scholarly journals What Is the Nature of Supramolecular Bonding? Comprehensive NBO/NRT Picture of Halogen and Pnicogen Bonding in RPH2···IF/FI Complexes (R = CH3, OH, CF3, CN, NO2)

Molecules ◽  
2019 ◽  
Vol 24 (11) ◽  
pp. 2090 ◽  
Author(s):  
Yinchun Jiao ◽  
Frank Weinhold
Keyword(s):  
Binding Energies ◽  
Classical Type ◽  
Resonance Theory ◽  
Binary Complexes ◽  
Donor Acceptor ◽  
Sigma Hole ◽  
Natural Resonance Theory ◽  
Type 3 ◽  
Supramolecular Complexation ◽  
Covalent Interactions

We employ a variety of natural bond orbital (NBO) and natural resonance theory (NRT) tools to comprehensively investigate the nature of halogen and pnicogen bonding interactions in RPH2···IF/FI binary complexes (R = CH3, OH, CF3, CN, and NO2) and the tuning effects of R-substituents. Though such interactions are commonly attributed to “sigma-hole”-type electrostatic effects, we show that they exhibit profound similarities and analogies to the resonance-type 3-center, 4-electron (3c/4e) donor-acceptor interactions of hydrogen bonding, where classical-type “electrostatics” are known to play only a secondary modulating role. The general 3c/4e resonance perspective corresponds to a continuous range of interatomic A···B bond orders (bAB), spanning both the stronger “covalent” interactions of the molecular domain (say, bAB ≥ ½) and the weaker interactions (bAB ˂ ½, often misleadingly termed “noncovalent”) that underlie supramolecular complexation phenomena. We show how a unified NBO/NRT-based description of hydrogen, halogen, pnicogen, and related bonding yields an improved predictive utility and intuitive understanding of empirical trends in binding energies, structural geometry, and other measurable properties that are expected to be manifested in all such supramolecular interaction phenomena.

scholarly journals Photoluminescence of GaN Grown by Molecular Beam Epitaxy on Freestanding GaN Template

2002 ◽  
Vol 722 ◽  
Author(s):  
M. A. Reshchikov ◽  
F. Yun ◽  
D. Huang ◽  
L. He ◽  
H. Morkoç ◽  
...  
Keyword(s):  
Molecular Beam Epitaxy ◽  
Molecular Beam ◽  
Broad Band ◽  
Shallow Donor ◽  
Binding Energies ◽  
Main Peak ◽  
Acceptor Pair ◽  
Pl Spectra ◽  
Frequency Plasma ◽  
Donor Acceptor

AbstractWe studied photoluminescence (PL) of GaN layers grown by molecular beam epitaxy on freestanding high-quality GaN templates. The layers with thickness of ∼ 1 νm were grown under Ga-rich conditions using radio-frequency plasma as a nitrogen source. The PL spectra from both the epilayer and the substrate contain a plethora of very sharp peaks related to excitonic transitions. Through the analysis of the excitonic part of the spectra, we have identified two shallow donors with the binding energies of 28.8 and 32.6 meV, attributed to SiGa and ON, respectively. The PL spectra involved also emissions due to shallow donor-acceptor pair transitions with the main peak at 3.26 eV and a broad band peaking at ∼2.5 - 2.6 eV (green band). The green bands in the GaN substrate and GaN overgrown layer have different energy positions invoking the suggestion that they must have their genesis in different defect centers.

Multi-mode ground state interaction terms in C60-based electron donor-acceptor complexes

Open Physics ◽  
2004 ◽  
Vol 2 (2) ◽  
Author(s):  
Elena Sheka
Keyword(s):  
Ground State ◽  
Singlet State ◽  
Molecular Complexes ◽  
Suggested Approach ◽  
Interaction Terms ◽  
Binary Complexes ◽  
Avoided Crossing ◽  
Donor Acceptor ◽  
Multi Mode ◽  
Chemical Testing

AbstractQuantum-chemical testing of donor-acceptor properties of binary molecular complexes, related to the singlet state, is suggested as QCh calculations of studied systems and their constituents by using both spin-nondependent (RHF) and spindependent (UHF) versions of the exploited computational tool. The avoided crossing of intermolecular interaction terms of neutral moleculesE int(A 0 B 0) and molecular ionsE int(A + B −) causes a multi-mode character of the ground state term. The dependence of D-A complex properties on the type of the term, space positions of the term minimum, and the interrelation of the corresponding energies are discussed. The suggested approach has been applied to binary complexes C60+X (X=TAE, TDAE, DMMA, COANP, 2Li, Mg).

