An efficient synthesis of selectively functionalized d-rhamnose derivatives

d-Rhamnose is an important component of bacterial lipopolysaccharides. This paper describes a short and highly efficient synthesis of d-rhamnose from d-mannose. The synthesis of selectively C-4 modified d-rhamnosides and 6-deoxy-d-talosides as potential building blocks for complex oligosaccharide synthesis is also discussed.     

Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features

Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.     

Temperature dependent Raman scattering study of l-ascorbic acid

Temperature dependent Raman study of l-ascorbic acid has been performed from 15 to 418 K. Changes in the wavenumber vs. temperature plots for some internal modes were interpreted as conformational molecular change and the discontinuity in the wavenumber vs. temperature plots along with the appearance of a new vibrational mode in the temperature range 200-270 K suggests that l-ascorbic acid undergoes a structural phase transition. For temperatures higher than 300 K, no relevant modification was observed on the Raman spectra thus indicating a stable structure at high temperatures. Additionally, a correlation between OH stretching wavenumber and the behavior of hydrogen bond is also made.     

Intermolecular hydrogen bonding in the binary mixture [(C2H5)2CO + CH3OH] probed by polarized Raman measurements and DFT calculations

The Raman spectra of neat (C₂H₅)₂Cclass="glyphImg">O (pentanone) and its binary mixtures with hydrogen donor solvent (CH₃OH), [(C₂H₅)₂Cclass="glyphImg">O + CH₃OH] having different mole fractions of the reference system, (C₂H₅)₂Cclass="glyphImg">O in the range 0.1-0.9 at a regular interval of 0.1 were recorded in the Cclass="glyphImg">O stretching region. In neat liquid, the Raman peak appears asymmetric. The asymmetric nature of the peak has been attributed to the Cclass="glyphImg">O stretching mode of the two conformers of (C₂H₅)₂Cclass="glyphImg">O having C₂ and C_2v point groups and the corresponding bands at ∼1711 and ∼1718 cm⁻¹, respectively. A careful analysis of the I_iso (isotropic component of the Raman scattered intensity) at different concentrations reveals that upon dilution with methanol, at mole fraction C = 0.6, an additional peak in the Cclass="glyphImg">O stretching region is observed at ∼1703 cm⁻¹ which is attributed to the hydrogen bonding with methanol. A peculiar feature in this study is that upon dilution, the peak at ∼1718 cm⁻¹ shows a minimum at C = 0.6, but on further dilution it shows a blue shift. However, the other peak at ∼1711 cm⁻¹ shows a continuous red shift with dilution as well as a maximum at C = 0.7 in the linewidth vs. concentration plot, which is essentially due to competition between motional narrowing and diffusion phenomena. A significant amount of narrowing in the Raman band at ∼1718 cm⁻¹ can be understood in terms of caging effect of the reference molecule by the solvent molecules at high dilution. A density functional theoretic (DFT) calculation on optimized geometries and vibrational frequencies of two conformers of neat (C₂H₅)₂Cclass="glyphImg">O in C₂ ad C_2v forms and the complexes with one and two CH₃OH molecules with both the conformers was performed. The experimental results and theoretical calculations together indicate a co-existence of two conformers as well as hydrogen bonded complex with methanol in the binary mixture, [(C₂H₅)₂Cclass="glyphImg">O + CH₃OH] at intermediate concentrations.     

On the specificity of the amide VI band for the secondary structure of proteins

In this work we analyzed the specificity of the amide VI band for different types of secondary structure elements in protein structures. This band involves the bending motion of the Cclass="glyphImg">O group of the peptide chain that is typically observed in the spectral region from 590 to 490 cm⁻¹. The infrared absorbance spectra of a set of polypeptide model compounds of well known secondary structure was obtained at defined pH, including poly (l-lysine), poly (l-tyrosine), poly (l-alanine) and poly (l-histidine). In addition spectra of membrane proteins from the respiratory chain, namely the NADH:ubiquinone oxidoreductase, the cytochrome c oxidase and its Cu_A fragment, the cytochrome bc₁ complex, a Rieske-type protein and in addition myoglobin, have been comparatively investigated. The systematic analysis of the amide VI band of the polypeptides and the proteins allowed correlating the signal appearing at ∼525 cm⁻¹ to α-helical structures and signals at ∼545 cm⁻¹ to β-sheet contributions. Random coils have been found to contribute at ∼535 cm⁻¹ while the β-turns were observed at ∼560 cm⁻¹.     

