Solvating Effects

The treatment of equilibrium solvation effects in condensed-phase kmetics on the basis of TST has a long history and the literature on this topic is extensive. As the basic ideas can be found m most physical chemistry textbooks and excellent reviews and monographs on more advanced aspects are available (see, for example, the recent review article by Tnihlar et al [6] and references therein), the following presentation will be brief and far from providing a complete picture. 

Onsager s reaction field model in its original fonn offers a description of major aspects of equilibrium solvation effects on reaction rates in solution that includes the basic physical ideas, but the inlierent simplifications seriously limit its practical use for quantitative predictions. It smce has been extended along several lines, some of which are briefly sunnnarized in the next section. 

Mineva T, Russo N and Sicilia E 1998 Solvation effects on reaction profiles by the polarizable continuum model coupled with Gaussian density functional method J. Oomp. Ohem. 19 290-9... 

Hydrogen-bonded clusters are an important class of molecular clusters, among which small water clusters have received a considerable amount of attention [148, 149]. Solvated cluster ions have also been produced and studied [150, 151]. These solvated clusters provide ideal model systems to obtain microscopic infonnation about solvation effect and its influence on chemical reactions. 

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. 

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

Two important contributions to the study of solvation effects were made by Bom (in 192( and Onsager (in 1936). Bom derived the electrostatic component of the free energ) c solvation for placing a charge within a spherical solvent cavity [Bom 1920], and Onsagi extended this to a dipole in a spherical cavity (Figure 11.21) [Onsager 1936]. In the Bor... 

The simulation of molecules in solution can be broken down into two categories. The first is a list of elfects that are not defined for a single molecule, such as diffusion rates. These types of effects require modeling the bulk liquid as discussed in Chapters 7 and 39. The other type of effect is a solvation effect, which is a change in the molecular behavior due to the presence of a solvent. This chapter addresses this second type of effect. 

In a few cases, where solvent effects are primarily due to the coordination of solute molecules with the solute, the lowest-energy solvent configuration is sufficient to predict the solvation effects. In general, this is a poor way to model solvation effects. 

This chapter focuses on the simulation of bulk liquids. This is a dilferent task from modeling solvation effects, which are discussed in Chapter 24. Solvation effects are changes in the properties of the solute due to the presence of a solvent. They are defined for an individual molecule or pair of molecules. This chapter discusses the modeling of bulk liquids, which implies properties that are not defined for an individual molecule, such as viscosity. 

A number of types of calculations can be performed. These include optimization of geometry, transition structure optimization, frequency calculation, and IRC calculation. It is also possible to compute electronic excited states using the TDDFT method. Solvation effects can be included using the COSMO method. Electric fields and point charges may be included in the calculation. Relativistic density functional calculations can be run using the ZORA method or the Pauli Hamiltonian. The program authors recommend using the ZORA method. 

COSMO (conductor-like screening model) a method for including solvation effects in orbital-based calculations... 

GAPT (generalized atomic polar tensor) a charge calculation method GB/SA (generalized Born/surface area) method for computing solvation effects... 

OPW (orthogonalized plane wave) a band-structure computation method P89 (Perdew 1986) a gradient corrected DFT method parallel computer a computer with more than one CPU Pariser-Parr-Pople (PPP) a simple semiempirical method PCM (polarized continuum method) method for including solvation effects in ah initio calculations... 

Photoelectron spectroscopic studies show that the first ionization potential (lone pair electrons) for cyclic amines falls in the order aziridine (9.85 eV) > azetidine (9.04) > pyrrolidine (8.77) >piperidine (8.64), reflecting a decrease in lone pair 5-character in the series. This correlates well with the relative vapour phase basicities determined by ion cyclotron resonance, but not with basicity in aqueous solution, where azetidine (p/iTa 11.29) appears more basic than pyrrolidine (11.27) or piperidine (11.22). Clearly, solvation effects influence basicity (74JA288). 

Pinto-Graham Pinto and Graham studied multicomponent diffusion in electrolyte solutions. They focused on the Stefan-Maxwell equations and corrected for solvation effects. They achieved excellent results for 1-1 electrolytes in water at 25°C up to concentrations of 4M. 

