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.     

Molecular hydrogen occupancy in binary THF-H2 clathrate hydrates by high resolution neutron diffraction

We have determined the time-space average filling of hydrogen molecules in a binary tetrahydrofuran (THF)-d(8) + D(2) sII clathrate hydrate using high resolution neutron diffraction. The filling of hydrogen in the lattice of a THF-d(8) clathrate hydrate occurred upon pressurization. The hydrogen molecules were localized in the small dodecahedral cavities at 20 K, with nuclear density from the hydrogen approximately spherically distributed and centered in the small cavity. With a formation pressure of 70 MPa, molecular hydrogen was found to only singly occupy the sII small cavity. This result helps explain discrepancies about the hydrogen occupancy in the THF binary hydrate system.     

A TD‐DFT Study on the Effect of Intermolecular Hydrogen Bonding on the Photophysical Properties of N‐Methyl‐1,8‐naphthalimide

The effect of intermolecular hydrogen bonding on the photophysical properties of N‐methyl‐1,8‐naphthalimide ( 2 ) has been investigated by time‐dependent density functional theory (TD‐DFT) method. The UV and IR spectra of 2 monomer and its hydrogen‐bonded complexes formed with 2,2,2‐trifluoroethanol (TFE) 2 +TFE and 2 +2TFE have been calculated, which confirm the presence of intermolecular hydrogen bonding interactions between the carbonyl groups of the aromatic imide and the hydroxyl group of the polyfluorinated alcohol. The absorption and fluorescence intensities going from 2 monomer via hydrogen‐bonded complex 2 +TFE to 2 +2TFE were found to be gradually enhanced with the wavelength gradually red‐shifted. The enhancements of the fluorescence intensities from 2 monomer to hydrogen‐bonded complexes 2 +TFE and 2 +2TFE were attributed to the decrease of the intersystem crossing (ISC) efficiency from the first excited singlet state S₁ ¹(ππ*) to the second excited triplet state T₂ ³(nπ*), whose energy was increased relative to its ground state due to the intermolecular hydrogen bonding interactions.     

Excited‐State Hydrogen Bonding Strengthening and Weakening with Intramolecular Charge Transfer in Resorufin‐Water Complexes: A TD‐DFT Study

The geometric structures, infrared spectra and hydrogen bond binding energies of the various hydrogen‐bonded Res^?‐water complexes in states S0 and S1 have been calculated using the density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods, respectively. Based on the changes of the hydrogen bond lengths and binding energies as well as the spectral shifts of the vibrational mode of the hydroxyl groups, it is demonstrated that hydrogen bonds HB‐II, HB‐III and HB‐IV are strengthened while hydrogen bond HB‐I is weakened in the four singly hydrogen‐bonded Res^?‐Water complexes upon photoexcitation. When the four hydrogen bonds are formed simultaneously between one resorufin anion and four water molecules in the Res^?‐4Water complex, all the hydrogen bonds are weakened in both the ground and excited states compared with those in the corresponding singly hydrogen‐bonded Res^?‐Water complexes. Furthermore, in complex Res^?‐4Water, hydrogen bonds HB‐II and HB‐IV are strengthened while hydrogen bonds HB‐I and HB‐III are weakened after the electronic excitation. The hydrogen bond strengthening and weakening in the various hydrogen‐bonded Res^?‐water complexes should be due to the redistribution of the charges among the four heteroatoms (O_1‐3 and N₁) within the resorufin molecule upon the optical excitation.     

Tuning the Halogen/Hydrogen Bond Competition: A Spectroscopic and Conceptual DFT Study of Some Model Complexes Involving CHF2I

Insight into the key factors driving the competition of halogen and hydrogen bonds is obtained by studying the affinity of the Lewis bases trimethylamine (TMA), dimethyl ether (DME), and methyl fluoride (MF) towards difluoroiodomethane (CHF₂I). Analysis of the infrared and Raman spectra of solutions in liquid krypton containing mixtures of TMA and CHF₂I and of DME and CHF₂I reveals that for these Lewis bases hydrogen and halogen‐bonded complexes appear simultaneously. In contrast, only a hydrogen‐bonded complex is formed for the mixtures of CHF₂I and MF. The complexation enthalpies for the C?H ??? Y hydrogen‐bonded complexes with TMA, DME, and MF are determined to be ?14.7(2), ?10.5(5) and ?5.1(6) kJ mol^?1, respectively. The values for the C?I ??? Y halogen‐bonded isomers are ?19.0(3) kJ mol^?1 for TMA and ?9.9(8) kJ mol^?1 for DME. Generalization of the observed trends suggests that, at least for the bases studied here, softer Lewis bases such as TMA favor halogen bonding, whereas harder bases such as MF show a substantial preference for hydrogen bonding.     