Using one halogen bond to change the nature of a second bond in ternary complexes with P⋯Cl and F⋯Cl halogen bonds

2017 ◽  
Vol 203 ◽  
pp. 29-45 ◽  
Author(s):  
Janet E. Del Bene ◽  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Halogen Bond ◽  
Synergistic Effects ◽  
Ternary Complexes ◽  
Binding Energies ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Halogen Bonds ◽  
Binary Complexes ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to determine the effect of the presence of one halogen bond on the nature of the other in ternary complexes H2XP:ClF:ClH and H2XP:ClF:ClF, for X = F, Cl, H, NC, and CN. The P⋯Cl bonds remain chlorine-shared halogen bonds in the ternary complexes H2XP:ClF:ClH, although the degree of chlorine sharing increases relative to the corresponding binary complexes. The F⋯Cl bonds in the ternary complexes remain traditional halogen bonds. The binding energies of the complexes H2XP:ClF:ClH increase relative to the corresponding binary complexes, and nonadditivities of binding energies are synergistic. In contrast, the presence of two halogen bonds in the ternary complexes H2XP:ClF:ClF has a dramatic effect on the nature of these bonds in the four most strongly bound complexes. In these, chlorine transfer occurs across the P⋯Cl halogen bond to produce complexes represented as (H2XP–Cl)+:−(F:ClF). In the ion-pair, the cation is also halogen bonded to the anion by a Cl⋯F− halogen bond, while the anion is stabilized by an −F⋯Cl halogen bond. The central ClF molecule no longer exists as a molecule. The binding energies of the ternary H2XP:ClF:ClF complexes are significantly greater than the binding energies of the H2XP:ClF:ClH complexes, and nonadditivities exhibit large synergistic effects. The Wiberg bond indexes for the complexes H2XP:ClF, H2XP:ClF:ClH, and H2XP:ClF:ClF, and the cations (H2XP–Cl)+ reflect the changes in the P–Cl and Cl–F bonds. Similarly, EOM-CCSD spin–spin coupling constants are also consistent with the changes in these same bonds. In particular, 1xJ(P–Cl) in H2XP:ClF complexes becomes 1J(P–Cl) in the ternary complexes with chlorine-transferred halogen bonds. A plot of these coupling constants shows a change in the curvature of the trendline as chlorine-shared halogen bonds in H2XP:ClF:ClH become chlorine-transferred halogen bonds in H2XP:ClF:ClF. 1xJ(F–Cl) coupling constants also reflect changes in the nature of F⋯Cl halogen bonds.

scholarly journals Theoretical Description of R–X⋯NH3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 530
Author(s):  
Juan Zurita ◽  
Vladimir Rodriguez ◽  
Cesar Zambrano ◽  
Jose Ramón Mora ◽  
Luis Rincón ◽  
...  
Keyword(s):  
Halogen Bond ◽  
Theoretical Description ◽  
Binding Energies ◽  
Complex Stability ◽  
Ethyl Vinyl ◽  
Cooperative Effects ◽  
Pair Density ◽  
Leibler Divergence ◽  
Sigma Hole ◽  
The Stability

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.

scholarly journals A Halogen Bonding Perspective on Iodothyronine Deiodinase Activity

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1328 ◽  
Author(s):  
Eric S. Marsan ◽  
Craig A. Bayse
Keyword(s):  
Active Site ◽  
Polybrominated Diphenyl Ethers ◽  
Density Functional ◽  
Endocrine System ◽  
Halogen Bonding ◽  
Binding Energies ◽  
Active Site Residues ◽  
Iodothyronine Deiodinase ◽  
Donor Acceptor ◽  
Small Models

Iodothyronine deiodinases (Dios) are involved in the regioselective removal of iodine from thyroid hormones (THs). Deiodination is essential to maintain TH homeostasis, and disruption can have detrimental effects. Halogen bonding (XB) to the selenium of the selenocysteine (Sec) residue in the Dio active site has been proposed to contribute to the mechanism for iodine removal. Polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) are known disruptors of various pathways of the endocrine system. Experimental evidence shows PBDEs and their hydroxylated metabolites (OH-BDEs) can inhibit Dio, while data regarding PCB inhibition are limited. These xenobiotics could inhibit Dio activity by competitively binding to the active site Sec through XB to prevent deiodination. XB interactions calculated using density functional theory (DFT) of THs, PBDEs, and PCBs to a methyl selenolate (MeSe−) arrange XB strengths in the order THs > PBDEs > PCBs in agreement with known XB trends. THs have the lowest energy C–X*-type unoccupied orbitals and overlap with the Se lp donor leads to high donor-acceptor energies and the greatest activation of the C–X bond. The higher energy C–Br* and C–Cl* orbitals similarly result in weaker donor-acceptor complexes and less activation of the C–X bond. Comparison of the I···Se interactions for the TH group suggest that a threshold XB strength may be required for dehalogenation. Only highly brominated PBDEs have binding energies in the same range as THs, suggesting that these compounds may inhibit Dio and undergo debromination. While these small models provide insight on the I···Se XB interaction itself, interactions with other active site residues are governed by regioselective preferences observed in Dios.

An MEDT study of the carbenoid-type [3 + 2] cycloaddition reactions of nitrile ylides with electron-deficient chiral oxazolidinones

2016 ◽  
Vol 14 (44) ◽  
pp. 10427-10436 ◽  
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
Patricia Pérez
Keyword(s):  
Cycloaddition Reactions ◽  
Evolution Theory ◽  
Non Covalent Interactions ◽  
Type 3 ◽  
Covalent Interactions

A combination of the bonding evolution theory and non-covalent interactions analyses of TSs makes it possible to characterise both the carbenoid-type 32CA reaction between a NY and a chiral oxazolidinone, and the diastereoselectivity experimentally observed.

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