Electrostatic potential calculating

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 ... 

Table I. Electrostatic potentials calculated from pKobs values for A — x (3) with various charge densities [42]...

Figure 4 shows the electrostatic potential calculated as a function of E, at distances 5, 10, and 15 A from the cylinder axis by using the data given in Fig. 1. Experimental points come fairly close to the calculated values at 10 A, when > 1.

Fig. 4. Relationship between the electrostatic potential calculated from the PB equation and the charge density parameter at distances 5,10, and 15 A from the axis of a cylinder with 3 A radius. Points indicate experimental data listed in Table 1 [42]...

Espinosa, E., C. Lecomte, N. E. Ghermani, J. Devemy, M. M. Rohmer, M. Benard, and E. Molins. 1996. Hydrogen Bonds First Quantitative Agreement between Electrostatic Potential Calculations from Experimental X-(X+N) and Theoretical Ab Initio SCF Models. J. Am Chem. Soc. 118, 2501. 

The electrostatic potential calculations have shown that the minor groove of AT rich B-DNA sequence has the lowest negative potential.15 This led to the implication that the cationic drugs will exhibit binding specificity to the minor groove regions of AT rich sequences. The crystal structure of a DNA distamycin complex showed that there is only one molecule bound to the minor groove of an AATT DNA site.2 However, experimental studies... 

The use of molecular electrostatic potentials calculated from the wave function of ligands, as has been recently suggested 50—54) seems to present a less ambiguous alternative to the more empirical approach described above. This potential can either be calculated exactly for each point of interest according to Eq. (3), or it is approximated by a suitable distribution of point charges choosen either by intuitive guess or by a less arbitrary method like the one of Hall 182>. 

Fig. 4 B3LYP/6-311+G electrostatic potentials calculated for phosphole (left) and phosphole oxide (right). Red and blue colors denote positive and negative charge, respectively (Holloczki and Nyulaszi, unpublished result)...

B. Electrostatic Potential Calculation from X-ray Diffraction Data.284... 

Another method is to calculate the molecular electronic electrostatic potential by replacing p(r ) in Eq. 19 by its multipole formulation (Eq. 8). The quantity obtained represents the electrostatic potential of a molecule removed from the crystal lattice. First calculations have been performed by the Pittsburgh group (Stewart, Craven, He, and co-workers) [43] electrostatic potential calculations were also derived from the Hansen Coppens [lib] electron density model [41,44], The atomic total electrostatic potential including nuclear contribution may be calculated as ... 

The electrostatic potential calculated for one molecule removed from the crystal lattice in the histidine plane (Figure 19a) shows a very small minimum of potential (-0.18 elk 1) around the nitrogen atom which becomes positive when the calculation is made for a cluster of two hydrogen-bonded molecules [53] (N4—Ns = 2.856 A) (Figure 19b). 

This review only focuses on experimental results. The experimental topological analysis is made for molecules removed from the crystal lattice in the same way than for the electrostatic potential calculations (see above). The crystal field effects are therefore not absent. 

It has been suggested in the case of offretite that minima of the electrostatic potential calculated for the Al-substituted framework, in the absence of... 

The electrostatic potential calculated at neutral pH is positive in the phosphate-binding site defined in the other three structures while it is negative at neutral pH in the phosphate-binding site proposed in the 2-deoxy-glucitol-6-phosphate complex structure. 

Espinosa, E., Lecomte, C., Ghermani, N. E., Devemy, J., Rohmer, M. M., Benard, M., and Molins, E, Hydrogen bonds First quantitative agreement between electrostatic potential calculations from experimental X-(X + N) and theoretical ab initio SCF models, J. Am. Chem. Soc. 118, 2501-2502(1996). 

In complementary computational studies, Gunner et al. have explored the role of long-range electrostatic interaction on electron transfer processes in the Rhodo-bacter sphaeroides reaction center [38]. The interaction domains were identified by mapping electrostatic potentials, calculated from the Poisson-Boltzmann equation, on to calculated encounter surfaces for each of the components of the reaction center. From qualitative correlation of electron transfer processes with these low-resolution potential maps, it is apparent that long-range interactions profoundly affect the reduction potential of the cofactors in the reaction center. 

Fits are to HF/3-21G(" ) electrostatic potential calculated at 1000 points in a shell between 1.0 and 3.0 times the van der Waals surface of the molecule. The rank estimate is taken as the number of singular values for which the ratio s to Sj does not exceed 10. ... 

Elsewhere (22) a model for the highly acidic sites is discussed that is supported by electrostatic potential calculations. According to that model the activity is due to generation of protons coordinated to oxygen ions that connect the silicon-containing tetrahedra with aluminium-containing octrahedra. Such sites, however, can only contribute to catalysis at lateral planes, at lattice dislocations in the basal plane or at the edges of the lateral and basal planes. 

It is defined as the average deviation of the surface —> molecular electrostatic potential calculated as [Brinck, Murray et al., 1993 Murray, Brinck et al., 1993] ... 

A roman reference number is appended to each molecule. Not all the electrostatic potential calculations at present available are discussed here, though other examples are considered in the next section. The calculations of W (r) for molecules XII, XV, XX, XXI are presented for the first time. The others have been published before, but some of the maps have been drawn specially for this paper. The kind permission of authors and editors to reproduce some material is here acknowledged. 

---