Density functional calculations of large systems containing heavy elements by means of the regionalization algorithm

The compounds containing transition metals orother heavy elements play important roles in chemistry.They possess diverse properties which have been util-ized in numerous functional materials. Some of theseproperties are also involved in biological processes.However, it is very difficult to study these compoundsdeeply by means of quantum chemical methods, be-cause in these systems usually there are a large amountof electrons, the distribution of the frontier orbitals isdense, the correlation be…     

Preparation of trout liver microsomes for iron speciation in P-450 enzymes by AE–FPLC with ICP–(ORS)MS detection

Cytochromes P-450 are members of a superfamily of hemoproteins involved in the oxidative metabolism of various physiological and xenobiotic compounds in eukaryotes and prokaryotes. The multiplicity of this group of enzymes has been widely studied by chromatographic techniques, mainly high-performance liquid chromatography (HPLC). Because these enzymes are membrane-bound proteins, sample preparation for chromatographic separation of P-450 enzymes requires a solubilization step. The sample-preparation procedures are critical, because detergents affect not only the efficiency of protein solubilization but also their further chromatographic resolution. Trout liver microsomes have been taken here as a model sample to investigate iron speciation in cytochrome P-450. Trouts were treated intraperitoneally with -naphthoflavone, a potent inducer of some P-450 enzymes, and a microsomal suspension containing 7.4±0.1 nmol mL^–1 P-450 enzymes was obtained by ultracentrifugation. Lubrol PX was selected as detergent for solubilization, resulting in about 90% solubilization recovery. The solubilized cytochromes P-450 were further separated by AE–FPLC, with UV detection, or coupled to ICP–MS with an octapole reaction system, ICP–(ORS)MS (monitoring Fe signals at masses 54, 56, and 57). A sampling procedure and chromatographic conditions are developed and were successfully applied to iron speciation in trout liver P-450 enzymes. ICP–(ORS)MS detection of P-450 enzymes is Fe-specific and so will give accurate information on the prosthetic group of the protein, which can constitute an advantageous alternative to classical methods for detection of these hemoproteins.     

Analysis of organic acids in wines by Fourier-transform infrared spectroscopy

Fourier-transform infrared (FTIR) spectroscopy has been a major point of development in many wine laboratories in recent years. It enables almost instant analysis of several properties of wine, usually with very good precision and accurate results. Nevertheless, validation procedures should not be forgotten and should be fully performed. Recovery experiments were performed by spiking wine samples with different amounts of organic acids (tartaric, malic, lactic, acetic and citric—the most prominent in wines). After FTIR analysis of the total acidity and of each organic acid concentration, recoveries were calculated. For total acidity recovery results were, in general, good and very close to 100% (64–111%). On the other hand, for individual organic acid concentrations, the recovery results were lower than 100% (11–73%) for all spiking additions. These results could be explained by spectroscopic interferences between the organic acids. Because they have similar infrared spectra, it is not easy to distinguish between them and, therefore, to achieve accurate calibration. When total acidity, with a different infrared spectrum from the other abundant compounds in the wine, was taken as a single property the recovery results were acceptable.     

Dissociation of Fumaric Acid: Spectrophotometric Investigation in Aqueous Solutions from 10 to 90 <Superscript>∘</Superscript>C and Theoretical Considerations

The dissociation constants of fumaric acid were extracted from UV-vis spectra in the 10–90 ^∘C range. These values were used to extract thermodynamic parameters that showed the temperature effects on the dissociations reactions to be dominantly driven by the solvent. The molar absorption coefficients for the fumaric acid, the bifumarate and fumarate species, can be accurately reproduced with the two-term Gauss–Lorentz equation. Deconvolution of these bands showed strong π–π^∗ transitions for all species and weaker charge-transfer-to-solvent transitions for the charged species. TD-DFT calculations were used to identify the most important molecular orbitals involved in the vertical excitations of the fumaric acid species. The electron population and their states of delocalization were also estimated with topological analyses of the electron density and of the Becke–Edgecombe Electron Localization Function.     

