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.

Mukaiyama Aldol Reaction Catalyzed by (Benz)imidazolium-Based Halogen Bond Donors

2020 ◽  
Author(s):  
Revannath L. Sutar ◽  
Nikita Erochok ◽  
Stefan Huber
Keyword(s):  
Halogen Bond ◽  
Aldol Reaction ◽  
Mukaiyama Aldol Reaction ◽  
Mukaiyama Aldol ◽  
Background Reaction ◽  
Strong Performance ◽  
The Stability ◽  
Elemental Iodine

A series of cationic monodentate and bidentate iodo(benz)­imidazolium-based halogen bond (XB) donors were employed as catalysts in a Mukaiyama aldol reaction. While 5 mol% of a monodentate variant showed noticeable activity, a <i>syn</i>-preorganized bidentate XB donor provided a strong performance even with 0.5 mol% loading. In contrast to the very active BAr<sup>F</sup><sub>4</sub> salts, PF<sub>6</sub> or OTf salts were either inactive or showed background reaction. Repetition experiments clearly ruled out a potential hidden catalysis by elemental iodine and demonstrated the stability of our catalyst over three consecutive cycles.

scholarly journals Nanotechnology-based approaches for targeting and delivery of drugs via Hexakis (m-PE) macrocycles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samaneh Pasban ◽  
Heidar Raissi
Keyword(s):  
Drug Delivery ◽  
Density Functional ◽  
Water Solution ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Partial Density ◽  
High Propensity ◽  
The Stability ◽  
Novel Applications

AbstractHexakis (m-phenylene ethynylene) (m-PE) macrocycles, with aromatic backbones and multiple hydrogen-bonding side chains, had a very high propensity to self-assemble via H-bond and π–π stacking interactions to form nanotubular structures with defined inner pores. Such stacking of rigid macrocycles is leading to novel applications that enable the researchers to explored mass transport in the sub-nanometer scale. Herein, we performed density functional theory (DFT) calculations to examine the drug delivery performance of the hexakis dimer as a novel carrier for doxorubicin (DOX) agent in the chloroform and water solvents. Based on the DFT results, it is found that the adsorption of DOX on the carrier surface is typically physisorption with the adsorption strength values of − 115.14 and − 83.37 kJ/mol in outside and inside complexes, respectively, and so that the essence of the drug remains intact. The negative values of the binding energies for all complexes indicate the stability of the drug molecule inside and outside the carrier's cavities. The energy decomposition analysis (EDA) has also been performed and shown that the dispersion interaction has an essential role in stabilizing the drug-hexakis dimer complexes. To further explore the electronic properties of dox, the partial density of states (PDOS and TDOS) are calculated. The atom in molecules (AIM) and Becke surface (BS) methods are also analyzed to provide an inside view of the nature and strength of the H-bonding interactions in complexes. The obtained results indicate that in all studied complexes, H-bond formation is the driving force in the stabilization of these structures, and also chloroform solvent is more favorable than the water solution. Overall, our findings offer insightful information on the efficient utilization of hexakis dimer as drug delivery systems to deliver anti-cancer drugs.

Effect of delocalization of nonbonding electron density on the stability of the M–Ccarbene bond in main group metal-imidazol-2-ylidene complexes: a computational and structural database study

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Samuel Tetteh ◽  
Albert Ofori
Keyword(s):  
Electron Density ◽  
Lone Pair ◽  
Main Group ◽  
Binding Energies ◽  
Electrostatic Model ◽  
Group Metal ◽  
Main Group Metal ◽  
Structural Database ◽  
The Stability ◽  
Lone Pair Electrons

