Comparison between Hydrogen and Halogen Bonds in Complexes of 6-OX-Fulvene with Pnicogen and Chalcogen Electron Donors

Quantum chemical calculations are applied to complexes of 6-OX-fulvene (X=H, Cl, Br, I) with ZH₃/H₂Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H-bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order O<S<Se<Te, whereas the pattern is murkier for the pnicogen donors. In terms of competition, most halogen bonds to pnicogen donors are stronger than their H-bond analogues, but there is no clear pattern with respect to chalcogen donors. O prefers a H-bond, while halogen bonds are favored by Te. For S and Se, I-bonds are strongest, followed Br, H, and Cl-bonds in that order.     

On the Stability of Interactions between Pairs of Anions – Complexes of MCl3− (M=Be,Mg, Ca,Sr, Ba) with Pyridine and CN−

The ability of the central M atom of the MCl₃⁻ anion, with M=Be, Mg, Ca, Sr, Ba, to engage in a noncovalent bond with an approaching nucleophile is gauged by ab initio methods. The N atom of pyridine forms a M⋅⋅⋅N bond with an interaction energy between 12 and 21 kcal mol⁻¹, even though the π-hole above the M atom is not necessarily positive in sign. Despite a strong Coulombic repulsion between two anions, CN⁻ is also able to approach the M atom so as to engage in a metastable complex that is higher in energy than the individual anions. The energy barrier separating this complex from its constituent anion pair is roughly 20 kcal mol⁻¹. Despite the endothermic formation reaction energy of the CN⁻⋅⋅⋅MCl₃⁻ complex, the electron topology signals a strong interaction, more so than in pyridine⋅⋅⋅MCl₃⁻ with its exothermic binding energy. The dianionic complex is held together largely on the strength of interorbital interactions, thereby overcoming a repulsive electrostatic component. The latter is partially alleviated by the pyramidalization of the MCl₃ unit which makes its π-hole more positive. The complex sinks below the separate monomers in energy when the system is immersed in an aqueous medium, with a binding energy that varies from as much as 20 kcal mol⁻¹ for Be down to 1.2 kcal mol⁻¹ for Ba.     

A–X⋯σ Interactions—Halogen Bonds with σ-Electrons as the Lewis Base Centre

CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F₂, Cl₂, Br₂ and I₂ molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds.     

The Different Story of π Bonds

We revisit “classical” issues in multiply bonded systems between main groups elements, namely the structural distortions that may occur at the multiple bonds and that lead, e.g., to trans-bent and bond-length alternated structures. The focus is on the role that orbital hybridization and electron correlation play in this context, here analyzed with the help of simple models for σ- and π-bonds, numerically exact solutions of Hubbard Hamiltonians and first principles (density functional theory) investigations of an extended set of systems.     

Creating σ‐Holes through the Formation of Beryllium Bonds

Through the use of ab initio theoretical models based on MP2/aug‐cc‐pVDZ‐optimized geometries and CCSD(T)/aug‐cc‐pVTZ and CCSD(T)/aug‐c‐pVDZ total energies, it has been shown that the significant electron density rearrangements that follow the formation of a beryllium bond may lead to the appearance of a σ‐hole in systems that previously do not exhibit this feature, such as CH₃OF, NO₂F, NO₃F, and other fluorine‐containing systems. The creation of the σ‐hole is another manifestation of the bond activation–reinforcement (BAR) rule. The appearance of a σ‐hole on the F atoms of CH₃OF is due to the enhancement of the electronegativity of the O atom that participates in the beryllium bond. This atom recovers part of the charge transferred to Be by polarizing the valence density of the F into the bonding region. An analysis of the electron density shows that indeed this bond becomes reinforced, but the F atom becomes more electron deficient with the appearance of the σ‐hole. Importantly, similar effects are also observed even when the atom participating in the beryllium bond is not directly attached to the F atom, as in NO₂F, NO₃F, or NCF. Hence, whereas the isolated CH₃OF, NO₂F, and NO₃F are unable to yield F ??? Base halogen bonds, their complexes with BeX₂ derivatives are able to yield such bonds. Significant cooperative effects between the new halogen bond and the beryllium bond reinforce the strength of both noncovalent interactions.     

