Electrostatic Maps

Thermodynamically, molecular recognition is dominantly controlled by free energy changes as defined by 

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Within the CoMFA electrostatic map, red contours are displayed in areas where negative charge is associated with increased activity of the database analogues. Red contours are visible near the peroxide bridge, supporting the important role the peroxide plays in activity and near 0-11 (or N-l 1). There are also red contours in... 

Graphical pre- and postprocessor for semiempirical molecular orbital programs extended Hiickel, MOPAC, and ZINDO. Structure building from library of fragments and molecules manipulation. Stick, ball-and-stick, and space-filling display. Orbital, electron density, and electrostatic maps. Reaction energy surfaces. IR and UV spectra. MM2 energy minimization. Dynamics. 

Figure 4. Pictorial representation of 3D-QSAR models. The color code is as follows sterically favourable and unfavourable interactions, green and red regions, respectively favourable and unfavourable influence of high electron density, cyan and yellow zones respectively. To aid interpretation the template 26, idazoxan compounds 35 and 40 have been added to the electrostatic map, whereas clonidine, compounds 5, 8 and 34 are shown in the steric map. n, number of data points q and r, cross-validated and non-cross-validated correlation coefficient, respectively s, standard deviation one, optimal number of components.

It turns out that the flatness of the analyte alone is not the only factor needed for good complex-ation with CTA. To probe the electronics of these interactions the authors computed molecular electrostatic maps as in Figure 7 and extracted from them a normalized electrostatic interaction energy. 

A number of questions remain open, including extension of the present approach to objects in 3D space. Are the binary shape codes sufficiently general, i.e., can they be extended to 3D structures We cannot answer these questions since they have not yet been considered. We will, however, outline briefly an approach to the 3D case. A generalization from planar contours to surfaces in a 3D space is possible even if not unique. For example, we first derive for a 3D surface a set of 2D contours. Such are, for example, the electrostatic maps that have found use in QSAR in the well-known CoMFA method. Once we have the contours, each contour can be encoded by the binary code as illustrated in this chapter. A list of such contours, with specifications of their relative positions, will lead to a 3D code for molecular shapes. Comparisons of 3D shapes will now be more involved. 

At the time we solved the crystal structure of Serratia nuclease, comparative sequence data, mutagenesis data and chemical modification data were not available. After we completed the building and refinemoit of the Serratia nuclease structure, visual inspection did not reveal the active site location. Since there were no other nuclease structures to use to help locate the active site, we analyzed the structure in terms of its electrostatic surface potential. Inspection of electrostatic maps calculated in GRASP (32) revealed that one side of the nuclease monomer displayed a broad area of positive electrostatic potential while the opposite side displayed negative electrostatic... 

The electrical properties of OmpF have been measured for long times, both with patch-clamp techniques and on planar lipid membranes." A high-resolution electrostatic mapping of the trimer was obtained with atomic probe microscopy,while a systematic electrostatic modeling of the pore lumen has been recently performed by two groups who did not limit their study to the wild protein, but comparatively analyzed several mutants. The electrostatic landscape of OmpF is a typical example of how the balance between strong interactions finely tunes the properties of a channel. Ionic trajectories have been simulated both with Brownian and molecular dynamics simulation codes,and the role of ion-ion interaction within the pore has been stressed as being important. 

S-atomic affinity map file H-atomic affinity map file electrostatics map file... 

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