On Entropy-Based Molecular Descriptors: Statistical Analysis of Real and Synthetic Chemical Structures

This paper presents an analysis of entropy-based molecular descriptors. Specifically, we use real chemical structures, as well as synthetic isomeric structures, and investigate properties of and among descriptors with respect to the used data set by a statistical analysis. Our numerical results provide evidence that synthetic chemical structures are notably different to real chemical structures and, hence, should not be used to investigate molecular descriptors. Instead, an analysis based on real chemical structures is favorable. Further, we find strong hints that molecular descriptors can be partitioned into distinct classes capturing complementary information.

A Simple Algorithm for Unique Representation of Chemical Structures - Cyclic/ Acyclic Functionalized Achiral Hydrocarbons

An algorithm, based on ‘vertex priority values’ has been proposed to uniquely sequence and represent connectivity matrix of chemical structures of cyclic/ acyclic functionalized achiral hydrocarbons and their derivatives. In this method ‘vertex priority values’ have been assigned in terms of atomic weights, subgraph lengths, loops, and heteroatom contents. Subsequently the terminal vertices have been considered upon completing the sequencing of the core vertices. This approach provides a multilayered connectivity graph, which can be put to use in comparing two or more structures or parts thereof for any given purpose. Furthermore the basic vertex connection tables generated here are useful in the computation of characteristic matrices/ topological indices, automorphism groups, and in storing, sorting and retrieving of chemical structures from databases.

Chemical characterization of oligosaccharides in the milk of six species of New and Old World monkeys.

Human and great ape milks contain a diverse array of milk oligosaccharides, but little is known about the milk oligosaccharides of other primates, and how they differ among taxa. Neutral and acidic oligosaccharides were isolated from the milk of three species of Old World or catarrhine monkeys (Cercopithecidae: rhesus macaque (Macaca mulatta), toque macaque (Macaca sinica) and Hamadryas baboon (Papio hamadryas)) and three of New World or platyrrhine monkeys (Cebidae: tufted capuchin (Cebus apella) and Bolivian squirrel monkey (Saimiri boliviensis); Atelidae: mantled howler (Alouatta palliata)). The milks of these species contained 6-8% total sugar, most of which was lactose: the estimated ratio of oligosaccharides to lactose in Old World monkeys (1:4 to 1:6) was greater than in New World monkeys (1:12 to 1:23). The chemical structures of the oligosaccharides were determined mainly by (1)H-NMR spectroscopy. Oligosaccharides containing the type II unit (Gal(β1-4)GlcNAc) were found in the milk of the rhesus macaque, toque macaque, Hamadryas baboon and tufted capuchin, but oligosaccharides containing the type I unit (Gal(β1-3)GlcNAc), which have been found in human and many great ape milks, were absent from the milk of all species studied. Oligosaccharides containing Lewis x (Gal(β1-4)[Fuc(α1-3)]GlcNAc) and 3-fucosyl lactose (3-FL, Gal(β1-4)[Fuc(α1-3)]Glc) were found in the milk of the three cercopithecid monkey species, while 2-fucosyl lactose (5'-FL, Fuc(α1-2)Gal(β1-4)Glc) was absent from all species studied. All of these milks contained acidic oligosaccharides that had N-acetylneuraminic acid as part of their structures, but did not contain oligosaccharides that had N-glycolylneuraminic acid, in contrast to the milk or colostrum of great apes which contain both types of acidic oligosaccharides. Two GalNAc-containing oligosaccharides, lactose 3'-O-sulfate and lacto-N-novopentaose I (Gal(β1-3)[Gal(β1-4)GlcNAc(β1-6)]Gal(β1-4)Glc) were found only in the milk of rhesus macaque, hamadryas baboon and tufted capuchin, respectively. Further research is needed to determine the extent to which the milk oligosaccharide patterns observed among these taxa represent wider phylogenetic trends among primates and how much variation occurs among individuals or species.

