Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Proton inventory studies of alpha-thrombin-catalyzed reactions of substrates with selected P and P' sites

Deuterium kinetic solvent isotope effects for the human alpha-thrombin-catalyzed hydrolysis of (1) substrates with selected P(1)-P(3) sites, Z-Pro-Arg-7-amido-4-methylcoumarin (7-AMC), N-t-Boc-Val-Pro-Arg-7-AMC, Bz-Phe-Val-Arg-4-nitroanilide (pNA), and H-D-Phe-L-Pip-Arg-pNA, are (DOD)k(cat) = (2.8-3.3) +/- 0.1 and (DOD)(k(cat)/K(m)) = (0.8-2.1) +/- 0.1 and (2) internally fluorescence-quenched substrates (a) (AB)Val-Phe-Pro-Arg-Ser-Phe-Arg-Leu-Lys(DNP)-Asp-OH, an optimal sequence, and (b) (AB)Val-Ser-Pro-Arg-Ser-Phe-Gln-Lys(DNP)-Asp-OH, recognition sequence for factor VIII, are (DOD)k(cat) = 2.2 +/- 0.2 and (DOD)(k(cat)/K(m)) = (0.8-0.9) +/- 0.1, at the pL (L = H, D) maximum, 8.4-9.0, and (25.0-26.0) +/- 0.1 degrees C. The most plausible models fitting the partial isotope effect (proton inventory) data have been selected on the basis of lowest values of the reduced chi squared and consistency of fractionation factors at all substrate concentrations, assuming rate-determining acylation. The data for Z-Pro-Arg-7-AMC are consistent with a single-proton bridge at the transition state phi(TS) = 0.39 +/- 0.05 and components for solvent reorganization phi(S) = 0.8 +/- 0.1 and phi(S) = 1.22 for k(cat) and k(cat)/K(m), respectively. The data for tripeptide amides fit bowl-shaped curves; an example is N-t-Boc-Val-Pro-Arg-7-AMC: phi(TS)(1) = phi(TS)(2) = 0.57 +/- 0.01 and phi(S) = 1 for k(cat) and 1.6 +/- 0.1 for k(cat)/K(m). Proton inventories for the nonapeptide (2b) are linear. The data for k(cat) for H-D-Phe-L-Pip-Arg-pNA and the decapeptide (2a) are most consistent with two identical fractionation factors for catalytic proton bridging, phi(TS)(1) = phi(TS)(2) = 0.68 +/- 0.02 and a large inverse component (phi(S) = 3.1 +/- 0.5) for the latter, indicative of substantial solvent reorganization upon leaving group departure. Proton inventory curves for k(cat)/K(m) for nearly all substrates are dome-shaped with an inverse isotope effect component (phi(S) = 1.2-2.4) originating from solvent reorganization during association of thrombin with substrate. These large contributions from medium effects are in full accord with the conformational adjustments required for the fulfillment of the dual, hemostatic and thrombolytic, functions of thrombin.     

Equilibrium Topology and Partial Inversion of Janus Drops: A Numerical Analysis

The equilibrium topology of an aqueous Janus emulsion of two oils, O1 and O2, with water, W, [(O1+O2)/W], is numerically evaluated with the following realistic interfacial tensions (γ): γ_O2/W=5 mN m⁻¹, γ_O1/O2=1 mN m⁻¹, and γ_O1/W varies within the range 4–5 mN m⁻¹, which is the limiting range for stable Janus drop topology. The relative significance of the two independently pivotal factors for the topology is evaluated, that is, the local equilibrium at the line of contact between the three liquids and the volume fraction of the two dispersed liquids within the drop. The results reveal a dominant effect of the local equilibrium on the fraction of the O2 drop surface that is covered by O1. In contrast, for a constant volume of O2, the impact of the interfacial tension balance on the limit of the coverage is modest for an infinite volume of O1. Interestingly, when the O1 volume exceeds this value, an emulsion inversion occurs, and the O1 portion of the (O1+O2)/W topology becomes a continuous phase, generating a (W+O2)/O1 Janus configuration.     

Fingerprinting pre-historical symbolic artefacts by a non-destructive methodological approach

Journal of Radioanalytical and Nuclear Chemistry - A contribution to the discussion about Vila Nova de São Pedro (VNSP) as a production centre of symbolic lithic artefacts, the origin of raw...     

The development and assessment of high‐throughput mass spectrometry‐based methods for the quantification of a nanoparticle drug delivery agent in cellular lysate

The safe use of lipid‐based drug delivery agents requires fast and sensitive qualitative and quantitative assessment of their cellular interactions. Many mass spectrometry (MS) based analytical platforms can achieve such task with varying capabilities. Therefore, four novel high‐throughput MS‐based quantitative methods were evaluated for the analysis of a small organic gene delivery agent: N,N‐bis(dimethylhexadecyl)‐1,3‐propane‐diammonium dibromide (G16‐3). Analysis utilized MS instruments that detect analytes using low‐resolution tandem MS (MS/MS) analysis (i.e. QTRAP or linear ion trap in this work) or high‐resolution MS analysis (i.e. time of flight (ToF) or Orbitrap). Our results indicate that the validated fast chromatography (FC)‐QTRAP‐MS/MS, FC‐ LTQ‐Orbitrap‐MS, desorption electrospray ionization‐collision‐induced dissociation (CID)‐MS/MS and matrix assisted laser desorption ionization‐ToF/ToF‐MS MS methods were superior in the area of method development and sample analysis time to a previously developed liquid chromatography (LC)‐CID‐MS/MS. To our knowledge, this is the first evaluation of the abilities of five MS‐based quantitative methods that target a single pharmaceutical analyte. Our findings indicate that, in comparison to conventional LC‐CID‐MS/MS, the new MS‐based methods resulted in a (1) substantial reduction in the analysis time, (2) reduction in the time required for method development and (3) production of either superior or comparable quantitative data. The four new high‐throughput MS methods, therefore, were faster, more efficient and less expensive than a conventional LC‐CID‐MS/MS for the quantification of the G16‐3 analyte within tissue culture. When applied to cellular lysate, no significant change in the concentration of G16‐3 gemini surfactant within PAM212 cells was observed between 5 and 53 h, suggesting the absence of any metabolism/excretion from PAM212 cells. Copyright © 2014 John Wiley & Sons, Ltd.     

