Solvation models calculation comparison

Fig. 2.6 Comparison of the calculated structures for glycine in the gas-phase and in water (COSMO solvation model). Note that the central bond angle in the zwitterionic form 1 is distorted by the hydrogen bond length of 1.96A computed for this structure in the gas phase. When solvation effects are included in the calculation using COSMO, the electrostatic interaction is reduced in magnitude due to charge screening by water, and the bond angle distortion is no longer present.

Three different sets of experimental aqueous-phase pKa s allow us to judge to what extent solvent effects can be ignored and, where they cannot be ignored, assess the performance of the SMS. 4 model in accounting for solvation. The first involves a diverse set of carboxylic acids and the second a diverse series of alcohols and phenols. Calculated acidities (relative to acetic acid in the case of carboxylic acids and relative to ethanol in the case of alcohols and phenols) have been obtained from the Hartree-Fock 6-311+G model. Previous comparisons with gas-phase acidities suggest that this should be as satisfactory as any other model for this purpose (see, for example. Tables 6-18 and A6-50). 6-3IG geometries have been used in place of 6-311+G geometries in order to save computation time. (See... 

Of course, the simplicity of the QM/MM operator does not imply diat it has only a small effect. Large atomic partial charges placed near the QM fragment would be expected to polarize the system strongly. Table 13.2 compares the dipole moments of the standard nucleic acid bases at the AMI level evaluated in the gas phase and in a QM/MM calculation carried out modeling aqueous solvation with a periodic box of TIP31 water molecules. Eor comparison, results from the AM1-SM2 aqueous continuum solvation model are also provided. 

Comparisons of Calculations Employing Explicit and Implicit Solvation Models... 

Brunne, R.M., Liepinsh, E., Otting, G., Wuthrich, K., and Vangunsteren, WF. (1993) Hydration of proteins a comparison of experimental residence times of water-molecules solvating the bovine pancreatic trypsin-inhibitor with theoretical-model calculations. Journal of Molecular Biology, 231, 1040-1048. 

Table 12.1 Solvation energies calculated with the differential geometry nonpolar solvation model for a set of 11 alkanes in comparison with an explicit solvent model [154]...

To date the SMx family is probably the best parametrized model for calculations of the energy of hydration, especially in the case of local minima. Nevertheless, the last versions of the PCM and SCRF models which do not contain the parametric expressions, at least for the electrostatics, look very promising. For the choice of the most efficient application, a careful comparison of the results of these three versions of solvation models is needed. 

For comparison with real reactions, it is usually necessary to strip the chemical system to its essentials to reduce the number of atoms in the reaction system and permit computational feasibility. Most reactions are run in solution whereas the computations apply to the gas phase thus, solvation needs to be considered at some level. Solvation is particularly important when ions are involved. It is less important for the reactions of neutral polar organometallics but these compounds generally have significant dipole moments and solvation is not insignificant. Nevertheless, most calculations of reaction systems have generally ignored solvation at least explicitly. In some recent cases solvation was modeled by coordination of one or more solvent molecules with the metal or by use of a continuum model for solvation (see Solvation Modeling). 

In the IPCM calculations, the molecule is contained inside a cavity within the polarizable continuum, the size of which is determined by a suitable computed isodensity surface. The size of this cavity corresponds to the molecular volume allowing a simple, yet effective evaluation of the molecular activation volume, which is not based on semi-empirical models, but also does not allow a direct comparison with experimental data as the second solvation sphere is almost completely absent. The volume difference between the precursor complex Be(H20)4(H20)]2+ and the transition structure [Be(H20)5]2+, viz., —4.5A3, represents the activation volume of the reaction. This value can be compared with the value of —6.1 A3 calculated for the corresponding water exchange reaction around Li+, for which we concluded the operation of a limiting associative mechanism. In the present case, both the nature of [Be(H20)5]2+ and the activation volume clearly indicate the operation of an associative interchange mechanism (156). 

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