Mechanistic aspects of hydrogen abstraction for phenolic antioxidants. Electronic structure and topological electron density analysis

2005 ◽  
Vol 7 (4) ◽  
pp. 614-619 ◽  
Author(s):  
Nakul Singh ◽  
Patrick J. O’Malley ◽  
Paul L. A. Popelier
Keyword(s):  
Electronic Structure ◽  
Electron Density ◽  
Hydrogen Abstraction ◽  
Phenolic Antioxidants ◽  
Density Analysis ◽  
Electron Density Analysis

Interpretation of neighboring group interactions in crystal structures. A solid state and quantum-chemical study of "incipient nucleophilic attack" in 2-diazonium benzoic acid and its benzoate

1996 ◽  
Vol 74 (6) ◽  
pp. 1200-1214 ◽  
Author(s):  
Rainer Glaser ◽  
Christopher J. Horan
Keyword(s):  
Electronic Structure ◽  
Electron Density ◽  
Nucleophilic Attack ◽  
Neighboring Group ◽  
Group Interactions ◽  
Diazonium Ions ◽  
Attraction Model ◽  
Density Analysis ◽  
Bridging Attraction ◽  
Electron Density Analysis

The concept of the Bürgi–Dunitz angle of attack on carbonyls is compatible with the electronic structure of carbonyls. However, it is argued here that the generalization asserted to describe the interaction of nucleophiles with diazonium ions is inappropriate. Distortions in crystal structures of diazonium ions with proximate nucleophiles were interpreted by an incipient nucleophilic attack (INA) on the formally positive-charged Nα. This "Nα attraction model" relies on the assumption that the formal charge in the most commonly used Lewis structure of diazonium ions represents actual charge. We proposed that the close approach of the proximate nucleophile to the diazonium group occurs to enhance attractive 1,3-(C,Nβ)-bridging interactions and despite repulsion between Nα and the proximate oxygen (Opr). The present study combines theoretical analysis of rotamers of 2-diazonium benzoic acid and its conjugate base with experimental results on the same system to provide compelling evidence that the more general conclusions drawn from analyses of neighboring group interactions in propenoic acid models are fully warranted. The crystallographic record is more fully consistent with the "1,3-bridging attraction model." Combined analysis of solid state and gas phase structures reveals the intrinsic features due to INA. Both electrostatic models can account for these features but with different postulates about the electron density distribution. While the structural analysis alone cannot distinguish between the alternative interpretations, the study of the electronic structure allows one to clearly differentiate between these competing interpretations. A method (ESI) for the quantitative evaluation of electrostatic neighboring group interactions has been devised and this ESI concept employs atomic electrical moments (charges, dipoles, and quadrupoles) determined via topological electron density analysis. The results of the ESI analysis support the 1,3-bridging attraction model and eliminate the Nα attraction model. Key words: electrostatic interactions, electron density analysis, atoms in molecules. X-ray crystallography, ab initio molecular orbital theory, incipient nucleophilic attack, bonding models, ESI analysis.

scholarly journals Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3960
Author(s):  
Nadezhda Palko ◽  
Maria Grishina ◽  
Vladimir Potemkin
Keyword(s):  
Electronic Structure ◽  
Rna Polymerase ◽  
Electron Density ◽  
Research Methodology ◽  
Electronic Structures ◽  
Positive Relationship ◽  
Electron Densities ◽  
Rna Dependent Rna Polymerase ◽  
Density Analysis ◽  
Electron Density Analysis

The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.

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