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Bond Critical Points (bond + critical_point)
Selected AbstractsRelationship between substituent effect and aromaticity , Part III: naphthalene as a transmitting moiety for substituent effectJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 5 2007Tadeusz M. Krygowski Abstract Molecular geometry of 10 isomeric nitronaphtholate ions (excluding peri - and ortho -type substituted systems), 1- and 2-naphtholate ions, 1- and 2-nitronaphthalene, meta - and para -nitrophenolate, phenolate, and nitrobenzene were optimized at B3LYP/6-311G** level of approximation. Substituent effect stabilization energy (SESE), geometry-based aromaticity index HOMA, magnetism-based indices NICS, NICS(1), NICS(1)zz, and parameters characterizing Bond Critical Points (BCP) (,, ,2,, ellipticity, ion/cov) of the Bader AIM theory were used to characterize transmitting properties for substituent effect through the naphthalene moiety. It results from our study that the studied systems could be clearly divided into two groups, (i) a para -type group, where the intramolecular charge transfer between the , -electron donating and , -electron accepting substituents can be described by canonical forms with charge separation (as in the case of para -nitrophenolate) and (ii) a meta -type group, where this transfer requires using canonical forms with double charge separation (as in the case of meta -nitrophenolate). Copyright © 2007 John Wiley & Sons, Ltd. [source] Hydrogen bonding strength,measures based on geometric and topological parameters,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2004awomir Janusz Grabowski Abstract Different methods of estimating H-bond strength are presented. The studies are based on the results of MP2/6,311++G** calculations and the binding energies are corrected for the basis set superposition error (BSSE). The wavefunctions were further applied to localize bond critical points and ring critical points. The characteristics based on the Bader theory are also applied as indicators and measures of hydrogen bonding. This study compares samples of different compounds. The H-bond strength measures such as the proton,acceptor distance (H···Y), the length of the proton donating bond, the electron density at H···Y bond critical point, the H-bond energy and others are analysed. The case of the intramolecular hydrogen bonding is also analysed, and its special characteristics are given. Copyright © 2003 John Wiley & Sons, Ltd. [source] Theoretical Prediction of the Phenoxyl Radical Formation Capacity and Cyclooxygenase Inhibition Relationships by Phenolic CompoundsMOLECULAR INFORMATICS, Issue 6 2002Juan Ruiz Abstract Due to the importance of the O-H bond dissociation in the antioxidant mechanism of anti-inflammatory phenols, we studied the biradical process Ph-OH,PhO.+H. for 25 phenolic compounds using ab initio calculations. Enthalpies of reaction (,Hr), changes in the electron density at the O-H bond critical point (,OH) and total atomic charges of ortho and para carbon atoms strongly correlate with the in vitro inhibition of cyclooxygenase activity by phenols. The most active compounds have large values of the electron density at the O-H bond (,OH), thus favouring the O-H bond dissociation. In contrast, inactive compounds have small values of the electron density at the O-H bond (,OH), thus reducing the hydrogen donation ability. These results are also supported by the representation of the molecular electrostatic potentials maps. The prediction of the cyclooxygenase inhibitory activity of the proposed QSAR equations is analysed using the multilineal (MLR) method. Finally, the differences in biological activity are examined by analysing the binding interactions of active compounds in the pocket site of human COX-2 enzyme structure derived from crystallographic X -ray data. [source] Hydrogen bonding strength,measures based on geometric and topological parameters,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2004awomir Janusz Grabowski Abstract Different methods of estimating H-bond strength are presented. The studies are based on the results of MP2/6,311++G** calculations and the binding energies are corrected for the basis set superposition error (BSSE). The wavefunctions were further applied to localize bond critical points and ring critical points. The characteristics based on the Bader theory are also applied as indicators and measures of hydrogen bonding. This study compares samples of different compounds. The H-bond strength measures such as the proton,acceptor distance (H···Y), the length of the proton donating bond, the electron density at H···Y bond critical point, the H-bond energy and others are analysed. The case of the intramolecular hydrogen bonding is also analysed, and its special characteristics are given. Copyright © 2003 John Wiley & Sons, Ltd. [source] On the origin of topological differences between experimental and theoretical crystal charge densitiesACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2000Anatoliy Volkov Topological analysis of experimental and theoretical (molecular and crystal) electron densities of p -nitroaniline and p -amino- p,-nitrobiphenyl reveals considerable discrepancies between experiment and theory for the bond critical points properties. Particularly large differences occur for the positive curvature along the bond path (,3). The differences become somewhat smaller when more extended basis sets and correlation effects are introduced in the theoretical calculations. The effect of the crystal matrix on the properties of bond critical points is evaluated for the p -nitroaniline molecule using the 6-21G** and 6-31G** basis sets. The differences between the isolated molecule and the molecule in the crystal are too small to explain the quantitative disagreement between the theoretical and experimental topologies reported in the literature and found in the current study. For most bonds, the observed changes in the properties of the electron density agree well for both basis sets but some discrepancies are found for changes in ,3 for N,H and aromatic C,C bonds. When the theoretical densities are projected into the multipole density functions through refinement of the theoretical structure factors, the topological properties change and differences between theory and experiment are reduced. The main origin of the observed discrepancies is attributed to the nature of the radial functions in the experimental multipole model. [source] Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Jeanette Netzel Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T, 20,K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (lmax = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C,C, C,N and C,O bonds, and for hydrogen bonds together with covalent C,H and N,H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. [source] Accurate charge density of the tripeptide Ala-Pro-Ala with the maximum entropy method (MEM): influence of data resolutionACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2007Andreas Hofmann The accurate electron density of Ala-Pro-Ala is determined by the maximum entropy method (MEM), employing the same reflection data measured at 100,K which was used for a multipole refinement by Kalinowski et al. [(2007), Acta Cryst. Accepted for publication]. Properties of the electron density are compared with the corresponding properties of the static electron density from the multipole model and to the dynamic MEM electron density of trialanine at 20,K. It is thus shown that the increased thermal smearing at 100,K leads to lower electron densities in the bond critical points and atomic charges closer to zero for Ala-Pro-Ala than has been obtained for trialanine at 20,K. The influence of the resolution of the data is investigated by a series of MEM calculations. Atomic charges and atomic volumes are found not to depend on the resolution, but the charge density in the BCPs decreases with decreasing resolution of the dataset. The origin of this dependence is found to lie mostly in the more accurate estimate of the atomic displacement parameters (ADPs) for the higher-resolution datasets. If these effects are taken into account, meaningful information on chemical bonding can be obtained with data at a resolution better than dmin = 0.63,Å. Alternatively, low-resolution X-ray diffraction data can be used in accurate electron-density studies by the MEM, if another source of accurate values of the ADPs is available, e.g. from refinements with multipole parameters from a database of transferable multipole parameters. [source] | ||||||||||