Polyhedral clathrate hydrates of a strong base: Phase relations and crystal structures in the system tetramethylammonium hydroxide-water

The tetramethylammonium hydroxide-water system has been studied by low-temperature differential thermal analysis and X-ray powder diffraction. The melting diagram was constructed for concentrations between 66.7 and 100 mol% H₂O. It shows the existence and stability ranges of as many as eight crystalline hydrate phases:- and-Me₄NOH·2H₂O (phase transition at –85°C, decomposition atca. 105°C), Me₄NOH·4 H₂O (melting point 44°C, incongruent), and-Me₄NOH·5 H₂O (phase transition at 42°C, melting point 68°C, congruent),- and-Me₄NOH·7.5 H₂O (phase transition at 6°C, melting point 16°C, incongruent), and Me₄NOH·10 H₂O (melting point –20°C, incongruent). The structures of all these phases, except the already known one of-Me₄NOH·5 H₂O, were determined from single-crystal MoK diffractometer data. The decahydrate and the high-temperature forms of the 7.5-hydrate and the pentahydrate are genuinepolyhedral clathrate hydrates, the first ones reported of a strong base. Their mostly novel three-dimensional anionic host structures, formed by the hydrogen-bonded OH^– ions and H₂O molecules, arefour-connected throughout, in spite of their proton deficiency which is apparently leveled by disorder. Disorder also affects the enclosed cationic Me₄N⁺ guest species. Like the low-temperature form of the pentahydrate, that of the 7.5-hydrate has a clathrate-related, but not fully polyhedral structure, some of the oxygen atoms being three-connected only. The tetrahydrate presents the rare case of both a hydrogen bond of the type OH^–...OH₂ and a (deprotonated) water-channel structure. This is fully ordered and apart from that can be derived from the polyhedral one of the-pentahydrate just by removing the appropriate number of water molecules from certain positions. The structures of- and-Me₄NOH·2 H₂O contain identical one-dimensionalspiro chains [HO^–(HOH)_/42] with the hydroxide protonnot participating in the hydrogen bonding. The Me₄N⁺ ion is ordered in the and disordered in the phase.Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82076 (66 pages).Dedicated to Dr D. W. Davidson in honor of his great contributions to the sciences of inclusion phenomena.     

Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.     

Energetic and topological analyses of the oxidation reaction between Mo(n) (n = 1, 2) and N2O

The interaction between molybdenum, atom, and dimer, with nitrous oxide has been investigated using density functional theory. The analysis of the potential energy surfaces for both reactions has revealed that a single molybdenum atom can activate the N--O bond of N2O requiring a small activation energy. However, the presence of several intersystem crossings between three different spin states, namely, septet, quintet and triplet states, seems to be the major constraint to the Mo + N2O reaction. Contrarily, the low-lying excited states (triplet and quintet) do not participate in the reaction between the molybdenum dimer and N2O. The latter reaction fully evolves on the singlet spin surface. Three different regions have been distinguished along the pathway: formation of an adduct complex, formation of an inserted compound, and the N2 detachment. The connection between the two first regions has been characterized by the formation of a special complex in which the N--O bond is so weakened that it could be considered as a first step in the insertion process. It has been shown that the topological changes along the pathways provide a clear explanation for the geometrical changes that occur along the reaction pathway. In summary, the detachment of the N2 molecule is found to be kinetically an effective process for both reactions, owing to the high exothermicity and consequently to the high internal energy of the insertion intermediates. However, in the case of Mo atom, the reaction should be a slow process due to the presence of spin-forbidden transitions. These results fully agree with previous experimental works.     

Intermolecular-medium and intramolecular-weak hydrogen bonding chains in the crystals of chiral trifluoromethylated amino alcohols

A structural feature of hydrogen bonding chains found in the crystals of trifluoromethylated amino alcohols is reported. Hydrogen bondings of 3-(N,N-dialkylamino)-1,1,1-trifluoro-2-propanols construct chiral spiral hydrogen bonding chains. Lone pairs on the nitrogen atoms of the amino alcohols participate in two hydrogen bondings. Detailed structural analysis of the hydrogen bonds of the 3-(N,N-dimethylamino)-1,1,1-trifluoro-2-propanol suggested that the chain built up with alternating intermolecular-medium and intramolecular-weak hydrogen bonds. The medium intermolecular hydrogen bond, which transfers a proton from the hydroxy group to the amino nitrogen, would make a tentative zwitterionic form of the molecule. Then, electrostatic attraction between the charges in the zwitterion centers induced a weak intramolecular hydrogen bond.     

Solid-State NMR Study of Phase Separation and Order of Water Molecules and Silanol Groups in Polysiloxane Networks

Homogeneity and structure of organically modified polysiloxane networks prepared by sol-gel co-condensation, as well as location and nature of water molecules and silanol groups were studied by 1D and 2D solid-state NMR. ¹H–²⁹Si and ¹H–¹H interatomic distances were estimated from variable contact-time CP/MAS experiments, ¹H NMR chemical shifts and off-resonance WISE NMR. A structure model of these networks is proposed and discussed. The fraction of proton-inaccessible units Q⁴ in the networks decreases with increasing amounts of dimethylsiloxane (D) and methylsiloxane (T) units. In contrast to systems prepared by co-condensation of tetraethoxysilane (TEOS) with dimethyl(diethoxy)silane (DMDEOS), proton-inaccessible units form essential fraction in networks prepared by co-condensation of TEOS with methyl(triethoxy)silane (MTEOS). The proton-accessible part of the networks with high O/Si ratios is nano-heterogeneous phase, which is composed of water containing Q ⁱ particles separated by copolymer domains. The overall homogeneity and uniformity of binding sites around silanol groups increases by co-condensation TEOS with DMDEOS or MTEOS, while the amount of physisorbed water as well as the hydrogen bond strength decreases, as compared with neat silica gel prepared by polycondensation of TEOS.     

