Molecular electrostatic potentials calculation

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>. 

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] ... 

C. D. Crowder, G. P. Alldredge, and H. W. White, Phys. Rev., B31,6676 (1985). Study of the Orientation of Thiourea Adsorbed on Aluminum Oxide by Tunneling Spectroscopy. I. Determination of Partial Charges from Molecular Electrostatic Potential Calculations for Thiourea and Urea. 

Complexes of anions with electron-deficient r-tetrazine aromatic rings and other binding units have been studied and compared using both high-level MP2/6-311-l-G ab initio and molecular interaction potential with and without polarization and molecular electrostatic potential calculations, in order to explore the physical nature of the interactions <2003CPL(370)7>. 

Independent evidence pointing to heightened A1 site acidity comes from molecular electrostatic potential calculations [9]. 

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 ... 

In the present work, we shall investigate the problem of the amount of correlation accounted for in the DF formalism by comparing the molecular electrostatic potentials (MEPs) and dipole moments of CO and N2O calculated by DF and ab initio methods. It is indeed well known that the calculated dipole moment rf these compounds is critically dependent on the level of theory implemented and, in particular, that introduction of correlation is essential for an accurate prediction [13,14]. As the MEP property reflects reliably the partial charges distribution on the atoms of the molecule, it is expected that the MEP will exhibit a similar dependence and that its gross features correlate with the changes in the value of dipole moment when switching from one level of theory to the other. Such a behavior has indeed been reported recently by Luque et al. [15], but their study is limited to the ab initio method and we found it worthwhile to extend it to the DF formalism. Finally, the proton affinity and the site of protonation of N2O, as calculated by both DF and ab initio methods, will be reported. 

The calculated molecular electrostatic potential is particularly well suited for the analysis of noncovaient interactions, which do not involve making or breaking covalent bonds and which occur without any extensive polarization or charge transfer between the interacting species. As we have discussed in the previous section, V(r) has been shown to be useful... 

Etchebest, C., R. Lavery, and A. Pullman. 1982. The Calculations of Molecular Electrostatic Potential from a Multipole Expansion Based on Localized Orbitals and Developed at Their Centroids Accuracy and Applicability for Macromolecular Computations. Theor. Chim. Acta 62, 17. 

Murray, J. S., S. Ranganathan, and P. Politzer. 1991. Correlations Between the Solvent Hydrogen Bond Acceptor Parameter (3 and the Calculated Molecular Electrostatic Potential. J. Org. Chem. 56, 3734. 

Rabinowitz, J. R., K. Namboodiri, and H. Weinstein. 1986. A Finite Expansion Method for the Calculation and Interpretation of Molecular Electrostatic Potentials. Int. J. Quant. Chem. 29,1697. 

St.-Amant, A., W. D. Cornell, P. Kollman, and T. A. Halgren. 1995. Calculation of Molecular Geometries, Relative Conformation Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Functional Theory. J. Comp. Chem. 16, 1483. 

To make an accurate FEP calculation, a good description of the system is required. This means that the parameters for the chosen force field must reproduce the dynamic behaviour of both species correctly. A realistic description of the environment, e.g. size of water box, and the treatment of the solute-solvent interaction energy is also required. The majority of the parameters can usually be taken from the standard atom types of a force field. The electrostatic description of the species at both ends of the perturbation is, however, the key to a good simulation of many systems. This is also the part that usually requires tailoring to the system of interest. Most force fields require atom centered charges obtained by fitting to the molecular electrostatic potential (MEP), usually over the van der Waals surface. Most authors in the studies discussed above used RHF/6-31G or higher methods to obtain the MEP. 

The final part is devoted to a survey of molecular properties of special interest to the medicinal chemist. The Theory of Atoms in Molecules by R. F.W. Bader et al., presented in Chapter 7, enables the quantitative use of chemical concepts, for example those of the functional group in organic chemistry or molecular similarity in medicinal chemistry, for prediction and understanding of chemical processes. This contribution also discusses possible applications of the theory to QSAR. Another important property that can be derived by use of QC calculations is the molecular electrostatic potential. J.S. Murray and P. Politzer describe the use of this property for description of noncovalent interactions between ligand and receptor, and the design of new compounds with specific features (Chapter 8). In Chapter 9, H.D. and M. Holtje describe the use of QC methods to parameterize force-field parameters, and applications to a pharmacophore search of enzyme inhibitors. The authors also show the use of QC methods for investigation of charge-transfer complexes. 

Fig. 9.9 Molecular electrostatic potentials of the H2-antagonists. The MEP have been calculated on the basis of AMI point charges and...

Physicochemical properties rather than reactivities were also explored. Molecular electrostatic potential (MEP) was calculated for the [l,2,4]triazolo[4,3- ]pyridine fragment 23, according to the CHELPG algorithm. This afforded a prediction of its H-bond acceptor ability in view of the synthesis of p38 MAP kinase inhibitors <2005JME5728>. Tautomerism was also examined for compound 24, also postulated as two possible acyclic structures. The ab initio self-consistent field (SCF)-calculated energies support 24a as the most stable tautomer <1999MRC493>. 

In Eqs. (16) and (17), a and P refer to atoms of the solute and solvent, respectively q is the permittivity of free space, Qa and Qp are atomic charges, and Rap is the distance between atoms a and p. The parameters eap, aap, Aap, Bap and Cap can either be assigned by fitting to experimental data or can be the arithmetic or geometric means of literature values for the individual atom types.10,65,66 The atomic charges are commonly determined by requiring that they reproduce the calculated molecular electrostatic potentials.10 In order to provide better descriptions of the solvent s structure, Eqs. (16) and (17) are generally extended to include solvent-solvent intermolecular interactions. 

These results are given for the DNA bases in Table 4. The calculated effects are quite substantial, with the predicted increases in dipole moments essentially parallelling the magnitudes of the polarization energies. Given (p solute solution molecular electrostatic potentials can also be obtained in solution, and used to derive atomic charges.85,86... 

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