Theoretical study on the asymmetric Michael addition of cyclohexanone with trans‐β‐nitrostyrene catalyzed by a pyrrolidine‐type chiral ionic liquid

The Michael addition of cyclohexanone with trans‐β‐nitrostyrene catalyzed by a chiral ionic liquid (CIL) pyrrolidine‐imidazolium bromide, which represents a prototype of CIL‐promoted asymmetric syntheses, has been investigated by performing density functional theory calculations. We show the details of the mechanism and energetics, the influence of the acid additive on the reactivity, and the functional role of the CIL in the asymmetric addition. It is found that the reaction proceeds via two stages, i.e., the initial enamine formation, where the imine complex is first created and then isomerizes into the enamine intermediate, and the subsequent Michael addition involving a three‐step mechanism. The calculations show that the presence of the acid additive changes the imine formation mechanism and lowers the reaction barrier, as well as, more importantly, makes the reaction become highly thermodynamically favored. It is also suggested that both the anion and cation of the CIL synergically facilitate the reaction, which act as the proton acceptor in the imine‐enamine tautomerism and the stabilizer of the negative charge in the C? C bond formation process, respectively. The present theoretical study rationalizes the early experimental findings well and provides aid to some extent for the rational design of efficient CIL catalysts. Chirality 2010. © 2010 Wiley‐Liss, Inc.     

Detection and identification of 4‐hydroxy‐2‐nonenal Schiff‐base adducts along with products of Michael addition using data‐dependent neutral loss‐driven MS3 acquisition: Method evaluation through an in vitro study on cytochrome c oxidase modifications

We report a data‐dependent neutral‐loss‐driven MS³ acquisition to enhance, in addition to abundant Michael adducts, the detection of Schiff‐base adducts of proteins and 4‐hydroxy‐2‐nonenal, a reactive end product of lipid peroxidation. In vitro modification of cytochrome c oxidase, a mitochondrial protein complex, was used as a model to evaluate the method. The technique allowed for a confident validation of modification sites and also identified a Schiff‐base adduct in subunit Vb of the protein complex.     

The resolution of acyclic P‐stereogenic phosphine oxides via the formation of diastereomeric complexes: A case study on ethyl‐(2‐methylphenyl)‐phenylphosphine oxide

As an example of acyclic P‐chiral phosphine oxides, the resolution of ethyl‐(2‐methylphenyl)‐phenylphosphine oxide was elaborated with TADDOL derivatives, or with calcium salts of the tartaric acid derivatives. Besides the study on the resolving agents, several purification methods were developed in order to prepare enantiopure ethyl‐(2‐methylphenyl)‐phenylphosphine oxide. It was found that the title phosphine oxide is a racemic crystal‐forming compound, and the recrystallization of the enantiomeric mixtures could be used for the preparation of pure enantiomers. According to our best method, the (R)‐ethyl‐(2‐methylphenyl)‐phenylphosphine oxide could be obtained with an enantiomeric excess of 99% and in a yield of 47%. Complete racemization of the enantiomerically enriched phosphine oxide could be accomplished via the formation of a chlorophosphonium salt. Characterization of the crystal structures of the enantiopure phosphine oxide was complemented with that of the diastereomeric intermediate. X‐ray analysis revealed the main nonbonding interactions responsible for enantiomeric recognition.     

On the Permeation by Dioxygen of the Cofactor‐Independent Unusual Oxygenase RhCC,in Complex with Substrate 4‐Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation

This work deals with a trimeric bacterial protein, RhCC, which, although belonging to the tautomerase superfamily, shows oxygenase activity. A model of the complex from RhCC and substrate 4‐hydroxyphenylenolpyruvate (4HPP), fitting the observation of extra electron densities from X‐ray diffraction of the crystal, could be built by autodocking. When subjected to molecular dynamics (MD) aided by an external random force applied to a O₂ molecule placed above 4HPP, this model evolved with O₂ egressing toward the bulk solvent from two nearly opposite gates. These were located between the nearly parallel helices 75 – 91 and 15 – 33 of either chain C (gate SE) or chain B (gate FL). Alternatively, with four O₂ molecules in the bulk solvent, unbiased MD led to O₂ entering the protein from gate SE and getting to 4HPP, while forming a stabilizing salt bridge between the 4HPP carboxylate and P1.C ⁺NH₂, thus providing scientific ground for a refined model of the complex.     