Chemical structural effects on γ-ray spectra of positron annihilation in fluorobenzenes

Spectra of ?-ray Doppler shifts for positron annihilation in benzene and its fluoro-derivatives are simulated using low energy plane wave positron (LEPWP) approximation. The results are compared with available measurements. It is found that the Doppler shifts in these larger aromatic compounds are dominated by the contributions of the valence electrons and that the LEPWP model overestimates the measurements by approximately 30%, in agreement with previous findings in noble gases and small molecules. It is further revealed that the halogen atoms not only switch the sign of the charges on carbon atoms that they bond to, but that they also polarize other C-H bonds in the molecule leading to a redistribution of the molecular electrostatic potentials. As a result, it is likely that the halogen atoms contribute more significantly to the annihilation process. The present study also suggests that, while the Doppler shifts are sensitive to the number of valence electrons in the molecules, they are less sensitive to the chemical structures of isomers that have the same numbers and type of atoms and, hence, the same numbers of electrons. Further investigation of this effect is warranted. © EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2012.

Chemical Composition of Lipids Present in Cat and Dog Oocyte by Matrix-Assisted Desorption Ionization Mass Spectrometry (MALDI- MS)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Processi di biorefining per l'estrazione di secondary chemical building blocks da sottoprotti dell'agro-industria

Phenol and cresols represent a good example of primary chemical building blocks of which 2.8 million tons are currently produced in Europe each year. Currently, these primary phenolic building blocks are produced by refining processes from fossil hydrocarbons: 5% of the world-wide production comes from coal (which contains 0.2% of phenols) through the distillation of the tar residue after the production of coke, while 95% of current world production of phenol is produced by the distillation and cracking of crude oil. In nature phenolic compounds are present in terrestrial higher plants and ferns in several different chemical structures while they are essentially absent in lower organisms and in animals. Biomass (which contain 3-8% of phenols) represents a substantial source of secondary chemical building blocks presently underexploited. These phenolic derivatives are currently used in tens thousand of tons to produce high cost products such as food additives and flavours (i.e. vanillin), fine chemicals (i.e. non-steroidal anti-inflammatory drugs such as ibuprofen or flurbiprofen) and polymers (i.e. poly p-vinylphenol, a photosensitive polymer for electronic and optoelectronic applications). European agrifood waste represents a low cost abundant raw material (250 millions tons per year) which does not subtract land use and processing resources from necessary sustainable food production. The class of phenolic compounds is essentially constituted by simple phenols, phenolic acids, hydroxycinnamic acid derivatives, flavonoids and lignans. As in the case of coke production, the removal of the phenolic contents from biomass upgrades also the residual biomass. Focusing on the phenolic component of agrifood wastes, huge processing and marketing opportunities open since phenols are used as chemical intermediates for a large number of applications, ranging from pharmaceuticals, agricultural chemicals, food ingredients etc. Following this approach we developed a biorefining process to recover the phenolic fraction of wheat bran based on enzymatic commercial biocatalysts in completely water based process, and polymeric resins with the aim of substituting secondary chemical building blocks with the same compounds naturally present in biomass. We characterized several industrial enzymatic product for their ability to hydrolize the different molecular features that are present in wheat bran cell walls structures, focusing on the hydrolysis of polysaccharidic chains and phenolics cross links. This industrial biocatalysts were tested on wheat bran and the optimized process allowed to liquefy up to the 60 % of the treated matter. The enzymatic treatment was also able to solubilise up to the 30 % of the alkali extractable ferulic acid. An extraction process of the phenolic fraction of the hydrolyzed wheat bran based on an adsorbtion/desorption process on styrene-polyvinyl benzene weak cation-exchange resin Amberlite IRA 95 was developed. The efficiency of the resin was tested on different model system containing ferulic acid and the adsorption and desorption working parameters optimized for the crude enzymatic hydrolyzed wheat bran. The extraction process developed had an overall yield of the 82% and allowed to obtain concentrated extracts containing up to 3000 ppm of ferulic acid. The crude enzymatic hydrolyzed wheat bran and the concentrated extract were finally used as substrate in a bioconversion process of ferulic acid into vanillin through resting cells fermentation. The bioconversion process had a yields in vanillin of 60-70% within 5-6 hours of fermentation. Our findings are the first step on the way to demonstrating the economical feasibility for the recovery of biophenols from agrifood wastes through a whole crop approach in a sustainable biorefining process.

