Acyclic peptides as conformational models Crystal structure of Boc-Aib-Leu-Pro-NHMe± 2H2O

The tripeptide Boc-Aib-Leu-Pro-NHMe crystallizes in the orthorhombic space group P212121 with a = 9.542, b = 15.200, c = 18.256 Å and Z = 4. Each peptide is associated wth two water molecules in the asymmetric unit of the crystal. The structure has been solved by direct methods and refined to an R-value of 0.069. The peptide adopts a structure without any intramolecular hydrogen bond. The three residues occupy distinctly different regions of the Ramachandran map: Aib in the left-handed 310-helical region (± = 67°, ± = 23°), Leu in the β-sheet region (± = - 133°, ± = 142°) and Pro in the poly (Pro) II region (± = - 69°, ± = 151°). An interesting observation is that each water molecule participates in four hydrogen bonds with distorted tetrahedral coordination about the oxygen atom.

Resonance raman intensity analysis of polyatomic molecules

A time-dependent quantum mechanical (TDQM) method of wavepacket propagation in computing resonance Raman intensities for polyatomic systems, has been developed and demonstrated by applying it tocis-stilbene andtrans-azobenzene. In the case of the former, Raman excitation profiles (REPs) for the various vibrational modes have also been computed. It is observed that the calculated absorption spectrum and the REPs compare very well with the experimental results. A comparison of these results with those of the often semiclassical approach reveals that the TDQM method can be used to study polyatomic systems with as much ease as the semiclassical wavepacket method.

A comparative Raman study of the interaction of electron donor and acceptor molecules with graphene prepared by different methods

Interaction of tetrathiafulvalene (TTF) and tetracyanoethylene (TCNE) with few-layer graphene samples prepared by the exfoliation of graphite oxide (EG), conversion of nanodiamond (DG) and arc-evaporation of graphite in hydrogen (HG) has been investigated by Raman spectroscopy to understand the role of the graphene surface. The position and full-width at half maximum of the Raman G-band are affected on interaction with TTF and TCNE and the effect is highest with EG and least with HG. The effect of TTF and TCNE on the 2D-band is also maximum with EG. The magnitude of interaction between the donor/acceptor molecules varies in the same order as the surface areas of the graphenes. (C) 2009 Published by Elsevier B. V.

NMR spectra of oriented biologically important molecules - The structure of and the internal rotation in N,N'-dimethyluracil

From the proton NMR spectra of Nfl-dimethyluracil oriented in two different nematic solvents, the internal rotation of the methyl groups about the N-C bonds is studied. It has been observed that the preferred conformation of the methyl group having one carbonyl in the vicinity is the one where a C-H bond is in the ring plane pointing toward the carbonyl group. The results are not sensitive to the mode of rotation of the other methyl group. These data are interpreted in terms of the bond polarizations.

Omega-Hydroxylation of acyclic monoterpene alcohols by rat lung microsomes

Rat lung microsomes were shown to �-hydroxylate acyclic monoterpene alcohols in the presence of NADPH and O2. NADH could neither support hydroxylation efficiently nor did it show synergistic effect. The hydroxylase activity was greater in microsomes prepared from β-naphthoflavone (BNF)-treated rats than from phenobarbital (PB)-treated or control microsomal preparations. Hydroxylation was specific to the C-8 position in geraniol and has a pH optimum of 7.8. The inhibition of the hydroxylase activity by SKF-525A, CO, N-ethylmaleimide, ellipticine, α-naphthoflavone, cyt. Image and p-CMB indicated the involvement of the cyt. P-450 system. However, NaN3 stimulated the hydroxylase activity to a significant level. Rat kidney microsomes were also capable of �-hydroxylating geraniol although the activity was lower than that observed with lungs.

First hyperpolarizability of bacteriorhodopsin, retinal and related molecules revisited

The previously reported beta values of BR and retinal based chromophores were very high but subsequent measurements found them to be much less. We have found that the beta values of these compounds do not vary so much with experimental conditions as with the method of analysis. Hyper-Rayleigh scattering measurements at 1543 and 1907 nm produce more realistic beta values close to the intrinsic (static) hyperpolarizability, beta(0) which for BR is still very high (275 x 10 (30) esu). The optical nonlinearity of BR arises entirely due to the protonated retinal Schiff Base (PRSB) which in its isolated form has the same intrinsic hyperpolarizability as that of the rotein.

A note on acyclic edge coloring of complete bipartite graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic (2-colored) cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). Let Delta = Delta(G) denote the maximum degree of a vertex in a graph G. A complete bipartite graph with n vertices on each side is denoted by K-n,K-n. Alon, McDiarmid and Reed observed that a'(K-p-1,K-p-1) = p for every prime p. In this paper we prove that a'(K-p,K-p) <= p + 2 = Delta + 2 when p is prime. Basavaraju, Chandran and Kummini proved that a'(K-n,K-n) >= n + 2 = Delta + 2 when n is odd, which combined with our result implies that a'(K-p,K-p) = p + 2 = Delta + 2 when p is an odd prime. Moreover we show that if we remove any edge from K-p,K-p, the resulting graph is acyclically Delta + 1 = p + 1-edge-colorable. (C) 2009 Elsevier B.V. All rights reserved.

