The Cyclic Hydrogen‐Bonded 6‐Azaindole Trimer and its Prominent Excited‐State Triple‐Proton‐Transfer Reaction

The compound 6‐azaindole undergoes self‐assembly by formation of N(1)?H???N(6) hydrogen bonds (H bonds), forming a cyclic, triply H‐bonded trimer. The formation phenomenon is visualized by scanning tunneling microscopy. Remarkably, the H‐bonded trimer undergoes excited‐state triple proton transfer (ESTPT), resulting in a proton‐transfer tautomer emission maximized at 435 nm (325 nm of the normal emission) in cyclohexane. Computational approaches affirm the thermodynamically favorable H‐bonded trimer formation and the associated ESTPT reaction. Thus, nearly half a century after Michael Kasha discovered the double H‐bonded dimer of 7‐azaindole and its associated excited‐state double‐proton‐transfer reaction, the triply H‐bonded trimer formation of 6‐azaindole and its ESTPT reaction are demonstrated.     

On‐Surface Assembly of Hydrogen‐ and Halogen‐Bonded Supramolecular Graphyne‐Like Networks

Demonstrated here is a supramolecular approach to fabricate highly ordered monolayered hydrogen‐ and halogen‐bonded graphyne‐like two‐dimensional (2D) materials from triethynyltriazine derivatives on Au(111) and Ag(111). The 2D networks are stabilized by N???H?C(sp) bonds and N???Br?C(sp) bonds to the triazine core. The structural properties and the binding energies of the supramolecular graphynes have been investigated by scanning tunneling microscopy in combination with density‐functional theory calculations. It is revealed that the N???Br?C(sp) bonds lead to significantly stronger bonded networks compared to the hydrogen‐bonded networks. A systematic analysis of the binding energies of triethynyltriazine and triethynylbenzene derivatives further demonstrates that the X₃‐synthon, which is commonly observed for bromobenzene derivatives, is weaker than the X₆‐synthon for our bromotriethynyl derivatives.     

Microwave spectrum, structure, and internal dynamics of the nitric acid dihydrate complex

A-type rotational spectra of the complex HNO3-(H2O)2 have been observed by rotational spectroscopy in a supersonic jet. Extensive isotopic substitution and analysis of the resulting moments of inertia reveals that the complex adopts a cyclic geometry in which a second water inserts into the weak secondary hydrogen bond of the (also cyclic) HNO3-H2O dimer. The complex is planar, except for one free proton from each water unit that lies above or below the plane. The primary hydrogen bond, formed between the HNO3 proton and the first water molecule in the trimer, is 1.643(76) A in length. All intermolecular distances are smaller than those of the constituent dimers. Internal motion, inferred from spectral doubling and studied by isotopic substitution experiments, likely corresponds to proton interchange involving the second water unit, but no such motion is revealed by the a-type spectrum for the first water unit. The degree of proton transfer across the hydrogen bond is discussed in terms of the proton-transfer parameter, rhoPT, which assesses the degree of ionization on the basis of interatomic distances. Measured in this way, the complex is best described as hydrogen bonded, in accord with numerous theoretical predictions. However, an increase in the degree of ionization relative to that in HNO3-H2O is discernible. Using rhoPT as a metric, two water molecules do less to ionize nitric acid than one water does to ionize sulfuric acid.     

Directionality of Dihydrogen Bonds: The Role of Transition Metal Atoms

A theoretical study on two series of electron‐rich group 8 hydrides is carried out to evaluate involvement of the transition metal in dihydrogen bonding. To this end, the structural and electronic parameters are computed at the DFT/B3PW91 level for hydrogen‐bonded adducts of [(PP₃)MH₂] and [Cp*MH(dppe)] (M=Fe, Ru, Os; PP₃=κ⁴‐P(CH₂CH₂PPh₂)₃, dppe= κ²‐Ph₂PCH₂CH₂PPh₂) with CF₃CH₂OH (TFE) as proton donor. The results are compared with those of adduct [Cp₂NbH₃] ? TFE featuring a “pure” dihydrogen bond, and classical hydrogen bonds in pyridine ? TFE and Me₃N ? TFE. Deviation of the H ??? H? A fragment from linearity is shown to originate from the metal participation in dihydrogen bonding. The latter is confirmed by the electronic parameters obtained by NBO and AIM analysis. Considered together, orbital interaction energies and hydrogen bond ellipticity are salient indicators of this effect and allow the MH ??? HA interaction to be described as a bifurcate hydrogen bond. The impact of the M ??? HA interaction is shown to increase on descending the group, and this explains the experimental trends in mechanisms of proton‐transfer reactions via MH ??? HA intermediates. Strengthening of the M ??? H interaction in the case of electron‐rich 5d metal hydrides leads to direct proton transfer to the metal atom.     

