On the Importance of π-Hole Beryllium Bonds: Theoretical Study and Biological Implications

Strong Be-N Interaction Induced Complementary Chemical Tuning to Design a Dual-gated Single Molecule Junction

The interaction between pyridines and the π-hole of BeH2 leads to the formation of strong beryllium-bonded complexes. Theoretical investigations demonstrate that the Be-N bonding interaction can effectively regulate the electronic current through a molecular junction. The electronic conductance exhibits distinct switching behavior depending on the substituent groups at the para position of pyridine, highlighting the role of Be-N interaction as a potent chemical gate in the proposed device. The complexes exhibit short intermolecular distances ranging from 1.724 to 1.752 Å, emphasizing their strong binding. Detailed analysis of electronic rearrangements and geometric perturbations upon complex formation provides insights into the underlying reasons for the formation of such strong Be-N bonds, with bond strengths varying from -116.25 to -92.96 kJ/mol. Moreover, the influence of chemical substituents on the local electronic transmission of the beryllium-bonded complex offers valuable insights for the implementation of a secondary chemical gate in single-molecule devices. This study paves the way for the development of chemically gateable, functional single-molecule transistors, advancing the design and fabrication of multifunctional single-molecule devices in the nanoscale regime.

Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance

The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends.

Noble-gas compounds: A general procedure of bonding analysis

This paper accounts for a general procedure of bonding analysis that is, expectedly, adequate to describe any type of interaction involving the noble-gas (Ng) atoms. Building on our recently proposed classification of the Ng-X bonds (X = binding partner) [New J. Chem. 44, 15536 (2020)], these contacts are first distinguished into three types, namely, A, B, or C, based on the topology of the electron energy density H(r) and on the shape of its plotted form. Bonds of type B or C are, then, further assigned as B-loose (B^l) or B-tight (B^t) and C-loose (C^l) or C-tight (C^t) depending on the sign that H(r) takes along the Ng-X bond path located from the topological analysis of ρ(r), particularly at around the bond critical point (BCP). Any bond of type A, B^l/B^t, or C^l/C^t is, finally, assayed in terms of contribution of covalency. This is accomplished by studying the maximum, minimum, and average value of H(r) over the volume enclosed by the low-density reduced density gradient (RDG) isosurface associated with the bond (typically, the RDG isosurface including the BCP) and the average ρ(r) over the same volume. The bond assignment is also corroborated by calculating the values of quantitative indices specifically defined for the various types of interactions (A, B, or C). The generality of our taken approach should encourage its wide application to the study of Ng compounds.

Yet another perspective on hole interactions

Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.

The competition and cooperativity of hydrogen/halogen bond and π-hole bond involving the heteronuclear ethylene analogues

The noncovalent interactions involving heteronuclear ethylene analogues H₂ CEH₂ (E = Si, Ge and Sn) have been studied by the Møller-Plesset perturbation theory to investigate the competition and cooperativity between the hydrogen/halogen bond and π-hole bond. H₂ CEH₂ has a dual role of being a Lewis base and acid with the region of π-electron accumulation above the carbon atom and the region of π-electron depletion (π-hole) above the E atom to participate in the NCX···CE (X = H and Cl) hydrogen/halogen bond and CE···NCY (Y = H, Cl, Li and Na) π-hole bond, respectively. When HCN/ClCN interacts with H₂ CEH₂ by two sites, the strength of hydrogen bond/halogen bond is stronger than that of π-hole bond. The π-hole bond becomes obviously stronger when the metal substituent of YCN (Y = Li and Na) interacting with H₂ CEH₂ , showing the character of partial covalent, its strength is much greater than that of hydrogen/halogen bond. In the ternary complexes, both hydrogen/halogen bond and π-hole bond are simultaneously strengthened compared to those in the binary complexes, especially in the systems containing alkali metal.

Mutual Influence of Pnicogen Bonds and Beryllium Bonds: Energies and Structures in the Spotlight

Pnicogen bonds, which are weak noncovalent interactions (NCIs), can be significantly modified by the presence of beryllium bonds, one of the strongest NCIs known. We demonstrate the importance of this influence by studying ternary complexes in which both NCIs are present, that is, the ternary complexes formed by a nitrogen base (NH₃, NHCH₂, and NCH), a phosphine (fluorophosphane, PH₂F) and a beryllium derivative (BeH₂, BeF₂, BeCl₂, BeCO₃, and BeSO₄). Energies, structures, and nature of the chemical bonding in these complexes are studied by means of ab initio computational methods. The pnicogen bond between the nitrogen base and the phosphine and the beryllium bond between the fluorine atom of fluorophosphane and the beryllium derivative show large cooperativity effects both on energies and geometries, with dissociation energies up to 296 kJ mol^-1 and cooperativity up to 104 kJ mol^-1 in the most strongly bound complex, CH₂HN:PH₂F:BeSO₄. In the complexes between the strongest nitrogen bases and the strongest beryllium donors, phosphorus-shared and phosphorus-transfer bonds are found.

