Effect of Guest–Host Hydrogen Bonding on the Structures and Properties of Clathrate Hydrates

To provide improved understanding of guest–host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single‐crystal X‐ray crystallography has been used to detect guest–host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert‐butylamine (tBA) sII clathrate with H₂S/Xe help gases and the pinacolone + H₂S binary sH clathrate. X‐ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 Å from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 Å from the closest water oxygen atom. These distances are compatible with guest–water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X‐ray crystallographic observations. The tBA guest shows long‐lived guest–host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest–host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100–250 K. Guest–host hydrogen bonding leads to the formation of Bjerrum L‐defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen‐bonded guest–host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.     

Distribution of Butane in the Host Water Cage of Structure II Clathrate Hydrates

To understand host–guest interactions of hydrocarbon clathrate hydrates, we investigated the crystal structure of simple and binary clathrate hydrates including butane (n‐C₄H₁₀ or iso‐C₄H₁₀) as the guest. Powder X‐ray diffraction (PXRD) analysis using the information on the conformation of C₄H₁₀ molecules obtained by molecular dynamics (MD) simulations was performed. It was shown that the guest n‐C₄H₁₀ molecule tends to change to the gauche conformation within host water cages. Any distortion of the large 5¹²6⁴ cage and empty 5¹² cage for the simple iso‐C₄H₁₀ hydrate was not detected, and it was revealed that dynamic disorder of iso‐C₄H₁₀ and gauche‐nC₄H₁₀ were spherically extended within the large 5¹²6⁴ cages. It was indicated that structural isomers of hydrocarbon molecules with different van der Waals diameters are enclathrated within water cages in the same way owing to conformational change and dynamic disorder of the molecules. Furthermore, these results show that the method reported herein is applicable to structure analysis of other host–guest materials including guest molecules that could change molecular conformations.     

Physicochemical Properties of Ionic Clathrate Hydrates

Ionic clathrate hydrates are known to be formed by the enclathration of hydrophobic cations or anions into confined cages and the incorporation of counterions into the water framework. As the ionic clathrate hydrates are considered for their potential applicability in various fields, including those that involve solid electrolytes, gas separation, and gas storage, numerous studies of the ionic clathrate hydrates have been reported. This review concentrates on the physicochemical properties of the ionic clathrate hydrates and the notable characteristics of these materials regarding their potential application are addressed.     

Probing the Hydrogen Bonding Structure in the Rieske Protein

The use of the far‐infrared spectral range presents a novel approach for analysis of the hydrogen bonding in proteins. Here it is presented for the analysis of Fe? S vibrations (500–200 cm^?1) and of the intra‐ and intermolecular hydrogen bonding signature (300–50 cm^?1) in the Rieske protein from Thermus thermophilus as a function of temperature and pH. Three pH values were adequately chosen in order to study all the possible protonation states of the coordinating histidines. The Fe? S vibrations showed pH‐dependent shifts in the FIR spectra in line with the change of protonation state of the histidines coordinating the [2Fe? 2S] cluster. Measurements of the low‐frequency signals between 300 and 30 K demonstrated the presence of a distinct overall hydrogen bonding network and a more rigid structure for a pH higher than 10. To further support the analysis, the redox‐dependent shifts of the secondary structure were investigated by means of an electrochemically induced FTIR difference spectroscopic approach in the mid infrared. The results confirmed a clear pH dependency and an influence of the immediate environment of the cluster on the secondary structure. The results support the hypothesis that structure‐mediated changes in the environment of iron? sulfur centers play a critical role in regulating enzymatic catalysis. The data point towards the role of the overall internal hydrogen bonding organization for the geometry and the electronic properties of the cluster.     

Phenylacetylene: A Hydrogen Bonding Chameleon

Molecules with multiple hydrogen bonding sites offer the opportunity to investigate competitive hydrogen bonding. Such an investigation can become quite interesting, particularly when the molecule of interest has neither lone‐pair electrons nor strongly acidic/basic groups. Phenylacetylene is one such molecule with three hydrogen bonding sites that cannot be ranked into any known hierarchical pattern. Herein we review the structures of several binary complexes of phenylacetylene investigated using infrared optical double‐resonance spectroscopy in combination with high‐level ab initio methods. The diversity of intermolecular structures formed by phenylacetylene with various reagents is remarkable. The nature of intermolecular interaction with various reagents is the result of a subtle balance between various configurations and competition between the electrostatic and dispersion energy terms, while trying to maximize the total interaction strength.     

