... 

A Fully Implicit, Three Dimensional, Three-Phase Simulator with Automatic History-Matching Capability... 

Jonsson H, Mills G, Jacobsen K (1998) In Berne BJ, Ciccotti G, Coker DF (eds) Nudged Elastic Band Method , in Classical and quantum dynamics in condensed phase simulations, World Scientific, Singapore, pp 387 101... 

Field MJ (1997) Hybrid quantum mechanical molecular mechanical fluemating charge models for condensed phase simulations. Mol Phys 91(5) 835-845... 

Figure 20. Dense phase simulation by Peng, Tomita and Tashiro (1991),...

Although quite a few studies of the coadsorption of water and alkalis on metal surfaces in UHV. have been reported /19-21/ the possibility of complete hydration of the alkali adsorbate has not been considered in most cases The reason is probably that, as yet, all the experimental evidence suggests that the alkali 10ns are "specifically" adsorbed in such gas-phase simulation experiments, even when an excess of water (several multilayers) is made available. This result is not yet understood, although one should again keep in mind that the simulation experiments are typically performed 150 K below room temperature. 

Gas-phase results provide insight into the reaction pathways for isolated HE molecules however, the absence of the condensed-phase environment is believed to affect reaction pathways strongly. Some key questions related to condensed-phase decomposition are as follows (1) How do the temperature and pressure affect the reaction pathways (2) Are there temperature or pressure-induced phase-transitions that play a role in the reaction pathways that may occur (3) What happens to the reaction profiles in a shock-induced detonation These questions can be answered with condensed-phase simulations, but such simulations would require large-scale reactive chemical systems consisting of thousands of atoms. Here we present results of condensed-phase atomistic simulations, which are pushing the envelope toward reaching the required simulation goal. 

The retention times of test solutes are correlated with reference compounds whose partition coefficients in octanol/water (Kow) are known The reliability of this technique depends on the extent to which the stationary and mobile phases simulate the octanol/water system... 

Analytical shape computation techniques were applied for the detection of cavities and the calculation of molecular surface properties of isolated cavity features and other ordered formations within these resultant alkyl stationary-phase simulation models [227]. Deep cavities (8-10 A wide) within the alkyl chains were identified for Cig polymeric models representing shape selective stationary phases (Figure 5.23). Similar-structure cavities with significant alkyl-chain ordered regions (>11 A) were isolated from two independent Cig models (differing in temperature,... 

FIGURE 5.26 (See color insert following page 280.) A representation of the slot model illustrating potential constrained-shape solute (BaP) interactions with the conformational ordered cavities of a polymeric Cjg stationary-phase simulation model. Also included on the chromatographic surface is an identical-scale molecular structure of 1,2 3,4 5,6 7,8-tetrabenzonaphthalene (TBN). 

Quantum and Classical Dynamics in Condensed Phase Simulations, B. J. Berne, G. Ciccotti, and D. F. Coker, eds.. World Scientific, Singapore, 1998. 

The UOP Ebex process has been available for license since the 1970s. This process is a rejective simulated moving bed process where the ethylbenzene is the least adsorbed member of the mixed xylenes and is recovered in high purity in the raffinate stream [47]. Other liquid phase simulated moving bed concepts selective for ethylbenzene have been considered. These would ostensibly require less adsorbent circulation per unit feed because ethylbenzene is typically at <20% concentrahon in mixed xylenes [48, 49]. A process is disclosed by Broughton [50] that produces a pure m-xylene stream along with a pure ethylbenzene stream. 

Berne, B.J., Ciccotti, G., Coker, D.F. (eds), Classical and Quantum Dynamics in Condensed Phase Simulations, World Scientific, River Edge, NJ, 1998. 

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