Solvation term

Stouten, P.F.W., Frdmmel, C., Nakamura, H., Sander, C. An effective solvation term based on atomic occupancies for use in protein simulations. Mol. Simul. 10 (1993) 97-120. 

The most ambitious approaches to the protein folding problem attempt to solve it from firs principles (ab initio). As such, the problem is to explore the coirformational space of th molecule in order to identify the most appropriate structure. The total number of possibl conformations is invariably very large and so it is usual to try to find only the very lowes energy structure(s). Some form of empirical force field is usually used, often augmente with a solvation term (see Section 11.12). The global minimum in the energy function i assumed to correspond to the naturally occurring structure of the molecule. 

Finally, Nagaoka et al have made a very interesting study applying MC-FEP techniques to the vinyl alcohol - acetaldehyde tautomerism.32 Using a cluster of the solute with three water molecules as a solute , the free energy for the tautomerism was calculated along different reaction pathways, which had been previously found by ab initio calculations including an SCRF solvation term. They were able to deduce that a two-step mechanism is favoured over a concerted one for the transfer of the proton. 

Equation 5.7 indicates that l)//°(A B) = Z)//s°n(A-B) when the solvation terms cancel out. This is seldom observed in practice, but there is some experimental evidence that the net solvation effect on the enthalpy of reaction 5.6 may be small. For instance, it has been shown that the solvation enthalpies of an alkyl radical (R) and the parent hydrocarbon (RH) are similar both in polar and in nonpolar solvents [72], Hence, the solvation terms in equation 5.7 are approximated by Asoiv77°(RH) - A T/ R) - A /rdl) s -Asolv/7°(H). Surprisingly, the solvation enthalpy of the hydrogen atom is not readily available in the literature. Estimates based on the relationship Asoiv//°(H) Asoiv//0(H2) yield Asoiv °(H) 5 kJ mol-1 in most organic solvents and Asoiv7f°(H) -4 kJ mol-1 in water [73]. 

Another attempt to find solute geometries without explicitly including solvent molecules in the calculations is due to Sinanoglu 245,246). jn a recent paper he proposed a C-potential" effective for molecules in solution, which is derived from the potential surface of a naked solute molecule by inclusion of additive solvation terms obtainable from simple macroscopic properties of the pure liquid solvent. This method is an extension of an earlier formalism applicable to intermolecular potentials between solvated molecules 247,248). 

The partial molal property of the solute is thus composed of one ) plus one solvation ) term i.e., for a generic ion j, nonsolvation term... 

The compressibility of a generic ion or electrolyte in solution is given by the variation with P of the nonsolvation and solvation terms ... 

Qy. = Born solvation term B = coulombic repulsion term Kh+ = adsorption constant for H ). An excellent correlation resulted between the experimentally determined and calculated pHp c for nine different solids, namely quartz, kaolinite, rutile, magnetite, goethite, hematite, corundum gibbsite and MgO. For the Fe oxides, the predicted (experimentally determined) values were magnetite 7.1 (6.6), hematite 8.47 (8.5) and goethite 9.0 (9.4). 

Some stability constants for ion pairs on Fe oxides are listed in Table 10.4. This model was applied by Davis and Leckie (1978, 1980) to adsorption of various cations and anions on ferrihydrite. The extended triple layer model of Sahai and Svenjensky (1997) incorporates recent advances in aqueous electrolyte chemistry which enable aqueous activity coefficients for electrolytes to be calculated over a wide range of ionic strengths. The model also considers the free energy of adsorption of an ion to be the sum of the contributions from an electrostatic term, a Born solvation term and a ion intrinsic term. This extended model has been applied to adsorption of Co and Cd on goethite. 

Both expressions (29 a, b) reduce to the zero solvation term P = 0 at the theta point, where 8Q/K - 0, kg - kg and e, -> 0 for any P. After eliminating it, the relationship between the chain contributions to the heat of polymer transfer gel - sol in a flow-equilibrium and in a reversible-thermodynamic equilibrium can be obtained ... 

Density Functional Theory does not require specific modifications, in relation to the solvation terms [9], with respect to the Hartree-Fock formalism presented in the previous section. DFT also absorbs all the properties of the HF approach concerning the analytical derivatives of the free energy functional (see also the contribution by Cossi and Rega), and as a matter of fact continuum solvation methods coupled to DFT are becoming the routine approach for studies of solvated systems. 

There is continuous progress in molecular dynamics and energy minimization. The main topics are force field improvement [26,53-56], incorporation of effective solvation term [57], b Initio modeling of small protein [49—5155.59], the incorporation of real data for x-ray refinement [60] and NMR structure determination [61], However, much work still has to be done to improve the force fields used for ensr"1 calculations before sn,r but trivial errors be detected... 

Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations. 

---