Energetic effects between halogen bonds and anion-π or lone pair-π interactions: a theoretical study

Energetic effects between halogen bonds and anion-π or lone pair-π interactions have been investigated by means of ab initio MP2 calculations. 1,4-diiodo-perfluorobenzene, a very effective building block for crystal engineering based on halogen bonding, is selected in this work both as electron-deficient π aromatic ring and as halogen bond donor. Additive and diminutive effects are observed when halogen bonds and anion-π/lone pair-π interactions coexist in the same complex, which can be ascribed to the same direction of charge transfer for the two interactions. These effects have been analyzed in detail by the structural, energetic, and AIM properties of the complexes. Finally, experimental evidence of the combination of the interactions has been obtained from the Cambridge Structural Database.     

Modelling fundamental arene-borane contacts: spontaneous formation of a dibromoborenium cation driven by interaction between a borane Lewis acid and an arene π system

Reaction of 2,6-dimesityl pyridine (L(py)) with BBr(3) leads to the spontaneous formation of the trigonal dibromoborenium cation [L(py)·BBr(2)](+)via bromide ejection. Systematic structural and computational studies, and the reactivity displayed by a closely related N-heterocyclic carbene (NHC) donor, reveal the role played by arene-borane interactions in this chemistry. [L(py)·BBr(2)](+) features a structurally characterized (albeit weak) electrostatic interaction between the borane Lewis acid and flanking arene π systems.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Interplay between halogen bonds and π-π stacking interactions: CSD search and theoretical study

According to our survey of the Cambridge Structural Database (CSD), a great number of crystal structures, in which halogen bonds and aromatic stacking interactions are present and play an important role in crystal packing, have been extracted. In this work, ab initio calculations at the MP2 level of theory were performed to investigate the mutual influence between halogen bonds and π-π stacking interactions. Different energetic effects are observed in the studied complexes where the two kinds of noncovalent interactions coexist, which can be rationalized by the direction of charge transfer for the two interactions. These effects have been analyzed in detail in terms of the structural, energetic, and charge transfer properties of the complexes. In addition, the quantum theory of atoms in molecules (QTAIM) was also employed to characterize the interactions and to examine the strengthening or weakening of the interactions, depending on the variations of electron density on the bond and cage critical points. Finally, certain crystal structures retrieved from the CSD have been selected to provide experimental evidence of the combination of the two interactions.     

Strong intramolecular hydrogen bonds and steric effects involving C═S groups: An NMR and computational study

A number of 5-acyl rhodanines and thiorhodanines with bulky acyl groups (pivaloyl and adamantoyl), not previously available, have been synthesized. The compounds are shown to exist in the enol form. Structures have been calculated using both the MP2 approach and the B3LYP-GD3BJ functional and the 6-311++G(d,p) basis set. Hydrogen bond energies are estimated by subtracting energies of a structure with the OH group turned 180° from those of the intramolecularly hydrogen-bonded one. Properties such as OH chemical shifts, two-bond isotope effects on ¹³C chemical shifts, electron densities at the bond critical point from atoms in molecules analysis, and the hydrogen bond energies show that the sterically hindered compounds have stronger hydrogen bonds than methyl or isopropyl derivatives. The combination of oxygen and sulfur derivatives enables a detailed analysis of hydrogen bond energies.     

Ouroboros: Heterocycles closed by dative σ bonds and stabilized by π delocalization

Heteroarenes such as (aza and oxa)borines are increasingly important as synthetic targets and reagents. We map the intramolecular cyclization of saturated heterocyclic chains through dative bonding. A related set of planar unsaturated aza-, oxa-, and fluora-rings that feature dative σ bonding enhanced by π delocalization are identified. The systems have, in general, the formulae A′(CH₂)_mD′ and A′(CH)_mD′, where m?=?3 and 4, and A′ and D′ are acceptor and donor sites, respectively. In each case, the ring isomers, achievable via A′←D' internal coordination (in the manner of Kekulé’s ouroboros), are more stable than chains. Unsaturated aromatic rings examined herein include a oxadiborine with a hypervalent oxygen center and a dioxadiborine. They are isoelectronic with an azaborine, which was synthesized more recently, and benzene.     

