An Experimental Exploration of C−H⋅⋅⋅X Hydrogen Bond in [CHCl3−X(CH3)2] Complexes (X=O,S, and Se)

Among the conglomeration of hydrogen bond donors, the C−H group is prevalent in chemistry and biology. In the present work, CHCl₃ has been selected as the hydrogen bond donor and are X(CH₃)₂ are the hydrogen bond acceptors. Formation of C−H⋅⋅⋅X hydrogen bond under the matrix isolation condition is confirmed by the observation of red-shift in the C−H stretching frequency of CHCl₃ and comparison with the simulated spectra. Stabilisation energy of all the three complexes is almost equal although the observed red-shift for the C−H⋅⋅⋅O complex is less compared to the C−H⋅⋅⋅S/Se complexes. The nature and origin of the hydrogen bond have been delineated using Natural Bond Orbital, Atoms in Molecules, Non-Covalent Interaction analyses, and Energy Decomposition Analysis. Charge transfer is found to be proportional to the observed red-shift. This work provides the first impression of C−H⋅⋅⋅Se hydrogen bond and its comparison with C−H⋅⋅⋅O/S hydrogen bond interaction under experimental condition.     

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.     

Non-Classical Synthons: Supramolecular Recognition by S⋅⋅⋅O Chalcogen Bonding in Molecular Complexes of Riluzole

Classical examples of supramolecular recognition units or synthons are the ones formed by hydrogen bonds. Here, we report the ubiquity of a S⋅⋅⋅O chalcogen bonded synthon observed in a series of supramolecular complexes of the amyotrophic lateral sclerosis drug riluzole. Although the potential of higher chalcogens such as Se and Te to form robust and directional chalcogen bonded motifs is known, intermolecular sulfur chalcogen bonding is considered to be weak owing to the lower polarizability of S atoms. Here, the robustness and electronic nature of a S⋅⋅⋅O chalcogen bonding non-classical synthon, and the origin of its exceptional directionality have been explored. Bond orders of the drug–coformer chalcogen bonding are found to be as high as one third of a single bond, and they are largely ionic in nature. The contribution of the S⋅⋅⋅O chalcogen bonded motifs to the lattice energies of a series of crystals from the Cambridge Structural Database has been analyzed, showing they can be indeed significant, especially in molecules devoid of strong hydrogen bond donor groups.     

Spectroscopic and Crystallographic Characterization of the R3N+−C−H⋅⋅⋅X Interaction

As appreciation for nonclassical hydrogen bonds has progressively increased, so have efforts to characterize these interesting interactions. Whereas several kinds of C−H hydrogen bonds have been well-studied, much less is known about the R₃N⁺−C−H⋅⋅⋅X variety. Herein, we present crystallographic and spectroscopic evidence for the existence of these interactions, with special relevance to Selectfluor chemistry. Of particular note is the propensity for Lewis bases to engage in nonclassical hydrogen bonding over halogen bonding with the electrophilic F atom of Selectfluor. Further, the first examples of ¹H NMR experiments detailing R₃N⁺−C−H⋅⋅⋅X (X=O, N) hydrogen bonds are described.     

Resonance Assisted Hydrogen Bonding Phenomenon Unveiled through Both Experiments and Theory: A New Family of Ethyl N-Salicylideneglycinate Dyes

