An evaluation of british columbian beetle-killed hybrid spruce for bioethanol production

The development of bioconversion technologies for production of fuels, chemicals, and power from renewable resources is currently a high priority for developed nations such as the United States, Canada, and the European Union as a way to improve national energy security and reduce greenhouse gas emissions. The widespread implementation of such technologies will require a sustainable supply of biomass from forestry and agriculture. Forests are a major source of feedstocks for biofuels production in Canada. Woody biomass includes residues from logging and forest thinning, and from wood processing and pulp production. More recently, damaged wood caused by beetle infestations has become available on a large scale in Western Canada. This study evaluates beetle-killed British Columbian hybrid spruce (HS) (Picea glauca x P. engelmannii) as a feedstock for the production of bioethanol. In the past 30 yr, attack by the beetle Dendroctonus rufipennis and associated fungi has resulted in estimated losses of more than three billion board feet in British Columbia alone. Here we describe the chemical and some physical characteristics of both healthy (HHS) and beetle-killed (BKHS) British Columbian HS and evaluate the technical feasibility of using these feedstocks as a source of biomass for bioethanol production. Untreated HHS and BKHS did not differ significantly in chemical composition except for the moisture content, which was significantly lower in BKHS (approx 10%) compared with HHS (approx 18%). However, the yields of carbohydrates in hydrolyzable and fermentable forms were higher at mild pretreatment conditions (H-Factor <1000) for BKHS compared with HHS. At medium (H-Factor 1000-2000) and severe (H-Factor >2000) pretreatment conditions HHS and BKHS behaved similarly. Organosolv pretreated HHS and BKHS demonstrated good ethanol theoretical yields, approx 70 and 80%, respectively.     

Unraveling solvent-driven equilibria between alpha- and 3(10)-helices through an integrated spin labeling and computational approach

In this work we present an effective and flexible computational approach, which is the result of an ongoing development in our groups, allowing the complete a priori simulation of the ESR spectra of complex systems in solution. The usefulness and reliability of the method are demonstrated on the very demanding playground represented by the tuning of the equilibrium between 3(10)- and alpha-helices of polypeptides by different solvents. The starting point is the good agreement between computed and X-ray diffraction structures for the 3(10)-helix adopted by the double spin-labelled heptapeptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe. Next, density functional computations, including dispersion interactions and bulk solvent effects, suggest another energy minimum corresponding to an alpha-helix in polar solvents, which, eventually, becomes the most stable structure. Computation of magnetic and diffusion tensors provides the basic ingredients for the building of complete spectra by methods rooted in the Stochastic Liouville Equation (SLE). The remarkable agreement between computed and experimental spectra at different temperatures allowed us to identify helical structures in the various solvents. The generality of the computational strategy and its implementation in effective and user-friendly computer codes pave the route toward systematic applications in the field of biomolecules and other complex systems.     

Exploring the subtleties of drug-receptor interactions: the case of matrix metalloproteinases

By solving high-resolution crystal structures of a large number (14 in this case) of adducts of matrix metalloproteinase 12 (MMP12) with strong, nanomolar, inhibitors all derived from a single ligand scaffold, it is shown that the energetics of the ligand-protein interactions can be accounted for directly from the structures to a level of detail that allows us to rationalize for the differential binding affinity between pairs of closely related ligands. In each case, variations in binding affinities can be traced back to slight improvements or worsening of specific interactions with the protein of one or more ligand atoms. Isothermal calorimetry measurements show that the binding of this class of MMP inhibitors is largely enthalpy driven, but a favorable entropic contribution is always present. The binding enthalpy of acetohydroxamic acid (AHA), the prototype zinc-binding group in MMP drug discovery, has been also accurately measured. In principle, this research permits the planning of either improved inhibitors, or inhibitors with improved selectivity for one or another MMP. The present analysis is applicable to any drug target for which structural information on adducts with a series of homologous ligands can be obtained, while structural information obtained from in silico docking is probably not accurate enough for this type of study.     

