Biomedical subjects

Robert Ponec

Publications and source records attributed to Robert Ponec.

17 recordsLinked to original sources

PubMed2007

Electron pairing and chemical bonds: pair localization in ELF domains from the analysis of domain averaged Fermi holes.

This article reports the application of a recently proposed formalism of domain averaged Fermi holes to the problem of the localization of electron pairs in electron localization function (ELF) domains and its possible implications for the electron pair model of chemical bond. The main focus was on the systems, such as H2O or N2, in which the "unphysical" population of ELF domains makes the parallel between these domains and chemical bond questionable. On the basis of the results of the Fermi-hole analysis, we propose that the above problems could be due to the fact that in some cases the boundaries of the ELF domains need not be determined precisely enough.

Journal Article↗

PubMed2007

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.

Journal Article↗

PubMed2006

Local aromaticity in polycyclic aromatic hydrocarbons: electron delocalization versus magnetic indices.

The local aromaticity of benzenoid rings is examined by means of the Polansky index (P) and generalized population analysis (GPA). The results are found to agree very well with recently published circuit-condensed ring currents and magnetic-energetic aromaticity indices, but no correlation is found with nucleus independent chemical shifts (NICS). This is usually seen as a manifestation of the more general multidimensional nature of aromaticity. This paper examines the sources for the observed correlations, showing that some indices give conflicting results because they inherently reflect different phenomena.

Journal Article↗

PubMed2006

Electron delocalization and aromaticity in linear polyacenes: atoms in molecules multicenter delocalization index.

Molecular aromaticity in the linear polyacenes is investigated using an atoms in molecules based six center index (SCI-AIM) which measures the electron delocalization. SCI-AIM values for the linear polyacenes indicate decreasing aromaticity going from outer to inner rings in the polyacene series. The SCI-AIM approach is compared to a Mulliken-like approach, and a critical comparison to the PDI index is made.

Journal Article↗

PubMed2006

Multicenter bonding in carbocations with tetracoordinate protons.

The nature of the bonding in a set of nonclassical carbocations with tetracoordinated protons "sandwiched" between two C=C pi bonds was scrutinized using the new computational methodology of generalized population analysis. The results of this theoretical analysis strongly corroborate the conclusions of a previous study in which the occurrence of delocalized 5-center 4-electron (5c-4e) bonding in the C-C-H-C-C fragments of such cations was anticipated.

Journal Article↗

PubMed2005

Multicenter bond indices as a new means for the quantitative characterization of homoaromaticity.

This study reports the use of multicenter bond indices as a new tool for the quantitative characterization of homoaromaticity. The approach was applied to the series bicyclic systems whose homoaromaticity was recently discussed in terms of traditional aromaticity index, namely, NICS. In this study we found that the multicenter bond indices are indeed able to quantify the degree of homoaromaticity of the studied systems as reflected in the classification of these molecules into classes of homoaromatic, non-homoaromatic, and anti-homoaromatic systems suggested on the basis of NICS values.

Models, Chemical↗

PubMed2005

Chemical structures from the analysis of domain-averaged fermi holes. Nature of the Mn-Mn bond in bis(pentacarbonylmanganese).

Because of conflicting and contradictory classification based on traditional AIM characteristics, the nature of the Mn-Mn bond has been and still is the subject of continuing discussions. To overcome the existing inconsistencies in the interpretation of the nature of this bond, the bonding in Mn2(CO)10 has been analyzed and discussed in terms of new recently proposed methodology known as the analysis of domain-averaged Fermi holes. It has been shown that this analysis is able to reconcile the conflicting conclusions of earlier AIM-based studies with traditional anticipations based on simple electron counting rules. According to Fermi hole analysis, the Mn-Mn bond has the character of the more or less ordinary covalent single sigma bond, but the analysis also brings clear evidence in favor of Mn . . . (CO) intramolecular interactions between the metal atom and the ligands bonded to the other metal atom. These interactions could be responsible for the observed decrease of electron density at the bond critical point detected in AIM studies.