Investigation of the chemical origin and evidential value of differences in the SERS spectra of blue gel inks

Highly swellable polymer films doped with Ag nanoparticle aggregates (poly-SERS films) have been used to record very high signal:noise ratio, reproducible surface-enhanced (resonance) Raman (SER(R)S) spectra of in situ dried ink lines and their constituent dyes using both 633 and 785 nm excitation. These allowed the chemical origins of differences in the SERRS spectra of different inks to be determined. Initial investigation of pure samples of the 10 most common blue dyes showed that the dyes which had very similar chemical structures such as Patent Blue V and Patent Blue VF (which differ only by a single OH group) gave SERRS spectra in which the only indications that the dye structure had been changed were small differences in peak positions or relative intensities of the bands. SERRS studies of 13 gel pen inks were consistent with this observation. In some cases inks from different types of pens could be distinguished even though they were dominated by a single dye such as Victoria Blue B (Zebra Surari) or Victoria Blue BO (Pilot Acroball) because their predominant dye did not appear in other inks. Conversely, identical spectra were also recorded from different types of pens (Pilot G7, Zebra Z-grip) because they all had the same dominant Brilliant Blue G dye. Finally, some of the inks contained mixtures of dyes which could be separated by TLC and removed from the plate before being analysed with the same poly-SERS films. For example, the Pentel EnerGel ink pen was found to give TLC spots corresponding to Erioglaucine and Brilliant Blue G. Overall, this study has shown that the spectral differences between different inks which are based on chemically similar, but nonetheless distinct dyes, are extremely small, so very close matches between SERRS spectra are required for confident identification. Poly-SERS substrates can routinely provide the very stringent reproducibility and sensitivity levels required. This, coupled with the awareness of the reasons underlying the observed differences between similarly coloured inks allows a more confident assessment of the evidential value of inks SERS and should underpin adoption of this approach as a routine method for the forensic examination of inks.

Ordering induced by chemical, thermal and mechanical constraints at solid interfaces

We know that classical thermodynamics even out of equilibrium always leads to stable situation which means degradation and consequently d sorder. Many experimental evidences in different fields show that gradation and order (symmetry breaking) during time and space evolution may appear when maintaining the system far from equilibrium. Order through fluctuations, stochastic processes which occur around critical points and dissipative structures are the fundamental background of the Prigogine-Glansdorff and Nicolis theory. The thermodynamics of macroscopic fluctuations to stochastic approach as well as the kinetic deterministic laws allow a better understanding of the peculiar fascinating behavior of organized matter. The reason for the occurence of this situation is directly related to intrinsic non linearities of the different mechanisms responsible for the evolution of the system. Moreover, when dealing with interfaces separating two immiscible phases (liquid - gas, liquid -liquid, liquid - solid, solid - solid), the situation is rather more complicated. Indeed coupling terms playing the major role in the conditions of instability arise from the peculiar singular static and dynamic properties of the surface and of its vicinity. In other words, the non linearities are not only intrinsic to classical steps involving feedbacks, but they may be imbedded with the non-autonomous character of the surface properties. In order to illustrate our goal we discuss three examples of ordering in far from equilibrium conditions: i) formation of chemical structures during the oxidation of metals and alloys; ii) formation of mechanical structures during the oxidation of metals iii) formation of patterns at a solid-liquid moving interface due to supercooling condition in a melt of alloy. © 1984, Walter de Gruyter. All rights reserved.

