Robert Ponec

Electron pairing and chemical bonds. Chemical structure, valences and structural similarities from the analysis of the Fermi holes

A new method of visualisation of bonding in molecules is introduced. The method is based on the analysis of Fermi holes associated with conditional probabilities of finding one electron of the pair provided the second, reference, electron is localised in a certain molecular region. Based on this analysis it is possible to get a clear and highly visual insight into the structure of molecular fragments (functional groups) in molecules. In addition to this visualisation, the new approach opens the possibility of the new definition of atomic and group valence and, also, can be applied as a new means of the quantitative characterisation of similarity of structural fragments in the series of related molecules.

Electron pairing and chemical bonds. Molecular structure from the analysis of pair densities and related quantities

The Fermi holes are presented as a new means of analysis and visualisation of molecular structure. Based on these quantities it is possible to get clear and highly visual insight into the structure of molecular fragments (functional groups) even in molecules with complex bonding patterns like multicenter bonding, hypervalence, etc. In addition to allowing the detection and localization of multicenter bonding, the new approach also brings some new interesting possibilities for the quantitative evaluation of molecular similarity.

Molecular basis of quantitative structure-properties relationships (QSPR): A quantum similarity approach

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett σ constants and the logarithm of the octanol- water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

Electron pairing and chemical bonds: Bonding in hypervalent molecules from analysis of Fermi holes

Bonding in the hypervalent molecules SF4, BrF5, PF5, and SF6 was studied using multicenter bond order indices and examination of the eigenvalues and the eigenvectors of the Fermi holes of the constituent atoms. Diagonalization of the Fermi holes provided quantitative validation of Mushers categorization of hypervalency with SF4 and BrF5 representative of type I, and PF5 and SF6 belonging to type II. The eigenvalues and eigenvectors of type I molecules distinguished between classic two‐center two‐electron bonds and three‐center four‐electron bonds, whereas the results of diagonalization for type II molecules demonstrated the presence of substantial reorganization of the valence state of the central atom leading to equivalent bonds and the highest expected symmetry of the molecule. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 760–771, 1999

Structure and bonding in binuclear metal carbonyls from the analysis of domain averaged Fermi holes. I. Fe2(CO)9 and Co2(CO)8

The nature of the bonding in the above carbonyls was studied using the analysis of domain averaged Fermi holes (DAFH). The results straightforwardly confirm the conclusions of earlier theoretical studies in which the existence of direct metal–metal bond, anticipated for the above carbonyls on the basis of 18‐electron rule, was questioned. In addition to indicating the lack of direct metal–metal bond, the DAFH analysis also allowed to characterize the nature of the electron pairs involved in the bonding of the bridging ligands. The analysis has shown that because the number of available electron pairs is not sufficient for the formation of ordinary localized 2c‐2e bonds between terminal M(CO)3 fragments and the bridging ligands, the bonding in both carbonyls exhibits typical features of electron deficiency and one bonding electron pair is effectively involved in multicenter 3c‐2e bonding. Because of the symmetry of the complexes the bridging ligands are not distinguishable and all M‐C‐M bridges have a partial 3c‐2e nature via resonance of the localized structures.

Aromaticity in linear polyacenes: Generalized population analysis and molecular quantum similarity approach

The relative aromaticity of benzenoid rings in the linear polyacenes is investigated using two novel aromaticity approaches. According to the first, the aromaticity of individual benzene rings was gauged by the values of six‐center bond indices (SCI) calculated within the so‐called Generalized Population Analysis (GPA). In the second approach, the same goal is addressed using the theory of Molecular Quantum Similarity (MQS). Both independent approaches are found to correlate very well, and both point toward decreasing aromaticity in any linear polyacenes upon going from the outer to inner rings.

Molecular quantum similarity measures as an alternative to log P values in QSAR studies

A new molecular descriptor of hydrophobicity based on molecular quantum similarity measures (MQSM), which can be used to replace the log P parameter in QSAR studies, is proposed. Unlike the majority of existing approaches for calculation of log P, the present methodology does not rely on the use of fragment additive contributions, but rather it is based on the comparison of quantum chemically calculated electron density distributions of a given molecule in water and in 1‐octanol, using MQSM. The method has been tested on a broad series of 58 molecules including such structural types as aliphatic hydrocarbons, alcohols, amines, halides, carboxylic acids, esters, amides, and ketones, as well as more complex systems with two functional groups. In all cases investigated, an excellent linear relationship between calculated MQSM and log P values was found. Additionally, an example of QSAR analysis is presented using MQSM instead of log P values, corresponding to predict the narcosis of tadpoles. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1575–1583, 1998

Anatomy of bond formation. Bond length dependence of the extent of electron sharing in chemical bonds from the analysis of domain-averaged Fermi holes

We demonstrate that domain-average Fermi hole (DAFH) analysis, which has previously been used at the Hartree–Fock level, remains useful after the proper introduction of electron correlation. We perform a systematic investigation of the variation of the picture of bonding with increasing bond length in simple diatomic molecules such as N2 and LiH. Alongside values of a shared-electron distribution index (SEDI), this analysis provides further insight into the geometry dependence of the extent of electron sharing in polar and non-polar systems. We also use DAFH analysis, with correlated wave functions, to evaluate the (potential) multicentre bonding in the electron-deficient and electron-rich molecules CH2Li2 and CH2N2, respectively.

Identification of active molecular sites using quantum-self-similarity measures.

A novel approach to construct theoretical QSAR models is proposed. This technique, based on the systematic use of quantum similarity measures as theoretical molecular descriptors, opens the possibility to localize and to identify the position of the bioactive part of drug molecules in situations, where the nature of the pharmacophore is not known. To test the reliability of this new approach, the method has been applied to the study of steroids binding to corticosteroid-binding human globulin. The studied molecules involved the set of 31 Cramers steroids, often used as a benchmark set in QSAR studies. It has been shown that theoretical QSAR models based on the present procedure are superior to those derived from alternative existing approaches. In addition, a new method to measure the statistical significance of multiparameter QSAR models is also proposed.

Electron pairing and chemical bonds. On the accuracy of the electron pair model of chemical bond

Abstract The accuracy of the Lewis electron pair model of the chemical bond is reinvestigated. It is shown that, contrary to previous pessimistic findings, the accuracy of this model is high enough to represent a good basis for the understanding and interpretation of molecular structure, not only for molecules well described by a classical structural formula with localised two-centre two-electron (2c2e) bonds, but also for molecules with more complex bonding patterns such as three- or multicentre bonding.