Preparation and Diels-Alder Reactivity of 2,3,5,6,7,8-Hexamethylidenebicyclo [2.2.2]octane (‘[2.2.2]Hericene’). Force-field calculations of exocyclic dienes as a moiety of bicyclic skeletons

The [2.2.2]hericene ( 6 ), a bicyclo[2.2.2]octane bearing three exocyclic s-cis-butadiene units has been prepared in eight steps from coumalic acid and maleic anhydride. The hexaene 6 adds successively three mol-equiv. of strong dienophiles such as ethylenetetracarbonitrile (TCE) and dimethyl acetylenedicarboxylate (DMAD) giving the corresponding monoadducts 17 and 20 (k₁), bis-adducts 18 and 21 (k₂) and tris-adducts 19 and 22 (k₃), respectively. The rate constant ratio k₁/k₂ is small as in the case of the cycloadditions of 2,3,5,6-tetramethylidene-bicyclo [2.2.2]octane ( 3 ) giving the corresponding monoadducts 23 and 27 (k₁) and bis-adducts 25 and 29 (k₂) with TCE and DMAD, respectively. Constrastingly, the rate constant ratio k₂/k₃ is relatively large as the rate constant ratio k₁/k₂ of the Diels-Alder additions for 5,6,7,8-tetramethylidenebicyclo [2.2.2]oct-2-ene ( 4 ) giving the corresponding monoadducts 24 and 28 (k₁) and bis-adducts 26 and 30 (k₂). The following second-order rate constants (toluene, 25°) and activation parameters were obtained for the TCE additions: 3 +TCE→ 23 : k₁ = 0.591±0.012 mol^?1·l·s^?1, ΔH^≠=10.6±0.4 kcal/mol, and ΔS^≠ = ?24.0±1.4 cal/mol·K (e.u.); 23 +TCE→ 25 : k₂=0.034±0.0010 mol^?1·l·s^?1, ΔH^≠ = 10.6±0.6 kcal/mol, and ΔS^≠ = ?29.7±2.0 e.u.; 4 +TCE→ 26 : k₁ = 0.172±0.035 mol^?1·l·s^?1, ΔH^≠ 11.3±0.8 kcal/mol, and ΔS^≠ = ?24.0±2.8 e.u.; 24 +TCE→ 26 : k₂ = (6.1±0.2)·10^?4 mol^?1·l·s^?1, ΔH^≠ = 13.0±0.3 kcal/mol, and ΔS^≠ = ?29.5±0.8 e.u.; 6 +TCE→ 17 : k₁ = 0.136±0.002 mol^?1·l·s^?1, ΔH^≠ = 11.3±0.2 kcal/mol, and ΔS^≠ = ?24.5±0.8 e.u.; 17 +TCE→ 18 : k₂ = 0.0156±0.0003 mol^?1·l·s^?1, ΔH^≠ = 10.9±0.5 kcal/mol, and ΔS^≠ = ?30.1 ± 1.5 e.u.; 18 +TCE→ 19 : k₃=(5±0.2) · 10^?5 mol^?1 mol^?1 ·l·s^?1, ΔH^≠ = 15±3 kcal/mol, and ΔS^≠ = ?28 ± 8 e.u. The following rate constants were evaluated for the DMAD additions (CD₂Cl₂, 30°): 6 +DMAD→ 20 : k₁ = (10±1)·10^?4 mol^?1 · l·s^?1; 20 +DMAD→ 21 : k₂ = (6.5±0.1) · 10^?4 mol^?1 ·l·^?1; 21 +DMAD→ 22 : k₃ = (1.0±0.1) · 10^?4 mol^?1 ·l·s^?1. The reactions giving the barrelene derivatives 19, 22, 26 and 30 are slower than those leading to adducts that are not barrelenes. The former are estimated less exothermic than the latter. It is proposed that the Diels-Alder reactivity of exocyclic s-cis-butadienes grafted onto bicycle [2.2.1]heptanes and bicyclo [2.2.2]octanes that are modified by remote substitution of the bicyclic skeletons can be affected by changes inthe exothermicity of the cycloadditions, in agreement with the Dimroth and Bell-Evans-Polanyi principle. Force-field calculations (MMPI 1) of 3, 4, 6 and related exocyclic s-cis-butadienes as a moiety of bicyclo [2.2.2]octane suggested single minimum energy hypersurfaces for these systems (eclipsed conformations, planar dienes). Their flexibility decreases with the degree of unsaturation of the bicyclic skeleton. The effect of an endocyclic double bond is larger than that of an exocyclic diene moiety.     