(Isocyano group)⋯lone pair interactions involving coordinated isocyanides: experimental, theoretical and CSD studies

Both carbon and nitrogen centers in the coordinated isocyano group are capable of acting as a π-hole donor toward lone pairs.

Weak Interactions Get Strong: Synergy between Tetrel and Alkaline-Earth Bonds

Weak and strong noncovalent interactions such as tetrel bonds and alkaline-earth bonds, respectively, cooperate and get reinforced when acting together in ternary complexes of general formula RN··· SiH₃F···MY, where MY is a Be or Mg derivative and RN is a N-containing Lewis base with different hybridization patterns. Cooperativity has been studied in the optimized MP2/aug'-cc-pVTZ ternary complexes by looking at changes on geometries, binding energies, ²⁹Si NMR chemical shifts, and topological features according to the atoms in molecules theoretical framework. Our study shows that cooperativity in terms of energy is in general significant: more than 40 kJ/mol, and up to 83.6 kJ/mol in the most favorable case. The weakest the isolated interaction, the strongest the reinforcement in the ternary complex; in this sense, the tetrel bond is shortened enormously, between 0.3 and 0.6 Å. This dramatic reinforcement of the tetrel bond is also nicely reflected in the positive variations of the ²⁹Si chemical shifts in all the ternary complexes. At the same time the ternary complexes are characterized by the presence of totally planar silyl group, due to the pentacoordination of the Si atom. Both the hybridization of the N base and the geometry imposed by the alkaline-earth ligands have a strong influence on the binding energies, as they modify the donor ability of N and the Lewis acid character of the alkaline-earth metal.

Ligation-Enhanced π-Hole···π Interactions Involving Isocyanides: Effect of π-Hole···π Noncovalent Bonding on Conformational Stabilization of Acyclic Diaminocarbene Ligands

The reaction of cis-[PdCl₂(CNXyl)₂] (Xyl = 2,6-Me₂C₆H₃) with the aminoazoles [1 H-imidazol-2-amine (1), 4 H-1,2,4-triazol-3-amine (2), 1 H-tetrazol-5-amine (3), 1 H-benzimidazol-2-amine (4), 1-alkyl-1 H-benzimidazol-2-amines, where alkyl = Me (5), Et (6)] in a 2:1 ratio in the presence of a base in CHCl₃ at RT proceeds regioselectively and leads to the binuclear diaminocarbene complexes [(ClPdCNXyl)₂{μ-C(N-azolyl)N(Xyl)C═NXyl}] (7-12; 73-91%). Compounds 7-12 were characterized by C, H, N elemental analyses, high-resolution ESI⁺-MS, Fourier transform infrared spectroscopy, 1D (¹H, ¹³C) and 2D (¹H,¹H-COSY, ¹H,¹H-NOESY, ¹H,¹³C-HSQC, ¹H,¹³C-HMBC) NMR spectroscopies, and X-ray diffraction (XRDn). Inspection of the XRDn data and results of the Hirshfeld surface analysis suggest the presence in all six structures of intramolecular π-hole_isocyanide···π_arene interactions between the electrophilic C atom of the isocyanide moiety and the neighboring arene ring. These interactions also result in distortion of the Pd-C≡N-Xyl fragment from the linearity. Results of density functional theory calculations [M06/MWB28 (Pd) and 6-31G* (other atoms) level of theory] for model structures of 7-9 followed by the topological analysis of the electron density distribution within the framework of Bader's theory (QTAIM method) reveal the presence of these weak interactions also in a CHCl₃ solution, and their calculated strength is 1.9-2.2 kcal/mol. The natural bond orbital analysis of 7-9 revealed that π(C-C)Xyl → π*(C-N)isocyanide charge transfer (CT) takes place along with the intramolecular π-hole_isocyanide···π_arene interactions. The observed π(C-C)_Xyl → π*(C-N)_isocyanide CT is due to ligation of the isocyanide to the metal center, whereas in the cases of the uncomplexed p-CNC₆H₄NC and CNXyl species, the effects of CT are negligible. Available CCDC data were processed from the perspective of isocyanide-involving π-hole···π interactions, disclosed the role of metal coordination in the π-hole donor ability of isocyanides, and verified the π-hole_isocyanide···π_arene interaction effect on the stabilization of the in-conformation in metal-bound acyclic diaminocarbenes.

Viable aromatic BenHn stars enclosing a planar hypercoordinate boron or late transition metal

Similar to B_n rings, star-like Be_nH_n rings can serve as the n-electron σ-donors for designing species with planar hypercoordinate atom.

On the σ, π and δ hole interactions: a molecular orbital overview

With molecular orbital theory it is possible to distinguish and design σ, π and the elusive δ electrostatic holes.

Alkyl groups as electron density donors in π-hole bonding

A combined structural and computational analysis has demonstrated that alkyl groups can act as Lewis bases in π-hole bonding.