Stabilizing Otherwise Unstable Anions with Halogen Bonding

Clathrate Hydrates as a Kind of Promising Ice Nanoreactors

Since their discovery, clathrate hydrates (CHs) have received great attention both from theoretical and experimental aspects due to their great potential for gas storage and prospective applications as icy crystal materials. However, there has been limited research on the decomposition, reduction or other reactions of gases enclosed in CHs. Thanks to their unique hydrogen bonding network and cavity structures, CHs can serve as the promising nanoreactors to achieve chemical conversions, e. g. reducing greenhouse gases. In this review-type article, we characterize the potential performance of such CHs nanoreactors by discussing their multiple functions including important roles of hydrogen bonds in CHs, e. g. the confinement effect and proton source, and then discuss the enhanced electron-binding ability of guest molecules and the structures and properties of trapped electrons in the stacked nanocages, which contribute to our understanding of chemical reactions occurring in CHs. Finally, we provide detailed analyses of representative reaction mechanisms underwent in CH nanoreactors and effective calculational and molecular dynamics simulation methods. This review-type article aims to provide a detailed summary about the functional characteristics of CHs and reactivity in CHs, which make CHs a kind of promising icy nanoreactors.

Chemical bonding misnomer in AeF- (Ae = Be-Ca) anions

Chemical bonding is the fundamental concept in chemistry and multiple bonding holds a special position. Recent quantum chemical calculations predicted the presence of triple dative bonds in BeF- and MgF- and quadruple dative bonds in CaF- anions. The present quantum chemical calculations based on quantum theory of atoms in molecules (QTAIM), electron localization function (ELF) and adaptive density partitioning (AdNDP) analyses find no sign of multiple dative bonding in these anions. In fact, the bond is actually an electron-sharing covalent one, rather than dative. Charge distribution analysis and comparison with a neutral AeF molecule reveal no difference in bonding between the neutral AeF molecule and its anion.

Stabilizing Halogen-Bonded Complex between Metallic Anion and Iodide

Halogen bonds (XBs) between metal anions and halides have seldom been reported because metal anions are reactive for XB donors. The pyramidal-shaped Mn(CO)₅^- anion is a candidate metallic XB acceptor with a ligand-protected metal core that maintains the negative charge and an open site to accept XB donors. Herein, Mn(CO)₅^- is prepared by electrospray ionization, and its reaction with CH₃I in gas phase is studied using mass spectrometry and density functional theory (DFT) calculation. The product observed experimentally at m/z = 337 is assigned as [IMn(CO)₄(OCCH₃)]^-, which is formed by successive nucleophilic substitution and reductive elimination, instead of the halogen-bonded complex (XC) CH₃-I···Mn(CO)₅^-, because the I···Mn interaction is weak within XC and it could be a transient species. Inspiringly, DFT calculations predict that replacing CH₃I with CF₃I can strengthen the halogen bonding within the XC due to the electro-withdrawing ability of F. More importantly, in so doing, the nucleophilic substitution barrier can be raised significantly, ~30 kcal/mol, thus leaving the system trapping within the XC region. In brief, the combination of a passivating metal core and the introduction of an electro-withdrawing group to the halide can enable strong halogen bonding between metallic anion and iodide.

Computational Studies of Coinage Metal Anion M- + CH3X (X = F, Cl, Br, I) Reactions in Gas Phase

We characterized the stationary points along the nucleophilic substitution (S_N2), oxidative insertion (OI), halogen abstraction (XA), and proton transfer (PT) product channels of M⁻ + CH₃X (M = Cu, Ag, Au; X = F, Cl, Br, I) reactions using the CCSD(T)/aug-cc-pVTZ level of theory. In general, the reaction energies follow the order of PT > XA > S_N2 > OI. The OI channel that results in oxidative insertion complex [CH₃–M–X]⁻ is most exothermic, and can be formed through a front-side attack of M on the C-X bond via a high transition state OxTS or through a S_N2-mediated halogen rearrangement path via a much lower transition state invTS. The order of OxTS > invTS is inverted when changing M⁻ to Pd, a d¹⁰ metal, because the symmetry of their HOMO orbital is different. The back-side attack S_N2 pathway proceeds via typical Walden-inversion transition state that connects to pre- and post-reaction complexes. For X = Cl/Br/I, the invS_N2-TS’s are, in general, submerged. The shape of this M⁻ + CH₃X S_N2 PES is flatter as compared to that of a main-group base like F⁻ + CH₃X, whose PES has a double-well shape. When X = Br/I, a linear halogen-bonded complex [CH₃−X∙··M]⁻ can be formed as an intermediate upon the front-side attachment of M on the halogen atom X, and it either dissociates to CH₃ + MX⁻ through halogen abstraction or bends the C-X-M angle to continue the back-side S_N2 path. Natural bond orbital analysis shows a polar covalent M−X bond is formed within oxidative insertion complex [CH₃–M–X]⁻, whereas a noncovalent M–X halogen-bond interaction exists for the [CH₃–X∙··M]⁻ complex. This work explores competing channels of the M⁻ + CH₃X reaction in the gas phase and the potential energy surface is useful in understanding the dynamic behavior of the title and analogous reactions.

