Characterization and sequence confirmation of unnatural amino acid containing peptide libraries using electrospray ionization mass spectrometry

The content of 24 12-membered heptapeptide libraries was investigated using capillary liquid chromatography coupled with an electrospray ionization quadrupole orthogonal acceleration time-of-flight mass spectrometer. Adjustment of the chromatographic parameters led to the separation of most of the components. Extraction of the [M + 2H]2+ ions allowed us to demonstrate the presence of all expected species in the library and to evaluate their relative abundance in the mixture. Rapid sequence confirmation was achieved by subtraction of product ion spectra, a way to eliminate common ions and to simplify the spectra for interpretation. This technique can also easily be applied to other libraries consisting of components with a common core.     

Amplification of Chirality in Helical Supramolecular Columns

Strong amplification of chirality occurs in dynamic, but highly ordered, helical columns in n-butanol, for which one chiral seed molecule suffices to render a column of 400 molecules to become homochiral. The chiral columns are formed in a thermally dependent stepwise process. The transition from achiral stacks to helical columns is highly cooperative owing to well-defined intermolecular interactions. `Sergeant and Soldiers' measurements allow for the calculation of the association constant and cooperativity length of the homochiral segments. The `Sergeant and Soldiers' data on the number of molecules within a column show a strikingly good match with data obtained from a theoretical model describing the self-assembly of the discotic molecules as a function of temperature and concentration.     

Iterative tandem catalysis of racemic AB monomers

Racemic AB monomers encompassing a secondary hydroxy group and a methyl ester moiety were synthesized and converted to chiral polyesters by iterative tandem catalysis (ITC). The concurrent action of an enantioselective acylation catalyst (Novozym 435) and a racemization catalyst (Ru(Shvo)) results in the high conversion of the racemic monomers to enantio‐enriched polymers. Several factors are important for attaining high ee's and high molecular weights. The enantioselectivities observed for the novel AB monomers by Novozym 435 are high enough at 70 °C (E ratio ≥ 200) for the monomers to be useful for ITC. ITC of methyl 6‐hydroxyheptanoate showed that a catalyst loading of ～1.4 mol % Ru(Shvo), 25 mg Novozym 435/mmol AB monomer, and 0.5 mmol DMP/mmol monomer employing a monomer concentration of 1 mol/L gave a monomer conversion of 94%, an ee of 91%, and an M_p of 6.0 kg/mol. Application of these conditions to the other AB monomers revealed the sensitivity of the system. Reduced enantioselectivities were observed when longer reaction times were required for attaining high conversions. These long reaction times were necessary due to the slow (or absent) racemization activity of the Ru(Shvo) catalyst as a result of catalyst deactivation. Since quantitative conversions are crucial to attain high molecular weight polymers in polycondensation reactions, we could significantly improve the system by switching to isopropyl esters of the AB monomers and/or by strict exclusion of oxygen during the ITC. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2721–2733, 2008     

Radiation damage in Si1−x Ge x heteroepitaxial devices

Results are presented of an extended study on the induced lattice defects and their effects on the degradation of Si_1−x Ge _x devices, subjected to a 20 MeV alpha-ray, 1 MeV electron, 1 MeV fast neutron, and 20 and 86 MeV proton irradiations. The degradation of the electrical device performance increase with increasing fluence, while it decreases with increasing germanium content. In the Si_1−x Ge _x epitaxial layers, electron capture levels associated with an interstitial-substitutional boron complex are induced. The radiation source dependence of performance degradation is attributed to the difference of mass and the probability of nuclear collision for the formation of lattice defects.     

Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed

Recently, it has been shown that the red fluorescent protein DsRed undergoes photoconversion on intense irradiation, but the mechanism of the conversion has not yet been elucidated. Upon irradiation with a nanosecond-pulsed laser at 532 nm, the chromophore of DsRed absorbing at 559 nm and emitting at 583 nm (R form) converts into a super red (SR) form absorbing at 574 nm and emitting at 595 nm. This conversion leads to a significant change in the fluorescence quantum yield from 0.7 to 0.01. Here we demonstrate that the photoconversion is the result of structural changes of the chromophore and one amino acid. Absorption, fluorescence, and vibrational spectroscopy as well as mass spectrometry suggest that a cis-to-trans isomerization of the chromophore and decarboxylation of a glutamate (E215) take place upon irradiation to form SR. At the same time, another photoproduct (B) with an absorption maximum at 386 nm appears upon irradiation. This species is assigned as a protonated form of the DsRed chromophore. It might be a mixture of several protonated DsRed forms as there is at least two ways of formation. Furthermore, the photoconversion of DsRed is proven to occur through a consecutive two-photon absorption process. Our results demonstrate the importance of the chromophore conformation in the ground state on the brightness of the protein as well as the importance of the photon flux to control/avoid the photoconversion process.     

