Electrostatic and hydrogen-bonding

Im W, Chen J, Brooks CL III (2006) Peptide and protein folding and conformational equilibria Theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem 72 173-198. 

The first three terms, stretch, bend and torsion, are common to most force fields although their explicit form may vary. The nonbonded terms may be further divided into contributions from Van der Waals (VdW), electrostatic and hydrogen-bond interactions. Most force fields include potential functions for the first two interaction types (Lennard-Jones type or Buckingham type functions for VdW interactions and charge-charge or dipole-dipole terms for the electrostatic interactions). Explicit hydrogen-bond functions are less common and such interactions are often modeled by the VdW expression with special parameters for the atoms which participate in the hydrogen bond (see below). 

One of the most important characteristics of micelles is their ability to enclose all kinds of substances. Capture of these compounds in micelles is generally driven by hydrophobic, electrostatic and hydrogen-bonding interactions. The dynamics of solubilization into micelles are similar to those observed for entrance and exit of individual surfactant molecules, but the micelle-bound substrate will experience a reaction environment different from bulk water, leading to kinetic medium effects308. Hence, micelles are able to catalyse or inhibit reactions. The catalytic effect on unimolecular reactions can be attributed exclusively to the local medium effect. For more complicated bimolecular or higher-order reactions, the rate of the reaction is affected by an additional parameter the local concentrations of the reacting species in or at the micelle. 

These studies are continuing to evaluate the effects of different potential functions, contributions from electrostatic and hydrogen bond attractions, ten erature, etc. The effects of solvents, complexing agents, and adjacent surfaces of crystalline regions will be investigated in due course. 

Sum of van der Waals, electrostatic and hydrogen bond energy terms. 

The interaction on silanated slides is thought to be the result of a combination of electrostatic and hydrogen bonding. Aminosilane surfaces are positively charged at neutral pH. Printing under alkaline conditions shifts... 

The protonated endo-endo isomers of the diazabicycloalkanes, catapinands, were among the first macrocycles found to be capable of incorporating halide anions (78).54 Electrostatic and hydrogen bond interactions are undoubtedly the primary driving forces for complex stability. The crystal structure of the chloride catapinate of (78) has confirmed the inclusion nature of the complex and... 

During the extraction process three types of interactions are usually disrupted, these are van der Waals forces in lipid-lipid, lipid-protein, and liquid-carbohydrate complexes electrostatic and hydrogen bonding interactions between lipids andproteins andcovalent bonding between lipids, carbohydrates, and proteins (Roby t and White, 1987). The solvent of choice depends on the type of lipid and the interactions to be disrupted. Thus, neutral lipids may be extracted with nonpolar solvents, while phospholipids and glycolipids are extracted with more polar solvent mixtures (Shahidi and Wanasundara, 1998). 

Alkylation Alkylation of the phenylindanone 31 with catalyst 3a by the Merck group demonstrates the reward that can accompany a careful and systematic study of a particular phase-transfer reaction (Scheme 10.3) [5d,5f,9,36], The numerous reaction variables were optimized and the kinetics and mechanism of the reaction were studied in detail. It has been proposed that the chiral induction step involves an ion-pair in which the enolate anion fits on top of the catalyst and is positioned by electrostatic and hydrogen-bonding effects as well as 71—71 stacking interactions between the aromatic rings in the catalyst and the enolate. The electrophile then preferentially approaches the ion-pair from the top (front) face, because the catalyst effectively shields the bottom-face approach. A crystal structure of the catalyst as well as calculations of the catalyst-enolate complex support this interpretation [9a,91]. Alkylations of related active methine compounds, such as 33 to 34 (Scheme 10.3), have also appeared [10,11]. 

The third factor, ZR, in Eq. (5.1) is called the residual contribution in the chemical engineering notation and it arises from all kinds of non-steric interactions between molecules, i.e., usually from vdW, electrostatic, and hydrogen bond interactions. Despite its name, it is the most important contribution in most liquids. The basic assumption of surface-pair interaction models is that residual—i.e., non-steric—interactions can be described as local pairwise interactions of surface segments. The residual contribution is just the partition sum of an ensemble of pairwise interacting surface segments. 

The model must provide for electrostatic and hydrogen bonding in order to fix the substrate properly. 

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