Dynamics of the concerted triple proton transfer in cyclic water trimer using the multiconfiguration molecular mechanics algorithm

Cyclic water clusters are important molecular species to understand the nature of hydrogen bonded networks. Theoretical studies for the dynamics of triple proton transfer in the cyclic water trimer were performed. The potential energy surface (PES) of triple proton transfer is generated by the multiconfiguration molecular mechanics (MCMM) algorithm. We have used the MP2/6-31G(d,p) level for high-level ab initio data (energies, gradients, and Hessians), which are used in the Shepard interpolation. Eight high-level reference points were added step by step, including two points for the critical configurations of the large curvature tunneling paths. The more high-level points are used, the better the potential energy surfaces become. The rate constant and kinetic isotope effect (KIE) for the triple proton transfer at 300 K, which have been calculated by the canonical variational transition-state theory with microcanonical optimized multidimensional semiclassical tunneling approximation, are 1.6 x 10(-3) s(-1) and 230, respectively. Tunneling is very important not only for the triple proton transfer but also for the triple deuterium transfer. The MCMM results show good agreement with those from the direct ab initio dynamics calculations.     

Probing the CH⋅⋅⋅π Weak Hydrogen Bond in Anesthetic Binding: The Sevoflurane–Benzene Cluster

Cooperativity between weak hydrogen bonds can be revealed in molecular clusters isolated in the gas phase. Here we examine the structure, internal dynamics, and origin of the weak intermolecular forces between sevoflurane and a benzene molecule, using multi‐isotopic broadband rotational spectra. This heterodimer is held together by a primary C? H???π hydrogen bond, assisted by multiple weak C? H???F interactions. The multiple nonbonding forces hinder the internal rotation of benzene around the isopropyl C? H bond in sevoflurane, producing detectable quantum tunneling effects in the rotational spectrum.     

The Barrier to Proton Transfer in the Dimer of Formic Acid: A Pure Rotational Study

The rotational spectra of three C‐deuterated isotopologues of the dimer of formic acid have been measured, thanks to the small dipole moment induced by asymmetric H→D substitution(s). For the DCOOH–HCOOH species, the concerted double proton transfer of the two hydroxy hydrogen atoms takes place between two equivalent minima and generates a tunneling splitting of 331.2(6) MHz. This splitting can be reproduced by a 3D model with a barrier of 2559 cm^?1 (30.6 kJ mol^?1) as obtained from theoretical calculations.     

Using (FH)2 and (FH)3 to Bridge the σ‐Hole and the Lone Pair at P in Complexes with H2XP,for X=CH3, OH,H, CCH,F, Cl,NC, and CN

