Local geometry effects hydrogen bonding

The chelate effect in proteins is also important, since the three-dimensional (3-D) structure of the protein can impose particular coordination geometry on the metal ion. This determines the ligands available for coordination, their stereochemistry and the local environment, through local hydrophobicity/hydrophilicity, hydrogen bonding by nearby residues with bound and non-bound residues in the metal ion s coordination sphere, etc. A good example is illustrated by the Zn2+-binding site of Cu/Zn superoxide dismutase, which has an affinity for Zn2+, such that the non-metallated protein can extract Zn2+ from solution into the site and can displace Cu2+ from the Zn2+ site when the di-Cu2+ protein is treated with excess Zn2+. 

Pratt and co-workers have proposed a quasichemical theory [118-122] in which the solvent is partitioned into inner-shell and outer-shell domains with the outer shell treated by a continuum electrostatic method. The cluster-continuum model, mixed discrete-continuum models, and the quasichemical theory are essentially three different names for the same approach to the problem [123], The quasichemical theory, the cluster-continuum model, other mixed discrete-continuum approaches, and the use of geometry-dependent atomic surface tensions provide different ways to account for the fact that the solvent does not retain its bulk properties right up to the solute-solvent boundary. Experience has shown that deviations from bulk behavior are mainly localized in the first solvation shell. Although these first-solvation-shell effects are sometimes classified into cavitation energy, dispersion, hydrophobic effects, hydrogen bonding, repulsion, and so forth, they clearly must also include the fact that the local dielectric constant (to the extent that such a quantity may even be defined) of the solvent is different near the solute than in the bulk (or near a different kind of solute or near a different part of the same solute). Furthermore... 

The validity of this model requires that the intermolecular forces (most often van der Waals) be much weaker than their intramolecular analogs, which are associated with the chemical bonds. To be more precise, provided the exact local field factors are used, the microscopic quantities deduced from or do not correspond to the p (first hyperpolarizability) and y (second hyperpolarizability) values of the gas phase species but rather to those of the molecule dressed by its surroundings. Conversely, using the hyperpolarizabilities of the isolated molecules, Eq. (3) provides the susceptibilities of an artificial crystal because the geometry and/or the electronic properties of the constituent units may not be consistent with the true crystal. Of course, the gap between the model and the true values depends upon how large the van der Waals forces, the intermolecular charge transfer effects, the hydrogen bonds, and so on, are. Its... 

The polarizable continuum model (PCM) by Tomasi and coworkers [77-79] was selected to describe the effects of solvent, because it was used to successfully investigate the effect of solvent upon the energetics and equilibria of other small molecular systems. The PCM method has been described in detail [80]. The solvents and dielectric constants used were benzene (s = 2.25), methylene chloride (g = 8.93), methanol (g = 32.0), and water (g = 78.4). Full geometry optimizations were carried out for the discrete and PCM models. To simultaneously account for localized hydrogen bonding and bulk solvation effects, PCM single-point energy calculations have been conducted on stationary points of the acrolein and butadiene reaction with two waters explicitly... 

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