The Role of Hydrogen Bonds in Interactions between [PdCl4]2− Dianions in Crystal

[PdCl₄]²⁻ dianions are oriented within a crystal in such a way that a Cl of one unit approaches the Pd of another from directly above. Quantum calculations find this interaction to be highly repulsive with a large positive interaction energy. The placement of neutral ligands in their vicinity reduces the repulsion, but the interaction remains highly endothermic. When the ligands acquire a unit positive charge, the electrostatic component and the full interaction energy become quite negative, signalling an exothermic association. Raising the charge on these counterions to +2 has little further stabilizing effect, and in fact reduces the electrostatic attraction. The ability of the counterions to promote the interaction is attributed in part to the H-bonds which they form with both dianions, acting as a sort of glue.     

Anionic CH⋅⋅⋅X− Hydrogen Bonds: Origin of Their Strength,Geometry, and Other Properties

CF₃H as a proton donor was paired with a variety of anions, and its properties were assessed by MP2/aug‐cc‐pVDZ calculations. The binding energy of monoanions halide, NO₃^?, formate, acetate, HSO₄^?, and H₂PO₄^? lie in the 12–17 kcal mol^?1 range, although F^? is more strongly bound, by 26 kcal mol^?1. Dianions SO₄^2? and HPO₄^2? are bound by 27 kcal mol^?1, and trianion PO₄^3? by 45 kcal mol^?1. When two O atoms are available on the anion, the CH???O^? H‐bond (HB) is usually bifurcated, although asymmetrically. The CH bond is elongated and its stretching frequency redshifted in these ionic HBs, but the shift is reduced in the bifurcated structures. Slightly more than half of the binding energy is attributed to Coulombic attraction, with smaller contributions from induction and dispersion. The amount of charge transfer from the anions to the σ*(CH) orbital correlates with many of the other indicators of bond strength, such as binding energy, CH bond stretch, CH redshift, downfield NMR spectroscopic chemical shift of the bridging proton, and density at bond critical points.     

Enantioseparation of 5,5′-Dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on Polysaccharide-Based Chiral Stationary Phases: Exploring Chalcogen Bonds in Liquid-Phase Chromatography

The chalcogen bond (ChB) is a noncovalent interaction based on electrophilic features of regions of electron charge density depletion (σ-holes) located on bound atoms of group VI. The σ-holes of sulfur and heavy chalcogen atoms (Se, Te) (donors) can interact through their positive electrostatic potential (V) with nucleophilic partners such as lone pairs, π-clouds, and anions (acceptors). In the last few years, promising applications of ChBs in catalysis, crystal engineering, molecular biology, and supramolecular chemistry have been reported. Recently, we explored the high-performance liquid chromatography (HPLC) enantioseparation of fluorinated 3-arylthio-4,4′-bipyridines containing sulfur atoms as ChB donors. Following this study, herein we describe the comparative enantioseparation of three 5,5′-dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on polysaccharide-based chiral stationary phases (CSPs) aiming to understand function and potentialities of selenium σ-holes in the enantiodiscrimination process. The impact of the chalcogen substituent on enantioseparation was explored by using sulfur and non-chalcogen derivatives as reference substances for comparison. Our investigation also focused on the function of the perfluorinated aromatic ring as a π-hole donor recognition site. Thermodynamic quantities associated with the enantioseparation were derived from van’t Hoff plots and local electron charge density of specific molecular regions of the interacting partners were inspected in terms of calculated V. On this basis, by correlating theoretical data and experimental results, the participation of ChBs and π-hole bonds in the enantiodiscrimination process was reasonably confirmed.     

