Hydration computer simulation

In summary, the MD, MC, and LD (lattice dynamic) techniques are very powerful tools to investigate hydrate phenomena. Indeed, hydrate computer simulations may shortly outnumber hydrate experimental observations, because simulations are generally more accessible than experiments. However, such tools investigate phenomena which are on much smaller time and space dimensions than normally observed, outside of spectroscopy. Even with spectroscopy, the relevant peaks may be subject to some interpretation. As a result there may be several microscopic interpretations (based upon hundreds to thousands of molecules) of macroscopic phenomena which involve typically 1023 molecules. Such a scale-up may cause misinterpretation. 

Structural Aspects of DNA Hydration Dynamics of DNA Hydration Computer Simulations Protein-DNA Recognition Concluding Remarks... 

The ideas of Frank, Evans and Kauzmann had a profound influence on the way chemists thought about hydrophobic effects in the decades that followed However, after the study of the hydrophobic hydration shell through computer simulations became feasible, the ideas about the hydrophobic hydration gradually changed. It became apparent that the hydrogen bonds in the hydrophobic hydration shell are nof or only to a minor extent, stronger than in normal water which is not compatible with an iceberg character of the hydration shell. 

In summary, a wealtli of experimental data as well as a number of sophisticated computer simulations univocally indicate that two important effects underlie the acceleration of Diels-Alder reactions in aqueous media hydrogen bonding and enforced hydrophobic interactionsIn terms of transition state theory hydrophobic hydration raises the initial state more tlian tlie transition state and hydrogen bonding interactions stabilise ftie transition state more than the initial state. The highly polarisable activated complex plays a key role in both of these effects. 

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. 

Figure 5 shows pn distributions for spherical observation volumes calculated from computer simulations of SPC water. For the range of solute sizes studied, the In pn values are found to be closely parabolic in n. This result would be predicted from the flat default model, as shown in Figure 5 with the corresponding results. The corresponding excess chemical potentials of hydration of those solutes, calculated using Eq. (7), are shown in Figure 6. As expected, /x x increases with increasing cavity radius. The agreement between IT predictions and computer simulation results is excellent over the entire range d < 0.36 nm that is accessible to direct determinations of po from simulation.

Smith, P. E., Computer simulation of cosolvent effects on hydrophobic hydration, J. Phys. Chem. B 1999,103, 525-534... 

Engberts, Molecular dynamics computer simulation of the hydration of two simple organic solutes. Comparison with the simulation of an empty cavity, Mol. Phys. 53 1517 (1984). 

Schwartz, B. J. and Rossky, P. J. Aqueous solvation dynamics with a quantum mechanical solute computer simulation studies of the photoexcited hydrated electron, J.Chem.Phys., 101 (1994), 6902-6916... 

Severance, D. L. and Jorgensen, W. L. Effects of hydration on the Claisen rearrangement of allyl vinyl ether from computer simulations, JAm.Chem.Soc., 114(1992), 10966-10968... 

The main goal of the molecular dynamics computer simulation of ionic solvation and adsorption on a metal surface has been to test the above model and to provide more quantitative information about the different factors that influence the structure of hydrated ions at the interface. Unfortunately, most of the experimental information about these issues has been obtained from indirect measurements such as capacity and current-potential plots, although in recent years in situ experimental techniques have begun to provide an accurate test of the above model. For a recent review of experimental techniques and the theory of ionic adsorption at the water/metal interface, see the excellent paper by Philpott. ... 

The parameters used for simulation of the absorptions in the perpendicular region, AhJ and AAj, were slightly lower at S-band, compared with X-band. A plausible reason for this effect might be a rhombic distortion in the local symmetry of the hydrated cation. The result would be an additional splitting in the perpendicular direction which is expected to be more evident at higher microwave frequencies. If the assumption that axial symmetry is maintained, larger values for AA and AhJ would be required for the computer simulation at X-band, as we indeed observed. 

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. 

Computer simulations provide a means of examining the early stages of hydrate formation (nucleation) on a molecular level (Baez and Clancy, 1994 Radhakrishnan and Trout, 2002 Moon et al., 2003, 2005). Computer simulation has also been applied to study hydrate dissociation (Baez and Clancy, 1994 English and MacElroy, 2004) and the effects on dissociation kinetics of external electromagnetic fields (English and MacElroy, 2004). 

The pentagonal and hexagonal faces are central to hydrate cavities, and therefore, their geometries are considered here. Small clusters, such as pentamers can be studied via geometric considerations, computer simulation, and more recently spectroscopy. 

