Continuum basis calculation

Due to the numerous potential cycles using explicit molecules, levels of theory, basis sets, and types of molecules, it is impossible to determine one specific method that produces the most accurate pKa values. Rather, this review serves to summarize the current literature and illustrate various schemes that have been successful. Accurate attention to detail and the use of benchmark calculations or experimental values to assist in determination of the correct method to use for a particular system is highly recommended. Further research on thermodynamic cycles using explicit cycles, clustered water structures, conformational effects, and advances in continuum solvation calculations will continue to advance this field. 

In an early work by Mertz and Pettitt, an open system was devised, in which an extended variable, representing the extent of protonation, was used to couple the system to a chemical potential reservoir [67], This method was demonstrated in the simulation of the acid-base reaction of acetic acid with water [67], Recently, PHMD methods based on continuous protonation states have been developed, in which a set of continuous titration coordinates, A, bound between 0 and 1, is propagated simultaneously with the conformational degrees of freedom in explicit or continuum solvent MD simulations. In the acidostat method developed by Borjesson and Hiinenberger for explicit solvent simulations [13], A. is relaxed towards the equilibrium value via a first-order coupling scheme in analogy to Berendsen s thermostat [10]. However, the theoretical basis for the equilibrium condition used in the derivation seems unclear [3], A test using the pKa calculation for several small amines did not yield HH titration behavior [13],... 

Although continuum solvation models do appear to reproduce the structural and spectroscopic properties of many molecules in solution, parameterization remains an issue in studies involving solvents other than water. In addition, the extension of these approaches to study proteins embedded in anisotropic environments, such as cell membranes, is clearly a difficult undertaking96. As a result, several theoretical studies have been undertaken to develop semi-empirical methods that can calculate the electronic properties of very large systems, such as proteins28,97 98. The principal problem in describing systems comprised of many basis functions is the method for solving the semi-empirical SCF equations ... 

Tomas et al. [281] have calculated the tautomeric equilibrium of 1,2,3-benzotriazole in the gas phase and compared their results to experimental data [282] derived from ultraviolet spectroscopy. Experiment suggests that 35 is about 4 kcal/mol more stable than 34 this result is consistent with calculations [281] at the MP2/6-31G level, which predict 35 to be 2.5 kcal/mol more stable than 34. The same level of theory predicts 33 to be 5.0 kcal/mol more stable than 32 in the parent triazole system. Although experimental data are available indicating 35 to be the dominant tautomer in CDCf and d6-dimethyl sulfoxide solutions [279, 283], this equilibrium does not appear to have been the subject of any modeling, continuum or otherwise. It may prove to be somewhat challenging, however. Tomas et al. point out that correlation effects favor 35 by about 5 kcal/mol at the MP2 level AMI, PM3, and HF calculations with moderate basis sets all predict... 

In order to utilise our colloids as near hard spheres in terms of the thermodynamics we need to account for the presence of the medium and the species it contains. If the ions and molecules intervening between a pair of colloidal particles are small relative to the colloidal species we can treat the medium as a continuum. The role of the molecules and ions can be allowed for by the use of pair potentials between particles. These can be determined so as to include the role of the solution species as an energy of interaction with distance. The limit of the medium forms the boundary of the system and so determines its volume. We can consider the thermodynamic properties of the colloidal system as those in excess of the solvent. The pressure exerted by the colloidal species is now that in excess of the solvent, and is the osmotic pressure II of the colloid. These ideas form the basis of pseudo one-component thermodynamics. This allows us to calculate an elastic rheological property. Let us consider some important thermodynamic quantities for the system. We may apply the first law of thermodynamics to the system. The work done in an osmotic pressure and volume experiment on the colloidal system is related to the excess heat adsorbed d Q and the internal energy change d E ... 

In turning to cases where strong, specific interactions with the solvent are expected, the picture can change considerably and it is no longer obvious that dielectric continuum theory provides a reasonable basis for calculating x It is apparent that dielectric continuum theory can not be used to account for solvent induced variations in AE but, as mentioned earlier, there is hope that a combination of dielectric continuum theory and the use of empirically determined solvent parameters can provide a framework for understanding solvent effects. The importance of specific solvent effects shows up dramatically for MLCT or LMCT transitions in complexes such as shown below (21) ... 

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