Photochemical cleavage and release of carboxylic acids from alpha-keto amides

In aqueous media, alpha-keto amides LGCH(2)COCON(R)CH(R')CH(3) (1a, R = Et, R' = H; 1b, R = (i)()Pr, R' = Me; 1c, R = Ph, R' = H) with various carboxylate leaving groups (LG) at the C-3 position undergo photocleavage and release of carboxylic acids with formation of diastereomeric 5-hydroxyoxazolidin-4-ones 2a,c in the cases of 1a,c or 5-methyleneoxazolidin-4-ones 3b in the case of 1b. For 1a,b, Phi(photocleavage) = 0.24-0.38, whereas Phi(photocleavage) = ca. 0.05 for 1c. The proposed mechanism involves transfer of hydrogen from an N-alkyl group to the keto oxygen to produce zwitterionic intermediates 4a-c that eliminate carboxylate anions. The resultant imminium ions, H(2)C=C(OH)CON(+)(R)=C(R')CH(3) 5a-c, cyclize intramolecularly to 3b or undergo intermolecular addition of water followed by tautomerization and cyclization to give 2a,c. These inter- or intramolecular trapping reactions of 5 release protons that decrease the pH and cause bleaching of the 620 nm band of the pH indicator, bromocresol green. Determination of the bleaching kinetics by laser flash photolysis methods in the case of 1a gives time constants of 18-137 mus, depending on the leaving group ability of the carboxylate anion, whereas amides 1b show only a small leaving group effect. For 1a, the large leaving group effect is consistent with rate-limiting carboxylate elimination from 4a, whereas the proton release step would be largely rate determining for 1b. Photolyses of 1a (LG = CH(3)CO(2)(-), PhCH(2)CO(2)(-)) in neat CH(3)CN results in carboxylate elimination to form imminium ion 5a, followed by internal return to give aminals.     

Speciation of cyclo(Pro-Gly)<Subscript>3</Subscript> and its divalent metal-ion complexes by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to study the binding of selected group II and divalent transition-metal ions by cyclo(Pro-Gly)3 (CPG3), a model ion carrier peptide. Metal salts (CatXn) were combined with the peptide (M) at a molar ratio of 1:10 M/Cat in aqueous solvents containing 50% vol/vol acetonitrile or methanol and 1 or 10 mM ammonium acetate (NH4Ac). Species detected include [M+H]+, [M+Cat-H]+, [M2+Cat]2+, [M+Cat+Ac]+, and [M+Cat+X]+. The relative stabilities of complexes formed with different cations (Mg2+, Ca2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, and Zn2+) were determined from the abundance of 1:1 and 2:1 M/Cat species relative to that of the unbound peptide. The largest metal ions (Ca2+, Sr2+, and Mn2+) formed the most stable complexes. Reducing the buffer concentration increased the overall extent of metal binding. Results show that the binding specificity of CPG3 depends upon the size of the metal ion and its propensity for electrostatic interaction with oxygen atoms. Product ion tandem mass spectrometry of [M+H]+ and [M+Cu-H]+ confirmed the cyclic structure of the peptide, although the initial site(s) of metal attachment could not be determined.     

Evaluation of different quantitative approaches for the determination of noneasily ionizable molecules by different atmospheric pressure interfaces used in liquid chromatography tandem mass spectrometry: Abamectin as case of study

The liquid chromatography tandem mass spectroscopy residue determination of compounds without any acidic or basic centers such as abamectin has been investigated. Several approaches regarding the interface used and adduct formation have been compared. The low acidity of the hydroxyl groups only made deprotonation feasible using the atmospheric pressure chemical ionization (APCI) interface. To obtain sufficient sensitivity for residue analysis, the Ion Sabre APCI interface was necessary. However, the sensitivity attained was lower than for monitoring adducts in positive ion mode. Using electrospray ionization, different adducts with Na+, NH4+, and Li+ were tested and compared. The best results were obtained for the ammoniated adduct in electrospray ionization (ESI) because of its high sensitivity and the presence of several product ions with similar abundance. The highest sensitivity was reached using an in-source fragment as precursor ion, leading to a limit of detection (LOD) of 2 microg/L with low relative standard deviation. The relatively high abundance of other transitions allowed abamectin confirmation at concentrations close to the LOD (6 microg/L). Alkali ions were found to be a suitable alternative to determine and confirm abamectin at residue levels. The [M + Na]+ also presented various product ions with similar abundance, which allowed confirmation at LOD levels. However, this LOD was found to be almost four times higher than with [M + NH4]+ because of the poor sensitivity of the transitions obtained. Although the use of Li+ facilitated the fragmentation of the adduct [M + Li]+, with similar sensitivity to [M + NH4]+, this fragmentation preferentially generated only one product ion, which did not allow confirmation at concentration levels lower than 15 microg/L. The use of APCI for monitoring adducts was also feasible, but with less sensitivity. The sensitivity increased with the Ion Sabre APCI, although it was still five times lower than with ESI. Other adduct formers such as Co2+ and Ni2+ also were tested with unsatisfactory results.     

