Testing for the non-separability of bi-ambiguous compounds

Separability is a concept that is very difficult to define, and yet much of our scientific method is implicitly based upon the assumption that systems can sensibly be reduced to a set of interacting components. This paper examines the notion of separability in the creation of bi-ambiguous compounds that is based upon the CHSH and CH inequalities. It reports results of an experiment showing that violations of the CHSH and CH inequality can occur in human conceptual combination.

Anhydrous 1:1 proton-transfer compounds of isonipecotamide with picric acid and 3,5-dinitrosalicylic acid: 4-carbamoylpiperidinium 2,4,6-trinitrophenolate and two polymorphs of 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate

The structures of the anhydrous 1:1 proton-transfer compounds of isonipecotamide (4-carbamoylpiperidine) with picric acid and 3,5-dinitrosalicylic acid, namely 4-carbamoylpiperidinium 2,4,6-trinitrophenolate, C6H13N2O8+ C6H2N3O7- (I) and 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate, C6H13N2O8+ C7H3N2O7-: two forms, the monoclinic alpha-polymorph (II) and the triclinic beta-polymorph (III) have been determined at 200 K. All compounds form hydrogen-bonded structures, one-dimensional in (II), two-dimensional in (I) and three-dimensional in (III). In (I), the cations form centrosymmetric cyclic head-to-tail hydrogen-bonded homodimers [graph set R2/2(14)] through lateral duplex piperidinium N---H...O(amide) interactions. These dimers are extended into a two-dimensional network structure through further interactions with anion phenolate-O and nitro-O acceptors, including a direct symmetric piperidinium N-H...O(phenol),O(nitro) cation--anion association [graph set R2/1(6)]. The monoclinic polymorph (II) has a similar R2/1(6) cation-anion hydrogen-bonding interaction to (I) but with an additional conjoint symmetrical R1/2(4) interaction as well as head-to-tail piperidinium N-H...O(amide) O hydrogen bonds and amide N-H...O(carboxyl) hydrogen bonds, give a network structure which include large R3/4(20) rings. The hydrogen bonding in the triclinic polymorph (III) is markedly different from that of monoclinic (II). The asymmetric unit contains two independent cation-anion pairs which associate through cyclic piperidinium N-H...O,O'(carboxyl) interactions [graph set R2/1(4)]. The cations also show the zig-zag head-to-tail piperidinium N-H...O(amide) hydrogen-bonded chain substructures found in (II) but in addition feature amide N-H...O(nitro) and O(phenolate) and amide N-H...O(nitro) associations. As well there is a centrosymmetric double-amide N-H...O(carboxyl) bridged bis(cation-anion) ring system [graph set R2/4(8)] in the three-dimensional framework. The structures reported here demonstrate the utility of the isonipecotamide cation as a synthon with previously unrecognized potential for structure assembly applications. Furthermore, the structures of the two polymorphic 3,5-dinitrosalicylic acid salts show an unusual dissimilarity in hydrogen-bonding characteristics, considering that both were obtained from identical solvent systems.

Hydrogen bonding in the anhydrous 1:1 proton-transfer compounds of isonipecotamide with nitro-substituted benzoic acids: the salts of the three isomeric mononitrobenzoic acids and of 3,5-dinitrobenzoic acid