The Role of Molecular Electrostatic Potentials in the Formation of a Halogen Bond in Furan⋅⋅⋅XY and Thiophene⋅⋅⋅XY Complexes

The halogen bonding of furan???XY and thiophene???XY (X=Cl, Br; Y=F, Cl, Br), involving σ‐ and π‐type interactions, was studied by using MP2 calculations and quantum theory of “atoms in molecules” (QTAIM) studies. The negative electrostatic potentials of furan and thiophene, as well as the most positive electrostatic potential (V_S,max) on the surface of the interacting X atom determined the geometries of the complexes. Linear relationships were found between interaction energy and V_S,max of the X atom, indicating that electrostatic interactions play an important role in these halogen‐bonding interactions. The halogen‐bonding interactions in furan???XY and thiophene???XY are weak, “closed‐shell” noncovalent interactions. The linear relationship of topological properties, energy properties, and the integration of interatomic surfaces versus V_S,max of atom X demonstrate the importance of the positive σ hole, as reflected by the computed V_S,max of atom X, in determining the topological properties of the halogen bonds.     

A new QM/MM method oriented to the study of ionic liquids

The interest on room temperature ionic liquids has grown in the last decades because of their use as all‐purpose solvent and their low environmental impact. In the present work, a new theoretical procedure is developed to study pure ionic liquids within the framework of the quantum mechanics/molecular mechanics method. Each type of ion (cation or anion) is considered as an independent entity quantum mechanically described that follows a differentiated path in the liquid. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1‐ethyl‐3‐methylimidazolium tetrafluoroborate. It was found that, similar to non‐polar liquids and as a consequence of the low value of the reaction field, the cation and anion charge distributions are hardly polarized by the rest of molecules in the liquid. Their structure is characterized by an alternance between anion and cation shells as evidenced by the coincidence of the first maximum of the anion–anion and cation–cation radial distribution functions with the first minimum of the anion‐cation. Some degree of stacking between the cations is also found. © 2015 Wiley Periodicals, Inc.     

Theoretical Studies on the Hydrogen Bonds of Different Position Action Mechanisms of Thymine with Uracil

In this research, the hydrogen bonds Y···H-X(X = C, N; Y = N, O) of thymine and uracil have been theoretically studied. The results show that hydrogen bond leads to bond length elongation and stretches the frequency red-shift of N-H···Y. Meanwhile, the C-H···O bonds shorten and stretch the frequency blue-shift. They all belong to traditional hydrogen bonds. The intermolecular charge transfer caused by the intermolecular hyperconjugation ρ*(N–H) →n(Y) and intramolecular charge redistribution by intramolecular hyperconjugation ρ(C-H)→ρ*(C-N) play important roles in the formation of hydrogen bonds. According to the judgment standards proposed by Bader and Popelier, these hydrogen bonds have typical electron density topological properties. Electrostatic surface potential(ESP) is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as the prediction of likely sites of electrophilic and nucleophilic metabolic attack.     

Chiral Nanoparticles/Lewis Acids as Cooperative Catalysts for Asymmetric 1,4‐Addition of Arylboronic Acids to α,β‐Unsaturated Amides

Cooperative catalysts consisting of chiral Rh/Ag nanoparticles and Sc(OTf)₃ have been developed that catalyze asymmetric 1,4‐addition reactions of arylboronic acids with α,β‐unsaturated amides efficiently. The reaction has been considered one of the most challenging reactions because of the low reactivity of the amide substrates. The new catalysts provide the desired products with outstanding enantioselectivities (>98 % ee) in the presence of low loadings (<0.5 mol %) of the catalyst.     

An experimental and theoretical approach to the molecular structure of 3‐{[4‐(3‐Methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐hydrazono}‐1,3‐dihydro‐ indol‐2‐one

The title molecule, 3‐{[4‐(3‐methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐hydrazono}‐1,3‐dihydro‐indol‐2‐one (C₂₂H₂₀N₄O₁S₁), was prepared and characterized by ¹H NMR, ¹³C NMR, IR, UV–visible, and single‐crystal X‐ray diffraction. The compound crystallizes in the monoclinic space group P21 with a = 8.3401(5), b = 5.6976(3), c = 20.8155(14) Å, and β = 95.144(5)°. Molecular geometry from X‐ray experiment and vibrational frequencies of the title compound in the ground state has been calculated using the Hartree–Fock with 6‐31G(d, p) and density functional method (B3LYP) with 6‐31G(d, p) and 6‐311G(d, p) basis sets, and compared with the experimental data. The calculated results show that optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies values show good agreement with experimental data. Density functional theory calculations of the title compound and thermodynamic properties were performed at B3LYP/6‐31G(d, p) level of theory. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Jumping Crystals of Pyrene Tweezers: Crystal‐to‐Crystal Transition Involving π/π‐to‐CH/π Assembly Mode Switching