Chemometric Optimization of Biologically Active Compounds Extraction from Grape Marc: Composition and Antimicrobial Activity

The article focuses on the optimization of the extraction process of biologically active compounds (BAC) from grape marc—a by-product of the wine industry. The influence of temperature, specifically 30 °C, 45 °C and 65 °C, and ethanol concentration in solutions, specifically 0–96% (v/v) on the extraction yield of polyphenols, flavonoids, tannins and anthocyanins, were investigated. The composition of individual polyphenols, anthocyanins and organic acids, antioxidant activity (DPPH and ABTS) and CIELab chromatic characteristics of the grape marc extracts (GME), were characterized. The microbiostatic and microbicidal effects in direct contact of GME with pathogenic microorganisms, Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, were determined in vitro. The influence of extraction parameters on the total polyphenol content (TPC), total flavonoid content (TFC), tannin content (TC), total anthocyanin content (TAC) and their interdependencies were studied using information analysis. A mathematical model was developed on cubic spline functions. The analysis of individual compounds showed the presence of a wide range of flavonoids (procyanidin B2, procyanidin B1, hyperoside and quercetin), flavones (catechin), hydroxybenzoic acid derivatives (gallic, protocatechuic, p-hydroxybenzoic acids, m-hydroxybenzoic acid, syringic acid), hydroxycinic acid derivatives and ferulic acid methyl ester. The malvidol-3-glucoside was the main anthocyanin identified in the extract. A high amount of tartaric acid was also found. GME showed significant antimicrobial activity against Gram-positive bacteria and lower activity against Gram-negative bacteria.     

Beyond linear least squares regression

Regression is a collection of statistical methods that are used to study relationships among predictor and response variables. In addition to the most popular linear model, solved by least squares, several other techniques have found an application in analytical chemistry. Biased methods such as stepwise regression, ridge regression, principal components regression, and partial least squares regression are especially useful in cases of poorly or underdetermined systems with collinearity. When structural and/or distributional assumptions associated with linear least squares are violated, nonlinear regression, robust regression or generalized least squares estimators may offer potential remedies.     

Tandem mass spectrometric analysis of novel diquaternary ammonium gemini surfactants and their bromide adducts in electrospray-positive ion mode ionization

Gemini surfactants are cationic lipids which are utilized for both in vitro and in vivo gene delivery. Structurally, they are comprised of two hydrophobic tail regions with polar head termini that are attached to one another through a spacer region. Structural elucidation and characterization of 29 novel diquaternary ammonium gemini surfactant molecules were achieved using a quadrupole time-of-flight mass spectrometer (QqToF-MS) and a quadrupole-hexapole-quadrupole mass spectrometer (QhQ-MS). The tested compounds were categorized into four distinct structural families based upon the composition of the spacer region. Single stage (MS), tandem stage (MS/MS) and quasimulti-stage (quasi MS(3)) mass spectrometric analysis allowed for confirmation of each gemini surfactant's molecular composition and structure through the identification of common and unique product ions. Identification of similarities in the gemini surfactants' fragmentation behaviour resulted in the production of a universal fragmentation pathway that can assist in the future MS/MS analysis of novel quaternary ammonium gemini surfactants, with unique product ions being indicative of specific structural elements. Furthermore, evidence for the association of agemini surfactant with bromine counter ion was confirmed during MS analysis of tested gemini surfactants regardless of their chemical composition; previously, evidence for bromine and gemini surfactant association was only observed with compounds bearing short alkyl spacer regions. MS/MS analysis of the bromine adducts was also confirmatory to the molecular structure.Understanding the ionization and fragmentation behaviour of gemini surfactants, including bromine adducts, will allow for future qualitative and quantitative identification of these novel drug delivery agents within biological samples.     

The 1(5)Π(g) state of C2

We report ab initio spectroscopic constants for the recently identified 1(5)Π(g) state of C(2) [P. Bornhauser, Y. Sych, G. Knopp, T. Gerber, and P. P. Radi, J. Chem. Phys. 134, 044302 (2011)]. The calculations are performed at the multi-reference configuration interaction level of theory with Davidson's correction using aug-cc-pV6Z basis sets and include core-valence correlation and relativistic corrections obtained with quadruple-zeta bases. Such treatment accurately reproduces the experimentally observed constants of the a(3)Π(u) and other states. Thus, we expect our calculated ω(e) value for the 1(5)Π(g) state to be within a few cm(-1), and rotational constants to be within 0.1% of experiment. Agreement with available spectroscopic data is excellent, with the calculations strongly suggesting that the 1(5)Π(g) vibrational level observed by Bornhauser et al. is v = 0.