Sequential Orientation of Cycles in Gas Hydrate Frameworks

The role of sequentially oriented cycles of hydrogen-bonded molecules in gas hydrate frameworks is analyzed in the framework of the topological model of strong and weak H-bonds. A close correlation is found between the number of strong H-bonds corresponding to trans-conformations, which are more stable, and the number of sequentially oriented cycles. The boundary values of the fractions of such cycles in gas hydrate frameworks are estimated. It is concluded that the high percent of such cycles is an important structural indicator of low-energy configurations, useful in physical analyses of gas hydrates.     

Nanostructural Approach to Proton Ordering in Gas Hydrate Cages

A nanostructural approach to analysis of proton ordering in gas hydrate cages has been worked out within the framework of the topological model of strong and weak H-bonds. The approach involves rejection of the periodic boundary conditions, decomposition of the H-bond net into spherical layers, and two-dimensional drawing of the structure of spherical (spheroidal) fragments in the form of conjugate Schlegel diagrams. To analyze proton ordering in the spherical fragments composed of gas hydrate voids, we used the simulated annealing procedure and the correlation extension method proposed earlier.     

Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength

Matsuda and coworkers demonstrated that imidazopyridopyrimidine nucelobases (N ^N , O ^O , N ^O , tO ^O , and O ^N ) can mimic Watson–Crick nucleobase in forming H-bonds in DNA double helix. In the present study, we address the question about the strengths of the H-bonds in imidazopyridopyrimidine base pairs compared to those in Watson–Crick ones by focusing particularly on the nature of these interactions. Optimized structures of imidazopyridopyrimidine, imidazopyridopyrimidine–Watson–Crick, and Watson–Crick base pairs are obtained at the DFTB3LYP/6-311++G (d,p). The nature and strength of the intramolecular H-bonds in these base pairs have been investigated based on natural bond orbital (NBO method) to consider the effect of charge transfer, “atoms-in-molecules” (AIM) topological parameters, and decomposition of the interaction energies using the energy decomposition analysis (EDA). These investigations imply that N ^N –O ^O and N ^O –O ^N can form base pairs with four H-bonds (most stable than those of Watson–Crick base pairs) when they incorporated into DNA double helix. Furthermore, it can be deduced that O ^N and N ^N nucleobases form energetically more favorable pairs with adenine and guanine than the normal Watson–Crick counter parts. These results can be helpful for the stabilization and regulation of a variety of new base-pairing motif of DNA structures.     

The effective dipole moments of isobutyric acid in the liquid state and dilute solutions in methanol

The dipole moments of isobutyric acid (I) were determined in the liquid state (μ₁) and dilute solutions in methanol (μ₁) at 20–50°C. The permittivity of I in the liquid state was found to increase as the temperature grew, and the permittivity of solutions of I was lower than that of pure methanol; it decreased as the concentration of I and the temperature of solutions increased. The effective dipole moments of I were calculated using the Onsager polarization theory for the pure liquid and the Buckingham statistical polarization theory for solutions with various acid concentrations in methanol. The small μ₁ (～0.8 D) and higher μ₂ (～3.0 D) values compared with the dipole moment of I in the gas phase μ₀ (1.9 D) were analyzed as determined by the character of acid-acid, acid-solvent, and solvent-solvent intermolecular interactions, a key role in which was played by H-bonds. An analysis of the dipole moments of I in methanolic solutions led us to conclude that the μ₁ and μ₂ values corresponded to the dipole moments of associates and solvates comprising like and unlike molecules linked by intermolecular H-bonds. Their stoichiometry changed as the temperature increased.     

Atlas of Optimal Proton Configurations of Water Clusters in the Form of Gas Hydrate Cavities

All nonisomorphic proton configurations of water clusters in the form of gas hydrate cavities that are most stable in the number of strong hydrogen bonds corresponding to trans conformations have been found. The symmetry of these configurations is analyzed with allowance for the antisymmetry peration changing the directions of all Hbonds. The proton configurations of a cluster shaped like a pentagonal dodecahedron are considered in more detail.     

Molecular-dynamic study of liquid ethylenediamine

Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293–363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.     

