Aqueous solutions molecular dynamics simulations

Zeolites can contain charge-compensating cations. These cations can be mobile and can be exchanged, usually with an aqueous solution. Molecular dynamics simulations of the cation mobility in anhydrous zeolite A have been performed by Shin et al.2S2 Xhe most complete studies to date of a real zeolite are molecular dynamics simulations of zeolite A containing both sodium cations and water.283-285... 

For most electrolyte solutions at or near room temperature, there have been two main approaches, exemplified by the Pitzer and HKF models to be described below. (These two approaches were also mentioned on page 304.) In one, referred to as ion-interaction theory and embodied in the Pitzer equations, no attempt is made (except if there are very strong complexes present) to identify species. Components are treated stoichiometrically, and all ion interactions are accounted for in the form of fit coefficients in some form of equation. Advocates of this approach point to the rather uncertain nature of our knowledge of aqueous species. Molecular dynamics simulations of these solutions... 

One of the main advantages of the stochastic dynamics methods is that dramatic tirn savings can he achieved, which enables much longer stimulations to he performed. Fc example, Widmalm and Pastor performed 1 ns molecular dynamics and stochastic dynamic simulations of an ethylene glycol molecule in aqueous solution of the solute and 259 vvatc jnolecules [Widmalm and Pastor 1992]. The molecular dynamics simulation require 300 hours whereas the stochastic dynamics simulation of the solute alone required ju 24 minutes. The dramatic reduction in time for the stochastic dynamics calculation is du not only to the very much smaller number of molecules present hut also to the fact the longer time steps can often he used in stochastic dynamics simulations. 

You can detect hydroxyl group transitions by plotting dihedral angles versus time over the course of the simulation. This is the distance history. Brady investigated the distance history of water 19. Brady, J.W. Molecular dynamics simulations of a-d-glucose in aqueous solution. 

A good understanding of the properties of water is thus essential as we move to more complicated systems. We have been involving in the study of aqueous solution of many important biological molecules, such as acetylcholine, Gramicidin, deoxydinucleoside phosphate and proflavin, and DNA, etc., first at the Monte Carlo level and slowly moving to the molecular dynamics simulations. We will discuss some of the new results on the hydration structure and the dynamics of B- and Z-DNA in the presence of counterions in the following. 

Heinje, G., Luck, W. A. P. Heinzinger, K. (1987). Molecular dynamics simulation of an aqueous sodium perchlorate solution. Journal of Physical Chemistry, 91, 331-8. 

Santiveri, C. M., Jimenez, M. A., Rico, M., van Gunsteren, W. F., and Daura, X. (2002). /3-Hairpin folding and stability Molecular dynamics simulations of designed peptides in aqueous solution. Submitted. 

Fig. 6.10. Comparison of overlap sampling and FEP calculation results for the free energy change along the mutation of an adenosine in aqueous solution (between A = 0.05 and 0.45) in a molecular dynamics simulation. The results represent the average behavior of 14 independent runs. (MD time step.) The sampling interval is 0.75 ps. The upper half of the plot presents the standard deviation of the mean (with gives statistical error) for AA as a function of sample size N the lower half of the plot gives the estimate of A A - for comparison of the accuracy, the correct value of AA is indicated by the bold horizontal line...

Simonson, T. Perahia, D., Microscopic dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution, J. Am. Chem. Soc. 1995, 117, 7987-8000... 

Figure 2 The molecular dynamics simulation picture of [Gd(DOTA)(H20)] in aqueous solution shows the inner sphere water, directly bound to the metal (its oxygen is dark) the second sphere water molecules, bound to the carboxylates of the ligand through hydrogen bridges (their oxygens are gray) and outer sphere or bulk water molecules without preferential orientation (in white).

