Competition of C(sp2)–X···O Halogen Bonding and Lone Pair···π Interactions: Cryospectroscopic Study of the Complexes of C2F3X (X = F, Cl, Br, and I) and Dimethyl Ether

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

A Combined Experimental/Quantum-Chemical Study of Tetrel, Pnictogen, and Chalcogen Bonds of Linear Triatomic Molecules

Linear triatomic molecules (CO₂, N₂O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO₂ and OCS) or pnictogen (N₂O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency to form end-on chalcogen bonds. Comparison of the IR spectra of the complexes with the corresponding monomers in cryogenic solutions in liquid argon enables to determine the stoichiometry and the nature of the complexes. In the present cases, perpendicular tetrel and pnictogen 1:1 complexes are identified mainly on the basis of the lifting of the degenerate ν 2 bending mode with the appearance of both a blue and a red shift. Van ′t Hoff plots of equilibrium constants as a function of temperature lead to complexation enthalpies that, when converted to complexation energies, form the first series of experimental complexation energies on sp¹ tetrel bonds in the literature, directly comparable to quantum-chemically obtained values. Their order of magnitude corresponds with what can be expected on the basis of experimental work on halogen and chalcogen bonds and previous computational work on tetrel bonds. Both the order of magnitude and sequence are in fair agreement with both CCSD(T) and DFA calculations, certainly when taking into account the small differences in complexation energies of the different complexes (often not more than a few kJ mol⁻¹) and the experimental error. It should, however, be noted that the OCS chalcogen complexes are not identified experimentally, most probably owing to entropic effects. For a given Lewis base, the stability sequence of the complexes is first successfully interpreted via a classical electrostatic quadrupole–dipole moment model, highlighting the importance of the magnitude and sign of the quadrupole moment of the Lewis acid. This approach is validated by a subsequent analysis of the molecular electrostatic potential, scrutinizing the σ and π holes, as well as the evolution in preference for chalcogen versus tetrel bonds when passing to “higher” chalcogens in agreement with the evolution of the quadrupole moment. The energy decomposition analysis gives further support to the importance/dominance of electrostatic effects, as it turns out to be the largest attractive term in all cases considered, followed by the orbital interaction and the dispersion term. The natural orbitals for chemical valence highlight the sequence of charge transfer in the orbital interaction term, which is dominated by an electron-donating effect of the N or O lone-pair(s) of the base to the central atom of the triatomics, with its value being lower than in the case of comparable halogen bonding situations. The effect is appreciably larger for TMA, in line with its much higher basicity than DME, explaining the comparable complexation energies for DME and TMA despite the much larger dipole moment for DME.

Structural Characterization, DFT Calculation, NCI, Scan-Rate Analysis and Antifungal Activity against Botrytis cinerea of (E)-2-{[(2-Aminopyridin-2-yl)imino]-methyl}-4,6-di-tert-butylphenol (Pyridine Schiff Base)

Botrytis cinerea is a ubiquitous necrotrophic filamentous fungal phytopathogen that lacks host specificity and can affect more than 1000 different plant species. In this work, we explored L1 [(E)-2-{[(2-aminopyridin-2-yl)imino]-methyl}-4,6-di-tert-butylphenol], a pyridine Schiff base harboring an intramolecular bond (IHB), regarding their antifungal activity against Botrytis cinerea. Moreover, we present a full characterization of the L1 by NMR and powder diffraction, as well as UV–vis, in the presence of previously untested different organic solvents. Complementary time-dependent density functional theory (TD-DFT) calculations were performed, and the noncovalent interaction (NCI) index was determined. Moreover, we obtained a scan-rate study on cyclic voltammetry of L1. Finally, we tested the antifungal activity of L1 against two strains of Botrytis cinerea (B05.10, a standard laboratory strain; and A1, a wild type strains isolated from Chilean blueberries). We found that L1 acts as an efficient antifungal agent against Botrytis cinerea at 26 °C, even better than the commercial antifungal agent fenhexamid. Although the antifungal activity was also observed at 4 °C, the effect was less pronounced. These results show the high versatility of this kind of pyridine Schiff bases in biological applications.

