DNA nucleosides and their radical anions: molecular structures and electron affinities

The deoxyribonucleosides have been studied to determine the properties of combinations of 2-deoxyribose with each of the isolated DNA bases for both neutral and anionic species. We have used a carefully calibrated theoretical method [Chem. Rev. 2002, 102, 231], employing the B3LYP hybrid Hartree-Fock/DFT functional with the DZP++ basis set. Predictions are made of the geometric parameters, adiabatic electron affinities, charge distributions based on natural population analysis, and decomposition enthalpy for the neutral and anionic forms of the four 2'-deoxyribonucleosides in DNA: 2'-deoxyriboadenosine (dA), 2'-deoxyribocytidine (dC), 2'-deoxyriboguanosine (dG), and 2'-deoxyribothymidine (dT). Geometric changes in the anions show that the glycosidic bond exhibits little change with excess charge for the guanosine but significant shortening for the adenosine and for the pyrimidines. The zero-point corrected adiabatic electron affinities in eV for each of the 2'-deoxyribonucleosides are as follows: 0.06, dA; 0.09, dG; 0.33, dC; and 0.44, dT. These values are uniformly greater than those of the corresponding isolated bases (-0.28, A; -0.07, G; 0.03, C; 0.20, T) and the isolated 2-deoxyribose (-0.38) at the same level of theory. The vertical detachment energies of dT and dC are substantial, 0.72 and 0.94 eV, and these anions should be observable. A high VDE, 0.91 eV, is also found for dA but its anion is unlikely to be stable due to the small AEA of 0.06 eV. The high VDE reflects the fact that the molecular structures of the anions and the corresponding neutral species are quite different. Valence character is displayed for the SOMOs of dA, dC, and dT, while some component of diffuse character is visible in the SOMO of dG. Further analysis of electronic changes upon electron attachment include an examination of the NPA charges, which show that in the neutral 2'-deoxyribonucleosides the sum of NPA charges for every base is the same, -0.28 with the sum of 2-deoxyribose charges being positive, +0.28. In the anions, the trend in charge division varies based on the nature of the excess electron in the anions. Thermodynamically, the overall enthalpy change for the reaction of water with the neutral nucleosides to give bases and ribose is approximately zero. The analogous decomposition is exothermic by 8 to 11 kcal mol-1 for the anions, indicating possible challenges for anionic gas-phase nucleoside exploration in the presence of water.     

Continuous and simultaneous fermentation and recovery of lactic acid in a biparticle fluidized-bed bioreactor

Applied Biochemistry and Biotechnology - A continuous biparticle fluidized-bed reactor (BFBR) is developed for the simultaneous fermentation and recovery of lactic acid. In this processing scheme,...     

Production of succinic acid by anaerobiospirillum succiniciproducens

The effect of an external supply of carbon dioxide and pH on the production of succinic acid byAnaerobiospirillum succiniciproducens was studied. In a rich medium containing yeast extract and peptone, when the external carbon dioxide supply was provided by a 1.5M Na₂CO₃ solution that also was used to maintain the pH at 6.0, no additional carbon dioxide supply was needed. In fact, sparging CO₂ gas into the fermenter at 0.025 L/L-min or higher rates resulted in significant decreases in both production rate and yield of succinate. Under the same conditions, the production of the main by-product acetate was not affected by sparging CO₂ gas into the fermenter. The optimum pH (pH 6.0) for the production of succinic acid was found to be in agreement with results previously reported in the literature. Succinic acid production also was studied in an industrial-type inexpensive medium in which light steep water was the only source of organic nutrients. At pH 6.0 and with a CO₂ gas sparge rate of 0.08 L/L-min, succinate concentration reached a maximum of 32 g/L in 27 h with a yield of 0.99 g succinate/g glucose consumed.     

Preparation of functionalized tertiary thiols and nitrosothiols

The development and preparation of five series of tertiary thiols and nitrosothiols as nitric oxide releasing molecules functionalized with acid, alcohol, or amine groups for future conjugation are reported.     

Synthesis and characterization of water-soluble amino fullerene derivatives

[formula: see text] A series of amino-substituted methanofullerene derivatives were prepared by mono-, tris-, and hexa-Bingel-Hirsch reactions using an N-protected malonate derivative. Upon scission of the protecting groups, the e,e,e-tris- and octahedral Th hexa-methano amino fullerenes were found to be among the most water-soluble fullerene derivatives yet prepared. 3He NMR data on corresponding adducts of 3He/C60 helped verify the assigned structures. UV spectral studies confirmed the influence of aggregation on solubility of these adducts in water.     

