Electrofluorination of uracil

In view of the importance of the medical applications of fluorinated uracil and derivatives, synthetic methods directed to obtain such compounds are of particular interest. Several aspects of the electrochemical fluorination of uracil in different experimental conditions will be discussed.     

A rapidly convergent method for solving the static Hartree-Fock problem

An improved version of the direct density method for solving the static Hartree-Fock equations is presented. A simple relation with the imaginary time method is exhibited.     

Comparison of the metabolism of baicalin in rats orally administered with Radix scutellariae extract and Shuang-Huang-Lian extract

Shuang-Huang-Lian (SHL) is a traditional Chinese formula containing Flos lonicerae, Radix scutellariae (RS) and Fructus forsythiae, and is commonly used for treating acute upper respiratory tract infection, acute bronchitis and light pneumonia. The aim of the present study is to compare the metabolites of baicalin in rats when orally administered with SHL and Radix scutellariae, and try to explore the principle of SHL compatibility. By using LC-MS(n) and HPLC-DAD, the metabolites of baicalin were analyzed from bile, urine and feces of rats dosed with SHL and RS. Our results showed significant difference of baicalin metabolism between RS and SHL. However, baicalein was found to be the main metabolites of baicalin in intestinal tract after oral administration of RS and SHL, glucuronide, glucoside and methylated products were also found in rat urine after administration of either RS or SHL. Meanwhile, several sulphates were found in rat urine after RS administration, but not found after SHL. Among the metabolites of the SHL, potentially there existed a isomerized baicalin and methylated product: 5,7-dihydroxy-6-methoxyisoflavone-7-O-beta-glucopyranuronoside, but without unidentified metabolite M3. Baicalein-6-O-beta-glucopyranuronoside-7-O-beta-glucopyranuronoside and baicalein-6-O-beta-glucose-7-O-beta-glucopyranuronoside were first reported by this study. The major metabolites of baicalin of RS and SHL in rat bile were the same, including baicalin-6-O-beta-glucopyranuronoside-7-O-beta-glucopyranuronoside, baicalin-6-beta-glucopyranuronoside and 6-O-methyl-baicalin-7-O-beta-glucopyranuronoside. Moreover, baicalein-6-O-beta-glucose-7-O-beta-glucopyranuronoside was also first found in rat bile by this study. Although baicalin-6-O-sulfate-7-O-beta-glucopyranuronoside was found in rat bile after RS administration, no sulphated products were found after oral administration of SHL. These differences of baicalin metabolism between RS and SHL indicated that compatibility of medicines could result in the differences of metabolites.     

Evaluation by chemical parameters of the pollution state of the agricultural-industrial settlement of the Fucino Plain

In the present work are reported the results of a monitoring on a vast scale, carried out through evaluation of opportune chemical parameters, of the pollution state of the agricultural-industrial settlement of the Fucino Plain. The parameters took into consideration have been the presence of wide consumption pesticides and of ionic species as Cl-, NO2-, NO3-, NH4+, the quantification of the dissolved oxygen, of the temperature, of the conductivity, of pH and eH. Collected data are used for chemometric elaboration. The water systems examined, by means of drawing campaigns carried out at regular intervals in winter, spring, summer, and autumnal seasons, are represented by superficial waters constituting a network of irrigation canals fed by stratum and meteoric waters. In this work are reported the results relative to the drawing campaigns.     

First structural characterization of a protactinium(V) single oxo bond in aqueous media

The present work describes the first structural studies of protactinium(V) in sulfuric and hydrofluoric acid media using X-ray absorption spectroscopy. The results show unambiguously the absence of the trans-dioxo bond that characterizes the other early actinide elements such as U and Np. In concentrated sulfuric acid (13 M), Pa(V) is proved to exhibit a single oxo bond as postulated in the literature for species in more dilute media. In a 0.5 M HF medium, XANES and EXAFS spectra indicate the absence of any oxo bond: Pa(V) exists in the form of a pure fluoro complex.     

