Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent

The exchange for deuterium of the C-6 protons of uridine 5'-monophosphate (UMP) and 5-fluorouridine 5'-monophosphate (F-UMP) catalyzed by yeast orotidine 5'-monophosphate decarboxylase (ScOMPDC) at pD 6.5-9.3 and 25 °C was monitored by (1)H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for k(cat) give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10(-5) and 0.041 s(-1), respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pK(a) of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pK(a) values for proton transfer from C-6 of uridine (pK(CH) = 28.8) and 5-fluorouridine (pK(CH) = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 10(9)-fold increase in the equilibrium constant for proton transfer from C-6, so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for k(cat)/K(m) for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M(-1) s(-1). This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 10(10) M(-1), which corresponds to a transition-state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition-state stabilization for the decarboxylation of orotidine 5'-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction.     

Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations

We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A? associated with the shorter U(IV)-(OH(-)) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.     

First principles investigation of19F* nuclear quadrupole interaction in fourth group tetrafluorides

Using the Hartree-Fock-Roothaan procedure the nuclear quadrupole interactions of the¹⁹F (spin 5/2) nucleus in CF₄, SiF₄ and GeF₄ are studied. The theoretical results explain within 10% the observed experimental measurements by the time-differential perturbed angular distribution technique, including the important feature of sharp decrease of the¹⁹F^* nuclear quadrupole coupling constant in going from CF₄ to SiF₄, followed by an increase in going to GeF₄, while a simple consideration of the ionic characters of the C-F, Si-F and Ge-F bonds together with Townes and Dailey theory would lead to a continuous decrease from CF₄ to GeF₄. The dependence of the results on the choice of basis sets and the role of many-body effects is discussed.     

A portable gas chromatograph with simultaneous detection by mass spectrometry and electroantennography for the highly sensitive in situ measurement of volatiles

Mating disruption is a sustainable method for the control of insect pests, involving the release of synthetic sex pheromones that disrupt the olfactory localization of females by males. However, the development and refinement of this strategy is hampered because current instruments lack the sensitivity to detect volatile organic chemicals in the field, and portable electroantennograms produce non-comparable relative units and distorted results in the presence of plant volatiles. To address the demand for more sensitive instruments that are suitable for the rapid in situ detection of airborne pheromones, we have developed a portable, automated needle trap device connected to a gas chromatograph, mass spectrometer, and electroantennographic detector (NTD-GC-MS/EAD) suitable for field applications. We tested the instrument by measuring the concentration of the sex pheromone (E,Z)-7,9-dodecadienyl acetate, which is used to disrupt the mating of the European grapevine moth Lobesia botrana (Lepidoptera: Tortricidae). Our data confirm that the instrument generates highly reproducible results and is highly sensitive, with a detection threshold of 3 ng/m³ (E,Z)-7,9-dodecadienyl acetate in outside air.     

Efficacy analysis of a body-mass-reduction treatment using mathematical modelling

Obesity was categorized as a chronic disease by the World Health Organization (WHO) in 1997 because the problem had reached at pandemic level and presented a serious risk factor with respect to people who have been developing type-2 diabetes, hyperdyslipidaemia and hypertension. These four risk factors tend to accelerate the development of cardiovascular diseases. As a result, obesity has also become a significant social and economic burden. An important observation with regard to the population exhibiting increased body mass is the fact that they would like to decrease their weight, although they are frequently not successful. In this paper, a modelling-and-simulation approach is used for the presentation, analysis and explanation of the reasons that have an important influence on the treatment’s efficacy. The presented modelling results are based on the observation and treatment experiences of patients in a specialized institution over a period of 15 years, where each year around 100 new patients enter the treatment programme. The introduction of the motivation principle in the model structure allows strong support for the actions of the therapeutic team in a closed-loop manner, as the checking of different scenarios for the individual patient is easily realized. The efficacy of the treatment can, in this way, be significantly improved. In the past 6 years, which mainly involved open-loop treatments, the dropout rate was 70%. After the introduction of proposed closed-loop approach, this was reduced to 27% in the past year. As a consequence, the effect on body-mass control was significantly improved.     

The preparation of N-(1H-pyrazol-3-yl)arylamides and 1H-pyrazol-3-amines from polylithiated C(α),N-thiosemicarbazones and C(α),N-semicarbazones

C(α),N-Thiosemicarbazones or C(α),N-semicarbazones were polylithiated with excess lithium diiso-propylamide, and the resulting cyclized intermediates were condensed with aromatic esters to afford N-(1H-pyrazol-3-yl)arylamides. The polylithiated intermediates were also quenched with aqueous acid to give 5-substituted, 1H-pyrazol-3-amines.     

Lithiation of trimethylsilyl substituted acetamide derivatives : Addition to carbonyl compounds

The lithio anions of N,O-bis(trimethylsilyl)acetamide and N-(trimethylsilyl)-N-methylacetamide were prepared and reacted with several carbonyl compounds to form β hydroxy acetamide and N-methylacetamide derivatives.     

Half-sandwich arene ruthenium(II)-enzyme complex

The 1.6 [Angstrom] X-ray crystal structure of [(eta(6)-p-cymene)Ru(lysozyme)Cl(2)], the first of a half-sandwich complex of a protein, shows selective ruthenation of Nepsilon of the imidazole ring of His15.     

Current best practice for traceability in testing laboratories,when certified reference materials are unavailable

Since the implementation of ISO/IEC 17025 in 2002, all accredited laboratories (at the least) need to establish traceability in all their tests and calibration methods. Traceabilty, though well understood in the calibration field (through an unbroken chain of comparisons to the International System of Units —SI), is less straight forward and not so well understood in the testing laboratories. Traceability in analytical and biological testing is found through the use of reference materials, and the validated steps of a test method. This article describes the possibilities to comply with the traceability requirement of ISO/IEC 17025 in testing laboratories , when certified reference materials are unavailable.Presented at the Second International Conference on Metrology—Trends and Applications in Calibration and Testing Laboratories, 4–6 November, 2003, Eilat, Israel