Can we quantitatively evaluate the mutual impacts of intramolecular metal-ligand bonds the same as intermolecular noncovalent bonds?

In this paper, we have reviewed several equations for calculating the cooperative energy of two chemical bonds between three fragments/species, regardless of whether they are atoms, ions or molecules, and whether the bonds between them are intra- or intermolecular. It is emphasized that two chemical bonds upon cooperation in a new compound change the bond dissociation energy of each other exactly by the same quantitative value, their cooperative energy, regardless of the nature of the bonds or whether one bond is very weak and another one is very strong. However, the final benefit/drawback of weak bonds from this cooperation can be considerably larger than that of strong bonds. The above statements are supported by a computational study on the various types of inter- and intramolecular chemical bonds.

Elucidating the Role of Electron-Donating Groups in Halogen Bonding

Computational quantum chemical techniques were utilized to systematically examine how electron-donating groups affect the electronic and spectroscopic properties of halogen bond donors and their corresponding complexes. Unlike the majority of studies on halogen bonding, where electron-withdrawing groups are utilized, this work investigates the influence of electron-donating substituents within the halogen bond donors. Statistical analyses were performed on the descriptors of halogen bond donors in a prescribed set of archetype, halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond systems. The σ-hole magnitude, binding and interaction energies, and the vibrational X···N local force constant (where X = Cl, Br, I, and At) were found to correlate very well in a monotonic and linear manner with all other properties studied. In addition, enhanced halogen bonds were found when the systems contained electron-donating groups that could form intramolecular hydrogen bonds with the electronegative belt of the halogen atom and adjacent linker features.

Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds

The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately - 60 kcal mol-1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.

Metal-free synthesis of selenoesters directly from carboxylic acids using bifunctional selenoureas under batch and continuous-flow conditions

A new metal-free method for the synthesis of selenoesters directly from carboxylic acids in a flow reactor is reported. The carboxylic acids, Michael acceptors, and bifunctional selenoureas (source of selenium and nucleophile, activator of carbonyl group) were reacted to obtain selenoesters (up to 70% yield). An evidence-backed plausible mechanism is also presented.

Enhancement of Halogen Bond Strength by Intramolecular H-Bonds

Quantum calculations study the potential of an intramolecular H-bond between the halogen atom (X) of a halobenzene and a substituent placed ortho to it, to amplify the ability of X to engage in a halogen bond (XB) with a Lewis base. H-bonding substituents NH₂, CH₂CH₂OH, CH₂OH, OH, and COOH were added to halobenzenes (X = Cl, Br, I). The amino group had little effect, but those containing OH increased the CX···N XB energy to a NH₃ nucleophile by about 0.5 kcal/mol; the increment associated with COOH is larger, nearly 2 kcal/mol. These energy increments were approximately doubled if two such H-bonding substituents are present. Combining a pair of ortho COOH groups with an electron-withdrawing NO₂ group in the para position has a particularly large effect, raising the XB energy by about 4 kcal/mol, which can amount to as much as a 4-fold magnification.

Ability of Peripheral H Bonds to Strengthen a Halogen Bond

Quantum calculations study the manner in which the involvement of a halogen atom as a proton acceptor in one or more H bonds (HBs) affects the strength of the halogen bond (XB) it can form with a nucleophile aligned with the X σ-hole. A variety of Lewis acids wherein X = F, Cl, Br, and I are attached to a tetrel atom C or Ge engaged in a XB with nucleophile NH₃. One, two, and three HF molecules were positioned perpendicular to the XB axis so that they could form a HB to the X atom. Each such HB strengthened the XB by an increment of 1 kcal/mol or more that does not attenuate as each new HB is added, potentially increasing the interaction energy manyfold. Additionally, the presence of one or more HBs facilitates the formation of a XB by molecules which are reluctant to engage in such a bond in the absence of these auxiliary interactions. Even the F atom, which avoids such a XB, can be coaxed to participate in a XB of moderate strength by one or more of these external HBs.

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.

Assessing the effects of covalent, dative and halogen bonds on the electronic structure of selenoamides

The C–NMe2 bond rotation of a selenoamide is proposed as an experimental probe to compare different chemical interactions.

Tautomeric Equilibrium of an Asymmetric β-Diketone in Halogen-Bonded Cocrystals with Perfluorinated Iodobenzenes

In order to study the effect of halogen bond on tautomerism in β-diketones in the solid-state, we have prepared a series of cocrystals derived from an asymmetric β-diketone, benzoyl-4-pyridoylmethane (b4pm), as halogen bond acceptor and perfluorinated iodobenzenes: iodopentaflourobenzene (ipfb), 1,2-, 1,3- and 1,4-diiodotetraflorobenzene (12tfib, 13tfib and 14tfib) and 1,3,5-triiodo-2,4,6-trifluorobenzene (135titfb). All five cocrystals are assembled by I···N halogen bonds involving pyridyl nitrogen and iodoperfluorobenzene iodine resulting in 1:1 (four compounds) or 1:2 (one compound) cocrystal stoichiometry. Tautomer of b4pm in which hydrogen atom is adjacent to the pyridyl fragment was found to be more stable in vacuo than tautomer with a benzoyl hydroxyl group. This tautomer is also found to be dominant in the majority of crystal structures, somewhat more abundantly in crystal structures of cocrystals in which additional I···O halogen bond with the benzoyl oxygen has been established. Attempts have also been made to prepare an equivalent series of cocrystals using a closely related asymmetric β-diketone, benzoyl-3-pyridoylmethane (b3pm); however, all attempts were unsuccessful, which is attributed to more effective crystal packing of b3pm isomer compared to b4pm, which reduced the probability of cocrystal formation.