Extensive experimental and theoretical investigations are reported on the nature of resonance-assisted hydrogen bonding phenomenon (RAHB) and its influence on photophysical properties of the newly designed dyes differing in donor–acceptor properties, namely ethyl N-salicylideneglycinate ( 1 ), ethyl N-(5-methoxysalicylidene)glycinate ( 2 ), ethyl N-(5-bromosalicylidene)glycinate ( 3 ) and ethyl N-(5-nitrosalicylidene)glycinate ( 4 ). All compounds are thermochromic in the solid state and they contain a typical intramolecular O−H⋅⋅⋅N hydrogen bond formed between the hydroxyl hydrogen atom and the imine nitrogen atom, yielding the enol form in the solid state. It is unveiled, that the magnitude of RAHB effect fine tunes the strength of the O−H⋅⋅⋅N bonding and accordingly the relative populations of the enol, cis-keto and trans-keto forms leading to variation of the photophysical properties of 1 – 4 . It is determined, that the electron-withdrawing NO₂ in 4 amplifies the most RAHB effect causing the breaking of the O−H⋅⋅⋅N hydrogen bond and accordingly formation of the dominant cis-keto isomer in both the solid state and EtOH. To this end, the UV/Vis spectra of 1 – 3 in EtOH revealed the exclusive presence of the enol form, while the prevalent contribution of the cis-keto form was found for 4 . Furthermore, only compound 4 is emissive in the solid state in ambient condition due to dual emission arising from the cis-keto* and trans-keto* forms, while 2 was found to be highly emissive in EtOH. It is revealed qualitatively and quantitatively, based on the ETS-NOCV charge and energy decomposition scheme and the EDDB population-based method, that RAHB is strongly a non-local phenomenon based on electrons pumping or sucking through both the π- and σ-channels, which accordingly exerts chemical bonding changes at both the phenyl ring and predominantly a distant O−H⋅⋅⋅N area.     

Chalcogen Bonding with Diaryl Ditellurides: Evidence from Solid State and Solution Studies.

The chalcogen bonding (ChB) ability of Te is studied in symmetrical diaryl ditellurides ArTeTeAr. Among the two Te σ-holes, the one along the less polarized Te−Te bond was calculated as the more electropositive. This counter-intuitive situation is due to the hyperconjugation contribution from Te lone pair to the σ* of the adjacent Te which coincides with σ-hole along the more polarized Te−Ar bond. ArTeTeAr showed notable structural features in the solid state as a result of intermolecular Te⋅⋅⋅Te ChB, such as a Te₄ rectangle through dimer aggregation or a triangular Te₃ motif, where one Te interacts with both Te atoms of a neighboring molecule through both its σ-hole and lone pair, in a slightly frustrated geometry. Lewis acidity of ArTeTeAr was also evaluated by NMR with R₃PO as σ-hole acceptors in different solvents. Thus, ¹²⁵Te NMR allowed monitoring Te⋅⋅⋅O interaction and delivering association constants (K_a) for 1 : 1 adducts. The highest value of K_a=90 M⁻¹ was measured for the adduct between ArTeTeAr bearing CF₃ groups and Et₃PO in cyclohexane. Notably, by using nBu₃PO, Te⋅⋅⋅O interaction was revealed by ¹⁹F-¹H HOESY showing spatial proximity between CF₃ and CH₃ of nBu₃PO.     

(6‐Oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylato‐κ2O5,O6)bis[2‐(2‐pyridyl)‐1H‐benzimidazole‐κ2N2,N3]manganese(II) monohydrate

In the title compound, [Mn(C₅H₂N₂O₄)(C₁₂H₉N₃)₂]·H₂O, the Mn^II centre is surrounded by three bidentate chelating ligands, namely, one 6‐oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylate (or uracil‐5‐carboxylate, Huca²⁻) ligand [Mn—O = 2.136 (2) and 2.156 (3) Å] and two 2‐(2‐pyridyl)‐1H‐benzimidazole (Hpybim) ligands [Mn—N = 2.213 (3)–2.331 (3) Å], and it displays a severely distorted octahedral geometry, with cis angles ranging from 73.05 (10) to 105.77 (10)°. Intermolecular N—H...O hydrogen bonds both between the Hpybim and the Huca²⁻ ligands and between the Huca²⁻ ligands link the molecules into infinite chains. The lattice water molecule acts as a hydrogen‐bond donor to form double O...H—O—H...O hydrogen bonds with the Huca²⁻ O atoms, crosslinking the chains to afford an infinite two‐dimensional sheet; a third hydrogen bond (N—H...O) formed by the water molecule as a hydrogen‐bond acceptor and a Hpybim N atom further links these sheets to yield a three‐dimensional supramolecular framework. Possible partial π–π stacking interactions involving the Hpybim rings are also observed in the crystal structure.     

Enhancement of the Tetrel Bond by the Effects of Substituents,Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond

The T⋅⋅⋅N tetrel bond (TB) formed between TX₃OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH₃OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF₃OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T−O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl₂ to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.     

