Structural and dynamical properties of methane clathrate hydrates

Equilibrium molecular dynamics (MD) simulations have been performed in both the NVT and NPT ensembles to study the structural and dynamical properties of fully occupied methane clathrate hydrates at 50, 125, and 200 K. Five atomistic potential models were used for water, ranging from fully flexible to rigid polarizable and nonpolarizable. A flexible and a rigid model were utilized for methane. The phonon densities of states were evaluated and the localized rattling modes for the methane molecules were found to couple to the acoustic phonons of the host lattice. The calculated methane density of states was found to be in reasonable agreement with available experimental data.     

Topology of polyhedral clathrate frameworks. 2. Frameworks constructed of polyhedral stories

The main features of the most widespread class of polyhedra clathrate frameworks formed of polyhedral stories are investigated. An algorithm for constructing such frameworks is suggested. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Struktumoi Khimii, Vol. 37, No. 1, pp. 123–130, January–February, 1996. Translated by L. Smolina     

Structural principles of biomembranes

The determination of the electron density distribution of the membrane cross sections of nerve myelin and the discs of the outer segments of retinal rods by a new X-ray evaluation method indicates, as in the case of the cross-sectional structure of the photosynthetic membrane, an “asymmetric” mass distribution. In connection with the detection of planar protein lattices in the membranes of photosynthetic bacteria, the chloroplasts of higher plants, erythrocytes, and retinal discs as well as the detection of a new category of lipid characteristics, comprising isothermal confromational and phase changes by specific ligand binding, a basis is established for the development of a general concept of biomembrane structure.     

ChemInform Abstract: Structural Principles of Semiconducting Group 14 Clathrate Frameworks.

The basic clathrate frameworks, together with their polytypes, intergrowth clathrate frameworks, and extended frameworks based on larger icosahedral building blocks of carbon, silicon, germanium, and tin are investigated by quantum chemical DFT computations.     

Structural properties and phase transitions in a silica clathrate

Melanophlogite, a low-pressure silica polymorph, has been extensively studied at different temperatures and pressures by molecular dynamics simulations. While the high-temperature form is confirmed as cubic, the low-temperature phase is found to be slightly distorted, in agreement with experiments. With increasing pressure, the crystalline character is gradually lost. At 8 GPa, the radial distribution function is consistent with an amorphous state. Like pristine glass, the topology changes, plastic behavior, and permanent densification appear above ～12 GPa, triggered by Si coordination number changes. We predict that a partial crystalline and amorphous sample can be obtained by recovering the sample from a pressure of ～12-16 GPa.     

Structural transformation due to Co-host inclusion in ionic clathrate hydrates

The present findings on the co-host role in restructuring the host water framework might provide important information on tuning the cage dimensions via lattice distortion and promoting the total number of cages via structural transformation. This co-host-induced structural modification can improve the physicochemical properties of ionized clathrate hydrates, particularly given that the host framework is able to function as a pathway to deliver protons or electrons.     

Structural Principles and Thermoelectric Properties of Polytypic Group 14 Clathrate‐II Frameworks

We have investigated the structural principles and thermoelectric properties of polytypic group 14 clathrate‐II frameworks using quantum chemical methods. The experimentally known cubic 3C polytype was found to be the energetically most favorable framework, but the studied hexagonal polytypes (2 H, 4 H, 6 H, 8 H, 10 H) lie energetically close to it. In the case of germanium, the energy difference between the 3C and 6H clathrate‐II polytypes is ten times smaller than the difference between the experimentally known 3C‐Ge (α‐Ge) and 4H‐Ge polytypes. The thermoelectric properties of guest‐occupied clathrate‐II structures were investigated for compositions Na–Rb–Ga–Ge and Ge–As–I. The clathrate‐II structures show promising thermoelectric properties and the highest Seebeck coefficients and thermoelectric power factors were predicted for the 3C polytype. The structural anisotropy of the largest studied hexagonal polytypes affects their thermoelectric power factors by over a factor of two.     