Bis-Selenoureas for Anion Binding: A 1H NMR and Theoretical Study

The anion binding ability of a family of bis-selenoureas L1-L3 obtained by the reaction of 1,3-bis(aminomethyl)-benzene and phenylisoselenocyanate, p-methoxyphenylisoselenocyanate and naphtylisoselenocyanate, for L1, L2, and L3, respectively, has been tested and compared to that of previously described bis-urea analogues. Results suggest that the introduction of selenium leads to an increase in the acidity of the urea NH hydrogen atoms, and therefore to a stronger affinity (more than three-fold higher) towards anion species, in particular dihydrogen phosphate, in DMSO-d₆ . Theoretical calculations allowed for the optimization of the adducts receptors corroborating the experimental results.

Halogenated isophthalamides and dipicolineamides: the role of the halogen substituents in the anion binding properties

A novel family of amide-based receptors is herein described. Specifically, the role of the halogen substituents at the aryl moieties in the anion binding properties of a series of halogenated isophthalamides and dipicolineamides (L1-L6) was investigated both in solution and in the solid state in order to evaluate the incidence of all possible different and combined weak host-guest interactions. Only L5 and L6 bearing pentafluorophenyl rings as substituents have some affinities for the set of anions studied. In particular, in the case of L5 an interesting behaviour with the formation of a non-symmetric adduct with benzoate and dihydrogen phosphate was hypothesised by ¹H- and ¹⁹F-NMR spectroscopy studies in solution and confirmed by theoretical calculation. The study of the crystal structures of the receptors demonstrated that the steric hindrance determined by the halogen substituents in the receptor molecules influences the accessibility of the anions to the isophthalamide or dipicoline amide NH moieties, thus modulating the affinity for the anion guests.

Some interesting features of the rich chemistry around electron-deficient systems

In this short review, different phenomena that are triggered by the interaction of different compounds or clusters of compounds with electron-deficient systems, in particular beryllium and boron compounds, have been discussed in some detail. Particular attention was devoted to the huge acidity enhancements that can be induced through the interaction of conventional bases with B or Be containing compounds, which change these conventional bases in extremely strong proton donors. We have paid also attention to the cooperativity between Be bonds with other weak interactions, which results in a substantial increase of their strength, that can lead in some specific cases to the spontaneous formation of ion-pairs in the gas phase. Finally, the behavior of different Be derivatives as electron and anion sponges is discussed as well as the conditions needed to have clusters exhibiting rather strong Be–Be bonds, even though the Be–Be interaction in Be2 dimer is extremely weak. Finally, some attention was paid to systems with extremely short Be–Be distances but without a bond.

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

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.

Hybrid Molecular Dynamics for Elucidating Cooperativity Between Halogen Bond and Water Molecules During the Interaction of p53-Y220C and the PhiKan5196 Complex

The cooperativity between hydrogen and halogen bonds plays an important role in rational drug design. However, mimicking the dynamic cooperation between these bonds is a challenging issue, which has impeded the development of the halogen bond force field. In this study, the Y220C–PhiKan5196 complex of p53 protein was adopted as a model, and the functions of three water molecules that formed hydrogen bonds with halogen atoms were analyzed by the simulation method governed by the hybrid quantum mechanical/molecular mechanical molecular dynamics. A comparison with the water-free model revealed that the strength of the halogen bond in the complex was consistently stronger. This confirmed that the water molecules formed weak hydrogen bonds with the halogen atom and cooperated with the halogen atom to enhance the halogen bond. Further, it was discovered that the roles of the three water molecules were not the same. Therefore, the results obtained herein can facilitate a rational drug design. Further, this work emphasizes on the fact that, in addition to protein pockets and ligands, the role of voids should also be considered with regard to the water molecules surrounding them.

Disentanglement of orthogonal hydrogen and halogen bonds via natural orbital for chemical valence: A charge displacement analysis

As known, the electron density of covalently bound halogen atoms is anisotropically distributed, making them potentially able to establish many weak interactions, acting at the same time as halogen bond donors and hydrogen bond acceptors. Indeed, there are many examples in which the halogen and hydrogen bond coexist in the same structure and, if a correct bond analysis is required, their separation is mandatory. Here, the advantages and limitations of coupling the charge displacement analysis with natural orbital for chemical valence method (NOCV-CD) to separately analyze orthogonal weak interactions are shown, for both symmetric and asymmetric adducts. The methodology gives optimal results with intermolecular adducts but, in the presence of an organometallic complex, also intramolecular interactions can be correctly analyzed. Beyond the methodological aspects, it is shown that correctly separate and quantify the interactions can give interesting chemical insights about the systems.