Journal Article↗

PubMed2005

Electron pairing and chemical bonds. Electron fluctuation and pair localization in ELF domains.

This article reports the numerical comparison of the quantities characterizing the extent of electron fluctuation and pair localization in the domains determined by the direct minimization of electron fluctuation with the domains resulting from the partitioning of the molecules based on the topological analysis of the so-called electron localization function (ELF). Such a comparison demonstrates that the ELF partitioning can be regarded as a feasible alternative to computationally much more demanding direct optimization of minimum fluctuation domains. This opened the possibility of the systematic scrutiny of the electron pair model of the chemical bond, and as it was demonstrated, the previous pessimistic claims about the applicability of this model are not completely justified.

Journal Article↗

PubMed2004

Multicenter bonding in organic chemistry. Geometry-sensitive 3c-2e bonding in (C...H...C) fragments of organic cations.

This paper reports the application of a new general tool for the study of multicenter bonding, namely the so-called generalized population analysis, to the investigation of interesting geometry dependent variation of 3c-2e bonding in the (C...H...C) fragments of ingeniously designed organic cations I and II. This phenomenon was previously characterized by the correlation between experimental (1)H NMR chemical shifts of the central hydrogen in the (C...H...C) fragment and the changes in the corresponding C-H-C bond angle. The observed values of both chemical shifts and C-H-C angles are shown herein to correlate with the calculated 3-center bond indices but the dependence displays splitting into two separate lines according to the type of corresponding cation.

Journal Article↗

PubMed2004

Similarity approach to QSAR. Application to antimycobacterial benzoxazines.

The antimycobacterial activity in six series of substituted 3-phenyl-2H-benzoxazine-2,4(3H)-dithiones and 3-(phenyl)-4-thioxo-2H-benzoxazine-2,4(3H)-diones has been studied using a quantum molecular similarity approach. The approach is based on the use of fragment self-similarity measures as new universal molecular descriptors applicable for the design of novel theoretical QSAR models. Using this approach it was possible to show that while traditional QSAR models were able to describe the activity only within each of the six sets of studied molecules individually, the proposed approach is much more general and a single universal QSAR model describing the activity of all the 39 studied molecules in all the studied series together was built. The replacement of the oxo group by the thioxo group in position 4 on the benzoxazine ring of the antitubercular 3-(phenyl)-2H-benzoxazine-2,4(3H)-diones increases the activity, as well as the similar replacement in position 2.

Anti-Bacterial Agents↗

PubMed2003

Chemical structures from the analysis of domain-averaged Fermi holes: multiple metal-metal bonding in transition metal compounds.

The recently proposed approach based on the analysis of domain-averaged Fermi holes was applied to the study of the nature of metal-metal bonding in transition metal complexes and clusters. The main emphasis was put on the scrutiny of the systems assumed to contain direct multiple metal-metal bonds. The studied systems involve: (1) systems of the type M(2)X(6) (M = Mo, W, X = CH(3)) anticipated to contain metal-metal triple bonds; (2) the molecule of W(2)Cl(8) ((4-)) as the representative of the systems with quadruple metal-metal bonding; (3) diatomic molecules Mo(2) and V(2) considered as the potential candidates for higher than quadruple metal-metal bonding. Although the resulting picture of bonding has been usually shown to agree with the original expectations based on early simple MO models, some examples were also found in which the conclusions of the reported analysis display dramatic sensitivity to the quality of the wave function used for the generation of the Fermi holes. In addition to this we also report some examples where the original theoretical predictions of multiplicity of metal-metal bonds have to be corrected.

Journal Article↗

PubMed2003

Evidence for 5-center 4-electron bonding in (C...H...C...H...C) array.

This paper brings new independent evidence for 5-center 4-electron bonding, whose existence in (C...H...C...H...C) fragment of the molecule I was anticipated in the recent study by Tantillo and Hoffmann. The evidence is based on the applications of the so-called multicenter bond indices, recently proposed as new efficient tool for the detection and localization of multicenter bonding in molecules.

Journal Article↗

PubMed2003

Virtual generation of agents against Mycobacterium tuberculosis. A QSAR study.

