Confined model systems examples

Uncovering of the three dimentional structure of catalytic groups at the active site of an enzyme allows to theorize the catalytic mechanism, and the theory accelerates the designing of model systems. Examples of such enzymes are zinc ion containing carboxypeptidase A 1-5) and carbonic anhydrase6-11. There are many other zinc enzymes with a variety of catalytic functions. For example, alcohol dehydrogenase is also a zinc enzyme and the subject of intensive model studies. However, the topics of this review will be confined to the model studies of the former hydrolytic metallo-enzymes. 

As is the case with any scientific development with important technological consequences, basic research plays a fundamental role whereby appropriate models are designed to explore and predict the physical and chemical behavior of a system. A confined quantum system is a clear example where theory constitutes a cornerstone for explanation and prediction of new properties of spatially limited atoms, molecules, electrons, excitons, etc. Theoretical study of possible confined structures might also suggest and stimulate further experimental investigations. In essence, the design of novel materials with exceptional properties requires proper theoretical modeling. 

The lipidic cubic phase has recently been demonstrated as a new system in which to crystallize membrane proteins [143, 144], and several examples [143, 145, 146] have been reported. The molecular mechanism for such crystallization is not yet clear, but the interfacial water and transport are believed to play an important role in nucleation and crystal growth [146, 147], Using a related model system of reverse micelles, drastic differences in water behavior were observed both experimentally [112, 127, 128, 133-135] and theoretically [117, 148, 149]. In contrast to the ultrafast motions of bulk water that occurs in less than several picoseconds, significantly slower water dynamics were observed in hundreds of picoseconds, which indicates a well-ordered water structure in these confinements. 

The purpose of this chapter is to account for the more recent developments pertaining to the structure and dynamics of bulk and confined water as a function of temperature. Examples relative to interactions of water molecules with model systems as well as with biological macromolecules will be presented. 

After illustrating the rather fascinating structural and rheological properties of confined fluids we conclude our discussion of MC simulations of continuous model systems (i.e., models in which fluid molecules move along continuous trajectories in space) with yet another example of the imique behavior of confined fluids. For pedagogic reasons we selected a topic that is standard in physical chemistry textbooks [26, 199-203] as far as bulk fluids are concerned, namely the Joule-Thomson effect. 

It is well known that confinement simulated via impenetrable boxes overestimates the effects on the atomic systems analyzed here. For example, transitions to the continuum and related properties are beyond the scope of such models. Even though resorting to cavities of soft or penetrable walls would provide a more realistic model, systems under impenetrable confinement represent the most broadly used models and the predictions resulting thereof are in general qualitatively correct. 

This type of model may be used to confine a system to a lower dimension, and a particularly well known example of such a model is two-dimensional confined hydrogen (treated later), which has been applied to the theory of quantum dots so that the atoms are essentially confined to a plane. 

More recently, there has been renewed interest in confined atomic systems in several areas of research for reviews and references see Jaskolski [7], Sako and Diercksen [8,9] and Dolmatov et al. [10], as well as papers here in the present volume. In addition to the spherical box model, the hydrogen atom has also been studied under various types of confinement (see, for example, Ley-Koo and Rubinstein [4], Froman et al. [5], Connerade et al. [11] and Saha et al. [12]), and off-centre investigations of the spherical cavity model have been performed as well [13]. 

Numerical computations on model systems have, in fact, revealed erratic wave functions for some systems that are classically mixing. An example is shown in Fig. 23, where the system is a particle confined by infinite potential walls to a region that is the shape of a racetrack (the so-called stadium system). The nodal patterns are clearly highly disordered and in marked contrast with the simple nodal lines associated with, for example, the separable particle in a rectangle case. Unfortunately, there is no one-to-one correspondence between systems that display chaotic classical behavior and the observation of erratic wave function nodal patterns. 

The investigation of the interaction between water and such interfaces is relevant to the study of such problems as the behavior of water in living organisms [4,5] and sludge dewatering [6], Moreover, water enclosed in very small volumes plays a dominant role as the medium that contfols structure and behavior near biological membranes, for example, and microemulsions may weU serve as model systems for the study of water in confined spaces [2,7,8],... 

The first step in the DG calculations is the generation of the holonomic distance matrix for aU pairwise atom distances of a molecule [121]. Holonomic constraints are expressed in terms of equations which restrict the atom coordinates of a molecule. For example, hydrogen atoms bound to neighboring carbon atoms have a maximum distance of 3.1 A. As a result, parts of the coordinates become interdependent and the degrees of freedom of the molecular system are confined. The acquisition of these distance restraints is based on the topology of a model structure with an arbitrary, but energetically optimized conformation. 

Without any doubt, the zeolite framework porous characteristics (micropores sizes and topology) largely govern the zeolite properties and their industrial applications. Nevertheless for some zeolite uses, as for instance, host materials for confined phases, the zeolite inner surface characteristics should be precised to understand their influence on such low dimensionality sorbed systems. In that paper, we present illustrative examples of zeolite inner surface influence on confined methane phases. Our investigation extends from relatively complex zeolite inner surface types (as for MOR structural types) to the model inner surface ones (well illustrated by the AFI zeolite type). Sorption isotherm measurements associated with neutron diffraction experiments are used in the present study. 

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