Molecular orientational order of nitroxide radicals in liquid crystalline media

The orientational distribution of a set of stable nitroxide radicals in aligned liquid crystals 5CB (nematic) and 8CB (smectic A) was studied in detail by numerical simulation of EPR spectra. The order parameters up to the 10th rank were measured. The directions of the principal orientation axes of the radicals were determined. It was shown that the ordering of the probe molecules is controlled by their interaction with the matrix molecules more than the inherent geometry of the probes themselves. The rigid fused phenanthrene-based (A5) and 2-azaphenalene (A4) nitroxides as well as the rigid core elongated C11 and 5α-cholestane (CLS) nitroxides were found to be most sensitive to the orientation of the liquid crystal matrixes.

Applications of the Vilsmeier reaction. 13. Vilsmeier approach to polycyclic aromatic hydrocarbons

The Synthesis of three typical polycyclic hydrocarbons (PAH) has been described, wherein the Vilsmeier reaction plays a major role. Vilsmeier reaction of the tetraloll gives the dihydronaphthaldehyde 2 which on cyclodehydration gives the dihydroarene 3. Ita dehydrogenation affords 3-methoxybenz[a]anthracene (4). Vilsmeier reaction on the dimethoxydihydronaphthalene 5 gives the versatile dimethoxydihydronaphthaldehyde 6 which has been converted to the dimethoxybenzo[c]fluorene 7 by direct cyclodehydration and the fulvene 10 by cyclodehydration of allylic alcohol 8 derived from 6 followed by dehydrogenation. The saturated alcohol 12 corresponding to 8 undergoes cyclodehydration to give the dimethoxyhexahydrobenzo[c]phenanthrene (13). Some of the advantages of the Vilsmeier approach to PAH have been pointed out.

Microbial activities in boreal soils: Biodegradation of organic contaminants at low temperature and ammonia oxidation

This thesis deals with the response of biodegradation of selected anthropogenic organic contaminants and natural autochthonous organic matter to low temperature in boreal surface soils. Furthermore, the thesis describes activity, diversity and population size of autotrophic ammonia-oxidizing bacteria (AOB) in a boreal soil used for landfarming of oil-refinery wastes, and presents a new approach, in which the particular AOB were enriched and cultivated in situ from the landfarming soil onto cation exchange membranes. This thesis demonstrates that rhizosphere fraction of natural forest humus soil and agricultural clay loam soil from Helsinki Metropolitan area were capable of degrading of low to moderate concentrations (0.2 50 µg cm-3) of PCP, phenanthrene and 2,4,5-TCP at temperatures realistic to boreal climate (-2.5 to +15 °C). At the low temperatures, the biodegradation of PCP, phenanthrene and 2,4,5-TCP was more effective (Q10-values from 1.6 to 7.6) in the rhizosphere fraction of the forest soil than in the agricultural soil. Q10-values of endogenous soil respiration (carbon dioxide evolution) and selected hydrolytic enzyme activities (acetate-esterase, butyrate-esterase and β-glucosidase) in acid coniferous forest soil were 1.6 to 2.8 at temperatures from -3 to +30 °C. The results indicated that the temperature dependence of decomposition of natural autochthonous soil organic matter in the studied coniferous forest was only moderate. The numbers of AOB in the landfarming (sandy clay loam) soil were determined with quantitative polymerase chain reaction (real-time PCR) and with Most Probable Number (MPN) methods, and potential ammonium oxidation activity was measured with the chlorate inhibition technique. The results indicated presence of large and active AOB populations in the heavily oil-contaminated and urea-fertilised landfarming soil. Assessment of the populations of AOB with denaturing gradient gel electrophoresis (DGGE) profiling and sequence analysis of PCR-amplified 16S rRNA genes showed that Nitrosospira-like AOB in clusters 2 and 3 were predominant in the oily landfarming soil. This observation was supported by fluorescence in situ hybridization (FISH) analysis of the AOB grown on the soil-incubated cation-exchange membranes. The results of this thesis expand the suggested importance of Nitrosospira-like AOB in terrestrial environments to include chronically oil-contaminated soils.

Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.

Two ex situ fungal technologies to treat contaminated soil

Wood-degrading fungi are able to degrade a large range of recalcitrant pollutants which resemble the lignin biopolymer. This ability is attributed to the production of lignin-modifying enzymes, which are extracellular and non-specific. Despite the potential of fungi in bioremediation, there is still an understanding gap in terms of the technology. In this thesis, the feasibility of two ex situ fungal bioremediation methods to treat contaminated soil was evaluated. Treatment of polycyclic aromatic hydrocarbons (PAHs)-contaminated marsh soil was studied in a stirred slurry-phase reactor. Due to the salt content in marsh soil, fungi were screened for their halotolerance, and the white-rot fungi Lentinus tigrinus, Irpex lacteus and Bjerkandera adusta were selected for further studies. These fungi degraded 40 - 60% of a PAH mixture (phenanthrene, fluoranthene, pyrene and chrysene) in a slurry-phase reactor (100 ml) during 30 days of incubation. Thereafter, B. adusta was selected to scale-up and optimize the process in a 5 L reactor. Maximum degradation of dibenzothiophene (93%), fluoranthene (82%), pyrene (81%) and chrysene (83%) was achieved with the free mycelium inoculum of the highest initial biomass (2.2 g/l). In autoclaved soil, MnP was the most important enzyme involved in PAH degradation. In non-sterile soil, endogenous soil microbes together with B. adusta also degraded the PAHs extensively, suggesting a synergic action between soil microbes and the fungus. A fungal solid-phase cultivation method to pretreat contaminated sawmill soil with high organic matter content was developed to enhance the effectiveness of the subsequent soil combustion. In a preliminary screening of 146 fungal strains, 28 out of 52 fungi, which extensively colonized non-sterile contaminated soil, were litter-decomposing fungi. The 18 strains further selected were characterized by their production of lignin-modifying and hydrolytic enzymes, of which MnP and endo-1,4-β-glucanase were the main enzymes during cultivation on Scots pine (Pinus sylvestris) bark. Of the six fungi selected for further tests, Gymnopilus luteofolius, Phanerochaete velutina, and Stropharia rugosoannulata were the most active soil organic matter degraders. The results showed that a six-month pretreatment of sawmill soil would result in a 3.5 - 9.5% loss of organic matter, depending on the fungus applied. The pretreatment process was scaled-up for a 0.56 m3 reactor, in which perforated plastic tubes filled with S. rugosoannulata growing on pine bark were introduced into the soil. The fungal pretreatment resulted in a soil mass loss of 30.5 kg, which represents 10% of the original soil mass (308 kg). Despite the fact that Scots pine bark contains several antimicrobial compounds, it was a suitable substrate for fungal growth and promoter of the production of oxidative enzymes, as well as an excellent and cheap natural carrier of fungal mycelium. This thesis successfully developed two novel fungal ex situ bioremediation technologies and introduce new insights for their further full-scale application. Ex situ slurry-phase fungal reactors might be applied in cases when the soil has a high water content or when the contaminant bioavailability is low; for example, in wastewater treatment plants to remove pharmaceutical residues. Fungal solid-phase bioremediation is a promising remediation technology to ex situ or in situ treat contaminated soil.

Dipole moments and molecular structure of picrates of aromatic hydrocarbons and heterocyclic amines

Dipole moment measurements have been made in the case of a few aromatic hydrocarbon picrates, the values obtained being 2·18, 2·25, 2·97 (all in Debye units) for picrates of naphthalene, acenaphthene and phenanthrene respectively and the results discussed in terms of Mulliken's theory. Measurements have also been extended to include a few salt-like heterocyclic amine picrates.