A QSAR approach based on the use of various topological indices as new theoretical molecular descriptors was applied to the study of a set of 64 anti-tuberculosis agents involving the substituted benzoxazines and phenylquinazolines. In order to evaluate the reliability of the proposed linear QSAR model, several statistical tests were proposed. The resulting model was subsequently applied to a wider virtual molecular library, which, together with the original set of 64 molecules with known activities contained another 512 molecules for which the predictions were made. Based on this prediction some new structures were proposed as especially promising candidates for active anti-tuberculotic drugs.

Algorithms↗

PubMed1997

Theoretical Analysis of the Stereoselectivity in the Ozonolysis of Olefins. Evidence for a Modified Criegee Mechanism.

The Criegee mechanism of the ozonolysis of cis and trans symmetric alkenes of the type RCH=CHR is investigated by semiempirical AM1 calculations. The observed stereoselectivity trends are qualitatively explained in terms of the original Criegee mechanism. However, it is shown that in order to elucidate some subtle stereochemical effects as well as to account for the vain attempts to detect the carbonyloxide intermediate, a modification is required. This is done by adopting a proposal made by Cremer et al. (Chem. Phys. Lett. 1991, 187, 491) for the specific case of ethylene and applying it to all systems. The carbonyl oxide and aldehyde formed upon dissociation of the primary ozonide are not separated but form a strongly bound complex that subsequently transforms to the secondary ozonide.

Journal Article↗

PubMedDate not supplied

Molecular basis of linear free energy relationships. The nature of inductive effect in aliphatic series.

The nature of inductive substituent effect on the acidity of aliphatic carboxylic acids was analyzed in terms of a quantum chemical model based on the Longuet-Higgins theory of proton affinity. It has been shown that the effect is generally composed of two additive components, the electrostatic one and the polarization one. The relative weights of these components depend in any given case on the type of the reaction series. Thus, for example, the substituent-induced variation of gas-phase acidity in a series of 4-substituted bicyclo[2.2.2]octane-1-carboxylic acids is due to the electrostatic component classically described by the Kirkwood-Westheimer theory. On the other hand, the gas-phase basicity in a series of aliphatic amines is primarily determined by the polarization term that in traditional description corresponds to the concept of inductive effect.

Journal Article↗

PubMedDate not supplied

Molecular basis of LFER. Modeling of the electronic substituent effect using fragment quantum self-similarity measures.

A new approach allowing the theoretical modeling of the electronic substituent effect is proposed. The approach is based on the use of fragment Quantum Self-Similarity Measures (MQS-SM) calculated from domain averaged Fermi Holes as new theoretical descriptors allowing for the replacement of Hammett sigma constants in QSAR models. To demonstrate the applicability of this new approach its formalism was applied to the description of the substituent effect on the dissociation of a broad series of meta and para substituted benzoic acids. The accuracy and the predicting power of this new approach was tested on the comparison with a recent exhaustive study by Sullivan et al. It has been shown that the accuracy and the predicting power of both procedures is comparable, but, in contrast to a five-parameter correlation equation necessary to describe the data in the study, our approach is more simple and, in fact, only a simple one-parameter correlation equation is required.

Journal Article↗

PubMedDate not supplied

Molecular Quantum Similarity Measures from Fermi hole densities: modeling Hammett sigma constants.

A new approach, based on the use of fragment Quantum Self-Similarity Measures (MQS-SM) as descriptors of electronic substituent effect in aromatic series, was proposed. The novelty of this approach consists of the fact that the corresponding MQS-SM are not derived, as usual, from ordinary density functions (DF) but from the so-called domain averaged Fermi holes. This approach was applied to the study of substituent effects on the acidobasic dissociation constants in 6 series of para-substituted aromatic carboxylic acids. It has been shown that MQS-SM calculated for each particular set of acids correlate with the Hammett substituent constants. As a consequence, the corresponding similarity measures can be used as new efficient descriptors of the substituent effect, which hopefully could replace empirical sigma constants in QSAR models.

Models, Theoretical↗