Other Interactions Involving Ions

Many commonly encountered materials include ionic and molecular units that may interact by mechanisms that may be considered to be hybrids between strictly coulombic phenomena and the van der Waals interactions to be considered below. Although weaker and perhaps more subtle, interactions involving a charged species and a neutral (but usually polar) unit can make a significant contribution to the total interaction energy of a system. 

Dipoles and Polarization Phenomena. Many molecules do not carry formal electrical charges, so that their mutual interactions do not involve the direct coulombic interactions discussed above. However, if one examines the structures of many useful chemical species, including polymers, proteins, and drugs, it is apparent that they often include bonds that can impart an overall polar nature to the molecule as permanent dipoles, or they can be polarized by the effect of neighboring electric fields producing induced dipoles. The presence of permanent or induced dipoles means that the molecules can become involved in specific interactions with charged species, other dipoles, or nonpolar molecules, and those interactions can significantly affect the physical characteristics of the system. 

Some molecules have dipoles that result from differences in the electronegativity of the bonded atoms, an example being the commonly encountered carbonyl group =0 ) found in many organic molecules. Other important 

In water at the isoelectric point, the molecule is electrically neutral, but the charge separation in the zwitterion produces a strong dipole that to a great extent governs the nature of the interactions of the molecule. At pH values other than the isoelectric point, the molecule becomes formally charged and 

The Dipole Moment. A dipole results from the presence of an unsymmetrical distribution of electron density within a molecule, due either to a formal charge separation, such as in amino acids, or due to differences in the electronegativities of the atoms forming a covalent bond, as in carbonyl compounds, water, and alcohols. An isolated, neutral atom, of course, cannot have an unsymmetrical electron distribution therefore atoms cannot be dipolar in nature. That is not to say, of course, that they cannot be polarized, or have their electron cloud distorted by an external electric field, but that subject is considered later. The dipole momenl, of a molecule is defined as 

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As the solute descriptors (E, S, A, B and V) represent the solute influence on various solute-solvent phase interachons, the regression coefficients e, s, a, h and V correspond to the complementary effect of the solvent phases on these interactions. As an example, consider the product aA in Eq. (4). Since A is the H-bond acidity of the solute, a is the H-bond basicity of the system. In other words, the intermolecular forces discussed in Sections 12.1.1.2 and 12.1.1.3 are present in all Abraham s log P factorization equations, with the exception of those interactions involving ions. This is the reason why Abraham s equahons are valid for neutral species only. 

This interface is critically important in many applications, as well as in biological systems. For example, the movement of pollutants tln-ough the enviromnent involves a series of chemical reactions of aqueous groundwater solutions with mineral surfaces. Although the liquid-solid interface has been studied for many years, it is only recently that the tools have been developed for interrogating this interface at the atomic level. This interface is particularly complex, as the interactions of ions dissolved in solution with a surface are affected not only by the surface structure, but also by the solution chemistry and by the effects of the electrical double layer [31]. It has been found, for example, that some surface reconstructions present in UHV persist under solution, while others do not. 

Chemical ionization (Cl) The formation of new ionized species when gaseous molecules interact with ions. This process may involve the transfer of an electron, proton, or other charged species between the reactants in an ion-molecule reaction. Cl refers to positive ions, and negative Cl is used for negative ions. 

Effect of off-diagonal dynamic disorder (off-DDD). The interaction of the electron with the fluctuations of the polarization and local vibrations near the other center leads to new terms VeP - V P, Vev - Vev and VeAp - VAPd, VA - VAd in the perturbation operators V°d and Vfd [see Eqs. (14)]. A part of these interactions corresponding to the equilibrium values of the polarization P0l and Po/ results in the renormalization of the electron interactions with ions A and B, due to their partial screening by the dielectric medium. However, at arbitrary values of the polarization P, there is another part of these interactions which is due to the fluctuating electric fields. This part of the interaction depends on the nuclear coordinates and may exceed the renormalized interactions of the electron with the donor and the acceptor. The interaction of the electron with these fluctuations plays an important role in processes involving solvated, trapped, and weakly bound electrons. 

The QM/MM and ab initio methodologies have just begun to be applied to challenging problems involving ion channels [73] and proton motion through them [74]. Reference [73] utilizes Hartree-Fock and DFT calculations on the KcsA channel to illustrate that classical force fields can fail to include polarization effects properly due to the interaction of ions with the protein, and protein residues with each other. Reference [74] employs a QM/MM technique developed in conjunction with Car-Parrinello ab initio simulations [75] to model proton and hydroxide ion motion in aquaporins. Due to the large system size, the time scale for these simulations was relatively short (lOps), but the influences of key residues and macrodipoles on the short time motions of the ions could be examined. 

If, on the other hand, loose ion pairs (between soft ions) are involved, microwave acceleration is limited, because ionic interactions are only slightly modified from GS to TS. 

Carboxypeptidase A was the first zinc enzyme to yield a three-dimensional structure to the X-ray crystallographic method, and the structure of an enzyme-pseudosubstrate complex provided a model for a precatalytic zinc-carbonyl interaction (Lipscomb etai, 1968). Comparative studies have been performed between carboxypeptidase A and thermolysin based on the results of X-ray crystallographic experiments (Argosetai, 1978 Kesterand Matthews, 1977 Monzingoand Matthews, 1984 Matthews, 1988 Christianson and Lipscomb, 1988b). Models of peptide-metal interaction have recently been utilized in studies of metal ion participation in hydrolysis (see e.g., Schepartz and Breslow, 1987). In these examples a dipole-ion interaction is achieved by virtue of a chelate interaction involving the labile carbonyl and some other Lewis base (e.g.. 

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