Dynamic Internal Cavities of Dendrimers as Constrained Media. A Study of Photochemical Isomerizations of Stilbene and Azobenzene Using Poly(alkyl aryl ether) Dendrimers

Dendritic rnicroenvironments defined by dynamic internal cavities of a dendrimer were probed through geometric isomerization of stilbene and azobenzene. A third-generation poly(alkyl aryl ether) dendrimer with hydrophilic exterior and hydrophobic interior was used as a reaction cavity in aqueous medium. The dynamic inner cavity sizes were varied by utilizing alkyl linkers that connect the branch junctures from ethyl to n-pentyl moiety (C(2)G(3)-C(5)G(3)). Dendrimers constituted with n-pentyl linker were found to afford higher solubilities of stilbene and azobenzene. Direct irradiation of trans-stilbene showed that C(5)G(3) and C(4)G(3) dendrimers afforded considerable phenanthrene formation, in addition to cis-stilbene, whereas C(3)G(3) and C(2)G(3) gave only cis-stilbene. An electron-transfer sensitized trans-cis isomerization, using cresyl violet perchlorate as the sensitizer, also led to similar results. Thermal isomerization of cis-azobenzene to trans-azobenzene within dendritic microenvironments revealed that the activation energy of the cis- to trans-isomer was increasing in the series C(5)G(3) < C(4)G(3) < C(3)G(3)

Nanoindentation as a probe for mechanically-induced molecular migration in layered organic donor-acceptor complexes

Nanoindentation and scratch experiments on 1:1 donor-acceptor complexes, 1 and 2, of 1,2,4,5-tetracyanobenzene with pyrene and phenanthrene, respectively, reveal long-range molecular layer gliding and large interaction anisotropy. Due to the layered arrangements in these crystals, these experiments that apply stress in particular directions result in the breaking of interlayer interactions, thus allowing molecular sheets to glide over one another with ease. Complex 1 has a layered crystal packing wherein the layers are 68° skew under the (002) face and the interlayer space is stabilized by van der Waals interactions. Upon indenting this surface with a Berkovich tip, pile-up of material was observed on just one side of the indenter due to the close angular alignment of the layers with the half angle of the indenter tip (65.35°). The interfacial differences in the elastic modulus (21 ) and hardness (16 ) demonstrate the anisotropic nature of crystal packing. In 2, the molecular stacks are arranged in a staggered manner; there is no layer arrangement, and the interlayer stabilization involves C-H�N hydrogen bonds and ��� interactions. This results in a higher modulus (20 ) for (020) as compared to (001), although the anisotropy in hardness is minimal (4 ). The anisotropy within a face was analyzed using AFM image scans and the coefficient of friction of four orthogonal nanoscratches on the cleavage planes of 1 and 2. A higher friction coefficient was obtained for 2 as compared to 1 even in the cleavage direction due to the presence of hydrogen bonds in the interlayer region making the tip movement more hindered. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The application of metallointercalators in recognition of and charge transport in nucleic acids

Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety bind to DNA through the major groove. These metallointercalators can recognize DNA sites and perform reactions on DNA as a substrate. The site-specific metallointercalator Λ-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription factor, yAP-1, from an oligonucleotide that contains a common binding site. The demonstration that metal complexes can prevent transcription factor binding to DNA site-specifically is an important step in using metallointercalators as therapeutics.

The distinctive photochemistry of metallointercalators can also be applied to promote long range charge transport in DNA. Experiments using duplexes with regions 4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying order showed that radical migration is more dependent on the sequence of bases, and less dependent on the distance between the guanine doublets. This result suggests that mechanistic proposals of long range charge transport must involve all the bases.

RNA/DNA hybrids show charge migration to guanines from a remote site, thus demonstrating that nucleic acid stacking other than B-form can serve as a radical bridge. Double crossover DNA assemblies also provide a medium for charge transport at distances up to 100 Å from the site of radical introduction by a tethered metal complex. This radical migration was found to be robust to mismatches, and limited to individual, electronically distinct base stacks. In single DNA crossover assemblies, which have considerably greater flexibility, charge migration proceeds to both base stacks due to conformational isomers not present in the rigid and tightly annealed double crossovers.

Finally, a rapid, efficient, gel-based technique was developed to investigate thymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated via the bases of a thymine-thymine interface; reversal of this ligation is easily visualized by gel electrophoresis. This assay was used to show that the repair of thymine dimers from a distance through DNA charge transport can be accomplished with different photooxidants.