Ab initio MP2/aug′‐cc‐pVTZ calculations are used to investigate the binary complexes H₂XP:HF, the ternary complexes H₂XP:(FH)₂, and the quaternary complexes H₂XP:(FH)₃, for X=CH₃, OH, H, CCH, F, Cl, NC, and CN. Hydrogen‐bonded (HB) binary complexes are formed between all H₂XP molecules and FH, but only H₂FP, H₂ClP, and H₂(NC)P form pnicogen‐bonded (ZB) complexes with FH. Ternary complexes with (FH)₂ are stabilized by F?H???P and F?H???F hydrogen bonds and F???P pnicogen bonds, except for H₂(CH₃)P:(FH)₂ and H₃P:(FH)₂, which do not have pnicogen bonds. All quaternary complexes H₂XP:(FH)₃ are stabilized by both F?H???P and F?H???F hydrogen bonds and P???F pnicogen bonds. Thus, (FH)₂ with two exceptions, and (FH)₃ can bridge the σ‐hole and the lone pair at P in these complexes. The binding energies of H₂XP:(FH)₃ complexes are significantly greater than the binding energies of H₂XP:(FH)₂ complexes, and nonadditivities are synergistic in both series. Charge transfer occurs across all intermolecular bonds from the lone‐pair donor atom to an antibonding σ* orbital of the acceptor molecule, and stabilizes these complexes. Charge‐transfer energies across the pnicogen bond correlate with the intermolecular P?F distance, while charge‐transfer energies across F?H???P and F?H???F hydrogen bonds correlate with the distance between the lone‐pair donor atom and the hydrogen‐bonded H atom. In binary and quaternary complexes, charge transfer energies also correlate with the distance between the electron‐donor atom and the hydrogen‐bonded F atom. EOM‐CCSD spin‐spin coupling constants ^2hJ(F–P) across F?H???P hydrogen bonds, and ^1pJ(P–F) across pnicogen bonds in binary, ternary, and quaternary complexes exhibit strong correlations with the corresponding intermolecular distances. Hydrogen bonds are better transmitters of F–P coupling data than pnicogen bonds, despite the longer F???P distances in F?H???P hydrogen bonds compared to P???F pnicogen bonds. There is a correlation between the two bond coupling constants ^2hJ(F–F) in the quaternary complexes and the corresponding intermolecular distances, but not in the ternary complexes, a reflection of the distorted geometries of the bridging dimers in ternary complexes.     

Seeking Extremes in Molecular Design: To What Extent May Two “Non‐Bonded” Hydrogen Atoms be Squeezed in a Hydrocarbon?

A series of novel and possibly synthetically accessible rigid hydrocarbon structures is computationally introduced, maintaining ultrashort non‐bonded hydrogen–hydrogen (H???H) contacts smaller than 1.2 Å. These are the shortest non‐bonded H???H contacts reported to date, bypassing previous world records of both experimentally observed, 1.56 Å, and computationally derived, 1.4 Å, H???H contacts in any stable molecular structure.     

Supramolecular Cl⋅⋅⋅H and O⋅⋅⋅H Interactions in Self‐Assembled 1,5‐Dichloroanthraquinone Layers on Au(111)

The role of halogen bonds in self‐assembled networks for systems with Br and I ligands has recently been studied with scanning tunneling microscopy (STM), which provides physical insight at the atomic scale. Here, we study the supramolecular interactions of 1,5‐dichloroanthraquinone molecules on Au(111), including Cl ligands, by using STM. Two different molecular structures of chevron and square networks are observed, and their molecular models are proposed. Both molecular structures are stabilized by intermolecular Cl???H and O???H hydrogen bonds with marginal contributions from Cl‐related halogen bonds, as revealed by density functional theory calculations. Our study shows that, in contrast to Br‐ and I‐related halogen bonds, Cl‐related halogen bonds weakly contribute to the molecular structure due to a modest positive potential (σ hole) of the Cl ligands.     

Construction of halogen and hydrogen bond‐based multicomponent nanostructures at liquid‐solid interface

The cooperative effect of hydrogen and halogen bonds on the 2‐dimensional molecular arrangement of highly oriented pyrolytic graphite has been studied by scanning tunneling microscopy. The scanning tunneling microscopy observations demonstrate that the self‐assembled hydrogen‐bonded molecular chicken‐wire networks of trimesic acid have been significantly transformed after annealing and the introduction of tribromobenzene guest molecules. Bromine atoms and carboxyl groups were found to form 2 different multicomponent structures via hydrogen and halogen bonds. Owing to the effect of halogen and hydrogen bonds, tribromobenzene with trimesic acid formed the 3‐fold symmetry networks.     