Properties of lignin and poly(hydroxybutyrate) blends

The Queensland University of Technology (QUT) allows the presentation of a thesis for the Degree of Doctor of Philosophy in the format of published or submitted papers, where such papers have been published, accepted or submitted during the period of candidature. This thesis is composed of Seven published/submitted papers and one poster presentation, of which five have been published and the other two are under review. This project is financially supported by the QUTPRA Grant. The twenty-first century started with the resurrection of lignocellulosic biomass as a potential substitute for petrochemicals. Petrochemicals, which enjoyed the sustainable economic growth during the past century, have begun to reach or have reached their peak. The world energy situation is complicated by political uncertainty and by the environmental impact associated with petrochemical import and usage. In particular, greenhouse gasses and toxic emissions produced by petrochemicals have been implicated as a significant cause of climate changes. Lignocellulosic biomass (e.g. sugarcane biomass and bagasse), which potentially enjoys a more abundant, widely distributed, and cost-effective resource base, can play an indispensible role in the paradigm transition from fossil-based to carbohydrate-based economy. Poly(3-hydroxybutyrate), PHB has attracted much commercial interest as a plastic and biodegradable material because some its physical properties are similar to those of polypropylene (PP), even though the two polymers have quite different chemical structures. PHB exhibits a high degree of crystallinity, has a high melting point of approximately 180°C, and most importantly, unlike PP, PHB is rapidly biodegradable. Two major factors which currently inhibit the widespread use of PHB are its high cost and poor mechanical properties. The production costs of PHB are significantly higher than for plastics produced from petrochemical resources (e.g. PP costs $US1 kg-1, whereas PHB costs $US8 kg-1), and its stiff and brittle nature makes processing difficult and impedes its ability to handle high impact. Lignin, together with cellulose and hemicellulose, are the three main components of every lignocellulosic biomass. It is a natural polymer occurring in the plant cell wall. Lignin, after cellulose, is the most abundant polymer in nature. It is extracted mainly as a by-product in the pulp and paper industry. Although, traditionally lignin is burnt in industry for energy, it has a lot of value-add properties. Lignin, which to date has not been exploited, is an amorphous polymer with hydrophobic behaviour. These make it a good candidate for blending with PHB and technically, blending can be a viable solution for price and reduction and enhance production properties. Theoretically, lignin and PHB affect the physiochemical properties of each other when they become miscible in a composite. A comprehensive study on structural, thermal, rheological and environmental properties of lignin/PHB blends together with neat lignin and PHB is the targeted scope of this thesis. An introduction to this research, including a description of the research problem, a literature review and an account of the research progress linking the research papers is presented in Chapter 1. In this research, lignin was obtained from bagasse through extraction with sodium hydroxide. A novel two-step pH precipitation procedure was used to recover soda lignin with the purity of 96.3 wt% from the black liquor (i.e. the spent sodium hydroxide solution). The precipitation process is presented in Chapter 2. A sequential solvent extraction process was used to fractionate the soda lignin into three fractions. These fractions, together with the soda lignin, were characterised to determine elemental composition, purity, carbohydrate content, molecular weight, and functional group content. The thermal properties of the lignins were also determined. The results are presented and discussed in Chapter 2. On the basis of the type and quantity of functional groups, attempts were made to identify potential applications for each of the individual lignins. As an addendum to the general section on the development of composite materials of lignin, which includes Chapters 1 and 2, studies on the kinetics of bagasse thermal degradation are presented in Appendix 1. The work showed that distinct stages of mass losses depend on residual sucrose. As the development of value-added products from lignin will improve the economics of cellulosic ethanol, a review on lignin applications, which included lignin/PHB composites, is presented in Appendix 2. Chapters 3, 4 and 5 are dedicated to investigations of the properties of soda lignin/PHB composites. Chapter 3 reports on the thermal stability and miscibility of the blends. Although the addition of soda lignin shifts the onset of PHB decomposition to lower temperatures, the lignin/PHB blends are thermally more stable over a wider temperature range. The results from the thermal study also indicated that blends containing up to 40 wt% soda lignin were miscible. The Tg data for these blends fitted nicely to the Gordon-Taylor and Kwei models. Fourier transform infrared spectroscopy (FT-IR) evaluation showed that the miscibility of the blends was because of specific hydrogen bonding (and similar interactions) between reactive phenolic hydroxyl groups of lignin and the carbonyl group of PHB. The thermophysical and rheological properties of soda lignin/PHB blends are presented in Chapter 4. In this chapter, the kinetics of thermal degradation of the blends is studied using thermogravimetric analysis (TGA). This preliminary investigation is limited to the processing temperature of blend manufacturing. Of significance in the study, is the drop in the apparent energy of activation, Ea from 112 kJmol-1 for pure PHB to half that value for blends. This means that the addition of lignin to PHB reduces the thermal stability of PHB, and that the comparative reduced weight loss observed in the TGA data is associated with the slower rate of lignin degradation in the composite. The Tg of PHB, as well as its melting temperature, melting enthalpy, crystallinity and melting point decrease with increase in lignin content. Results from the rheological investigation showed that at low lignin content (.30 wt%), lignin acts as a plasticiser for PHB, while at high lignin content it acts as a filler. Chapter 5 is dedicated to the environmental study of soda lignin/PHB blends. The biodegradability of lignin/PHB blends is compared to that of PHB using the standard soil burial test. To obtain acceptable biodegradation data, samples were buried for 12 months under controlled conditions. Gravimetric analysis, TGA, optical microscopy, scanning electron microscopy (SEM), differential scanning calorimetry (DSC), FT-IR, and X-ray photoelectron spectroscopy (XPS) were used in the study. The results clearly demonstrated that lignin retards the biodegradation of PHB, and that the miscible blends were more resistant to degradation compared to the immiscible blends. To obtain an understanding between the structure of lignin and the properties of the blends, a methanol-soluble lignin, which contains 3× less phenolic hydroxyl group that its parent soda lignin used in preparing blends for the work reported in Chapters 3 and 4, was blended with PHB and the properties of the blends investigated. The results are reported in Chapter 6. At up to 40 wt% methanolsoluble lignin, the experimental data fitted the Gordon-Taylor and Kwei models, similar to the results obtained soda lignin-based blends. However, the values obtained for the interactive parameters for the methanol-soluble lignin blends were slightly lower than the blends obtained with soda lignin indicating weaker association between methanol-soluble lignin and PHB. FT-IR data confirmed that hydrogen bonding is the main interactive force between the reactive functional groups of lignin and the carbonyl group of PHB. In summary, the structural differences existing between the two lignins did not manifest itself in the properties of their blends.