Halogen bonding with the halogenabenzene bird structure, halobenzene, and halocyclopentadiene

The ability of the "bird-like" halogenabenzene molecule, referred to as X-bird (XCl to At), to form halogen-bonded complexes with the nucleophiles H₂ O and NH₃ was investigated using double-hybrid density functional theory and the aug-cc-pVTZ/aug-cc-pVTZ-PP basis set. The structures and interaction energies were compared with 5-halocyclopenta-1,3-diene (halocyclopentadiene; an isomer of halogenabenzene) and halobenzene, also complexed with H₂ O and NH₃ . The unusual structure of the X-bird, with the halogen bonded to two carbon atoms, results in two distinct σ-holes, roughly at the extension of the C-X bonds. Based on the behavior of the interaction energy (which increases for heavier halogens) and van der Waals (vdW) ratio (which decreases for heavier halogens), it is concluded that the X-bird forms proper halogen bonds with H₂ O and NH₃ . The interaction energies are larger than those of the halogen-bonded complexes involving halobenzene and halocyclopentadiene, presumably due to the presence of a secondary interaction. © 2019 Wiley Periodicals, Inc.

Halogen bonding in mono- and dihydrated halobenzene

Density functional theory calculations were performed on halogen-bonded and hydrogen-bonded systems consisting of a halobenzene (XPh; X = F, Cl, Br, I, and At) and one or two water molecules, using the M06-2X density functional with the 6-31+G(d) (for C, H, F, Cl, and Br) and aug-cc-pVDZ-PP (for I, At) basis sets. The counterpoise procedure was performed to counteract the effect of basis set superposition error. The results show halogen bonds form in the XPh-H₂ O system when X > Cl. There is a trend toward stronger halogen bonding as the halogen group is descended, as assessed by interaction energy and X•••O_w internuclear separation (where O_w is the water oxygen). For all XPh-H₂ O systems hydrogen-bonded systems exist, containing a combination of CH•••O_w and O_w H_w •••X hydrogen bonds. For all systems except X = At the X•••H_w hydrogen-bonding interaction is stronger than the X•••O_w halogen bond. In the XPh-(H₂ O)₂ system halogen bonds form only for X > Br. The two water molecules prefer to form a water dimer, either located around the CH bond (for X = Br, At, and I) or located above the benzene ring (for all halogens). Thus, even in the absence of competing strong interactions, halogen bonds may not form for the lighter halogens due to (1) competition from cooperative weak interactions such as CH•••O and OH•••X hydrogen bonds, or (2) if the formation of the halogen bond would preclude the formation of a water dimer. © 2018 Wiley Periodicals, Inc.

S⋯S and S⋯P chalcogen bonding in solution: a cryospectroscopic study of the complexes of 2,2,4,4-tetrafluoro-1,3-dithietane with dimethyl sulfide and trimethylphosphine

Experimental evidence on the formation of S⋯S and P⋯S chalcogen bonded complexes between 2,2,4,4-tetrafluoro-1,3-dithiethane and the Lewis bases dimethyl sulfide and trimethylphosphine is obtained using infrared spectroscopy of solutions in liquid krypton.

Effect of Fluorination on the Competition of Halogen Bonding and Hydrogen Bonding: Complexes of Fluoroiodomethane with Dimethyl Ether and Trimethylamine

To further rationalize the competition between halogen and hydrogen bonding, a combined experimental and theoretical study on the weakly bound molecular complexes formed between the combined halogen bond/hydrogen bond donor fluoroiodomethane and the Lewis bases dimethyl ether and trimethylamine (in standard and fully deuterated form) is presented. The experimental data are obtained by recording infrared and Raman spectra of mixtures of the compounds in liquid krypton, at temperatures between 120 and 156 K. The experiments are supported by ab initio calculations at the MP2/aug-cc-pVDZ-PP level, statistical thermodynamics and Monte Carlo free energy perturbation calculations. For the mixtures containing fluoroiodomethane and dimethyl ether a hydrogen-bonded complex with an experimental complexation enthalpy of -7.0(2) kJ mol^-1 is identified. Only a single weak spectral feature is observed which can be tentatively assigned to the halogen-bonded complex. For the mixtures involving trimethylamine, both halogen- and hydrogen-bonded complexes are observed, the experimental complexation enthalpies being -12.5(1) and -9.6(2) kJ mol^-1 respectively. To evaluate the influence of fluorination on the competition between halogen and hydrogen bonding, the results obtained for fluoroiodomethane are compared with those of a previous study involving difluoroiodomethane.