Structural studies of 2,2-Diphenyl-1-picrylhydrazine: A clathrate forming compound

2,2-Diphenyl-1-picrylhydrazine was crystallized from both tetrahydrofuran and chloroform. The crystal structures of samples from both preparations were determined by X-ray diffraction at low temperatures. Both crystals are clathrates with solvent molecules included as guest species in a host framework formed by the diphenylpicrylhydrazine molecules. The structures are rhombohedral, space groupR3. For the crystal from tetrahydrofuran, at 228 K,a = 25.820(4),c = 15.096(2) Å,Z = 18,R = 0.084 andwR = 0.133. For the crystal from chloroform, at 115 K,a = 25.453(12),c = 15.083(3) Å,Z = 18,R = 0.117 andwR = 0.153. Each unit cell contains three cavities which have approximate cylindrical shape with diameter 7.8 Å and height 6.0 Å, and 3 point symmetry. The integrity of the host framework is maintained only through van der Waals forces rather than through intermolecular hydrogen bonding as is found in many other known organic cathrates. The conformation of the trinitroanilino group of the hydrazine molecule is similar to that in the related trinitroanilinocarbazole molecule. The N-N bond approximates a single bond, and both hydrazine N atoms aresp ² hybridized.     

Pnictogen‐containing iron and chromium carbonyl complexes: From complexes to semiconducting frameworks

Recently, main group elements containing transition metal carbonyl complexes have received much attention due to their novel bonding modes and versatile reactivities. In this article, we will focus on the development of pnictogen (Bi, Sb, and As)‐containing Fe or Cr carbonyl complexes reported in our previous study, in which their rational synthetic methodologies, intriguing reactivities, as well as their special properties will be described and systematically compared. Importantly, a unique zig‐zag Bi‐Fe polymer was synthesized, and several Bi‐Cr complexes were found to exhibit surprising semiconducting behaviors with varied ultra‐low energy gaps via the through‐bond or through‐space electron communication.     

Group 14 triple-decker cations

The triple-decker cations trans-[(Cp*Sn)(2)(mu-eta(5):eta(5)-Cp*)](+) and trans-[(Cp*Pb)(2)(mu-eta(5):eta(5)-Cp*)](+) have been prepared and structurally characterized as their [B(C(6)F(5))(4)](-) salts from the reactions of [Cp*M][B(C(6)F(5))(4)](M = Sn, Pb) with the appropriate decamethylmetallocene. Both triple-decker cations adopt a cisoid arrangement of terminal Cp* groups, whereas the two known triple-decker main-group anions possess a transoid arrangement of terminal Cp groups. The reason for this conformational difference has been probed on the basis of DFT calculations.     

Structural relationships in tetrahedral frameworks: Reflections on cristobalite

Twinning on the unit cell level of the idealized cristobalite structure, using a mirror plane as the twin and composition plane, provides a simple relationship between 14 tetrahedral frameworks. Of these, 9 are found among the aluminosilicates with examples ranging from (stuffed) silicas to zeolites and include the framework types of nepheline hydrate I, zeolite LiA(BW), gismondine, phillipsite, merlinoite, tridymite, paracelsian, and monoclinic CaAl₂Si₂O₈. Similar twinning relates the frameworks of natrolite, thomsonite, and edingtonite.     

Structural transformation and guest dynamics of methanol-loaded hydroquinone clathrate observed by temperature-dependent Raman spectroscopy

The structural transformations and guest dynamics of methanol-loaded β-form hydroquinone (HQ) clathrate were investigated using temperature-dependent Raman spectroscopy. Methanol-loaded β-form HQ clathrate was obtained by recrystallization and characterized by elemental analysis, synchrotron X-ray diffraction, solid-state (13)C NMR spectroscopy, and Raman spectroscopy. Temperature-dependent Raman spectra of methanol-loaded β-form HQ clathrate were measured in the temperature range 300-412 K at increments of 4 K. Although no significant changes were evident in the temperature range 300-376 K, abrupt changes in the relative intensity and shape of the Raman bands were observed between 380 and 412 K indicating the structural transition from methanol-loaded β-form HQ clathrate to pure α-form HQ. Methanol molecules were gradually released from the β-form HQ clathrate in the range 364-380 K. Upon returning to ambient conditions, the crystal structure of the HQ sample remained identical to that of pure α-form HQ. Therefore, the temperature-induced structural transition of methanol-loaded HQ clathrate is completely irreversible and α-form HQ is more stable at ambient conditions.     

