Nature of halogen bonding involving π-systems, nitroxide radicals and carbenes: a highlight of the importance of charge transfer

An orbital-overlap complement to σ-hole electrostatic potentials

A σ-hole is an electron-deficient region of positive electrostatic potential (ESP) opposite from a half-filled p orbital involved in forming a covalent bond. The σ-hole concept helps rationalize directional noncovalent interactions, known as σ-hole bonds, between covalently bonded group V-VII atoms and electron-pair donors. The magnitude and orientation of σ-holes are correlated with the strength and geometry of halogen bonds. However, ESP computed for isolated σ-holes are not always predictive of interaction energies. For example, the σ-holes of isolated CHFBr2 and isolated CH2FI have identical ESP on the molecule surface, but halogen bonds to these molecules generally have different strengths. Here we show that the compact/diffuse nature of the orbitals involved plays an important role. Our orbital overlap distance quantifies the compact/diffuse nature of the "test orbital" that best overlaps with a systems orbitals at each point. The overlap distance captures the response properties of σ-holes: diffuse σ-holes with large overlap distance are typically "softer" and more polarizable. This aids visualization and interpretation. A linear fit to overlap distance and ESP is predictive of the halogen bond strengths of CH3X and CF3X (X = Cl, Br and I). We suggest that the overlap distance will be a useful partner to ESP for characterizing σ-holes.

Wolfium bonds in homodimers of MX4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se)

The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.

Catalytic activation via π-backbonding in halogen bonds

The role of halogen bonding (XB) in chemical catalysis has largely involved using XB donors as Lewis acid activators to modulate the reactivity of partner Lewis bases. We explore a more uncommon scenario, where a Lewis base modulates reactivity via a spectator halogen bond interaction. Our computational studies reveal that spectator halogen bonds may play an important role in modulating the rate of SN2 reactions. Most notably, π acceptors such as PF3 significantly decrease the barrier to substitution by decreasing electron density in the very electron rich transition state. Such π-backbonding represents an example of a heretofore unexplored situation in halogen bonding: the combination of both σ-donation and π-backdonation in this "non-covalent" interaction. The broader implications of this observation are discussed.

Phenylalanine Residues in the Active Site of CYP2E1 Participate in Determining the Binding Orientation and Metabolism-Dependent Genotoxicity of Aromatic Compounds

The composition of amino acids forming the active site of a CYP enzyme is impactful in its substrate selectivity. For CYP2E1, the role of PHE residues in the formation of effective binding orientations for its aromatic substrates remains unclear. In this study, molecular docking and molecular dynamics analysis were performed to reflect the interactions between PHEs in the active site of human CYP2E1 and various aromatic compounds known as its substrates. The results indicated that the orientation of 1-methylpyrene (1-MP) in the active site was highly determined by the presence of PHEs, PHE478 contributing to the binding free energy most significantly. Moreover, by building a random forest model the relationship between each of 19 molecular descriptors of polychlorinated biphenyl (PCB) compounds (from molecular docking, quantum mechanics, and physicochemical properties) and their human CYP2E1-dependent mutagenicityas established mostly in our lab, was investigated. The presence of PHEs did not appear to significantly modify the electronic or structural feature of each bound ligand (PCB), instead, the flexibility of the conformation of PHEs contributed substantially to the effective binding energy and orientation. It is supposed that PHE residues adjust their own conformation to permit a suitablly shaped cavity for holding the ligand and forming its orientation as favorable for a biochemical reaction. This study has provided some insights into the role of PHEs in guiding the interactive adaptation of the active site of human CYP2E1 for the binding and metabolism of aromatic substrates.

Force Decomposition Analysis: A Method to Decompose Intermolecular Forces into Physically Relevant Component Contributions

Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to noncovalent interactions. Herein, we formulate, implement, and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis.

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand-protein complexes may shed light on rational design of potent ligands in the future.

Investigation of the influence of chirality and halogen atoms on the anticancer activity of enantiopure palladium(ii) complexes derived from chiral amino-alcohol Schiff bases and 2-picolylamine

In order to evaluate the impact of chirality and halogen-substitution pattern on biological activity, four mixed-ligand enantiomeric pairs of Pd(ii) complexes were synthesized and characterized.

Maximal occupation by bases of π-hole bands surrounding linear molecules

Linear molecules such as CO₂ contain a positive π-hole ring that surrounds C on the molecule's equator. Quantum calculations examine the question as to how many bases can simultaneously bind to this ring. Linear molecules examined are TO₂ , where T = C, Si, Ge, Sn; bases are NCH and NH₃ . CO₂ engages in the weakest of the tetrel bonds, and can bind up to three NCH and two NH₃ . Unlike σ-hole tetrel bonds, Si forms the strongest tetrel bonds, with interaction energies as high as 43 kcal/mol with NH₃ . But like GeO₂ , SiO₂ can sustain only two bases in its equatorial ring. The π-hole ring of SnO₂ can engage in up to four tetrel bonds with either NCH or NH₃ , even though these bonds are weaker than those with GeO₂ or SiO₂ . As all of these complexes cast TO₂ in the role of multiple electron acceptor, the resulting negative cooperativity makes each successive bond weaker than its predecessor as bases are added, as well as reducing the magnitude of the central molecule's π-hole.

