UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting

We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.     

Carbon Participation in the Solvolysis of 6-exo-substituted 2-exo- and 2-endo-Norbornyl p-Toluenesulfonates. Norbornanes part 5

The solvolysis rates and products of the 6-exo-substituted 2-exo- 1a - 1u , and 2-endo-norbornyl p-toluenesulfonates 2a - 2u , have been determined. In general, the rate constants for 1 and 2 (log k) correlate well with the inductive constants σ of the substitutents at C(6); however, their sensitivity to σ is much larger in the 2-exo-series 1 than in the 2-endo-series 2 . This differential transmission of polar effects is the cause of decreasing 2-exo/2-endo rate ratios from 2388 for R = t-C₄H₉ to 0.37 for R = Br, i. e. with increasing electron attraction by the substituent. The high sensitivity of the rate constants for the 2-exo-p-toluenesulfonates 1 to σ indicates an unusually strong inductive interaction between C(6) and the incipient cationic center at C(2). This interaction is ascribed to the participation of the pentacoordinate C(6)-atom, i. e. to 1,3-bridging, a consequence of steric hindrance of nucleophilic solvent participation in norbornanes. Donor substituents enhance 1,3-bridging, lead to faster reactions and to the formation of 2-exo substitution products. Conversely, acceptor substituents reduce 1,3-bridging, decrease rates and facilitate the formation of 2-endo substitution products. Graded 1,3-bridging is discussed in the light of Winstein's nonclassical ion concept.     

Formation of spatially patterned colloidal photonic crystals through the control of capillary forces and template recognition

We report the formation of microscopic patterns of substrate-supported, 3D planar colloidal crystals using physical confinement in conjunction with surfaces displaying predetermined binary patterns of hydropholicity. The formation process involves a primary self-assembly wherein nano- and microscale colloids order into a photonic fcc lattice via capillary interactions followed by a secondary template-induced crystal cleavage step. Following this method, arbitrary arrays of pattern elements, which preserve structural and orientational properties of the parent crystal, can be easily obtained.     

Photoelectron spectroscopy of S1 toluene: II. Intramolecular dynamics of selected vibrational levels in S1 toluene studied by nanosecond and picosecond time-resolved photoelectron spectroscopies

We present results which suggest that the photophysics of S(1) toluene is significantly more complicated than that of the related molecules p-fluorotoluene or p-difluorobenzene. We have measured a range of photoelectron spectra for a number of S(1) internal energies, on different time scales and at different temperatures, in an attempt to unravel the competing processes, but the final conclusion remains outstanding.     

Compositionally modulated Fermi surfaces, structured diffuse scattering and ternary derivatives of 1T-TaS2

Ternary derivatives of 1T-TaS₂ have been synthesized and the variation in the highly structured diffuse intensity distributions characteristic of such materials carefully monitored to investigate the effect that such substitution has upon the band structures and Fermi surfaces (FSs) of the materials. Removal of d electrons via the replacement of Ta ions with lower valent transition metal ions leads to a systematic increase in the radii of the characteristic structured diffuse intensity distribution. Extended Hückel tight binding calculations of the FSs of the doped samples are carried out and used to predict possible nesting wave-vectors. The results are in reasonably good agreement with the radii of the experimentally observed diffuse intensity distributions.     

Properties of nucleic acid staining dyes used in gel electrophoresis

Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed? was the most sensitive and safest dye to use with UV light excitation, and both GelGreen? and Diamond? Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.     