The structures of the anhydrous 1:1 proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with the three isomeric mononitro-substituted benzoic acids and 3,5-dinitrobenzoic acid, namely 4-carbamoylpiperidinium 2-nitrobenzoate (I), 4-carbamoylpiperidinium 3-nitrobenzoate (II), 4-carbamoylpiperidinium 4-nitrobenzoate (III), (C6H13N2O+ C7H4NO4-) and 4-carbamoylpiperidinium 3,5-dinitrobenzoate (IV) (C6H13N2O+ C7H5N2O6-)respectively, have been determined at 200 K. All salts form hydrogen-bonded structures: three-dimensional in (I), two-dimensional in (II) and (III) and one-dimensional in (IV). Featured in the hydrogen bonding of three of these [(I), (II) and (IV)] is the cyclic head-to-head amide--amide homodimer motif [graph set R2/2~(8)] through a duplex N---H...O association, the dimer then giving structure extension via either piperidinium or amide H-donors and carboxylate-O and in some examples [(II) and (IV)], nitro-O atom acceptors. In (I), the centrosymmetric amide-amide homodimers are expanded laterally through N-H...O hydrogen bonds via cyclic R2/4(8) interactions forming ribbons which extend along the c cell direction. These ribbons incorporate the 2-nitrobenzoate cations through centrosymmetric cyclic piperidine N-H...O(carboxyl) associations [graph set R4/4(12)], giving inter-connected sheets in the three-dimensional structure. In (II) in which no amide-amide homodimer is present, duplex piperidinium N-H...O(amide) hydrogen-bonding homomolecular associations [graph set R2/2(14)] give centrosymmetric head-to-tail dimers. Structure extension occurs through hydrogen-bonding associations between both the amide H-donors and carboxyl and nitro O-acceptors as well as a three-centre piperidinium N-H...O,O'(carboxyl) cyclic R2/1(4) association giving the two-dimensional network structure. In (III), the centrosymmetric amide-amide dimers are linked through the two carboxyl O-atom acceptors of the anions via bridging piperidinium and amide N-H...O,O'...H-N(amide) hydrogen bonds giving the two-dimensional sheet structure which features centrosymmetric cyclic R4/4(12) associations. In (IV), the amide-amide dimer is also centrosymmetric with the dimers linked to the anions through amide N-H...O(nitro) interactions. The piperidinium groups extend the structure into one-dimensional ribbons via N-H...O(carboxyl) hydrogen bonds. The structures reported here further demonstrate the utility of the isonipecotamide cation in molecular assembly and highlight the efficacy of the cyclic R2/2(8) amide-amide hydrogen-bonding homodimer motif in this process and provide an additional homodimer motif type in the head-to-tail R2/2(14) association.

The application of a profluorescent nitroxide probe to detect reactive oxygen species derived from combustion-generated particulate matter

Particulate pollution has been widely recognised as an important risk factor to human health. In addition to increases in respiratory and cardiovascular morbidity associated with exposure to particulate matter (PM), WHO estimates that urban PM causes 0.8 million premature deaths globally and that 1.5 million people die prematurely from exposure to indoor smoke generated from the combustion of solid fuels. Despite the availability of a huge body of research, the underlying toxicological mechanisms by which particles induce adverse health effects are not yet entirely understood. Oxidative stress caused by generation of free radicals and related reactive oxygen species (ROS) at the sites of deposition has been proposed as a mechanism for many of the adverse health outcomes associated with exposure to PM. In addition to particle-induced generation of ROS in lung tissue cells, several recent studies have shown that particles may also contain ROS. As such, they present a direct cause of oxidative stress and related adverse health effects. Cellular responses to oxidative stress have been widely investigated using various cell exposure assays. However, for a rapid screening of the oxidative potential of PM, less time-consuming and less expensive, cell-free assays are needed. The main aim of this research project was to investigate the application of a novel profluorescent nitroxide probe, synthesised at QUT, as a rapid screening assay in assessing the oxidative potential of PM. Considering that this was the first time that a profluorescent nitroxide probe was applied in investigating the oxidative stress potential of PM, the proof of concept regarding the detection of PM–derived ROS by using such probes needed to be demonstrated and a sampling methodology needed to be developed. Sampling through an impinger containing profluorescent nitroxide solution was chosen as a means of particle collection as it allowed particles to react with the profluorescent nitroxide probe during sampling, avoiding in that way any possible chemical changes resulting from delays between the sampling and the analysis of the PM. Among several profluorescent nitroxide probes available at QUT, bis(phenylethynyl)anthracene-nitroxide (BPEAnit) was found to be the most suitable probe, mainly due to relatively long excitation and emission wavelengths (λex= 430 nm; λem= 485 and 513 nm). These wavelengths are long enough to avoid overlap with the background fluorescence coming from light absorbing compounds which may be present in PM (e.g. polycyclic aromatic hydrocarbons and their derivatives). Given that combustion, in general, is one of the major sources of ambient PM, this project aimed at getting an insight into the oxidative stress potential of combustion-generated PM, namely cigarette smoke, diesel exhaust and wood smoke PM. During the course of this research project, it was demonstrated that the BPEAnit probe based assay is sufficiently sensitive and robust enough to be applied as a rapid screening test for PM-derived ROS detection. Considering that for all three aerosol sources (i.e. cigarette smoke, diesel exhaust and wood smoke) the same assay was applied, the results presented in this thesis allow direct comparison of the oxidative potential measured for all three sources of PM. In summary, it was found that there was a substantial difference between the amounts of ROS per unit of PM mass (ROS concentration) for particles emitted by different combustion sources. For example, particles from cigarette smoke were found to have up to 80 times less ROS per unit of mass than particles produced during logwood combustion. For both diesel and wood combustion it has been demonstrated that the type of fuel significantly affects the oxidative potential of the particles emitted. Similarly, the operating conditions of the combustion source were also found to affect the oxidative potential of particulate emissions. Moreover, this project has demonstrated a strong link between semivolatile (i.e. organic) species and ROS and therefore, clearly highlights the importance of semivolatile species in particle-induced toxicity.

