Bioluminescent sensor for naphthalene in air: Cell immobilization and evaluation with a dynamic standard atmosphere generator

A dynamic atmosphere generator with a naphthalene emission source has been constructed and used for the development and evaluation of a bioluminescence sensor based on the bacteria Pseudomonas fluorescens HK44 immobilized in 2% agar gel (101 cell mL(-1)) placed in sampling tubes. A steady naphthalene emission rate (around 7.3 nmol min(-1) at 27 degrees C and 7.4 mLmin(-1) of purified air) was obtained by covering the diffusion unit containing solid naphthalene with a PTFE filter membrane. The time elapsed from gelation of the agar matrix to analyte exposure (""maturation time"") was found relevant for the bioluminescence assays, being most favorable between 1.5 and 3 h. The maximum light emission, observed after 80 min, is dependent on the analyte concentration and the exposure time (evaluated between 5 and 20 min), but not on the flow rate of naphthalene in the sampling tube, over the range of 1.8-7.4 nmol min(-1). A good linear response was obtained between 50 and 260 nmol L-1 with a limit of detection estimated in 20 nmol L-1 far below the recommended threshold limit value for naphthalene in air. (c) 2008 Elsevier B.V. All rights reserved.

Theoretical studies of mononuclear non-heme iron active sites

The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined. The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.

Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Investigation of heterogeneous catalysts for the synthesis of fine chemicals

In order to match the more stringent environmental regulations, heterogenization of traditional homogeneous processes is one of the main challenges of the modern chemical industry. Great results have been achieved in the fields of petrochemicals and base chemicals, whereas in fine chemical industry most of the synthetic procedures are based on multistep processes catalyzed by homogeneous catalysts mainly used in stoichiometric amounts. In the fine chemicals manufacture not so much efforts have been devoted to the investigation of suitable solid catalysts for the development of greener processes, then this sector represent a very attractive field of research. In this context, the present work deals with the extensive investigation of the possibility to heterogenize existing processes, in particular two different classes of reactions have been studied: alkylation of aromatic and heteroaromatic compounds and selective oxidation of aromatic alcohols. Traditional solid acid catalysts, such as zeolites, clays and alumina have been tested in the gas phase alkylation of 1,2-methylendioxybenzene, core building block of many drugs, pesticides and fragrances. The observed reactivity were clarified through a deep FTIR investigation complemented by ab initio calculation. The same catalysts were tested in the gas phase isopropylation of thiophene with the aim of clearly attribute the role of the reaction parameters in the reaction proceeding and verify the possibility to enhance the selectivity of one of the two possible isomers. Finally various Au/CeO2 catalysts were tested in the synthesis of benzaldehyde and piperonal, two aldehydes largely employed in the manufacture of fine chemical products, through liquid phase oxidation of the corresponding alcohols in very mild conditions.

Molecular characterization of aromatic peroxygenase from Agrocybe aegerita

Recently, a novel group of fungal peroxidases, known as the aromatic peroxygenases (APO), has been discovered. Members of these extracellular biocatalysts produced by agaric basidiomycetes such as Agrocybe aegerita or Coprinellus radians catalyze reactions--for example, the peroxygenation of naphthalene, toluene, dibenzothiophene, or pyridine--which are actually attributed to cytochrome P450 monooxygenases. Here, for the first time, genetic information is presented on this new group of peroxide-consuming enzymes. The gene of A. aegerita peroxygenase (apo1) was identified on the level of messenger RNA and genomic DNA. The gene sequence was affirmed by peptide sequences obtained through an Edman degradation and de novo peptide sequencing of the purified enzyme. Quantitative real-time reverse transcriptase polymerase chain reaction demonstrated that the course of enzyme activity correlated well with that of mRNA signals for apo1 in A. aegerita. The full-length sequences of A. aegerita peroxygenase as well as a partial sequence of C. radians peroxygenase confirmed the enzymes' affiliation to the heme-thiolate proteins. The sequences revealed no homology to classic peroxidases, cytochrome P450 enzymes, and only little homology (<30%) to fungal chloroperoxidase produced by the ascomycete Caldariomyces fumago (and this only in the N-terminal part of the protein comprising the heme-binding region and part of the distal heme pocket). This fact reinforces the novelty of APO proteins. On the other hand, homology retrievals in genetic databases resulted in the identification of various APO homologous genes and transcripts, particularly among the agaric fungi, indicating APO's widespread occurrence in the fungal kingdom.

Excitonic couplings and electronic coherence in bridged naphthalene dimers

The electronic excitations of naphthalene and a family of bridged naphthalene dimers are calculated and analyzed by using the Collective Electronic Oscillator method combined with the oblique Lanczos algorithm. All experimentally observed trends in absorption profiles and radiative lifetimes are reproduced. Each electronic excitation is linked to the corresponding real-space transition density matrix, which represents the motions of electrons and holes created in the molecule by photon absorption. Two-dimensional plots of these matrices help visualize the degree of exciton localization and explain the dependence of the electronic interaction between chromophores on their separation.

The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.

