C–H···Y (Y=N, O, π) Hydrogen Bond: A Unique Unconventional Hydrogen Bond

Halogen Bonding to the π-Systems of Polycyclic Aromatics

The propensity of the π-electron system lying above a polycyclic aromatic system to engage in a halogen bond is examined by DFT calculations. Prototype Lewis acid CF3I is placed above the planes of benzene, naphthalene, anthracene, phenanthrene, naphthacene, chrysene, triphenyl, pyrene, and coronene. The I atom positions itself some 3.3-3.4 Å above the polycyclic plane, and the associated interaction energy is about 4 kcal/mol. This quantity is a little smaller for benzene, but is roughly equal for the larger polycyclics. The energy only oscillates a little as the Lewis acid slides across the face of the polycyclic, preferring regions of higher π-electron density over minima of the electrostatic potential. The binding is dominated by dispersion which contributes half of the total interaction energy.

Symmetry of Pyridine Derivatives Controlled Two-Dimensional Nanostructural Diversity by Co-Assembly with Aromatic Carboxylic Acids

The self-assembly behaviors of aromatic carboxylic acids are commonly investigated at the liquid/solid interfaces because of their rigid skeletons and both hydrogen-bond donors and receptors. However, self-assemblies of aromatic carboxylic acids with low symmetry and interactions between carboxylic acid and pyridine derivatives are worth exploring. In this work, the self-assembled structural transitions of a kind of low-symmetric aromatic carboxylic acid (H4QDA) are regulated by the coadsorption of two pyridine derivatives (DPE and T4PT) with different symmetry, which are investigated by scanning tunneling microscopy under ambient conditions. For the H4QDA/DPE system, the grid structure appears. For the H4QDA/T4PT system, the coassembled morphologies display an obvious concentration dependence. With the increase of solution concentration of T4PT, three coassembled patterns (network structure, chiral linear structure, and brick-like structure) are observed. Corresponding structural models suggest that the O-H···N hydrogen bonds have great contributions to stabilizing these coassembled structures. Our studies will help to explore the complexity, diversity, and functionality of multiple component systems and are conducive to further understanding the underlying mechanisms in the assembly process.

Non-covalent interactions in the monohydrated complexes of 1,2,3,4-tetrahydroisoquinoline

The eleven monohydrates of 1, 2, 3, 4-tetrahydroisoquinoline (THIQ) are analyzed through natural bond orbital (NBO) analysis and QTAIM methods employing M06-2X functional in DFT and MP2 methods. Here, the role of OH bonds as an acceptor and donor is critically analyzed. The role of lone pairs of O is critically monitored in two of the complexes, where N-H···O hydrogen bonds are present. The relative contributions of rehybridisation and hyperconjugation are compared in detail. Popelier criteria are satisfied in all the complexes barring a few exceptions involving weak hydrogen bonds. At the bond critical points (BCP), four monohydrates show higher values of electron density (ρ_C) and negative values of total electron energy density (H_C), while Laplacian [Formula: see text] remains positive. These complexes satisfy the criteria of partial covalency. All these are O-H⋅⋅⋅N-type bonds. Remaining h-bonds are weaker in nature. These are also confirmed by the smaller values of ρ_C at the respective BCP. The variation of potential energy density (V_C) among the complexes seems to be the most important factor in determining the nature of non-covalent interactions.

Molecular dynamics study on the hydrogen bond formation between α-hydrogen atom of L-Phe and N5 atom of FAD in the enzyme-substrate complex of the L-Phe oxidase reaction

It is difficult to observe the structure of the enzyme-substrate complex (ES complex) experimentally, since the complex changes to the enzyme and its product during observation. The molecular dynamics (MD) approach is ideal to observe the structural change of enzyme and of substrate in the ES complex. Analyses on the complex of L-Phe oxidase with L-Phe by MD showed 1) the distance between the α-hydrogen atom of L-Phe and the N5 atom of isoalloxazine ring of FAD to be 2.64 ± 0.19 Å, and 2) the angle CA-HA-N5 atoms to be 141.5 ± 10.7°. This result clearly showed that the α-hydrogen atom forms the hydrogen bond with the N5 atom of isoalloxazine ring of FAD in the enzyme-substrate complex. Thus, the complex is ready for the hydrogen transfer from substrate to FAD in the key step of the oxidation of substrate by the enzyme.