Hydrogen in Porous Tetrahydrofuran Clathrate Hydrate

The lack of practical methods for hydrogen storage is still a major bottleneck in the realization of an energy economy based on hydrogen as energy carrier. ¹ Storage within solid‐state clathrate hydrates, ² – ⁴ and in the clathrate hydrate of tetrahydrofuran (THF), has been recently reported. ⁵ , ⁶ In the latter case, stabilization by THF is claimed to reduce the operation pressure by several orders of magnitude close to room temperature. Here, we apply in situ neutron diffraction to show that—in contrast to previous reports^{[5, 6]}—hydrogen (deuterium) occupies the small cages of the clathrate hydrate only to 30 % (at 274 K and 90.5 bar). Such a D₂ load is equivalent to 0.27 wt. % of stored H₂. In addition, we show that a surplus of D₂O results in the formation of additional D₂O ice Ih instead of in the production of sub‐stoichiometric clathrate that is stabilized by loaded hydrogen (as was reported in ref. ⁶ ). Structure‐refinement studies show that [D₈]THF is dynamically disordered, while it fills each of the large cages of [D₈]THF?17D₂O stoichiometrically. Our results show that the clathrate hydrate takes up hydrogen rapidly at pressures between 60 and 90 bar (at about 270 K). At temperatures above ≈220 K, the H‐storage characteristics of the clathrate hydrate have similarities with those of surface‐adsorption materials, such as nanoporous zeolites and metal–organic frameworks, ⁷ , ⁸ but at lower temperatures, the adsorption rates slow down because of reduced D₂ diffusion between the small cages.     

Tuning the Composition of Guest Molecules in Clathrate Hydrates: NMR Identification and Its Significance to Gas Storage

Gas hydrates represent an attractive way of storing large quantities of gas such as methane and carbon dioxide, although to date there has been little effort to optimize the storage capacity and to understand the trade‐offs between storage conditions and storage capacity. In this work, we present estimates for gas storage based on the ideal structures, and show how these must be modified given the little data available on hydrate composition. We then examine the hypothesis based on solid‐solution theory for clathrate hydrates as to how storage capacity may be improved for structure II hydrates, and test the hypothesis for a structure II hydrate of THF and methane, paying special attention to the synthetic approach used. Phase equilibrium data are used to map the region of stability of the double hydrate in P–T space as a function of the concentration of THF. In situ high‐pressure NMR experiments were used to measure the kinetics of reaction between frozen THF solutions and methane gas, and ¹³C MAS NMR experiments were used to measure the distribution of the guests over the cage sites. As known from previous work, at high concentrations of THF, methane only occupies the small cages in structure II hydrate, and in accordance with the hypothesis posed, we confirm that methane can be introduced into the large cage of structure II hydrate by lowering the concentration of THF to below 1.0 mol %. We note that in some preparations the cage occupancies appear to fluctuate with time and are not necessarily homogeneous over the sample. Although the tuning mechanism is generally valid, the composition and homogeneity of the product vary with the details of the synthetic procedure. The best results, those obtained from the gas–liquid reaction, are in good agreement with thermodynamic predictions; those obtained for the gas–solid reaction do not agree nearly as well.     

氢键识别超分子聚合物的新进展

近年来,由于氢键作用对聚合物的热力学性质、微观自组装、结晶及液晶行为的重要影响,氢键识别在超分子聚合物的分子设计与结构控制方面的应用受到广泛关注。本文系统介绍了氢键识别体系的类型与性质,以及分子结构、分子内氢键对氢键识别强度的影响,讨论了羧酸与吡啶间氢键识别体系、与核苷相关的氢键识别体系以及四重氢键识别体系在超分子聚合物中的最新应用,主要介绍了氢键识别超分子聚合物的合成、结构、性质及功能。     

Intramolecular N−H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4-Anilino-5-Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects

The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (d_H,F∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (^1hJ_NH,F) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.     