Raman spectroscopy of hydrogene-arsenate group (AsO3OH) in solid-state compounds: cobalt mineral phase burgessite Co2(H2O)4[AsO3OH]2•H2O

Raman spectrum of burgessite, Co2(H2O)4[AsO3OH]2.H2O was studied, interpreted and compared with its infrared spectrum. The stretching and bending vibrations of (AsO3) and As-OH units together with the stretching, bending and libration modes of water molecules and hydroxyl ions were assigned. The range of O-H...O hydrogen bond lengths was inferred from the Raman and infrared spectra of burgessite. The presence of (AsO3OH)2- units in the crystal structure of burgessite was proved in agreement with its recently solved crystal structure. Raman and infrared spectra of erythrite inferred from the RRUFF database are used for comparison.

Apoptosis is induced in Chlamydia trachomatis infected HEp-2 cells by the addition of a combination innate immune activation compounds and the inhibitor wedelolactone

Problem: Innate immune activation of human cells, for some intracellular pathogens, is advantageous for vacuole morphology and pathogenic viability. It is unknown whether innate immune activation is advantageous to Chlamydia trachomatis viability. ----- ----- Method of study: Innate immune activation of HEp-2 cells during Chlamydia infection was conducted using lipopolysaccharide (LPS), polyI:C, and wedelolactone (innate immune inhibitor) to investigate the impact of these conditions on viability of Chlamydia. ----- ----- Results: The addition of LPS and polyI:C to stimulate activation of the two distinct innate immune pathways (nuclear factor kappa beta and interferon regulatory factor) had no impact on the viability of Chlamydia. However, when compounds targeting either pathway were added in combination with the specific innate immune inhibitor (wedelolactone) a major impact on Chlamydia viability was observed. This impact was found to be due to the induction of apoptosis of the HEp-2 cells under these conditions. ----- ----- Conclusion: This is the first time that induction of apoptosis has been reported in C. trachomatis-infected cells when treated with a combination of innate immune activators and wedelolactone.