Low-Barrier Hydrogen Bonds in Negative Thermal Expansion Material H3[Co(CN)6]

The covalent nature of the low-barrier N−H−N hydrogen bonds in the negative thermal expansion material H₃[Co(CN)₆] has been established by using a combination of X-ray and neutron diffraction electron density analysis and theoretical calculations. This finding explains why negative thermal expansion can occur in a material not commonly considered to be built from rigid linkers. The pertinent hydrogen atom is located symmetrically between two nitrogen atoms in a double-well potential with hydrogen above the barrier for proton transfer, thus forming a low-barrier hydrogen bond. Hydrogen is covalently bonded to the two nitrogen atoms, which is the first experimentally confirmed covalent hydrogen bond in a network structure. Source function calculations established that the present N−H−N hydrogen bond follows the trends observed for negatively charge-assisted hydrogen bonds and low-barrier hydrogen bonds previously established for O−H−O hydrogen bonds. The bonding between the cobalt and cyanide ligands was found to be a typical donor–acceptor bond involving a high-field ligand and a transition metal in a low-spin configuration.     

A Series of Isolable Silanoic Thio‐, Seleno‐, and Telluroesters (LSi(X)OR) with Donor‐Supported SiX Double Bonds (L=β‐Diketiminate; X=S,Se, Te)

The first silicon analogues of carbonic (carboxylic) esters, the silanoic thio‐, seleno‐, and tellurosilylesters 3 (Si?S), 4 (Si?Se), and 5 (Si?Te), were prepared and isolated in crystalline form in high yield. These thermally robust compounds are easily accessible by direct reaction of the stable siloxysilylene L(Si:)OSi(H)L′ 2 (L=HC(CMe)₂[N(aryl)₂], L′=CH[(C?CH₂)‐CMe][N(aryl)]₂; aryl=2,6‐iPr₂C₆H₃) with the respective elemental chalcogen. The novel compounds were fully characterized by methods including multinuclear NMR spectroscopy and single‐crystal X‐ray diffraction analysis. Owing to intramolecular N→Si donor–acceptor support of the Si?X moieties (X=S, Se, Te), these compounds have a classical valence‐bond N⁺–Si–X^? resonance betaine structure. At the same time, they also display a relatively strong nonclassical Si?X π‐bonding interaction between the chalcogen lone‐pair electrons (n_π donor orbitals) and two antibonding Si? N orbitals (σ*_π acceptor orbitals mainly located at silicon), which was shown by IR and UV/Vis spectroscopy. Accordingly, the Si?X bonds in the chalcogenoesters are 7.4 ( 3 ), 6.7 ( 4 ), and 6.9 % ( 5 ) shorter than the corresponding Si? X single bonds and, thus, only a little longer than those in electronically less disturbed Si?X systems (“heavier” ketones).     

Aromaticity and Chemical Bonding of Chalcogen-Bonded Capsules Featuring Enhanced Magnetic Anisotropy

We present a theoretical study of chalcogen bonded container capsules ( A_X+A_X ) where X=O, S, Se, and Te, and their encapsulation complexes with n-C₉H₂₀ (n-C₉H₂₀@ A_X+A_X ). Both Se and Te encapsulation complexes have significant experimental and computed binding energies, analogous to the hydrogen bonded counterparts, while the S and O capsules and their encapsulation complexes show only weak binding energies, which are attributed to different types of bonding: chalcogen S⋅⋅⋅N bonds for S-capsules and π–π stacking and weak hydrogen bonds for the O case. All A_X+A_X and C₉H₂₀@ A_X+A_X present unusually high magnetic anisotropies in their interiors. The ¹H NMR spectra of the encapsulation complexes display the proton signals of the encapsulated n-nonane highly upfield shifted, in agreement with the available experimental data for the Se capsule. We found that different factors contribute to the observed magnetic anisotropy of the capsule's interior: for the Te capsule the most important factor is Te's large polarizability; for the O analogue the inductive effects produced by the electronegative nature of the O and N heteroatoms; and for the S and Se capsules, the polarizability of the heteroatoms combines with electric field effects.     

