Electrostatic effects, modeling

When dealing with the modification induced on the UV/ VIS spectra of a chromophore embedded in a macromo-lecular environment, one has to take into account three main effects the geometric deformation induced by the rather rigid environment, the electrostatic effect modeled by the polarization of the wavefunction induced by the MM point charges, and finally the electronic polarization of the environment due to the modification of the electronic density of the environment to adapt itself to the new excited state electronic density. 

The model adopted by Ri and Eyring is not now acceptable, but some of the more recent treatments of electrostatic effects are quite close to their method in principle. In dealing with polar substituents some authors have concentrated on the interaction of the substituent with the electrophile whilst others have considered the interaction of the substituent with the charge on the ring in the transition state. An example of the latter method was mentioned above ( 7.2.1), and both will be encountered later ( 9.1.2). They are really attempts to explain the nature of the inductive effect, and an important question which they raise is that of the relative importance of localisation and electrostatic phenomena in determining orientation and state of activation in electrophilic substitutions. 

In the models discussed thus far in this section, emphasis has been placed on electrostatic effects and solvent polarity. An alternative view that to some extent takes other forces into account begins with the idea that, in order to dissolve a solute molecule in a solvent, energy is required to create a cavity in the solvent the solute is then inserted into this cavity. In Section 8.2 we saw that the energy to create a cavity can be expressed as a product of the surface area of the cavity and the surface tension of the solvent. An equivalent expression is obtained as the product of the volume of the cavity and the pressure exerted by the solvent, and we now explore this concept. 

MODELING CHEMISTRY AND ELECTROSTATIC EFFECTS 6.3.1. A Simple VB Formulation... 

FIGURE 6.10. Comparing the energetics of the EVB configurations in solution and in the active site of lysozyme. The calculations were done by using the PDLD and related models (Refs. 6 and 7) and they represent a study of a stepwise mechanism. The energetics of a more concerted pathway (e.g., that of Fig. 6.9) is almost identical to that of the stepwise mechanism and correlated in a similar way with the electrostatic effect of the protein. 

Theories and simulation of the operation of AFM in liquid have been attempted [102-104], In principle, molecular dynamics or NEMD may be a suitable method to mimic the operation of a scanning tip. The time scale, however, precludes simulating a long-enough scan to see a complete atom. Most studies, therefore, were made with equilibrium conditions and a fixed position of the AFM tip. Explicit consideration of electrolytes and electrostatic effects has not been modeled. 

Hydrogen bonding and electrostatic interactions between the sample molecules and the phospholipid bilayer membranes are thought to play a key role in the transport of such solute molecules. When dilute 2% phospholipid in alkane is used in the artificial membrane [25,556], the effect of hydrogen bonding and electrostatic effects may be underestimated. We thus explored the effects of higher phospholipid content in alkane solutions. Egg and soy lecithins were selected for this purpose, since multicomponent mixtures such as model 11.0 are very costly, even at levels of 2% wt/vol in dodecane. The costs of components in 74% wt/vol (see below) levels would have been prohibitive. 

For acids, the membrane retention actually increases in the case of egg lecithin, compared to soy lecithin. This may be due to decreased repulsions between the negatively charged sample and negatively charged phospholipid, allowing H-bond-ing and hydrophobic forces to more fully realize in the less negatively charged egg lecithin membranes. The neutral molecules display about the same transport properties in soy and egg lecithin, in line with the absence of direct electrostatic effects. These differences between egg and soy lecithins make soy lecithin the preferred basis for further model development. 

Figure 2-3. Protonated Schiff-base of retinal (PSBR) and computational models used in ONIOM QM QM calculations (left). Electrostatic effects of the surrounding protein on excitation energies in bacteriorhodopsin evaluated using TD-B3LYP Amber right). (Adapted from Vreven and Morokuma [37] (Copyright American Institute of Physics) and Vreven et al. [38], Reprinted with permission.)...

Since electrostatic effects dominate the thermodynamic cycle as shown in Figure 10-2, major development efforts have focused on the calculation of electrostatic energy for transferring the neutral and charged forms of the ionizable group from water with dielectric constant of about 80 to the protein with a low dielectric constant (see later discussions). This led to the development of continuum based models, where water and protein are described as uniform dielectric media, and enter into the linearized Poisson-Boltzmann (PB) electrostatic equation,... 

Warshel A, Sharmaa PK, Katoa M, Parson WW (2006) Modeling electrostatic effects in proteins. Biochim Biophys Acta 1764 1647—1676. 

Fitzgerald et al. (1984) measured pressure fluctuations in an atmospheric fluidized bed combustor and a quarter-scale cold model. The full set of scaling parameters was matched between the beds. The autocorrelation function of the pressure fluctuations was similar for the two beds but not within the 95% confidence levels they had anticipated. The amplitude of the autocorrelation function for the hot combustor was significantly lower than that for the cold model. Also, the experimentally determined time-scaling factor differed from the theoretical value by 24%. They suggested that the differences could be due to electrostatic effects. Particle sphericity and size distribution were not discussed failure to match these could also have influenced the hydrodynamic similarity of the two beds. Bed pressure fluctuations were measured using a single pressure point which, as discussed previously, may not accurately represent the local hydrodynamics within the bed. Similar results were... 

Section 2 presents a review of the theory underlying self-consistent continuum models, with section 2.1 devoted to electrostatics and section 2.2 devoted to the incorporation of non-electrostatic effects into continuum solvation... 

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