Cytenamide-1,4-dioxane (2/1)

In the crystal structure of the title compound [systematic name: 5H-dibenzo[a,d]cycloheptatriene-5-carboxamide-1,4dioxane(2/1)], 2C(16)H(13)NO center dot C4H8O2, the cytenamide molecules form a hydrogen-bonded R-2(2)(8) dimer. The solvent molecule is located between two adjacent cytenamide dimers and forms N-H center dot center dot center dot O hydrogen bonds with one cytenamide molecule from each dimer.

Stochiometrically governed molecular interactions in drug: Poloxamer solid dispersions

This study probes the molecular interactions between model drugs and poloxamers that facilitate dissolution rate improvements using solid dispersions. Ibuprofen and ketoprofen solid dispersions were prepared at different mole ratios using poloxamers 407 and 188. The carbonyl stretching vibration of the ibuprofen dimer shifted to higher wavenumber in the infrared spectra of 2:1 drug:carrier mole ratio solid dispersions, indicating disruption of the ibuprofen dimer concomitant with hydrogen bond formation between the drug and carrier. Solid dispersions with mole ratios >2:1 drug:carrier (up to 29:1) showed both ibuprofen hydrogen-bonded to the poloxamer, and excess drug present as dimers. X-ray diffraction studies confirmed these findings with no evidence of crystalline drug in 2:1 mole ratio systems whereas higher drug loadings retained crystalline ibuprofen. Similar results were found with ketoprofen-poloxamer solid dispersions. Thermal analysis of ibuprofen-poloxamer 407 solid dispersions and their resultant phase diagram suggested solid solutions and a eutectic system were formed, depending on drug loading. Dissolution studies showed fastest release from the solid solutions; dissolution rates from solid solutions were 12-fold greater than the dissolution of ibuprofen powder whereas the eutectic system gave a 6-fold improvement over the powder. When designing solid dispersions to improve the delivery of poorly-water soluble drugs, the nature of drug:carrier interactions, which are governed by the stochiometry of the composition, can affect the dissolution rate improvement.

Structure of single-wall peptide nanotubes: in situ flow aligning X-ray diffraction

The structure of single wall peptide nanotubes is presented for the model surfactant-like peptide A6K. Capillary flow alignment of a sample in the nematic phase at high concentration in water leads to oriented X-ray diffraction patterns. Analysis of these, accompanied by molecular dynamics simulations, suggests the favourable self-assembly of antiparallel peptide dimers into beta-sheet ribbons that wrap helically to form the nanotube wall.

Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Global and local expression of chirality in serine on the Cu{110} surface

Establishing a molecular-level understanding of enantioselectivity and chiral resolution at the organic−inorganic interfaces is a key challenge in the field of heterogeneous catalysis. As a model system, we investigate the adsorption geometry of serine on Cu{110} using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The chirality of enantiopure chemisorbed layers, where serine is in its deprotonated (anionic) state, is expressed at three levels: (i) the molecules form dimers whose orientation with respect to the substrate depends on the molecular chirality, (ii) dimers of l- and d-enantiomers aggregate into superstructures with chiral (−1 2; 4 0) lattices, respectively, which are mirror images of each other, and (iii) small islands have elongated shapes with the dominant direction depending on the chirality of the molecules. Dimer and superlattice formation can be explained in terms of intra- and interdimer bonds involving carboxylate, amino, and β−OH groups. The stability of the layers increases with the size of ordered islands. In racemic mixtures, we observe chiral resolution into small ordered enantiopure islands, which appears to be driven by the formation of homochiral dimer subunits and the directionality of interdimer hydrogen bonds. These islands show the same enantiospecific elongated shapes those as in low-coverage enantiopure layers.

SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding

Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel-shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of (15)N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel beta-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.