Thus, nucleic acids that support long range charge transport have been shown to include A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a method for thymine dimer repair detection using charge transport was developed. These observations underscore and extend the remarkable finding that DNA can serve a medium for charge transport via the heteroaromatic base stack.

Aplicações de métodos de classificação e calibração multivariada acoplados com técnicas espectroscópicas em amostras ambientais e alimentos

Este trabalho de pesquisa descreve dois estudos de caso de métodos quimiométricos empregados para a quantificação de hidrocarbonetos policíclicos aromáticos HPAs (naftaleno, fluoreno, fenantreno e fluoranteno) em água potável usando espectroscopia de fluorescência molecular e a classificação e caracterização de sucos de uva e seus parâmetros de qualidade através de espectroscopia de infravermelho próximo. O objetivo do primeiro estudo é a aplicação combinada de métodos quimiométricos de segunda ordem (N-PLS, U-PLS, U-PLS/RBL e PARAFAC) e espectrofluorimetria para determinação direta de HPAs em água potável, visando contribuir para o conhecimento do potencial destas metodologias como alternativa viável para a determinação tradicional por cromatografia univariada. O segundo estudo de caso destinado à classificação e determinação de parâmetros de qualidade de sucos de uva, densidade relativa e teor de sólidos solúveis totais, foi medida por espectroscopia de infravermelho próximo e métodos quimiométricos. Diversos métodos quimiométricos, tais como HCA, PLS-DA, SVM-DA e SIMCA foram investigados para a classificação amostras de sucos de uva ao mesmo tempo que métodos de calibração multivariada de primeira ordem, tais como PLS, iPLS e SVM-LS foram usadas para a predição dos parâmetros de qualidade. O princípio orientador para o desenvolvimento dos estudos aqui descritos foi a necessidade de metodologias analíticas com custo, tempo de execução e facilidade de operação melhores e menor produção de resíduos do que os métodos atualmente utilizados para a quantificação de HPAs, em água de torneira, e classificação e caracterização das amostras de suco de uva e seus parâmetros de qualidade

Desenvolvimento e produção de metabólitos de arruda (Ruta graveolens L.) exposta a substratos contaminados por hidrocarbonetos de petróleo

A indução da síntese de moléculas biologicamente ativas é conhecida como uma estratégia de defesa do organismo vegetal às condições adversas, onde plantas medicinais e/ou aromáticas são foco de pesquisa na terapêutica médica, na indústria farmacêutica, de cosméticos e de alimentos. A possibilidade de que os hidrocarbonetos de petróleo presentes no solo possam agir como agentes elicitores do metabolismo vegetal tem despertado interesse científico. O presente trabalho teve como objetivo avaliar o desenvolvimento in vivo e in vitro de Ruta graveolens L. (Rutaceae), considerando as respostas morfológicas e metabólicas na presença de petróleo e derivados. Além disso, verificar o potencial de desenvolvimento dessa espécie em áreas contaminadas, com base na hipótese de que tais substâncias podem influenciar na produção de substâncias de interesse, sem que haja redução significativa da biomassa vegetal. Foram realizados experimentos de (i) germinação in vivo em solo contaminado e parcialmente biorremediado, assim como solo com contaminação recente com óleo cru (0,8 % e 2,8 %) e diesel comercial S50 (0 % a 6,0 %), sendo que neste último foi avaliado o desenvolvimento e a produção de biomassa das plântulas; (ii) germinação in vitro em meio MS contaminado com fenantreno (1,0; 5,0 e 10,0 mg/L de meio) ou benzo[a]pireno (0,001; 0,010 e 0,100 mg/L de meio), sendo avaliado o desenvolvimento e a produção de biomassa; e (iii) resposta fisiológica de plantas oriundas do estoque in vitro à exposição de fenantreno ou benzo[a]pireno. R. graveolens teve redução significativa da germinação em solos contaminados, principalmente os solos parcialmente biorremediados pelo do processo de bioestímulo; não teve redução significativa da germinação in vivo nos solos contaminados com óleo cru, biorremediado e contaminado com diesel, porém o desenvolvimento pósgerminação foi afetado. Na exposição in vitro aos hidrocarbonetos, não houve alteração significativa na germinação nem na capacidade de desenvolvimento e produção de biomassa nas concentrações testadas de até 10 mg/L de fenantreno e até 0,1 mg/L de benzo[a]pireno. Em relação à propagação in vitro, foi possível a multiplicação de plantas em meio de cultura sem suplementação hormonal, na presença dos contaminantes. A presença de fenantreno e benzo[a]pireno in vitro não promoveu mudanças significativas nos níveis de compostos fenólicos e flavonoides totais produzidos, não havendo também alteração no perfil fitoquímico da espécie, quanto à presença de rutina. Pelo exposto, conclui-se que a espécie tem potencial para uso em biomonitoramento de solos contaminados , considerando a sua capacidade de produzir metabólitos e tolerar a presença dos hidrocarbonetos selecionados, sendo indicada ao cultivo em áreas contaminadas nos níveis investigados