Supramolecular structures containing ‘isolated’ pentaborate anions and non-metal cations: Crystal structures of [Me3NCH2CH2OH][B5O6(OH)4] and [4-MepyH, 4-Mepy][B5O6(OH)4]

The solid-state structures of two non-metal pentaborates [Me₃NCH₂CH₂OH][B₅O₆(OH)₄] (1) and [4-MepyH, 4-Mepy][B₅O₆(OH)₄] (2) have been determined by single-crystal X-ray diffraction methods. Structures 1 and 2 both contain supramolecular pentaborate frameworks held together by extensive H-bond interactions. The framework of 1 exists essentially as planes of pentaborate anions linked via three pairwise ‘planar’ β → α interactions, with a fourth β → β interaction crosslinking the planes. The framework of 2 is very similar except that one of the three pairwise linkages within the plane is replaced by pairwise ‘step-like’ bifurcated H-bonds to both α sites of a neighboring anion. The cations in 1 and the cations and neutral 4-Mepy ligands in 2 are present in the framework cavities and channels, with additional H-bond interactions existing between cations and anions.     

Tryst with a molecular and supramolecular oddity: an anti-Fürst-Plattner epoxide opening product as a designer additive for accessing an elusive polymorph

Additive induced polymorphism of a conformationally locked tetraacetate 3 in presence of its diastereomer 4 is described. The ester 3 was specially crafted on a trans-decalin backbone to relegate the O-H?O H-bond donors to the molecular interior and have the peripheral H-bond acceptors in 1,3-syndiaxial relationship. The supramolecular assembly of 3 was destined to evolve along two mutually exclusive pathways, namely one, which employs intermolecular O-H?O H-bonds (pathway 1) and the other that sacrifices these for intramolecular O-H?O H-bonds and settles for a crystal packing dictated by weak intermolecular interactions alone (pathway 2). Exploiting the similarity between the self-assemblies of 4 and the two recently reported dimorphs of 3, the ester 3 has been stimulated to follow the elusive non-hierarchical pathway 2 through preferential inhibition of pathway 1. Interestingly, the inhibitor 4 was obtained serendipitously en route3 via an apparent breakdown of Fürst-Plattner rule.     

Gas Hydrate Frameworks of Allen's Polyhedra. 2. Frameworks on 3–6 and 3–5–6 Nets

The structure of two classes of water molecule frameworks built up of 5¹²(D), 5¹²6²(T), 5¹²6³(P), and 5¹²6⁴(H) polyhedra is discussed. Polyhedral layers can be distinguished in the frameworks. The centers of the polyhedra belonging to a layer are at the nodes of planar networks consisting of triangular, pentagonal, and hexagonal meshes. The structure of one network determines exclusively the topology of the entire framework. Frameworks on 3–6 nets can be constructed of two types of polyhedral blocks: D₃T₂P₂and D₂T₆. Frameworks on 3–5–6 nets might include both specific blocks and the blocks involved in the frameworks on 3–5 and 3–6 nets. The paper analyzes the structure of frameworks on the nets built as a series of rows, each of these rows being constructed of pentagons or hexagons exclusively. These frameworks are described by the formula (D₃T₂P₂) _x (D₄H₂) _y (D₂T₆) _z , where x 1, y 0, and z 0 (x, y, and z are integers). Since all known frameworks of Allen's polyhedra satisfy this formula, they can be constructed of fragments of gas hydrate lattices with the CS1, CS2, and HS1 structures because they are derivatives of these key structures. Similar frameworks can be constructed of other tetrahedral particles (C, Si, SiO₂, etc.).     

Synthesis,characterization and magnetic properties of cobalt(II) and manganese(II) metal–organic frameworks assembled from 4,6-bis(imidazol-1-yl)isophthalic acid ligands

Two metal–organic frameworks of 4,6-bis(imidazol-1-yl)isophthalic acid (H₂biip), of general formula, {[M₂(biip)₂(H₂O)]·EtOH₂}_n (M?=?Co (1), Mn (2)), have been synthesized under solvothermal conditions. Complexes 1 and 2 are isomorphic and exhibit three-dimensional metal–organic frameworks with a 2-nodal (4,8)-connected topological network, Point Symbol {4¹⁶.6¹²}{4⁴.6²}₂. The magnetic properties of the complexes were examined, indicating antiferromagnetic interactions between the metal centers in the temperature range from 2 to 300 K.     