Two-dimensional sheet based on C–H···N hydrogen bonds within an organic cocrystal: a crystallographic,spectroscopic and theoretical study

The cocrystal containing 1,2,4,5-tetracyanobenzene (TCNB) and trans-1,2-bis(4-pyridyl)ethylene (4,4′-BPE) has been realised (TCNB)·(4,4′-BPE) 1. Compound 1 produces a two-dimensional sheet based on two different types of C–H···N hydrogen bonds. Each molecule within the cocrystal functions as both a donor and an acceptor of hydrogen bonds. Weak hydrogen bonds such as these, acting as the driving force to produce a polymeric assembly, are not investigated as frequently as stronger and more traditional O–H···O and O–H···N hydrogen bonds within multicomponent cocrystals. The existence of the different types of C–H···N hydrogen bonds was confirmed by single-crystal X-ray diffraction as well as infrared spectroscopy. The overall interaction energies for both types of hydrogen bonds were determined by computational calculations at various levels of theory.     

Stabilization of a π double bond between two boron atoms: A theoretical approach

The low-lying states of HBBH, HBBNH₂ and H₂NBBNH₂ are investigated by means of ab initio CI calculations using a double-zeta + polarization basis set. Diborene is found to have a ³∑_g⁻ ground state. Replacement of hydrogen by amino groups on each side of the BB bond leads to an ethylene-like bond which corresponds to a ¹A_g state of D_2h symmetry. π back-donation by the amino lone pairs is responsible for the stabilization of this state.     

AIM and NBO analyses on hydrogen bonds formation in sugar-based surfactants (α/β-d-mannose and n-octyl-α/β-d-mannopyranoside): a density functional theory study

Density functional theory calculations on α/β-d-mannose (α/β-d-Man) and the corresponding glycosides of n-octyl-α/β-d-mannopyranoside (C₈O-α/β-d-Man) were carried out for geometrical optimisation and stability predictions at the B3LYP/6-31G level of theory. These compounds are related anomerically, since they differ by only the orientation of the hydroxyl group at the C1 position. The aim of this study is to investigate the effect of the hydroxyl group's orientations (axial vs. equatorial) at the C1 position on the intra-molecular interactions and the conformational stability of these isomers. The structural parameters of X-H???Y intra-molecular hydrogen bonds were analysed, while the nature of these bonds was considered using the atoms-in-molecules (AIM) approach. Natural bond orbital (NBO) analysis was used to determine bond orders and the effective non-bonding interactions. We have also reported thermodynamic properties and the electronic properties, such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, ionisation energy, electron affinity, electronic chemical potential, chemical hardness, softness and electrophilicity index in the gas phase for all compounds. These results showed that while α-anomers possess only one intra-molecular hydrogen bond, β-anomers possess two intra-molecular hydrogen bonds, which further confirms the anomalous stability of the latter in the self-assembly phenomena.     

Charge transport and electronic properties of N-heteroquinones: quadruple weak hydrogen bonds and strong π–π stacking interactions

The charge transport and photophysical properties of N-heteroquinones, which can function as n-type organic semiconductors in organic field-effect transistors (OFETs) with high electron mobility, were systematically investigated using hopping model, band theory, and time-dependent density functional theory (TDDFT). The calculated absorption spectra and electron mobility are in good agreement with experimental results. To the studied compounds, subtle structural modifications can greatly reduce the reorganization energy. There are two main kinds of intermolecular interaction forces of the studied compounds in the crystal, which result from intermolecular π–π and hydrogen bonds interactions, respectively. The results of hopping model show that the electron transport properties are mainly determined by pathways containing intermolecular π–π interactions, and hole transport properties are mainly determined by pathways containing intermolecular hydrogen bonds from the standpoint of transfer integral. Moreover, electronic transfer integral value increases with the enhancement of intermolecular overlap corresponding to the overlap extent of π–π packing. Hole transfer integral value decreases with decreasing the number of hydrogen bonds. This means that charge transport properties can be efficiently tuned by controlling the relative positions of the molecules and the number of hydrogen bonds. The analysis of band structure also supports the conclusion of hopping model.     

Quantum chemical study of the nature of interactions between the boraphosphinine and alumaphosphinine with some of the mono- and divalent cations: cation–π or cation–lone pair?

Structural Chemistry - Quantum chemical study of the nature of interactions between the boraphosphinine (BP) and alumaphosphinine (AlP) with some of the alkali metal cations (Li+, Na+, K+) and...     