Determination of PAH, PCB, and OCP in water from the Three Gorges Reservoir accumulated by semipermeable membrane devices (SPMD)

Bioavailable water concentrations of polycyclic aromatic hydrocarbons (PAH), polychlorinated biphenyls (PCB) and organochlorine pesticides (OCP) were measured in the water column from Three Gorges Reservoir (TGR) collected in May 2008 using semipermeable membrane devices (SPMDs). The sampling sites spanned the whole reservoir from the upstream Chongqing to the great dam covering more than 600 km long distance with water flow velocities ranging from <0.05 to 1.5 m s(-1). This is the first experience of SPMD application in the biggest reservoir in the world. The results of water sampling rates based on performance reference compounds (PRC) were tested to be significantly correlated with water flow velocities in the big river. Results of back-calculated aqueous concentrations based on PRC showed obvious regional variations of PAH, PCB and OCP levels in the reservoir. Total PAH ranged from 13.8 to 97.2 ng L-1, with the higher concentrations occurring in the region of upstream and near the dam. Phenanthrene, fluoranthene, pyrene and chrysene were the predominant PAH compounds in TGR water. Total PCB ranged from 0.08 to 0.51 ng L-1, with the highest one occurring in the region near the dam. PCB 28, 52, 101, 138, 153, 180, 118 were the most abundant PCB congeners in the water. The total OCP ranged from 2.33 to 3.60 ng L-1 and the levels showed homogenous distribution in the whole reservoir. HCH, DDT and HCB, PeCB were the major compounds of OCP fingerprints. Based on water quality criteria, the TGR water could be designated as being polluted by HCB and PAH. Data on PAH, PCB and OCP concentrations found in this survey can be used as reference levels for future POP monitoring programmes in TGR. (C) 2009 Elsevier Ltd. All rights reserved.

微生物的固定化及其降解土壤中菲、芘的研究

该论文是在综合分析中国典型土壤的污染特性与土壤环境背景的基础上，研制开发出适合中国国情的有机污染土壤的污染特性与土壤环境背景的基础上，研制开发出适合中国国情的有机污染土壤清洁技术.采用固定化进行有机物降解试验，目的是以期开发出一条提高有机污染土壤降解效率的新途径.该论文首先通过菌种的筛选与鉴定后，进行微生物的固定化包埋，挑选出最佳的固定化载体.最合理的载体配比是：聚乙烯醇100（p/gL<'-1>），活性炭50（p/gL<'-1>）.同时确定细菌采用化学方法进行固定化包埋，载体形状为球形;真菌采用物理方法进行固定化包埋，载体形状为莲藕型.并将固定化微生物应用于有机污染土壤菲、芘的降解.通过不同接种量的固定化微生物对菲、芘的降解、固定化微生物对不同系列浓度菲和芘的降解以及固定化微生物在自然土壤中对菲、芘降解的各参数测定，说明固定化微生物用于降解土壤中有机污染物具有一定的应用前景.该研究首次将固定化微生物用于降解土壤中有机污染物，为将来的实际应用奠定了一定的理论基础.同时首次采用了新的载体形状——莲藕型，具有一定的创新性.