A Theoretical Study of Correlation between Hydrogen‐Bond Stability and J‐Coupling through a Hydrogen Bond

trans‐Hydrogen‐bond hyperfine splitting via magnetic interaction, which is observed as J‐coupling in NMR experiments, was theoretically studied. trans‐Hydrogen‐bond hyperfine splitting should be closely related to the orbital interaction between the lone‐pair orbital of the H‐bond acceptor and the antibond orbital of the H‐bond donor. A linear relationship was observed between magnetic interaction hyperfine splitting through a H‐bond and the H‐bond strength. The relationship was dependent on the type of the nucleus forming the H‐bond; linear correlation was observed in N H⋅⋅⋅O/N type or O H⋅⋅⋅N type H‐bonded complexes, but not in O H⋅⋅⋅O type H‐bonded complexes.     

Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor

In this article, we explored the noncovalent bonding interactions between O?C?S, S?C?S, F₂C?S, Cl₂C?S, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of C?S bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH₂. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

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.     

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D₂Ch⋅⋅⋅A⁻ (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO−LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A⁻ to D₂Ch.     

Coordination-Induced N−H Bond Splitting of Ammonia and Primary Amine of CuI−MOFs

We report a porous three-dimensional anionic tetrazolium based Cu^I−MOF 1 , which is capable of cleaving the N−H bond of ammonia and primary amine, as well as the O−H bond of H₂O along with spontaneous H₂ evolution. In the gas-solid phase reaction of 1 with ammonia and water vapor, Cu^I−MOF 1 was gradually oxidized to NH₂−Cu^II−MOF and OH−Cu^II−MOF, through single-crystal-to-single-crystal (SCSC) structural transformations, which was confirmed by XPS, PXRD and X-ray single-crystal diffraction. Density functional theory (DFT) demonstrated that Cu^I−MOF could lower N−H bond dissociation free energy of ammonia through coordination-induced bond weakening and promote H₂ evolution by the reduction potential of 1 . To our knowledge, this is the first example of MOFs that activate ammonia and amine in gas-solid manner.     

Microwave Detection of Wet Triacetone Triperoxide (TATP): Non-Covalent Forces and Water Dynamics

The water adducts of triacetone triperoxide (TATP) have been observed by using broadband rotational spectroscopy. This work opens a new way for the gas-phase detection of this improvised explosive. The observed clusters exhibit unusual water dynamics and rarely observed multicenter interactions. TATP-H₂O is formed from the D₃ symmetry conformer of TATP with water lying close to the C₃ axis. Water rotation around this axis with a very low barrier gives rise to the rotational spectrum of a symmetric top. The main interaction of the monohydrate is a four-center trifurcated donor O_w-H⋅⋅⋅O hydrogen bond, not observed previously in the gas phase, reinforced by a weak four-center trifurcated acceptor C−H⋅⋅⋅O_w interaction. Surprisingly, all structural signatures show the weakness of these interactions. The complex TATP-(H₂O)₂ is formed from the monohydrated TATP by the self-association of water.     

Correlated one‐electron wave functions

Using four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. By contrast with above the three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Gas-Phase Conformational Map of the Amino Acid Isovaline

Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and ¹⁴N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N−H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H−O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.     

Confinement inside a Crystalline Sponge Induces Pyrrole To Form N−H⋅⋅⋅π Bonded Tetramers

Based on the DFT-level-calculated molecular volume (V_mol) of pyrrole and its liquid density, pyrrole manifests the highest liquid density coefficient LD_c (defined as [V_mol×density ×0.6023]/FW) value of 0.7. Normal liquids have LD_c <0.63. This very high LD_c is due to the strong N−H⋅⋅⋅π interactions in solution, and hence pyrrole can be considered to be a pseudo-crystalline liquid. When trapped inside the confined space of a crystalline sponge, a reorientation of the N−H⋅⋅⋅π interaction is observed leading to specific cyclic N−H⋅⋅⋅π tetramers and N−H⋅⋅⋅π dimers, as verified by single-crystal X-ray crystallographic and computational methods. These tetramers are of the same size as four pyrrole molecules in the solid-state of pyrrole, yet the cyclic N−H⋅⋅⋅π intermolecular interactions are circularly oriented instead of being in the linear zigzag structure found in the X-ray structure of a solid pyrrole. The confinement thus acts as an external driving force for tetramer formation.