Strongly nucleophilic RhI centre in square-planar complexes with terdentate (κ3) 2,2′:6′,2′′-terpyridine ligands: crystallographic, electrochemical and density functional theoretical studies

Rh-I-terpyridine complexes have been unambiguously formed for the first time. The 2,21:6',2"-terpyridine (tpy), 4'-chloro-2,2':6',2"-terpyridine (4'-Cl-tpy) and 4'-(tert-butyldimethylsilyl-ortho-carboranyl)-2,2':6',2"-terpyridine (carboranyl-tpy) ligands were used for successful syntheses and characterisation of the corresponding Rh-I complexes with halide coligands, [Rh(X)(4'-Y-terpyridine)] (X = Cl, Y = H, Cl, carboranyl; X = Br, Y = H). All four neutral Rh-tpy complexes are square planar, with Rh-X bonds in the plane of the 4'-Y-terpyridine ligands. Full characterisation of these dark blue, highly air-sensitive compounds was hampered by their poor solubility in various organic solvents. This is mainly due to the formation of pi-stacked aggregates, as evidenced by the crystal structure of [Rh(Cl)(tpy)]; in addition, [Rh(Cl)(carboranyl-tpy)] merely forms discrete dimers. The (bonding) properties of the novel Rh-I-terpyridine complexes have been studied with single-crystal X-ray diffraction, (time-dependent) density functional theoretical (DFT) calculations, far-infrared spectroscopy, electronic absorption spectroscopy and cyclic voltammetry. From DFT calculations, the HOMO of the studied Rh-I-terpyridine complexes involves predominantly the metal centre, while the LUMO resides on the terpyridine ligand. Absorption bands of the studied complexes in the visible region (400-900 nm) can be assigned to MLCT and MLCT/XLCT transitions. The relatively low oxidation potentials of [Rh(X)(tpy)] (X = Cl, Br) point to a high electron density on the metal centre. This makes the Rh-I-terpyridine complexes strongly nucleophilic and (potentially) highly reactive towards various (small) substrate molecules containing carbon-halide bonds.

Hydrogen-bond assisted stabilization of the less favored conformation of a tridentate Schiff base ligand in dinuclear nickel(II) complex: an experimental and theoretical study

The Schiff base ligand, HL (2-[1-(3-methylamino-propylimino)-ethyl]-phenol), the 1:1 condensation product of 2-hydroxy acetophenone and N-methyl-1,3-diaminopropane, has been synthesized and characterized by X-ray crystallography as the perchlorate salt [H2L]ClO4 (1). The structure consists of discrete [H2L](+) cations and perchlorate anions. Two dinuclear Ni-II complexes, [Ni2L2(NO2)(2)] (2), [Ni2L2(NO3)(2)] (3) have been synthesized using this ligand and characterized by single crystal X-ray analyses. Complexes 2 and 3 are centrosymmetric dimers in which the Ni-II ions are in distorted fac- and mer-octahedral environments, respectively, bridged by two mu(2)-phenolate ions of deprotonated ligand, L. The plane of the phenyl rings and the Ni2O2 basal plane are nearly coplanar in 2 but almost perpendicular in 3. We have studied and explained this different behavior using high level DFT calculations (RI-BP86/def2-TZVP level of theory). The conformation observed in 3, which is energetically less favorable, is stabilized via intermolecular non-covalent interactions. Under the excitation of ultraviolet light, characteristic fluorescence of compound 1 was observed; by comparison fluorescence intensity decreases in case of compound 3 and completely quenched in compound 2.

Transition metal clusters on graphite

The topic of this work is 3d transition metals deposited on graphite. Spin-polarised density-functional calculations are used to obtain the magnetic moments of deposited adatoms and dimers. Interatomic potentials are also deduced. These are used in molecular dynamics simulations to study cluster formation and to investigate cluster morphology.