Reaction of Aromatic Peroxyl Radicals with Alkynes: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

The reaction of the aromatic distonic peroxyl radical cations N-methyl pyridinium-4-peroxyl (PyrOO center dot+) and 4-(N,N,N-trimethyl ammonium)-phenyl peroxyl (AnOO center dot+), with symmetrical dialkyl alkynes 10?ac was studied in the gas phase by mass spectrometry. PyrOO center dot+ and AnOO center dot+ were produced through reaction of the respective distonic aryl radical cations Pyr center dot+ and An center dot+ with oxygen, O2. For the reaction of Pyr center dot+ with O2 an absolute rate coefficient of k1=7.1X10-12 cm3 molecule-1 s-1 and a collision efficiency of 1.2?% was determined at 298 K. The strongly electrophilic PyrOO center dot+ reacts with 3-hexyne and 4-octyne with absolute rate coefficients of khexyne=1.5X10-10 cm3 molecule-1 s-1 and koctyne=2.8X10-10 cm3 molecule-1 s-1, respectively, at 298 K. The reaction of both PyrOO center dot+ and AnOO center dot+ proceeds by radical addition to the alkyne, whereas propargylic hydrogen abstraction was observed as a very minor pathway only in the reactions involving PyrOO center dot+. A major reaction pathway of the vinyl radicals 11 formed upon PyrOO center dot+ addition to the alkynes involves gamma-fragmentation of the peroxy O?O bond and formation of PyrO center dot+. The PyrO center dot+ is rapidly trapped by intermolecular hydrogen abstraction, presumably from a propargylic methylene group in the alkyne. The reaction of the less electrophilic AnOO center dot+ with alkynes is considerably slower and resulted in formation of AnO center dot+ as the only charged product. These findings suggest that electrophilic aromatic peroxyl radicals act as oxygen atom donors, which can be used to generate alpha-oxo carbenes 13 (or isomeric species) from alkynes in a single step. Besides gamma-fragmentation, a number of competing unimolecular dissociative reactions also occur in vinyl radicals 11. The potential energy diagrams of these reactions were explored with density functional theory and ab initio methods, which enabled identification of the chemical structures of the most important products.

Ecionines A and B, two new cytotoxic pyridoacridine alkaloids from the Australian marine sponge, Ecionemia geodides

Chemical investigations of the Australian marine sponge Ecionemia geodides resulted in the isolation of two new pyridoacridine alkaloids, ecionines A (1) and B (2), along with the previously isolated marine natural products, biemnadin (3) and meridine (4). Compounds 1 and 2 both contain an imine moiety, which is rare for the pyridoacridine structure class. The chemical structures of 1 and 2 were determined by extensive 1D and 2D NMR and MS data analyses. All compounds were tested against a panel of human bladder cancer cell lines, the increasingly metastatic TSU-Pr1 series (TSU-Pr1, TSU-Pr1-B1 and TSU-Pr1- B2) and the superficial bladder cancer cell line 5637. Ecionine A (1) displayed cytotoxicity against all cell lines, with IC50 values ranging from 3 to 7 mM. This is the first report of chemistry from the sponge genus Ecionemia.