Comparative study of recent wide-pore materials of different stationary phase morphology, applied for the reversed-phase analysis of recombinant monoclonal antibodies

Various recent wide-pore reversed-phase stationary phases were studied for the analysis of intact monoclonal antibodies (mAbs) of 150 kDa and their fragments possessing sizes between 25 and 50 kDa. Different types of column technology were evaluated, namely, a prototype silica-based inorganic monolith containing mesopores of ～250 Å and macropores of ～?1.1 μm, a column packed with 3.6 μm wide-pore core-shell particles possessing a wide pore size distribution with an average around 200 Å and a column packed with fully porous 1.7 μm particles having pore size of ～300 Å. The performance of these wide-pore materials was compared with that of a poly(styrene–divinyl benzene) organic monolithic column, with a macropore size of approximately 1 μm but without mesopores (stagnant pores). A systematic investigation was carried out using model IgG1 and IgG2 mAbs, namely rituximab, panitumumab, and bevacizumab. Firstly, the recoveries of intact and reduced mAbs were compared on the two monolithic phases, and it appeared that adsorption was less pronounced on the organic monolith, probably due to the difference in chemistry (C18 versus phenyl) and the absence of mesopores (stagnant zones). Secondly, the kinetic performance was investigated in gradient elution mode for all columns. For this purpose, peak capacities per meter as well as peak capacities per time unit and per pressure unit (PPT) were calculated at various flow rates, to compare performance of columns with different dimensions. In terms of peak capacity per meter, the core-shell 3.6 μm and fully porous 1.7 μm columns outperformed the two monolithic phases, at a temperature of 60 °C. However, when considering the PPT values, the core-shell 3.6 μm column remained the best phase while the prototype silica-based monoliths became very interesting, mostly due to a very high permeability compared with the organic monolith. Therefore, these core-shell and silica-based monolith provided the fastest achievable separation. Finally, at the maximal working temperature of each column, the core-shell 3.6 μm column was far better than the other one, because it is the only one stable up to 90 °C. Lastly, the loading capacity was also measured on these four different phases. It appeared that the organic monolith was the less interesting and rapidly overloaded, due to the absence of mesopores. On the other hand, the loading capacity of prototype silica-based monolith was indeed reasonable.     

Photo- and thermal-oxidation of polyethylene: Comparison of mechanisms and influence of unsaturation content

The behaviour of polyethylene with different contents in vinyl and t-vinylene groups have been studied by photooxidation with λ ≥ 300 nm light or by thermooxidation at a temperature of 100 °C. The oxidation was studied by infrared spectroscopy and it was shown that the same oxidation products were obtained, but with different relative concentrations depending on the conditions of ageing, i.e. photochemical or thermal conditions. The mechanisms by which the oxidation products are formed were recalled. The differences between photo- and thermo-oxidation were evidenced on the basis of the stability of ketones that do not accumulate in photochemical conditions, as a result of Norrish reactions. The influence of the initial amount of unsaturated groups on the rates of oxidation was characterized. It was shown that the concentration of unsaturations had no effect on the rate of photooxidation but dramatically influenced the stability in thermooxidative conditions.     

Synthesis of unnatural 3′-phospha-2′-deoxyfuranose nucleoside analogues

This Letter describes the synthesis of racemic analogues of unnatural 2′-deoxy nucleoside with a phosphorus atom replacing the carbon atom in the 3′-position. A seven-step sequence was developed in racemic series to afford unnatural 3′-phospha-2′-deoxyfuranose nucleosides. The phospha nucleoside analogues were tested against HCV, but did not show any antiviral activity at a 10 μM maximum concentration used for the inhibition assays of analogues 2-T, 2-C and 4-Tα.     

Characterization of glycosyl inositol phosphoryl ceramides from plants and fungi by mass spectrometry