Ab Initio MP2 and Density Functional Theory Computational Study of AcAlaNH2 Peptide Hydration: A Bottom‐Up Approach

AcAlaNH₂?n H₂O (n=1–13) complexes have been proposed as models to account for water solvent effects on the molecular properties of N‐acetyl‐L ‐alanine amide. Ab initio computations are planned to evaluate peptide–water interactions and to provide a means for approximating relative effects of the short‐range many‐body interactions arising in real solution without introducing any external parameters intended to quantify empirical or semiempirical potential‐energy functions. The present bottom‐up approach reveals the formation of compact ring clusters of water molecules strongly bonded to peptidic polar groups throughout hydrogen bonds. The explicit coordination of water molecules around the peptide renders the fully extended (FE) and polyproline II (PPII) conformers more stable with respect to the 3₁₀ helix or γ turn. The alternance of donor and acceptor groups on both sides of the FE and PPII conformers allows for synergy and extensive H‐bonding.     

Unusually Strong Dipole–Dipole and Dipole–Quadrupole Interactions in a Nanoporous Solid. Crystal Structure and Related Properties of (VO)3[M(CN)6]2·nH2O (M = Fe,Co)

In porous Prussian blue (PB) analogues, the partially naked central metal atoms found at the cavities surface are responsible for many of their physical properties, among them the adsorption potentials. In the as‐synthesized PB analogues, such metal sites stabilize water molecules inside the cavity through coordination bond formation. The filling of the cavity volume is completed with water molecules linked to the coordinated ones through hydrogen bonds formation. Vanadyl‐based PB analogue shows quite different features. The metal(V) at the cavities surface has saturated its coordination sphere with the O atom of the vanadyl ion (V=O). In this material, the V=O group preserves enough strong dipole moment to stabilize adsorbed species at the cavity through dipole–dipole and dipole–quadrupole interactions. This contribution reports the preparation, crystal structure and properties for (VO)₃[M(CN)₆]₂ · nH₂O (M = Fe, Co). According to the refined crystal structure, IR spectra and TG data, six water molecules remain stabilized inside the cavities through a strong dipole–dipole coupling with the vanadyl group. The cavity contains additional water molecules interacting through hydrogen bond bridges with the water molecules coupled to the V=O group. The vanadyl ion is free of hydrogen bonding interactions with the water molecules. The recorded adsorption isotherms for N₂, CO₂ and H₂, three molecules with only quadrupole moment, reveal presence of relative strong adsorption forces due to dipole‐quadrupole interactions.     

Complexation of peptides with crown ethers. Structure and thermal behaviour of ternary compounds: 18-crown-6/glycylglycine/water and 18-crown-6/L-α-alanyl-L-α-alanine/water

Abstract

X-ray structures of ternary complexes composed of small dipeptides, i.e. glycylglycine or L-α-alanyl-L-α-alanine, 18-crown-6 and water molecules are determined based on single-crystal studies. It has been concluded that both dipeptides exist in the complex as zwitterions and are bonded to the 18-crown-6 macrocycle by the -NH⁺ ₃ end group through N-H…O hydrogen bonds. The carboxylic groups at the opposite side of the peptide molecules take part in hydrogen bonding with water molecules. This scheme of water-peptide hydrogen bonding is particularly interesting in the glycylglycine compound where the water content is rather high (approximately 16 moles per mole of crown/dipeptide, 6 of which are found in the X-ray study) and may have interesting relevance with respect to the structure of gel solutions which easily form in these systems. The DSC and TGA thermograms of different hydrated forms of the complexes were obtained. Two types of water, i.e. weakly and strongly bonded, were observed upon heating of the hydrated complex. On further heating the anhydrous complexes have at least two transitions in the range 320–470 K: melting of complexes at 373–383 K and decomposition above 410 K.     

