scholarly journals Hydrogen vs. Halogen Bonds in 1-Halo-Closo-Carboranes

Materials ◽  
2020 ◽  
Vol 13 (9) ◽  
pp. 2163 ◽  
Author(s):  
Ibon Alkorta ◽  
Jose Elguero ◽  
Josep M. Oliva-Enrich
Keyword(s):  
Electron Density ◽  
Halogen Bond ◽  
Noncovalent Interactions ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Bond Critical Point ◽  
Total Energy Density ◽  
Comparison Of The Results ◽  
Intermolecular Distances

A theoretical study of the hydrogen bond (HB) and halogen bond (XB) complexes between 1-halo-closo-carboranes and hydrogen cyanide (NCH) as HB and XB probe has been carried out at the MP2 computational level. The energy results show that the HB complexes are more stable than the XBs for the same system, with the exception of the isoenergetic iodine derivatives. The analysis of the electron density with the quantum theory of atoms in molecules (QTAIM) shows the presence of a unique intermolecular bond critical point with the typical features of weak noncovalent interactions (small values of the electron density and positive Laplacian and total energy density). The natural energy decomposition analysis (NEDA) of the complexes shows that the HB and XB complexes are dominated by the charge-transfer and polarization terms, respectively. The work has been complemented with a search in the CSD database of analogous complexes and the comparison of the results, with those of the 1-halobenzene:NCH complexes showing smaller binding energies and larger intermolecular distances as compared to the 1-halo-closo-carboranes:NCH complexes.

scholarly journals Through-Bond and Through-Space Interactions in [2,2]Cyclophanes

2021 ◽  
Author(s):  
Sérgio Galembeck ◽  
Renato Orenha ◽  
Rafael Madeira ◽  
Letícia Peixoto ◽  
Renato Parreira
Keyword(s):  
Electron Density ◽  
Noncovalent Interactions ◽  
Topological Analysis ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Relative Importance ◽  
Energy Decomposition ◽  
Covalent Contribution ◽  
Pauli Repulsion ◽  
Open Question

The interpretation of the distortions of the electron distribution in [2,2]cyclophanes (22-CPs) is controversial. Some studies indicate that there is an accumulation of electron density (ρ) outside the cavity of 22-CPs. The nature of through-space (ts) interaction is still under debate. The relative importance of ts and through-bond (tb) is an open question. In an attempt to clarify these points, we have investigated five 22-CPs and their corresponding toluene dimers by molecular orbitals analysis, electron density difference analysis, some topological analysis of ρ (quantum theory of atoms in molecules (QTAIM), electron localization function (ELF) and noncovalent interactions (NCI)), and energy decomposition analysis with natural orbitals for chemical valence (EDA-NOCV). ρ is concentrated inside the inter-ring region. All the analyses indicated that ts is predominant. The ts is composed by attractive dispersion and Pauli repulsion, with a small covalent contribution. Except for 1 and 6, all the compounds present inter-ring bond paths.

Short is strong: experimental electron density in a very short N···I halogen bond

2018 ◽  
Vol 233 (9-10) ◽  
pp. 733-744 ◽  
Author(s):  
Ruimin Wang ◽  
Daniel Hartnick ◽  
Ulli Englert
Keyword(s):  
Critical Point ◽  
Electron Density ◽  
Halogen Bond ◽  
Bond Critical Point ◽  
Total Energy Density ◽  
Covalent Bonds ◽  
Secondary Interaction ◽  
Bona Fide ◽  
Atoms In Molecules Theory ◽  
Experimental Electron Density

Abstract 2,3,5,6-Tetrafluoro-1,4-diiodobenzene and 4-(dimethylamino)pyridine co-crystallize in 1:2 stoichiometry. A diffraction experiment at standard resolution was already conducted in 2010 and revealed one of the shortest N···I contacts ever reported. We collected X-ray intensities at 100 K up to a very high resolution of 1.23 Å−1. These experimental data allowed to refine a structure model based on atom-centered multipoles according to the Hansen-Coppens approach and provided an experimental electron density. A subsequent analysis with the help of Bader’s atoms in molecules theory showed a strong interaction between the pyridine N atom and the σ hole of its closest iodine neighbor on the halogenated benzene. This contact is characterized by a distance of 2.6622(4) Å and associated with a remarkably large electron density of 0.359(5) e⋅Å−3 in the (3, −1) critical point, unprecedented for a secondary interaction. This bona fide shortest halogen bond ever investigated by an experimental charge density study is associated with a significantly negative total energy density in the bond critical point and thus can reliably be classified as strong. Both the electron density and the position of the bond critical point suggest to compare the short N···I contact to coordinative or covalent bonds rather than to σ hole interactions.

