Molecular modeling current uses

Furthermore, the molecular scheme for the gel point prediction and viscoelasticity calculation in the course of the network formation were described in Section 3 and 4, respectively. Although some simpler models are in demand, the frameworks currently used are too complicated to use conventionally. However, the effect of unequal reactivity on the delay of gel point could be derived by drawing the detailed molecular scheme. Conversely, it is necessary to set the model up to details to meet with the realistic experimental data. Such molecular parameters allows us to prepare materials near the gel point with a wide range of properties for applications, like adhesives, absorbents, vibration dampers, sealants, membranes etc. With suitable design, it will be possible to control network structures, relaxation character, and then mechanical properties to the requirements. 

The availability of thermodynamically reliable quantities at liquid interfaces is advantageous as a reference in examining data obtained by other surface specific techniques. The model-independent solid information about thermodynamics of adsorption can be used as a norm in microscopic interpretation and understanding of currently available surface specific experimental techniques and theoretical approaches such as molecular dynamics simulations. This chapter will focus on the adsorption at the polarized liquid-liquid interfaces, which enable us to externally control the phase-boundary potential, providing an additional degree of freedom in studying the adsorption of electrified interfaces. A main emphasis will be on some aspects that have not been fully dealt with in previous reviews and monographs [8-21]. 

Biochemistry and chemistry takes place mostly in solution or in the presence of large quantities of solvent, as in enzymes. As the necessary super-computing becomes available, molecular dynamics must surely be the method of choice for modeling structure and for interpreting biological interactions. Several attempts have been made to test the capability of molecular dynamics to predict the known water structure in crystalline hydrates. In one of these, three amino acid hydrates were used serine monohydrate, arginine dihydrate and homoproline monohydrate. The first two analyses were by neutron diffraction, and in the latter X-ray analysis was chosen because there were four molecules and four waters in the asymmetric unit. The results were partially successful, but the final comments of the authors were "this may imply that methods used currently to extract potential function parameters are insufficient to allow us to handle the molecular-level subtleties that are found in aqueous solutions" (39). 

Even for purely adiabatic reactions, the inadequacies of classical MD simulations are well known. The inability to keep zero-point energy in all of the oscillators of a molecule leads to unphysical behavior of classical trajectories after more than about a picosecond of their time evolution." It also means that some important physical organic phenomena, such as isotope effects, which are easily explained in a TST model, cannot be reproduced with classical molecular dynamics. So it is clear that there is much room for improvement of both the computational and experimental methods currently employed by those of us interested in reaction dynamics of organic molecules. Perhaps some of the readers of this book will be provide some of the solutions to these problems. 

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