Hydrogen bonding solvation models

Molecular mechanics with special treatment of hydrogen bonding, solvation, and metal ions. Also Yak for receptor modeling based on directionality of potential binding points on a ligand. VAX, Silicon Graphics, and Evans 8c Sutherland. 

The goal of this section is to describe a semiempirical model of nanoscale solvation that captures the dielectric modulation brought about by the approach of a hydrophobe to a protein hydrogen bond. In essence, the model captures the solvent-ordering effect promoted by the hydrophobe and quantifies the effect of this induced organization on the electrostatics of a pre-formed amide-carbonyl hydrogen bond. This model reproduces the crossover point in hydrogen bond dehydration... 

It should be noted that the regular solution theory, upon which Eqs. (3.31) and (3.32) are based, is valid only for solute-solvent systems that are free of strong associative behavior, such as hydrogen bonding, solvation, or complex formation (Modell and Reid 1983). As such, Eq. (3.32) is correctly applied to ideal systems or nonideal systems that exhibit positive, as opposed to negative. 

The most important noncovalent interactions in these transitions are hydrogen bonding, solvation, and hydrophobic interactions. The dynamics of these processes have been extensively studied in model systems, and the results obtained provide some insight into the corresponding processes in proteins [21]. 

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. 

Solvent effects on chemical equilibria and reactions have been an important issue in physical organic chemistry. Several empirical relationships have been proposed to characterize systematically the various types of properties in protic and aprotic solvents. One of the simplest models is the continuum reaction field characterized by the dielectric constant, e, of the solvent, which is still widely used. Taft and coworkers [30] presented more sophisticated solvent parameters that can take solute-solvent hydrogen bonding and polarity into account. Although this parameter has been successfully applied to rationalize experimentally observed solvent effects, it seems still far from satisfactory to interpret solvent effects on the basis of microscopic infomation of the solute-solvent interaction and solvation free energy. 

Pant and Levinger have measured the solvation dynamics of water at the surface of semiconductor nanoparticles [48,49]. In this work, nanoparticulate Zr02 was used as a model for the Ti02 used in dye-sensitized solar photochemical cells. Here, the solvation dynamics for H2O and D2O at the nanoparticle surface are as fast or faster than bulk water motion. This is interpreted as evidence for reduced hydrogen bonding at the particle interface. 

Fig. 12.9. Structure and relative energies of four modes of hydrogen bonding in transition structures for epoxidation of 2-propen-l-ol by peroxyformic acid. Relative energies are from B3I.YP/6-311G -level computations with a solvation model for CH2C12, e = 8.9. Reproduced from / Org. Chem., 64, 3853 (1999), by permission of the American Chemical Society.

Other studies conducted on mixed protonated clusters of ammonia bound with TMA showed that the ion intensity distributions of (NH3)n(TMA)mH+191 display local maxima at (n,m) = (1,4), (2,3), (2,6), (3,2), and (3,8). Observation that the maximum ion intensity occurs at (n,m) = (1,4), (2,3), and (3,2) indicates that a solvation shell is formed around the NHJ ion with four ligands of any combination of ammonia and TMA molecules. In the situation where the maximum of the ion intensity occurs at (n,m) = (2,6) and (3,8), the experimental results suggest that another solvation shell forms which contains the core ions [H3N-H-NH3]+ (with six available hydrogen-bonding sites) and [H3N-H(NH2)H-NH3]+ (with eight available hydrogen-bonding sites). The observed metastable unimolecular decomposition processes support the above solvation model. 

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.

Marten, B., K. Kim, C. Cortis, R. A. Friesner, R. B. Murphy, M. N. Ringnalda, D. Sitkoff, and B. Honig. 1996. New Model for Calculation of Solvation Free Energies Correction to Self-consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects. J. Phys. Chem. 100, 11775. 

---