Azoporphyrin : the porphyrin analogue of azobenzene

Azobenzenes (1,2-diaryldiazenes) are very important organic pigments, and they have a unique place in the field of photoresponsive conjugated molecules due to their (usually) reversible E/Z photoisomerisation. The current intense interest in molecular analogues of mechanical components and information storage and processing elements has stimulated research into conjugated molecules whose shape and/or optical properties can be switched electro- or photochemically. Among the classes of conjugated pigments being explored in these contexts are the porphyrinoids, which offer advantages of intense light absorption, a variety of accessible oxidation states, and synthetic control of properties through peripheral or central substitution. Extension of porphyrinoid conjugation can be achieved by linking the peripheral carbons either by three direct bonds (as in the “porphyrin tapes” of Osuka et al.) or through potentially conjugating bridges such as alkenes or, even better, alkynes.

meso-Porphyrinylphosphine Oxides: Mono- and Bidentate Ligands for Supramolecular Chemistry and the Crystal Structures of Monomeric [10,20-Diphenylporphyrinatonickel(II)-5,15-diyl]-bis-[P(O)Ph2] and Polymeric Self-Coordinated ([10,20-Diphenylporphyrinatozinc(II)-5,15-diyl]-bis-[P(O)Ph2])

A series of porphyrins substituted in one or two meso-positions by diphenylphosphine oxide groups has been prepared by the palladium catalysed reaction of diphenylphosphine or its oxide with the corresponding bromoporphyrins. Compounds {MDPP-[P(O)Ph2]n} (M = H2, Ni, Zn; H2DPP = 5,15-diphenylporphyrin; n = 1, 2) were isolated in yields of 60-95%. The reaction is believed to proceed via the conventional oxidative addition, phosphination and reductive elimination steps, as the stoichiometric reaction of η1-palladio(II) porphyrin [PdBr(H2DPP)(dppe)] (H2DPP = 5,15-diphenylporphyrin; dppe = 1,2-bis(diphenylphosphino)ethane) with diphenylphosphine oxide also results in the desired mono-porphyrinylphosphine oxide [H2DPP-P(O)Ph2]. Attempts to isolate the tertiary phosphines failed due to their extreme air-sensitivity. Variable temperature 1H NMR studies of [H2DPP-P(O)Ph2] revealed an intrinsic lack of symmetry, while fluorescence spectroscopy showed that the phosphine oxide group does not behave as a "heavy atom" quencher. The electron withdrawing effect of the phosphine oxide group was confirmed by voltammetry. The ligands were characterised by multinuclear NMR and UV-visible spectroscopy as well as mass spectrometry. Single crystal X-ray crystallography showed that the bis(phosphine oxide) nickel(II) complex {[NiDPP-[P(O)Ph2]2} is monomeric in the solid state, with a ruffled porphyrin core and the two P=O fragments on the same side of the average plane of the molecule. On the other hand, the corresponding zinc(II) complex formed infinite chains through coordination of one Ph2PO substituent to the neighbouring zinc porphyrin through an almost linear P=O---Zn unit, leaving the other Ph2PO group facing into a parallel channel filled with disordered water molecules. These new phosphine oxides are attractive ligands for supramolecular porphyrin chemistry.

Reduction of nitroaromatic compounds on supported gold nanoparticles by visible and ultraviolet light

Shedding light: Nitroaromatic compounds on gold nanoparticles (3 wt %) supported on ZrO2 can be reduced directly to the corresponding azo compounds when illuminated with visible light or ultraviolet light at 40 °C (see picture). The process occurs with high selectivity and at ambient temperature and pressure, and enables the selection of intermediates that are unstable in thermal reactions.

Raman spectroscopy of hydrogen arsenate group (AsO3OH)2− in solid-state compounds: cobalt-containing zinc arsenate mineral, koritnigite (Zn,Co)(AsO3OH)·H2O

Raman spectra of two well-defined types of koritnigite crystals from the Jáchymov ore district, Czech Republic, were recorded and interpreted. No substantial differences were observed between both crystal types. Observed Raman bands were attributed to the (AsO3OH)2- stretching and bending vibrations, stretching and bending vibrations of water molecules and hydroxyl ions. Non-interpreted Raman spectra of koritnigite from the RRUFF database, and published infrared spectra of cobaltkoritnigite were used for comparison. The O-H...O hydrogen bond lengths in the crystal structure of koritnigite were inferred from the Raman spectra and compared with those derived from the X-ray single crystal refinement. The presence of (AsO3OH)2- units in the crystal structure of koritnigite was proved from the Raman spectra which supports the conclusions of the X-ray structure analysis.