Spectroscopic Investigation of Chalcogen Bonding: Halide-Carbon Disulfide Complexes

A combined experimental and theoretical approach has been used to study intermolecular chalcogen bonding. Specifically, the chalcogen bonding occurring between halide anions and CS₂ molecules has been investigated using both anion photoelectron spectroscopy and high-level CCSD(T) calculations. The relative strength of the chalcogen bond has been determined computationally using the complex dissociation energies as well as experimentally using the electron stabilisation energies. The anion complexes featured dissociation energies on the order of 47 kJ/mol to 37 kJ/mol, decreasing with increasing halide size. Additionally, the corresponding neutral complexes have been examined computationally, and show three loosely-bound structural motifs and a molecular radical.

F-Halogen Bond: Conditions for Its Existence

The question as to whether the F atom can engage in a halogen bond (XB) remains unsettled. This issue is addressed via density functional theory calculations which pair a wide range of organic and inorganic F-acids with various sorts of Lewis bases. From an energetic perspective, perfluorinated hydrocarbons with sp, sp², or sp³ C-hybridization are unable to form an XB with an N-base, but a very weak bond can be formed if electron-withdrawing C≡N substituents are added to the acid. There is little improvement for inorganic acids O₂NF, FOF, ClF, BrF, SiF₄, or GeF₄, but F₂ is capable of a stronger XB of up to 5 kcal/mol. These results are consistent with a geometric criterion, which compares the intermolecular equilibrium distance with the sum of atomic van der Waals radii. The intensity of the σ-hole on the F atom has predictive value in that a V_s,max of at least 10-15 kcal/mol is required for XB formation. Adding a positive charge to the Lewis acid enhances the strength of any XB and even more so if the base is anionic. The acid-base interaction induces a contraction of the r(AF) covalent bond in the acid in most cases and a deshielding of the NMR signal of the F nucleus.

Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore

The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferred for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found that the color of the neutral chromophore can be more sensitive to protein electrostatics than can the anionic counterpart. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model as compared to that of the anionic state, which requires only two forms ( J. Am. Chem. Soc. 2019, 141, 15250-15265). Specifically, an underlying zwitterionic charge-transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to excited-state proton transfer (ESPT) of the protonated chromophore, we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The three-form model could also be applied to similar biological and nonbiological dyes and complements the failure of the two-form model for donor-acceptor systems with localized ground-state electronic distributions.

Reply to the Comment on "Realization of Lewis Basic Sodium Anion in the NaBH3 - Cluster"

We reply to the comment by S. Pan and G. Frenking who challenged our interpretation of the Na^- :→BH₃ dative bond in the recently synthesized NaBH₃ ^- cluster. Our conclusion remains the same as that in our original paper (https://doi.org/10.1002/anie.201907089 and https://doi.org/10.1002/ange.201907089). This conclusion is additionally supported by the energetic pathways and NBO charges calculated at UCCSD and CASMP2(4,4) levels of theory. We also discussed the suitability of the Laplacian of electron density (QTAIM) and Adaptive Natural Density Partitioning (AdNDP) method for bond type assignment. It seems that AdNDP yields more sensible results. This discussion reveals that the complex realm of bonding is full of semantic inconsistencies, and we invite experimentalists and theoreticians to elaborate this topic and find solutions incorporating different views on the dative bond.

Halogen Bonding Facilitates Intersystem Crossing in Iodo-BODIPY Chromophores

BODIPY chromophores can serve as organic-based triplet photosensitizers for a wide range of applications. To perform this function, the formation of the triplet state is critical, and a better understanding of how to modulate the formation of the triplet state could lead to further advances in BODIPY-based sensitizers for solar energy conversion and photodynamic therapy. In this work we investigate the ability of halogen bonding, a noncovalent solvent interaction, to facilitate intersystem crossing in a diiodo-BODIPY. Ultrafast transient absorption spectroscopy is applied to diiodo-BODIPY in the presence of pyridine-based halogen bonding solvent molecules to determine the rate constants for intersystem crossing. We find that halogen bonding facilitates the formation of the triplet state by increasing the intersystem crossing rate constant of diiodo-BODIPY. The results are interpreted in terms of the Marcus expression for intersystem crossing. Quantum chemical calculations show that halogen bonding acts to alter both the spin-orbit coupling terms and the relative energetics of the singlet and triplet states.

Realization of Lewis Basic Sodium Anion in the NaBH3 - Cluster

We report a Na:^- →B dative bond in the NaBH₃ ^- cluster, which was designed on the principle of minimum-energy rupture, prepared by laser vaporization, and characterized by a synergy of anion photoelectron spectroscopy and electronic structure calculations. The global minimum of NaBH₃ ^- features a Na-B bond. Its preferred heterolytic dissociation conforms with the IUPAC definition of dative bond. The lone electron pair revealed on Na and the negative Laplacian of electron density at the bond critical point further confirm the dative nature of the Na-B bond. This study represents the first example of a Lewis adduct with an alkalide as the Lewis base.

The metallo-formate anions, M(CO2)−, M = Ni, Pd, Pt, formed by electron-induced CO2 activation

The metallo-formate anions, M(CO₂)⁻, M = Ni, Pd, and Pt, were formed by electron-induced CO₂ activation.

Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization

Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.