The adsorptive separation of aromatic hydrocarbon mixtures

A detailed study has been made of the feasibility of adsorptive purification of slack waxes from traces of aromatic compounds using type 13X molecular sieves to achieve 0.01% aromatics in the product. The limited literature relating to the adsorption of high molecular weight aromatic compounds by zeolites was reviewed. Equilibrium isotherms were determined for typical individual aromatic compounds. Lower molecular weight, or more compact, molecules were preferentially adsorbed and the number of molecules captured by one unit cell decreased with increasing molecular weight of the adsorbate. An increase in adsorption temperature resulted in a decrease in the adsorption value. The isosteric heat of adsorption of differnt types of aromatic compounds was determined from pairs of isotherms at 303 K to 343 K at specific coverages. The lowest heats of adsorption were for dodecylbenzene and phenanthrene. Kinetics of adsorption were studied for different aromatic compounds. The diffusivity decreased significantly when a long alkyl chain was attached to the benzene ring e.g. in dodecylbenzene; molecules with small cross-sectional diameter e.g. cumene were adsorbed most rapidly. The sorption rate increased with temperature. Apparent activation energies increased with increasing polarity. In a study of the dynamic adsorption of selected aromatic compounds from binary solutions in isooctane or n-alkanes, naphthalene exhibited the best dynamic properties followed by dibenzothiophene and finally dodecylbenzene. The dynamic adsorption of naphthalene from different n-alkane solvents increased with a decrease in solvent molecular weight. A tentative mathematical approach is proposed for the prediction of dynamic breakthrough curves from equilibrium isotherms and kinetic data. The dynamic properties of liquid phase adsorption of aromatics from slack waxes were studied at different temperatures and concentrations. The optimum operating temperature was 543 K. The best dynamic performance was achieved with feeds of low aromatic content. The studies with individual aromatic compounds demonstrated the affinity of type NaX molecular sieves to adsorb aromatics in the concentration range 3% - 5% . Wax purification by adsorption was considered promising and extension of the experimental programme was recommended.

Technology of repair for corroded reinforced concrete

A number of factors relating to various methods of repair for chloride initiated corrosion damage of reinforced concrete have been studied. A novel methodology has been developed to facilitate the measurement of macro and micro-cell corrosion rates for steel electrodes embedded in mortar prisms containing a chloride gradient. The galvanic bar specimen comprised electrically isolatable segmental mild steel electrodes and was constructed such that macro-cell corrosion currents were determinable for a number of electrode combinations. From this, the conditions giving rise to an incipient anode were established. The influence of several reinforcement and substrate primer systems upon macro-cell corrosion, arising from an incipient anode, within a patch repair have been investigated. Measurements of electrochemical noise were made in order to investigate the suitability of the technique as an on-site means of assessing corrosion activity within chloride contaminated reinforced concrete. For this purpose the standard deviation of potential noise was compared to macro-cell galvanic current data and micro-cell corrosion intensity determined by linear polarisation. Hydroxyl ion pore solution analyses were carried out on mortar taken from cathodically protected specimens. These specimens, containing sodium chloride, were cathodically protected over a range of polarisation potentials. Measurement of the hydroxyl ion concentrations were made in order to examine the possibility of alkali-silica reactions initiated by cathodic protection of reinfored concrete. A range of mortars containing a variety of generic type additives were examined in order to establish their resistances to chloride ion diffusion. The effect of surfactant addition rate was investigated within a cement paste containing various dosages of naphthalene sulphonate.

Singlet and triplet molecular interaction in excimers

A perturbative approach is developed to determine, term by term, the contributions of the various forces to the excimer potentials of the singlet and triplet excimers. The results show that the singlet excimer of naphthalene is more stable than the corresponding triplet excimer primarily due to large contributions of the exciton-resonance and the dispersion energy terms. The variation of the various terms with the conformations of the excimers suggests that the singlet and triplet excimers of naphthalene cannot have identical structure.

Some Themes in Chemical Crystallography Pertinent to the Indian Contribution

It is particularly appropriate that the Journal of the Indian Institute of Science is bringing out a commemorative issue to mark the International Year of Crystallography 2014 (IYCr2014). India has had a strong crystallographic tradition, and the earliest work in what may be described as structural crystallography from this country is the work of K. Banerjee on the determination of the crystal structure of naphthalene in 1930. The Indian Institute of Science itself has played no small part in establishing and sustaining the subject of crystallography in this country. A large number of papers in this special issue are written by authors who have either have been trained in the Institute or who have some kind of professional association with this organization. In this article I will try to capture some unique features that characterize the intersection of the crystallographic and the chemical domains, mostly as they pertain to the Indian contribution to this subject. Crystallography is of course is as old as chemistry itself, and some would say it is even older. The relationships between chemistry and crystallography go back to much before the discovery of diffraction of X-rays by crystals.The discovery of polymorphism by Mitscherlisch in 1822, Haüy’s formulation of the molecule integrante, and the work of Fedorov and Groth on the identification of crystals from their morphology alone, are well known examples of such relationships.A very early article by Tutton speaks of “crystallo-chemical analysis”. In this article, I shall, however, be dealing with the interplay of chemistry and crystallography only in the post diffraction era, that is, after 1912. Much had been written and said about chemical crystallography, and even within the context of the present special issue, there is a review of chemical crystallography in India including some futuristic trends. This topic was also reviewed by Nangia in a special publication brought out by Indian Academy of Sciences in 2009,and by Desiraju in a special publication brought out by the Indian National Science Academy in 2010. A rather detailed account of crystallography in India appeared in 2007 in the newsletter of the International Union of Crystallography (IUCr) in which chemical crystallography was detailed. Since all these publications are fairly recent there is little need for me to attempt a comprehensive coverage of chemical crystallography in India in this short review