The Double‐Faced Nature of Hydrogen Bonding in Hydroxy‐Functionalized Ionic Liquids Shown by Neutron Diffraction and Molecular Dynamics Simulations

We characterize the double‐faced nature of hydrogen bonding in hydroxy‐functionalized ionic liquids by means of neutron diffraction with isotopic substitution (NDIS), molecular dynamics (MD) simulations, and quantum chemical calculations. NDIS data are fit using the empirical potential structure refinement technique (EPSR) to elucidate the nearest neighbor H???O and O???O pair distribution functions for hydrogen bonds between ions of opposite charge and the same charge. Despite the presence of repulsive Coulomb forces, the cation–cation interaction is stronger than the cation–anion interaction. We compare the hydrogen‐bond geometries of both “doubly charged hydrogen bonds” with those reported for molecular liquids, such as water and alcohols. In combination, the NDIS measurements and MD simulations reveal the subtle balance between the two types of hydrogen bonds: The small transition enthalpy suggests that the elusive like‐charge attraction is almost competitive with conventional ion‐pair formation.     

Creation of Ternary Multicomponent Crystals by Exploitation of Charge‐Transfer Interactions

Four new ternary crystalline molecular complexes have been synthesised from a common 3,5‐dinitrobenzoic acid (3,5‐dnda) and 4,4′‐bipyridine (bipy) pairing with a series of amino‐substituted aromatic compounds (4‐aminobenzoic acid (4‐aba), 4‐(N,N‐dimethylamino)benzoic acid (4‐dmaba), 4‐aminosalicylic acid (4‐asa) and sulfanilamide (saa)). The ternary crystals were created through the application of complementary charge transfer and hydrogen‐bonding interactions. For these systems a dimer was created through a charge‐transfer interaction between two of the components, while hydrogen bonding between the third molecule and this dimer completed the construction of the ternary co‐crystal. All resulting structures display the same acid ??? pyridine interaction between 3,5‐dnba and bipy. However, changing the third component causes the proton of this bond to shift from neutral OH ??? N to a salt form, O^? ??? HN⁺, as the nature of the group hydrogen bonding to the carboxylic acid was changed. This highlights the role of the crystal environment on the level of proton transfer and the utility of ternary systems for the study of this process.     

Potential Proton‐Release Channels in Bacteriorhodopsin

The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton‐transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen‐bonded networks, which may include internal water molecules. The terminal step of the proton‐transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton‐release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen‐bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.     

Guest⊂Guest⊂Host Multicomponent Molecular Crystals: Entrapment of Guest⊂Guest in Honeycomb Networks Formed by Self‐Assembly of 1,3,5‐Tri(4‐hydroxyaryl)benzenes

Sterically‐engineered rigid trigonal molecular modules based on 1,3,5‐tri(4‐hydroxyphenyl)benzenes H1 and H2 undergo O‐H???O hydrogen‐bonded self‐assembly into eight‐fold catenated hexagonal (6,3) and two‐fold interpenetrated undulated square (4,4) networks, respectively. In the presence of [18]crown‐6 as a guest, the triphenol H1 is found to self‐assemble into a honeycomb network with hexagonal voids created between three triphenol building blocks. The guest [18]crown‐6 molecules are found to be nicely nested in hexagonal enclosures. The empty spaces within the crowns can be further filled with neutral (MeOH/water, MeOH/MeNO₂) or ionic guest species such as KI/KAcAc to furnish novel multicomponent assemblies, that is, guest ? guest ? host, that typify Russian dolls. In contrast, triphenol H2 is found to yield analogous multicomponent molecular crystals in which the guest crown–K⁺ acts as a spacers in the hydrogen‐bonded self‐assembly that leads to distorted chicken wire networks.     

Isolation and Structural Characterization of Eightfold Protonated Octacyanometalates [M(CNH)8]4+ (M=MoIV,WIV) from Superacids

Octacyanometalates K₄[Mo(CN)₈] and K₄[W(CN)₈] are completely protonated in superacidic mixtures of anhydrous hydrogen fluoride and antimony pentafluoride. The resulting hydrogen isocyanide complexes [Mo(CNH)₈]⁴⁺ [SbF₆]^?₄ and [W(CNH)₈]⁴⁺ [SbF₆]^?₄ are the first examples of eight‐coordinate homoleptic metal complexes containing hydrogen isocyanide (CNH) ligands. The complexes were crystallographically characterized, revealing hydrogen‐bonded networks with short N???H???F contacts. Low‐temperature NMR measurements in HF confirmed rapid proton exchange even at ?40 °C. Upon protonation, ν(C≡N) increases of about 50 cm^?1 which is in agreement with DFT calculations.     