Abstract The M–Ccarbene bond in metal (M) complexes involving the imidazol-2-ylidene (Im) ligand has largely been described using the σ-donor only model with donation of σ electrons from the sp-hybridized orbital of the carbene carbon into vacant orbitals on the metal centre. Analyses of the M–Ccarbene bond in a series of group IA, IIA and IIIA main group metal complexes show that the M-Im interactions are mostly electrostatic with the M–Ccarbene bond distances greater than the sum of the respective covalent radii. Estimation of the binding energies of a series of metal hydride/fluoride/chloride imidazol-2-ylidene complexes revealed that the stability of the M–Ccarbene bond in these complexes is not always commensurate with the σ-only electrostatic model. Further natural bond orbital (NBO) analyses at the DFT/B3LYP level of theory revealed substantial covalency in the M–Ccarbene bond with minor delocalization of electron density from the lone pair electrons on the halide ligands into antibonding molecular orbitals on the Im ligand. Calculation of the thermodynamic stability of the M–Ccarbene bond showed that these interactions are mostly endothermic in the gas phase with reduced entropies giving an overall ΔG > 0.

scholarly journals Using beryllium bonds to change halogen bonds from traditional to chlorine-shared to ion-pair bonds

2015 ◽  
Vol 17 (3) ◽  
pp. 2259-2267 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Otilia Mó ◽  
Manuel Yáñez ◽  
Janet E. Del Bene
Keyword(s):  
Halogen Bond ◽  
Ion Pair ◽  
Ternary Complexes ◽  
Halogen Bonds ◽  
Bond Type ◽  
Cooperative Effects ◽  
Pair Bonds

Dramatic synergistic cooperative effects between Be⋯F beryllium bonds and Cl⋯N halogen bonds in XYBe:FCl:N-base ternary complexes lead to changes in the halogen-bond type from traditional to chlorine-shared to ion-pair bonds.

Cyclic networks of halogen-bonding interactions in molecular self-assemblies: a theoretical N—X...NversusC—X...N investigation

2017 ◽  
Vol 73 (2) ◽  
pp. 179-187
Author(s):  
Ruben D. Parra ◽  
Álvaro Castillo
Keyword(s):  
Electron Density ◽  
Self Assembly ◽  
Metal Ion ◽  
Halogen Atom ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Nbo Analysis ◽  
Binding Energies ◽  
Cyclic Network ◽  
Ability To Drive

The geometries and energetics of molecular self-assembly structures that contain a sequential network of cyclic halogen-bonding interactions are investigated theoretically. The strength of the halogen-bonding interactions is assessed by examining binding energies, electron charge transfer (NBO analysis) and electron density at halogen-bond critical points (AIM theory). Specifically, structural motifs having intramolecular N—X...N (X= Cl, Br, or I) interactions and the ability to drive molecular self-assemblyviathe same type of interactions are used to construct larger self-assemblies of up to three unit motifs. N—X...N halogen-bond cooperativity as a function of the self-assembly size, and the nature of the halogen atom is also examined. The cyclic network of the halogen-bonding interactions provides a suitable cavity rich in electron density (from the halogen atom lone pairs not involved in the halogen bonds) that can potentially bind an electron-deficient species such as a metal ion. This possibility is explored by examining the ability of the N—X...N network to bind Na+. Likewise, molecular self-assembly structures driven by the weaker C—X...N halogen-bonding interactions are investigated and the results compared with those of their N—X...N counterparts.

Ab-Initio Calculation of the β-SiC/Ni Interface

2001 ◽  
Vol 680 ◽  
Author(s):  
A. Blasetti ◽  
G. Profeta ◽  
S. Picozzi ◽  
A. Continenza ◽  
A. J. Freeman
Keyword(s):  
First Principles ◽  
Ab Initio Calculation ◽  
Surface States ◽  
Binding Energies ◽  
Bonding Mechanism ◽  
Covalent Character ◽  
Adsorption Sites ◽  
Barrier Heights ◽  
Adsorption Energies ◽  
The Stability

ABSTRACTWe investigate the adsorption of a Ni monolayer on the β-SiC(001) surface by means of highly precise first-principles all-electron FLAPW calculations. Total energy calculations for the Si- and C-terminated surfaces reveal high Ni adsorption energies, with respect to other metals, confirming the strong reactivity and the stability of the transition metal/SiC interface. These high binding energies, about 7.3-7.4 eV, are shown to be related to strong p-d hybridization, common to both surface terminations and different adsorption sites, which, despite the large mismatch, may stabilize overlayer growth. A detailed analysis of the bonding mechanism, in terms of density of states and hybridization of the surface states, reveals the strong covalent character of the bonding. We also calculate and discuss the Schottky barrier heights at the Ni/SiC junction for both terminations.

