Reactions of simple and peptidic alpha-carboxylate radical anions with dioxygen in the gas phase

alpha-Carboxylate radical anions are potential reactive intermediates in the free radical oxidation of biological molecules (e. g., fatty acids, peptides and proteins). We have synthesised well-defined alpha-carboxylate radical anions in the gas phase by UV laser photolysis of halogenated precursors in an ion-trap mass spectrometer. Reactions of isolated acetate ((center dot)CH(2)CO(2)) and 1-carboxylatobutyl (CH(3)CH(2)CH(2)(center dot)CHCO(2)(-)) radical anions with dioxygen yield carbonate (CO(3)(center dot-)) radical anions and this chemistry is shown to be a hallmark of oxidation in simple and alkyl-substituted cross-conjugated species. Previous solution phase studies have shown that C(alpha)-radicals in peptides, formed from free radical damage, combine with dioxygen to form peroxyl radicals that subsequently decompose into imine and keto acid products. Here, we demonstrate that a novel alternative pathway exists for two alpha-carboxylate C(alpha)-radical anions: the acetylglycinate radical anion (CH(3)C(O)NH(center dot)CHCO(2)(-)) and the model peptide radical anion, YGGFG(center dot-). Reaction of these radical anions with dioxygen results in concerted loss of carbon dioxide and hydroxyl radical. The reaction of the acetylglycinate radical anion with dioxygen reveals a two-stage process involving a slow, followed by a fast kinetic regime. Computational modelling suggests the reversible formation of the C(alpha) peroxyl radical facilitates proton transfer from the amide to the carboxylate group, a process reminiscent of, but distinctive from, classical proton-transfer catalysis. Interestingly, inclusion of this isomerization step in the RRKM/ME modelling of a G3SX level potential energy surface enables recapitulation of the experimentally observed two-stage kinetics.

Isolation and characterization of charge-tagged phenylperoxyl radicals in the gas phase : direct evidence for products and pathways in low temperature benzene oxidation

The phenylperoxyl radical has long been accepted as a critical intermediate in the oxidation of benzene and an archetype for arylperoxyl radicals in combustion and atmospheric chemistry. Despite being central to many contemporary mechanisms underpinning these chemistries, reports of the direct detection or isolation of phenylperoxyl radicals are rare and there is little experimental evidence connecting this intermediate with expected product channels. We have prepared and isolated two charge-tagged phenyl radical models in the gas phase [i.e., 4-(N,N,N-trimethylammonium) phenyl radical cation and 4-carboxylatophenyl radical anion] and observed their reactions with dioxygen by ion-trap mass spectrometry. Measured reaction rates show good agreement with prior reports for the neutral system (k(2)[(Me3N+)C6H4 center dot + O-2] = 2.8 x 10(-11) cm(3) molecule(-1) s(-1), Phi = 4.9%; k(2)[(-O2C)C6H4 center dot + O-2] = 5.4 x 10(-1)1 cm(3) molecule(-1) s(-1), Phi = 9.2%) and the resulting mass spectra provide unequivocal evidence for the formation of phenylperoxyl radicals. Collisional activation of isolated phenylperoxyl radicals reveals unimolecular decomposition by three pathways: (i) loss of dioxygen to reform the initial phenyl radical; (ii) loss of atomic oxygen yielding a phenoxyl radical; and (iii) ejection of the formyl radical to give cyclopentadienone. Stable isotope labeling confirms these assignments. Quantum chemical calculations for both charge-tagged and neutral phenylperoxyl radicals confirm that loss of formyl radical is accessible both thermodynamically and entropically and competitive with direct loss of both hydrogen atom and carbon dioxide.

Stimulating organizational ingenuity with design methods

Organizations invest in ways to stimulate new ideas for new products and services for the benefit of the organization, engaging in tournaments and competitions to generate new ideas or to combine existing ideas in new ways for new products and services (Terweisch and Uhlrich, 2009). Specifically, some large companies have developed platforms for posting intractable problems to tap into the ideas and problem solving abilities of a broader range of people (Huston and Sakkab, 2006; Morgan and Wang, 2010), and to develop new and elegant solutions often in an open innovation approach (Chesbrough, 2003). The notion of ingenuity is often applied to individuals who create innovative solutions in situations of constraint, where ingenuity in the form of elegant solutions can be understood as one form of resourcefulness (Young, 2011). However, the notion of organizational ingenuity locates ingenuity more centrally to an organization's strategic decision making and implementation, embedding ingenuity into the company's culture. Studies of organizations displaying ingenuity indicate a range of possibilities from extreme ingenuity (Baker and Nelson, 2005) to less dramatic but substantial changes (Thomke, 2003), sometimes in an experimental phase or as part of a move towards a new and distinct identity for ongoing innovation.