Paramagnetism-based NMR restraints provide maximum allowed probabilities for the different conformations of partially independent protein domains

An innovative analytical/computational approach is presented to provide maximum allowed probabilities (MAPs) of conformations in protein domains not rigidly connected. The approach is applied to calmodulin and to its adduct with alpha-synuclein. Calmodulin is a protein constituted by two rigid domains, each of them composed by two calcium-binding EF-hand motifs, which in solution are largely free to move with respect to one another. We used the N60D mutant of calmodulin, which had been engineered to selectively bind a paramagnetic lanthanide ion to only one of its four calcium binding sites, specifically in the second EF-hand motif of the N-terminal domain. In this way, pseudocontact shifts (pcs's) and self-orientation residual dipolar couplings (rdc's) measured on the C-terminal domain provide information on its relative mobility with respect to the domain hosting the paramagnetic center. Available NMR data for terbium(III) and thulium(III) calmodulin were supplemented with additional data for dysprosium(III), analogous data were generated for the alpha-synuclein adduct, and the conformations with the largest MAPs were obtained for both systems. The MAP analysis for calmodulin provides further information on the variety of conformations experienced by the system. Such variety is somewhat reduced in the calmodulin-alpha-synuclein adduct, which however still retains high flexibility. The flexibility of the calmodulin-alpha-synuclein adduct is an unexpected result of this research.     

Measurements of lower carbonyls and hydrocarbons at Ny-Alesund, Svalbard

Measurements of gaseous organic compounds were carried out near Ny-Alesund, in the Norwegian Arctic, during September 2004. Twenty alkanes, alkenes and aromatic hydrocarbons from ethane to toluene and six aldehydes and ketones from formaldehyde to butanal, were identified and quantified in air samples. Hydrocarbons showed a quite uniform distribution, with ethane being by far the most abundant component (> 1 ppb), followed by propane (> 0.4 ppb) and butanes (> 0.3 ppb), while for unsaturated homologues, except ethene, concentrations never exceeding 0.05 ppb were observed. This distribution confirmed that hydrocarbon depletion during the transport time from Europe into the Arctic was depending upon their atmospheric lifetimes, calculated relatively to the OH reactivity scale. The presence of short lived hydrocarbons could be associated to local sources of anthropogenic and/or biogenic origin. Although the local air photochemistry played a primary role in the production of lower aldehydes in late summer, the observed mixing ratios of formaldehyde (in the 0.25 - 0.50 ppb range) could not be fully explained by known gas-phase chemistry. In this case additional sources, such as fluxes of formaldehyde from snow pack to the atmosphere and/or local anthropogenic activities, were to be taken into consideration. The possible influences of these sources on HCHO mixing ratios were analysed by means of a backward-trajectory circulation model.     

Solid phase extraction of food contaminants using molecular imprinted polymers

Food contamination from natural or anthropogenic sources poses severe risks to human health. It is now largely accepted that continuous exposure to low doses of toxic chemicals can be related to several chronic diseases, including some type of cancer and serious hormonal dysfunctions.Contemporary analytical methods have the sensitivity required for contamination detection and quantification, but direct application of these methods on food samples can be rarely performed. In fact, the matrix introduces severe disturbances, and analysis can be performed only after some clean-up and preconcentration steps. Current sample pre-treatment methods, mostly based on the solid phase extraction technique, are very fast and inexpensive but show a lack of selectivity, while methods based on immunoaffinity extraction are very selective but expensive and not suitable for harsh environments. Thus, inexpensive, rapid and selective clean-up methods, relaying on “intelligent” materials are needed. Recent years have seen a significant increase of the “molecularly imprinted solid phase extraction” (MISPE) technique in the food contaminant analysis. In fact, this technique seems to be particularly suitable for extractive applications where analyte selectivity in the presence of very complex and structured matrices represents the main problem. In this review, several applications of MISPE in food contamination analysis will be discussed, with particular emphasis on the extraction of pesticides, drugs residua, mycotoxins and environmental contaminants.     

Structural and thermodiffractometric analysis of coordination polymers. Part II: zinc and cadmium derivatives of the Bim ligand [Bim = bis(1-imidazolyl)methane

