sigma hole
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Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 377
Author(s):  
Frank Weinhold

Intermolecular bonding attraction at π-bonded centers is often described as “electrostatically driven” and given quasi-classical rationalization in terms of a “pi hole” depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO−, CN−) with simple atomic anions (H−, F−) or with one another. Such “anti-electrostatic” anion–anion attractions are shown to lead to robust metastable binding wells (ranging up to 20–30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi–Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that “deletion” of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi–Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency (“charge transfer”) rather than envisioned Coulombic properties of unperturbed monomers.


2021 ◽  
Author(s):  
Alexander Friedrich ◽  
Jürgen Pahl ◽  
Jonathan Eyselein ◽  
Jens Langer ◽  
Nico van Eikema Hommes ◽  
...  
Keyword(s):  

Complexes of a highly Lewis acidic Mg cation and the full series of Ph–X (X = F, Cl, Br, I) have been structurally characterized. The Mg⋯X–Ph angle decreases with halogen size on account of the growing halogen σ-hole.


2020 ◽  
Author(s):  
Thomas Fellowes ◽  
JONATHAN WHITE

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19, however<br>efforts to model ebselen in silico have been hampered by the lack of a efficient and accurate method to assess<br>its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which<br>incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to<br>simulate the sigma?-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach<br>is justified using an energy decomposition analysis of a number DFT optimised structures, which shows that the<br>?sigma-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting MD simulations<br>on a number of simple complexes, as well the clinically relevant SOD1, which is known to bind to ebselen.


2020 ◽  
Author(s):  
Thomas Fellowes ◽  
JONATHAN WHITE

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19, however<br>efforts to model ebselen in silico have been hampered by the lack of a efficient and accurate method to assess<br>its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which<br>incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to<br>simulate the sigma?-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach<br>is justified using an energy decomposition analysis of a number DFT optimised structures, which shows that the<br>?sigma-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting MD simulations<br>on a number of simple complexes, as well the clinically relevant SOD1, which is known to bind to ebselen.


Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 530
Author(s):  
Juan Zurita ◽  
Vladimir Rodriguez ◽  
Cesar Zambrano ◽  
Jose Ramón Mora ◽  
Luis Rincón ◽  
...  

In the present work, a number of R–X⋯NH3 (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme’s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R–Br⋯NH3 complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback–Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R–X bond is significantly polarized due to the presence of the NH3 molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br—CN]n system (n = 1–8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.


2020 ◽  
Vol 22 (20) ◽  
pp. 11558-11566 ◽  
Author(s):  
Jyoti Rani ◽  
Vratta Grover ◽  
Swati Dhamija ◽  
Hatem M. Titi ◽  
Ranjan Patra

A direct influence of porphyrin's ring current on the sigma-hole potential of halogen atoms at the axial position of metalloporphyrins during halogen bonded self-assembly is determined in this study.


2020 ◽  
Vol 22 (12) ◽  
pp. 6595-6605
Author(s):  
Niloufar Hendinejad ◽  
Qadir K. Timerghazin

S-Nitrosothiols, ubiquitous biological derivatives of nitric oxide, can engage in σ-hole/bonding with Lewis bases, which, in combination with hydrogen bonding with Lewis acids, could be the basis of enzymatic control of S-nitrosothiol reactions.


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