Denhaminols A–H, dihydro-β-agarofurans from the endemic Australian rainforest plant Denhamia celastroides

Eight new dihydro-β-agarofurans, denhaminols A–H (1–8), were isolated from the leaves of the Australian rainforest tree Denhamia celastroides. The chemical structures of 1–8 were elucidated following analysis of 1D/2D NMR and MS data. The absolute configuration of denhaminol A (1) was determined by single-crystal X-ray crystallography. All compounds were evaluated for cytotoxic activity against the human prostate cancer cell line LNCaP, using live-cell imaging and metabolic assays. Denhaminols A (1) and G (7) were also tested for their effects on the lipid content of LNCaP cells. This is the first report of secondary metabolites from D. celastroides.

Binding mechanism of affinity ligands for purification of plasmid DNA

Plasmid DNA for therapeutic and vaccination purposes must be highly purified. The high selectivity of affinity chromatography makes it ideal for the isolation of pDNA from complex biological feed stocks. Affinity chromatography makes use of the biological function and/or individual chemical structure of the interacting molecules. However, the success of any affinity purification protocol is dependent on the availability of suitable ligands. In this study, surface plasmon resonance (SPR) based Biacore system has been employed for the detection and quantification of the binding between lac operon (lacO) sequence contained in a pDNA and synthetic peptides based on the DNA-binding domain of the lac repressor protein, lad. The equilibrium dissociation constant (K D) and association and dissociation rate constants (ka, kd) for the interaction between plasmid DNA and designed peptides were determined.

The O-specific polysaccharide structure and biosynthetic gene cluster of Yersinia pseudotuberculosis serotype O:11

In the Yersinia pseudotuberculosis serotyping scheme, 21 serotypes are present originating from about 30 different O-factors distributed within the species. With regard to the chemical structures of lipopolysaccharides (LPSs) and the genetic basis of their biosynthesis, a number, but not all, of Y. pseudotuberculosis strains representing different serotypes have been investigated. In order to present an overall picture of the relationship between genetics and structures, we have been working on the genetics and structures of various Y. pseudotuberculosis O-specific polysaccharides (OPSs). Here, we present a structural and genetic analysis of the Y. pseudotuberculosis serotype O:11 OPS. Our results showed that this OPS structure has the same backbone as that of Y. pseudotuberculosis O:1b, but with a 6d-l-Altf side-branch instead of Parf. The 3′ end of the gene cluster is the same as that for O:1b and has the genes for synthesis of the backbone and for processing the completed repeat unit. The 5′ end has genes for synthesis of 6d-l-Altf and its transfer to the repeating unit backbone. The pathway for the synthesis of the 6d-l-Altf appears to be different from that for 6d-l-Altp in Y. enterocolitica O:3. The chemical structure of the O:11 repeating unit is [Figure]

Genetic characterisation and structural analysis of the O-specific polysaccharide of Yersinia pseudotuberculosis serotype O:1c

Many, but not all, of the current 21 serotypes of Yersinia pseudotuberculosis have been investigated with regard to the chemical structures of their O-specific polysaccharide (OPS) and the genetic basis of their biosynthesis. Completion of the genetics and structures of the remaining serotypes will enhance our understanding of the emerging relationship between genetics and structures within this species. Here, we present a structural and genetic analysis of the Y. pseudotuberculosis serotype O:1c OPS. Our results showed that this OPS has the same backbone as Y. pseudotuberculosis O:2b, but with a 3,6-dideoxy-D-ribo-hexofuranose (paratofuranose, Parf) side-branch instead of a 3,6-dideoxy-D-xylo-hexopyranose (abequopyranose, Abep). The 3'-end of the gene cluster is the same as for O:2b and has the genes for synthesis of the backbone and for processing the completed repeat unit. The 5'-end of the cluster consists of the same genes as O:1b for synthesis of Parf and a related gene for its transfer to the repeating unit backbone.