Weak matching rules for quasicrystals

Weak matching rules for a quasicrystalline tiling are local rules that ensure that fluctuations in perp-space are uniformly bounded. It is shown here that weak matching rules exist forN-fold symmetric tilings, whereN is any integer not divisible by four. The result suggests that, contrary to previous indications, quasicrystalline ground states are not confined to those symmetries for which the incommensurate ratios of wavevectors are quadratic irrationals. An explicit method of constructing weak matching rules forN-fold symmetric tilings in two dimensions is presented. It is shown that the generalization of the construction yields weak matching rules in the case of icosahedral symmetry as well.     

Synthesis of dityrosine cross-linked peptide dimers using the Miyaura-Suzuki reaction

[reaction: see text] Since peroxidase-catalyzed dityrosine formation is inefficient for peptides, we have developed alternative conditions for intermolecular dityrosine formation using the Miyaura-Suzuki reaction. A one-pot reaction is effective for cross-linking short peptides, but longer peptides inhibit the Suzuki step, mandating a traditional two-step procedure using potassium acetate for the Miyaura reaction and potassium carbonate for the Suzuki coupling. These palladium-based methods are complementary to the well-established peroxidase-catalyzed oxidative phenolic coupling of full-length proteins.     

In situ preparation of protein-"smart" polymer conjugates with retention of bioactivity

Protein-polymer conjugates are widely used in biotechnology and medicine, and new methods to prepare the bioconjugates would be advantageous for these applications. In this report, we demonstrate that bioactive "smart" polymer conjugates can be synthesized by polymerizing from defined initiation sites on proteins, thus preparing the polymer conjugates in situ. In particular, free cysteines, Cys-34 of bovine serum albumin (BSA) and Cys-131 of T4 lysozyme V131C, were modified with initiators for atom transfer radical polymerization (ATRP) either through a reversible disulfide linkage or irreversible bond by reaction with pyridyl disulfide- and maleimide-functionalized initiators, respectively. Initiator conjugation was verified by electrospray-ionization mass spectroscopy (ESI-MS), and the location of the modification was confirmed by muLC-MSMS (tandem mass spectrometry) analysis of the trypsin-digested protein macroinitiators. Polymerization of N-isopropylacrylamide (NIPAAm) from the protein macroinitiators resulted in thermosensitive BSA-polyNIPAAm and lysozyme-polyNIPAAm in greater than 65% yield. The resultant conjugates were characterized by gel electrophoresis and size exclusion chromatography (SEC) and easily purified by preparative SEC. The identity of polymer isolated from the BSA conjugate was confirmed by (1)H NMR, and the polydispersity index was determined by gel permeation chromatography (GPC) to be as low as 1.34. Lytic activities of the lysozyme conjugates were determined by two standard assays and compared to that of the unmodified enzyme prior to polymerization; no statistical differences in bioactivity were observed.     

OPTICAL AND THERMAL CHARACTERIZATION OF NATURAL (Sepia officinalis) MELANIN

Abstract The optical properties and the thermal diffusivity of natural cuttlefish ( Sepia officinalis ) melanin have been measured. The optical absorption and scattering properties of melanin particles were determined at 580 nm and 633 nm, using photometric and photothermal techniques. For the photometric studies, the absorption and the transport scattering coefficients were determined from the measurements of diffuse reflectance and transmittance. The scattering anisotropy was obtained from an additional measurement of the total attenuation coefficient and independently obtained by goniometry. For photothermal studies, pulsed photothermal radiometry was used to deduce the absorption and transport scattering coefficients via a model based on optical diffusion theory. Pulsed photothermal radiometry was also used to provide the thermal diffusivity of solid melanin pressed pellets.     

Collisional quenching of resonance states of rare gases

We report an experimental study of Xe(³P₁) → Xe(³P₂) electronic quenching by Ar in Xe/Ar mixtures optically excited by the 1470 Å line of Xe. The quenching process was monitored by the observation of the Xe^*₂ second emission continuum at low Xe pressures.     