Computer simulation studies by Stillinger and Rahman (1974) suggest that the pentamer is the most likely structure to spontaneously arise in water at many temperatures, followed in frequency by hexamers, and squares. In a review of water, Frank (1970) noted that closed rings of bonds are always more stable than the most stable open chains of the same cluster number, due to the extra energy of the hydrogen bond. Through molecular dynamics studies of many five-molecule clusters, Plummer and Chen (1987) argued that the cyclic pentamer that comprises many hydrate cavities is the only stable five-member cluster above 230 K. 

Hydrate nucleation is the process during which small clusters of water and gas (hydrate nuclei) grow and disperse in an attempt to achieve critical size for continued growth. The nucleation step is a microscopic phenomenon involving tens to thousands of molecules (Mullin, 1993, p. 173) and is difficult to observe experimentally. Current hypotheses for hydrate nucleation are based upon the better-known phenomena of water freezing, the dissolution of hydrocarbons in water, and computer simulations of both phenomena. Evidence from experiments shows that nucleation is a statistically probable (not deterministically certain see Section 3.1.3) process. 

Using Equations 3.3a and b, Englezos et al. (1987a) calculated the critical radius of methane hydrate to be 30-170 A. In comparison, critical cluster sizes using classical nucleation theory are estimated at around 32 A (Larson and Garside, 1986), while computer simulations predict critical sizes to be around 14.5 A (Baez and Clancy, 1994 Westacott and Rodger, 1998 Radhakrishnan and Trout, 2002). 

The engineer may finally turn to the computer simulation packages mentioned above to obtain a mixture hydrate dissociation pressure of 1.26 MPa. 

As with all hydrate theory, it is important to interpret calculations at every opportunity in terms of experiments. With computer simulations, it is deceptively alluring to interpret calculations without physical validation, yet such a path can lead to false conclusions. When physical confirmation is not available, simulations should be regarded with caution. For example, at the heart of both MD and MC methods is the potential energy between individual molecules, which is itself an approximation and limits the accuracy of the simulated macroscopic properties. Such potentials should be validated in terms of their ability to predict measured properties, such as phase equilibria. 

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]. 

The problems being addressed in recent work carried out in various laboratories include the fundamental nature of the solute-water intermolecular forces, the aqueous hydration of biological molecules, the effect of solvent on biomolecular conformational equilibria, the effect of biomolecule - water interactions on the dynamics of the waters of hydration, and the effect of desolvation on biomolecular association 17]. The advent of present generation computers have allowed the study of the structure and statistical thermodynamics of the solute in these systems at new levels of rigor. Two methods of computer simulation have been used to achieve this fundamental level of inquiry, the Monte Carlo and the molecular dynamics methods. 

Water pentagons as structural motif in computer simulation studies. In recent years, a number of publications reported computer simulations of aqueous solutions of biological molecules [831-834]. In most studies the overall distribution of water molecules around a solute molecule was considered, and the organization of water molecules into distinct motifs was described [847]. In simulations of hydrated amino acids and a nucleic acid fragment, three motifs are frequently found in the water structure (Fig. 23.12) ... 

Subramanian S, Ravishanker G, Beveridge DL (1988) Theoretical considerations of the spine of hydration in the minor groove of d(CGCGAATTCGCG) d(CGCGAATTCGCG) Monte Carlo computer simulation. Proc Natl Acad Sci USA 85 1836-1840... 

Mezei M, Mehrotra PK, Beveridge DL (1984) Monte Carlo computer simulation study of the aqueous hydration of the glycine zwitterion at 25 °C. J Biomol Struct Dynam 2 1-27... 

Beveridge DL, Maye PV, Jayaram B, Ravishanker G, Mezei M (1984) Aqueous hydration of nucleic acid constituents Monte Carlo computer simulation studies. J Biomol Struct Dynam 2 261-270... 

Fig. 2.59. Ion-0 radial distribution functions in the ion-( 2 )199 cluster, (a) Na, (b) K. 1 Gj q (ordinate to the left). 2 Number of H2O molecules in the sphere of radius R (ordinate to the right). (Reprinted from G. G. Malenkov, Models for the structure of Hydrated Shells of Simple Ions Based on Crystal Structure Data and Computer Simulation, in The Chemical Physics of Solvation, Part A, R. R. Dogo-nadze, E. Kalman, A. A. Komyshev, and J. Ulstrup, eds., Elsevier, New York, 1985.)...

---