Parchment et al. [271] have provided more recent calculations on the 3-hydroxypyrazole equilibrium at the ab initio level. They noted that tautomer 9, which was not considered by Karelson et al. [268], is the lowest-energy tautomer in the gas phase at levels of theory (including AMI) up to MP4/6-31G //HF/3-21G [271], Although 8 is the dominant tautomer observed experimentally in aqueous solution, in the gas phase 8 is predicted to be nearly 9 kcal/mol less stable than 9 at the MP4 level [271], Using a DO model with an unphysically small cavity radius of 2.5 A, Parchment et al. [271] were able to reproduce at the ab initio level the AMI-DO prediction of Karelson et al. [268], namely that 8 is the most stable tautomer in aqueous solution. With this cavity, though, 8 is predicted to be better solvated than 9 by -22.2 kcal/mol [271], This result is inconsistent with molecular dynamics simulations with explicit aqueous solvation [271], and with PCM and SCME calculations with more reasonable cavities [271] these predict that 8 is only about 3 kcal/mol better solvated than 9. In summary, the most complete models used by Parchment et al. do not lead to agreement with experiment... 

The 3H chemical shifts, coupling constants, temperature coefficients, exchange rates and inter-residual ROEs of the hydroxyl protons of various synthetic type II trisaccharides, analogues of (3-D-Galp-(l - 4)-p-D-GlcpNAc-(l - 2)-a-D-Man-(l - 0)(CH2)7CH3, were reported and interpreted,8 assisted with molecular dynamic simulations, to deduce key information on the conformational behavior of these important molecules in aqueous solution. 

Figure 7. Water oxygen-exocyclic methylene carbon pair distribution function, calculated from a molecular dynamics simulation of a-D-glucopyranose in aqueous solution, giving the normalized probability of finding a water oxygen atom a given distance r from the C6 carbon atom. (Reproduced from Ref. 32. Copyright 1989 American Chemical Society.)...

Nada, H. (2006). Growth mechanism of a gas clathrate hydrate from a dilute aqueous gas solution A molecular dynamics simulation of a three-phase system. J. Phys. Chem. B, 110 (33,1, 16526-16534. 

MacKerell, Jr., A. D. (1995) Molecular dynamics simulation analysis of a sodium dodecyl sulfate micelle in aqueous solution decreased fluidity of the micelle hydrocarbon interior. J. Phys. Chem. 99, 1846-1855. 

Engstrdm et al. [112] used molecular dynamics simulations to study quadrupole relaxation mechanism for Li+, Na+, and Cl ions in dilute aqueous solutions. They found that NMR relaxation rate for these ions was determined by the relaxation of water molecules in the first solvation shell. The simulations show nonexponential solvation dynamics which can be modeled by two relaxation time constants < 0.1 ps and x2 lps (see Table 4). 

In view of the studies [75] of aqueous NaCl solutions by using molecular-dynamics simulation, one may suggest that our models are applicable61 only at low salt concentrations Cm, for which the Kirkwood correlation factor g could be calculated from Eq. (414d), where the ionic contribution Ae on(0) is not involved. 

Crown ethers continue to be one of the most useful parts of supramolecular chemistry/91 From the beginning computations of metal ions complexes with synthetic ionophores/101 which have been aptly reviewed/111 emphasized the importance of including explicitly solvation in free energy calculations, also with ab initio calculations on calixarene complexes/121 Molecular dynamics simulations of 18-crown-6 ether complexes in aqueous solutions predict too low affinities, but at least correctly reproduce the sequence trend K+ > Rb+ > Cs+ > Na+. However, only the selection of K+ over Rb+ and Cs+ is ascribed to the cation size relative to that of the crown cavity, whereas K+ appears in these calculations to be selected over Na+ as consequence of the greater free energy penalty involved in displacing water molecules ftomNa/1131... 

Straatsma, T. P., McCammon, J. A. (1989), Treatment of Rotational Isomers in Free Energy Calculations. II. Molecular Dynamics Simulation of 18-Crown-6 in Aqueous Solution as an Example of Systems with Large Numbers of Rotational Isomeric States, J. Chem. Phys. 91, 3631-3637. 

Theoretical studies using the results of molecular dynamics simulation of A-methylazetidin-2-one in aqueous solution predicted a stepwise mechanism for the hydrolysis <1998JA2146>. In the alkaline hydrolysis, the first reaction step involved the formation of a tetrahedral intermediate, which required a desolvation of the hydroxyl anion, which is difficult to simulate by calculations. Afterwards, the reaction proceeded through either a concerted or stepwise mechanism for ring opening and proton transfer. 

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