Hydration layer computer simulations

To provide molecular-scale detail about these surface reactions, four types of computer simulation for layer-type silicates (clay minerals) are utilized quantum mechanics (QM), molecular mechanics (MM), molecular dynamics (MD), and Monte Carlo (MC) (Fig. 1). Molecular modeling of a clay mineral and its hydrates is a nontrivial task because of the relatively large cell size required for simulation (up to hundreds of atoms for a solid clay mineral surface, plus layers of water molecules, which also require up to hundreds of atoms) and complex... 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

In sharp contrast to the large number of experimental and computer simulation studies reported in literature, there have been relatively few analytical or model dependent studies on the dynamics of protein hydration layer. A simple phenomenological model, proposed earlier by Nandi and Bagchi [4] explains the observed slow relaxation in the hydration layer in terms of a dynamic equilibrium between the bound and the free states of water molecules within the layer. The slow time scale is the inverse of the rate of bound to free transition. In this model, the transition between the free and bound states occurs by rotation. Recently Mukherjee and Bagchi [14] have numerically solved the space dependent reaction-diffusion model to obtain the probability distribution and the time dependent mean-square displacement (MSD). The model predicts a transition from sub-diffusive to super-diffusive translational behaviour, before it attains a diffusive nature in the long time. However, a microscopic theory of hydration layer dynamics is yet to be fully developed. 

Simulations of three representative Cs-smectites revealed interlayer Cs+ to be strongly bound as inner sphere surface complexes, in agreement with published bulk diffusion coefficients [78]. Spectroscopic and surface chemistry methods have provided data suggesting that in stable 12.4 A Cs-smectite hydrates the interlayer water content is less than one-half monolayer. However, Smith [81] showed using molecular simulations of dry and hydrated Cs-montmorillonite that a 12.4 A simulation layer spacing was predicted at about one full water monolayer. The results of MD computer simulations of Na-, Cs-and Sr-substituted montmorillonites also provide evidence for a constant water content swelling transition between one-layer and two-layer spacings [82]. 

Spohr describes in detail the use of computer simulations in modeling the metal/ electrolyte interface, which is currently one of the main routes towards a microscopic understanding of the properties of aqueous solutions near a charged surface. After an extensive discussion of the relevant interaction potentials, results for the metal/water interface and for electrolytes containing non-specifically and specifically adsorbing ions, are presented. Ion density profiles and hydration numbers as a function of distance from the electrode surface reveal amazing details about the double layer structure. In turn, the influence of these phenomena on electrode kinetics is briefly addressed for simple interfacial reactions. 

In sharp contrast to the large number of experimental and computer simulation studies of the structure and dynamics of water in hydration layers reported in the literature and to be discussed in later chapters in this book, there have been only a few purely analytical (or model-independent) studies on the dynamics of the hydration layer found around biomolecules, within tissues and cells, and in and around self-assemblies. Some of the early theoretical studies invoked a simple... 

The above procedure provided historically the first estimate of the width of the protein hydration layer. The estimate (3—4 A) so obtained was believed to be fairly accurate for a long time, till newer time-dependent studies and computer simulations became available. 

Computer simulation studies show that the hydration layer of smaller proteins like HP36 extends only up to the first layer of solvent. For larger proteins, as emphasized earlier, researchers have concluded from their simulations that the hydration layer around the protein has a thickness of more than 10 A, which amounts to more than a three-monolayer thickness. 

However, it is important to note that the MRD experiments do not measure an explicit time correlation function that could characterize water dynamics occurring at different timescales. Thus it extracts only the average relaxation time of the system. It is interesting to note how these recent developments (particularly results from the NMRD technique and computer simulations) have changed our perception about the dynamics of the hydration layer, from a rigid ice-like layer to a dynamically mobile, somewhat slower than bulk but still active region. 

Understanding the protein hydration layer lessons from computer simulations... 

The above definitions are particularly suitable for investigations in computer simulations. They can be applied also to a fictitious layer in the bulk liquid, except that in the latter case decay can happen by molecules crossing across the region -that is, by penetrating the sphere not allowed in the case of protein. In the case of the protein hydration layer, these survival correlation functions decay slowly for the hydration layer. 

As discussed in Chapter 3, SD provides information on molecular motions (primarily rotation) by optically studying the energy fluctuations in a solute probe. In the experimental SD studies of the hydration layer of proteins, we need to either place an external probe in the layer, or use a natural probe such as tryptophan, which is a natural amino acid residue. An additional constraint is that the probe must be at least partly exposed to the solvent. However, in computer simulation studies we have the... 

Understanding the protein hydration layer lessons from computer simulations 9.6 Explanation of anomalous dynamics in the hydration layer... 

As we discussed above, the first model that attempts to explain this entropy loss was that of Frank and Evans, who proposed that water molecules in the first layer of the hydration shell form a eage-like strueture by forming HBs around the non-polar solute in a fence-like manner so as not to waste HBs by pointing them towards the solute. This ordering clearly eosts entropy. This iceberg model has sometimes been taken too literally, for example in understanding the hydration shell of proteins. The shell would certainly retain a eertain dynamic character, as it would be in dynamic equilibrium with the rest of the bulk. In fact, computer simulation studies indeed show that water molecules around methane or ethane have a residence time of a few tens of picoseconds at most, so the ieeberg model indeed has a limited validity. 

Computer simulation studies have explored translational and rotational dynamics in micellar solutions and shown that both translational and rotational dynamics in the hydration layer of micelles (Stem layer) are significantly slower than that in the bulk. The dipole-dipole time correlation function (which measures the rotational dynamics) shows the appearance of a long-time tail of the time constant in the 100 ps range or above. The dependence of the rotational dynamics on the probe location has also been investigated and it was found that the dynamics becomes faster as the probe moves away from the surface [7]. 

Abstract To understand the contribution of water to the repulsive force acting between phospholipid membrane molecules we performed molecular dynamics computer simulations on lamellar systems of phospholipid bilayers in water. Four simulations were performed. Two simulations were done on dilauroyl-phosphatidylethanolamine (DLPE) in water systems and two on dipal-mitoylphosphatidylcholine (DPPC) in water systems. The simulations differed by the amount of water per phospholipid headgroup. From the simulations we concluded that even at the hydration limit the headgroups of the opposing membranes come in to close proximity, so that they are separated by only one or two water layers. Since the water structure in the... 

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