Deciphering the complexity of sainfoin (Onobrychis viciifolia) proanthocyanidins by MALDI-TOF mass spectrometry with a judicious choice of isotope patterns and matrixes

Use of superdihydroxybenzoic acid as the matrix enabled the analysis of highly complex mixtures of proanthocyanidins from sainfoin (Onobrychis viciifolia) by MALDI-TOF mass spectrometry. Proanthocyanidins contained predominantly B-type homopolymers and heteropolymers up to 12- mers (3400 Da). Use of another matrix, 2,6-dihydroxyacetophenone, revealed the presence of A-type glycosylated dimers. In addition, we report here how a comparison of the isotopic adduct patterns, which resulted from Li and Na salts as MALDI matrix additives, could be used to confirm the presence of A-type linkages in complex proanthocyanidin mixtures. Preliminary evidence suggested the presence of A-type dimers in glycosylated prodelphinidins and in tetrameric procyanidins and prodelphinidins.

Water vapour continuum absorption in near-infrared windows derived from laboratory measurements

In most near-infrared atmospheric windows, absorption of solar radiation is dominated by the water vapor self-continuum and yet there is a paucity of measurements in these windows. We report new laboratory measurements of the self-continuum absorption at temperatures between 293 and 472 K and pressures from 0.015 to 5 atm in four near-infrared windows between 1 and 4 m (10000-2500 cm-1); the measurements are made over a wider range of wavenumber, temperatures and pressures than any previous measurements. They show that the self-continuum in these windows is typically one order of magnitude stronger than given in representations of the continuum widely used in climate and weather prediction models. These results are also not consistent with current theories attributing the self continuum within windows to the far-wings of strong spectral lines in the nearby water vapor absorption bands; we suggest that they are more consistent with water dimers being the major contributor to the continuum. The calculated global-average clear-sky atmospheric absorption of solar radiation is increased by 0.75 W/m2 (which is about 1% of the total clear-sky absorption) by using these new measurements as compared to calculations with the MT_CKD-2.5 self-continuum model.

Structure and spectra of dichloro(hydroxy-methoxy-di(2-pyridyl)methane)copper(II)

The non-electrolyte dichloro(hydroxy-methoxy-di(2-pyridylmethane)copper(II), resulting from the reaction of di(2-pyridyl)ketone and copper(II) chloride in methanol solution, was isolated and characterized and its structure was determined by X-ray diffraction. The pyridyl nitrogens and the chloride anions virtually from a basal plane in which lies the copper atom, while the oxygen of the methoxy group is in an apical position at a distance of 2.497 (3)Å. The nitrogenous base adopts the boat conformation with the pyridyl rings forming a dihedral angle of 108.72 (14)°. The nearest interatomic copper distance of 3.940(3)Å precludes copper-copper interactions, while the proximity of copper to the out-of-plane chlorine atoms [3.109(3)Å] suggests weakly bound chloro-bridged dimers. Spectral changes indicate that protic molecules displace the methoxy group and water affords the corresponding 1,1-diol.

Synthesis and structural characterisation of [Pd2(μ-Br)2(PBut3)2], an example of a palladium(I)-palladium(I) dimer

The syntheses, spectroscopic characterisation and in one case (X = Br) the single-crystal structure of the novel PdI–PdI dimers [Pd2(µ-X)2(PBut3)2](X = Br or I) have been determined; preliminary results on their reactions with CO, H2, CNC6H3Me2 and C2H2 have also been obtained.

7,8-dihydropyrido[2,3-d]pyrimidin-2-one; a bicyclic cytosine analogue capable of enhanced stabilisation of DNA duplexes

Incorporation of a bicyclic cytosine analogue, 3-beta-D-(2'-deoxyribofuranosyl)7,8- dihydropyrido[ 2,3-d] pyrimidine, into synthetic DNA duplexes results in a greatly enhanced thermal stability ( 3 - 4 degrees C per modification) compared to the corresponding unmodified duplex.

Fibrillisation of ring-closed amyloid peptides

Ring-closing olefin metathesis reactions are used to create intramolecularly ring closed peptides or inter-molecularly ring-closed peptide dimers based on a designed amyloid peptide sequence. The uncrosslinked peptide self-assembles into high aspect ratio nanotubes, however ring-closing leads to the formation of fibrillar and twisted/helical ribbon structures.