The biological application of cobalt

This review collects and summarises the biological applications of the element cobalt. Small amounts of the ferromagnetic metal can be found in rock, soil, plants and animals, but is mainly obtained as a by-product of nickel and copper mining, and is separated from the ores (mainly cobaltite, erythrite, glaucodot and skutterudite) using a variety of methods. Compounds of cobalt include several oxides, including: green cobalt(II) (CoO), blue cobalt(II,III) (Co3O4), and black cobalt(III) (Co2O3); four halides including pink cobalt(II) fluoride (CoF2), blue cobalt(II) chloride (CoCl2), green cobalt(II) bromide (CoBr2), and blue-black cobalt(II) iodide (CoI2). The main application of cobalt is in its metal form in cobalt-based super alloys, though other uses include lithium cobalt oxide batteries, chemical reaction catalyst, pigments and colouring, and radioisotopes in medicine. It is known to mimic hypoxia on the cellular level by stabilizing the α subunit of hypoxia inducing factor (HIF), when chemically applied as cobalt chloride (CoCl2). This is seen in many biological research applications, where it has shown to promote angiogenesis, erythropoiesis and anaerobic metabolism through the transcriptional activation of genes such as vascular endothelial growth factor (VEGF) and erythropoietin (EPO), contributing significantly to the pathophysiology of major categories of disease, such as myocardial, renal and cerebral ischaemia, high altitude related maladies and bone defects. As a necessary constituent for the formation of vitamin B12, it is essential to all animals, including humans, however excessive exposure can lead to tissue and cellular toxicity. Cobalt has been shown to provide promising potential in clinical applications, however further studies are necessary to clarify its role in hypoxia-responsive genes and the applications of cobalt-chloride treated tissues.

Analysis of the build-up of semi and non volatile organic compounds on urban roads

Vehicular traffic in urban areas may adversely affect urban water quality through the build-up of traffic generated semi and non volatile organic compounds (SVOCs and NVOCs) on road surfaces. The characterisation of the build-up processes is the key to developing mitigation measures for the removal of such pollutants from urban stormwater. An in-depth analysis of the build-up of SVOCs and NVOCs was undertaken in the Gold Coast region in Australia. Principal Component Analysis (PCA) and Multicriteria Decision tools such as PROMETHEE and GAIA were employed to understand the SVOC and NVOC build-up under combined traffic scenarios of low, moderate, and high traffic in different land uses. It was found that congestion in the commercial areas and use of lubricants and motor oils in the industrial areas were the main sources of SVOCs and NVOCs on urban roads, respectively. The contribution from residential areas to the build-up of such pollutants was hardly noticeable. It was also revealed through this investigation that the target SVOCs and NVOCs were mainly attached to particulate fractions of 75 to 300 µm whilst the redistribution of coarse fractions due to vehicle activity mainly occurred in the >300 µm size range. Lastly, under combined traffic scenario, moderate traffic with average daily traffic ranging from 2300 to 5900 and average congestion of 0.47 was found to dominate SVOC and NVOC build-up on roads.

Proton-transfer compounds of isnipecotamide with the aromatic dicarboxylic acids 4-nitrophthalic, 4,5-dichlorophthalic, 5-nitroisophthalic and terephthalic acid