Recovering methane from quartz sand-bearing hydrate with gaseous CO_2

The replacement method by CO_2 is regarded as a new approach to natural gas hydrate(NGH) exploitation method, by which methane production and carbon dioxide sequestration might be obtained simultaneously. In this study, CO_2 was used to recover CH_4 from hydrate reservoirs at different temperatures and pressures. During the CO_2–CH_4 recovery process, the pressure was selected from 2.1 to 3.4 MPa, and the temperature ranged from 274.2 to 281.2 K. Calculating the fugacity differences between the gas phase and the hydrate phase for CO_2 and CH_4 at different conditions, it has found rising pressure was positive for hydrates formation process that was helpful for the improvement of CH_4 recovery rate. Rising temperature promoted the trend of CH_4 hydrate decomposition for the whole process of CO_2–CH_4replacement.The highest recovery rate was 46.6 % at 3.4 MPa 281.2 K for CO_2–CH_4replacement reaction in this work.     

Tautomerism, structure and properties of 1,1′,1″-(2,4,6-trihydroxybenzene-1,3,5-triyl)triethanone

According to computational predictions 1,1′,1″-(2,4,6-trihydroxybenzene-1,3,5-triyl)triethanone (triacetylphloroglucinol) (TTT, form a) can exist in five tautomeric forms, among which 2,4,6-tris(1-hydroxyethylidene)-1,3,5-cyclohexanetrione (form e) exhibits thermodynamic stability comparable to that of form a. X-ray investigations reveal that the compound exists in form a in the crystalline solid phase. Analysis of the arrangement of atoms involved in the three intramolecular H-bonds, responsible for the stabilization of tautomer a by 55.4 kcal/mol, suggests that there could be fast H atom (proton) transfer within the hydrogen bonds, bringing about the transformation of a into e and vice versa. Such an effect could explain the unique behaviour and spectral properties of TTT in solutions.     

Clathrate Hydrates of Sulfur Hexafluoride at High Pressures

The pressure dependence (0.4 Mpa–1.3 GPa) of the hydrate decomposition temperatures in the sulfur hexafluoride-water system has been studied. In addition to the known low-pressure hydrate SF₆17H₂O of Cubic Structure II, two new high-pressure hydrates have been found. X-ray analysis in situ showed the gas hydrate forming in the sulfur hexafluoride-water system above 50 MPa at room temperature to be of Cubic Structure I. The ability of water to form hydrates whose structures depend on the guest molecule size under normal conditions and at high pressures is discussed.     

Gas Hydrate Frameworks of Allen's Polyhedra. 3. Chemical and Structural Implications of the Topological Properties of the Frameworks

The topology of frameworks of 5¹²(D), 5¹²6² (T) 5¹²6³ (P), and 5¹²6⁴ (H) polyhedra, belonging to the most widespread class of gas hydrate frameworks, is discussed. The frameworks of formula (D₃T₂P₂)_x (D₄H₂)_y (D₂T₆)_z, where x, y, and z are integers, have low strain energies of hydrogen bonds. For these frameworks, formulas relating their topological characteristics (the number of water molecules and hydrogen bonds in the unit cell, etc.) to x, y, and z are given. The tendencies of variation of hydration numbers in clathrate and semiclathrate hydrates are considered. Compounds with new structures of water frameworks are predicted, and approaches to selection of possible chemical systems with such compounds are discussed. The structural regularities found for the frameworks and the relationships between their topological characteristics may be used for analyzing Frank–Kasper structures of intermetallic compounds that are dualists of the polyhedral frameworks under study.     

Functionalized proline with double hydrogen bonding potential: highly enantioselective Michael addition of carbonyl compounds to β-nitrostyrenes in brine

Simple synthetic manipulation of S-proline allows access to prolinamides 5-7 as organocatalysts capable of double hydrogen bonding for enantioselective Michael addition reactions of carbonyl compounds to β-nitrostyrenes. It is shown that prolinamide catalyst 7 leads to addition products with a high diastereo- as well as enantioselectivity. The transition state structure involving the binding of electrophilic nitrostyrene via two H-bonds is believed to be further stabilized by π,π stacking interactions mediated by the tosyl ring.     