Crystals of pyrene tweezers 1 with interdigitating pyrenyl blades jump vigorously at around 160 °C. Single‐crystal X‐ray diffraction analysis before jumping revealed the presence of a “pyrene tetrad” in the crystal lattice, where four pyrenyl blades are π ‐stacked on top of each other. Upon heating the crystal to induce the jumping event, inner two pyrenyl blades in the “pyrene tetrad” probably rotate to switch off their π ‐stacking interaction with the neighboring outer pyrenyl blades and form new CH−π bonds. Different from reported salient crystals, our crystal jumps with the release of CHCl₃ as inclusion solvent.     

Comparison of the Ability of N-Bases to Engage in Noncovalent Bonds

The lone pair of the N atom is a common electron donor in noncovalent bonds. Quantum calculations examine how various aspects of the base on which the N is located affect the strength and other properties of complexes formed with Lewis acids FH, FBr, F₂Se, and F₃As that respectively encompass hydrogen, halogen, chalcogen, and pnicogen bonds. In most cases the halogen bond is the strongest, followed in order by chalcogen, hydrogen, and pnicogen. The noncovalent bond strength increases in the sp<sp²<sp³ order of hybridization of N. Replacement of H substituents on the base by a methyl group or substituting N by C atom to which the base N is attached, strengthens the bond. The strongest bonds occur for trimethylamine and the weakest for N₂.     

Cooperation of σ–π and σ*–π* Conjugation in the UV/Vis and Fluorescence Spectra of 9,10-Disilylanthracene

In 1996, we reported that silyl groups of 9,10-disilylanthracenes significantly affect the UV/Vis and fluorescence spectra. Although the results indicate that the silyl groups have strong electronic effects on anthracene, the details of the mechanisms responsible for this have not yet been clarified. This article describes the analysis of the UV/Vis and fluorescence spectra of 9,10-bis(diisopropylsilyl)anthracene by theoretical calculations. This study reveals that π conjugation of anthracene is extended by cooperation of σ–π and σ*–π* conjugation between the silyl groups and anthracene. This effect increases the transition moment of the π–π* transition of anthracene. As a result, the molecular extinction coefficient of the ¹L_a band and the fluorescence quantum yield are increased.     

The Effects of Substituents on the Geometry of π–π Interactions

We have designed and utilized a simple molecular recognition system to study the substituent effects in aromatic interactions. Recently, we showed that 3‐ and 3,5‐disubstituted benzoyl leucine diethyl amides with aromatic rings of varying electronic character organized into homochiral dimers in the solid state through a parallel displaced π–π interaction and two hydrogen bonds, but no such homochiral dimerization was observed for the unsubstituted case. This phenomenon supports the hypothesis that substituents stabilize π–π interactions regardless of their electronic character. To further investigate the origin of substituent effects for π–π interactions, we synthesized and crystallized a series of 4‐substituted benzoyl leucine diethyl amides. Surprisingly, only two of the 4‐substituted compounds formed homochiral dimers. A comparison among the 4‐substituted compounds that crystallized as homochiral dimers and their 3‐substituted counterparts revealed that there are differences in regard to the geometry of the aromatic rings with respect to each other, which depend on the electronic nature and location of the substituent. The crystal structures of the homochiral dimers that showed evidence of direct, local interactions between the substituents on the aromatic rings also displayed nonequivalent dihedral angles in the individual monomers. The crystallographic data suggests that such “flexing” may be the result of the individual molecules orienting themselves to maximize the local dipole interactions on the respective aromatic rings. The results presented here can potentially have broad applicability towards the development of molecular recognition systems that involve aromatic interactions.