Formation of [b(n−1)+OH+H]+ ion structural analogs by solution-phase chemistry

Derivatization of a variety of peptides by a method known to enhance anhydride formation is demonstrated by mass spectrometry to yield ions that have elemental composition and fragmentation properties identical to [b(n-1) + OH + H]+ ions formed by gas-phase rearrangement and fragmentation. The [b(n-1) + OH + H]+ ions formed by gas-phase rearrangement and fragmentation and the solution-phase [b(n-1) + OH + H]+ ion structural analogs formed by derivatization chemistry show two different forms of dissociation using multiple-collision CAD in a quadrupole ion trap and unimolecular decomposition in a TOF-TOF; one group yields identical product ions as a truncated form of the peptide with a free C-terminal carboxylic acid and fragments at the same activation energy; the other group fragments differently from the truncated peptide, being more resistant to fragmentation than the truncated peptide and yielding primarily the [b(n-2) + OH + H]+ product ion. Nonergodic electron capture dissociation MS/MS suggests that any structural differences between the specific-fragmenting [b(n-1) + OH + H]+ ions and the truncated peptide is at the C-terminus of the peptide. The specific-fragmentation can be readily observed by MS(n) experiments to occur in an iterative fashion, suggesting that the C-terminal structure of the original [b(n-1) + OH + H]+ ion is maintained after subsequent rearrangement and fragmentation events in peptides which fragment specifically. A mechanism for the formation of specific-fragmenting and nonspecific-fragmenting [b(n-1) + OH + H]+ ions is proposed.     

Solution structure of a beta-peptide ligand for hDM2

We recently reported a beta-peptide foldamer, beta53-1, that folds into a 14-helix in aqueous solution, binds the oncoprotein hDM2 with submicromolar affinity, and potently inhibits the interaction of hDM2 with a peptide derived from the activation domain of p53 (p53AD). Here, we present the solution structure of beta53-1 in methanol. Details of the structure illustrate fundamental and novel elements of beta-peptide folding and recognition. These elements include the detailed arrangement of a complex, 14-helix-stabilizing salt bridge on one helical face, and a unique "wedge into cleft" packing interaction along a second. The structure also reveals how a subtle distortion in the beta53-1 14-helix geometry alters the presentation of its recognition epitope, rendering it particularly well suited for alpha-helix mimicry. The solution structure of beta53-1 demonstrates that well folded beta-peptide oligomers can effectively present an extended, highly variable surface that could be used as a general platform for targeting critical protein-protein interfaces.     

Alanine racemase free energy profiles from global analyses of progress curves

Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1). steady-state kinetic constants, (2). solvent viscosity dependence, (3). spectral analysis of reaction intermediates, (4). equilibrium overshoots for progress curves measured in D(2)O, and (5). the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.     

Additional NMR data on compounds of the type cis-Ti(AA)2X2

Previous work has shown that $\text{cis}$-disubstituted (acac)₂ titanium (IV) complexes exist in solution as nonrigid molecules [1]. These studies were followed by variable temperature ¹H NMR spectroscopy. The spectra shows that for the dialkoxy and dihalo complexes the acetylacetonate (acac) rings exchange the methyl groups between the two nonequivalent sites of the cis isomer. These rearrangements take place $\text{via}$ an intramolecular rearrangement: both twisting and one bond rupture mechanisms have been suggested for these stero-chemical rearrangements [2-4].     

Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer

We demonstrate the existence of a simultaneous degeneracy (not required by symmetry) of three electronic states in malonaldehyde. This is one of the first reports of such a triple degeneracy involving S0, S1, and S2 in a molecule with a closed-shell ground state. We further report on a two-state S2/S1 conical intersection which is higher in energy than the three-state intersection, but closer to the Franck-Condon point. First-principles quantum dynamics calculations of the photochemistry after excitation to S2 show that there is a competition between these intersections, with more than half of the population decaying to S1 through the higher energy S2/S1 intersection. Surprisingly, much of the population which makes it to the triple degeneracy point is not funneled directly to S0, but rather remains trapped on S1. We attribute this to the large dimensionality of the branching plane at a three-state intersection (the degeneracy is lifted along at least five distinct molecular displacements).