Mechanism of sulfide oxidations by peroxymonocarbonate

A detailed mechanism for the oxidation of aryl sulfides by peroxymonocarbonate ion in cosolvent/water media is described. Kinetic studies were performed to characterize the transition state, including a Hammett correlation and variation of solvent composition. The results are consistent with a charge-separated transition state relative to the reactants, with an increase of positive charge on the sulfur following nucleophilic attack of the sulfide at the electrophilic oxygen of peroxymonocarbonate. In addition, an average solvent isotope effect of 1.5 +/- 0.2 for most aryl sulfide oxidations is consistent with proton transfer in the transition state of the rate-determining step. Activation parameters for oxidation of ethyl phenyl sulfide in tert-butyl alcohol/water are reported. From the pH dependence of oxidation rates and (13)C NMR equilibrium experiments, the estimated pK(a) of peroxymonocarbonate was found to be approximately 10.6.     

Conformational changes of a calix[8]arene derivative at the air-water interface

The particular behavior of a p-tert-butyl calix[8]arene derivative (C8A) has been studied at the air-water interface using surface pressure-area isotherms, surface potential-area isotherms, film relaxation measurements, Brewster angle microscopy (BAM), and infrared spectroscopy for Langmuir-Blodgett films. Thus, it is observed that the properties of the film, for example, isotherms, domain formation, and FTIR spectra, recorded during the first compression cycle differ appreciably from those during the second compression and following cycles. The results obtained are interpreted on the basis of the conformational changes of the C8A molecules by surface pressure, allowing us to inquire into the inter- and intramolecular interactions (hydrogen bonds) of those molecules. Thus, the compression induces changes in the kind of hydrogen bonds from intra- and intermolecular with other C8A molecules to hydrogen bonds with water molecules.     

Filipin III: Configuration Assignment and Confirmation by Synthetic Correlation

The stereochemical configuration of filipin III (1) was determined using the (13)C acetonide analysis. The relative configurations for the nine stereogenic centers in the top half of filipin were initially identified using just three acetonide derivatives (2, 3, and 4) arising from a two-step protection sequence. The structure was confirmed by synthesis and direct correlation of degradation products 8 (C26-C28) and 10 (C1-C16). Filipin tetraacetonide 2 and triacetonide 4 each contain an anti acetonide in a highly unusual chair conformation. Molecular modeling successfully reproduced the preference for a chair conformation over the normally more stable twist-boat conformation.     

Molecular orbital studies on the optical activity of chiral nitrosamines and nitramines

The chiroptical properties of the two lowest energy singlet-singlet transitions in a series of N-nitrosopiperidine derivatives are examined on a CNDO/S-CI molecular orbital (MO) model in which rotatory strengths are calculated directly from total molecular electronic wave functions. Similar calculations are carried out for the three lowest energy singlet-singlet transitions in a series of chiral N-nitropiperidine derivatives. The results obtained for the low energy n→π^* transitions in these compounds are compared to those predicted by sector rules proposed for chiral N-nitrosamine and N-nitramine systems.     

Conformational dependence of the 1Lb and n → π* rotatory strengths in α-substituted phenylacetic acids

The chiroptical properties of a series of chiral phenylacetic acid derivatives are examined on a theoretical model in which electronic rotatory strengths are calculated directly from molecular wave functions derived from semiempirical molecular orbital calculations. The CNDO/S SCF-MO model is used to calculate ground state wave functions and excited states are constructed in the virtual orbital-configuration interaction approximation. Of special interest are the rotatory strengths associated with the ¹L_b transition of the phenyl chromophore and the n → π^* transition of the carboxyl chromophore. Calculations are carried out on a large number of conformational isomers of the compounds: α-methyl phenylacetie acid (and its methyl ester), α-methylmandelic acid (and its methyl ester), and mandelic acid (and its methyl ester). The dependence of rotatory strength (¹L_b and n → π^*) on conformational variables is examined and discussed, and comparisons between available experimental data and the calculated results are made. Coupling between the phenyl and carboxyl chromophoric moieties is considered and possible spectra-structure relationships are examined.