Synthesis and crystal structure of two novel nickel (imidazole) complexes having hydrogen-bonded networks

Two nickel (imidazole) complexes, Ni(im)₆Cl₂·4H₂O (1) and Ni(im)₆(NO₃)₂ (2) (im=imidazole) have been synthesized and characterized by elemental analysis, IR, UV, TG and single crystal X-ray diffraction. 1 crystallizes in the triclinic space group P-1 with a=8.800(6) Å, b=9.081(6) Å, c=10.565(7) Å, =75.058(9)°, β=83.143(8)°, γ=61.722(8)°, V=718.3(8) Å³, Z=1 and R₁ (wR₂)=0.0469 (0.1497). 2 crystallizes in the trigonal space group R-3 with a=12.370(6) Å, b=12.370(6) Å, c=14.782(14) Å, =90.00°, β=90.00°, γ=120.00°, V=1959(2) Å³, Z=3 and R₁ (wR₂)=0.0358 (0.0955). 1 and 2 exhibit different supramolecular network due to their different counter anions and different hydrogen bonding connection. In compound 1, [Ni(im)₆]²⁺ cation and counter anions Cl⁻ alternatively array in an ABAB fashion via N–HCl hydrogen bonding. In compound 2, the plane of each NO₃²⁻ is almost parallel and each NO₃²⁻ connect three different [Ni(im)₆]²⁺ cations via N–HO hydrogen bonding.     

Chemical Bonding and Pressure‐Induced Change of the Electron Configuration of Ytterbium in β‐YbAgGa2

Single‐phase polycrystalline samples of the intermetallic compound β‐YbAgGa₂ were synthesized by inductive heating and subsequent annealing for eight weeks at 670 K. Magnetic properties were characterized by susceptibility measurements and indicated intermediate valence of ytterbium at ambient pressure. Angle‐dispersive X‐ray powder diffraction data of orthorhombic β‐YbAgGa₂ indicate stability of the phase in the investigated pressure range from 0.1 MPa (ambient pressure) to 19 GPa. The pressure‐induced volume decrease is accompanied by an increase of the effective valence from 2.17 at ambient conditions to 2.71 at 16 GPa as evaluated by X‐ray absorption spectroscopy at the Yb L_III threshold. Analysis of the chemical bonding in β‐YbAgGa₂ by integrating the electron density of the polyanion in basins as defined by the electron localization function results in an electron count Yb^2.7+[(Ag^0.2—)(Ga1(3b)^1.0—)(Ga2(4b)^1.5—)]. This finding is close to the expected values calculated by means of the Zintl rules and fits well the results of magnetic susceptibility measurements and XAS investigations.     

Nucleation of β-hairpin structure in a pyrrole amino acid containing peptide

Synthesis and conformational studies of two short peptides containing pyrrole amino acids (1, Paa), Boc-Paa-Paa-d-Pro-Gly-Xaa-Paa-Paa-OMe (2: Xaa=Ala; 3: Xaa=Val), were carried out in which it was established that replacement of Ala in 2 with a Val residue helps peptide 3 to adopt a well-defined β-hairpin conformation in a nonpolar solvent, like CDCl₃.     

Osmium catalyzed asymmetric dihydroxylation of methyl trans-cinnamate in ionic liquids, followed by supercritical CO2 product recovery

In this work, osmium-catalyzed asymmetric dihydroxylation (AD) of methyl trans-cinnamate was studied. Osmium and chiral ligand catalysts were immobilized in ionic liquid only, without any other reaction solvents, while the recovery of the product was performed by extraction with supercritical CO₂, and compared with results obtained by extractions with organic solvents such as hexane and diethyl ether. In supercritical CO₂ extraction experiments, optimal extraction pressure was found and ionic liquid chosen, so that the highest reaction yields coupled with lowest osmium content in the crude product can be achieved. Finally, recycle experiments of the same (ionic liquid + catalytic system) mixture were successfully conducted. Application of ionic liquids and supercritical CO₂ in osmium catalyzed AD allows for the isolation of the diol basically without contamination with osmium, in high yield and enantiomeric excess, and it makes possible the efficient reuse of ionic liquid solvent and the catalytic system.     

Supramolecular Assemblies of (±-2,2''''-Dihydroxy-1,1''''-binaphthyl with 2,2''''-Bipyridine and Naphthodiazine

Introduction Optically active 1,1'-bi-2-naphthol (BINOL) and its derivatives have been widely used as chiral ligands of catalysts for asymmetric reactions and effective host compounds for the isolation or optical resolution of a wide range of organic guest molecules through the for-mation of crystalline inclusion complexes.1,2 The wide-ranging and important applications of these com-pounds in organic synthesis have stimulated great inter-est in developing efficient methods for their prepara-…