Clathrate hydration molecular structure

In an oligonucleotide-drug hydrate complex, the appearance of a clathrate hydrate-like water structure prompt a molecular dynamics simulation (40). Again the results were only partially successful, prompting the statement, "The predictive value of simulation for use in analysis and interpretation of crystal hydrates remains to be established." However, recent molecular dynamics calculations have been more successful in simulating the water structure in Ae host lattice of a-cyclodextrin and P-cyclodextrin in the crystal structures of these hydrates (41.42). 

While si, sll, and sH are the most common clathrate hydrates, a few other clathrate hydrate phases have been identified. These other clathrate hydrates include new phases found at very high pressure conditions (i.e., at pressures of around 1 GPa and higher at ambient temperature conditions). Dyadin et al. (1997) first reported the existence of a new methane hydrate phase at very high pressures (500 MPa). This discovery was followed by a proliferation in molecular-level studies to identify the structure of the high pressure phases of methane hydrate (Chou et al., 2000 Hirai et al., 2001 Kurnosov et al., 2001 Loveday et al., 2001, 2003). 

It is clear from the above that molecular-level methods are required to determine the hydrate structure. Furthermore, these methods have identified several phenomena that shift the paradigm on our understanding of clathrate hydrates, including ... 

The most conceptually attractive model for these solutions is to consider that the organization of water resembles that in the clathrate hydrates (p. 225), the structure being based on pentagonal dodecahedra of hydrogen bonded water molecules (Glew and Moelwyn-Hughes, 1953). This model receives some support from the observation that there is an optimum molecular radius of 4-5 x 10 8 cm for solubility of apolar solutes in water (Franks and Reid, 1973). 

Hydrogen-bonding patterns in crystal structures of the cydodextrins and the simpler carbohydrates differ. The infinite, homodromic chains are common both in the low molecular-weight carbohydrates and in the cydodextrins. The principal difference lies in the frequency of occurrence of the homodromic and antidromic cycles, which are common in the cyclodextrin crystal structures and rare in the mono-, di-, and trisaccharides. The cyclic patterns are the rule in the clathrate hydrates and in the ices. From this point of view, the hydrogen-bonding patterns of the hydrated cydodextrins lie between those of the simpler hydrated carbohydrates and those of the hydrate inclusion compounds, discussed in Part IV, Chapter 21. 

We treat, in this chapter, mainly solid composed of water molecules such as ices and clathrate hydrates, and show recent significant contribution of simulation studies to our understanding of thermodynamic stability of those crystals in conjunction with structural morphology. Simulation technique adopted here is not limited to molecular dynamics (MD) and Monte Carlo (MC) simulations[l] but does include other method such as lattice dynamics. Electronic state as well as nucleus motion can be solved by the density functional theory[2]. Here we focus, however, our attention on the ambient condition where electronic state and character of the chemical bonds of individual molecules remain intact. Thus, we restrict ourselves to the usual simulation with intermolecular interactions given a priori. 

Much of the information on hydrate processes has come from macroscopic studies, that is, from the observation of gas consumption, pressure drop, particle size measurements, or crystal morphology observations. However clathrate hydrates in many ways are unique materials that make it imperative that studies on the molecular scale are also carried out. For instance, several structures of hydrate may coexist, and often this is not obvious from phase equilibrium studies ... 

In the molecular sciences, elueidation of the strueture and property of a van der Waals molecule is an important current researeh subject. The van der Waals molecule is unstable at room temperature, and it is quite difficult to get a concentrated system of van der Waals molecules [14,15]. There is another weakly interactive molecular complex compound, called a moleeular clathrate. Usually, molecular clathrates are unstable at ambient eonditions. Supercritical gas molecules such as N2 and NO are said to tend to produce dimers in micropores [16-20], In particular, NO molecules are adsorbed in micropores of activated carbon fiber (ACF) at ambient conditions in the form of dimers that are typical van der Waals molecules. Water molecules form an organized structure in the carbon micropore [21], The formation of NO hydrate and CH4 hydrate in micropores at a subatmospheric pressure has also been suggested [22,23]. Hence micropores accelerate the formation of van der Waals molecules or molecular clathrate hydrates. In the case of micropores that have a deep potential well, many molecules tend to be adsorbed in the deep potential well. Molecules confined in micropores should form the best dense structure according to the micropore geometry. Therefore, we can control the intermoleeular structure with inicropores even at supercritical conditions of the bulk gas. The molecular field of micropores can stabilize van der Waals molecules and molecular clathrates. 

The responsive behavior of ELRs has been defined as their ability to respond to external stimuli. This property is based on a molecular transition of the polymer chain in the presence of water at a temperature above a certain level, known as the Inverse Temperature Transition (ITT). This transition, whieh shares most of the properties of the lower critical solution temperature (LCST), although it also differs in some respects, particularly as regards the ordered state of the folded state, is clearly relevant for the application of new peptide-based polymers as molecular devices and biomaterials. Below a specific transition temperature (T,), the free polymer chains remain as disordered, random coils [20] that are fully hydrated in aqueous solution, mainly by hydrophobic hydration. This hydration is characterized by ordered, clathrate-like water structures somewhat similar to those described for crystalline gas hydrates [21, 22], although somewhat more heterogeneous and of varying perfection and stability [23], surrounding the apolar... 

Another confirmation of the close packing principle can be found in the rather common occurrence [17] of the formation of clathrates, hydrates, and solvates whenever the shape of the crystallizing molecule is too complex to allow efficient self-recognition with total space occupation, highly mobile solvent molecules slip in between and are incorporated in the crystal structure as space fillers. Incidentally, no numerical indicator of the ability or even the tendency of a given molecule to form solvate crystals has ever been found, a confirmation of the difficulties encountered in the definition of numerical descriptors of molecular shape. 

---