Charge Displacement Analysis-A Tool to Theoretically Characterize the Charge Transfer Contribution of Halogen Bonds

Theoretical bonding analysis is of prime importance for the deep understanding of the various chemical interactions, covalent or not. Among the various methods that have been developed in the last decades, the analysis of the Charge Displacement function (CD) demonstrated to be useful to reveal the charge transfer effects in many contexts, from weak hydrogen bonds, to the characterization of σ hole interactions, as halogen, chalcogen and pnictogen bonding or even in the decomposition of the metal-ligand bond. Quite often, the CD analysis has also been coupled with experimental techniques, in order to give a complete description of the system under study. In this review, we focus on the use of CD analysis on halogen bonded systems, describing the most relevant literature examples about gas phase and condensed phase systems. Chemical insights will be drawn about the nature of halogen bond, its cooperativity and its influence on metal-ligand bond components.

Influence of halogen bonding on gold(i)-ligand bond components and DFT characterization of a gold-iodine halogen bond

A gold(i) complex bearing nitrogen acyclic carbene (NAC) and selenourea (SeU) has been used to verify whether the second-sphere SeI halogen bond (XB) is able to modify the Dewar-Chatt-Duncanson components of the Au-C and Au-Se bonds. The chosen system was found to be thermically unstable but it allowed an in-depth theoretical study by means of Energy Decomposition Analysis, Natural Bond Orbital and Natural Orbitals for Chemical Valence methods, coupled with Charge Displacement analysis. Indeed, in the presence of iodoperfluoroalkanes as XB donors, iodine interacts with the lone pair of the coordinated selenium, enhancing the Au ← C σ donation and depressing the Au → C π back-donation, as demonstrated also by the increase of the rotational barrier of the C-N bond of the NAC (see G. Ciancaleoni and others, Chem. - Eur. J., 2015, 21, 2467). On the other hand, in the presence of N-iodosuccinimide (NIS), the gold directly establishes a XB with the iodine by using its d lone pairs. This AuI XB is favored by the low steric hindrance of the ligands coordinated to the gold and the presence of the amino protons of SeU, which establish additional hydrogen bonds with the NIS. Also in this case, the effect is to increase the σ acidity and decrease the π basicity of the metal.

Interplay between Gold(I)-Ligand Bond Components and Hydrogen Bonding: A Combined Experimental/Computational Study

The influence of weak interactions on the donation/back-donation bond components in the complex [(NHC)Au(SeU)]⁺ (NHC = N-heterocyclic carbene; SeU = selenourea) has been studied by coupling experimental and theoretical techniques. In particular, NMR ¹H and pulsed-field gradient spin-echo titrations allowed us to characterize the hydrogen bond (HB) between the -NH₂ moieties of SeU and the anions PF₆ ^- and ClO₄ ^-, whereas ⁷⁷Se NMR spectroscopy allowed us to characterize the Au-Se bond. Theoretically, the Au-Se and Au-C orbital interactions have been decomposed using the natural orbital for the chemical valence framework and the bond components quantified through the charge displacement analysis. This methodology provides the quantification of the Dewar-Chatt-Duncanson (DCD) components for the Au-C and Au-Se bonds in the absence and presence of the second-sphere HB. The results presented here show that the anion has a dual mode action: it modifies the conformation of the cation by ion pairing (and this already influences the DCD components) and it induces new polarization effects that depend on the relative anion/cation relative orientation. The perchlorate polarizes SeU, enhancing the Se → Au σ donation and the Au → C back-donation and depressing the C → Au σ donation. On the contrary, the hexafluorophosphate depresses both the Se → Au and C → Au σ donations.

Lewis Base Activation of Lewis Acid: A Detailed Bond Analysis

The effect of a Lewis base (LB) on the nucleophilic attack on chalcogeniranium (chalcogen = sulfur and selenium) cations, the so-called LB activation of a Lewis acid, has been studied coupling natural orbital for chemical valence decomposition of the orbital interaction energy with charge displacement analysis. This methodology provides a detailed and accurate description of all the interactions (LB···chalcogen, chalcogen···olefin and olefin···ammonia) present in the system and leads to a deeper understanding of how they influence each other at all stages of the reaction: reactant complex, transition state, and product complex. In particular, the bond between the chalcogen and the olefin has been decomposed in terms of σ donation/π back-donation and the bond components quantified. This allowed determination of a linear relationship between the activation barrier of the nucleophilic attack and the net amount of charge donated by the olefin to the chalcogen.

The effect of anions on noncovalent interactions in model clusters of chalcogen-containing (CH3)2X (X = O, S, Se) molecules

A computational study of F⁻⋯(CH₃)₂O⋯CH₃F with F⁻ bound to the protons of the two methyl groups, found significant enhancement of the O⋯C interaction relative to the neutral (CH₃)₂O⋯CH₃F dyad.