Supramolecular selection in molecular and framework co-crystals

An ongoing challenge in chemistry and crystal engineering is the synthesis of functional materials with predictable structures and customisable properties. This may be achieved by crystallising mixtures of different compounds. Co-crystals formed through this method have predictable structures and their properties may be tuned by varying the ratio of the compounds in the crystallising solution. This thesis examines single crystals formed by the co-crystallisation of metal complexes that have similar structures but different physical or chemical properties. A variety of new compounds with interesting properties were prepared, characterised and their significance in the context of crystal engineering was explored.

Direct detection of additives and degradation products from polymers by liquid extraction surface analysis employing chip-based nanospray mass spectrometry

RATIONALE: Polymer-based surface coatings in outdoor applications experience accelerated degradation due to exposure to solar radiation, oxygen and atmospheric pollutants. These deleterious agents cause undesirable changes to the aesthetic and mechanical properties of the polymer, reducing its lifetime. The use of antioxidants such as hindered amine light stabilisers (HALS) retards these degradative processes; however, mechanisms for HALS action and polymer degradation are poorly understood. METHODS: Detection of the HALS TINUVINW123 (bis(1-octyloxy-2,2,6,6-tetramethyl-4-piperidyl) sebacate) and the polymer degradation products directly from a polyester-based coil coating was achieved by liquid extraction surface analysis (LESA) coupled to a triple quadrupole QTRAPW 5500 mass spectrometer. The detection of TINUVINW123 and melamine was confirmed by the characteristic fragmentation pattern observed in LESA-MS/MS spectra that was identical to that reported for authentic samples. RESULTS: Analysis of an unstabilised coil coating by LESA-MS after exposure to 4 years of outdoor field testing revealed the presence of melamine (1,3,5-triazine-2,4,6-triamine) as a polymer degradation product at elevated levels. Changes to the physical appearance of the coil coating, including powder-like deposits on the coating's surface, were observed to coincide with melamine deposits and are indicative of the phenomenon known as polymer ' blooming'. CONCLUSIONS: For the first time, in situ detection of analytes from a thermoset polymer coating was accomplished without any sample preparation, providing advantages over traditional extraction-analysis approaches and some contemporary ambient MS methods. Detection of HALS and polymer degradation products such as melamine provides insight into the mechanisms by which degradation occurs and suggests LESA-MS is a powerful new tool for polymer analysis. Copyright (C) 2012 John Wiley & Sons, Ltd.

Co-creative media in remote Indigenous communities

This paper examines co-creative video outputs that have originated from, or relate to, remote Indigenous communities in Australia. Scholarly work on remote media has mostly operated at the interface of media studies and anthropology, seeking to identify how cultural systems shape the production, distribution and reception of media in Aboriginal communities. This paper looks instead at content themes, funding sources and institutions during the 2010-2013 period, and examines the factors that may be determining the quantity of co-creative outputs, as well as the types of stories that get produced. I argue that the focus on culture has obscured important shifts in remote media policy and funding, including a trend towards content designed to address social disadvantage.

Using ambient ozone for assignment of double bond position in unsaturated lipids

Unsaturated lipids deposited onto a range of materials are observed to react with the low concentrations of ozone present in normal laboratory air. Parent lipids and ozonolysis cleavage products are both detected directly from surfaces by desorption electrospray ionisation mass spectrometry (DESI-MS) with the resulting mass spectra providing clear evidence of the double bond position within these molecules. This serendipitous process has been coupled with thin-layer chromatography (TLC) to provide a simple but powerful approach for the detailed structural elucidation of lipids present in complex biological extracts. Lipid extracts from human lens were deposited onto normal phase TLC plates and then developed to separate components according to lipid class. Exposure of the developed plates to laboratory air for ca. 1 h prior to DESI-MS analysis gave rise to ozonolysis products allowing for the unambiguous identification of double bond positions in even low abundant, unsaturated lipids. In particular, the co-localization of intact unsaturated lactosylceramides (LacCer) with products from their oxidative cleavage provide the first evidence for the presence of three isomeric LacCer (d18:0/24:1) species in the ocular lens lipidome, i.e., variants with double bonds at the n-9, n-7 and n-5 positions.