New dsDNA‐Binding Hybrid Molecules Combining an Unnatural Peptide and an Intercalating Moiety

In our search for new dsDNA‐binding ligands, combinatorial chemistry was first applied to select unnatural oligopeptides with moderate affinity for dsDNA. To enhance the binding affinity of a heptapeptide lead structure, Ac‐Arg‐Ual‐Sar‐Chi‐Chi‐Tal‐Arg‐NH₂ (K_d=4.9?10^?4 M ), the compound was conjugated to different heteropolyaromatic moieties by means of a variety of linker arms. Glycine, β‐alanine, glycyl‐glycine, glycyl‐β‐alanine, γ‐aminobutyric acid, and 6‐aminocaproic acid were used as spacers, representing different lengths and/or flexibilities. The intercalators coupled to the oligopeptide were acridine, fluorenone, anthracene, anthraquinone, and 3,8‐diamino‐5‐methyl‐6‐phenylphenantridinium (methidium). The binding capacities of these new hybrid molecules to dsDNA have been investigated by gel retardation and footprinting assays. The results show that, by conjugating the unnatural oligopeptide to intercalators, the affinity for dsDNA could be enhanced more than 100‐fold. For methidium‐β‐alanyl‐glycyl‐Arg‐Ual‐Sar‐Chi‐Chi‐Tal‐Arg‐NH₂ (K_d of 2.1?10^?6 M ), the interaction with dsDNA was dominated by the intercalator in such a way that the sequence specificity of the heptapeptide was changed. The interaction with dsDNA of hybrid molecules of other intercalators was mainly governed by the oligopeptide, since the sequence selectivity of the heptapeptide was conserved. In general, the linker arm glycine (shortest spacer) and glycine‐β‐alanine were preferred over β‐alanine, glycyl‐glycine and the more‐flexible spacers γ‐aminobutyric acid and 6‐aminocaproic acid. This way new hybrid molecules endowed with dsDNA affinities of ca. 10^?6 M and displaying different sequence selectivities have been developed. Therefore, combinations of such unnatural peptides with intercalators can be used to broaden the knowledge about the sequence‐selective recognition of dsDNA.     

Toward poly(aminophthalimide), structures of dimers and trimers

Poly(aminophthalimide) (PAP) dimers and trimers have been synthesized by palladium-catalyzed cross-coupling reactions of 3-aminophthalimides with 3-chloro- and 3,6-dichlorophthalimide, respectively. When Pd(OAc)₂, XPhos (2-dicyclohexylphosphino-2′,4′,6′-triisopropylbiphenyl), and K₃PO₄ are used, the C-N bond-forming reactions proceed quantitatively. The structures of those oligomers are examined by experimental and theoretical techniques including NMR, IR, single-crystal X-ray diffraction, and DFT calculations. The strong preference for cisoid structure of the diphthalimidylamine unit bearing a bifurcate hydrogen bonding is disclosed. Therefore, the aminophthalimide backbone is a highly promising candidate for the construction of a dynamically ordered helical structure.     

Non-destructive Removal of the Bornanesultam Auxiliary in α-Substituted N-Acylbornane-10,2-sultanis under Mild Conditions: An efficient synthesis of enantiomerically pure ketones and aldehydes

α-Substituted N-acylbornane-10, 2 -sultams 6, 9 , and 10 can be converted into enantiomerically pure ketones 5. 13 , and 14 , respectively, via a two-step procedure involving a known mercaptolysis reaction followed by an [Fe(acac)₃]-mediated coupling of the resulting S-benzyl thioesters with Grignard reagents. Furthermore, enantiomerically pure aldehydes 23 can be obtained from α-substituted N-acylbornane-10,2-sultams 6 via a one-step reduction with (i-Bu)₂AIH. No epimerization at the α-chiral center is observed during the cleavage reaction whereby the chiral auxiliary, bornane-10,2-sultam 1 or ent- l , was recovered. By using this methodology, several natural products or precursors thereof can be prepared.     

Symmetrical electron-deficient materials incorporating azaheterocycles

To investigate the potential of di- and tri-azaheterocycles as building blocks for pi-conjugated materials with high electron affinity, linear oligomers incorporating pyrazine and a C(3)-symmetric discotic molecule based on triazine were synthesized. The tridodecyloxyphenyl end-capped ethynylene pyrazinylene oligomers showed remarkable solvatochroism in absorption and emission in solution. The oligomers containing one and two pyrazine rings displayed liquid crystallinity in the solid state. The largest ethynylene pyrazinylene oligomer containing three pyrazine rings had the lowest first reduction potential at -1.08 V. The triazine-derived discotic molecule exhibited UV/Vis and fluorescence behavior comparable to that of the linear oligomers and featured a first reduction potential at -1.49 V, somewhat lower than expected.