The structures of the 1:1 proton-transfer compounds of isonipecotamide (4-piperidinecarboxamide) with 4-nitrophthalic acid, 4-carbamoylpiperidinium 2-carboxy-4-nitrobenzoate, C6H13N2O8+ C8H4O6- (I), 4,5-dichlorophthalic acid, 4-carbamoylpiperidinium 2-carboxy-4,5-dichlorobenzoate, C6H13N2O8+ C8H3Cl2O4- (II) and 5-nitroisophthalic acid, 4-carbamoylpiperidinium 3-carboxy-5-nitrobenzoate, C6H13N2O8+ C8H4O6- (III) as well as the 2:1 compound with terephthalic acid, bis(4-carbamoylpiperidinium)benzene-1,2-dicarboxylate dihydrate, 2(C6H13N2O8+) C8H4O42- . 2H2O (IV)have been determined at 200 K. All salts form hydrogen-bonded structures, one-dimensional in (II) and three-dimensional in (I), (III) and (IV). In (I) and (III) the centrosymmetric R2/2(8) cyclic amide-amide association is found while in (IV) several different types of water-bridged cyclic associations are present [graph sets R2/4(8), R3/4(10), R4/4(12), R3/3(18) and R4/6(22)]. The one-dimensional structure of (I), features the common 'planar' hydrogen 4,5-dichlorophthalate anion together with enlarged cyclic R3/3(13) and R3/4(17) associations. With the structures of (I) and (III) the presence of head-to-tail hydrogen phthalate chain substructures is found. In (IV) head-to-tail primary cation-anion associations are extended longitudinally into chains through the water-bridged cation associations and laterally by piperidinium N-H...O(carboxyl) and water O-H...O(carboxyl) hydrogen bonds. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. An additional example of cation--anion association with this cation is also shown in the asymmetric three-centre piperidinium N-H...O,O'(carboxyl) interaction in the first-reported structure of a 2:1 isonipecotamide-carboxylate salt.

The spermostatic and microbicidal actions of quinones and malemides : towards a dual-purpose contraceptive agent

There is an urgent need to develop safe, effective, dual-purpose contraceptive agents that combine the prevention of pregnancy with protection against sexually transmitted diseases. Here we report the identification of a group of compounds that on contact with human spermatozoa induce a state of “spermostasis,” characterized by the extremely rapid inhibition of sperm movement without compromising cell viability. These spermostatic agents were more active and significantly less toxic than the reagent in current clinical use, nonoxynol 9, giving therapeutic indices (ratio of spermostatic to cytotoxic activity) that were orders of magnitude greater than this traditional spermicide. Although certain compounds could trigger reactive oxygen species generation by spermatozoa, this activity was not correlated with spermostasis. Rather, the latter was associated with alkylation of two major sperm tail proteins that were identified as A Kinase-Anchoring Proteins (AKAP3 and AKAP4) by mass spectrometry. As a consequence of disrupted AKAP function, the abilities of cAMP to drive protein kinase A-dependent activities in the sperm tail, such as the activation of SRC and the consequent stimulation of tyrosine phosphorylation, were suppressed. Furthermore, analysis of microbicidal activity using Chlamydia muridarum revealed powerful inhibitory effects at the same low micromolar doses that suppressed sperm movement. In this case, the microbicidal action was associated with alkylation of Major Outer Membrane Protein (MOMP), a major chlamydial membrane protein. Taken together, these results have identified for the first time a novel set of cellular targets and chemical principles capable of providing simultaneous defense against both fertility and the spread of sexually transmitted disease.

The relationship between building characteristics and the chemical composition of surface films found on glass windows in Brisbane, Australia

Films found on the windows of residential buildings have been studied. The main aim of the paper was to assess the roles of the films in the accumulation of potentially toxic chemicals in residential buildings. Thus the elemental and polycyclic aromatic hydrocarbon compositions of the surface films from the glass windows of eighteen residential buildings were examined. The presence of sample amounts of inorganic elements (4.0–1.2 × 106 μg m−2) and polycyclic aromatic hydrocarbons in the films (BDL - 620.1 ng m−2) has implications for human exposure and the fate of pollutants in the urban environment. To facilitate the interpretation of the results, data matrices consisting of the chemical composition of the films and the building characteristics were subjected to multivariate data analysis methods, and these revealed that the accumulation of the chemicals was strongly dependent on building characteristics such as the type of glass used for the window, the distance from a major road, age of the building, distance from an industrial activity, number of smokers in the building and frequency of cooking in the buildings. Thus, building characteristics which minimize the accumulation of pollutants on the surface films need to be encouraged.