An efficient conversion of the carboxylic group of N-Fmoc alpha-amino acids/peptide acids into N-formamides employing isocyanates as key intermediates

Reaction of 96% formic acid with isocyanates derived from N-Fmoc alpha-amino acids/peptide acids catalyzed by DMAP has yielded a new class of stable formamides as crystalline solids which have been characterized by IR, 1H NMR, 13C NMR, and mass spectroscopy. Conversion of the side chain carboxylic acid of N-Fmoc-5-oxazolidinones of Asp/Glu into the N-formyl group also has been accomplished. The reaction is simple, mild, and high yielding.     

Metastable intermediates in the formation of ozone by recombination

The rate of formation of ozone by O(³P) + O₂(³Σ_g⁻) recombination following an energy pulse such as flash photolysis or pulse radiolysis is typically only about half the rate of disappearance of O(³P). Measurements of the growth of the Hartley band of ozone under several experimental conditions are shown to be consistent with reaction of 0.62 of the available O(³P) to form a metastable state of ozone. Deactivation of the metastable state by ground state O₂ is slow (approximately 10⁻¹⁶ cm³ molecule⁻¹ s⁻¹), but it is significant because of its large excess. Deactivation and decomposition of the metastable state by singlet molecular oxygen is rapid.     

An experimental and theoretical study of the gas-phase decomposition of monoprotonated peptide nucleic acids

Peptide nucleic acids (PNAs) are DNA/RNA mimics which have recently generated considerable interest due to their potential use as antisense and antigene therapeutics and as diagnostic and molecular biology tools. These synthetic biomolecules were designed with improved properties over corresponding oligonucleotides such as greater binding affinity to complementary nucleic acids, enhanced cellular uptake, and greater stability in biological systems. Because of the stability and unique structure of PNAs, traditional sequence confirmation methods are not effective. Alternatively, electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry shows great potential as a tool for the characterization and structural elucidation of these oligonucleotide analogs. Extensive gas-phase fragmentation studies of a mixed nucleobase 4-mer (AACT) and a mixed nucleobase 4-mer with an acetylated N-terminus (N-acetylated AACT) have been performed. Gas-phase collision-induced dissociation of PNAs resulted in water loss, cleavage of the methylene carbonyl linker containing a nucleobase, cleavage of the peptide bond, and the loss of nucleobases. These studies show that the fragmentation behavior of PNAs resembles that of both peptides and oligonucleotides. Molecular mechanics (MM+), semiempirical (AM1), and ab initio (STO-3G) calculations were used to investigate the site of protonation and determine potential low energy conformations. Computational methods were also employed to study prospective intramolecular interactions and provide insight into potential fragmentation mechanisms.     

Reduction as a probe for benzothiirene intermediates: Thermal and photochemical decomposition of 1,2,3 -benzothiadiazoles.

Four benzothiadiazoles were either heated at reflux or irradiated at room temperature in tetrahydronaphthalene. The base soluble thiols which were obtained were converted to thiolacetates and analyzed by use of infrared and nmr shift-reagent spectroscopy.     

Carbon-carbon bond formation by ‘double activation’. The synthesis of piperolide and fadyenolide intermediates.

Buenolide anions do not react with orthoesters and butenolides do not react with carbocations derived from acetals and orthoesters. However double activation of the butenolide (as the carbanion) and the alkoxyalkanes (as the stabilised carbocations) leads to high yield carbon-carbon bond formation of some generality.     

Amino acids and peptides—V: Novel peptide bond formation catalyzed by metal ions—III Elucidation of the formation mechanism

Elucidation of the mechanism for peptide bond formation observed when an amino acid ester is treated with anhyd CuCl₂ in an anhyd alcoholic solvent, was attempted using results of IR and visible spectra measurements of the amino acid ester-CuCl₂ complex and accumulated experimental data.This novel reaction proceeds through a mechanism in which the amino anion produced by elimination of the proton from the Cu(II)-coordinating amino group, attacks the non-activated ester CO group of the amino acid ester which shares a common Cu(II) ion. It differs completely from the peptide formation reaction featuring a Co(III)-amino acid ester complex.     

Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42

We report all-atom molecular dynamics simulations of annular beta-amyloid (17-42) structures, single- and double-layered, in solution. We assess the structural stability and association force of Abeta annular oligomers associated through different interfaces, with a mutated sequence (M35A), and with the oxidation state (M35O). Simulation results show that single-layered annular models display inherent structural instability: one is broken down into linear-like oligomers, and the other collapses. On the other hand, a double-layered annular structure where the two layers interact through their C-termini to form an NC-CN interface (where N and C are the N and C termini, respectively) exhibits high structural stability over the simulation time due to strong hydrophobic interactions and geometrical constraints induced by the closed circular shape. The observed dimensions and molecular weight of the oligomers from atomic force microscopy (AFM) experiments are found to correspond well to our stable double-layered model with the NC-CN interface. Comparison with K3 annular structures derived from the beta 2-microglobulin suggests that the driving force for amyloid formation is sequence specific, strongly dependent on side-chain packing arrangements, structural morphologies, sequence composition, and residue positions. Combined with our previous simulations of linear-like Abeta, K3 peptide, and sup35-derived GNNQQNY peptide, the annular structures provide useful insight into oligomeric structures and driving forces that are critical in amyloid fibril formation.     

O-selectivity and utility of phosphorylation mediated by phosphite triester intermediates in the N-unprotected phosphoramidite method

Previously, O-selective phosphorylation on polymer supports in the N-unprotected phosphoramidite method could not be carried out because the amino groups of dA and dC have high reactivity toward tervalent phosphorus(III)-type phosphitylating reagents. In this paper, we developed a new coupling strategy named the "activated phosphite method" in which the phosphitylation is mediated by phosphite triester intermediates 1. Application of 1-hydroxybenzotriazole as the promoter to the solid-phase synthesis resulted in excellent O-selectivity of more than 99.7%. This O-selectivity was explained by the frontier molecular orbital interactions between the reactive intermediates and the nucleophiles such as the amino or hydroxyl groups of nucleosides. Furthermore, longer oligonucleotides were synthesized not only by a manual operation but also by a DNA synthesizer. The utility of our new method was demonstrated by the successful synthesis of a base-labile modified oligodeoxyribonucleotide having 4-N-acetyldeoxycytidine residues. Finally, DNA 20-mers containing dA or dC could be synthesized in good yields by use of a combined reagent of 6-trifluoromethyl-1-hydroxybenzotriazole and benzimidazolium triflate.