Bulk and nanoscale semiconducting materials: Structural advances using solid-state NMR spectroscopy

Solid-state nuclear magnetic resonance (NMR) spectroscopy continues to make major strides in the investigation of semiconducting materials. As an analytical technique, NMR offers an element-specific probe of virtually any chemical system and is uniquely suited to the selective study of materials exhibiting disorder or inhomogeneity, where long-range structural techniques may fail. With the advances in experimentation, hardware and high-polarization techniques realized over the past decade, challenging studies on difficult nuclei from bulk to nano-sized materials have now become practical. Below, we feature five recent works that have advanced our atomic-level understanding of new semiconducting materials using NMR spectroscopy.     

Structural Biochemistry 14. Permethylation of Nucleosides

Prominent molecular ions are generally observed in the field ionization (FI) mass spectra of unprotected nucleosides.² In the one exception so far observed, that of guanosine, we found the simple methyl derivative, N²,N²-dimethylguanosine, to afford an easily detectible molecular ion. The electron impact (EI) mass spectrum of N²,N²-dimethylguanosine also displayed a molecular ion and suggested that nucleoside methyl derivatives might be more easily studied by EI methods. For this purpose and the more important objective of developing methods for sequencing small nucleic acid units by computer assisted³ FI-EI mass spectrometry, a program was initiated (1967) to explore permethylation of nucleosides. We believe protection by permethylation to be superior to pertrimethylsilylation and acetylation principally for reasons involving molecular weight and stability. Concurrently it was anticipated that such nucleoside methylation studies would afford routes to partially mathylated nucleosides of value in characterizing such components of virus and cellular DNA and RNA⁴. Subsequently, using variations of the methanol-DCCI,⁵ diazomethane with various Lewis acids,⁶ methyl iodide in, for example, dimethylsulfoxide,⁷ methyl iodide-sodium hydride in dimethylformamide,⁸ methyl iodide-silver oxides⁹ and methyl iodidemethylsulfinyl carbanion in dimethylsulfoxide,¹⁰ techniques were evaluated but none was found to provide permethyl nucleosides in high yield.¹¹ The latter two methods have, however, been applied to methylating nucleosides for EI mass spectral investigations.¹²     

Developing some functional group chemistry at the Group 4 bent metallocene frameworks

Four series of reactions were explored that are aimed at the development of a functional group chemistry at the sensitive bent metallocenes of the Group 4 metals. First, we have tested and employed the olefin metathesis reaction. Two [C₅H₄-(CH₂)_n-CHCH₂]₂ZrCl₂ complexes (with n=4 and n=1) were treated with the Cl₂(PCy₃)₂RuCHPh catalyst in dilute solution. Intramolecular metathesis took place readily with liberation of ethene to yield the corresponding ansa-metallocene complexes [C₅H₄-(CH₂)_n-CHCH-(CH₂)_n-C₅H₄]ZrCl₂ that were isolated in ca. 28% (n=4, trans-CHCH-) or ca. 50% (n=1, cis-CHCH-) yield. Intermolecular olefin metathesis could also be effected using either a first or a second generation Grubbs catalyst to metathetically couple a variety of (L)Cl₂M(C₅H₄-CH₂CHCH₂)-type titanium or zirconium complexes to yield the respective dimetallic products. Alkenyl substituents were attached at the ligand stage at the indenyl 2-positions by means of a nickel-catalyzed cross-coupling reaction. Transmetallation eventually gave the bis(2-alkenylindenyl)ZrCl₂ complexes. Photolysis of three examples of this type of complexes (with 1-alkenyl substituents being methyl, cyclohexyl, or phenyl) resulted in a very efficient intramolecular [2 + 2] cycloaddition to yield the respective substituted cyclobutylene-bridged ansa-metallocenes. These complexes were MAO activated to give very active homogeneous metallocene catalysts for, e.g., ethene/1-octene copolymerization. The corresponding (s-trans-butadiene)-ansa-zirconocene complexes feature a pronounced C-H/phenylene π-interaction that probably helps to stabilize the s-trans-diene complex relative to its s-cis-isomer. Deprotonation of 7-dialkylaminofulvenes provides an easy access to enamino-cyclopentadienides. Transmetallation under carefully controlled conditions gave the respective bis(enamino-C₅H₄)ZrCl₂ complexes. Their treatment with a catalytic amount of a Lewis acid (TiCl₄) or a Brønsted-acid ([HNMe₂Ph⁺][BPh₄⁻]) led to a rapid intramolecular Mannich-type carbon-carbon coupling reaction that gave novel, very rigid C₃-bridged, -NR₂ functionalized ansa-metallocene systems. The analogous, readily performed Mannich-coupling reaction starting from 1,1^′-diacetylferrocene and a variety of secondary amines provided an interesting and useful novel entry to [3]ferrocenophane systems. Catalytic hydrogenation of the unsaturated bridge followed by additional functionalization opened a novel pathway to ferrocenophane-based chelate ligands (some optically active) for stereoselective catalytic transformations. Eventually, examples of direct attack of the electrophilic boranes B(C₆F₅)₃ or HB(C₆F₅)₂, respectively, to the Cp rings of bis(cyclopentadienyl)zirconacyclopentadienes are described, leading to novel types of Cp-borylated Group 4 metallocene complexes.     