Computational study of structures and proton transfer in hydrogen‐bonded ammonia complexes using semiempirical valence‐bond approach

In this study, the seGVB method was implemented for the N H bonding system, specifically for hydrogen‐bonded ammonia complexes, and the model well reproduces the MP2 geometries and energetics. A comparison between the ammonia dimer and water dimer is given from the viewpoint of valance‐bond structures in terms of the calculated bond energies and pair–pair interactions. The linear hydrogen bond is found to be stronger than the bent bonds in both cases, with the difference in energy between the linear and cyclic structures being comparable in both cases although the NH bonds are generally weaker. The energy decomposition clearly demonstrates that the changes in electronic energy are quite different in the two cases due to the presence of an additional lone pair on the water molecule, and it is this effect which leads to the net stabilization of the cyclic structure for the ammonia dimer. Proton‐transfer profiles for hydrogen‐bonded ammonia complexes [NH₂ H NH₂]⁻ and [NH₃ H NH₃]⁺ were calculated. The barrier for proton transfer in [NH₃ H NH₃]⁺ is larger than that in [NH₂ H NH₂]⁻, but smaller than that in the protonated water dimer. The different bonding structures substantially affect the barrier to proton transfer, even though they are isoelectronic systems. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 357–367, 1999     

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

Different supramolecular assemblies in two 1:1 proton‐transfer compounds of sulfobenzoic acids with aromatic amines

Two 1:1 proton‐transfer complexes of sulfobenzoic acids with aromatic amines, namely 4‐[2‐(4‐pyridyl)ethenyl]pyridinium 2‐carboxybenzenesulfonate, C₁₂H₁₁N₂⁺·C₇H₅O₅S⁻, (I), and 1,10‐phenanthrolin‐1‐ium 4‐carboxybenzenesulfonate dihydrate, C₁₂H₉N₂⁺·C₇H₅O₅S⁻·2H₂O, (II), have very different hydrogen‐bonding patterns compared with reported organic sulfobenzoic acid complexes. In (I), two cations and two anions form a four‐molecule loop, in which π–π interactions occur. In (II), the anions and water molecules form a three‐dimensional hydrogen‐bonding network, while the cations only act as pendant components. The water molecules play a central role in the formation of the abundant hydrogen‐bonding architecture in (II). The relative poorness and richness of hydrogen bonds in (I) and (II), respectively, give rise to novel hydrogen‐bonding patterns.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Chirality‐Assisted Synthesis of a Very Large Octameric Hydrogen‐Bonded Capsule

The strategy of chirality‐assisted synthesis, which makes use of enantiomerically pure building blocks that are designed to associate in a single geometric orientation, was applied to synthesize an octameric hydrogen‐bonded capsule with a cavity volume of 2300 ų. This cube‐shaped capsule forms even host–guest complexes with tetraalkylammonium ions, and accommodates the large tetrahexadecylammonium cation in its cavity. The use of an enantiopure building block was shown to be highly beneficial for capsule formation, whereas its racemate also generates a large amount of ill‐defined aggregates in solution and crystallizes as a hydrogen‐bonded network.     

Proton‐Conducting Hydrogen‐Bonded 3D Frameworks of Imidazo‐Pyridine‐Based Coordination Complexes Containing Naphthalene Disulfonates in Rhomboid Channels

Coordination complexes of an olefinic molecule (PIP) containing pyridine and imidazopyridine moieties with Zn^II/Ni^II metal salts were shown to exhibit appreciable proton conductivity. These complexes form 3D‐hydrogen bonded frameworks containing rhomboidal channels that are occupied by uncoordinated 1,5‐naphthalenedisulfonate (NDS). The extensive hydrogen bonding between the frameworks and NDS resulted in thermally stable and water‐insoluble materials. Irrespective of the metal atom present, both complexes exhibited moderate to high proton conduction in the range of 10^?5 to 0.5×10^?3 S cm^?1 depending on the temperature and humidity levels.     

