Spectral representation of reduced protein models

We consider a spectrum-like two-dimensional graphical representation of proteins based on a reduced protein model in which 20 amino acids are grouped into five classes. This particular grouping of amino acids was suggested by Riddle and co-workers in 1997. The graphical representation is based on depicting sequentially the amino acids on five horizontal lines at equal separations. One-letter codes, B, O, U, X and Y, to which numerical values 1 to 5 have been assigned, are suggested as labels for the fictional amino acids that represent all the amino acids within each group. The approach is illustrated on ND6 proteins of eight species having from 168 to 175 amino acids. While visual inspection of the novel spectral graphical representations of proteins may reveal local similarities and dissimilarities of protein sequences, arithmetic manipulations of spectra offer an elegant route to graphic visualization of the degree of similarity for selected pairs of proteins.     

Novel matrix invariants for characterization of changes of proteomics maps

Previous studies on mathematical characterization of proteomics maps by sets of map invariants were based on the construction of a set of distance-related matrices obtained by matrix multiplication of a single matrix by itself. Here we consider an alternative characterization of proteomics maps based on a set of matrices characterizing local features of an embedded zigzag curve over the map. It is shown that novel invariants can well characterize proteomics maps. Advantages of the novel approach are discussed.     

l‐Valyl‐l‐serine trihydrate

The valine side chains in the crystal structure of the title compound [systematic name: 2‐(2‐ammonio‐3‐methyl­butan­amido)‐3‐hydroxy­propano­ate tri­hydrate], C₈H₁₆N₂O₄·3H₂O, stack along an a axis of 4.77 Å to form hydro­phobic columns surrounded by remarkable water/hydroxyl shells. The peptide main chains are connected by hydrogen bonds in two‐dimensional layers. The peptide mol­ecules in each layer are related only by translation, and generate a very rare pattern. This is rendered possible through the formation of the shortest C^α—H·O(carboxyl­ate) inter­action ever recorded.     

Electron-microscopy studies of NaAlH4 with TiF3 additive: hydrogen-cycling effects

NaAlH₄ is a promising candidate material for hydrogen storage. Ti additives are effective in reducing the reaction temperatures and improving kinetics. In this work, the microstructure of NaAlH₄ with 2% TiF₃ has been studied in different conditions using a combination of transmission electron microscopy and scanning electron microscopy, both with energy-dispersive spectroscopic X-ray analysis. The effect of the additive on particle and grain size was examined after the initial ball-milling process and after 15 cycles. The additive has an uneven distribution in the sample after ball milling. Selected-area diffraction and high-resolution imaging confirmed the presence of TiF₃. This phase accounts for most of the Ti in the material at this stage and showed limited mixing with the alanate. The grain size within particles for TiF₃ is larger than for the alanate particles. Diffraction from the latter was dominated by metallic aluminium. After cycling, the TiF₃ has decomposed and energy-dispersive spectroscopic X-ray analysis maps showed some combination of Ti with the alanate phase. There is no significant change in the measurable grain size of the Al-containing alanate particles between the ball-milled and the 15-cycled samples, but more cycles result in agglomeration of the material. PACS 61.14.-x; 68.37.LP; 68.37.Hk     

Hybridization in some macrocyclic polyacetylenes

The hybridization in several cyclic polyacetylene compounds has been calculated by the maximum overlap method, assuming planar and non-planar geometries of the molecules. In the planar configuration the hybrids describing the molecular skeleton deviate from the corresponding bond directions. We have a few “bent” bonds, but in contrast to the situation in small rings, here the deviation angles are negative, i.e., the hybrids point toward the inside of the ring. Non-planar structures in which acetylene groups are kept in a plane and CCH₂ or CH₂ groups are displaced out of the plane show less deviation from the bond directions of bent bonds. Furthermore, the deviation angles decrease with an increase in the out-of-plane displacement of methylene groups. Finally, when the angle of bending of the molecules approaches 50°, the deviation vanishes, predicting a puckered conformation for the molecules. Correlation between CC stretching vibration frequencies and the corresponding CC bond overlap is discussed.     

Correlation between C-H and C-C spin-spin coupling constants and s character of hybrids calculated by the maximum overlap method

For some thirty hydrocarbons the s character of hybrids obtained by the application of the maximum overlap method have been correlated with C-H and C-C spin-spin coupling constants. The following relationships were obtained: $$J_{{\text{C}}^{{\text{13}}} - {\text{H}}} = 1079a_{{\text{CH}}}^{\text{2}} /(1 + S_{{\text{CH}}}^{\text{2}} ) - 54.9$$ , $$J_{{\text{C}}_{\text{1}}^{{\text{13}}} - {\text{C}}_{\text{2}}^{{\text{13}}} } = 1020.5a_{{\text{C}}_{\text{1}} }^2 a_{{\text{C}}_{\text{2}} }^{\text{2}} /(1 + S_{{\text{CC}}}^{\text{2}} ) - 8.2$$ . Here the coupling constants are expressed in cps units. In the calculation of the maximum overlap hybrids either the experimental bond lengths or a standard bond lengths were used. For the \(J_{{\text{C}}^{{\text{13}}} - {\text{H}}}\) and \(J_{{\text{C}}^{{\text{13}}} - {\text{H}}} \) coupling constants the standard deviations are 0.9 cps and 1.9 cps respectively. It has been suggested that the large additive constant in the \(J_{{\text{C}}^{{\text{13}}} - {\text{H}}}\) correlation may be attributed to the ionic character of C-H bonds. A good agreement with the experimental data strongly supports the idea that the Fermi contact term and the hybridization are dominant factors in determining carbon-hydrogen and carbon-carbon spin-spin coupling constants across one bond, at least in hydrocarbons.