Developing Co-operating Legal Knowledge Based Systems

In attempting to build intelligent litigation support tools, we have moved beyond first generation, production rule legal expert systems. Our work supplements rule-based reasoning with case based reasoning and intelligent information retrieval. This research, specifies an approach to the case based retrieval problem which relies heavily on an extended object-oriented / rule-based system architecture that is supplemented with causal background information. Machine learning techniques and a distributed agent architecture are used to help simulate the reasoning process of lawyers. In this paper, we outline our implementation of the hybrid IKBALS II Rule Based Reasoning / Case Based Reasoning system. It makes extensive use of an automated case representation editor and background information.

Prospects for the development of sugarcane biorefineries

Sugarcane biorefineries co-producing fuels, green chemicals and bio-products offer great potential for improving the profitability and sustainability of sugarcane industries around the world. Sugarcane bagasse is widely regarded as one of the best biomass feedstocks for early adoption and commercialisation of biorefining technologies because of the large scale of the resource and its availability at sugar factories. Biomass biorefineries aim to convert bagasse through biochemical and thermochemical processes to produce low cost fermentable sugars which are a platform for value-adding. Through subsequent fermentation technologies or chemical synthesis, the sugars can be converted to fuels including ethanol and butanol, oils, organic acids such as succinic and levulinic and polymer precursors. Other biorefinery products can include food and animal feeds, plastics, fibre products and resins. Recent advances in biorefinery production technologies are being demonstrated in a unique research facility at the Queensland University of Technology’s Mackay Renewable Biocommodities Pilot Plant in Mackay, Australia. This pilot scale production facility located at Mackay Sugar Ltd’s Racecourse Mill is demonstrating the production of a range of fuels and other products from sugarcane bagasse. This paper will address the opportunities available for sugarcane biorefineries to contribute to future profitability and sustainability of the sugarcane industry.

Sweet sorghum : opportunities for a new, renewable fuel and food industry in Australia

Sweet sorghum is receiving significant global interest as an agro-industrial crop because of its capacity to co-produce energy, food, and feed products in integrated biorefineries. This report assesses the opportunities to develop a sweet sorghum industry in Australia, reports on research demonstrating the production of energy, food, and feed products, and assesses the potential economic and sustainability benefits of sweet sorghum biorefineries in the Australian context.

An assessment of the geographical scale of recurrent gene flow in wild populations of two species of Mekong River carps (Henicorhynchus spp.)

The Mekong is the most productive river fishery in the world, and such as, the Mekong River Basin (MRB) is very important to very large human populations across the region as a source of revenue (through fishing and marketing of aquatic resources products) and as the major source for local animal protein. Threats to biodiversity in the MRB, either to the fishery sector itself or to other sectors are a major concern, even though currently, fisheries across this region are still very productive. If not managed properly however, fish population declines will cause significant economic impact and affect livelihoods of local people and will have a major impact on food security and nutrition. Biodiversity declines will undoubtedly affect food security, income and socio-economic status of people in the MRB that depend on aquatic resources. This is an indicator of unsustainable development and hence should be avoided. Genetic diversity (biodiversity) that can be measured using techniques based on DNA markers; refers to variation within and among populations within the same species or reproductive units. In a population, new genetic variation is generated by sexual recombination contributed by individuals with mutations in genes and chromosomes. Over time, populations of a species that are not reproducing together will diverge as differential impacts of selection and genetic drift change their genetic attributes. For mud carp (Henicorhynchus spp.), understanding the status of breeding units in the MRB will be important for their long term persistence, sustainability and for implementing effective management strategies. Earlier analysis of stock structure in two economically important mud carp species (Henicorhynchus siamensis and H. lobatus) in the MRB completed with mtDNA markers identified a number of populations of both species where gene flow had apparently been interrupted or reduced but applying these data directly to management unit identification is potentially compromised because information was only available about female dispersal patterns. The current study aimed to address this problem and to fully assess the extent of current gene flow (nDNA) and reproductive exchange among selected wild populations of two species of carp (Henicorhynchus spp.) of high economic importance in the MRB using combined mtDNA and nDNA markers. In combination, the data can be used to define effective management units for each species. In general, nDNA diversity for H. lobatus (with average allelic richness (A) 7.56 and average heterozygosity (Ho) 0.61) was very similar to that identified for H. siamensis (A = 6.81 and Ho = 0.75). Both mud carp species show significant but low FST estimates among populations as a result of lower genetic diversity among sampled populations compared with genetic diversity within populations that may potentially mask any 'real' population structure. Overall, population genetic structure patterns from mtDNA and nDNA in both Henicorhynchus species were largely congruent. Different population structures however, were identified for the two Henicorhynchus species across the same geographical area. Apparent co-similarity in morphology and co-distribution of these two relatively closely related species does not apparently imply parallel evolutionary histories. Differences in each species population structure likely reflect historical drainage rearrangement of the Mekong River. The data indicate that H. siamensis is likely to have occupied the Mekong system for much longer than has H. lobatus in the past. Two divergent stocks were identified for H. lobatus in the MRB below the Khone Falls while a single stock had been evident in the earlier mtDNA study. This suggests that the two Henicorhynchus species may possess different life history traits and that different patterns of gene flow has likely influenced modern genetic structure in these close congeners. In combination, results of the earlier mtDNA and the current study have implications for effective management of both Henicorhynchus species across the MRB. Currently, both species are essentially treated as a single management unit in this region. This strategy may be appropriate for H. lobatus as a single stock was evident in the main stream of the MRB, but may not be appropriate for H. siamensis as more than a single stock was identified across the same range for this species. Management strategies should consider this difference to conserve overall biodiversity (local discrete populations) and this will include maintaining natural habitat and migration pathways, provision of fish sanctuaries (refuges) and may also require close monitoring of any stock declines, a signal that may require effective recovery strategies.

Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes

Background Transcription factors (TFs) co-ordinately regulate target genes that are dispersed throughout the genome. This co-ordinate regulation is achieved, in part, through the interaction of transcription factors with conserved cis-regulatory motifs that are in close proximity to the target genes. While much is known about the families of transcription factors that regulate gene expression in plants, there are few well characterised cis-regulatory motifs. In Arabidopsis, over-expression of the MYB transcription factor PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1) leads to transgenic plants with elevated anthocyanin levels due to the co-ordinated up-regulation of genes in the anthocyanin biosynthetic pathway. In addition to the anthocyanin biosynthetic genes, there are a number of un-associated genes that also change in expression level. This may be a direct or indirect consequence of the over-expression of PAP1. Results Oligo array analysis of PAP1 over-expression Arabidopsis plants identified genes co-ordinately up-regulated in response to the elevated expression of this transcription factor. Transient assays on the promoter regions of 33 of these up-regulated genes identified eight promoter fragments that were transactivated by PAP1. Bioinformatic analysis on these promoters revealed a common cis-regulatory motif that we showed is required for PAP1 dependent transactivation. Conclusion Co-ordinated gene regulation by individual transcription factors is a complex collection of both direct and indirect effects. Transient transactivation assays provide a rapid method to identify direct target genes from indirect target genes. Bioinformatic analysis of the promoters of these direct target genes is able to locate motifs that are common to this sub-set of promoters, which is impossible to identify with the larger set of direct and indirect target genes. While this type of analysis does not prove a direct interaction between protein and DNA, it does provide a tool to characterise cis-regulatory sequences that are necessary for transcription activation in a complex list of co-ordinately regulated genes.

Competitive charge-remote and anion-induced fragmentations of the non-8-enoate anion. A charge-remote reaction which co-occurs with hydrogen scrambling

The non-8-enoate anion undergoes losses of the elements of C3H6, C4H8 and C6H12 on collisional activation, The mechanisms of these processes have been elucidated by a combination of product ion and labelling (H-2 and C-13) studies, together with a neutralisation reionisation mass spectrometric study. These studies allow the following conclusions to be made. (i) The loss of C3H6 involves cyclisation of the enolate anion of non-8-enoic acid to yield the cyclopentyl carboxylate anion and propene. (ii) The loss of 'C4H8' is a charge-remote process (one which proceeds remote from the charged centre) which yields the pent-4-enoate anion, butadiene and dihydrogen. This process co-occurs and competes with complex H scrambling. (iii) The major loss of 'C6H12' occurs primarily by a charge-remote process yielding the acrylate anion, hexa-1,5-diene and dihydrogen, but in this case no H scrambling accompanies the process. (iv) It is argued that the major reason why the two charge-remote processes occur in preference to anion-induced losses of but-l-ene and hex-l-ene from the respective 4- and 2-anions is that although these anions are formed, they have alternative and lower energy fragmentation pathways than those involving the losses of but-l-ene and hex-l-ene; viz. the transient 4-anion undergoes facile proton transfer to yield a more stable anion, whereas the 2-(enolate) anion undergoes preferential cyclisation followed by elimination of propene [see (i) above].