The contribution of non-classical CHaxOC hydrogen bonds to the anomeric effect in fluoro and oxa-methoxycyclohexanes

In this theory study we demonstrate the dominance of non-classical 1,3-diaxial CH_axOC hydrogen bonds (NCHBs) dictating a 'pseudo' anomeric effect in selectively fluorinated methoxycyclohexanes and also influencing the axial preference in the classical anomeric exhibitor 2-methoxytetrahydropyran, a phenomenon which is most often described as a consequence of hyperconjugation. Analogues of methoxycyclohexane where ring CH₂'s are replaced by CF₂ can switch to an axial preference and theory methods (NBO, QTAIM, NCI) indicate the dominance of 1,3-CH_axOMe interactions over hyperconjugation. For 2-methoxytetrahydropyran, it is revealed that the global contribution to the anomeric effect is from electrostatic interactions including NCHBs, not hyperconjugation, although hyperconjugation (n_O→σ*_CO or n_O→σ*_CC) remains the main contributor to the exo-anomeric phenomenon. When two and three ether oxygens are introduced into the ring, then both the NCHB interactions and hyperconjugative contributions become weaker, not stronger as might have been anticipated, and the equatorial anomers progressively dominate.

Observation of an Unusually Large IR Red-Shift in an Unconventional S-H···S Hydrogen-Bond

The S-H···S non-covalent interaction is generally known as an extremely unconventional weak hydrogen-bond in the literature. The present gas-phase spectroscopic investigation shows that the S-H···S hydrogen-bond can be as strong as any conventional hydrogen-bond in terms of the IR red-shift in the stretching frequency of the hydrogen-bond donor group. Herein, the strength of the S-H···S hydrogen-bond has been determined by measuring the red-shift (∼150 cm^-1) of the S-H stretching frequency in a model complex of 2-chlorothiophenol and dimethyl sulfide using isolated gas-phase IR spectroscopy coupled with quantum chemistry calculations. The observation of an unusually large IR red-shift in the S-H···S hydrogen-bond is explained in terms of the presence of a significant amount of charge-transfer interactions in addition to the usual electrostatic interactions. The existence of ∼750 S-H···S interactions between the cysteine and methionine residues in 642 protein structures determined from an extensive Protein Data Bank analysis also indicates that this interaction is important for the structures of proteins.

C-HS interaction exhibits all the characteristics of conventional hydrogen bonds

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant. Sulfur (S), being less electronegative (2.58) compared to its first row analogue oxygen (3.44), has not been considered as a potential HB acceptor for a long time. The C-HY (Y = HB acceptor) interaction has its own history of exhibiting omnidirectional shifts in the CH stretching frequency upon complex formation. Therefore, a systematic investigation of the C-HS interaction was the primary goal of the work presented here. Together with gas-phase vibrational spectroscopy and ab initio quantum chemical calculations, the nature and strength of the C-HS hydrogen bond (HB) have been investigated in the complexes of 1,2,4,5-tetracyanobenzene (TCNB) with various sulfur containing solvents. Despite the unconventional nature of both HB donor and HB acceptor (C-H and S, respectively), it was found that the C-HS hydrogen bond exhibits all the characteristics of the conventional hydrogen bond. The binding strength of the C-HS H-bond in these complexes was found to be comparable to that of the conventional hydrogen bonds. The unusual stabilities of these HBs have been mainly attributed to the attractive dispersion interaction.