scholarly journals Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons

2020 ◽  
Vol 21 (18) ◽  
pp. 6571
Author(s):  
Nicholas J. Thornton ◽  
Tanja van Mourik
Keyword(s):  
Base Pair ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Dna Bases ◽  
Halogen Bonds ◽  
Base Pairs ◽  
Rich Diversity ◽  
Different Types ◽  
Guanine Base ◽  
The Stability

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).

scholarly journals Encapsulation of l-menthol in hydroxypropyl-β-cyclodextrin and release characteristics of the inclusion complex

2016 ◽  
Vol 18 (3) ◽  
pp. 110-116 ◽  
Author(s):  
Guangyong Zhu ◽  
Zuobing Xiao ◽  
Guangxu Zhu ◽  
Yunwei Niu ◽  
Keyword(s):  
Inclusion Complex ◽  
Preexponential Factor ◽  
Binding Energies ◽  
Stable Complex ◽  
X Ray Diffraction ◽  
Molecular Mechanics Calculations ◽  
Cyclodextrin Inclusion Complexes ◽  
Cyclodextrin Inclusion ◽  
High Volatility ◽  
The Stability

Abstract l-menthol has been widely used in flavour, food and pharmaceuticals. Because of its high volatility and whisker growth, l-menthol-hydroxypropyl-β-cyclodextrin inclusion complex was produced to improve shelf-life, provide protection, and enhance the stability of l-menthol. The inclusion complex was characterized by Fourier transform infrared spectroscopy, X-ray diffraction. The results show that l-menthol was successfully encapsulated in hydroxypropyl-β-cyclodextrin. l-menthol loading capacity is about 8.44%. Geometries and binding energies of l-menthol-hydroxypropyl-β-cyclodextrin inclusion complexes were investigated using molecular mechanics calculations. The shape and orientation of the most stable complex, and the minimum binding energy were determined. L-menthol release from complex was determined by thermogravimetric analysis. Two l-menthol release rate peaks were observed at 69.3 and 279.1°C. The l-menthol release reaction order, release activation energy and the preexponential factor were obtained.

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 Strength, character, and directionality of halogen bonds involving cationic halogen bond donors

2017 ◽  
Vol 203 ◽  
pp. 47-60 ◽  
Author(s):  
Kevin E. Riley ◽  
Khanh-An Tran
Keyword(s):  
Potential Energy ◽  
Halogen Bond ◽  
Model System ◽  
Potential Energy Curves ◽  
Chloride Salt ◽  
Halogen Bonds ◽  
Charged Species ◽  
Implicit Solvation Model ◽  
The Stability

Halogen bonds involving cationic halogen bond donors and anionic halogen bond acceptors have recently been recognized as being important in stabilizing the crystal structures of many salts. Theoretical characterization of these types of interactions, most importantly in terms of their directionality, has been limited. Here we generate high-quality symmetry adapted perturbation theory potential energy curves of a H3N–CC–Br+⋯Cl− model system in order to characterize halogen bonds involving charged species, in terms of contributions from electrostatics, exchange, induction, and dispersion, with special emphasis on analyzing contributions that are most responsible for the directionality of these interactions. It is found that, as in the case of neutral halogen bonds, exchange forces are important contributors to the directionality of charged halogen bonds, however, it is also found that induction effects, which contribute little to the stability and directionality of neutral halogen bonds, play a large role in the directionality of halogen bonds involving charged species. Potential energy curves based on the ωB97X-D/def2-TZVP/C-PCM method, which includes an implicit solvation model in order to mimic the effects of the crystal medium, are produced for both the H3N–CC–Br+⋯Cl− model system and for the 4-bromoanilinium⋯Cl− dimer, which is based on the real 4-bromoanilinium chloride salt, whose crystal structure has been determined experimentally. It is found that, within a crystal-like medium, charged halogen bond are significantly weaker than in the gas phase, having optimum interaction energies up to approximately −20 kcal mol−1.

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