The loss of CO from the ortho, meta and para forms of deprotonated methyl benzoate in the gas phase

The ortho, meta and para anions of methyl benzoate may be made in the source of a mass spectrometer by the S(N)2(Si) reactions between HO- and methyl (o-, m-, and p-trimethylsilyl)benzoate respectively. All three anions lose CO upon collisional activation to form the ortho anion of anisole in the ratio ortho>>meta > para. The rearrangement process is charge directed through the ortho anion. Theoretical calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that the conversion of the meta and para anions to the ortho anion prior to loss of CO involve 1,2-H transfer(s), rather than carbon scrambling of the methoxycarbonylphenyl anion. There are two mechanisms which can account for this rearrangement, viz. (A) cyclisation of the ortho anion centre to the carbonyl group of the ester to give a cyclic carbonyl system in which the incipient methoxide anion substitutes at one of the two equivalent ring carbons of the three membered ring to yield an intermediate which loses CO to give the ortho anion of anisole, and (B) an elimination reaction to give an intermediate benzyne-methoxycarbonyl anion complex in which the MeOCO- species acts as a MeO- donor, which then adds to benzyne to yield the ortho anion of anisole. Calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that (i) the barrier in the first step (the rate determining step) of process A is 87 kJ mol(-1) less than that for the synchronous benzyne process B, and (ii) there are more low frequency vibrations in the transition state for benzyne process B than for the corresponding transition state for process A. Stepwise process A has the lower barrier for the rate determining step, and the lower Arrhenius factor: we cannot differentiate between these two mechanisms on available evidence.

Photoelectron spectroscopic study of the oxyallyl diradical

The photoelectron spectrum of the oxyallyl (OXA) radical anion has been measured. The radical anion has been generated in the reaction of the atomic oxygen radical anion (O center dot-) with acetone. Three low-lying electronic states of OXA have been observed in the spectrum. Electronic structure calculations have been performed for the triplet states (B-3(2) and B-3(1)) of OXA and the ground doublet state ((2)A(2)) of the radical anion using density, functional theory (DFT). Spectral simulations have been carried out for the triplet statics based on the results of the DFT calculations. The simulation identifies a vibrational progression of the CCC bending mode of the B-3(2) state of OXA in the lower electron binding energy (eBE) portion of the spectrum. On top of the B-3(2) feature, however, the experimental spectrum exhibits additional photoelectron peaks whose angular distribution is distinct from that for the vibronic peaks of the B-3(2) state. Complete active space self-consistent field (CASSCF) method and second-order perturbation theory based on the CASSCF wave function (CASPT2) have been employed to study the lowest singlet state ((1)A(1)) of OXA. The simulation based on the results of these electronic structure calculations establishes that the overlapping peaks represent the vibrational ground level of the (1)A(1) state and its vibrational progression of the CO stretching mode. The A, state is the lowest electronic state of,OXA, and the electron affinity (EA) of OXA is 1.940 +/- 0.010 eV. The B-3(2) state is the first excited state with an electronic term energy of 55 +/- 2 meV. The widths of the vibronic peaks of the (X) over tilde (1)A(1) state are much broader than those of the (a) over tilde B-3(2) state, implying that the (1)A(1) state is indeed a transition state. The CASSCF and CASPT2 calculations suggest that the (1)A(1) state is at a potential maximum along the nuclear coordinate representing disrotatory motion of the two methylene groups, which leads to three-membered-ring formation, i.e., cydopropanone. The simulation of (b) over tilde B-3(1) OXA reproduces the higher eBE portion of the spectrum very well. The term energy of the B-3(1) state is 0.883 +/- 0.012 eV. Photoelectron spectroscopic measurements have also been conducted for the other ion products of the O center dot- reaction with acetone. The photoelectron imaging spectrum of the acetylcarbene (AC) radical anion exhibits a broad, structureless feature, which is assigned to the (X) over tilde (3)A '' state of AC. The ground ((2)A '') and first excited ((2)A') states of the 1-methylvinoxy (1-MVO) radical have been observed in the photoelectron spectrum of the 1-MVO ion, and their vibronic structure has been analyzed.