C4‐consumers in southern europe: The case of friuli V.G. (NE‐Italy) during early and central middle ages

Isotope variations were studied in necropolises of the early (6th to 7th century CE) and central (10th to 11th century CE) medieval period located in Fruili‐Venezia Giulia (Northeastern Italy). The two periods each shortly followed two great barbarian invasions that changed the politics and economy of Italy: the arrivals of Langobards in 578 CE and the Hungarian incursions from the end of the 9th to the first half of the 10th century. These events had a tragic effect on the economy of Friuli‐Venezia Giulia: severe depopulation and the partial abandonment of the countryside with fall of agricultural production. Am J Phys Anthropol 154:561–574, 2014. © 2014 Wiley Periodicals, Inc.     

Effect of a nitrogen pulse on ecosystem N processing at different temperatures: A mesocosm experiment with 15NO3− addition

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The effect of β‐methylation on the conformation of α, β‐dehydrophenylalanine: a DFT study

Dehydroamino acids are non‐coded amino acids that offer unique conformational properties. Dehydrophenylalanine (ΔPhe) is most commonly used to modify bioactive peptides to constrain the topography of the phenyl ring in the side chain, which commonly serves as a pharmacophore. The Ramachandran maps (in the gas phase and in CHCl₃ mimicking environments) of ΔPhe analogues with methyl groups at the β position of the side chain as well as at the C‐terminal amide were calculated using the B3LYP/6‐31 + G** method. Unexpectedly, β‐methylation alone results in an increase of conformational freedom of the affected ΔPhe residue. However, further modification by introducing an additional methyl group at C‐terminal methyl amide results in a steric crowding that fixes the torsion angle ψ of all conformers to the value 123°, regardless of the Z or E position of the phenyl ring. The number of conformers is reduced and the accessible conformational space of the residues is very limited. In particular, (Z)‐Δ(βMe)Phe with the tertiary C‐terminal amide can be classified as the amino acid derivative that has a single conformational state as it seems to adopt only the β conformation. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Dissection of a β‐barrel motif leads to a functional dimer: The case of the intestinal fatty acid binding protein

A lingering issue in the area of protein engineering is the optimal design of β motifs. In this regard, the framework provided by intestinal fatty acid binding protein (IFABP) was successfully chosen to explore the consequences on structure and function of the redesign of natural motifs. A truncated form of IFABP (Δ98Δ) served to illustrate the nonintuitive notion that the integrity of the β‐barrel can indeed be compromised with no effect on the ability to attain a native‐like fold. This is most likely the outcome of the key role played by the preservation of essential core residues. In the search for the minimal structural determinants of this fold, Δ98Δ offered room for further intervention. A dissection of this protein leads to a new abridged variant, Δ78Δ, containing 60% of the amino acids of IFABP. Spectroscopic analyses indicate that Δ78Δ retains substantial β‐sheet content and preserves tertiary interactions, displaying cooperative unfolding and binding activity. Most strikingly, this construct adopts a remarkably stable dimeric structure in solution. This phenomenon takes advantage of the inherent structural plasticity of this motif, likely profitting from edge‐to‐edge interactions between β‐sheets, whereas avoiding the most commonly occurring outcome represented by aggregation.     

Some introductory formalizations on the affine Hilbert spaces model of the origin of life. I. On quantum mechanical measurement and the origin of the genetic code: a general physical framework theory

A physical (affine Hilbert spaces) frame is developed for the discussion of the interdependence of the problem of the origin (symbolic assignment) of the genetic code and a possible endophysical (a kind of "internal") quantum measurement in an explicite way, following the general considerations of Balázs (Balázs, A., 2003. BioSystems 70, 43-54; Balázs, A., 2004a. BioSystems 73, 1-11). Using the Everett (a dynamic) interpretation of quantum mechanics, both the individual code assignment and the concatenated linear symbolism is discussed. It is concluded that there arises a skewed quantal probability field, with a natural dynamic non-linearity in codon assignment within the physical model adopted (essentially corresponding to a much discussed biochemical frame of self-catalyzed binding (charging) of t RNA like proto RNAs (ribozymes) with amino acids). This dynamic specific molecular complex assumption of individual code assignment, and the divergence of the code in relation to symbol concatenation, are discussed: our frame supports the former and interpret the latter as single-type codon (triplet), also unambiguous and extended assignment, selection in molecular evolution, corresponding to converging towards the fixedpoint of the internal dynamics of measurement, either in a protein- or RNA-world. In this respect, the general physical consequence is the introduction of a fourth rank semidiagonal energy tensor (see also Part II) ruling the internal dynamics as a non-linear in principle second-order one. It is inferred, as a summary, that if the problem under discussion could be expressed by the concepts of the Copenhagen interpretation of quantum mechanics in some yet not quite specified way, the matter would be particularly interesting with respect to both the origin of life and quantum mechanics, as a dynamically supported natural measurement-theoretical split between matter ("hardware") and (internal) symbolism ("software") aspects of living matter.     