An understanding of a wide variety of phenomena concerning conformational stabilities and molecule-molecule association (protein-protein, protein-ligand, and protein-nucleic acid) requires consideration of solvation effects. In particular, a quantitative assessment of the relative contribution of hydrophobic and electrostatic interactions in macromolecular recognition is a problem of central importance in biology. 

III. SOLVATION EFFECT ON A VARIETY OF CHEMICAL PROCESSES IN SOLUTION... 

The substituent stabilization effects calculated for the methyl cation and the methyl anion refer to the gas phase, where no solvation effects are present, and therefore are substantially larger, in terms of eneigy, than would be the case in solution, where solvation contributes to stabilization and attenuates the substituent effects. 

Whether AH for a projected reaction is based on bond-energy data, tabulated thermochemical data, or MO computations, there remain some fundamental problems which prevent reaching a final conclusion about a reaction s feasibility. In the first place, most reactions of interest occur in solution, and the enthalpy, entropy, and fiee energy associated with any reaction depend strongly on the solvent medium. There is only a limited amount of tabulated thermochemical data that are directly suitable for treatment of reactions in organic solvents. Thermodynamic data usually pertain to the pure compound. MO calculations usually refer to the isolated (gas phase) molecule. Estimates of solvation effects must be made in order to apply either experimental or computational data to reactions occurring in solution. 

It should always be home in mind that solvent effects can modify the energy of both tile reactants and the transition slate. It is the difference in the two solvation effects that is the basis for changes in activation energies and reaction rates. Ihus, although it is conimon to express solvent effects solely in terms of reactant solvation or transition-slate solvation,... 

Having considered how solvents can affect the reactivities of molecules in solution, let us consider some of the special features that arise in the gas phase, where solvation effects are totally eliminated. Although the majority of organic preparative reactions and mechanistic studies have been conducted in solution, some important reactions are carried out in the gas phase. Also, because most theoretical calculations do not treat solvent effects, experimental data from the gas phase are the most appropriate basis for comparison with theoretical results. Frequently, quite different trends in substituent effects are seen when systems in the gas phase are compared to similar systems in solution. 

This is opposite from the order in solution as revealed by the pK data in water and DMSO shown in Table 4.14. These changes in relative acidity can again be traced to solvation effects. In the gas phase, any substituent effect can be analyzed directly in terms of its stabilizing or destabilizing effect on the anion. Replacement of hydrogen by alkyl substituents normally increases electron density at the site of substitution, but this effect cannot be the dominant one, because it would lead to an ordering of gas-phase acidity opposite to that observed. The dominant effect is believed to be polarizability. The methyl... 

Shifts in the SEC fractionation range are not new. It has been known for decades that adding chaotropes to mobile phases causes proteins to elute as if they were much larger molecules. Sodium dodecyl sulfate (SDS) (9) and guanidinium hydrochloride (Gd.HCl) (9-12) have been used for this purpose. It has not been clearly determined in every case if these shifts reflect effects of the chaotropes on the solutes or on the stationary phase. Proteins are denatured by chaotropes the loss of tertiary structure increases their hydrodynamic radius. However, a similar shift in elution times has been observed with SEC of peptides in 0.1% trifluoroacetic acid (TEA) (13-15) or 0.1 M formic acid (16), even if they were too small to have significant tertiary structure. Speculation as to the cause involved solvation effects that decreased the effective pore size of the... 

Earlier analyses making use of AH vs. AS plots generated many p values in the experimentally accessible range, and at least some of these are probably artifacts resulting from the error correlation in this type of plot. Exner s treatment yields p values that may be positive or negative and that are often experimentally inaccessible. Some authors have associated isokinetic relationships and p values with specific chemical phenomena, particularly solvation effects and solvent structure, but skepticism seems justified in view of the treatments of Exner and Krug et al. At the present time an isokinetic relationship should not be claimed solely on the basis of a plot of AH vs. A5, but should be examined by the Exner or Krug methods. 

---