New polynuclear coordination species containing the ditopic bis(1-imidazolyl)methane (Bim) ligand have been prepared as microcrystalline powders and structurally characterized by ab initio X-ray powder diffraction methods. [Zn(CH3COO)2(Bim)]n contains 1D chains with tetrahedral metal atoms bridged by Bim ligands; [CdBr2(Bim)]n shows a dense packing with hexacoordinated Cd(II) ions and mu-Br and mu-Bim bridges; at variance, the isomorphous [ZnCl2(Bim)]n and [ZnBr2(Bim)]n species contain cyclic dimers based on tetrahedral Zn(II) ions. Thermodiffractometric analysis allowed estimation of the linear thermal expansion coefficients and strain tensors derived there from. Bim-rich phases, with 2:1 ligand-to-metal ratio, were also isolated: ZnBr2(Bim)2(H2O)3 and [Cd(CH3COO)2(Bim)2]n containing cis and trans MN4O2 chromophores, respectively, show 1D polymers built upon M2Bim2 cycles, hinged on the metal ions. In all species the conformation of the Bim ligands is Cs (or nearly so), while in the few sparse reports of similar coordination polymers the alternative C2 one was preferentially observed.     

Synthesis, reactivity, spectroscopic characterization, X-ray structures, PGSE, and NOE NMR studies of (eta5-C5Me5)-rhodium and -iridium derivatives containing bis(pyrazolyl)alkane ligands

Rhodium(III) and iridium(III) complexes containing bis(pyrazolyl)methane ligands (pz = pyrazole, L' in general; specifically, L1 = H2C(pz)2, L2 = H2C(pzMe2)2, L3 = H2C(pz4Me)2, L4 = Me2C(pz)2), have been prepared in a study exploring the reactivity of these ligands toward [Cp*MCl(mu-Cl)]2 dimers (M = Rh, Ir; Cp* = pentamethylcyclopentadienyl). When the reaction was carried out in acetone solution, complexes of the type [Cp*M(L')Cl]Cl were obtained. However, when L1 and L2 ligands have been employed with excess [Cp*MCl(mu-Cl)]2, the formation of [Cp*M(L')Cl][Cp*MCl3] species has been observed. PGSE NMR measurements have been carried out for these complexes, in which the counterion is a cyclopentadienyl metal complex, in CD2Cl2 as a function of the concentration. The hydrodynamic radius (rH) and, consequently, the hydrodynamic volume (VH) of all the species have been determined from the measured translational self-diffusion coefficients (Dt), indicating the predominance of ion pairs in solution. NOE measurements and X-ray single-crystal studies suggest that the [Cp*MCl3]- approaches the cation, orienting the three Cl-legs of the "piano-stool" toward the CH2 moieties of the bis(pyrazolyl)methane ligands. The reaction of 1 equiv of [Cp*M(L')Cl]Cl or [Cp*M(L')Cl][Cp*MCl3] with 1 equiv of AgX (X = ClO4 or CF3SO3) in CH2Cl2 allows the generation of [Cp*M(L')Cl]X, whereas the reaction of 1 equiv of [Cp*M(L')Cl] with 2 equiv of AgX yields the dicationic complexes [Cp*M(L')(H2O)][X]2, where single water molecules are directly bonded to the metal atoms. The solid-state structures of a number of complexes were confirmed by X-ray crystallographic studies. The reaction of [Cp*Ir(L')(H2O)][X]2 with ammonium formate in water or acetone solution allows the generation of the hydride species [Cp*Ir(L')H][X].     

Ugi multicomponent reaction followed by an intramolecular nucleophilic substitution: convergent multicomponent synthesis of 1-sulfonyl 1,4-diazepan-5-ones and of their benzo-fused derivatives

A short, two-step approach to the synthesis of diazepane or diazocane systems, based on a Ugi multicomponent reaction followed by a subsequent intramolecular SN2 reaction was studied. 1-sulfonyl tetrahydrobenzo[e]-1,4-diazepin-1-ones 1 were obtained in very high yield through a Ugi multicomponent reaction followed by Mitsunobu cyclization. On the other hand, aliphatic 1-sulfonyl 1,4-diazepan-5-ones 2 could be obtained employing different cyclization conditions (sulfuryl diimidazole). A similar approach toward diazocane rings using hydroxamates as nucleophiles was less successful, affording only O-cyclized adducts or unexpected side products. A mechanistic explanation of the observed outcomes is proposed.     

An efficient diastereoselective route to differentially protected anti-4-amino-1-alken-3-ols

Zinc-promoted hydroxyallylation of alpha-amidoalkyl arylsulfones 4 using 3-bromo-propenyl methyl carbonate 5 proceeds smoothly in DMF at room temperature to afford high yields of differentially protected anti-1,2-amino alcohols 6.