Investigating the change in the photophysical properties of a trio of tetraphenylcyclopentadienone derivatives with varied groups on the aromatic rings in the 3‐ and 4‐positions

Organic compounds with electronic properties, such as a small band gap, are useful in areas ranging from organic field effect transistors to solar cells. Such organic compounds can possess conjugation and/or aromatic systems, with one example being tetraphenylcyclopentadienone and its derivatives. A trio of dramatically coloured tetraphenylcyclopentadienone derivatives with varied substituents on the aromatic rings in the 3‐ and 4‐positions were prepared. Their identities were confirmed using the usual methods, for example ¹H nuclear magnetic resonance (NMR) spectroscopy, and their purity quantified using elemental analysis. The X‐ray crystal structure of compound 2 was determined. Its notable structural features involved the cyclopentadienone core with its distinct C?C and C=C bond lengths and its overall nonplanarity, both of which served to mitigate its antiaromatic nature. Chloroform solutions of compounds 2 – 4 exhibited absorption spectra with three absorption bands at approximately 250, 350, and 500 nm that were assigned to (π)→(π*) transitions. Computational chemistry methods assisted in assigning the observed transitions to a specific molecular orbital combination in the structures of 2 – 4 . Emission in the red end of the visible spectrum (550–625 nm) was observed from chloroform solutions of all three of the prepared compounds.     

A validated HPLC method for the determination of dimethyl‐4,4′‐dimethoxy‐5,6,5′,6′‐dimethylene dioxybiphenyl‐2,2′‐dicarboxylate (DDB) with fluorescence detection in raw material and pill form: application to an in vitro dissolution test and a content uniformity test

A simple, sensitive and rapid HPLC method with fluorescence detection for the determination of dimethyl‐4,4′‐dimethoxy‐5,6,5′,6′‐dimethylene dioxybiphenyl‐2,2′‐dicarboxylate (DDB) in the raw material and pill form was developed. Liquid chromatography was performed on a C₁₈ column (250 × 4.6 mm i.d., 5 µm particle size), the mobile phase consisted of methanol and 0.05 M sodium dihydrogen phosphate buffer (80 : 20, v/v), and the apparent pH of the mobile phase was adjusted to 3. The fluorescence detector was operated at excitation/emission wavelengths of 275/400 nm. The proposed method allows the determination of DDB within concentration range 0.1–1.5 µg/mL with a limit of detection of 0.032 µg/mL, a limit of quantification of 0.097 µg/mL and a correlation coefficient of 0.9997. The proposed method has been successfully applied for the analysis of DDB in its pills with a percentage recovery of 98.45 ± 0.32. The method was fully validated according to ICH guidelines. Moreover, the high sensitivity of the method permits its use in an in vitro dissolution test for DDB under simulated intestinal conditions. In addition, the proposed method was extended to a content uniformity test according to USP guidelines. Copyright © 2014 John Wiley & Sons, Ltd.     

Leptosphaeria maculans AvrLm9: a new player in the game of hide and seek with AvrLm4‐7

Blackleg disease of Brassica napus caused by Leptosphaeria maculans (Lm) is largely controlled by the deployment of race‐specific resistance (R) genes. However, selection pressure exerted by R genes causes Lm to adapt and give rise to new virulent strains through mutation and deletion of effector genes. Therefore, a knowledge of effector gene function is necessary for the effective management of the disease. Here, we report the cloning of Lm effector AvrLm9 which is recognized by the resistance gene Rlm9 in B. napus cultivar Goéland. AvrLm9 was mapped to scaffold 7 of the Lm genome, co‐segregating with the previously reported AvrLm5 (previously known as AvrLmJ1). Comparison of AvrLm5 alleles amongst the 37 re‐sequenced Lm isolates and transgenic complementation identified a single point mutation correlating with the AvrLm9 phenotype. Therefore, we renamed this gene as AvrLm5‐9 to reflect the dual specificity of this locus. Avrlm5‐9 transgenic isolates were avirulent when inoculated on the B. napus cultivar Goéland. The expression of AvrLm5‐9 during infection was monitored by RNA sequencing. The recognition of AvrLm5‐9 by Rlm9 is masked in the presence of AvrLm4‐7, another Lm effector. AvrLm5‐9 and AvrLm4‐7 do not interact, and AvrLm5‐9 is expressed in the presence of AvrLm4‐7. AvrLm5‐9 is the second Lm effector for which host recognition is masked by AvrLm4‐7. An understanding of this complex interaction will provide new opportunities for the engineering of broad‐spectrum recognition.     

