Hydration molecular dynamics

Smirnov, G.S., Stegailov, V.V. Melting and supeiheating of si methane hydrate molecular dynamics study. J. Chem. Phys. 136, 044523 (2012)... 

Keywords clathrate hydrates, molecular dynamics, equilibrium temperature 1. Introduction... 

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. 

Tieleman, D.P., Berendsen, H.J.C. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated POPE bilayer. Biophys. J., in print (1998). 

D. Beglov and B. Roux. Dominant solvations effects from the primary shell of hydration Approximation for molecular dynamics simulations. Biopolymers, 35 171-178, 1994. 

Essex J W, M M Harm and W G Richards 1994. Molecular Dynamics of a Hydrated Phospholipi Bilayer. Philosophical Transactions of the Royal Society of London 8344 239-260. 

In our last example we return to the issue of the possible damaging effects of the standard geometry constraints. Two long trajectories have been computed for a partially hydrated dodecamer DNA duplex of the previous example, first by using ICMD and second with Cartesian coordinate molecular dynamics without constraints [54]. Both trajectories started from the same initial conformation with RMSD of 2.6 A from the canonical B-DNA form. Figure 5 shows the time evolution of RMSD from the canonical A and B conformations. Each point in the figure corresponds to a 15 ps interval and shows an average RMSD value. We see that both trajectories approach the canonical B-DNA, while the RMSD... 

This chapter has given an overview of the structure and dynamics of lipid and water molecules in membrane systems, viewed with atomic resolution by molecular dynamics simulations of fully hydrated phospholipid bilayers. The calculations have permitted a detailed picture of the solvation of the lipid polar groups to be developed, and this picture has been used to elucidate the molecular origins of the dipole potential. The solvation structure has been discussed in terms of a somewhat arbitrary, but useful, definition of bound and bulk water molecules. 

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. 

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. 

Armrmanto, R., Schwenk, C.F. and Rode, B.M. (2003) Structure and Dynamics of Hydrated Ag (I) Ab Initio Quantum Mechanical-Molecular Mechanical Molecular Dynamics Simulation. The Journal of Physical Chemistry A, 107, 3132-3138. 

Wei, D., Salahub, D. R., 1997, Hydrated Proton Clusters Ab Initio Molecular Dynamics Simulation and Simulated Annealing , J. Chem. Phys., 106, 6086. 

Noskov S Y, Lamoureux G, Roux B (2005) Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field. J Phys Chem B 109(14) 6705-6713... 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

Chipot, C. Millot, C. Maigret, B. Kollman, P. A., Molecular dynamics free energy perturbation calculations. Influence of nonbonded parameters on the free energy of hydration of charged and neutral species, J. Phys. Chem. 1994, 98,11362-11372... 

Straatsma, T. R Berendsen, H. J. C. Postma, J. P. M., Free energy of hydrophobic hydration. A molecular dynamics study of noble gases in water, J. Chem. Phys. 1986, 85, 6720-6727... 

Grossman, J. C. Schwegler, E. Galli, G., Quantum and classical molecular dynamics simulations of hydrophobic hydration structure around small solutes, J. Phys. Chem. B 2004,108, 15865-15872... 

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). 

Molecular dynamics calculations have been performed (35-38). One ab initio calculation (39) is particularly interesting because it avoids the use of pairwise potential energy functions and effectively includes many-body interactions. It was concluded that the structure of the first hydration shell is nearly tetrahedral but is very much influenced by its own solvation. 

Schwartz, B. J. and Rossky, P. J. Pump-probe spectroscopy of the hydrated electron a quantum molecular dynamics simulation, J. Chem.Phys., 101 (1994), 6917-6926... 

Figure 1 (Plate 1). A molecular view of a small section of a flat lipid bilayer generated by molecular dynamics simulations. The bilayers are composed of l-stearoyl-2-docosa-hexaenoyl-5M-g]ycero-3-phosphatidylcholine lipids, i.e. the sn 1 chain is 18 C atoms long and the sn2 chain has 22 carbons, including six cis double bonds. The hydrophobic core is in the centre of the picture, and the hydrated head-group regions are both on top and bottom of the view graph. The head group is zwitterionic and no salt has been added. From [102], Reproduced by permission of the American Physical Society. Copyright (2003)...

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