Thermodynamics hydration, simulations

Aromatic molecules are hydrophobic but their thermodynamic hydration parameters are essentially different from those of aliphatic hydrocarbons (Table 2.5). The data in this table reveal that for benzene and toluene the A Gtr values are negative, primarily resulting from less unfavorable A Str values. Advanced MD simulations of the hydration of benzene and cyclohexane have shown that there is a definite tendency for H-bond interactions of the waters with the tt-electron system of the aromatics. This is confirmed by the solubility... 

Straatsma, T.P, Berendsen, H.J.C. Free energy of ionic hydration Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations. J. Chem. Phys. 89 (1988) 5876-5886. 

Hummer, G., Fast-growth thermodynamic integration results for sodium ion hydration, Mol. Simul. 2002, 28, 81-90... 

So far, CG approaches offer the most viable route to the molecular modeling of self-organization phenomena in hydrated ionomer membranes. Admittedly, the coarse-grained treatment implies simplifications in structural representation and in interactions, which can be systematically improved with advanced force-matching procedures however, it allows simulating systems with sufficient size and sufficient statishcal sampling. Structural correlations, thermodynamic properties, and transport parameters can be studied. 

Tsuji, H. Kobayashi, T. Okano, Y. Ohmura, R. Yasuoka, K. Mori, Y.H. (2005b). Thermodynamic Simulations of Isobaric Hydrate-Forming Operations Formulation of Computational Scheme and Its Application to Hydrate Formation from a Methane + Ethane + Propane Mixture. Energy and Fuel, 19, 1587-1597. 

Chapter 5 details the modified statistical thermodynamic prediction method of van der Waals and Platteeuw (1959). The application of molecular simulation methods to hydrates is outlined in Section 5.3. 

The molecular dynamic technique has been validated for water structures through comparison of calculated properties with experimental thermodynamic water data, such as the density maximum, the high heat capacity, and diffraction patterns (Stillinger and Rahman, 1974) as well as the hydrate infrared (vibrational) spectral data by Bertie and Jacobs (1977, 1982). With acceptable comparisons of many computed and experimental properties of water structures, there is little doubt that a substance similar to water has been simulated. 

In addition to the change in the theoretical methods applied to hydrates, there have been significant advancements and widespread use of meso- and microscopic tools in hydrate research. Conversely, the typical static experimental apparatus used today to measure macroscopic properties, such as phase equilibria properties, is based on the same principles as the apparatus used by Deaton and Frost (1946). In part, this is due to the fact that the simplest apparatus is both the most elegant and reliable simulation of hydrate formation in industrial systems. In Section 6.1.1 apparatuses for the determination of hydrate thermodynamic and transport macroscopic properties are reviewed. 

The FREZCHEM model was designed to characterize aqueous electrolyte solutions. To work properly, there must always be ions in solution, even if only hypothetical. To simulate pure water, pure gas hydrate, pure ice, or other nonion equilibria, you need to add minor concentrations of ions (e.g., Na = Cl = 1 x 10 6m). Such minor concentrations do not significantly affect the thermodynamic properties, but they do allow for proper model calculations. 

According to the MD simulations examined for cesium iodide solutions of 2.78 mol dm-3 (Csl H20 = 1 20) at 25 and 64°C and 5.56 mol dm-3 (Csl H20 = 1 10) at 64°C (34), higher ion pairs than 1 1 form in the 2.78 mol dm-3 solution, but formation is suppressed as the temperature is raised. Thus, ion-pair formation reactions between cesium and iodide, both of which are weakly hydrated, must be exothermic, although no thermodynamic data are available in the literature. The increase in concentration at a given temperature (64°C) enhances the formation of the ionic aggregates from raCsI = 1.07 to 1.80. 