Although glycosyl inositol phosphoryl ceramides (GIPCs) represent the most abundant class of sphingolipids in plants, they still remain poorly characterized in terms of structure and biodiversity. More than 50 years after their discovery, little is known about their subcellular distribution and their exact roles in membrane structure and biological functions. This review is focused on extraction and characterization methods of GIPCs occurring in plants and fungi. Global methods for characterizing ceramide moieties of GIPCs revealed the structures of long-chain bases (LCBs) and fatty acids (FAs): LCBs are dominated by tri-hydroxylated molecules such as monounsaturated and saturated phytosphingosine (t18:1 and t18:0, respectively) in plants and mainly phytosphingosine (t18:0 and t20:0) in fungi; FA are generally 14–26 carbon atoms long in plants and 16–26 carbon atoms long in fungi, these chains being often hydroxylated in position 2. Mass spectrometry plays a pivotal role in the assessment of GIPC diversity and the characterization of their structures. Indeed, it allowed to determine that the core structure of GIPC polar heads in plants is Hex(R1)-HexA-IPC, with R1 being a hydroxyl, an amine, or a N-acetylamine group, whereas the core structure in fungi is Man-IPC. Notably, information gained from tandem mass spectrometry spectra was most useful to describe the huge variety of structures encountered in plants and fungi and reveal GIPCs with yet uncharacterized polar head structures, such as hexose–inositol phosphoceramide in Chondracanthus acicularis and (hexuronic acid)₄–inositol phosphoceramide and hexose–(hexuronic acid)₃–inositol phosphoceramide in Ulva lactuca.

A two-point calibration method for quantifying organic binary mixtures using secondary ion mass spectrometry in the presence of matrix effects

Quantification of the composition of binary mixtures in secondary ion mass spectrometry (SIMS) is required in the analyses of technological materials from organic electronics to drug delivery systems. In some instances, it is found that there is a linear dependence between the composition, expressed as a ratio of component volumes, and the secondary ion intensities, expressed as a ratio of intensities of ions from each component. However, this ideal relationship fails in the presence of matrix effects and linearity is observed only over small compositional ranges, particularly in the dilute limits. In this paper, we assess an empirical method, which introduces a power law dependence between the intensity ratio and the volume fraction ratio. A previously published physical model of the organic matrix effect is employed to test the limits of the method and a mixed system of 3,3′-bis(9-carbazolyl) biphenyl and tris(2-phenylpyridinato)iridium (III) is used to demonstrate the method. This paper introduces a two-point calibration, which determines both the exponent in the power law and the sensitivity factor for the conversion of ion intensity ratio into volume fraction ratio. We demonstrate that this provides significantly improved accuracy, compared with a one-point calibration, over a wide compositional range in SIMS quantification and with a weak dependence on matrix effects. Because the method enables the use of clearly identifiable secondary ions for quantitative purposes and mitigates commonly observed matrix effects in organic materials, the two-point calibration method could be of significant benefit to SIMS analysts.     

CORSICA: correction of structured noise in fMRI by automatic identification of ICA components

When applied to functional magnetic resonance imaging (fMRI) data, spatial independent component analysis (sICA), a data-driven technique that addresses the blind source separation problem, seems able to extract components specifically related to physiological noise and brain movements. These components should be removed from the data to achieve structured noise reduction and improve any subsequent detection and analysis of signal fluctuations related to neural activity. We propose a new automatic method called CORSICA (CORrection of Structured noise using spatial Independent Component Analysis) to identify the components related to physiological noise, using prior information on the spatial localization of the main physiological fluctuations in fMRI data. As opposed to existing spectral priors, which may be subject to aliasing effects for long-TR data sets (typically acquired with TR >1 s), such spatial priors can be applied to fMRI data, regardless of the TR of the acquisitions. By comparing the proposed automatic selection to a manual selection performed visually by a human operator, we first show that CORSICA is able to identify the noise-related components for long-TR data with a high sensitivity and a specificity of 1. On short-TR data sets, we validate that the proposed method of noise reduction allows a substantial improvement of the signal-to-noise ratio evaluated at the cardiac and respiratory frequencies, even in the gray matter, while preserving the main fluctuations related to neural activity.     

Diversity of potential hydrogen bonds in cellulose I revealed by molecular dynamics simulation

We have performed molecular dynamics calculations using a revised version of the Gromos56A_carbo force field to understand the consequences of the different potential hydrogen bonding patterns on the structural stability and thermal behavior of the I_α and I_β forms of native cellulose. For each allomorph, we considered three patterns of hydrogen bonds: two patterns obtained from neutron diffraction data refinement and a regular mixture of the two. Upon annealing, the hydrogen bonding schemes of cellulose I_β, irrespective of the starting structure, re-arranged into the main hydrogen bond pattern experimentally observed (pattern A). On the other hand, the I_α structures, irrespective of the starting hydrogen bonding pattern, converged to a non-experimental structure where the adjacent chains are shifted along the chain direction by 0.12 nm in the hydrogen-bonded plane, and the hydroxymethyl group conformation alternates between gt and tg along the chain. The exotic structure in I_α might be a consequence of a deficiency in force field parameters and/or potential molecular arrangement in less crystalline cellulose.