Anatomy of π-hole bonds: Linear systems

The list of σ-hole bonds is long and growing, encompassing both H-bonds and its closely related halogen, chalcogen, etc., sisters. These bonds rely on the asymmetric distribution of electron density, whose depletion along the extension of a covalent bond leaves a positive region of electrostatic potential from which these bonds derive their name. However, the density distributions of other molecules contain analogous positive regions that lie out of the molecular plane known as π-holes, which are likewise capable of engaging in noncovalent bonds. Quantum calculations are applied to study such π-hole bonds that involve linear molecules, whose positive region is a circular belt surrounding the molecule, rather than the more restricted area of a σ-hole. These bonds are examined in terms of their most fundamental elements arising from the spatial dispositions of their relevant molecular orbitals and the π-holes in both the total electron density and the electrostatic potential to which they lead. Systems examined comprise tetrel, chalcogen, aerogen, and triel bonds, as well as those involving group II elements, with atoms drawn from various rows of the Periodic Table. The π-hole bonds established by linear molecules tend to be weaker than those of comparable planar systems.

Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization

Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.

Experimental evidence that halogen bonding catalyzes the heterogeneous chlorination of alkenes in submicron liquid droplets

A key challenge in predicting the multiphase chemistry of aerosols and droplets is connecting reaction probabilities, observed in an experiment, with the kinetics of individual elementary steps that control the chemistry that occurs across a gas/liquid interface. Here we report evidence that oxygenated molecules accelerate the heterogeneous reaction rate of chlorine gas with an alkene (squalene, Sqe) in submicron droplets. The effective reaction probability for Sqe is sensitive to both the aerosol composition and gas phase environment. In binary aerosol mixtures with 2-decyl-1-tetradecanol, linoleic acid and oleic acid, Sqe reacts 12-23× more rapidly than in a pure aerosol. In contrast, the reactivity of Sqe is diminished by 3× when mixed with an alkane. Additionally, small oxygenated molecules in the gas phase (water, ethanol, acetone, and acetic acid) accelerate (up to 10×) the heterogeneous chlorination rate of Sqe. The overall reaction mechanism is not altered by the presence of these aerosol and gas phase additives, suggesting instead that they act as catalysts. Since the largest rate acceleration occurs in the presence of oxygenated molecules, we conclude that halogen bonding enhances reactivity by slowing the desorption kinetics of Cl2 at the interface, in a way that is analogous to decreasing temperature. These results highlight the importance of relatively weak interactions in controlling the speed of multiphase reactions important for atmospheric and indoor environments.

Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage

Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.

π covalency in the halogen bond

Halogen bonds are a highly directional class of intermolecular interactions widely employed in chemistry and chemical biology. This linear interaction is commonly viewed to be analogous to the hydrogen bond because hydrogen bonding models also intuitively describe the σ-symmetric component of halogen bonding. The possibility of π-covalency in a halogen bond is not contemplated in any known models. Here we present evidence of π-covalency being operative in halogen bonds formed between chloride and halogenated triphenylamine-based radical cations. We reach this conclusion through computational analysis of chlorine K-edge X-ray absorption spectra recorded on these halogen bonded pairs. In light of this result, we contend that halogen bonding is better described by analogy to metal coordination bonds rather than hydrogen bonds. Our revised description of the halogen bond suggests that these interactions could be employed to influence the electronic properties of conjugated molecules in unique ways.

Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H₂O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H₂O) and ˙OH(H₂O)₂), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH₃CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.

Application of Halogen Bonding to Organocatalysis: A Theoretical Perspective

The strong, specific, and directional halogen bond (XB) is an ideal supramolecular synthon in crystal engineering, as well as rational catalyst and drug design. These attributes attracted strong growing interest in halogen bonding in the past decade and led to a wide range of applications in materials, biological, and catalysis applications. Recently, various research groups exploited the XB mode of activation in designing halogen-based Lewis acids in effecting organic transformation, and there is continual growth in this promising area. In addition to the rapid advancements in methodology development, computational investigations are well suited for mechanistic understanding, rational XB catalyst design, and the study of intermediates that are unstable when observed experimentally. In this review, we highlight recent computational studies of XB organocatalytic reactions, which provide valuable insights into the XB mode of activation, competing reaction pathways, effects of solvent and counterions, and design of novel XB catalysts.

Probing Blue-Shifting Hydrogen Bonds with Adiabatic Energy Decomposition Analysis

The physical origin of blue-shifting hydrogen bonds remains a subject of debate, although many plausible explanations have been proposed. Using a molecular property decomposition analysis based on absolutely localized molecular orbitals, we investigated several representative F₃CH···Y (Y = H₂O, NH₃, Cl^-) complexes. We reveal that features of a blue-shifting H-bond already appear on the frozen surface where both polarization and charge transfer (CT) are "turned off", and that the final frequency shift observed depends on the strength of CT. Further decomposition of forces at the frozen level shows that Pauli repulsion is the only component that shortens the C-H bond in the short-range, while both permanent electrostatics and dispersion lengthen the bond. The effects of these forces from the medium to long-range are also discussed. Our analysis provides a complete picture for blue-shifting H-bonds and suggests two necessary conditions for their features to be observed at equilibrium structures: (i) stronger Pauli repulsion than the combination of electrostatic and dispersion forces; (ii) relatively weak CT that is insufficient to compensate for the blue-shifting effect of the frozen interaction.

Unraveling the regioselectivity of odd electron halogen bond formation using electrophilicity index and chemical hardness parameters

1e and 3e regioselective XB formation by a free radical. 1e and 3e bond formation are realized when the free radical acts as nucleophile and electrophile, respectively, which are parametrized by electrophilicity index and chemical hardness parameters.

On the capability of metal–halogen groups to participate in halogen bonds

Halogens in a M–X bond are inhibited from forming a halogen bond but can do so in certain circumstances, with or without a σ-hole.