Surface miscibility of EPC/DOTAP/DOPE in binary and ternary mixed monolayers

Surface pressure (π)-molecular area (A) curves were used to characterize the packing of pseudo-ternary mixed Langmuir monolayers of egg phosphatidylcholine (EPC), 1,2-dioleoyl-3-trimethylammonium propane (DOTAP) and L-α-dioleoyl phosphatidylethanolamine (DOPE). This pseudo-ternary mixture EPC/DOPE/DOTAP has been successfully employed in liposome formulations designed for DNA non-viral vectors. Pseudo-binary mixtures were also studied as a control. Miscibility behavior was inferred from π-A curves applying the additivity rule by calculating the excess free energy of mixture (ΔG(Exc)). The interaction between the lipids was also deduced from the surface compressional modulus (C(s)(-1)). The deviation from ideality shows dependence on the lipid polar head type and monolayer composition. For lower DOPE concentrations, the forces are predominantly attractive. However, if the monolayer is DOPE rich, the DOTAP presence disturbs the PE-PE intermolecular interaction and the net interaction is then repulsive. The ternary monolayer EPC/DOPE/DOTAP presented itself in two configurations, modulated by the DOPE content, in a similar behavior to the DOPE/DOTAP monolayers. These results contribute to the understanding of the lipid interactions and packing in self-assembled systems associated with the in vitro and in vivo stability of liposomes.     

In-site mineralization of amorphous calcium carbonate particles: A facile and efficient approach to fabricate poly(l-lactic acid) based hybrids

The aim of this investigation is to obtain a polymer-based hybrid material with biodegradability, biocompatibility, and good mechanical properties and this object was realized via. in-situ introduction of the unmodified calcium carbonate (CaCO₃) into a poly(l-lactic acid) (PLLA) matrix. As verified by the measurements from scanning electron microscopy (SEM), optical microscopy, dynamic mechanical analysis (DMA) and thermogravimetric analysis (TGA), the hybrid films which possesses a uniform dispersion of calcium carbonate CaCO₃ in nano-meter scale, mechanically robustness and thermal stability could be fabricated by a mineralization-alike process. For example, the storage modulus increases from 441 MPa of neat PLLA to 1034 MPa of hybrid film containing 2% (w/w) CaCO₃. In addition, the hybrid films display a significant improvement in its UV-exposure resistance.     

Simultaneous analysis of citrulline and arginine in serum and tissue

We developed a method for simultaneously determining l-citrulline and l-arginine levels in serum and tissue samples using RP-HPLC with ultraviolet (UV) detection. The serum was deproteinized by trichloroacetic acid and heat; the tissue was homogenized by trichloroacetic acid and deproteinized as the same as serum. Phenyl-isothiocyanate (PITC) solution was used as derivatization reagent and a gradient elution was carried out. The linearity for l-arginine and l-citrulline ranged from 0 to at least 1000 μmol/L. R² values were above 0.9999 for both. LODs for l-arginine and l-citrulline were 0.0462 μmol/L and 0.0195 μmol/L, respectively, while LOQs were 0.530 μmol/L and 0.417 μmol/L, respectively. Intra- and inter-day CVs were less than 3.5% and 7.5% in serum, respectively. The average recovery was from 85.5% to 116.5% in serum. Intra-assay CVs were 3.8% and 10.3%, and inter-assay CVs were 13.7% and 10.7% for l-arginine and l-citrulline respectively in tissue. The average recovery was from 92.8% to 113.5% in tissue. This is a reliable and convenient analytical method which is suitable for most clinical laboratories.     

New bicyclic phosphorous ligands: synthesis, structure and catalytic applications in ionic liquids

New azadioxaphosphabicyclo[3.3.0]octane ligands showing a trans arrangement with regard to the two five-membered heterocycles, were obtained as a mixture of three conformers, in agreement with molecular modelling studies. The stability of oxaphosphane ligands was studied under basic catalytic conditions, monitored by NMR spectroscopy. Palladium catalytic systems containing these ligands were active in Suzuki C-C cross-coupling reactions between phenylboronic acid and aryl halides (bromide and chloride derivatives) bearing electron-donor or electron-withdrawing substituents, in both organic and ionic liquid solvents. The catalytic systems showed a high stability even under the most severe reaction conditions used in this work. The ionic liquid catalytic phase could be recycled up to ten times without significant activity loss.