Ubiquitous strategy for probing ATR surface-enhanced infrared absorption at platinum group metal-electrolyte interfaces

A versatile two-step wet process to fabricate Pt, Pd, Rh, and Ru nanoparticle films (simplified as nanofilms hereafter) for in situ attenuated total reflection Fourier transform infrared (ATR-FTIR) study of electrochemical interfaces is presented, which incorporates an initial chemical deposition of a gold nanofilm on the basal plane of a silicon prism with the subsequent electrodepostion of desired platinum group metal overlayers. Galvanostatic electrodeposition of Pt, Rh, and Pd from phosphate or perchloric acid electrolytes, or potentiostatic electrodeposition of Ru from a sulfuric acid electrolyte, yields sufficiently "pinhole-free" overlayers as evidenced by electrochemical and spectroscopic characterizations. The Pt group metal nanofilms thus obtained exhibit strongly enhanced IR absorption. In contrast to the corresponding metal films electrochemically deposited directly on glassy carbon and bulk metal electrodes, the observed enhanced absorption for the probe molecule CO exhibits normal unipolar band shapes. Scanning tunneling microscopic (STM) images reveal that fine nanoparticles of Pt group metals are deposited around wavy and stepped bunches of Au nanoparticles of relatively large sizes. This ubiquitous strategy is expected to open a wide avenue for extending ATR surface-enhanced IR absorption spectroscopy to explore molecular adsorption and reactions on technologically important transition metals, as exemplified by successful real-time spectroscopic and electrochemical monitoring of the oxidation of CO at Pd and that of methanol at Pt nanofilm electrodes. The spectral features of free water molecules coadsorbed with CO on Pt, Pd, Rh, and Ru are also discussed.     

Probing stereoselective inhibition of the acyl binding site of cholesterol esterase with four diastereomers of 2'-<Emphasis Type="Italic">N</Emphasis>-α-methylbenzylcarbamyl-1, 1'-bi-2-naphthol

Background  

Recently there has been increased interest in pancreatic cholesterol esterase due to correlation between enzymatic activity in vivo and absorption of dietary cholesterol. Cholesterol esterase plays a role in digestive lipid absorption in the upper intestinal tract, though its role in cholesterol absorption in particular is controversial. Serine lipases, acetylcholinesterase, butyrylcholinesterase, and cholesterol esterase belong to a large family of proteins called the α/β-hydrolase fold, and they share the same catalytic machinery as serine proteases in that they have an active site serine residue which, with a histidine and an aspartic or glutamic acid, forms a catalytic triad. The aim of this work is to study the stereoselectivity of the acyl chain binding site of the enzyme for four diastereomers of an inhibitor.     

Low-magnesium, <Emphasis Type="Italic">trans</Emphasis>-cleavage activity by type III,tertiary stabilized hammerhead ribozymes with stem 1 discontinuities

Background  

Low concentrations of free magnesium in the intracellular environment can present critical limitations for hammerhead ribozymes, especially for those that are designed for intermolecular (trans) cleavage of a host or pathogen RNA. Tertiary stabilizing motifs (TSM's) from natural and artificial ribozymes with a "type I" topology have been exploited to stabilize trans-cleaving hammerheads. Ribozymes with "type II" or "type III" topologies might seem incompatible with conversion to trans-cleavage designs, because opening the loop at the end of stem 1 or stem 2 to accommodate substrate binding is expected to disrupt the TSM and eliminate tertiary stabilization.