Structural and chiroptical properties of the two coordination isomers of YbDOTA-type complexes

Studies of the structural, physical, and chemical properties of the lanthanide(III) complexes of DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) and related ligands are often complicated by the presence of two coordination isomers in solution. Since these coordination isomers are in exchange and cannot be separated, many techniques offer information only on the weighted average of the two isomers. Lanthanide ion complexes formed with the ligands S(RRRR)NO2BnDOTMA and S(SSSS)NO2BnDOTMA preferentially adopt only one of the two common coordination isomers in solution, so the ytterbium complexes of these ligands offer a unique opportunity to study the near-infrared circular dichroism (NIR-CD) characteristics of each coordination geometry in isolation. The spectra acquired support many of the conclusions and assumptions of previous studies and demonstrate that this spectroscopy is particularly sensitive to the distortion of the coordination polyhedron. This will have particularly relevant consequences when studying achiral YbDOTA-like systems forming labile adducts with (chiral) hosts and receptors.     

Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation

We present methods that introduce concepts from Rosenbluth sampling [M. N. Rosenbluth and A. W. Rosenbluth, J. Chem. Phys. 23, 356 (1955)] into the Jarzynski nonequilibrium work (NEW) free-energy calculation technique [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. The proposed hybrid modifies the way steps are taken in the NEW process. With it, each step is selected from a range of alternatives, with bias given to steps that contribute the least work. The definition of the work average is modified to account for the bias. We introduce two variants of this method, lambda-bias sampling and configuration-bias sampling, respectively; a combined lambda- and configuration-bias method is also considered. By reducing the likelihood that large nonequilibrated work values enter the ensemble average, the Rosenbluth sampling aids in remedying problems of inaccuracy of the calculation. We demonstrate the performance of the proposed methods through a model system of N independent harmonic oscillators. This model captures the difficulties involved in calculating free energies in real systems while retaining many tractable features that are helpful to the study. We examine four variants of this model that differ qualitatively in the nature of their phase-space overlap. Results indicate that the lambda-bias sampling method is most useful for systems with entropic sampling barriers, while the configuration-bias methods are best for systems with energetic sampling barriers. The Rosenbluth-sampling schemes yield much more accurate results than the unbiased nonequilibrium work method. Typically the accuracy can be improved by about an order of magnitude for a given amount of sampling; this improvement translates into two or more orders of magnitude less sampling required to obtain a given level of accuracy, owing to the generally slow convergence of the NEW calculation when the inaccuracy is large.     

Dynamical Aspects of TEM-1 β-Lactamase Probed by Molecular Dynamics

The dynamical aspects of the fully hydrated TEM-1 β-lactamase have been determined by a 5 ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is reached and the molecule fluctuates around an equilibrium conformation. The results obtained in the first nanosecond are in agreement with those of a previous simulation (Diaz et al., J. Am. Chem. Soc., (2003) 125, 672–684). The successive equilibrium conformation in solution shows an increased mobility characterized by the following aspects. A flap-like translational motion anchores the Ω-loop to the body of the enzyme. A relevant part of the backbone dynamics implies a rotational motion of one domain relative to the other. The water molecules in the active site can exchange with different residence times. The H-bonding networks formed by the catalytic residues are frequently interrupted by water molecules that could favour proton transfer reactions. An additional simulation, where the aspartyl dyad D214–D233 was considered fully deprotonated, shows that the active site is destabilized.     

Hybrid Siloxane-Based Nano Building Blocks for Optical Applications: Optimization of the Synthetic Procedures by Spectroscopic Analysis

Diphenylsilanediol (DPDO) reacts with triethoxysilane (TREOS) in anhydrous conditions and in the presence of pyridine, to form complex mixtures of linear and cyclic condensation products which were identified by ²⁹Si NMR and ATR/FTIR spectroscopies. The distribution of products can be varied by modifying the reaction conditions. Spectroscopic analysis allowed to identify the optimal reagents ratio and concentration for the production of hetero-condensation products minimizing the number of residual –OH groups whose presence would affect the performance of optical waveguides based on the synthesised nano building blocks.