Dimers or trimers? A characterization of the halogen bonded complexes of CF3X (X=I or Br) with dimethyl ether and acetone in cryosolutions

Acetone molecules dissolved in liquid krypton are inclined to self-associate into dimers. This behavior affects its use as a prototype Lewis base in studies of weak intermolecular interactions. In this study infrared spectra of mixed solutions of dimethyl ether and CF₃X and of acetone and CF₃X (with X=I or Br) dissolved in liquid argon and liquid krypton are recorded at constant temperature. The dataset for dimethyl ether is used to validate a numerical method based on least-squares fitting of a model including contributions of both monomers and a heterodimer with 1:1 stoichiometry. The resulting monomer and dimer spectra show excellent agreement with previous studies found in literature. The analysis of the dataset for acetone requires an extension of the model with contributions for the acetone homodimer and for (acetone)₂·CF₃X and acetone·(CF₃X)₂ trimers. The results show that many signals for acetone·CF₃I and (acetone)₂·CF₃I are observed, while only a few bands due to acetone·(CF₃I)₂ occur. The use of numerical approaches adjusted to the specificities of a mixture of two compounds allows to reliably resolve overlapping spectra of monomers and heterocomplexes and characterizing heterocomplex features that could not be deduced using earlier methods. To support the assignments made, ab initio calculations predicting geometries, relative stabilities and harmonic vibrational frequencies for the species envisaged are performed.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

Self-Associating Behavior of Acetone in Liquid Krypton

Acetone molecules are inclined to self-associate through dipole-dipole interactions because of their large dipole moment. Infrared spectroscopy of compounds dissolved in liquid noble gases supported by high level ab initio calculations allows investigating the self-associating behavior and determining the thermodynamical properties. In this study, infrared spectra of various concentrations of acetone dissolved in liquid krypton are recorded at constant temperature. Overlapping monomer and dimer spectra are separated by analyzing the obtained data sets with numerical methods based on least-squares fitting. Although acetone is known to self-associate, only a few spectral features have been presented in literature before. In this study, the application of new numerical approaches succeeds in resolving overlapping spectra and allows observing isolated acetone dimer absorption bands for the complete mid infrared spectrum. By use of data sets of spectra recorded at temperatures between 134 and 142 K, the experimental standard dimerization enthalpy was determined to be -10.8 kJ mol(-1). MP2/aug-cc-pVDZ calculations predicted a stacked and planar dimer geometry of which the stacked geometry is more stable. Combining MP2 energies and single point corrections involving CCSD(T) calculations and complete basis set extrapolations based on the MP2/aug-cc-pVDZ equilibrium geometry lead to complexation energy of -28.4 kJ mol(-1) for the stacked geometry and -15.1 kJ mol(-1) for the planar geometry. The corresponding values for the complexation enthalpies in solution, obtained by combining these values with corrections for thermal and solvent influences are -13.7 and -5.8 kJ mol(-1).

Exploring the limits of cryospectroscopy: Least-squares based approaches for analyzing the self-association of HCl

To rationalize the concentration dependent behavior observed for a large spectral data set of HCl recorded in liquid argon, least-squares based numerical methods are developed and validated. In these methods, for each wavenumber a polynomial is used to mimic the relation between monomer concentrations and measured absorbances. Least-squares fitting of higher degree polynomials tends to overfit and thus leads to compensation effects where a contribution due to one species is compensated for by a negative contribution of another. The compensation effects are corrected for by carefully analyzing, using AIC and BIC information criteria, the differences observed between consecutive fittings when the degree of the polynomial model is systematically increased, and by introducing constraints prohibiting negative absorbances to occur for the monomer or for one of the oligomers. The method developed should allow other, more complicated self-associating systems to be analyzed with a much higher accuracy than before.

Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

The competition between hydrogen- and halogen-bonding interactions in complexes of 5-halogenated 1-methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5-X and C4=O4 is investigated with M06-2X/6-31+G(d). In the singly-hydrated systems, the water molecule forms a hydrogen bond with C4=O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5-X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4=O and C5-X (through hydrogen- and halogen-bonding interactions) exist for all halogens except F. The absence of a halogen-bonded structure in singly-hydrated ClmU is therefore attributed to the competing hydrogen-bonding interaction with C4=O4. The halogen-bond angle in the doubly-hydrated structures (150-160°) is far from the expected linearity of halogen bonds, indicating that significantly non-linear halogen bonds may exist in complex environments with competing interactions.

NX⋯Y halogen bonds. Comparison with NH⋯Y H-bonds and CX⋯Y halogen bonds

Quantum calculations examine how the NH⋯Y H-bond compares to the equivalent NX⋯Y halogen bond, as well as to comparable CH/CX donors.

PCl3–C6H6 heterodimers: evidence for P⋯π phosphorus bonding at low temperatures

A phosphorous trichloride (PCl₃)–benzene (C₆H₆) heterodimer was generated in a low temperature N₂ matrix and was characterized using infrared spectroscopy.