The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization

A new method for constrained nonlinear optimization known as the ellipsoid algorithm is evaluated as a means of determining and refining the conformations of peptides. Advantages of the ellipsoid algorithm over conventional optimization methods include that it avoids many local minima that other methods would be trapped by, and that it is sometimes able to find optimum solutions in which the constraints are satisfied exactly. The dihedral angles about single bonds were used as variables to keep the dimensionality low (the rate of convergence decreases rapidly with increasing dimensionality of the problem). The method is evaluated on problems involving distance constraints, and for minimization of conformational energy functions. In an initial application, conformations consistent with an experimental set of NMR distance constraints were obtained in a problem involving 48 variable dihedral angles.     

Studies on the preparation and exchange reactions of 5-deuterated uracils

The mechanism of base catalyzed proton exchange at the 5-position of uracil and its N-methylated derivatives has been studied. These reactions proceed by addition — elimination across the 5,6-double bond when the 1-nitrogen is substituted with a methyl group, or with anchimeric assistance of the N-1 anion if the 1-position is unsubstituted. The base catalyzed hydrolyses of 1,3-dimethyluracil and 3-methyluracil also appear to proceed through hydrated intermediates. A facile method for an acid catalyzed preparation of 5-deuterated uracils is described as well as a simple and accurate method for analysis of deuterium content.     

Ion exchange resins in steel analysis

The metals vanadium, chromium and molybdenum may be separated from the other constituents of steel by passing an acetate buffered solution of the steel through a strongly basic onion exchanger and selectively eluting the above metals from the resin column with aqueous solutions of 0.6 N sodium hydroxide, 8 N hydrochloric acid and 1 N hydrochloric acid, respectively.     

Dramatic changes in geometry after ionization: experimental and theoretical studies on the electronic properties of fluorocarbonyl (mono-, di-, and tri-) sulfur compounds

In this work, we present a complete study on He I photoelectron spectroscopy (PES) for the fluorocarbonyl mono-, di-, and trisulfur compounds FC(O)SCl, FC(O)SSCH(3), and FC(O)SSSC(O)F. After optimizations of the structure for stable conformers at different levels of theory, a complete theoretical study involving the calculation of the ionization energies using orbital valence Green's functional (OVGF) was performed. Calculations of radical-cationic forms were carried out in order to compare their properties with those of the neutral molecules. The first IP values are 10.7, 9.0, and 10.5 eV for FC(O)SCl, FC(O)SSCH(3), and FC(O)SSSC(O)F, respectively. The groups bonded to the S atom mainly influence the ionizations originating from the sulfur lone pairs. A wide electronic delocalization in the FC(O)S moiety can be deduced from experimental and theoretical results, which leads to a strong energetic stabilization of the n' '(S) (sulfur lone pair pi orbital). Other conclusions relate to effects on the substituents attached to the S atom and the importance of the molecular planarity in the orbital stabilization of the FC(O)S moiety for the neutral molecules. It is worthwhile mentioning that FC(O)SCl retains its planar structure after ionization, but drastic changes occur in the geometry of both FC(O)SSCH(3) and FC(O)SSSC(O)F. The FC(O)SSCH(3) molecule adopts a heavy atom planar structure after ionization. The FC(O)SSS moiety becomes a planar form after the ionization of the FC(O)SSSC(O)F molecule, whereas the second C(O)F group maintains its original conformation with respect to the SSS group.     

The Adsorption and Thermal Decomposition of CH2CO (CD2CO) on Si(111)-7 × 7

The adsorption and thermal decomposition of ketene on Si(l 11)-7 × 7 were investigated using various surface analysis techniques. When the surface was exposed to ketene at 120 K, two CO stretching modes at 220 and 273 meV appeared in HREELS, corresponding to two adsorbed ketene states. After the sample was annealed at ?250 K, the 273 and the 80 meV peaks vanished, indicating the disappearance of one of the adsorption states by partial desorption of the adsorbate. In a corresponding TPD measurement, a desorption peak for ketene species was noted at 220 K. Annealing the sample at 450 K caused the decomposition of the adsorbate, producing CH_x and O adspecies. Further annealing of the surface at higher temperatures resulted in the breaking of the CH bond, the desorption of H and O species and the formation of Si carbide. The desorption of H at 800 K was confirmed by the appearance of the D₂ (m/e = 4) TPD peak at that temperature when CD₂CO was used instead of CH₂CO.     

Elevated plasma levels of haptoglobin in Duchenne muscular dystrophy:electrophoretic variants in patients with a severe form of the disease

Analysis of plasma proteins of Duchenne muscular dystrophy (DMD) patients and normal age-matched boys using two dimensional gel electrophoresis and densitometry indicated a three-fold increase in the average haptoglobin level in DMD plasma. Two electrophoretic variants of haptoglobin in which the alpha 2 chain had more basic or more acidic spots were found in DMD patients with a rapidly progressing form of the disease. The basic variant was present in relatively low amount. Possible reasons for the elevated haptoglobin levels are discussed.     

The 7-nitroindole nucleoside as a photochemical precursor of 2'-deoxyribonolactone: access to DNA fragments containing this oxidative abasic lesion

On the basis of molecular modeling studies, the 7-nitroindole nucleoside 1 was selected as a suitable photochemical precursor for photochemical generation of the C1' deoxyribosyl radical under irradiation, which led to 2'-deoxyribonolactone. The nitro-indole nucleoside derivatives 1a and 1b were prepared and their conformation was determined by X-ray crystallography and NMR spectroscopy. The photoreaction of these nucleosides gave the corresponding deoxyribonolactone derivatives efficiently, with release of 7-nitrosoindole. This reaction was successfully applied to synthesis of oligonucleotides containing the deoxyribonolactone lesion.     

Reactions de redistribution avec des molecules dinucleaires fluorees et chlorees. Mise en evidence d'un heterocomplexe contenant du molybdene et du tungstene en equilibre avec les molecules dinucleaires symetriques

Redistribution reactions have been undertaken in dinuclear ions with μ-oxalato group. The fluoro-chloro species appear in solution.The accumulation of fluoride on tungsten atoms is always favored, whereas chlorine redistributes essentially on molybdenum, there is a preferential affinity of fluorine for tungsten.In solution a slow dynamic exchange is observed to occur between the two symetrical fluorospecies, the formation of the F₂O₂W(C₂O₄)Mo0₂F₂^2- heterofluoroanion is reported.     

Molecular mechanics of organic halides. III. Fluorinated olefins

A molecular mechanical force field for fluorinated ethylenes and propylenes is described. The field computes geometries, dipole moments, and energy differences between isomers and rotamers. Component analysis indicates that “classical” strains alone (skeletal, nonbonded, electrostatic) cannot account for energy relationships. The discussion is supplemented by a semiempirical quantum chemical comparison of cis- and trans-FCH?CHF and of gauche- and anti-FCH₂CH₂F.