CH⋯π and π⋯π interaction in benzene–acetylene clusters

Spodium Bonding to Dicoordinated Group 12 Atoms

DFT calculations consider the interactions between linear MR2 and a series of N-bases, where M is Hg or Zn and its R substituents are CCH, CN, or NO2. NCH, NH3, and NMe3 were considered as three different N-bases. Zn forms stronger bonds with the N bases than does Hg, and they strengthen along with the electron-withdrawing power of the R substituent, varying over a wide range from 3.4 to 43.9 kcal/mol. Another factor contributing to the bond strength is the nucleophilicity of the base: NCH < NH3 < NMe3. All MR2 Lewis acids can bind at least two bases, which are situated along the R-M-R bisecting plane, fairly close to one another, with θ(N-M-N) angles between 67° and 117°. The presence of a more electron-withdrawing substituent R and more powerful nucleophile allows up to 4 bases to bind to M. The properties of these bonds place them along a continuum, some clearly noncovalent, while other contain a good deal of covalent character.

Influence of Internal Angular Arrangement on Pnicogen Bond Strength

The three Z-X covalent bonds of a ZX3 unit (Z = P, As, Sb, Bi) are normally arranged in a pyramidal structure. Quantum chemical calculations show that pnicogen bonds (ZBs) to the central Z are weakened if ZX3 is flattened, as in the opening of an umbrella. The partial closing of the umbrella has the opposite effect of substantially strengthening these ZBs, even amounting to a 2- or 3-fold magnification in certain cases. The strongest such bonds, wherein Sb and Bi are in a strained configuration within a ZO3CH model system, have interaction energies of 20 kcal/mol with an NH3 base. Most of these systems, whether flattened or more pyramidal, are capable of engaging in three ZBs simultaneously, despite a certain amount of negative cooperativity.

Transition between the Noncovalency and Covalency of σ-Hole Bonds

The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.

Competition between Binding to Various Sites of Substituted Imidazoliums

The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH₃ base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.

Structural and dynamical studies of CH-πbonded CH4-C6H6dimer by ultrafast intermolecular Coulombic decay

The inner-valence ionization and fragmentation dynamics of CH₄-C₆H₆dimer induced by 200 eV electron impact is studied utilizing a multi-particle coincidence momentum spectroscopy. The three-dimensional momentum vectors and kinetic energy release (KER) of the CH₄⁺+C₆H₆⁺ion pairs are obtained by coincident momentum measurement. Our analysis on the absolute cross sections indicates that the intermediate dication CH₄⁺-C₆H₆⁺is preferentially produced by the removal of an inner-valence electron from CH₄or C₆H₆and subsequent relaxation of ultrafast intermolecular Coulombic decay followed by two-body Coulomb explosion. Combining withab initiomolecular dynamics (AIMD) simulations, the real-time fragmentation dynamics including translational, vibrational and rotational motions are presented as a function of propagation time. The revealed fragmentation dynamics are expected to have a potential implication for crystal structure imaging with various radiation sources.

Highly efficient synthesis of non-planar macrocycles possessing intriguing self-assembling behaviors and ethene/ethyne capture properties

It has been a challenging topic and perpetual task to design and synthesize covalent macrocycles with characteristic self-assembling behaviors and excellent host-guest properties in supramolecular chemistry. Herein, we present a family of macrocyclic diphenylamine[n]arenes (DPA[n]s, n = 3-7) consisting of methyldiphenylamine units through a facile one-pot synthesis strategy. Unlike many other reported macrocyclic arenes, the resultant non-planar DPA[n]s feature intrinsic π-π stacking interactions, interesting self-assembling behaviors and ethene/ethyne capture properties. Specifically, strong multiple intermolecular edge-to-face aromatic interactions in DPA[3] have been systematically investigated both in solid and solution states. The intriguing findings on the intermolecular edge-to-face stacking interaction mode in the macrocycle would further highlight the importance of noncovalent π-π interaction in supramolecular self-assembly. This study will also shed light on the macrocyclic and supramolecular chemistry and, we expect, will provide a direction for design and synthesis of covalent macrocycles in this area.

Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-π interactions

Oligoethylene glycols are used as crowding agents in experiments that aim to understand the effects of intracellular environments on DNAs. Moreover, DNAs with covalently attached oligoethylene glycols are used as cargo carriers for drug delivery systems. To investigate how oligoethylene glycols interact with DNAs, we incorporated deoxythymidine modified with oligoethylene glycols of different lengths, such as tetraethylene glycol (TEG), into DNAs that form antiparallel G-quadruplex or hairpin structures such that the modified residues were incorporated into loop regions. Thermodynamic analysis showed that because of enthalpic differences, the modified G-quadruplexes were stable and the hairpin structures were slightly unstable relative to unmodified DNA. The stability of G-quadruplexes increased with increasing length of the ethylene oxides and the number of deoxythymidines modified with ethylene glycols in the G-quadruplex. Nuclear magnetic resonance analyses and molecular dynamics calculations suggest that TEG interacts with bases in the G-quartet and loop via CH–π and lone pair–π interactions, although it was previously assumed that oligoethylene glycols do not directly interact with DNAs. The results suggest that numerous cellular co-solutes likely affect DNA function through these CH–π and lone pair–π interactions.

Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds

The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl^- , Br^- , and I^- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol^-1 for the Ge⋅⋅⋅F^- interaction. The receptors have a pronounced selectivity for F^- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.

Does borazine-water behave like benzene-water? A matrix isolation infrared and ab initio study

Borazine is isoelectronic with benzene and is popularly referred to as inorganic benzene. The study of non-covalent interactions with borazine and comparison with its organic counterpart promises to show interesting similarities and differences. The motivation of the present study of the borazine-water interaction, for the first time, stems from such interesting possibilities. Hydrogen-bonded complexes of borazine and water were studied using matrix isolation infrared spectroscopy and quantum chemical calculations. Computations were performed at M06-2X and MP2 levels of theory using 6-311++G(d,p) and aug-cc-pVDZ basis sets. At both the levels of theory, the complex involving an N-H⋯O interaction, where the N-H of borazine serves as the proton donor to the oxygen of water was found to be the global minimum, in contrast to the benzene-water system, which showed an H-π interaction. The experimentally observed infrared spectra of the complexes corroborated well with our computations for the complex corresponding to the global minimum. In addition to the global minimum, our computations also located two local minima on the borazine-water potential energy surface. Of the two local minima, one corresponded to a structure where the water was the proton donor to the nitrogen of borazine, approaching the borazine ring from above the plane of the ring; a structure that resembled the global minimum in the benzene-water H-π complex. The second local minimum corresponded to an interaction of the oxygen of water with the boron of borazine, which can be termed as the boron bond. Clearly the borazine-water system presents a richer landscape than the benzene-water system.

Effect of aromatic ring fluorination on CH⋯π interactions: microwave spectrum and structure of the 1,2-difluorobenzene⋯acetylene dimer

The H⋯π distance increases ino-C₆H₄F₂⋯HCCH, compared to C₆H₅F⋯HCCH or C₆H₆⋯HCCH, consistent with weaker interactions with increased ring fluorination.

C-H···π interactions and the nature of the donor carbon atom

The influence of multiple substituents (F, CH3, NO2, CN, Cl, OH and NH2) on the C-H···π interaction in benzene-ethylene complex was investigated using the estimated CCSD(T) method and complete basis set limit. The results were compared with our earlier reported complexes of benzene-acetylene and benzene-methane, thus completing the sp, sp(2) and sp(3) series of C-H donors. The stabilization energy values for multiple fluoro-substituted benzene-ethylene complexes are found to be very close to those of the multiple fluoro-substituted benzene-methane complexes. Expectedly, the stabilization energies for the multiple methyl-substituted benzene-ethylene complexes lie between those of the multiple methyl-substituted benzene-methane and benzene-acetylene complexes. Energy decomposition analysis using the DFT-SAPT method predicts the dispersion energy to be dominant, similar to the benzene-methane complexes. For the symmetrically disubstituted complexes (-OH, -Cl, -NH2, -CN and -NO2), additional C-H···X interaction was observed, possibly due to the angular orientation of the ethylene molecule. Multidimensional correlation analysis between the electrostatic, dispersion and exchange-repulsion with the C-H···π interaction distance (r), Hammett constant (σ) and the molar refractivity (MR) revealed strong correlation between dispersion energy and the C-H···π interaction distance (r) as well as molar refractivity (MR).

Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis

Recent studies have demonstrated that the active sites of S-adenosylmethionine (AdoMet)-dependent methyltransferases form strong carbon-oxygen (CH···O) hydrogen bonds with the substrate's sulfonium group that are important in AdoMet binding and catalysis. To probe these interactions, we substituted the noncanonical amino acid p-aminophenylalanine (pAF) for the active site tyrosine in the lysine methyltransferase SET7/9, which forms multiple CH···O hydrogen bonds to AdoMet and is invariant in SET domain enzymes. Using quantum chemistry calculations to predict the mutation's effects, coupled with biochemical and structural studies, we observed that pAF forms a strong CH···N hydrogen bond to AdoMet that is offset by an energetically unfavorable amine group rotamer within the SET7/9 active site that hinders AdoMet binding and activity. Together, these results illustrate that the invariant tyrosine in SET domain methyltransferases functions as an essential hydrogen bonding hub and cannot be readily substituted by residues bearing other hydrogen bond acceptors.

Benzene⋯acetylene: a structural investigation of the prototypical CH⋯π interaction

The benzene⋯acetylene dimer is a symmetric top with μ = 0.438(11) D and H⋯π = 2.4921(1) Å.