Toward a general mixed quantum/classical method for the calculation of the vibronic ECD of a flexible dye molecule with different stable conformers: Revisiting the case of 2,2,2‐trifluoro‐anthrylethanol

We extend a recently proposed mixed quantum/classical method for computing the vibronic electronic circular dichroism (ECD) spectrum of molecules with different conformers, to cases where more than one hindered rotation is present. The method generalizes the standard procedure, based on the simple Boltzmann average of the vibronic spectra of the stable conformers, and includes the contribution of structures that sample all the accessible conformational space. It is applied to the simulation of the ECD spectrum of (S)‐2,2,2‐trifluoroanthrylethanol, a molecule with easily interconvertible conformers, whose spectrum exhibits a pattern of alternating positive and negative vibronic peaks. Results are in very good agreement with experiment and show that spectra averaged over all the sampled conformational space can deviate significantly from the simple average of the contributions of the stable conformers. The present mixed quantum/classical method is able to capture the effect of the nonlinear dependence of the rotatory strength on the molecular structure and of the anharmonic couplings among the modes responsible for molecular flexibility. Despite its computational cost, the procedure is still affordable and promises to be useful in all cases where the ECD shape arises from a subtle balance between vibronic effects and conformational variety.     

Physicochemical studies on the biopolymer inulin: A critical evaluation of its self‐aggregation,aggregate‐morphology,interaction with water,and thermal stability

Physicochemical properties viz., aggregation, molar mass, shape, and size of chicory inulin in solution were determined by fluorimetry, DLS, SLS, TEM, and viscometry methods. The thermal stability of the biopolymer was examined by TGA, DTA, and DSC measurements. The water vapor adsorption of desiccated inulin was also studied by the isopiestic method, and the data were analyzed in the light of the BET equation. On the basis of the obstruction to ion conductance by the inulin aggregates in solution and analysis of the data, the extent of hydration of inulin in solution was estimated. The result was coupled with the intrinsic viscosity, [η], of inulin to ascertain the shape of the biopolymer aggregates in aqueous solution. The critical aggregation concentration (cac) of inulin in aqueous as well as in salt solution was assessed by fluorimetry. The weight average molar mass, , of inulin monomer and its aggregate was found to be 4468 and 1.03 × 10⁶ g/mol, respectively, in aqueous solution. This aggregated mass was 2.4 × 10⁶ g/mol in 0.5M NH₄SCN solution. The [η] values of the soft supramolecular aggregates in solution (without and with salt) were small and comparable with globular proteins evidencing spherical geometry of the biopolymer aggregates as supported by the TEM results. In DMSO, rod‐like aggregates of inulin was found by the TEM study. The [η] of the biopolymer in the DMSO medium was therefore, higher than that in the aqueous medium. Unlike aqueous medium, the aggregation in DMSO was not associated with a cac. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 687–699, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Changing gull diet in a changing world: A 150‐year stable isotope (δ13C, δ15N) record from feathers collected in the Pacific Northwest of North America

The world's oceans have undergone significant ecological changes following European colonial expansion and associated industrialization. Seabirds are useful indicators of marine food web structure and can be used to track multidecadal environmental change, potentially reflecting long‐term human impacts. We used stable isotope (δ¹³C, δ¹⁵N) analysis of feathers from glaucous‐winged gulls (Larus glaucescens) in a heavily disturbed region of the northeast Pacific to ask whether diets of this generalist forager changed in response to shifts in food availability over 150 years, and whether any detected change might explain long‐term trends in gull abundance. Sampled feathers came from birds collected between 1860 and 2009 at nesting colonies in the Salish Sea, a transboundary marine system adjacent to Washington, USA and British Columbia, Canada. To determine whether temporal trends in stable isotope ratios might simply reflect changes to baseline environmental values, we also analysed muscle tissue from forage fishes collected in the same region over a multidecadal timeframe. Values of δ¹³C and δ¹⁵N declined since 1860 in both subadult and adult gulls (δ¹³C, ~ 2–6‰; δ¹⁵N, ~4–5‰), indicating that their diet has become less marine over time, and that birds now feed at a lower trophic level than previously. Conversely, forage fish δ¹³C and δ¹⁵N values showed no trends, supporting our conclusion that gull feather values were indicative of declines in marine food availability rather than of baseline environmental change. Gradual declines in feather isotope values are consistent with trends predicted had gulls consumed less fish over time, but were equivocal with respect to whether gulls had switched to a more garbage‐based diet, or one comprising marine invertebrates. Nevertheless, our results suggest a long‐term decrease in diet quality linked to declining fish abundance or other anthropogenic influences, and may help to explain regional population declines in this species and other piscivores.