Self-Assembly of Bile Steroid Analogues: Molecules, Fibers, and Networks

Structural and rheological features of a series of molecular hydrogels formed by synthetic bile salt analogues have been scrutinized. Among seven gelators, two are neutral compounds, while the others are cationic systems among which one is a tripodal steroid derivative. Despite the fact that the chemical structures are closely related, the variety of physical characteristics is extremely large in the structures of the connected fibers (either plain cylinders or ribbons), in the dynamical modes for stress relaxation of the associated SAFINs, in the scaling laws of the shear elasticity (typical of either cellular solids or fractal floc-like assemblies), in the micron-scale texture and the distribution of ordered domains (spherulites, crystallites) embedded in a random mesh, in the type of nodal zones (either crystalline-like, fiber entanglements, or bundles), in the evolution of the distribution and morphology of fibers and nodes, and in the sensitivity to added salt. SANS appears to be a suitable technique to infer all geometrical parameters defining the fibers, their interaction modes, and the volume fraction of nodes in a SAFIN. The tripodal system is particularly singular in the series and exhibits viscosity overshoots at the startup of shear flows, an “umbrella-like” molecular packing mode involving three molecules per cross section of fiber, and scattering correlation peaks revealing the ordering and overlap of 1d self-assembled polyelectrolyte species.

Acyclic Edge Coloring of Graphs with Maximum Degree 4

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). It was conjectured by Alon, Sudakov, and Zaks that for any simple and finite graph G, a'(G) <= Delta+2, where Delta=Delta(G) denotes the maximum degree of G. We prove the conjecture for connected graphs with Delta(G)<= 4, with the additional restriction that m <= 2n-1, where n is the number of vertices and m is the number of edges in G. Note that for any graph G, m <= 2n, when Delta(G)<= 4. It follows that for any graph G if Delta(G)<= 4, then a'(G) <= 7.

Binary decompositions and acyclic schemes

It is well known that the notions of normal forms and acyclicity capture many practical desirable properties for database schemes. The basic schema design problem is to develop design methodologies that strive toward these ideals. The usual approach is to first normalize the database scheme as far as possible. If the resulting scheme is cyclic, then one tries to transform it into an acyclic scheme. In this paper, we argue in favor of carrying out these two phases of design concurrently. In order to do this efficiently, we need to be able to incrementally analyze the acyclicity status of a database scheme as it is being designed. To this end, we propose the formalism of "binary decompositions". Using this, we characterize design sequences that exactly generate theta-acyclic schemes, for theta = agr,beta. We then show how our results can be put to use in database design. Finally, we also show that our formalism above can be effectively used as a proof tool in dependency theory. We demonstrate its power by showing that it leads to a significant simplification of the proofs of some previous results connecting sets of multivalued dependencies and acyclic join dependencies.

Hydroxylation of oxygen-covered Cu(110) and Zn(0001) surfaces by interaction with CH3OH, (CH3)2NH, H2S, HCl and other proton donor molecules

EELS studies provide definitive evidence for the hydroxylation of oxygen-covered Cu(110) and Zn(0001) surfaces on interaction with proton donor molecules such as H2O, CH3OH, HCOOH, NH3 and (CH3)2NH. The occurrence of surface hydroxylation is unambigouusly shown by a study of the interaction of H2S and HCl with an oxygen covered Cu(110) surface.

Side-band intensities in the deuterium magnetic resonance spectra of oriented molecules spinning near the magic angle

The appearance of spinning side bands in the 2H NMR spectra of oriented molecules is investigated. A theoretical interpretation of the side-band intensities is carried out. Information derived on the director orientation and distribution as a function of spinning speedis reported.

A necessary and sufficient condition for acyclic graphs

This letter gives a new necessary and sufficient condition to determine whether a directed graph is acyclic.

Electron-Energy Loss Spectroscopy (Eels) Of Organic-Molecules In Vapor-Phase - Design And Fabrication Of An Indigenous Eel Spectrometer

An indigenous electron energy loss spectrometer has been designed and fabricated for the study of free molecules. The spectrometer enables the recording of low-resolution electronic spectra of molecules inthe vapour phase with ready access to the vacuum ultraviolet region. Electron energy loss spectra of aliphatic alcohols and carbonyl compounds as wellas of benzene derivatives have been recorded with the indigenous spectrometer and the electronic transitions in these molecules discussed.

Jump Reorientation of Water Molecules Confined in Narrow Carbon Nanotubes

We used molecular dynamics (MD) simulations to study the reorientational dynamics of water molecules confined inside narrow carbon nanotubes immersed in a bath of water. Our simulations show that the confined water molecules exhibit bistability in their reorientational relaxation, which proceeds by angular jumps between the two stable states. The angular jump of a water molecule in the bulk involves the breaking of a hydrogen bond with one of its neighbors and the formation of a hydrogen bond with a different neighbor. In contrast, the angular jump of a confined water molecule corresponds to an interchange of the two hydrogen atoms that can form a hydrogen bond with the same neighbor. The free energy barrier between these two states is a few k(B)T. The analytic solution of a simplified two-state jump model that qualitatively explains the reorientational behavior observed in simulations is also presented.