Electrostatic potential on molecular surface

The possibilities for the application for neural networks in chemistry arc huge [10. They can be used for various tasks for the classification of structures or reactions, for establishing spcctra-strncturc correlations, for modeling and predicting biological activities, or to map the electrostatic potential on molecular surfaces. 

In a series of studies, reviewed on several occasions [13,88,89], we have found that a variety of physical properties that depend upon noncovalent interactions, including AHvap and AHsub, can be related quantitatively to certain features of the electrostatic potentials on molecular surfaces. The electrostatic potential V(r) that the electrons and nuclei of a molecule create at any point r is given by,... 

In analyzing the electrostatic potentials on molecular surfaces, our emphasis so far has been on the locations and magnitudes of the most positive and most negative values, Fs,max and Fs,min, and on the qualitative general pattern of Vs(r). However, already some years ago, it seemed desirable to develop the means for quantitatively characterizing the overall features of Fs(r). For this purpose, we gradually introduced... 

Lavery, R., and B. Pullman. 1981. Molecular Electrostatic Potential on the Surface Envelopes of Macromolecules B-DNA. Int. J. Quant. Chem. 20, 259. 

It might seem that the Vs,min and Vs,max on a suitable molecular surface should indicate sites susceptible to electrophilic and nucleophilic reactants, respectively. Such reasoning has had some success in the past [3,14,16,17], but it is not reliable. For example, shown in Figure 17.2 is the electrostatic potential on a surface of anisole (methoxybenzene), 1, which is well known to undergo electrophilic attack at the ortho and para positions. 

Hasegawa, K., Matsuoka, S., Arakawa, M. and Funatsu, K. (2003) Multi-way PLS modeling of structure-activity data by incorporating electrostatic and lipophilic potentials on molecular surface. Comp. Biol. Chem., 27, 381-386. 

The interpretation of biological recognition interactions has continued, since the earliest days, to be one of the most active areas of application of electrostatic potentials [2,3,16,42-44,68-71,78,101-114]. The original studies of two-dimensional V(r) plots have evolved into detailed quantitative characterization of the potentials on molecular surfaces and the investigation of factors such as shape, similarity, and flexibility. In this section, we shall focus on one specific example a qualitative analysis of the molecular determinants of toxicity among the dibenzo-p-dioxins. We shall proceed to some more quantitative treatments in a later section, after establishing a basis for them. 

Lavery R, Pullman B. Molecular electrostatic potential on the surface envelopes of macromolecules B-DNA. Int J Quantum Chem 1981 20 259-272. 

To display properties on molecular surfaces, two different approaches are applied. One method assigns color codes to each grid point of the surface. The grid points are connected to lines chicken-wire) or to surfaces (solid sphere) and then the color values are interpolated onto a color gradient [200]. The second method projects colored textures onto the surface [202, 203] and is mostly used to display such properties as electrostatic potentials, polarizability, hydrophobidty, and spin density. 

This review article attempts to summarize and discuss recent developments in the studies of photoinduced electron transfer in functionalized polyelectrolyte systems. The rates of photoinduced forward and thermal back electron transfers are dramatically changed when photoactive chromophores are incorporated into polyelectrolytes by covalent bonding. The origins of such changes are discussed in terms of the interfacial electrostatic potential on the molecular surface of the polyelectrolyte as well as the microphase structure formed by amphiphilic polyelectrolytes. The promise of tailored amphiphilic polyelectrolytes for designing efficient photoinduced charge separation systems is afso discussed. 

Sites susceptible to nucleophilic attack can also be identified and ranked by means of positive electrostatic potential regions, but it is necessary to analyze the latter at distances at least 1 to 2 A away from the nuclei, e.g., in planes removed from the molecular framework (Murray, Lane, and Politzer 1990 Politzer, Abrahmsen, and Sjoberg 1984 Politzer et al. 1984) or on molecular surfaces (Murray et al. 1991b Murray and Politzer 1991 Murray and Politzer 1992 Pullman, Perahia, and Cauchy 1979 Sjoberg and Politzer 1990). This is because the electrostatic potentials of atoms and molecules have local maxima only at the nuclei (Pathak and Gadre 1990). To identify sites for nucleophilic attack, it is necessary, accordingly, to look for the most positive values in planes or on surfaces that are at some distance from the nuclei. (These are, of course, not true local minima.)... 

Fig. 3.2 Calculated electrostatic potential on the molecular surface of guanine (1). Three ranges of V(r) are depicted, in kcal/mole. These are white for V(r) < 0 light gray for F(r) from 0 to 10 dark gray for V(r) >10.

The macroscopic property of interest, e.g., heat of vaporization, is represented in terms of some subset of the computed quantities on the right side of Eq. (3.7). The latter are measures of various aspects of a molecule s interactive behavior, with all but surface area being defined in terms of the electrostatic potential computed on the molecular surface. Vs max and Fs min, the most positive and most negative values of V(r) on the surface, are site-specific they indicate the tendencies and most favorable locations for nucleophilic and electrophilic interactions. In contrast, II, a ot and v are statistically-based global quantities, which are defined in terms of the entire molecular surface. II is a measure of local polarity, °fot indicates the degree of variability of the potential on the surface, and v is a measure of the electrostatic balance between the positive and negative regions of V(r) (Murray et al. 1994 Murray and Politzer 1994). 

Murray, J. S., P. Lane, T. Brinck, P. Politzer, and P. Sjoberg. 1991b. Electrostatic Potentials on the Molecular Surface of Some Cyclic Ureides. J. Phys. Chem. 95, 844. 

Murray, J. S., K. Paulsen, and P. Politzer. 1994. Molecular Surface Electrostatic Potentials on the Analysis of Non-Hydrogen-Bonding Noncovalent Interactions. Proc. Ind. Acad. Sci. (Chem. Sci.) 106, 267. 

Fig. 8.2 Calculated electrostatic potential on the molecular surface of aniline (1), in kcal mob1, (a) The side of the aromatic ring with the nitrogen lone pair. Ranges black is more negative than -25 gray is between -25 and 0 off-white is between 0 and 20. (b) The side of the aromatic ring opposite to the nitro-...

The quantities defined by Eqs. (2)—(7) plus Vs max, Vs min, and the positive and negative areas, A and, enable detailed characterization of the electrostatic potential on a molecular surface. Over the past ten years, we have shown that subsets of these quantities can be used to represent analytically a variety of liquid-, solid-, and solution-phase properties that depend on noncovalent interactions [14-17, 84] these include boiling points and critical constants, heats of vaporization, sublimation and fusion, solubilities and solvation energies, partition coefficients, diffusion constants, viscosities, surface tensions, and liquid and crystal densities. 

The variances indicate the variabilities, or ranges, of the positive, the negative and the overall electrostatic potentials on the molecular surfaces. They are particularly sensitive to the extrema, Vs,max and Vs,min, due to the terms being squared. This also means that they may be much... 

The quantities that have been presented do effectively characterize the electrostatic potential on a molecular surface. We have shown that a number of macroscopic, condensed-phase properties that depend upon noncovalent interactions can be expressed in terms of some subset of these quantities (frequently... 

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