An Enantiopure Hydrogen‐Bonded Octameric Tube: Self‐Sorting and Guest‐Induced Rearrangement

The assembly of a discrete hydrogen‐bonded molecular tube from eight small identical monomers is reported. Tube assembly was accomplished by means of selective heterodimerization between isocytosine and ureidopyrimidinone hydrogen‐bonding motifs embedded in an enantiopure bicyclic building block, leading to the selective formation of an octameric supramolecular tube. Upon introduction of a fullerene guest molecule, the octameric tube rearranges into a tetrameric inclusion complex and the hydrogen‐bonding mode is switched. The dynamic behavior of the system is further explored in solvent‐ and guest‐responsive self‐sorting experiments.     

From Single Hydrogen Bonds to Extended Hydrogen‐Bond Wires: Low‐Dimensional Model Systems for Vibrational Spectroscopy of Associated Liquids

It is fair to say that if we ever wish to understand the anomalous properties of water, we need to study hydrogen bonds. Such a statement is based on statistical mechanics, which tells us how to calculate the structure and the thermodynamic properties of fluids and dense liquids from the forces between the particles. However, in the case of complex associated liquids, such calculations present a formidable—if not even insurmountable—challenge, which largely reflects our still‐limited understanding of the hydrogen‐bonding phenomenon itself. More experimental research on hydrogen‐bonded systems is required to develop a comprehensive, satisfactory theory for associated liquids. This Review gives an introduction to the latest experimental technique currently being used to study the ultrafast structural dynamics of hydrogen bonds, namely two‐dimensional infrared spectroscopy, and its applications to hydrogen‐bonded systems of systematically increasing complexity, starting from the single hydrogen bond of a diol to low‐dimensional extended networks of stereoselectively synthesized polyalcohols.     

Hydrogen Bonding in Phosphine Oxide/Phosphate–Phenol Complexes

To develop a new solvent‐impregnated resin (SIR) system for the removal of phenols and thiophenols from water, complex formation by hydrogen bonding of phosphine oxides and phosphates is studied using isothermal titration calorimetry (ITC) and quantum chemical modeling. Six different computational methods are used: B3LYP, M06‐2X, MP2, spin component‐scaled (SCS) MP2 [all four with 6‐311+G(d,p) basis set], a complete basis set extrapolation at the MP2 level (MP2/CBS), and the composite CBS‐Q model. This reveals a range of binding enthalpies (ΔH) for phenol–phosphine oxide and phenol–phosphate complexes and their thio analogues. Both structural (bond lengths/angles) and electronic elements (charges, bond orders) are studied. Furthermore, solvent effects are investigated theoretically by the PCM solvent model and experimentally via ITC. From our calculations, a trialkylphosphine oxide is found to be the most promising extractant for phenol in SIRs, yielding ΔH=?14.5 and ?9.8 kcal mol^?1 with phenol and thiophenol, respectively (MP2/CBS), without dimer formation that would hamper the phenol complexation. In ITC measurements, the ΔH of this complex was most negative in the noncoordinating solvent cyclohexane, and slightly less so in π–π interacting solvents such as benzene. The strongest binding is found for the dimethyl phosphate–phenol complex [?15.1 kcal mol^?1 (MP2/CBS)], due to the formation of two H‐bonds (P?O???H‐O‐ and P‐O‐H???O‐H); however, dimer formation of these phosphates competes with complexation of phenol, and would thus hamper their use in industrial extractions. CBS‐Q calculations display erroneous trends for sulfur compounds, and are found to be unsuitable. Computationally relatively cheap SCS‐MP2 and M06‐2X calculations did accurately agree with the much more elaborate MP2/CBS method, with an average deviation of less than 1 kcal mol^?1.     

Bare Histidine–Serine Models: Implication and Impact of Hydrogen Bonding on Nucleophilicity

A new family of 2‐hydroxyalk(en/yn)ylimidazoles has been evaluated as serine–histidine bare dyad models for the ring‐opening reaction of L ‐lacOCA, a cyclic O‐carboxyanhydride. These models were selected to unravel the implication of intramolecular hydrogen bonding and to substantiate its influence on the nucleophilicity of the alcohol moiety, as it is suspected to occur in enzyme active sites. Although designed to exclusively facilitate the preliminary step of proton transfer during the studied ring‐opening reaction, these minimalistic models depicted a measureable increase in reactivity relative to the isolated fragments. A couple of reliable experimental and theoretical methods have been developed to readily monitor the strength of the intramolecular hydrogen bond in dilute solution. Results show that the folded conformers are the most nucleophilic species because of the intramolecular hydrogen bond.