Because of the ease with which molecular mechanics calculations may be obtained, there was early recognition that inclusion of solvation effects, particularly for biological molecules associated with water, was essential to describe experimentally observed structures and phenomena [32]. The solvent, usually an aqueous phase, has a fundamental influence on the structure, thermodynamics, and dynamics of proteins at both a global and local level [3/]. Inclusion of solvent effects in a simulation of bovine pancreatic trypsin inhibitor produced a time-averaged structure much more like that observed in high-resolution X-ray studies with smaller atomic amplitudes of vibration and a fewer number of incorrect hydrogen bonds [33], High-resolution proton NMR studies of protein hydration in aqueous... 

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. 

Michael E. Paulaitis is Professor of Chemical and Biomolecular Engineering and Ohio Eminent Scholar at Ohio State University. He is also Director of the Institute of Multiscale Modeling of Biological Interactions at Johns Hopkins University. His research focuses on molecular thermodynamics of hydration, protein solution thermodynamics, and molecular simulations of biological macromolecules. 

Full internal motions of protein Dynamic and thermodynamic coupling between hydration water and protein, seen in Mossbauer spectroscopy and computer simulations... 

Nicolas C, Boutin A, Levy B, Borgis D. (2003) Molecular simulation of a hydrated electron at different thermodynamic state points. J Chem Phys 118 9689-9696. 

Realistic three-dimensional computer models for water were proposed already more than 30 years ago (16). However, even relatively simple effective water model potentials based on point charges and Leimard-Jones interactions are still very expensive computationally. Significant progress with respect to the models ability to describe water s thermodynamic, structural, and dynamic features accurately has been achieved recently (101-103). However, early studies have shown that water models essentially capture the effects of hydrophobic hydration and interaction on a near quantitative level (81, 82, 104). Recent simulations suggest that the exact size of the solvation entropy of hydrophobic particles is related to the ability of the water models to account for water s thermodynamic anomalous behavior (105-108). Because the hydrophobic interaction is inherently a multibody interaction (105), it has been suggested to compute pair- and higher-order contributions from realistic computer simulations. However, currently it is inconclusive whether three-body effects are cooperative or anticooperative (109). 

Thermodynamic properties for cation-water complexes have also been evaluated for PCM-based potentials. In one case [131], the hydration free energies of complexes with different numbers of hydration waters have been calculated by an appropriate thermodynamic cycle. It turned out that the best agreement with experimental results, always quite satisfactory, was reached when the number of waters considered was that found in the simulation. 

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. 

The most expensive part of a simulation of a system with explicit solvent is the computation of the long-range interactions because this scales as Consequently, a model that represents the solvent properties implicitly will considerably reduce the number of degrees of freedom of the system and thus also the computational cost. A variety of implicit water models has been developed for molecular simulations [56-60]. Explicit solvent can be replaced by a dipole-lattice model representation [60] or a continuum Poisson-Boltzmann approach [61], or less accurately, by a generalised Bom (GB) method [62] or semi-empirical model based on solvent accessible surface area [59]. Thermodynamic properties can often be well represented by such models, but dynamic properties suffer from the implicit representation. The molecular nature of the first hydration shell is important for some systems, and consequently, mixed models have been proposed, in which the solute is immersed in an explicit solvent sphere or shell surrounded by an implicit solvent continuum. A boundary potential is added that takes into account the influence of the van der Waals and the electrostatic interactions [63-67]. 

The modem era of hydrate research is marked by the industrial adoption of the van der Waals and Platteeuw statistical thermodynamics model for the hydrate phase. The spectroscopic measurement of the hydrate phase, abetted with molecular simulation, led to accuracy improvements, and industrial applications to energy, seafloor stability, and climate change. With the above historical advances, consider modem thermodynamics of the hydrate phase itself. 

Straatsma, T. P. and H. J. C. Berendsen (1988). Free Energy of Ionic Hydration Analysis of a Thermodynamic Technique to Evaluate Free Energy Differences by Molecular Dynamics Simulations. L Chem. Phvs. 89(9) 5876. 

---