Gas-phase fragmentation of long-lived cysteine radical cations formed via no loss from protonated S-nitrosocysteine

In this work, we describe two different methods for generating protonated S-nitrosocysteine in the gas phase. The first method involves a gas-phase reaction of protonated cysteine with t-butylnitrite, while the second method uses a solution-based transnitrosylation reaction of cysteine with S-nitrosoglutathione followed by transfer of the resulting S-nitrosocysteine into the gas phase by electrospray ionization mass spectrometry (ESI-MS). Independent of the way it was formed, protonated S-nitrosocysteine readily fragments via bond homolysis to form a long-lived radical cation of cysteine (Cys^•+), which fragments under collision-induced dissociation (CID) conditions via losses in the following relative abundance order: •COOH ≫ CH₂S > •CH₂SH-H₂S. Deuterium labeling experiments were performed to study the mechanisms leading to these pathways. DFT calculations were also used to probe aspects of the fragmentation of protonated S-nitrosocysteine and the radical cation of cysteine. NO loss is found to be the lowest energy channel for the former ion, while the initially formed distonic Cys^•+ with a sulfur radical site undergoes proton and/or H atom transfer reactions that precede the losses of CH₂S, •COOH, •CH₂SH, and H₂S.     

A Review of Surface Functionalized Amine Terminated Dendrimers for Application in Biological and Molecular Sensing

Dendrimers are three dimensional nanosized synthetic molecules that have internal cavities and numerous surface groups. In recent times they have received increased attention in sensing applications. For dendrimers to be used as sensors, they most commonly require functionalization at their surface. This is because the surface is generally the first point of contact between the dendrimer and the outside world, hence surface functionalization serves to selectively home in on the target analyte. Further, sensor signals may be transmitted through surface functionalities e.g. fluorochromic molecules. It is therefore important to document surface functionalization approaches. Dendrimers with amine surface groups have the advantage of being able to be conjugated to other molecules via an amide linkage, which is one of the most fundamental and widespread chemical bonds in nature. In this paper we demonstrate the properties of dendrimers that make them so applicable to sensing. We review several methods for functionalizing dendrimers via an amide linkage, as well as present a review of surface functionalized polyamidoamine, polyamine, and polypeptide dendrimers that have been employed for biological, chemical and molecular sensing.     

Stöber silica particles as basis for redox modifications: particle shape, size, polydispersity, and porosity

The synthesis of Stöber silica particles as basis for redox modifications is optimized for desired properties, in particular diameter in a wide sub-micrometer range, spherical shape, monodispersity, the absence of porosity, and aggregation free isolability for characterization and later covalent modification. The materials are characterized by SEM, DLS, nitrogen sorption isotherms, helium as well as Gay-Lussac (water) pycnometry, and DRIFT spectroscopy. Particles with diameters between approximately 50 and 800 nm are obtained by varying the concentrations of the reagents and reactants, the type of solvent as well as the temperature. The use of high water concentrations and post-synthetic calcination at 600 °C results in silica particles that can be considered as nonporous with respect to the size of the active molecules to be immobilized. The effect of reaction temperature on size distribution is identified. Low polydispersity is achieved by performing the reaction in a temperature range in which a change in temperature has only a weak or no effect on the final particle diameter. Upon optimization of the sol–gel process, the shape of the particles is still spherical. The agreement between experimental and geometric data is within the expected precision of the characterization techniques.     

Structure and stability of the (001) alpha-quartz surface

The structure and surface energies of the cleaved, reconstructed, and fully hydroxylated (001) alpha-quartz surface of various thicknesses are investigated with periodic density functional theory (DFT). The properties of the cleaved and hydroxylated surface are reproduced with a slab thickness of 18 atomic layers, while a thicker 27-layer slab is necessary for the reconstructed surface. The performance of the hybrid DFT functional B3LYP, using an atomic basis set, is compared with the generalised gradient approximation, PBE, employing plane waves. Both methodologies give similar structures and surface energies for the cleaved and reconstructed surfaces, which validates studying these surfaces with hybrid DFT. However, there is a slight difference between the PBE and B3LYP approach for the geometry of the hydrogen bonded network on the hydroxylated surface. The PBE adsorption energy of CO on a surface silanol site is in good agreement with experimental values, suggesting that this method is more accurate for hydrogen bonded structures than B3LYP. New hybrid functionals, however, yield improved weak interactions. Since these functionals also give superior activation energies, we recommend applying the new functionals to contemporary issues involving the silica surface and adsorbates on this surface.