Protonated hydrates molecular dynamics calculations

Architecture of Hydrates and Local Structure of Acetic Acid Aqueous Solution Ab Initio Calculations and Car-Parrinello Molecular Dynamics (CPMD) Simulations on Hydrogen-Bonding Rings, Network, and Intra-Hydrate Protonation in Multi-Hydrates of Acetic Acid Monomer... 

Both the experimental and theoretical studies indicate that the interactions between acetic acid and water molecules are more competitive in dilute aqueous solution. However to our knowledge, the specific interactions between acetic acid and water molecules are still not well understood, especially in such as the nature of hydrogen bonding, the bonds networking, the rule in architecture of larger hydration compounds, deprotonation of acetic acid in solution, stability of the hydrated proton, the local structure of its aqueous solution, and so on. In the present work, we have performed ab initio calculations on multi-hydrates (rich water hydration compounds) of acetic acid, and ab initio Car-Parrinello molecular dynamics (CPMD) [20] simulations on acetic acid monomer and water system (at dilute aqueous solution condition) to find something helpful for interpreting the nature of acetic acid aqueous solution. 

Theoretical studies on protonated hydrates (PH) are illustrative of the progress realized in theoretical chemistry over several decades. The evolution of such studies is presented. The main methods used (quantum chemistry, Monte Carlo or Molecular Dynamics calculations...) and the problems encountered are briefly recalled. Some of the results obtained are commented. 

This short and very limited review gives an idea of the wide variety and complexity of the problems encountered in the study of protonated hydrates. This selection of topics is illustrative of the new possibilities offered by the present developments of theoretical treatments and shows the progress realised in this field, especially within the last few years. Besides the improvement of the accuracy of some of the methods used, in particular to treat the correlation contribution to the intermolecular energies, other categories of methods of lower accuracy bring other kinds of information. This has been exemplified by the results obtained from Monte Carlo and Molecular Dynamics calculations based on the use of DFT or analytical potentials. Though great care must be taken to the possibility of artefacts due to the approximations included in these treatments, such work is complementary to more accurate determinations. We can expect all these methods to be more and more coupled in the near future. 

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... 

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