Thermodynamic studies of clathrate hydrates

Thermodynamic studies of clathrate hydrates, mainly of structures I and II, are considered in this review which is based on 147 references. There are two main subjects. The first is the host lattice energy and the guest-host interaction energy, both of these quantities being related to the enthalpy of dissociation and composition of the hydrates. The second subject concerns orientational ordering phenomena occurring in both host and guest, as reflected in the low temperature heat capacity. The classical theoretical treatment of clathrate formation has been reconsidered on the basis of recent experimental results. Particular emphasis has been given to orientational ordering since this topic is undoubtedly central to clarifying the nature of clathrate hydrates.Ausgehend von 147 Literaturangaben wurden in diesem Review thermodynamische Untersuchungen von Klathrathydraten hauptsächlich der Struktur I und II betrachtet. Es gibt zwei Hauptaugenmerke. Als erstes die Wirtsgitterenergie und die Gast-Wirt-Wechselwirkungsenergie, beide bezogen auf die Dissoziationsenthalpie und die Bildungsenthalpie der Hydrate. Das zweite Hauptaugenmerk betrifft Orientierungs-Konditionierungserscheinungen sowohl in Wirt als auch Gast, wie in den Wärmekapazitäten bei niedrigen Temperaturen widergespiegelt wird. Auf der Basis jüngster experimenteller Ergebnisse wurde die klassische theoretische Betrachtung über die Bildung von Klathraten überprüft. Der Orientierung-Konditionierung wurde besonderer Nachdruck verliehen, da dies zweifellos eine entscheidende Rolle bei der Klärung der Natur der Klathrathydrate spielt. 147 I II. . «» « — », . «» « », . . , .

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Contribution No. 155 from the Chemical Thermodynamics Laboratory.     

High-pressure clathrate hydrate of acetone

X-ray diffraction study of quenched sample of acetone clathrate hydrate synthesized at 0.8 GPa was carried out. It was shown that the host frameworks of the hydrate comprise uniform cavities which are similar to that of recently characterized structure of high-pressure tetrahydrofurane hydrate. The unique peculiarity of investigated hydrate is decrease in the crystallographic symmetry of the hydrate arising from ordering in guest subsystem.     

Half-century history of clathrate chemistry

This paper is devoted to the history of a new field of knowledge — clathrate chemistry, whose 50th anniversary is being celebrated. The Historical Dates section contains data on clathrates from the first observations of these compounds (late 18th century) to the pioneering works (1947–1948) of the English crystallographer Herbert Marcus Powell explaining their nature. Major trends of research into clathrate chemistry since Powell’s works are discussed. Translated fromZhurnal Strukturnoi Khimii, Vol. 40, No. 5, pp. 797–808, September–October, 1999     

Structural Characteristics of the Carboxylic Amide Group

Average bond distances and bond angles as well as conformational preferences in the φ and ψ torsion angles of carboxylic amides with different substitution patterns have been derived by analyzing data from many crystal structures retrieved from the Cambridge Structural Database (CSD).     

Structural Characteristics of the Carboxylic Ester Group

Average bond distances and bond angles in carboxylic esters with different substitution patterns have been derived by analyzing data from many crystal structures retrieved from the Cambridge Structural Database (CSD). Conformation-al preferences in the attachment of substituents are found.