Molecular orbital theory of the hydrogen bond. 27. Substituent effects in water: 4-R-pyrimidine complexes

Ab initio SCF calculations with the STO -3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH₃, NH₂, OH, F, C₂H₃, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N₃, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N₃, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N₁, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N₃ a poorer site for hydrogen bonding than N₁, primarily because of a stronger π electron-withdrawing effect at N₃. However, the relative stabilities of complexes hydrogen bonded at N₁ and N₃ are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N₃. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

(Glycylglycinato‐κ3O,N,N′)(2‐methyl‐1H‐benzimidazole‐κN3)copper(II) trihydrate

In the title compound, [Cu(C₄H₆N₂O₃)(C₈H₈N₂)]·3H₂O, the Cu^II atom is coordinated in a square‐planar manner by one O atom and three N atoms from glycylglycinate and 2‐methyl­benzimidazole ligands. The ternary complexes assemble into one‐dimensional chains through C—H⋯π inter­actions and direct N—H⋯O hydrogen bonding, as well as into hydrogen‐bonded water helices with branches which also link the complex chains into a three‐dimensional supra­molecular structure.     

Desvenlafaxine succinate monohydrate

The title compound {systematic name: [2‐(1‐hydroxycyclohexyl)‐2‐(4‐hydroxyphenyl)ethyl]dimethylammonium 3‐carboxypropanoate monohydrate}, C₁₆H₂₆NO₂⁺·C₄H₅O₄⁻·H₂O, is a succinate salt of O‐desmethylvenlafaxine (desvenlafaxine). The present structure is one of four reported polymorphs of this salt, which is a new antidepressant drug. The carboxyl group of the succinate anion adopts a rare anti conformation and is engaged in a very short O—H...O⁻ hydrogen‐bond contact. Both cations and anions are involved separately in the formation of distinct O—H...O hydrogen‐bonded networks. Desvenlafaxine cations and water molecules self‐assemble to generate a honeycomb layer, while the succinate anions form a linear tape structure. These hydrogen‐bonded networks are interlinked via N—H...O and O—H...O hydrogen bonds. The hydrogen‐bonding network is so strong that desolvation and melting occur together at approximately 402 K. Thus, the crystal structure may be used to understand the thermal stability and solubility of the compound at the molecular level.     

Time‐dependent density functional theory study on the electronic excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in aqueous solution: 4AP and 4AP–(H2O)1,2 clusters

The time‐dependent density functional theory (TDDFT) method has been carried out to investigate the excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in hydrogen‐donating water solvent. The infrared spectra of the hydrogen‐bonded solute?solvent complexes in electronically excited state have been calculated using the TDDFT method. We have demonstrated that the intermolecular hydrogen bond C? O···H? O and N? H···O? H in the hydrogen‐bonded 4AP?(H₂O)₂ trimer are significantly strengthened in the electronically excited state by theoretically monitoring the changes of the bond lengths of hydrogen bonds and hydrogen‐bonding groups in different electronic states. The hydrogen bonds strengthening in the electronically excited state are confirmed because the calculated stretching vibrational modes of the hydrogen bonding C?O, amino N? H, and H? O groups are markedly red‐shifted upon photoexcitation. The calculated results are consistent with the mechanism of the hydrogen bond strengthening in the electronically excited state, while contrast with mechanism of hydrogen bond cleavage. Furthermore, we believe that the transient hydrogen bond strengthening behavior in electroniclly excited state of chromophores in hydrogen‐donating solvents exists in many other systems in solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Products of the oxidation of 1‐(diaminomethylene)thiourea with hydrogen peroxide

Two oxidation products of 1‐(diaminomethylene)thiourea (HATU) are reported, obtained from reactions with hydrogen peroxide at two different concentrations; these are 3,5‐diamino‐1,2,4‐thiadiazole, C₂H₄N₄S, (I), related to HATU by intramolecular N—S bond formation, and 1‐(diaminomethylene)uronium hydrogen sulfate, C₂H₇N₄O⁺·HSO₄⁻, (II). In (I), molecular hydrogen‐bonded chains could be distinguished, further organized in a herring‐bone‐like pattern. The structure of (II) is stabilized by an extensive network of N—H...O and O—H...O hydrogen bonds, where hydrogen‐bonded anion chains and characteristic cation–anion motifs are present. The compounds are of importance not only with respect to crystal engineering, but also in the design of new synthetic routes to HATU transition metal complexes.