Electrostatic contour maps

Figure 13. CoMFA contour maps about (+)-artemisinin for the standard alignment database (n = 199, 2 A/C.3). In the steric contour map to the left, green contours indicate areas where steric bulk is predicted to increase antimalarial activity, while red contours indicate regions where steric bulk is predicted to decrease activity. The electrostatic contour map on the right displays yellow polyhedra where partial negative charge is correlated with antimalarial activity the blue polyhedra indicating a relationship between partial positive charge and activity.

Figure 7. Molecular electrostatic contour maps for molecules A, B and C in Fig.

Sequence of electrostatic contour maps through the intercalation plane of the nucleic acid receptor in mediating the receipt of ethidium bromide. Modified from ref. 41 (bottom). 

Fig. 11 Steric and electrostatic contour map for the dual-model showing the contributions from each model. A depicts the contributions made by the a-model and G depicts the contributions made by the y-model...

Find the molecular model of 18 crown 6 (see Figure 16 2) on Learning By Modeling and examine its electrostatic potential map View the map in vanous modes (dots contours and as a transparent surface) Does 18 crown 6 have a dipole moment Are vicinal oxygens anti or gauche to one another"d... 

The results of electrostatic potential calculations can be used to predict initial attack positions of protons (or other ions) during a reaction. You can use the Contour Plot dialog box to request a plot of the contour map of the electrostatic potential of a molecular system after you done a semi-empirical or ab initio calculation. By definition, the electrostatic potential is calculated using the following expression ... 

Figure 14-8. The 3D density contour maps (yellow) of Na+ ion distributions derived from the activated precursor simulation. The hammerhead ribozyme is shown in blue with the active site in red. Only the high-density contour is shown here to indicate the electrostatic recruiting pocket formed in the active site...

FIG. 8.6 Electrostatic potential maps in the region of one of the peptide links in iV-acetyl-a,/f-dehydrophenylalanine methylamide. (a) Observed, (b) From net charges fitted to the potential. Contours are at 0.05 eA 1 (1 eA) 1 = 332.1 kcal mol ). Zero and negative contours are dashed lines. Source Ghermani et al. (1993). 

In atomic force microscopy (AFM), the sharp tip of a microscopic probe attached to a flexible cantilever is drawn across an uneven surface such as a membrane (Fig. 1). Electrostatic and van der Waals interactions between the tip and the sample produce a force that moves the probe up and down (in the z dimension) as it encounters hills and valleys in the sample. A laser beam reflected from the cantilever detects motions of as little as 1 A. In one type of atomic force microscope, the force on the probe is held constant (relative to a standard force, on the order of piconewtons) by a feedback circuit that causes the platform holding the sample to rise or fall to keep the force constant. A series of scans in the x and y dimensions (the plane of the membrane) yields a three-dimensional contour map of the surface with resolution near the atomic scale—0.1 nm in the vertical dimension, 0.5 to 1.0 nm in the lateral dimensions. The membrane rafts shown in Figure ll-20b were visualized by this technique. 

Fig. 3.4. Experimental electrostatic potential map for the molecule of 9-methyladenine removed from the lattice. Note the marked difference between the electrostatic potentials around N-H (donor), (acceptor), and C-H (contours 0.05 e A-1) [218]...

Moreover, a final 3D-QSAR model vahdation was done using a prospective study with an external test set. The 82 compounds from the data set were used in a lead optimization project. A CoMFA model gave an (cross validated) value of 0.698 for four relevant PLS components and a conventional of 0.938 were obtained for those 82 compounds. The steric descriptors contributed 54% to the total variance, whereas the electrostatic field explained 46%. The CoMSIA model led to an (cross vahdated) value of 0.660 for five PLS components and a conventional of 0.933. The contributions for steric, electrostatic, and hydrophobic fields were 25, 44, and 31%. As a result, it was proved that the basic S4-directed substituents should be replaced against more hydrophobic building blocks to improve pharmacokinetic properties. The structural and chemical interpretation of CoMFA and CoMSIA contour maps directly pointed to those regions in the Factor Xa binding site, where steric, electronic, or hydrophobic effects play a dominant role in ligand-receptor interactions. 

J.J. Kaufman, P.C. Hariharan, F.L. Tobin, and C. Petrongolo, "Electrostatic Molecular Potential Contour Maps from Ab Initio Calculation", in Chemical Applications of Atomic and Molecular Electrostatic Potentials, P. Politzer and D.G. Truhlar (Eds.), Plenum, New York, 1981, pp. 335-380. 

Figure 1 Contour map of the negative of the molecular electrostatic potential for acetamide at the HF/3-21G( ) level calculated from the full molecular wavefunction. Shading indicates approximate value of the potential in the region. Thus, the MEP near the oxygen is negative, and the MEP near the amide hydrogens (not shown) is positive. The basis set has polarization functions only on second-row atoms.

Figure 2 Contour map of the negative of the molecular electrostatic potential for acetamide at the HF/S-ZIGI ) level calculated using the monopole approximation and the CHELP charges. Scale same as in Figure 1.

Such an expression has previously been used for comparative purposes, for the study of interaction between two molecular species, by computing the electrostatic potential of the first partner and by assuming some point charge model as representative of the charge distribution of the second partner. We also plan to extend this concept in a more subtle way by using an electron density contour map to describe the charge distribution of the second partner as a function of the space surrounding this second partner. 

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