Pore-water anomalies in gas hydrate-bearing sediments of the deeper continental margins: Facts and problems

Naturally occurring gas hydrates, discovered under the deeper parts of the continental margins (generally below 500 m water depth) during the Deep Sea Drilling Project and the Ocean Drilling Program, impregnate terrigenous sediments 0.5 to 1 km thick. They form from biogenic as well as thermogenic hydrocarbon gases and are associated with characteristic chemical and isotopic anomalies in the pore waters resulting from hydrate decomposition. Typical downward trends derived from water samples squeezed on board ship show decreasing chlorinity coupled with increases in the heavy oxygen and hydrogen isotopes resulting from the combined effects of sediment compaction and salt and isotope fractionation by hydrates. Carbon isotopes can be used to differentiate between biogenic ( ¹³C < –55) and thermogenic ( ¹³C > –559) gas hydrates except where acetate-derived methane is involved. Smooth downward trends in the chemical and isotopic anomalies suggest steady increases in the proportion of hydrates among the pore-filling substances. Spikes are attributed to high local hydrate concentrations (or massive hydrate layers or nodules). Problems encountered in delineating the detailed relationships between hydrate occurrence and pore-water anomalies concern (i) the roof-effect of a hydrate zone which should be marked by a positive Cl^– and a negative ¹⁸O anomaly (the opposite of the hydrate decomposition effect) (ii) the composition ofin-situ pore waters from within hydrate zones; (iii) the suppression of a positive ¹⁸O hydrate-decomposition anomaly due to superposition of other oxygen-isotope fractionation effects (such as volcanic glass alteration); and (iv) the non-linear correlation between Cl^– depletion and¹⁸O enrichment, and the magnitude of the¹⁸O enrichment. The hydrate-decomposition mechanism still provides the most successful explanation for the chemical and isotopic porewater anomalies observed in hydrate-bearing sediments, but the problems encountered underscore the urgency for future research through deep-sea drilling in hydrate zones.Dedicated to Dr D. W. Davidson in honor of his great contributions to the sciences of inclusion phenomena.     

The breaking and mending of porphyrins: reductive coupling of secochlorin bisaldehydes

The reaction of free base or Ni(II) complex secochlorin bisaldehydes 4H₂ and 4Ni regenerates the ultimate starting material of the bisaldehydes, meso-tetraphenylporphyrin 2H₂ and 2Ni, respectively. Depending on the reaction conditions employed (hydrazine hydrate in pyridine at reflux or hydrazine hydrate activated with sulfur in the presence of aqueous NaOH at ambient temperature), either porphyrin 2H₂ is formed together with known dihydroxymorpholinochlorin 9H₂ or known 2-hydroxychlorin 8H₂. Two different reaction pathways for the hydrazine reaction can be derived, either involving the formation of a meso-tetraphenyl-1,4,5-triazepinoporphyrin that loses spontaneously N₂ or a Wolff-Kishner-type pathway that also involves an intramolecular aldol-type reaction. Neither reaction is synthetically useful but both highlight in an impressive fashion the high thermodynamic stability of porphyrins. They also bring the ‘breaking and mending of porphyrin’ strategy to its ultimate conclusion by regenerating the starting porphyrin.     

Homochiral frameworks derived from magnesium, zinc and copper salts of l-tartaric acid

Five metal-organic frameworks derived from l-tartarate (l-tart=C₄H₄O₆) and the divalent metal ions magnesium, zinc or copper have been prepared and structurally characterized. The frameworks were prepared from the reaction of potassium l-tartrate [KC₄H₅O₆] with the appropriate metal salt in water solutions. The magnesium compound [Mg(l-tart)(H₂O)⊃1.5H₂O], 1, crystallizes as a two-dimensional 6³ sheet structure. The addition of the divergent linker molecules 4,4′-bipyridine (bipy) or trans-1,2-bispyridylethylene (bpe) to systems involving Zn²⁺ and Cu²⁺ results in the formation of the homochiral three-dimensional structures [Zn₂(l-tart)2(biyp)(H₂O)⊃5.25H₂O], 2, [Cu(l-tart)(bipy)⊃2.33H₂O], 3, and [Cu(l-tart)(bpe)⊃8H₂O], 5. Removal of solvent water molecules from 3 resulted in [Cu(l-tart)(bipy)⊃0.2H₂O], 4. Similar experiments on 2 and 5 resulted in breakdown of the frameworks, illustrating the dependence of the stability of these structures on the guest water molecules. This study reports the structures of two new topological types of binodal nets.