Atomic solvation potential

Presently, only the molecular dynamics approach suffers from a computational bottleneck [58-60]. This stems from the inclusion of thousands of solvent molecules in simulation. By using implicit solvation potentials, in which solvent degrees of freedom are averaged out, the computational problem is eliminated. It is presently an open question whether a potential without explicit solvent can approximate the true potential sufficiently well to qualify as a sound protein folding theory [61]. A toy model study claims that it cannot [62], but like many other negative results, it is of relatively little use as it is based on numerous assumptions, none of which are true in all-atom representations. 

Jiao D, King C, Grossfield A, Darden TA, Ren PY (2006) Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B 110(37) 18553—18559... 

Ligand. The redox potential of the single silver atom solvated in water was calculated with the aid of a thermodynamic cycle including the electrochemical potential of the bulk metal in aqueous solution and the subhmation energy of the metal (3). The hydration energy of the neutral species is considered neghgible relative to that of the cation. 

Jiao, D., et al.. Simulation of Ca2+ and Mg2+ solvation using poiarizabie atomic multipole potential./. Phys. Chem. B, 2006.110(37],... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

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. 

Examine atomic charges and display electrostatic potential maps for ammonium and trimethylammonium ions (protonated ammonia and trimethylamine, respectively). How many acidic hydrogens are there in each Assuming that solvent coordinates to acidic hydrogens, how many solvation sites are there in each ... 

Now knowing how to evaluate solvation-free energies, we are ready to explore the effect of the solvent on the potential surface of the reacting solute atoms. Adapting the EVB approach we can describe the reaction by including the solute-solvent interaction in the diagonal elements of the solute Hamiltonian, using... 

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