Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.     

Contrasting behavior in azide pyrolyses: an investigation of the thermal decompositions of methyl azidoformate, ethyl azidoformate and 2-azido-N, N-dimethylacetamide by ultraviolet photoelectron spectroscopy and matrix isolation infrared spectroscopy

The thermal decompositions of methyl azidoformate (N3COOMe), ethyl azidoformate (N3COOEt) and 2-azido-N,N-dimethylacetamide (N3CH2CONMe2) have been studied by matrix isolation infrared spectroscopy and real-time ultraviolet photoelectron spectroscopy. N2 appears as an initial pyrolysis product in all systems, and the principal interest lies in the fate of the accompanying organic fragment. For methyl azidoformate, four accompanying products were observed: HNCO, H2CO, CH2NH and CO2, and these are believed to arise as a result of two competing decomposition routes of a four-membered cyclic intermediate. Ethyl azidoformate pyrolysis yields four corresponding products: HNCO, MeCHO, MeCHNH and CO2, together with the five-membered-ring compound 2-oxazolidone. In contrast, the initial pyrolysis of 2-azido-N,N-dimethyl acetamide, yields the novel imine intermediate Me2NCOCH=NH, which subsequently decomposes into dimethyl formamide (HCONMe2), CO, Me2NH and HCN. This intermediate was detected by matrix isolation IR spectroscopy, and its identity confirmed both by a molecular orbital calculation of its IR spectrum, and by the temperature dependence and distribution of products in the PES and IR studies. Mechanisms are proposed for the formation and decomposition of all the products observed in these three systems, based on the experimental evidence and the results of supporting molecular orbital calculations.     

Studies on the synthesis of (+/-)-stenine: a combined intramolecular [4 + 2]-cycloaddition/rearrangement cascade

Several cyclic 2-(methylthio)-5-amidofurans containing tethered unsaturation were prepared via the reaction of dimethyl(methylthio)sulfonium tetrafluoroborate (DMSTF) with beta-alkoxy-gamma-dithiane lactams. Thermolysis of these furans resulted in an intramolecular Diels-Alder reaction (IMDAF). The resulting oxa-bridge cycloadducts underwent a subsequent 1,2-methylthio shift to form tricyclic lactams in high yield. Furan 9, annealed to an azepine ring, underwent the IMDAF reaction at or below room temperature. Conformational effects imposed by the placement of a carbonyl group within the tether, combined with a rotational bias about the C(2)-N bond, enhances the rate of the IMDAF reaction of the seven-ring system so that it occurs readily at 25 degrees C. The feasibility of using the cascade sequence in the context of a total synthesis of the Stemona alkaloid (+/-)-stenine was explored. The eventual synthesis of (+/-)-stenine was carried out by an intramolecular Diels-Alder reaction of a 2-amido-5-methylthio-substituted furan containing a trans-pent-3-enoic acid methyl ester side chain in order to create the desired azepinoindole skeleton. This was followed by a series of reductions to set the syn-anti stereochemical relationship at the incipient ring fusion sites present in stenine. All six stereocenters at the azepinoindole core were derived in high stereoselectivity from the functionality present in the rearranged cycloadduct 10. Compound 10 was converted to stenine in 11 additional steps via a sequence that features a Crabtree's-catalyst directed hydrogenation, iodolactonization, and a Keck allylation.     

Cu3(mu-S)2]3+ clusters supported by N-donor ligands: progress toward a synthetic model of the catalytic site of nitrous oxide reductase

By treating Cu(I) complexes of neutral, bidentate N-donor ligands with S8, clusters with novel delocalized mixed-valence [Cu3(mu-S)2]3+ cores have been isolated. X-ray crystal structures and UV-vis and resonance Raman spectral features of these clusters reveal similarities to the tetracopper-sulfide "CuZ" site in nitrous oxide reductase. A delocalized S = 1 ground state for the mixed-valent CuIIICu2II cores is supported by the observation of high symmetry in the X-ray structures and 10-line hyperfine features arising from coupling to three equivalent Cu ions in EPR spectra obtained at room temperature (shown) and 10 K. The delocalization we observe contrasts with the localization reported previously for a [Cu3(mu-O)2]3+ analogue (Root, D. E.; Henson, M. J.; Machonkin, T.; Mukherjee, P.; Stack, T. D. P.; Solomon, E. I. J. Am. Chem. Soc. 1998, 120, 4982), which we rationalized through DFT calculations.     

Optimization of the electrophoretic deposition of YBa2Cu3O7−x superconducting large area coatings

Large area coatings (>10cm²) of the high temperature superconductor YBa₂Cu₃O_7–x (x = 0.1 – 0.2) (YBCO) have been prepared by scale up an electrophoretic deposition technique using silver sheets and Si-wafers coated with Ag or Au as substrates. Several parameters, like the kind of the solvent, the applied voltage, the distance between the electrodes, the initial concentration of the suspension and the temperature during the electrophoresis were investigated in order to attain high deposition rates, as well as uniform YBCO coatings with the proper stoichiometry. To obtain a strongly adherent and dense coating a subsequent appropriate sintering and annealing procedure has been developed. The coatings obtained were characterized for their stoichiometry and superconducting properties by X-ray diffraction (XRD), Raman spectroscopy and magnetic measurements. The homogeneity and thickness of the films and the average grain size of the deposited particles have been investigated by optical and scanning electron microscopy (SEM).     

MNDO Study of reaction pathways for SN2 reactions. Menschutkin reaction potential energy surfaces

MNDO molecular orbital calculations have been employed to investigate limited reaction pathways and potential energy surfaces for a series of S_N2 reactions. Model calculations for X^? + CH₃X (X = H, F, OH, OCH₃, and CN) indicate that the MNDO method gives qualitative agreement with ab initio studies except for the hydride–CH₄ exchange. Studies involving alkylation of pyridine (Menschutkin reaction) were also carried out. For the reaction of pyridine with CH₃Cl, which involves charge separation, our MNDO studies (which do not include solvation effects) do not produce a characteristic S_N2 pathway. For the reaction of pyridine with trimethyloxonium cation [(CH₃)₃O⁺] as the alkylating agent, a well defined S_N2 reaction pathway was obtained; this reaction involves charge transfer. A potential energy surface for the pyridine–trimethyloxonium cation reaction shows the presence of a saddle point transition state that resembles starting materials, in agreement with the Hammond postulate for this exothermic reaction.     

The anhydride structure of several previously reported stable areneselenenic acids1

The compounds previously reported² to be the stable areneselenenic acids, $\text{o}$-nitro-($\text{la}$ and $\text{+o}$-benzoylbenzeneselenenic acid ($\text{lb}$), are shown actually to be the corresponding selenenic anhydrides (ArSeOSeAr). Solutions of the selenenic acids (ArSeOH), however, can be easily generated from the anhydrides byacid-catalyzed hydrolysis.