Characteristics of a σ-Hole and the Nature of a Halogen Bond

A quantum chemical perspective on the potency of electron donors and acceptors in pnicogen bonds (AS...N, P...N, N...N)

A quantum chemical perspective of 31 structures contains electron acceptors: ASCl₃ (arsenic trichloride), PCl₃ (phosphorous trichloride) and NCl₃ (nitrogen trichloride); forming non-covalent bond with various nitrogen-based electron donors that resulted in pnicogen bonds, AS...N, P...N and N...N were calculated at M062X/def2-QZVP level of theory. Besides the above method, MP2/def2-QZVP and CCSD(T)/def2-QZVP level of theories have also been analysed to have in depth knowledge about the bonds formed. The nature of the bonds was assumed from the electrostatic potential evaluated for all the monomers, where σ hole is positive for all the monomers. The strongest pnicogen bonds are ASCl₃-NF₂H, PCl₃-NCH₃CH₃CH₃ and NCl₃-NCH₃CH₃CH₃ having interaction energies as -4.15, -11.58 and -3.25 kcal/mol, respectively, at MP2/def2-QZVP level of theory. Further at CCSD(T)/def2-QZVP level of theory, ASCl₃-NF₂H and NCl₃-NCH₃CH₃CH₃ are found to be the most stable with interaction energies as -3.53 and -2.45 kcal/mol, respectively. The potential energy surface scan was performed for all the stable complexes in order to confirm the existences of energies are true minima. Moreover to confirm the halogen and pnicogen bonds, AIM analysis was carried out. The results from the above factors of pnicogen bond will help crystal growth, material science and engineering community to explore novel materials, which abide for modernization. Graphical abstract PCl₃-NCH₃CH₃CH₃ complex with 2.61 Å and pnicogen angle of 178.54° is strong, and interaction energy is -11.58 kcal/mol. Electron donors - ASCl₃, PCl₃ and NCl₃ and electron acceptors -NCH₃CH₃CH₃, NH₃C₂ and NHCO have strong electrostatic contribution. High and low values of (ρ) ∇²(ρ) reveal the strong and weak pnicogen bond. Schematic representation of acceptors surrounded by its donors and Electrostatic Potential map.

Halogen Bonding from the Bonding Perspective with Considerations for Mechanisms of Thyroid Hormone Activation and Inhibition

Halogen bonding interactions are often discussed in terms of an area of positive electrostatic potential on the halogen center along the bond axis called the σ-hole, yet various authors have noted a lack of completeness in this model. The nature of the XB interaction is explored from the perspective of bonding theories beginning from models that explain the electrostatic σ-hole and continuing to orbital-based donor-acceptor descriptions in which the donor lone pair MO mixes with the acceptor R-X and R-X* MOs to form a set of XB MOs related to three-center-four-electron bonding in hypervalent molecules. The strength of the XB interaction for a large series of RX···Cl- and RX···SeMe2 complexes correlate well with the energy of the acceptor R-X* MO and the contribution of the halide to the R-X and R-X* MOs, factors relevant to favourable overlap with the donor lone pair. An orbital-based focus accounts for the partial covalency of the XB interaction and can be extended to descriptions of enzymatic dehalogenation mechanisms. Applications of this MO perspective to the deiodination of thyroid hormones by the iodothyronine deiodinases and a possibly related mechanism of inhibition are discussed.

Comparison of the DFT-SAPT and Canonical EDA Schemes for the Energy Decomposition of Various Types of Noncovalent Interactions

Interaction energies computed with density functional theory can be divided into physically meaningful components by symmetry-adapted perturbation theory (DFT-SAPT) or the canonical energy decomposition analysis (EDA). In this work, the decomposition results obtained by these schemes were compared for more than 200 hydrogen-, halogen-, and pnicogen-bonded, dispersion-bound, and mixed complexes to investigate their similarity in the evaluation of the nature of noncovalent interactions. BLYP functional with D3(BJ) correction was used for the EDA scheme, whereas asymptotically corrected PBE0 functional for DFT-SAPT provided some of the best combinations for description of noncovalent interactions. Both schemes provide similar results concerning total interaction energies and insight into the individual energy components. For most complexes, the dominant energetic term was identified equally by both decomposition schemes. Because the canonical EDA is computationally less demanding than the DFT-SAPT, the former can be especially used in cases where the systems investigated are very large.

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding

In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.

Boron as an Electron-Pair Donor for B⋅⋅⋅Cl Halogen Bonds

MP2/aug'-cc-pVTZ calculations were performed to investigate boron as an electron-pair donor in halogen-bonded complexes (CO)₂ (HB):ClX and (N₂ )₂ (HB):ClX, for X=F, Cl, OH, NC, CN, CCH, CH₃ , and H. Equilibrium halogen-bonded complexes with boron as the electron-pair donor are found on all of the potential surfaces, except for (CO)₂ (HB):ClCH₃ and (N₂ )₂ (HB):ClF. The majority of these complexes are stabilized by traditional halogen bonds, except for (CO)₂ (HB):ClF, (CO)₂ (HB):ClCl, (N₂ )₂ (HB):ClCl, and (N₂ )₂ (HB):ClOH, which are stabilized by chlorine-shared halogen bonds. These complexes have increased binding energies and shorter B-Cl distances. Charge transfer stabilizes all complexes and occurs from the B lone pair to the σ* Cl-A orbital of ClX, in which A is the atom of X directly bonded to Cl. A second reduced charge-transfer interaction occurs in (CO)₂ (HB):ClX complexes from the Cl lone pair to the π* C≡O orbitals. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin-spin coupling constants, ^1x J(B-Cl), across the halogen bonds are also indicative of the changing nature of this bond. ^1x J(B-Cl) values for both series of complexes are positive at long distances, increase as the distance decreases, and then decrease as the halogen bonds change from traditional to chlorine-shared bonds, and begin to approach the values for the covalent bonds in the corresponding ions [(CO)₂ (HB)-Cl]⁺ and [(N₂ )₂ (HB)-Cl]⁺ . Changes in ¹¹ B chemical shieldings upon complexation correlate with changes in the charges on B.

σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond

The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.