Infrared study of hydrogen bonds involving 2,2′-bipyridine and 2,2′-bipyrimidine. Influence of equivalent nitrogen atoms on the hydrogen bond strength

Hydrogen bonding between proton donors (phenols and water) and 2,2′-bipyridine (BPR) or 2,2′-bipyrimidine (BPM) has been investigated by infrared and FT-infrared techniques. The thermodynamic parameters (K, - ΔH, - ΔS°) and the frequency shifts of the ν_OH stretching vibrations have been determined in carbon tetrachloride solution. The spectroscopic results suggest that the complexes formed between phenols covering a large pK_a range (10.3–3.50) and BPR or BPM are of the normal OH⋯N type. The thermodynamic and spectroscopic properties of the BPR and BPM complexes are compared with those previously reported for the interaction between the same proton donors and the model molecules pyridine and pyrimidine. The BPR and pyridine complexes belong to the same series. The behaviours of BPM and pyrimidine are in complete contrast, the thermodynamic parameters and the related proton affinity being much higher for BPM than for pyrimidine. The results are probably ascribable to the presence of two equivalent neighbouring nitrogen atoms, the approach of a hydroxylic proton donor being greatly favoured in this electron-rich region. This effect does not exist in BPR, owing to its transoid configuration in solvents of weak polarity.     

Excited-state N-H···S hydrogen bond between indole and dimethyl sulfide: time-dependent density functional theory study

The intermolecular hydrogen bond N-H···S between indole and dimethyl sulfide is theoretically investigated. The formation of N-H···S hydrogen bonds between indole and dimethyl sulfide in ground and excited states is confirmed by the analysis of geometric structure, Mulliken charge, and infrared spectra. The result shows that the S(1) state of hydrogen bonded indole-Me(2)S is mainly a charger transfer state, while the S(2) state is a local excited state and also the state corresponding to the experiment. More importantly, it is demonstrated that the intermolecular hydrogen bond N-H···S of indole-Me(2)S is strengthened in the S(1) and S(2) states compared to that in ground state. Moreover, the strengthening of intermolecular N-H···S hydrogen bond in excited state induces the fluorescence emission peak of indole shifts to the red. These findings may provide insights for further study of N-H···S hydrogen bonds existing in many biomolecular systems.     

A theoretical evidence for mutual influence between S···N(C) and hydrogen/lithium/halogen bonds: competition and interplay between π-hole and σ-hole interactions

Ab initio calculations were performed to investigate the cooperativity between the S···N(C) bond and the hydrogen/lithium/halogen bond interactions in O₂S···NCX···NCH and O₂S···CNX···CNH triads (X=H, Li, Cl, and Br). To understand the properties of the systems better, the corresponding dyads are also studied. It is evident that the lithium bond has a bigger influence on the chalcogen bond than vice versa. The results indicate that the enhanced interaction energies of the S···N(C) and X···N(C) interactions in the triad increase in the order NCCl < NCBr < NCH < NCLi and CNCl < CNBr < CNH < CNLi. This is the order of the increasing positive electrostatic potential V _S,max on the X atom. The nature of S···N(C) and X···N(C) interactions of the complexes is unveiled by energy decomposition analysis and natural bond orbital (NBO) theory. The cooperativity between both types of interaction is chiefly caused by the electrostatic effects.     

Isotopic labelling of peptides and isotope ratio analysis using LC–ICP–MS: a preliminary study

Bradykinin and substance P have been derivatised with cyclic diethylenetriaminepentaacetic anhydride (cDTPA) and subsequently labelled with natural and isotopically enriched Eu³⁺. This enabled the detection and relative quantitation of the peptides using element-selective detection by high-performance liquid chromatography inductively coupled plasma mass spectrometry (LC–ICP–MS). Relative quantitation was achieved by differentially labelling two peptide sources, after derivatisation with cDTPA, using natural and enriched ¹⁵¹Eu respectively. The ¹⁵¹Eu:¹⁵³Eu isotope ratio was measured and used to calculate the original peptide ratio. The measured ratios came within 5.2% of the known ratio. Derivatisation and chelation reactions were additionally confirmed using LC–ESI–MS.     

Formation of C4H4(•+) from the pyridine radical cation: a theoretical mechanistic and kinetic study

The potential energy surface (PES) for the formation of C(4)H(4)(?+) from the pyridine radical cation by loss of HCN was determined from quantum chemical calculations using the G3//B3LYP method. The complete reaction pathways for the formation of the low-energy C(4)H(4)(?+) isomers, radical cations of methylenecyclopropene (MCP(?+)), vinylacteylene (VA(?+)), cyclobutadiene, and butatriene were obtained. Based on the PESs, a Rice-Ramsperger-Kassel-Marcus model calculation was performed to investigate the dissociation kinetics. The calculated dissociation rate constants agreed with the previous experimental data. It was predicted that a mixture of MCP(?+) and VA(?+) was formed by loss of HCN. The formation of MCP(?+) was more favored near the dissociation threshold and at high energies, whereas the formation of VA(?+) was more favored at the low energies corresponding to the ion lifetime of microseconds.