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.

scholarly journals ELECTRON DENSITY STUDIES ON THE REGIOSELECTIVITY OF DEPROTONATION REACTIONS

2014 ◽  
Vol 70 (a1) ◽  
pp. C287-C287
Author(s):  
Juan Van der Maelen ◽  
Javier Cabeza
Keyword(s):  
Electron Density ◽  
Theoretical Calculations ◽  
Density Ratio ◽  
Atomic Charge ◽  
Heterocyclic Ring ◽  
Bond Critical Point ◽  
Electron Densities ◽  
Total Energy Density ◽  
Topological Parameters ◽  
Alkyl Groups

The C-alkyl groups of cationic triruthenium cluster complexes of the type [Ru3(µ-H)(µ-κ2N1,C2-EtnMemPyHk)(CO)10]+ (EtnMemPyHk represents a generic C-alkyl-N-methyl-pyrazium species) have been deprotonated to give kinetic products that contain unprecedented C-alkylidene derivatives and maintain the original edge-bridged decacarbonyl structure. When the starting complexes contain various C-alkyl groups, the selectivity of these deprotonation reactions is related to the atomic charges of the alkyl H atoms, as suggested by DFT/natural-bond orbital (NBO) calculations. Three additional electronic properties of the C-alkyl C-H bonds have also been found to correlate with the experimental regioselectivity since, in all cases, the deprotonated C-H bond has the smallest electron density at the bond critical point (bcp), the greatest Laplacian of the electron density at the bcp, and the greatest total energy density ratio at the bcp (computed by using the quantum theory of atoms in molecules, QTAIM). The kinetic decacarbonyl products evolve, under appropriate reaction conditions that depend upon the position of the C-alkylidene group in the heterocyclic ring, towards face-capped nonacarbonyl derivatives (thermodynamic products). Theoretical calculations support the proposal that the selectivity of these deprotonation reactions is primarily determined by the atomic charge of the alkyl H atoms: the higher the charge the easier the deprotonation when the starting complexes contain various C-alkyl groups. On the other hand, although QTAIM results have been obtained here only from theoretical electron densities for the above clusters, comparisons with local and integral topological parameters derived from both experimental and theoretical electron densities for the related triruthenium complex [Ru3(μ-H)2(μ3-MeImCH)(CO)9] (Me2Im = 1,3-dimethylimidazol-2-ylidene) may easily be made.

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.

scholarly journals Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis

2018 ◽  
Vol 20 (2) ◽  
pp. 905-915 ◽  
Author(s):  
Jonathan Thirman ◽  
Elric Engelage ◽  
Stefan M. Huber ◽  
Martin Head-Gordon
Keyword(s):  
Charge Transfer ◽  
Bond Strength ◽  
Halogen Bond ◽  
Decomposition Analysis ◽  
Halogen Bonding ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Pauli Repulsion

Variational energy decomposition analysis establishes charge-transfer as the origin of halogen bond strength differences that go against electrostatics.

scholarly journals Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 798
Author(s):  
Iñigo Iribarren ◽  
Goar Sánchez-Sanz ◽  
Cristina Trujillo
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Halogen Bond ◽  
Anion Recognition ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Binding Energies ◽  
Bond Critical Point ◽  
Density Values ◽  
Intramolecular Hydrogen

A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X⋯I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.

scholarly journals The Importance of Strain (Preorganization) in Beryllium Bonds

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5876
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Josep M. Oliva-Enrich ◽  
Manuel Yáñez ◽  
Otilia Mó ◽  
...  
Keyword(s):  
Decomposition Analysis ◽  
Orbital Energy ◽  
Strong Interactions ◽  
Energy Decomposition Analysis ◽  
Lewis Bases ◽  
Dissociation Energies ◽  
Polarization Term ◽  
Acidic Nature ◽  
Intermolecular Distances ◽  
Derivatives Of

In order to explore the angular strain role on the ability of Be to form strong beryllium bonds, a theoretical study of the complexes of four beryllium derivatives of orthocloso-carboranes with eight molecules (CO, N2, NCH, CNH, OH2, SH2, NH3, and PH3) acting as Lewis bases has been carried out at the G4 computational level. The results for these complexes, which contain besides Be other electron-deficient elements, such as B, have been compared with the analogous ones formed by three beryllium salts (BeCl2, CO3Be and SO4Be) with the same set of Lewis bases. The results show the presence of large and positive values of the electrostatic potential associated to the beryllium atoms in the isolated four beryllium derivatives of ortho-carboranes, evidencing an intrinsically strong acidic nature. In addition, the LUMO orbital in these systems is also associated to the beryllium atom. These features led to short intermolecular distances and large dissociation energies in the complexes of the beryllium derivatives of ortho-carboranes with the Lewis bases. Notably, as a consequence of the special framework provided by the ortho-carboranes, some of these dissociation energies are larger than the corresponding beryllium bonds in the already strongly bound SO4Be complexes, in particular for N2 and CO bases. The localized molecular orbital energy decomposition analysis (LMOEDA) shows that among the attractive terms associated with the dissociation energy, the electrostatic term is the most important one, except for the complexes with the two previously mentioned weakest bases (N2 and CO), where the polarization term dominates. Hence, these results contribute to further confirm the importance of bending on the beryllium environment leading to strong interactions through the formation of beryllium bonds.

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