Electrostatic isopotential

Naray-Szabo, G. 1979. Electrostatic Isopotential Maps for Large Biomolecules. Int. J. Quant. Chem. 16, 265. 

Electrostatic isopotential (EIP) minima186 often identify sites and ease of metabolism by epoxide hydrase, an enzyme responsible for the conversion of epoxides to diols by the addition of water. Molecular electrostatic potential energy calculations also are probably the best means of identifying positions of epoxidation and, possibly, metabolism in general. In the case of aflatoxin B for example, EIP maxima and minima calculated by the CNDO/2 method all lie close to the known sites of metabolism and, in particular, the formation of the carcinogenic 2,3-epoxide is readily predicted.189... 

PAH, polycyclic aromatic hydrocarbon PCB, polychlorinated biphenyl TCDD, 2,3,7,8-tetrachlorodibenzo-p-dioxin PCDF, polychlorinated dibenzofuran E1P, electrostatic isopotential. 

Figure 2.3. Electrostatic potential dendrogram constructed from an electrostatic potential distance matrix for a set of 42 WW domains showing four clusters. WW domains are colored according to their peptide ligand binding preferences. FourWWdomains representative of the clusters are shown with positive (blue) and negative (red) electrostatic isopotential contours. In the cluster of...

Figure 1. Electrostatic isopotential maps as derived from a point charge model using MNDO charges -5 kcal mol , cyan +5 kcal mol , purple. Hydrogen atoms omitted. Top, 3 bottom left, 2 bottom...

Naray-Szabo G. Electrostatic isopotential maps for large biomolecules. Int J Quantum Chem 1979 16 265-272. 

Cover picture The molecule depicted on the cover is (+)-milbemycin pa along with its electrostatic isopotential surface. Milbemycin was chosen because the spiroketal portion of the structure was synthesized from both malic and tartaric acids. 

The distribution of electrostatic potential o over molecular surfaces is a useful model for the analysis of chemical reactivity and steric effects. i The shape group method can be adapted to this model, by using values of the electrostatic potential to define the truncations on the molecular surface, The shape description obtained can be used in correlations with biochemical activity. [Note that the analysis of electrostatic isopotential surfaces, whenever closed, can be accomplished by the same method used with isodensity surfaces. The characterization of potential surfaces is relevant to interpreting molecular recognition processes. O i ]... 

G. Naray-Szabo, Quantum. Chem. Program Exchange Catalog, 13, 396 (1980). ELPO. Electrostatic Isopotential Maps and Interaction Energies from Localized Orbital Contributions. 

G. Naray-Szabo, A. Grofcsik, K. Kosa, M. Kubinyi, and A. Martin, /. Comput. Chem., 2, 58 (1981). Simple Calculation of Electrostatic Isopotential Maps from Bond Fragments. 

Fig. 3-2. Molecular electrostatic potential with 6-31G //3-21G basis set in the molecular plane of (ii)-nitrous acid. Black dots refer to four different protonation sites in potential minima. For values of isopotential contours see Nguyen and Hegarty, 1984.

Figure 3. Electrostatic potential map for the two bare defects and identification of the position of the atoms of the dissociated H2 molecule (H atoms in the Tfi configuration are in dark grey). The sections are in a vertical plane through the H atoms. Consecutive isopotential lines differ by 0.02 a.u. (0.54 V) continuous, dashed and dot-dashed curves refer to positive, negative, arid zero potential, respectively. Lines corresponding to absolute values larger than 0.3 a.u. are riot plotted.

The results are presented as maps of electrostatic interaction energies with a unit positive charge (isopotential maps). Fig. 9 gives such maps in the molecular plane for A, C and T. Fig. 10 gives the corresponding maps in selected planes perpendicular to the molecular plane. 

FI G U RE 28.10 The electrostatic potential distribution for the model I of hydrated state of silica surface. The p distribution within the plane perpendicular to the water molecule plane is given in upper left part of the picture. Isopotential lines correspond to p values in kJ/mol. 

FIGURE 28.11 The distribution of electrostatic potential for the model II of silica surface hydrated state. Isopotential lines... 

MO Calculations and Photoelectron Spectroscopy. Some all-valence-electron CNDO/2 SCF-MO calculations on fluorobenzene, hexafluorobenzene, pentafluoro-anisole, and some derived Wheland intermediates have been reported in a paper which is mainly concerned with derivatives of pyridine and the diazines (see p. 467). An MO-LCAO-SCF study of the electronic structure of fluorobenzene has yielded the electrostatic molecular potential and isopotential maps which are consistent with a poru-directing influence of fluorine in electrophilic substitution, ... 

Figure 36 On the left Structure of ice XI On the right Electrostatic potential at the (001) surface of ice XL Consecutive isodensity lines differ by 0.01 a.u. continuous, dashed, and dot-dashed curves correspond to positive, negative, and zero potential, respectively. Isopotential lines corresponding to potential values larger than 0.2 a.u. in module are not plotted.

Fig. 2. The effect of oxidation state on the electrostatic potential field surrounding spinach PC. The parameters used to calculate the electric field were protein/solvent dielectric constants = 2/80 solvent ionic strength = 150 mM Stern layer = 2 A. Isopotential lines are shown for kT/e of 4.0, 2.0, 1.0, 0.5, 0.25, -0.25, -0.5, -1.0, -2.0, -4.0. a) Oxidized PC b) Reduced PC c) Oxidized - reduced PC (Ionic strength = 30 mM).

The electrostatic potential of a molecule can be displayed in various ways. Originally, it was often presented as isopotential contours on planes through the molecule [20-22,24], A more recent practice is to show three-dimensional plots of just a single positive value and a single negative value of V(r). However, this necessarily gives an incomplete picture since other values may also be important. 

Display a structure with color of property-coded atoms. Display types should include stick, capped stick, ball and stick, and spacefill. It should also be possible to display electrostatic potentials and isopotential eontour maps. 

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