The Host/Guest Type of Excited‐State Proton Transfer; a General Review

Contemporary progress regarding guest/host types of excited‐state double proton transfer has been reviewed, among which are the biprotonic transfer within doubly H‐bonded host/guest complexes, the transfer through a solvent bridge relay, the intramolecular double proton transfer and solvation dynamics coupled proton transfer. Of particular emphases are the photophysical and photochemical properties of excited‐state double proton transfer (ESDPT) in 7‐azaindole and its corresponding analogues. From the chemical aspect, two types of ESDPT reaction, namely the catalytic and non‐catalytic types of ESDPT, have been classified and reviewed separately. For the case of static host/guest hydrogen‐bonded complexes both hydrogen‐bonding strength and configuration (i.e. geometry) play key roles in accounting for the reaction dynamics. In addition to the dynamical concern, excited‐state thermodynamics are of importance to fine‐tune the proton transfer reaction in the non‐catalytic host/guest type of ESDPT. The mechanisms of protic solvent assisted ESDPT, depending on host molecules and proton‐transfer models, have been reviewed where the plausible resolution is deduced. Particular attention has been given to the excited‐state proton transfer dynamics in pure water, aiming at its future perspective in biological applications. Finally, the differentiation in mechanism between solvent diffusive reorganization and solvent relaxation to affect the host/guest ESPT dynamics is made and discussed in de tail.     

Protonation of Pyridyl‐Substituted TTF Derivatives: Substituent Effects in Solution and in the Proton–Electron Correlated Charge‐Transfer Complexes

Protonated pyridyl‐substituted tetrathiafulvalene electron‐donor molecules (PyH⁺‐TTF) showed significant changes in the electron‐donating ability and HOMO–LUMO energy gap compared to the neutral analogues and gave a unique N⁺?H???N hydrogen‐bonded (H‐bonded) dimer unit in the proton–electron correlated charge‐transfer (CT) complex crystals. We have evaluated these features from the viewpoint of the molecular structure of the PyH⁺‐TTF derivatives, that is, the substitution position of the Py group and/or the presence or absence of the ethylenedithio (EDT) group. Among 2‐PyH⁺‐TTF ( 1 o H⁺ ), 3‐PyH⁺‐TTF ( 1 m H⁺ ), 4‐PyH⁺‐TTF ( 1 p H⁺ ), and 4‐PyH⁺‐EDT‐TTF ( 2 p H⁺ ) systems, the para‐pyridyl‐substituted donors 1 p H⁺ and 2 p H⁺ exhibit more marked changes upon protonation in solution; a larger redshift in the intramolecular CT absorption band and a larger decrease in the electron‐donating ability. Furthermore, the EDT system 2 p H⁺ has the smallest intramolecular Coulombic repulsion energy. These differences are reasonably interpreted by considering the energy levels and distributions of the HOMO and LUMO obtained by quantum chemical calculations. Such substituent effects related to protonation were also examined by comparing the structure and properties of a new H‐bonded CT complex crystal based on 2 p H⁺ with those of its 1 p H⁺ analogue recently prepared by us: Both of them form a similar type of H‐bonded dimer unit, however, its charge distribution as well as the overall molecular arrangement, electronic structure, and conductivity were significantly modulated by the introduction of the EDT group. These results provide a new insight into the structural and electronic features of the PyH⁺‐TTF‐based proton–electron correlated molecular conductors.     

1H NMR studies of solvent effects on hydrogen bonding in some pyridine trifluoroacetates

The chemical shifts of hydrogen bonded protons in complexes of 11 substituted pyridines with trifluoroacetic acid were examined, in five dry solvents of different activity, with respect to proton transfer and aggregation effects. The results were correlated with ΔpK_a, the Kirkwood function and E _T parameters. The solvent effect on the intersection point obtained from the plot of the chemical shift of the hydrogen bonded protons against ΔpK_a can be used, similar to an isotopic effect, to differentiate strong hydrogen bonds. The aggregation of acid–base complexes can lead to downfield or upfield shifts; the variation of chemical shift with aggregation depends on the position of the proton in the hydrogen bridge.